2018 |
Gazzo, Andrea Beyond monogenic diseases: a first collection and analysis of digenic diseases PhD Thesis 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/272617c, title = {Beyond monogenic diseases: a first collection and analysis of digenic diseases}, author = {Andrea Gazzo}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/272617}, year = {2018}, date = {2018-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Carcillo, Fabrizio 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/272119c, title = {Beyond Supervised Learning in Credit Card Fraud Detection: A Dive into Semi-supervised and Distributed Learning}, author = {Fabrizio Carcillo}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/272119}, year = {2018}, date = {2018-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Bizet, Martin Bioinformatic inference of a prognostic epigenetic signature of immunity in breast cancers PhD Thesis 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/265092c, title = {Bioinformatic inference of a prognostic epigenetic signature of immunity in breast cancers}, author = {Martin Bizet}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/265092}, year = {2018}, date = {2018-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Fimereli, Danai Computational analyses of gene fusions, viruses and parasitic genomic elements in breast cancer PhD Thesis 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/263609b, title = {Computational analyses of gene fusions, viruses and parasitic genomic elements in breast cancer}, author = {Danai Fimereli}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/263609}, year = {2018}, date = {2018-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Gazzo, Andrea Beyond monogenic diseases: a first collection and analysis of digenic diseases PhD Thesis 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/272617, title = {Beyond monogenic diseases: a first collection and analysis of digenic diseases}, author = {Andrea Gazzo}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/272617/5/ContratDiGazzo.pdf}, year = {2018}, date = {2018-01-01}, abstract = {In the next generation sequencing era many bioinformatics tools have been developed for assisting scientists in their studies on the molecular basis of genetic diseases, often with the aim of identifying the pathogenic variants. As a consequence, in the last decades more than one hundred new disease-gene associations have been discovered. Nevertheless, the genetic basis of many genetic diseases yet remains undisclosed. It has been shown that many diseases considered as monogenic with an imperfect genotype-phenotype correlation or incomplete penetrance are, on the contrary, caused or modulated by more than one mutated gene, meaning that they are in fact oligogenic. Current bioinformatics methods used for identifying pathogenic variants are trained and fine-tuned for identifying a single variant responsible of a disease. This monogenic-oriented approach cannot be used to explore the impact of combinations of variants in different genes on the complexity and genetic heterogeneity of rare diseases. Digenic diseases are the simplest form of oligogenic disease and thus they can provide a conceptual bridge between monogenic and the poorly understood polygenic diseases.The ambition of this thesis is to collect and analyse digenic data, introducing this topic in the bioinformatics field where digenic diseases are still an unexplored branch. This can be divided in two steps: the first consists in the creation of a central repository containing detailed information on digenic diseases; the second is an analysis of their peculiarities, using machine learning methods for studying subclasses of digenic effects.In the first step we developed DIDA (DIgenic diseases DAtabase), a novel database that provides for the first time a curated collection of genes and associated variants involved in digenic diseases. Detailed information related to the digenic mechanism have been manually mined from the medical literature. All instances in DIDA were also assigned to two sub classes of digenic effects, annotated as true digenic (both genes are required for developing the disease) and composite classes (one gene is sufficient to produce the disease phenotype, the second one alters it or change significantly the age of onset).In the second step, we hypothesized that the digenic effect may be related to some biological properties characterizing digenic combinations. Using machine learning methods, we show that a set of variant, gene and higher-level features can differentiate between the true digenic and composite classes with high accuracy. Moreover, we show that a digenic effect decision profile, extracted from the predictive model, motivates why an instance is assigned to either of the two classes.Together, our results show that digenic disease data generates novel insights, providing a glimpse into the oligogenic realm.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } In the next generation sequencing era many bioinformatics tools have been developed for assisting scientists in their studies on the molecular basis of genetic diseases, often with the aim of identifying the pathogenic variants. As a consequence, in the last decades more than one hundred new disease-gene associations have been discovered. Nevertheless, the genetic basis of many genetic diseases yet remains undisclosed. It has been shown that many diseases considered as monogenic with an imperfect genotype-phenotype correlation or incomplete penetrance are, on the contrary, caused or modulated by more than one mutated gene, meaning that they are in fact oligogenic. Current bioinformatics methods used for identifying pathogenic variants are trained and fine-tuned for identifying a single variant responsible of a disease. This monogenic-oriented approach cannot be used to explore the impact of combinations of variants in different genes on the complexity and genetic heterogeneity of rare diseases. Digenic diseases are the simplest form of oligogenic disease and thus they can provide a conceptual bridge between monogenic and the poorly understood polygenic diseases.The ambition of this thesis is to collect and analyse digenic data, introducing this topic in the bioinformatics field where digenic diseases are still an unexplored branch. This can be divided in two steps: the first consists in the creation of a central repository containing detailed information on digenic diseases; the second is an analysis of their peculiarities, using machine learning methods for studying subclasses of digenic effects.In the first step we developed DIDA (DIgenic diseases DAtabase), a novel database that provides for the first time a curated collection of genes and associated variants involved in digenic diseases. Detailed information related to the digenic mechanism have been manually mined from the medical literature. All instances in DIDA were also assigned to two sub classes of digenic effects, annotated as true digenic (both genes are required for developing the disease) and composite classes (one gene is sufficient to produce the disease phenotype, the second one alters it or change significantly the age of onset).In the second step, we hypothesized that the digenic effect may be related to some biological properties characterizing digenic combinations. Using machine learning methods, we show that a set of variant, gene and higher-level features can differentiate between the true digenic and composite classes with high accuracy. Moreover, we show that a digenic effect decision profile, extracted from the predictive model, motivates why an instance is assigned to either of the two classes.Together, our results show that digenic disease data generates novel insights, providing a glimpse into the oligogenic realm. |
Reggiani, Claudio 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/270994, title = {Bioinformatic discovery of novel exons expressed in human brain and their association with neurodevelopmental disorders}, author = {Claudio Reggiani}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/270994/5/ContratDiReggiani.pdf}, year = {2018}, date = {2018-01-01}, abstract = {An important quest in genomics since the publication of the first complete human genome in 2003 has been its functional annotation. DNA holds the instructions to the production of the components necessary for the life of cells and organisms. A complete functional catalog of genomic regions will help the understanding of the cell body and its dynamics, thus creating links between genotype and phenotypic traits. The need for annotations prompted the development of several bioinformatic methods. In the context of promoter and first exon predictors, the majority of models relies principally on structural and chemical properties of the DNA sequence. Some of them integrate information from epigenomic and transcriptomic data as secondary features. Current genomic research asserts that reference genome annotations are far from being fully annotated (human organism included).Physicians rely on reference genome annotations and functional databases to understand disorders with genetic basis, and missing annotations may lead to unresolved cases. Because of their complexity, neurodevelopmental disorders are under study to figure out all genetic regions that are involved. Besides functional validation on model organisms, the search for genotype-phenotype association is supported by statistical analysis, which is typically biased towards known functional regions.This thesis addresses the use of an in-silico integrative analysis to improve reference genome annotations and discover novel functional regions associated with neurodevelopemental disorders. The contributions outlined in this document have practical applications in clinical settings. The presented bioinformatic method is based on epigenomic and transcriptomic data, thus excluding features from DNA sequence. Such integrative approach applied on brain data allowed the discovery of two novel promoters and coding first exons in the human DLG2 gene, which were also found to be statistically associated with neurodevelopmental disorders and intellectual disability in particular. The application of the same methodology to the whole genome resulted in the discovery of other novel exons expressed in brain. Concerning the in-silico method itself, the research demanded a high number of functional and clinical datasets to properly support and validate our discoveries.This work describes a bioinformatic method for genome annotation, in the specific area of promoter and first exons. So far the method has been applied on brain data, and the extension to the whole body data would be a logical by-product. We will leverage distributed frameworks to tackle the even higher amount of data to analyse, a task that has already begun. Another interesting research direction that came up from this work is the temporal enrichment analysis of epigenomics data across different developmental stages, in which changes of epigenomic enrichment suggest time-specific and tissue-specific functional gene and gene isoforms regulation.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } An important quest in genomics since the publication of the first complete human genome in 2003 has been its functional annotation. DNA holds the instructions to the production of the components necessary for the life of cells and organisms. A complete functional catalog of genomic regions will help the understanding of the cell body and its dynamics, thus creating links between genotype and phenotypic traits. The need for annotations prompted the development of several bioinformatic methods. In the context of promoter and first exon predictors, the majority of models relies principally on structural and chemical properties of the DNA sequence. Some of them integrate information from epigenomic and transcriptomic data as secondary features. Current genomic research asserts that reference genome annotations are far from being fully annotated (human organism included).Physicians rely on reference genome annotations and functional databases to understand disorders with genetic basis, and missing annotations may lead to unresolved cases. Because of their complexity, neurodevelopmental disorders are under study to figure out all genetic regions that are involved. Besides functional validation on model organisms, the search for genotype-phenotype association is supported by statistical analysis, which is typically biased towards known functional regions.This thesis addresses the use of an in-silico integrative analysis to improve reference genome annotations and discover novel functional regions associated with neurodevelopemental disorders. The contributions outlined in this document have practical applications in clinical settings. The presented bioinformatic method is based on epigenomic and transcriptomic data, thus excluding features from DNA sequence. Such integrative approach applied on brain data allowed the discovery of two novel promoters and coding first exons in the human DLG2 gene, which were also found to be statistically associated with neurodevelopmental disorders and intellectual disability in particular. The application of the same methodology to the whole genome resulted in the discovery of other novel exons expressed in brain. Concerning the in-silico method itself, the research demanded a high number of functional and clinical datasets to properly support and validate our discoveries.This work describes a bioinformatic method for genome annotation, in the specific area of promoter and first exons. So far the method has been applied on brain data, and the extension to the whole body data would be a logical by-product. We will leverage distributed frameworks to tackle the even higher amount of data to analyse, a task that has already begun. Another interesting research direction that came up from this work is the temporal enrichment analysis of epigenomics data across different developmental stages, in which changes of epigenomic enrichment suggest time-specific and tissue-specific functional gene and gene isoforms regulation. |
Fimereli, Danai Computational analyses of gene fusions, viruses and parasitic genomic elements in breast cancer PhD Thesis 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/263609, title = {Computational analyses of gene fusions, viruses and parasitic genomic elements in breast cancer}, author = {Danai Fimereli}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/263609/5/ContratDanaiFimereli.pdf}, year = {2018}, date = {2018-01-01}, abstract = {Breast cancer is the most common cancer in women and research efforts to unravel the underlying mechanisms that drive carcinogenesis are continuous. The emergence of high-throughput sequencing techniques and their constant advancement, in combination with large scale studies of genomic and transcriptomic data, allowed the identification of important genetic changes that take place in the breast cancer genome, including somatic mutations, copy number aberrations and genomic rearrangements.The overall aim of this thesis is to explore the presence of genetic changes that take place in the breast cancer transcriptome and their possible contribution to carcinogenesis. The aim of the first research study was the identification of expressed gene fusions in breast cancer and the study of their association with other genomic events. For achieving this, transcriptome sequencing and Single Nucleotide Polymorphism arrays data for a cohort of 55 tumors and 10 normal breast tissues were combined. Gene fusions were detected in the majority of the samples, with evident differences between breast cancer subtypes, where HER2+ samples had significantly more fusions than the other subtypes. The genome-wide analysis uncovered localization of fusion genes in specific chromosomes like 17, 8 or 20. Additionally, a positive correlation between the number of gene fusions and the number of amplifications was observed, including the association between fusions on chromosome 17 and the amplifications in HER2+ samples, which can be attributed to the highly rearranged genomes of these subtypes. Finally, the absence of highly recurrent fusions across this cohort adds to the notion that gene fusions in breast cancer are most likely private events, with the majority being “passenger” events. In the second research study, the aim was to identify a connection between viral infections and breast cancer by devising five different computational methods for the analysis of both transcriptome and exome data in a cohort of 58 breast tumors. Despite being able to detect viral sequences in our testing dataset, no significantly high numbers of viral sequences were detected in our samples. Specifically, viral sequences (~2-30 reads) were extracted belonging to viruses EBV, HHV6 and Merkel cell polyomavirus. Such low levels of viral expression direct against a viral etiology for breast cancer but one should not exclude possible cases of integrated but silent viruses.In the third research project, we analyzed in silico the transcriptional profiles of human endogenous retroviruses in breast cancer. Despite being scattered across the genome in large numbers, a number of ERVs are actively transcribed, consisting of a small percentage of the total mapped reads. Alongside protein coding genes and lncRNAs, they show distinct expression profiles across the different breast cancer subtypes with luminal and basal-like samples clear separating from each other. Additionally, distinct profiles between ER+ and ER- samples were observed. Tumor specific ERV loci show an association with the immune status of the tumors, indicating that ERVs are reactivated in tumors and could play a role in the activation of the immune response cascade.The results presented in this thesis exhibit only in a small fragment the diversity and heterogeneity of the breast cancer transcriptome. The strength of the sequencing techniques allows the in depth detection of different genomic events. Gene fusions should be considered as part of the breast cancer transcriptome but their low recurrence across samples indicates for a role as passenger events. Under the light of existing results, viral infections do not play a significant role in breast cancer. On the other hand, human endogenous retroviruses, despite originating from exogenous viruses, seems to exhibit transcriptional profiles similar to those of normal genes, indicating that they are part of the genome’s transcriptional machinery.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } Breast cancer is the most common cancer in women and research efforts to unravel the underlying mechanisms that drive carcinogenesis are continuous. The emergence of high-throughput sequencing techniques and their constant advancement, in combination with large scale studies of genomic and transcriptomic data, allowed the identification of important genetic changes that take place in the breast cancer genome, including somatic mutations, copy number aberrations and genomic rearrangements.The overall aim of this thesis is to explore the presence of genetic changes that take place in the breast cancer transcriptome and their possible contribution to carcinogenesis. The aim of the first research study was the identification of expressed gene fusions in breast cancer and the study of their association with other genomic events. For achieving this, transcriptome sequencing and Single Nucleotide Polymorphism arrays data for a cohort of 55 tumors and 10 normal breast tissues were combined. Gene fusions were detected in the majority of the samples, with evident differences between breast cancer subtypes, where HER2+ samples had significantly more fusions than the other subtypes. The genome-wide analysis uncovered localization of fusion genes in specific chromosomes like 17, 8 or 20. Additionally, a positive correlation between the number of gene fusions and the number of amplifications was observed, including the association between fusions on chromosome 17 and the amplifications in HER2+ samples, which can be attributed to the highly rearranged genomes of these subtypes. Finally, the absence of highly recurrent fusions across this cohort adds to the notion that gene fusions in breast cancer are most likely private events, with the majority being “passenger” events. In the second research study, the aim was to identify a connection between viral infections and breast cancer by devising five different computational methods for the analysis of both transcriptome and exome data in a cohort of 58 breast tumors. Despite being able to detect viral sequences in our testing dataset, no significantly high numbers of viral sequences were detected in our samples. Specifically, viral sequences (~2-30 reads) were extracted belonging to viruses EBV, HHV6 and Merkel cell polyomavirus. Such low levels of viral expression direct against a viral etiology for breast cancer but one should not exclude possible cases of integrated but silent viruses.In the third research project, we analyzed in silico the transcriptional profiles of human endogenous retroviruses in breast cancer. Despite being scattered across the genome in large numbers, a number of ERVs are actively transcribed, consisting of a small percentage of the total mapped reads. Alongside protein coding genes and lncRNAs, they show distinct expression profiles across the different breast cancer subtypes with luminal and basal-like samples clear separating from each other. Additionally, distinct profiles between ER+ and ER- samples were observed. Tumor specific ERV loci show an association with the immune status of the tumors, indicating that ERVs are reactivated in tumors and could play a role in the activation of the immune response cascade.The results presented in this thesis exhibit only in a small fragment the diversity and heterogeneity of the breast cancer transcriptome. The strength of the sequencing techniques allows the in depth detection of different genomic events. Gene fusions should be considered as part of the breast cancer transcriptome but their low recurrence across samples indicates for a role as passenger events. Under the light of existing results, viral infections do not play a significant role in breast cancer. On the other hand, human endogenous retroviruses, despite originating from exogenous viruses, seems to exhibit transcriptional profiles similar to those of normal genes, indicating that they are part of the genome’s transcriptional machinery. |
Dierckxsens, Nicolas Targeted organelle genome assembly and heteroplamsy detection PhD Thesis 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/277507, title = {Targeted organelle genome assembly and heteroplamsy detection}, author = {Nicolas Dierckxsens}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/277507/5/ContratDiDierckxsens.pdf}, year = {2018}, date = {2018-01-01}, abstract = {Thanks to the development of next-generation sequencing (NGS) technology, whole genome data can be readily obtained from a variety of samples. Since the massive increase in available sequencing data, the development of efficient assembly algorithms has become the new bottleneck. Almost every new released tool is based on the De Brujin graph method, which focuses on assembling complete datasets with mathematical models. Although the decreasing sequencing costs made whole genome sequencing (WGS) the most straightforward and least laborious approach of gathering sequencing data, many research projects are only interested in the extranuclear genomes. Unfortunately, few of the available tools are specifically designed to efficiently retrieve these extranuclear genomes from WGS datasets. We developed a seed-and-extend algorithm that assembles organelle circular genomes from WGS data, starting from a single short seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina datasets and always outperformed other assemblers in assembly accuracy and contiguity. In our benchmark, NOVOPlasty assembled all genomes in less than 30 minutes with a maximum RAM memory requirement of 16 GB. NOVOPlasty is the only de novo assembler that provides a fast and straightforward manner to extract the extranuclear sequences from WGS data and generates one circular high quality contig.Heteroplasmy, the existence of multiple mitochondrial haplotypes within an individual, has been researched across different fields. Mitochondrial genome polymorphisms have been linked to multiple severe disorders and are of interest to evolutionary studies and forensic science. By utilizing ultra-deep sequencing, it is now possible to uncover previously undiscovered patterns of intra-individual polymorphism. However, it remains challenging to determine its source. Current available software can detect polymorphic sites but are not capable of determining the link between them. We therefore developed a new method to not only detect intra-individual polymorphisms within mitochondrial and chloroplast genomes, but also to look for linkage among polymorphic sites by assembling the sequence around each detected polymorphic site. Our benchmark study shows that this method can detect heteroplasmy more accurately than any method previously available and is the first tool that is able to completely or partially reconstruct the origin sequences for each intra-individual polymorphism.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } Thanks to the development of next-generation sequencing (NGS) technology, whole genome data can be readily obtained from a variety of samples. Since the massive increase in available sequencing data, the development of efficient assembly algorithms has become the new bottleneck. Almost every new released tool is based on the De Brujin graph method, which focuses on assembling complete datasets with mathematical models. Although the decreasing sequencing costs made whole genome sequencing (WGS) the most straightforward and least laborious approach of gathering sequencing data, many research projects are only interested in the extranuclear genomes. Unfortunately, few of the available tools are specifically designed to efficiently retrieve these extranuclear genomes from WGS datasets. We developed a seed-and-extend algorithm that assembles organelle circular genomes from WGS data, starting from a single short seed sequence. The algorithm has been tested on several new (Gonioctena intermedia and Avicennia marina) and public (Arabidopsis thaliana and Oryza sativa) whole genome Illumina datasets and always outperformed other assemblers in assembly accuracy and contiguity. In our benchmark, NOVOPlasty assembled all genomes in less than 30 minutes with a maximum RAM memory requirement of 16 GB. NOVOPlasty is the only de novo assembler that provides a fast and straightforward manner to extract the extranuclear sequences from WGS data and generates one circular high quality contig.Heteroplasmy, the existence of multiple mitochondrial haplotypes within an individual, has been researched across different fields. Mitochondrial genome polymorphisms have been linked to multiple severe disorders and are of interest to evolutionary studies and forensic science. By utilizing ultra-deep sequencing, it is now possible to uncover previously undiscovered patterns of intra-individual polymorphism. However, it remains challenging to determine its source. Current available software can detect polymorphic sites but are not capable of determining the link between them. We therefore developed a new method to not only detect intra-individual polymorphisms within mitochondrial and chloroplast genomes, but also to look for linkage among polymorphic sites by assembling the sequence around each detected polymorphic site. Our benchmark study shows that this method can detect heteroplasmy more accurately than any method previously available and is the first tool that is able to completely or partially reconstruct the origin sequences for each intra-individual polymorphism. |
Carcillo, Fabrizio 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/272119, title = {Beyond Supervised Learning in Credit Card Fraud Detection: A Dive into Semi-supervised and Distributed Learning}, author = {Fabrizio Carcillo}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/272119/5/ContratDiCarcillo.pdf}, year = {2018}, date = {2018-01-01}, abstract = {The expansion of the electronic commerce, as well as the increasing confidence of customers in electronic payments, makes of fraud detection a critical issue. The design of a prompt and accurate Fraud Detection System is a priority for many organizations in the business of credit cards. In this thesis we present a series of studies to increase the precision and the speed of fraud detection system. The thesis has three main contributions. The first concerns the integration of unsupervised techniques and supervised classifiers. We proposed several approaches to integrate outlier scores in the detection process and we found that the accuracy of a conventional classifier may be improved when information about the input distribution is used to augment the training set.The second contribution concerns the role of active learning in Fraud Detection. We have extensively compared several state-of-the-art techniques and found that Stochastic Semi-supervised Learning is a convenient approach to tackle the Selection Bias problem in the active learning process.The third contribution of the thesis is the design, implementation and assessment of SCARFF, an original framework for near real-time Streaming Fraud Detection. This framework integrates Big Data technology (notably tools like Kafka, Spark and Cassandra) with a machine learning approach to deal with imbalance, non-stationarity and feedback latency in a scalable manner. Experimental results on a massive dataset of real credit card transactions have showed that our framework is scalable, efficient and accurate over a big stream of transactions.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } The expansion of the electronic commerce, as well as the increasing confidence of customers in electronic payments, makes of fraud detection a critical issue. The design of a prompt and accurate Fraud Detection System is a priority for many organizations in the business of credit cards. In this thesis we present a series of studies to increase the precision and the speed of fraud detection system. The thesis has three main contributions. The first concerns the integration of unsupervised techniques and supervised classifiers. We proposed several approaches to integrate outlier scores in the detection process and we found that the accuracy of a conventional classifier may be improved when information about the input distribution is used to augment the training set.The second contribution concerns the role of active learning in Fraud Detection. We have extensively compared several state-of-the-art techniques and found that Stochastic Semi-supervised Learning is a convenient approach to tackle the Selection Bias problem in the active learning process.The third contribution of the thesis is the design, implementation and assessment of SCARFF, an original framework for near real-time Streaming Fraud Detection. This framework integrates Big Data technology (notably tools like Kafka, Spark and Cassandra) with a machine learning approach to deal with imbalance, non-stationarity and feedback latency in a scalable manner. Experimental results on a massive dataset of real credit card transactions have showed that our framework is scalable, efficient and accurate over a big stream of transactions. |
Porretta'S, Luciano MODELS AND METHODS IN GENOME WIDE ASSOCIATION STUDIES PhD Thesis 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/265314, title = {MODELS AND METHODS IN GENOME WIDE ASSOCIATION STUDIES}, author = {Luciano Porretta'S}, year = {2018}, date = {2018-01-01}, abstract = {The interdisciplinary field of systems biology has evolved rapidly over the last few years. Different disciplines have contributed to the development of both its experimental and theoretical branches.Although computational biology has been an increasing activity in computer science for more than a two decades, it has been only in the past few years that optimization models have been increasingly developed and analyzed by researchers whose primary background is Operations Research(OR). This dissertation aims at contributing to the field of computational biology by applying mathematical programming to certain problems in molecular biology.Specifically, we address three problems in the domain of Genome Wide Association Studies:(i) the Pure Parsimony Haplotyping Under uncertatind Data Problem that consists in finding the minimum number of haplotypes necessary to explain a given set of genotypes containing possible reading errors; (ii) the Parsimonious Loss Of Heterozygosity Problem that consists of partitioning suspected polymorphisms from a set of individuals into a minimum number of deletion areas; (iii) and the Multiple Individuals Polymorphic Alu Insertion Recognition Problem that consists of finding the set of locations in the genome where ALU sequences are inserted in some individual(s).All three problems are NP-hard combinatorial optimization problems. Therefore, we analyse their combinatorial structure and we propose an exact approach to solution for each of them. The proposed models are efficient, accurate, compact, polynomial-sized and usable in all those cases for which the parsimony criterion is well suited for estimation.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } The interdisciplinary field of systems biology has evolved rapidly over the last few years. Different disciplines have contributed to the development of both its experimental and theoretical branches.Although computational biology has been an increasing activity in computer science for more than a two decades, it has been only in the past few years that optimization models have been increasingly developed and analyzed by researchers whose primary background is Operations Research(OR). This dissertation aims at contributing to the field of computational biology by applying mathematical programming to certain problems in molecular biology.Specifically, we address three problems in the domain of Genome Wide Association Studies:(i) the Pure Parsimony Haplotyping Under uncertatind Data Problem that consists in finding the minimum number of haplotypes necessary to explain a given set of genotypes containing possible reading errors; (ii) the Parsimonious Loss Of Heterozygosity Problem that consists of partitioning suspected polymorphisms from a set of individuals into a minimum number of deletion areas; (iii) and the Multiple Individuals Polymorphic Alu Insertion Recognition Problem that consists of finding the set of locations in the genome where ALU sequences are inserted in some individual(s).All three problems are NP-hard combinatorial optimization problems. Therefore, we analyse their combinatorial structure and we propose an exact approach to solution for each of them. The proposed models are efficient, accurate, compact, polynomial-sized and usable in all those cases for which the parsimony criterion is well suited for estimation. |
Bizet, Martin Bioinformatic inference of a prognostic epigenetic signature of immunity in breast cancers PhD Thesis 2018, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/265092, title = {Bioinformatic inference of a prognostic epigenetic signature of immunity in breast cancers}, author = {Martin Bizet}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/265092/7/ContratDiBizet.pdf}, year = {2018}, date = {2018-01-01}, abstract = {L’altération des marques épigénétiques est de plus en plus reconnue comme une caractéristique fondamentale des cancers. Dans cette th`ese, nous avons utilisé des profils de méthylation de l’ADN en vue d’améliorer la classification des patients atteints du cancer du sein gr^ace `a une approche basée sur l’apprentissage automatique. L’objectif `a long terme est le développement d’outils cliniques de médecine personnalisée. Les données de méthylation de l’ADN furent acquises `a l’aide d’une puce `a ADN dédiée `a la méthylation, appelée Infinium. Cette technologie est récente comparée, par exemple, aux puces d’expression génique et son prétraitement n’est pas encore standardisé. La premi`ere partie de cette th`ese fut donc consacrée `a l’évaluation des méthodes de normalisation par comparaison des données normalisées avec d’autres technologies (pyroséquenccage et RRBS) pour les deux technologies Infinium les plus récentes (450k et 850k). Nous avons également évalué la couverture de régions biologiquement relevantes (promoteurs et amplificateurs) par les deux technologies. Ensuite, nous avons utilisé les données Infinium (correctement prétraitées) pour développer un score, appelé MeTIL score, qui présente une valeur pronostique et prédictive dans les cancers du sein. Nous avons profité de la capacité de la méthylation de l’ADN `a refléter la composition cellulaire pour extraire une signature de méthylation (c’est-`a-dire un ensemble de positions de l’ADN o`u la méthylation varie) qui refl`ete la présence de lymphocytes dans l’échantillon tumoral. Apr`es une sélection de sites présentant une méthylation spécifique aux lymphocytes, nous avons développé une approche basée sur l’apprentissage automatique pour obtenir une signature d’une tailleoptimale réduite `a cinq sites permettant potentiellement une utilisation en clinique. Apr`es conversion de cette signature en un score, nous avons montré sa spécificité pour les lymphocytes `a l’aide de données externes et de simulations informatiques. Puis, nous avons montré la capacité du MeTIL score `a prédire la réponse `a la chimiothérapie ainsi que son pouvoir pronostique dans des cohortes indépendantes de cancer du sein et, m^eme, dans d’autres cancers.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } L’altération des marques épigénétiques est de plus en plus reconnue comme une caractéristique fondamentale des cancers. Dans cette th`ese, nous avons utilisé des profils de méthylation de l’ADN en vue d’améliorer la classification des patients atteints du cancer du sein gr^ace `a une approche basée sur l’apprentissage automatique. L’objectif `a long terme est le développement d’outils cliniques de médecine personnalisée. Les données de méthylation de l’ADN furent acquises `a l’aide d’une puce `a ADN dédiée `a la méthylation, appelée Infinium. Cette technologie est récente comparée, par exemple, aux puces d’expression génique et son prétraitement n’est pas encore standardisé. La premi`ere partie de cette th`ese fut donc consacrée `a l’évaluation des méthodes de normalisation par comparaison des données normalisées avec d’autres technologies (pyroséquenccage et RRBS) pour les deux technologies Infinium les plus récentes (450k et 850k). Nous avons également évalué la couverture de régions biologiquement relevantes (promoteurs et amplificateurs) par les deux technologies. Ensuite, nous avons utilisé les données Infinium (correctement prétraitées) pour développer un score, appelé MeTIL score, qui présente une valeur pronostique et prédictive dans les cancers du sein. Nous avons profité de la capacité de la méthylation de l’ADN `a refléter la composition cellulaire pour extraire une signature de méthylation (c’est-`a-dire un ensemble de positions de l’ADN o`u la méthylation varie) qui refl`ete la présence de lymphocytes dans l’échantillon tumoral. Apr`es une sélection de sites présentant une méthylation spécifique aux lymphocytes, nous avons développé une approche basée sur l’apprentissage automatique pour obtenir une signature d’une tailleoptimale réduite `a cinq sites permettant potentiellement une utilisation en clinique. Apr`es conversion de cette signature en un score, nous avons montré sa spécificité pour les lymphocytes `a l’aide de données externes et de simulations informatiques. Puis, nous avons montré la capacité du MeTIL score `a prédire la réponse `a la chimiothérapie ainsi que son pouvoir pronostique dans des cohortes indépendantes de cancer du sein et, m^eme, dans d’autres cancers. |
2017 |
Fernandez-Domingos, Elias; Burguillo-Rial, Juan C; Lenaerts, Tom Reactive Versus Anticipative Decision Making in a Novel Gift-Giving Game Miscellaneous 2017, (Conference: 29nd Benelux conference on Artificial Intelligence(28-29 nov 2017: Groningen)). @misc{info:hdl:2013/263491, title = {Reactive Versus Anticipative Decision Making in a Novel Gift-Giving Game}, author = {Elias Fernandez-Domingos and Juan C Burguillo-Rial and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/263491}, year = {2017}, date = {2017-01-01}, note = {Conference: 29nd Benelux conference on Artificial Intelligence(28-29 nov 2017: Groningen)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Reggiani, Claudio; Coppens, Sandra; Sekhara, Tayeb; Dimov, Ivan; Pichon, Bruno; Lufin, Nicolas; Addor, Marie Claude; Belligni, Elga Fabia; Digilio, Maria Cristina; Faletra, Flavio; Ferrero, Giovanni Battista; Gerard, Marion; Isidor, Bertrand; Joss, Shelagh; Niel-Bütschi, Florence; Perrone, Maria Dolores; Petit, Florence; Renieri, Alessandra; Romana, Serge; Topa, Alexandra; Vermeesch, Joris Robert; Lenaerts, Tom; Casimir, Georges; Abramowicz, Marc; Bontempi, Gianluca; Vilain, Catheline; Deconinck, Nicolas; Smits, Guillaume Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability. Journal Article In: Genome medicine, 9 (1), pp. 67, 2017, (DOI: 10.1186/s13073-017-0452-y). @article{info:hdl:2013/258564c, title = {Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability.}, author = {Claudio Reggiani and Sandra Coppens and Tayeb Sekhara and Ivan Dimov and Bruno Pichon and Nicolas Lufin and Marie Claude Addor and Elga Fabia Belligni and Maria Cristina Digilio and Flavio Faletra and Giovanni Battista Ferrero and Marion Gerard and Bertrand Isidor and Shelagh Joss and Florence Niel-Bütschi and Maria Dolores Perrone and Florence Petit and Alessandra Renieri and Serge Romana and Alexandra Topa and Joris Robert Vermeesch and Tom Lenaerts and Georges Casimir and Marc Abramowicz and Gianluca Bontempi and Catheline Vilain and Nicolas Deconinck and Guillaume Smits}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/258564}, year = {2017}, date = {2017-01-01}, journal = {Genome medicine}, volume = {9}, number = {1}, pages = {67}, note = {DOI: 10.1186/s13073-017-0452-y}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lipski, D; Dewispelaere, Remi; Foucart, Vincent; Caspers, Laure; Defrance, Matthieu; Bruyns, Catherine; Willermain, Francois MHC class II expression and potential antigen-presenting cells in the retina during experimental autoimmune uveitis Journal Article In: Journal of neuroinflammation, 14 (1), 2017, (DOI: 10.1186/s12974-017-0915-5). @article{info:hdl:2013/258861, title = {MHC class II expression and potential antigen-presenting cells in the retina during experimental autoimmune uveitis}, author = {D Lipski and Remi Dewispelaere and Vincent Foucart and Laure Caspers and Matthieu Defrance and Catherine Bruyns and Francois Willermain}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/258861}, year = {2017}, date = {2017-01-01}, journal = {Journal of neuroinflammation}, volume = {14}, number = {1}, note = {DOI: 10.1186/s12974-017-0915-5}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
López-Ferrando, Víctor; Gazzo, Andrea; Cruz, Xavier De La; Orozco, Modesto; Gelpí, Josep Ll PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update Journal Article In: Nucleic acids research, 45 (W1), pp. W222-W228, 2017, (DOI: 10.1093/nar/gkx313). @article{info:hdl:2013/259491, title = {PMut: A web-based tool for the annotation of pathological variants on proteins, 2017 update}, author = {Víctor López-Ferrando and Andrea Gazzo and Xavier De La Cruz and Modesto Orozco and Josep Ll Gelpí}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/259491}, year = {2017}, date = {2017-01-01}, journal = {Nucleic acids research}, volume = {45}, number = {W1}, pages = {W222-W228}, note = {DOI: 10.1093/nar/gkx313}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Han, The Anh T A H; Pereira, Luís Moniz; Martinez-Vaquero, Luis L A; Lenaerts, Tom Centralized vs. Personalized Commitments and their influence on Cooperation in Group Interactions Inproceedings In: Proceedings of the 31st AAAI Conference on Artificial Intelligence (AAAI-17), 2017, (Conference: 31st AAAI Conference on Artificial Intelligence (AAAI-17)(4-9 February 2017: San Francisco, USA)). @inproceedings{info:hdl:2013/243939b, title = {Centralized vs. Personalized Commitments and their influence on Cooperation in Group Interactions}, author = {The Anh T A H Han and Luís Moniz Pereira and Luis L A Martinez-Vaquero and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243939}, year = {2017}, date = {2017-01-01}, booktitle = {Proceedings of the 31st AAAI Conference on Artificial Intelligence (AAAI-17)}, note = {Conference: 31st AAAI Conference on Artificial Intelligence (AAAI-17)(4-9 February 2017: San Francisco, USA)}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Orlando, Gabriele; Raimondi, Daniele; Khanna, T; Lenaerts, Tom; Vranken, Wim F SVM-dependent pairwise HMM: an application to Protein pairwise alignments. Journal Article In: Bioinformatics, 2017, (DOI: 10.1093/bioinformatics/btx391). @article{info:hdl:2013/254251b, title = {SVM-dependent pairwise HMM: an application to Protein pairwise alignments.}, author = {Gabriele Orlando and Daniele Raimondi and T Khanna and Tom Lenaerts and Wim F Vranken}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/254251}, year = {2017}, date = {2017-01-01}, journal = {Bioinformatics}, note = {DOI: 10.1093/bioinformatics/btx391}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Fernandez-Domingos, Elias; Burguillo-Rial, Juan C; Lenaerts, Tom Reactive Versus Anticipative Decision Making in a Novel Gift-Giving Game Inproceedings In: Proceedings of the 31st AAAI Conference on Artificial Intelligence (AAAI-17), 2017, (Conference: 31st AAAI Conference on Artificial Intelligence (AAAI-17)(4-9 February 2017: San Francisco, USA)). @inproceedings{info:hdl:2013/243947b, title = {Reactive Versus Anticipative Decision Making in a Novel Gift-Giving Game}, author = {Elias Fernandez-Domingos and Juan C Burguillo-Rial and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243947}, year = {2017}, date = {2017-01-01}, booktitle = {Proceedings of the 31st AAAI Conference on Artificial Intelligence (AAAI-17)}, note = {Conference: 31st AAAI Conference on Artificial Intelligence (AAAI-17)(4-9 February 2017: San Francisco, USA)}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Martinez-Vaquero, Luis L A; Han, The Anh T A H; Pereira, Luís Moniz; Lenaerts, Tom When agreement-accepting free-riders are a necessary evil for the evolution of cooperation. Journal Article In: Scientific reports, 7 (1), pp. 2478, 2017, (DOI: 10.1038/s41598-017-02625-z). @article{info:hdl:2013/256610b, title = {When agreement-accepting free-riders are a necessary evil for the evolution of cooperation.}, author = {Luis L A Martinez-Vaquero and The Anh T A H Han and Luís Moniz Pereira and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/256610}, year = {2017}, date = {2017-01-01}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2478}, note = {DOI: 10.1038/s41598-017-02625-z}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Fernandez-Domingos, Elias; Burguillo-Rial, Juan C; Nowe, Ann; Lenaerts, Tom Coordinating Human and Agent Behavior in Collective-Risk Scenarios Inproceedings In: Proceedings of the 31st AAAI Conference on Artificial Intelligence (AAAI-17), 2017, (Conference: 31st AAAI Conference on Artificial Intelligence (AAAI-17)(4-9 February 2017: San Francisco, USA)). @inproceedings{info:hdl:2013/243948b, title = {Coordinating Human and Agent Behavior in Collective-Risk Scenarios}, author = {Elias Fernandez-Domingos and Juan C Burguillo-Rial and Ann Nowe and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243948}, year = {2017}, date = {2017-01-01}, booktitle = {Proceedings of the 31st AAAI Conference on Artificial Intelligence (AAAI-17)}, note = {Conference: 31st AAAI Conference on Artificial Intelligence (AAAI-17)(4-9 February 2017: San Francisco, USA)}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Pham, Ngoc Cam; Haibe-Kains, Benjamin; Bellot, Pau; Bontempi, Gianluca; Meyer, Patrick E Study of Meta-analysis strategies for network inference using information-theoretic approaches Journal Article In: BioData Mining, 10 (1), 2017, (DOI: 10.1186/s13040-017-0136-6). @article{info:hdl:2013/259607b, title = {Study of Meta-analysis strategies for network inference using information-theoretic approaches}, author = {Ngoc Cam Pham and Benjamin Haibe-Kains and Pau Bellot and Gianluca Bontempi and Patrick E Meyer}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/259607}, year = {2017}, date = {2017-01-01}, journal = {BioData Mining}, volume = {10}, number = {1}, note = {DOI: 10.1186/s13040-017-0136-6}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pereira, Luís Moniz; Lenaerts, Tom; Martinez-Vaquero, Luis L A; Han, The Anh T A H Social manifestation of guilt leads to stable cooperation in multi-agent systems Journal Article In: Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS, 3 , pp. 1421-1430, 2017, (Language of publication: en). @article{info:hdl:2013/271395b, title = {Social manifestation of guilt leads to stable cooperation in multi-agent systems}, author = {Luís Moniz Pereira and Tom Lenaerts and Luis L A Martinez-Vaquero and The Anh T A H Han}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/271395}, year = {2017}, date = {2017-01-01}, journal = {Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS}, volume = {3}, pages = {1421-1430}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Han, The Anh T A H; Pereira, Luís Marcelo; Lenaerts, Tom Commitment and participation in public goods games Journal Article In: Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS, 3 , pp. 1431-1432, 2017, (Language of publication: en). @article{info:hdl:2013/290973, title = {Commitment and participation in public goods games}, author = {The Anh T A H Han and Luís Marcelo Pereira and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/290973}, year = {2017}, date = {2017-01-01}, journal = {Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS}, volume = {3}, pages = {1431-1432}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pham, Ngoc Cam; Haibe-Kains, Benjamin; Bellot, Pau; Bontempi, Gianluca; Meyer, Patrick E Study of Meta-analysis Strategies for Network Inference Using Information-Theoretic Approaches Journal Article In: Proceedings - International Workshop on Database and Expert Systems Applications, pp. 76-83, 2017, (DOI: 10.1109/DEXA.2016.030). @article{info:hdl:2013/247710b, title = {Study of Meta-analysis Strategies for Network Inference Using Information-Theoretic Approaches}, author = {Ngoc Cam Pham and Benjamin Haibe-Kains and Pau Bellot and Gianluca Bontempi and Patrick E Meyer}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/247710}, year = {2017}, date = {2017-01-01}, journal = {Proceedings - International Workshop on Database and Expert Systems Applications}, pages = {76-83}, note = {DOI: 10.1109/DEXA.2016.030}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pozzolo, Andrea Dal; Boracchi, Giacomo; Caelen, Olivier; Alippi, Cesare; Bontempi, Gianluca Credit Card Fraud Detection: A Realistic Modeling and a Novel Learning Strategy Journal Article In: IEEE Transactions on Neural Networks and Learning Systems, 99 , 2017, (DOI: 10.1109/TNNLS.2017.2736643). @article{info:hdl:2013/258224b, title = {Credit Card Fraud Detection: A Realistic Modeling and a Novel Learning Strategy}, author = {Andrea Dal Pozzolo and Giacomo Boracchi and Olivier Caelen and Cesare Alippi and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/258224}, year = {2017}, date = {2017-01-01}, journal = {IEEE Transactions on Neural Networks and Learning Systems}, volume = {99}, note = {DOI: 10.1109/TNNLS.2017.2736643}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Xu, Taosheng; Le, Thuc Duy; Liu, Lin; Su, Ning; Wang, Rujing; Sun, Bingyu; Colaprico, Antonio; Bontempi, Gianluca; Li, Jiuyong CancerSubtypes: An R/Bioconductor package for molecular cancer subtype identification, validation and visualization Journal Article In: Bioinformatics, 33 (19), pp. 3131-3133, 2017, (DOI: 10.1093/bioinformatics/btx378). @article{info:hdl:2013/260704b, title = {CancerSubtypes: An R/Bioconductor package for molecular cancer subtype identification, validation and visualization}, author = {Taosheng Xu and Thuc Duy Le and Lin Liu and Ning Su and Rujing Wang and Bingyu Sun and Antonio Colaprico and Gianluca Bontempi and Jiuyong Li}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/260704}, year = {2017}, date = {2017-01-01}, journal = {Bioinformatics}, volume = {33}, number = {19}, pages = {3131-3133}, note = {DOI: 10.1093/bioinformatics/btx378}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Garaud, Soizic; Roufosse, Florence; Silva, Pushpamali De; Gu-Trantien, Chunyan; Lodewyckx, Jean Nicolas; Duvillier, Hugues; Dedeurwaerder, Sarah; Bizet, Martin; Defrance, Matthieu; cc, Fran; cc, Fran; Willard-Gallo, Karen In: European Journal of Immunology, 47 (1), pp. 168-179, 2017, (DOI: 10.1002/eji.201646373). @article{info:hdl:2013/244657, title = {FOXP1 is a regulator of quiescence in healthy human CD4+ T cells and is constitutively repressed in T cells from patients with lymphoproliferative disorders}, author = {Soizic Garaud and Florence Roufosse and Pushpamali De Silva and Chunyan Gu-Trantien and Jean Nicolas Lodewyckx and Hugues Duvillier and Sarah Dedeurwaerder and Martin Bizet and Matthieu Defrance and Fran{cc}ois Fuks and Fran{cc}oise Bex and Karen Willard-Gallo}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/244657}, year = {2017}, date = {2017-01-01}, journal = {European Journal of Immunology}, volume = {47}, number = {1}, pages = {168-179}, note = {DOI: 10.1002/eji.201646373}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bontempi, Gianluca; "e, Yann-A; Stefani, Jacopo De A Dynamic Factor Machine Learning Method for Multi-variate and Multi-step-Ahead Forecasting Inproceedings In: 2017 IEEE International Conference on Data Science and Advanced Analytics (DSAA), pp. 222-231, 2017, (DOI: 10.1109/DSAA.2017.1). @inproceedings{info:hdl:2013/283239, title = {A Dynamic Factor Machine Learning Method for Multi-variate and Multi-step-Ahead Forecasting}, author = {Gianluca Bontempi and Yann-A{"e}l Le Borgne and Jacopo De Stefani}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/283239}, year = {2017}, date = {2017-01-01}, booktitle = {2017 IEEE International Conference on Data Science and Advanced Analytics (DSAA)}, pages = {222-231}, note = {DOI: 10.1109/DSAA.2017.1}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Jansen, Maarten; Amghar, Mohamed Multiscale Local Polynomial Decompositions using bandwidths as scales Journal Article In: Statistics and computing, 27 (5), pp. 1383-1399, 2017, (DOI: 10.1007/s11222-016-9692-8). @article{info:hdl:2013/239871, title = {Multiscale Local Polynomial Decompositions using bandwidths as scales}, author = {Maarten Jansen and Mohamed Amghar}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/239871}, year = {2017}, date = {2017-01-01}, journal = {Statistics and computing}, volume = {27}, number = {5}, pages = {1383-1399}, note = {DOI: 10.1007/s11222-016-9692-8}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lenaerts, Tom; Han, The Anh T A H; Pereira, Luis Moniz; Martinez-Vaquero, Luis A When apology is sincere, cooperation evolves, even when mistakes occur frequently Inproceedings In: Proceedings of the AISB Annual Convention, Symposium on Computational Modelling of Emotion: Theory and Applications, pp. 193-195, 2017, (Language of publication: en). @inproceedings{info:hdl:2013/262904b, title = {When apology is sincere, cooperation evolves, even when mistakes occur frequently}, author = {Tom Lenaerts and The Anh T A H Han and Luis Moniz Pereira and Luis A Martinez-Vaquero}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262904}, year = {2017}, date = {2017-01-01}, booktitle = {Proceedings of the AISB Annual Convention, Symposium on Computational Modelling of Emotion: Theory and Applications}, pages = {193-195}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Raimondi, Daniele; Orlando, Gabriele; Messens, Joris; Vranken, Wim Investigating the Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State Journal Article In: Human mutation, 38 (1), pp. 86-94, 2017, (DOI: 10.1002/humu.23129). @article{info:hdl:2013/242232, title = {Investigating the Molecular Mechanisms Behind Uncharacterized Cysteine Losses from Prediction of Their Oxidation State}, author = {Daniele Raimondi and Gabriele Orlando and Joris Messens and Wim Vranken}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/242232}, year = {2017}, date = {2017-01-01}, journal = {Human mutation}, volume = {38}, number = {1}, pages = {86-94}, note = {DOI: 10.1002/humu.23129}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Han, The Anh T A H; Pereira, Luís Moniz; Martinez-Vaquero, Luis A; Lenaerts, Tom Evolution of commitment and level of participation in public goods games. Inproceedings In: Proceedings of the 16th International Conference on Autonomous Agents and Multiagent Systems (AAMAS), pp. 1431-1432, 2017, (Language of publication: en). @inproceedings{info:hdl:2013/262902b, title = {Evolution of commitment and level of participation in public goods games.}, author = {The Anh T A H Han and Luís Moniz Pereira and Luis A Martinez-Vaquero and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262902}, year = {2017}, date = {2017-01-01}, booktitle = {Proceedings of the 16th International Conference on Autonomous Agents and Multiagent Systems (AAMAS)}, pages = {1431-1432}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Pereira, Luis Moniz; Lenaerts, Tom; Martinez-Vaquero, Luis A; others, Social manifestation of guilt leads to stable cooperation in multi-agent systems Inproceedings In: Proceedings of the 16th Conference on Autonomous Agents and MultiAgent Systems(AAMAS), pp. 1422-1430, 2017, (Language of publication: en). @inproceedings{info:hdl:2013/262903b, title = {Social manifestation of guilt leads to stable cooperation in multi-agent systems}, author = {Luis Moniz Pereira and Tom Lenaerts and Luis A Martinez-Vaquero and others}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262903}, year = {2017}, date = {2017-01-01}, booktitle = {Proceedings of the 16th Conference on Autonomous Agents and MultiAgent Systems(AAMAS)}, pages = {1422-1430}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Pereira, Luis Moniz; Lenaerts, Tom; Han, The Anh T A H; Martinez-Vaquero, Luis A Evolutionary Game Theory Modelling of Guilt Inproceedings In: Proceedings of the AISB Annual Convention, Symposium on Computational Modelling of Emotion: Theory and Applications, pp. 189-192, 2017, (Language of publication: en). @inproceedings{info:hdl:2013/262905b, title = {Evolutionary Game Theory Modelling of Guilt}, author = {Luis Moniz Pereira and Tom Lenaerts and The Anh T A H Han and Luis A Martinez-Vaquero}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262905}, year = {2017}, date = {2017-01-01}, booktitle = {Proceedings of the AISB Annual Convention, Symposium on Computational Modelling of Emotion: Theory and Applications}, pages = {189-192}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Stefani, Jacopo De; Caelen, Olivier; Hattab, Dalila; Bontempi, Gianluca Machine Learning for Multi-step Ahead Forecasting of Volatility Proxies Inproceedings In: 2nd Workshop on MIning DAta for financial applicationS (MIDAS), pp. 17-28, 2017, (Conference: MIDAS 2017(Skopje, Macedonia)). @inproceedings{info:hdl:2013/283252, title = {Machine Learning for Multi-step Ahead Forecasting of Volatility Proxies}, author = {Jacopo De Stefani and Olivier Caelen and Dalila Hattab and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/283252}, year = {2017}, date = {2017-01-01}, booktitle = {2nd Workshop on MIning DAta for financial applicationS (MIDAS)}, pages = {17-28}, series = {CEUR Workshop Proceedings}, note = {Conference: MIDAS 2017(Skopje, Macedonia)}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Amghar, Mohamed Multiscale local polynomial transforms in smoothing and density estimation PhD Thesis 2017, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/262040, title = {Multiscale local polynomial transforms in smoothing and density estimation}, author = {Mohamed Amghar}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262040}, year = {2017}, date = {2017-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Raimondi, Daniele 2017, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/251313c, title = {The effect of genome variation on human proteins: understanding variants and improving their deleteriousness prediction through extensive contextualisation}, author = {Daniele Raimondi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/251313}, year = {2017}, date = {2017-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Brown, David Norman 2017, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/260251b, title = {Application of phylogenetic inference methods to quantify intra-tumour heterogeneity and evolution of breast cancers}, author = {David Norman Brown}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/260251}, year = {2017}, date = {2017-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Devooght, Robin Similarity measures on graphs and novel methods for collaborative filtering PhD Thesis 2017, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/296124, title = {Similarity measures on graphs and novel methods for collaborative filtering}, author = {Robin Devooght}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/296124}, year = {2017}, date = {2017-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Raimondi, Daniele 2017, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/251313, title = {The effect of genome variation on human proteins: understanding variants and improving their deleteriousness prediction through extensive contextualisation}, author = {Daniele Raimondi}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/251313/5/ContratDiRaimondi.pdf}, year = {2017}, date = {2017-01-01}, abstract = {Rapid technological advances are providing unprecedented insights in the biologicalsciences, with massive amounts of data generated on genomic and protein sequences.These data continue to grow exponentially, and they are extremely valuable for com-putational tools where the effect of genomic variants on human health is predicted.State of the art tools in this field give varying results and only tend to agree in thecase of single variants that are strongly correlated to disease. The aim of this workis to increase the reliability of these methods, as well as our understanding of theunderlying biological mechanisms that lead to disease. We first developed machinelearning (ML) based structural bioinformatics predictors that are able to predictmolecular features of proteins from the sequence alone. We then used these tools forin silico analysis of the molecular effects of known variants on the affected proteins,and integrated these data with other sources heterogenous sources of information,such as the essentiality of a gene, that put the variants into their broader biologicalcontext. With this information we created DEOGEN, a novel predictor in this field,which is able to deal with the two most common forms of genomic variation, namelySingle Nucleotide Variants (SNVs) and short Insertions and DELetions (INDELs).DEOGEN performs at least on par with other state of the art methods in this fieldon different datasets. The method was then extended with additional contextualdata and is now available as DEOGEN2 via a web server, which visualizes the pre-dicted results for all variants in most human proteins through an interactive interfacetargeted to both bioinformaticians and clinicians.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } Rapid technological advances are providing unprecedented insights in the biologicalsciences, with massive amounts of data generated on genomic and protein sequences.These data continue to grow exponentially, and they are extremely valuable for com-putational tools where the effect of genomic variants on human health is predicted.State of the art tools in this field give varying results and only tend to agree in thecase of single variants that are strongly correlated to disease. The aim of this workis to increase the reliability of these methods, as well as our understanding of theunderlying biological mechanisms that lead to disease. We first developed machinelearning (ML) based structural bioinformatics predictors that are able to predictmolecular features of proteins from the sequence alone. We then used these tools forin silico analysis of the molecular effects of known variants on the affected proteins,and integrated these data with other sources heterogenous sources of information,such as the essentiality of a gene, that put the variants into their broader biologicalcontext. With this information we created DEOGEN, a novel predictor in this field,which is able to deal with the two most common forms of genomic variation, namelySingle Nucleotide Variants (SNVs) and short Insertions and DELetions (INDELs).DEOGEN performs at least on par with other state of the art methods in this fieldon different datasets. The method was then extended with additional contextualdata and is now available as DEOGEN2 via a web server, which visualizes the pre-dicted results for all variants in most human proteins through an interactive interfacetargeted to both bioinformaticians and clinicians. |
2016 |
Han, The Anh T A H; Pereira, Luís Moniz; Lenaerts, Tom Emergence of Cooperation in Group Interactions: Avoidance versus Restriction Inproceedings In: The 2016 AAAI Spring Symposium Series: Technical Reports, 2016, (Conference: AAAI Spring Symposium on “Ethical and Moral Considerations in Non-Human Agents”(21-23 March 2016: Stanford, USA)). @inproceedings{info:hdl:2013/243792b, title = {Emergence of Cooperation in Group Interactions: Avoidance versus Restriction}, author = {The Anh T A H Han and Luís Moniz Pereira and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243792}, year = {2016}, date = {2016-01-01}, booktitle = {The 2016 AAAI Spring Symposium Series: Technical Reports}, note = {Conference: AAAI Spring Symposium on “Ethical and Moral Considerations in Non-Human Agents”(21-23 March 2016: Stanford, USA)}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Świderska, Ewelina; Łasisz, Jakub; Byrski, Aleksander; Lenaerts, Tom; Samson, Dana; Indurkhya, Bipin; Nowe, Ann; Kisiel-Dorohinicki, Marek Measuring diversity of socio-cognitively inspired ACO search Journal Article In: Lecture notes in computer science, 9597 , pp. 393-408, 2016, (DOI: 10.1007/978-3-319-31204-0_26). @article{info:hdl:2013/231238b, title = {Measuring diversity of socio-cognitively inspired ACO search}, author = {Ewelina Świderska and Jakub Łasisz and Aleksander Byrski and Tom Lenaerts and Dana Samson and Bipin Indurkhya and Ann Nowe and Marek Kisiel-Dorohinicki}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/231238}, year = {2016}, date = {2016-01-01}, journal = {Lecture notes in computer science}, volume = {9597}, pages = {393-408}, note = {DOI: 10.1007/978-3-319-31204-0_26}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bugajski, Iwan; Listkiewicz, Piotr; Byrski, Aleksander; Kisiel-Dorohinicki, Marek; Korczynski, Wojciech; Lenaerts, Tom; Samson, Dana; Indurkhya, Bipin; Nowe, Ann Enhancing particle swarm optimization with socio-cognitive inspirations Journal Article In: Procedia Computer Science, 80 , pp. 804-813, 2016, (DOI: 10.1016/j.procs.2016.05.370). @article{info:hdl:2013/240085b, title = {Enhancing particle swarm optimization with socio-cognitive inspirations}, author = {Iwan Bugajski and Piotr Listkiewicz and Aleksander Byrski and Marek Kisiel-Dorohinicki and Wojciech Korczynski and Tom Lenaerts and Dana Samson and Bipin Indurkhya and Ann Nowe}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/240085}, year = {2016}, date = {2016-01-01}, journal = {Procedia Computer Science}, volume = {80}, pages = {804-813}, note = {DOI: 10.1016/j.procs.2016.05.370}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Martinez-Vaquero, Luis L A; Gruji'c, Jelena; Lenaerts, Tom Equivalence of cooperation indexes: Comment on Universal scaling for the dilemma strength in evolutionary games by Z. Wang et al. Journal Article In: Physics of life reviews, 16 , pp. 196-197, 2016, (DOI: 10.1016/j.plrev.2015.07.005). @article{info:hdl:2013/243586b, title = {Equivalence of cooperation indexes: Comment on Universal scaling for the dilemma strength in evolutionary games by Z. Wang et al.}, author = {Luis L A Martinez-Vaquero and Jelena Gruji'c and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243586}, year = {2016}, date = {2016-01-01}, journal = {Physics of life reviews}, volume = {16}, pages = {196-197}, note = {DOI: 10.1016/j.plrev.2015.07.005}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Han, The Anh T A H; Pereira, Luís Moniz; Lenaerts, Tom Evolution of commitment and level of participation in public goods games Journal Article In: Autonomous agents and multi-agent systems, pp. 24, 2016, (DOI: 10.1007/s10458-016-9338-4). @article{info:hdl:2013/243591b, title = {Evolution of commitment and level of participation in public goods games}, author = {The Anh T A H Han and Luís Moniz Pereira and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243591}, year = {2016}, date = {2016-01-01}, journal = {Autonomous agents and multi-agent systems}, pages = {24}, note = {DOI: 10.1007/s10458-016-9338-4}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bugajski, Iwan; Byrski, Aleksander; Kisiel-Dorohinicki, Marek; Lenaerts, Tom; Samson, Dana; Indurkhya, Bipin Adaptation of Population Structure in Socio-cognitive Particle Swarm Optimization Journal Article In: Procedia Computer Science, 101 , pp. 177-186, 2016, (DOI: 10.1016/j.procs.2016.11.022). @article{info:hdl:2013/247231b, title = {Adaptation of Population Structure in Socio-cognitive Particle Swarm Optimization}, author = {Iwan Bugajski and Aleksander Byrski and Marek Kisiel-Dorohinicki and Tom Lenaerts and Dana Samson and Bipin Indurkhya}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/247231}, year = {2016}, date = {2016-01-01}, journal = {Procedia Computer Science}, volume = {101}, pages = {177-186}, note = {DOI: 10.1016/j.procs.2016.11.022}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Silva, Tiago T C; Colaprico, Antonio; Olsen, Catharina; D'Angelo, Fulvio; Bontempi, Gianluca; Ceccarelli, Michele; Noushmehr, Houtan In: F1000Research, 5 , 2016, (DOI: 10.12688/F1000RESEARCH.8923.1). @article{info:hdl:2013/247761b, title = {TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 1; referees: 1 approved, 1 approved with reservations]}, author = {Tiago T C Silva and Antonio Colaprico and Catharina Olsen and Fulvio D'Angelo and Gianluca Bontempi and Michele Ceccarelli and Houtan Noushmehr}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/247761}, year = {2016}, date = {2016-01-01}, journal = {F1000Research}, volume = {5}, note = {DOI: 10.12688/F1000RESEARCH.8923.1}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
"e, Yann-A; Homolova, Adriana; Bontempi, Gianluca OpenTED browser: Insights into European Public Spendings Journal Article In: CEUR Workshop Proceedings, 1831 , 2016, (Language of publication: en). @article{info:hdl:2013/253331b, title = {OpenTED browser: Insights into European Public Spendings}, author = {Yann-A{"e}l Le Borgne and Adriana Homolova and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/253331}, year = {2016}, date = {2016-01-01}, journal = {CEUR Workshop Proceedings}, volume = {1831}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bontempi, Gianluca A blocking strategy for ranking features according to probabilistic relevance Journal Article In: Lecture notes in computer science, 10122 LNCS , pp. 59-69, 2016, (DOI: 10.1007/978-3-319-51469-7_5). @article{info:hdl:2013/247751b, title = {A blocking strategy for ranking features according to probabilistic relevance}, author = {Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/247751}, year = {2016}, date = {2016-01-01}, journal = {Lecture notes in computer science}, volume = {10122 LNCS}, pages = {59-69}, note = {DOI: 10.1007/978-3-319-51469-7_5}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Delatte, Benjamin; Wang, Feifei; Ngoc, Long Vo; Collignon, Evelyne; Bonvin, Elise; Deplus, Rachel; Calonne, Emilie; Hassabi, Bouchra; Putmans, Pascale; Awe, Stephan; Wetzel, Collin; Kreher, Judith; Soin, Romuald; Creppe, Catherine; Limbach, Patrick A; Gueydan, Cyril; Kruys, Véronique; Brehm, A; Minakhina, Svetlana; Defrance, Matthieu; Steward, Ruth; cc, Fran Transcriptome-wide distribution and function of RNA hydroxymethylcytosine Journal Article In: Science, 351 (6270), pp. 282-285, 2016, (DOI: 10.1126/science.aac5253). @article{info:hdl:2013/224506, title = {Transcriptome-wide distribution and function of RNA hydroxymethylcytosine}, author = {Benjamin Delatte and Feifei Wang and Long Vo Ngoc and Evelyne Collignon and Elise Bonvin and Rachel Deplus and Emilie Calonne and Bouchra Hassabi and Pascale Putmans and Stephan Awe and Collin Wetzel and Judith Kreher and Romuald Soin and Catherine Creppe and Patrick A Limbach and Cyril Gueydan and Véronique Kruys and A Brehm and Svetlana Minakhina and Matthieu Defrance and Ruth Steward and Fran{cc}ois Fuks}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/224506}, year = {2016}, date = {2016-01-01}, journal = {Science}, volume = {351}, number = {6270}, pages = {282-285}, note = {DOI: 10.1126/science.aac5253}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Brenner, Carmen; Luciani, Judith; Bizet, Martin; Ndlovu, Matladi N; Josseaux, Eléonore; Dedeurwaerder, Sarah; Calonne, Emilie; Putmans, Pascale; Cartron, Pierre Francois; Defrance, Matthieu; cc, Fran; Deplus, Rachel The interplay between the lysine demethylase KDM1A and DNA methyltransferases in cancer cells is cell cycle dependent Journal Article In: Oncotarget, 7 (37), pp. 58939-58952, 2016, (DOI: 10.18632/oncotarget.10624). @article{info:hdl:2013/243793, title = {The interplay between the lysine demethylase KDM1A and DNA methyltransferases in cancer cells is cell cycle dependent}, author = {Carmen Brenner and Judith Luciani and Martin Bizet and Matladi N Ndlovu and Eléonore Josseaux and Sarah Dedeurwaerder and Emilie Calonne and Pascale Putmans and Pierre Francois Cartron and Matthieu Defrance and Fran{cc}ois Fuks and Rachel Deplus}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243793}, year = {2016}, date = {2016-01-01}, journal = {Oncotarget}, volume = {7}, number = {37}, pages = {58939-58952}, note = {DOI: 10.18632/oncotarget.10624}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jansen, Maarten Non-equispaced B-spline wavelets Journal Article In: International Journal of Wavelets, Multiresolution and Information Processing, 14 (6), 2016, (DOI: 10.1142/S0219691316500569). @article{info:hdl:2013/239870, title = {Non-equispaced B-spline wavelets}, author = {Maarten Jansen}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/239870}, year = {2016}, date = {2016-01-01}, journal = {International Journal of Wavelets, Multiresolution and Information Processing}, volume = {14}, number = {6}, note = {DOI: 10.1142/S0219691316500569}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Wit, Nathalie De; Lenaerts, Tom Cluster analysis of neurodevelopmental diseases with Spark. Informatique Masters Thesis 2016, (Language of publication: fr). @mastersthesis{info:hdl:2013/243961b, title = {Cluster analysis of neurodevelopmental diseases with Spark. Informatique}, author = {Nathalie De Wit and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243961}, year = {2016}, date = {2016-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Steckelmacher, Denis; Lenaerts, Tom Reinforcement learning in complex environments: Evaluating algorithms on image classification. Informatique Masters Thesis 2016, (Language of publication: fr). @mastersthesis{info:hdl:2013/243960b, title = {Reinforcement learning in complex environments: Evaluating algorithms on image classification. Informatique}, author = {Denis Steckelmacher and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243960}, year = {2016}, date = {2016-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Velde, Thibaut Van De; Lenaerts, Tom Concevoir un mod`ele de jeu `a ressources communes au sein d'un cloud. Informatique Masters Thesis 2016, (Language of publication: fr). @mastersthesis{info:hdl:2013/243959b, title = {Concevoir un mod`ele de jeu `a ressources communes au sein d'un cloud. Informatique}, author = {Thibaut Van De Velde and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243959}, year = {2016}, date = {2016-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Zisis, Ioannis The Effect of Group Formation on Behaviour: An Experimental and Evolutionary Analysis PhD Thesis 2016, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/231974c, title = {The Effect of Group Formation on Behaviour: An Experimental and Evolutionary Analysis}, author = {Ioannis Zisis}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/231974}, year = {2016}, date = {2016-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Wit, Nathalie De; Lenaerts, Tom Cluster analysis of neurodevelopmental diseases with Spark. Informatique Masters Thesis 2016, (Language of publication: fr). @mastersthesis{info:hdl:2013/243961, title = {Cluster analysis of neurodevelopmental diseases with Spark. Informatique}, author = {Nathalie De Wit and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243961}, year = {2016}, date = {2016-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Steckelmacher, Denis; Lenaerts, Tom Reinforcement learning in complex environments: Evaluating algorithms on image classification. Informatique Masters Thesis 2016, (Language of publication: fr). @mastersthesis{info:hdl:2013/243960, title = {Reinforcement learning in complex environments: Evaluating algorithms on image classification. Informatique}, author = {Denis Steckelmacher and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243960}, year = {2016}, date = {2016-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Velde, Thibaut Van De; Lenaerts, Tom Concevoir un mod`ele de jeu `a ressources communes au sein d'un cloud. Informatique Masters Thesis 2016, (Language of publication: fr). @mastersthesis{info:hdl:2013/243959, title = {Concevoir un mod`ele de jeu `a ressources communes au sein d'un cloud. Informatique}, author = {Thibaut Van De Velde and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243959}, year = {2016}, date = {2016-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Tomás, Gil Da Rocha 2016, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/235915b, title = {Gene Expression Markers of Proliferation and Differentiation in Cancer & The Extent of Prognostic Signals in the Cancer Transcriptome}, author = {Gil Da Rocha Tomás}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/235915}, year = {2016}, date = {2016-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Tarabichi, Maxime Integrative analyses of genome-wide transcriptomic and genomic thyroid cancer profiles PhD Thesis 2016, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/225138b, title = {Integrative analyses of genome-wide transcriptomic and genomic thyroid cancer profiles}, author = {Maxime Tarabichi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/225138}, year = {2016}, date = {2016-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Zisis, Ioannis The Effect of Group Formation on Behaviour: An Experimental and Evolutionary Analysis PhD Thesis 2016, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/231974, title = {The Effect of Group Formation on Behaviour: An Experimental and Evolutionary Analysis}, author = {Ioannis Zisis}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/231974/5/contratZisis.pdf}, year = {2016}, date = {2016-01-01}, abstract = {The division of resources between a group of people may cause con- flicts: Individuals with varying roles and responsibilities will claim different shares of the surplus to be divided. In this dissertation, we analyze how the decision to form a group will influence the bargaining behaviour of the members of that group. People will act collectively as certain tasks may require the participation of a specific number of individuals before it can be completed. We examine whether certain mechanisms can efficiently promote group formation for the sake of surplus production, and then, what will be the effect of these mechanisms on the behaviour of the group members. For these reasons, we constructed a novel surplus production and distribution interaction which we call the Anticipation Game (AG). The AG can be played between only two players (pairwise interaction) or among more then two players (group interaction). In our study we will analyze both the pairwise AG and the group version of AG, first by obtaining our own empirical data and then by performing a stochastic evolutionary analysis. We aim to provide answers on: i) how will a reputation based partner approval mechanism influence the surplus distribution in both the pairwise and the group AG, ii) will then limitations in obtaining the reputation of a potential partner alter the results of the pairwise AG?, iii) will we notice any effect on the behaviour of players when they can repeatedly cooperate with the same partners in group interactions, iv) how natural selection may have shaped the behaviour of players in group formation interactions (both pairwise and group AG evolutionary analysis).}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } The division of resources between a group of people may cause con- flicts: Individuals with varying roles and responsibilities will claim different shares of the surplus to be divided. In this dissertation, we analyze how the decision to form a group will influence the bargaining behaviour of the members of that group. People will act collectively as certain tasks may require the participation of a specific number of individuals before it can be completed. We examine whether certain mechanisms can efficiently promote group formation for the sake of surplus production, and then, what will be the effect of these mechanisms on the behaviour of the group members. For these reasons, we constructed a novel surplus production and distribution interaction which we call the Anticipation Game (AG). The AG can be played between only two players (pairwise interaction) or among more then two players (group interaction). In our study we will analyze both the pairwise AG and the group version of AG, first by obtaining our own empirical data and then by performing a stochastic evolutionary analysis. We aim to provide answers on: i) how will a reputation based partner approval mechanism influence the surplus distribution in both the pairwise and the group AG, ii) will then limitations in obtaining the reputation of a potential partner alter the results of the pairwise AG?, iii) will we notice any effect on the behaviour of players when they can repeatedly cooperate with the same partners in group interactions, iv) how natural selection may have shaped the behaviour of players in group formation interactions (both pairwise and group AG evolutionary analysis). |
Tarabichi, Maxime Integrative analyses of genome-wide transcriptomic and genomic thyroid cancer profiles PhD Thesis 2016, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/225138, title = {Integrative analyses of genome-wide transcriptomic and genomic thyroid cancer profiles}, author = {Maxime Tarabichi}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/225138/5/ContratMaximeTarabichi.pdf}, year = {2016}, date = {2016-01-01}, abstract = {Cette th`ese en bioinformatique a été réalisée entre 2010 et 2015 dans le groupe du Pr. Vincent Detours `a l’Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire. Nous avons analysé des données génomiques et transcriptomiques provenant de carcinomes papillaires de la thyro"ide (CPTs) et leurs tissus non-cancéreux adjacents. La premi`ere partie étudiait les différences transcriptomiques entre CPTs post-Tchernobyl et CPTs sporadiques, et leur tissus non-cancéreux adjacents. Dans notre cohorte, les cas sporadiques étaient en moyenne et significativement un an plus jeunes. Apr`es un ajustement des données transcriptionnelles pour l'^age, pr`es de 400 g`enes étaient plus exprimés dans les tissus adjacents des patients exposés aux radiations. Cependant, nous n’avons pu détecter aucune surreprésentation de groupe de g`enes participant `a des fonctions biologiques connues. Il était possible de distinguer les cas sporadiques des cas post-Tchernobyl sur base des transcriptomes de leurs tissus adjacents, avec une précision de ~70%. Cette surexpression de g`enes dans les tissus non-cancéreux adjacents pourrait ^etre liée `a une radiosensibilité accrue dans le groupe des patients exposés aux radiations de Tchernobyl. Dans la deuxi`eme étude, nous avons intégré des données provenant des patients de la premi`ere partie, incluant les nombres de copies d'ADN des CPTs, le génotype de plus de 400.000 SNPs dans le sang et les données transcriptionnelles des CPTs et leurs tissus non-cancéreux adjacents. En reproduisant les résultats d'une étude précédente, nous avons retrouvé la région 7q11.23 dupliquée exclusivement dans un tiers des patients exposés aux radiations. Dans une étude indépendante, un autre groupe a montré que la duplication de cette région était plus fréquente dans une population de lignées cellulaires radiosensibles que dans la population humaine normale. Cependant, en analysant les transcriptomes des patients présentant cette duplication, nous n'avons pas détecté de différence d’expression des g`enes codés dans cette région génomique. En outre, aucun génotype de SNP n'était significativement lié `a l'exposition aux radiations. En conclusion, les résultats confirment qu'un tiers des CPTs post-Tchernobyl ont des traces d'un dég^at radio-sensibilsant dans leur ADN. Dans une troisi`eme étude, nous avons étudié les différences transcriptionnelles entre CPTs et leurs métastases ganglionnaires (MGs) associées, ainsi qu'entre des CPTs développant des MGs (N+) et des CPTs ne développant pas de MGs (N0). Des études précédentes comparant les MGs et leurs tumeurs associées impliquant d’autres organes ont montré une surexpression de g`enes dans les MGs, liés aux cellules immunitaires. Ce signal provient du tissu contaminant environnant les MGs. Pour se défaire de ce signal contaminant, d’autres études ont microdisséqué au laser les parties tumorales des MGs. Cependant, la microdissection retire aussi le stroma associé `a la tumeur, alors que celui-ci est justement impliqué dans la progression tumorale. Gr^ace `a une méthode originale, nous avons corrigé nos données d’expression des MGs pour leur contenu en contaminant ganglionnaire non-cancéreux. Apr`es cette correction, l’expression de g`enes liés au stroma était plus élevée dans les MGs que dans leurs CPTs. Les différences d’expression entre N0 et N+ n’étaient pas reproductibles entre 4 jeux de données indépendants de CPTs. Ceci démontre l’absence d’un signal transcriptionnelle lié au statut nodal dans ces données. Cependant, en utilisant des données publiques comprenant des centaines de tumeurs, il est possible de prédire le statut nodal (N0 ou N+) des CPTs ainsi que des cancers du sein et du colon `a partir de leurs transcriptomes. Des études précédentes montraient des taux de prédiction presque parfaits (>90%) du statut nodal `a partir des données transcriptomiques. Nous avons décelés dans ces études le m^eme biais technique de sélection des g`enes, qui peut expliquer ces taux artificiellement élevés. Dans notre étude, ce biais n’était pas présent et la précision de nos prédictions était limitée (<70%), questionnant l’intér^et clinique de telles prédictions. La présence d’un signal permettant de prédire le statut nodal et l’irreproductibilité de ce signal dans des jeux de données indépendants peuvent s'expliquer par l’association entre le statut nodal et des caractéristiques d'agressivité des tumeurs, qui pourraient, elles, avoir une influence reproductible sur les transcriptomes. Dans notre derni`ere étude, nous avons analysé les différences entre CPTs, liées `a la présence de BRAFV600E, une mutation commune `a 60% des CPTs. En utilisant un jeu de données public, nous avons montré que les CPTs présentant la mutation étaient plus dédifférenciés, et plus infiltrés en stroma, probablement en lymphocytes et fibroblastes; et que ces CPTs présentaient plus de fibrose et proliféraient sans doute plus. Tout ceci sugg`ere que les CPTs mutés pour BRAF constituent un groupe de CPTs plus agressif. Des caractéristiques d’agressivité pourraient ^etre détectées au front invasif, c’est-`a-dire la périphérie de la tumeur définissant son contact avec le stroma, notamment la présence de regroupement de cellules isolées du reste de la tumeur. Dans les CPTs, ces ^ilots cellulaires isolés sont observés sur des lames histologiques 2D et pourraient ^etre expliqués soit par un détachement cellulaire, signe d’agressivité lié au processus métastatique, soit une conformation complexe compatible avec une tumeur connexe en 3D. Dans un CPT, nous avons analysé la conformation 3D du front invasif d'un CPT muté. Nous avons reconstruit son volume 3D gr^ace `a une méthode originale. Les groupes de cellules cancéreuses qui semblaient isolées sur les images 2D d’histopathologie, étaient en fait connectés en 3D. L’hypoth`ese de la présence de détachement cellulaire suite `a la transition épithélio-mésenchymateuse n’est donc pas requise pour expliquer la présence de ces ^ilots cellulaires en 2D. La forme 3D du front invasif impliquait une surface de contact entre tumeur et stroma bien plus importante qu'impliquée par la forme ellipso"ide habituellement décrite. Les fibroblastes participaient autant `a la création de la masse tumorale que les cellules cancéreuses, puisque ces deux groupes de cellules proliféraient `a la m^eme vitesse. A l'avenir, le séquenccage du matériel génétique de cellules individuelles facilitera notre interprétation des signaux génomiques et transcriptomiques, qui jusqu’alors provenaient de tissu complet, i.e. un mélange de populations de cellules tumorales, stromales et de contaminant. Une signature de radiation pourrait ^etre extraite des profils mutationnels de cellules individuelles exposées aux radiations et `a l’H2O2 in vitro et comparée `a la signature des CTPs post-Tchernobyl. Les cellules tumorales et stromales individuelles des MGs pourraient ^etre comparées aux cellules tumorales et stromales invividuelles des CPTs. De m^eme les cellules individuelles mutées pour BRAFV600E pourraient ^etre comparées aux cellules non mutées.}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } Cette th`ese en bioinformatique a été réalisée entre 2010 et 2015 dans le groupe du Pr. Vincent Detours `a l’Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire. Nous avons analysé des données génomiques et transcriptomiques provenant de carcinomes papillaires de la thyro"ide (CPTs) et leurs tissus non-cancéreux adjacents. La premi`ere partie étudiait les différences transcriptomiques entre CPTs post-Tchernobyl et CPTs sporadiques, et leur tissus non-cancéreux adjacents. Dans notre cohorte, les cas sporadiques étaient en moyenne et significativement un an plus jeunes. Apr`es un ajustement des données transcriptionnelles pour l'^age, pr`es de 400 g`enes étaient plus exprimés dans les tissus adjacents des patients exposés aux radiations. Cependant, nous n’avons pu détecter aucune surreprésentation de groupe de g`enes participant `a des fonctions biologiques connues. Il était possible de distinguer les cas sporadiques des cas post-Tchernobyl sur base des transcriptomes de leurs tissus adjacents, avec une précision de ~70%. Cette surexpression de g`enes dans les tissus non-cancéreux adjacents pourrait ^etre liée `a une radiosensibilité accrue dans le groupe des patients exposés aux radiations de Tchernobyl. Dans la deuxi`eme étude, nous avons intégré des données provenant des patients de la premi`ere partie, incluant les nombres de copies d'ADN des CPTs, le génotype de plus de 400.000 SNPs dans le sang et les données transcriptionnelles des CPTs et leurs tissus non-cancéreux adjacents. En reproduisant les résultats d'une étude précédente, nous avons retrouvé la région 7q11.23 dupliquée exclusivement dans un tiers des patients exposés aux radiations. Dans une étude indépendante, un autre groupe a montré que la duplication de cette région était plus fréquente dans une population de lignées cellulaires radiosensibles que dans la population humaine normale. Cependant, en analysant les transcriptomes des patients présentant cette duplication, nous n'avons pas détecté de différence d’expression des g`enes codés dans cette région génomique. En outre, aucun génotype de SNP n'était significativement lié `a l'exposition aux radiations. En conclusion, les résultats confirment qu'un tiers des CPTs post-Tchernobyl ont des traces d'un dég^at radio-sensibilsant dans leur ADN. Dans une troisi`eme étude, nous avons étudié les différences transcriptionnelles entre CPTs et leurs métastases ganglionnaires (MGs) associées, ainsi qu'entre des CPTs développant des MGs (N+) et des CPTs ne développant pas de MGs (N0). Des études précédentes comparant les MGs et leurs tumeurs associées impliquant d’autres organes ont montré une surexpression de g`enes dans les MGs, liés aux cellules immunitaires. Ce signal provient du tissu contaminant environnant les MGs. Pour se défaire de ce signal contaminant, d’autres études ont microdisséqué au laser les parties tumorales des MGs. Cependant, la microdissection retire aussi le stroma associé `a la tumeur, alors que celui-ci est justement impliqué dans la progression tumorale. Gr^ace `a une méthode originale, nous avons corrigé nos données d’expression des MGs pour leur contenu en contaminant ganglionnaire non-cancéreux. Apr`es cette correction, l’expression de g`enes liés au stroma était plus élevée dans les MGs que dans leurs CPTs. Les différences d’expression entre N0 et N+ n’étaient pas reproductibles entre 4 jeux de données indépendants de CPTs. Ceci démontre l’absence d’un signal transcriptionnelle lié au statut nodal dans ces données. Cependant, en utilisant des données publiques comprenant des centaines de tumeurs, il est possible de prédire le statut nodal (N0 ou N+) des CPTs ainsi que des cancers du sein et du colon `a partir de leurs transcriptomes. Des études précédentes montraient des taux de prédiction presque parfaits (>90%) du statut nodal `a partir des données transcriptomiques. Nous avons décelés dans ces études le m^eme biais technique de sélection des g`enes, qui peut expliquer ces taux artificiellement élevés. Dans notre étude, ce biais n’était pas présent et la précision de nos prédictions était limitée (<70%), questionnant l’intér^et clinique de telles prédictions. La présence d’un signal permettant de prédire le statut nodal et l’irreproductibilité de ce signal dans des jeux de données indépendants peuvent s'expliquer par l’association entre le statut nodal et des caractéristiques d'agressivité des tumeurs, qui pourraient, elles, avoir une influence reproductible sur les transcriptomes. Dans notre derni`ere étude, nous avons analysé les différences entre CPTs, liées `a la présence de BRAFV600E, une mutation commune `a 60% des CPTs. En utilisant un jeu de données public, nous avons montré que les CPTs présentant la mutation étaient plus dédifférenciés, et plus infiltrés en stroma, probablement en lymphocytes et fibroblastes; et que ces CPTs présentaient plus de fibrose et proliféraient sans doute plus. Tout ceci sugg`ere que les CPTs mutés pour BRAF constituent un groupe de CPTs plus agressif. Des caractéristiques d’agressivité pourraient ^etre détectées au front invasif, c’est-`a-dire la périphérie de la tumeur définissant son contact avec le stroma, notamment la présence de regroupement de cellules isolées du reste de la tumeur. Dans les CPTs, ces ^ilots cellulaires isolés sont observés sur des lames histologiques 2D et pourraient ^etre expliqués soit par un détachement cellulaire, signe d’agressivité lié au processus métastatique, soit une conformation complexe compatible avec une tumeur connexe en 3D. Dans un CPT, nous avons analysé la conformation 3D du front invasif d'un CPT muté. Nous avons reconstruit son volume 3D gr^ace `a une méthode originale. Les groupes de cellules cancéreuses qui semblaient isolées sur les images 2D d’histopathologie, étaient en fait connectés en 3D. L’hypoth`ese de la présence de détachement cellulaire suite `a la transition épithélio-mésenchymateuse n’est donc pas requise pour expliquer la présence de ces ^ilots cellulaires en 2D. La forme 3D du front invasif impliquait une surface de contact entre tumeur et stroma bien plus importante qu'impliquée par la forme ellipso"ide habituellement décrite. Les fibroblastes participaient autant `a la création de la masse tumorale que les cellules cancéreuses, puisque ces deux groupes de cellules proliféraient `a la m^eme vitesse. A l'avenir, le séquenccage du matériel génétique de cellules individuelles facilitera notre interprétation des signaux génomiques et transcriptomiques, qui jusqu’alors provenaient de tissu complet, i.e. un mélange de populations de cellules tumorales, stromales et de contaminant. Une signature de radiation pourrait ^etre extraite des profils mutationnels de cellules individuelles exposées aux radiations et `a l’H2O2 in vitro et comparée `a la signature des CTPs post-Tchernobyl. Les cellules tumorales et stromales individuelles des MGs pourraient ^etre comparées aux cellules tumorales et stromales invividuelles des CPTs. De m^eme les cellules individuelles mutées pour BRAFV600E pourraient ^etre comparées aux cellules non mutées. |
2015 |
Pozzolo, Andrea Dal; Caelen, Olivier; Johnson, Reid; Bontempi, Gianluca Calibrating Probability with Undersampling for Unbalanced Classification Inproceedings In: 2015 IEEE Symposium on Computational Intelligence and Data Mining, 2015, (Language of publication: en). @inproceedings{info:hdl:2013/221670, title = {Calibrating Probability with Undersampling for Unbalanced Classification}, author = {Andrea Dal Pozzolo and Olivier Caelen and Reid Johnson and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/221670}, year = {2015}, date = {2015-01-01}, booktitle = {2015 IEEE Symposium on Computational Intelligence and Data Mining}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Zisis, Ioannis; Guida, Sibilla Di; Han, The Anh T A H; Kirchsteiger, Georg; Lenaerts, Tom Receivers’ acceptance drives the generosity of dictators in a dictator game with partner selection Miscellaneous 2015, (Conference: Student Conference on Complexity Science(9-11 September 2015: Granada, Spain)). @misc{info:hdl:2013/243680, title = {Receivers’ acceptance drives the generosity of dictators in a dictator game with partner selection}, author = {Ioannis Zisis and Sibilla Di Guida and The Anh T A H Han and Georg Kirchsteiger and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243680}, year = {2015}, date = {2015-01-01}, note = {Conference: Student Conference on Complexity Science(9-11 September 2015: Granada, Spain)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Zisis, Ioannis; Guida, Sibilla Di; Han, The Anh T A H; Kirchsteiger, Georg; Lenaerts, Tom An experimental and evolutionary analysis of group formation and gift giving Miscellaneous 2015, (Conference: Conference on Complex Systems(28 September - 2 October 2015: Tempe, USA)). @misc{info:hdl:2013/243679, title = {An experimental and evolutionary analysis of group formation and gift giving}, author = {Ioannis Zisis and Sibilla Di Guida and The Anh T A H Han and Georg Kirchsteiger and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243679}, year = {2015}, date = {2015-01-01}, note = {Conference: Conference on Complex Systems(28 September - 2 October 2015: Tempe, USA)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Zisis, Ioannis; Guida, Sibilla Di; Han, The Anh T A H; Kirchsteiger, Georg; Lenaerts, Tom Receivers’ acceptance drives the generosity of dictators in a dictator game with partner selection Miscellaneous 2015, (Conference: Physics Meets the Social Science, Granada Seminar on Computational and Statistical Physics(15-19 june 2015: La Herradura, Spain)). @misc{info:hdl:2013/243682, title = {Receivers’ acceptance drives the generosity of dictators in a dictator game with partner selection}, author = {Ioannis Zisis and Sibilla Di Guida and The Anh T A H Han and Georg Kirchsteiger and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243682}, year = {2015}, date = {2015-01-01}, note = {Conference: Physics Meets the Social Science, Granada Seminar on Computational and Statistical Physics(15-19 june 2015: La Herradura, Spain)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Martinez-Vaquero, Luis L A; Han, The Anh T A H; Pereira, Luís Moniz; Lenaerts, Tom Emergence of revenge and forgiveness in commitments Miscellaneous 2015, (Conference: Physics Meets the Social Science, Granada Seminar on Computational and Statistical Physics(15-19 June 2015: La Herradura, Spain)). @misc{info:hdl:2013/243683, title = {Emergence of revenge and forgiveness in commitments}, author = {Luis L A Martinez-Vaquero and The Anh T A H Han and Luís Moniz Pereira and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243683}, year = {2015}, date = {2015-01-01}, note = {Conference: Physics Meets the Social Science, Granada Seminar on Computational and Statistical Physics(15-19 June 2015: La Herradura, Spain)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Gazzo, Andrea; Daneels, Dorien; Smits, Guillaume; Dooren, Sonia Van; Cilia, Elisa; Lenaerts, Tom DIDA - A first digenic diseases database Miscellaneous 2015, (Conference: 15th Annual Meeting of the Belgian Society of Human Genetics(6 May 2015: Charleroi, Belgium)). @misc{info:hdl:2013/243685, title = {DIDA - A first digenic diseases database}, author = {Andrea Gazzo and Dorien Daneels and Guillaume Smits and Sonia Van Dooren and Elisa Cilia and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243685}, year = {2015}, date = {2015-01-01}, note = {Conference: 15th Annual Meeting of the Belgian Society of Human Genetics(6 May 2015: Charleroi, Belgium)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Conard, Ashley M; Cilia, Elisa; Lenaerts, Tom 2015, (Conference: The 23rd Annual International Conference on Intelligent Systems for Molecular Biology and the 14th European Conference on Computational Biology(10-14 July 2015: Dublin, ireland)). @misc{info:hdl:2013/243689, title = {Determining the winning SH3 coalition: how cooperative game theory reveals the importance of domain residues in peptide binding}, author = {Ashley M Conard and Elisa Cilia and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243689}, year = {2015}, date = {2015-01-01}, note = {Conference: The 23rd Annual International Conference on Intelligent Systems for Molecular Biology and the 14th European Conference on Computational Biology(10-14 July 2015: Dublin, ireland)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Gazzo, Andrea; Daneels, Dorien; Bonduelle, Maryse; Dooren, Sonia Van; Smits, Guillaume; Lenaerts, Tom Predicting oligogenic effects using digenic disease data Miscellaneous 2015, (Conference: 10th BeNeLux Bioinformatics Conference(7-8 December 2015: Antwerp, Belgium)). @misc{info:hdl:2013/243688, title = {Predicting oligogenic effects using digenic disease data}, author = {Andrea Gazzo and Dorien Daneels and Maryse Bonduelle and Sonia Van Dooren and Guillaume Smits and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243688}, year = {2015}, date = {2015-01-01}, note = {Conference: 10th BeNeLux Bioinformatics Conference(7-8 December 2015: Antwerp, Belgium)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Daneels, Dorien; Gazzo, Andrea; Bonduelle, Maryse; Smits, Guillaume; Cilia, Elisa; Lenaerts, Tom; Dooren, Sonia Van DIDA: a first database on digenic diseases Miscellaneous 2015, (Conference: VUB DS-LSM PhD day(31 March 2015: Jette, Belgium)). @misc{info:hdl:2013/243686, title = {DIDA: a first database on digenic diseases}, author = {Dorien Daneels and Andrea Gazzo and Maryse Bonduelle and Guillaume Smits and Elisa Cilia and Tom Lenaerts and Sonia Van Dooren}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243686}, year = {2015}, date = {2015-01-01}, note = {Conference: VUB DS-LSM PhD day(31 March 2015: Jette, Belgium)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Gazzo, Andrea; Daneels, Dorien; Smits, Guillaume; Dooren, Sonia Van; Cilia, Elisa; Lenaerts, Tom DIDA - A first digenic diseases database Miscellaneous 2015, (Conference: Cold Spring Harbor Laboratory conference on Genome Informatics(28-31 October 2015: Cold Spring Harbor, USA)). @misc{info:hdl:2013/243687, title = {DIDA - A first digenic diseases database}, author = {Andrea Gazzo and Dorien Daneels and Guillaume Smits and Sonia Van Dooren and Elisa Cilia and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243687}, year = {2015}, date = {2015-01-01}, note = {Conference: Cold Spring Harbor Laboratory conference on Genome Informatics(28-31 October 2015: Cold Spring Harbor, USA)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Huculeci, Radu; Cilia, Elisa; Buts, Lieven; Houben, Klaartje; van Nuland, Nico A J; Lenaerts, Tom SH2 sidechain dynamics may be key to unlock kinase activity Miscellaneous 2015, (Conference: Keystone symposium - The Biological Code of Cell Signaling: A Tribute to Tony Pawson(11-15 january 2015: Steamboat springs, Colorado, USA)). @misc{info:hdl:2013/243692, title = {SH2 sidechain dynamics may be key to unlock kinase activity}, author = {Radu Huculeci and Elisa Cilia and Lieven Buts and Klaartje Houben and Nico A J van Nuland and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243692}, year = {2015}, date = {2015-01-01}, note = {Conference: Keystone symposium - The Biological Code of Cell Signaling: A Tribute to Tony Pawson(11-15 january 2015: Steamboat springs, Colorado, USA)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Ruano, Ana Zafra; Cilia, Elisa; Couceiro, José JR; Sanz, Javier Ruiz; Schymkowitz, Joost J; Rousseau, Frédéric; Luque, Irene; Lenaerts, Tom On the evolutionary conservation of the dynamic changes predicted for a collection of SH3 domain structures Miscellaneous 2015, (Conference: Keystone symposium - The Biological Code of Cell Signaling: A Tribute to Tony Pawson(11-16 January 2015: Steamboat springs, Colorado, USA)). @misc{info:hdl:2013/243694, title = {On the evolutionary conservation of the dynamic changes predicted for a collection of SH3 domain structures}, author = {Ana Zafra Ruano and Elisa Cilia and José JR Couceiro and Javier Ruiz Sanz and Joost J Schymkowitz and Frédéric Rousseau and Irene Luque and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243694}, year = {2015}, date = {2015-01-01}, note = {Conference: Keystone symposium - The Biological Code of Cell Signaling: A Tribute to Tony Pawson(11-16 January 2015: Steamboat springs, Colorado, USA)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Lenaerts, Tom Bits and bytes of protein domain communication Miscellaneous 2015, (Conference: International Conference on Emergence in Chemical Systems(21-27 june 2015: Anchorage, USA)). @misc{info:hdl:2013/243701, title = {Bits and bytes of protein domain communication}, author = {Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243701}, year = {2015}, date = {2015-01-01}, note = {Conference: International Conference on Emergence in Chemical Systems(21-27 june 2015: Anchorage, USA)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Lenaerts, Tom 2015, (Conference: French Symposium on Games(26-30 May 2015: Paris, France)). @misc{info:hdl:2013/243706, title = {To apologize or not to apologize; the evolutionary viability of forgiveness in interrupted commitments in the iterated prisoners dilemma}, author = {Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243706}, year = {2015}, date = {2015-01-01}, note = {Conference: French Symposium on Games(26-30 May 2015: Paris, France)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Lenaerts, Tom Commitment to cooperate - the evolutionary viability of individual and group commitments in social dilemmas Miscellaneous 2015, (Conference: Granada Seminar on Computational and Statistical Physics(15-19 june 2015: La Herradura, Spain)). @misc{info:hdl:2013/243704, title = {Commitment to cooperate - the evolutionary viability of individual and group commitments in social dilemmas}, author = {Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243704}, year = {2015}, date = {2015-01-01}, note = {Conference: Granada Seminar on Computational and Statistical Physics(15-19 june 2015: La Herradura, Spain)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Pozzolo, Andrea Dal; Caelen, Olivier; Johnson, Reid; Bontempi, Gianluca Calibrating Probability with Undersampling for Unbalanced Classification Inproceedings In: 2015 IEEE Symposium on Computational Intelligence and Data Mining, 2015, (Language of publication: en). @inproceedings{info:hdl:2013/221670b, title = {Calibrating Probability with Undersampling for Unbalanced Classification}, author = {Andrea Dal Pozzolo and Olivier Caelen and Reid Johnson and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/221670}, year = {2015}, date = {2015-01-01}, booktitle = {2015 IEEE Symposium on Computational Intelligence and Data Mining}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Pozzolo, Andrea Dal; Boracchi, Giacomo; Caelen, Olivier; Alippi, Cesare; Bontempi, Gianluca Credit Card Fraud Detection and Concept-Drift Adaptation with Delayed Supervised Information Inproceedings In: Neural Networks (IJCNN), 2015 International Joint Conference on, 2015, (DOI: 10.1109/IJCNN.2015.7280527). @inproceedings{info:hdl:2013/221668b, title = {Credit Card Fraud Detection and Concept-Drift Adaptation with Delayed Supervised Information}, author = {Andrea Dal Pozzolo and Giacomo Boracchi and Olivier Caelen and Cesare Alippi and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/221668}, year = {2015}, date = {2015-01-01}, booktitle = {Neural Networks (IJCNN), 2015 International Joint Conference on}, note = {DOI: 10.1109/IJCNN.2015.7280527}, keywords = {}, pubstate = {published}, tppubtype = {inproceedings} } |
Huculeci, Radu; Garcia-Pino, Abel; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico A J Structural insights into the intertwined dimer of fyn SH2. Journal Article In: Protein science, 24 (12), pp. 1964-1978, 2015, (DOI: 10.1002/pro.2806). @article{info:hdl:2013/225650b, title = {Structural insights into the intertwined dimer of fyn SH2.}, author = {Radu Huculeci and Abel Garcia-Pino and Lieven Buts and Tom Lenaerts and Nico A J van Nuland}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/225650}, year = {2015}, date = {2015-01-01}, journal = {Protein science}, volume = {24}, number = {12}, pages = {1964-1978}, note = {DOI: 10.1002/pro.2806}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Zisis, Ioannis; Guida, Sibilla Di; Han, The Anh T A H; Kirchsteiger, Georg; Lenaerts, Tom Generocity motivated by acceptance - evolutionary analysis of an anticipation game Journal Article In: Scientific Reports, 5 , 2015, (Language of publication: en). @article{info:hdl:2013/228071b, title = {Generocity motivated by acceptance - evolutionary analysis of an anticipation game}, author = {Ioannis Zisis and Sibilla Di Guida and The Anh T A H Han and Georg Kirchsteiger and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/228071}, year = {2015}, date = {2015-01-01}, journal = {Scientific Reports}, volume = {5}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Colaprico, Antonio; Silva, Tiago Da; Olsen, Catharina; Garofano, Luciano; Cava, Claudia; Garolini, Davide; Sabedot, Thais TS; Malta, Tathiane TM; Pagnotta, Stefano SM; Castiglioni, Isabella; Ceccarelli, M; Bontempi, Gianluca; Noushmehr, Houtan TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Journal Article In: Nucleic acids research, 2015, (DOI: 10.1093/nar/gkv1507). @article{info:hdl:2013/222877b, title = {TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data.}, author = {Antonio Colaprico and Tiago Da Silva and Catharina Olsen and Luciano Garofano and Claudia Cava and Davide Garolini and Thais TS Sabedot and Tathiane TM Malta and Stefano SM Pagnotta and Isabella Castiglioni and M Ceccarelli and Gianluca Bontempi and Houtan Noushmehr}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/222877}, year = {2015}, date = {2015-01-01}, journal = {Nucleic acids research}, note = {DOI: 10.1093/nar/gkv1507}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lerman, Liran; Bontempi, Gianluca; Markowitch, Olivier The bias–variance decomposition in profiled attacks Journal Article In: Journal of Cryptographic Engineering, 5 (4), pp. 255-267, 2015, (DOI: 10.1007/s13389-015-0106-1). @article{info:hdl:2013/220673b, title = {The bias–variance decomposition in profiled attacks}, author = {Liran Lerman and Gianluca Bontempi and Olivier Markowitch}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220673}, year = {2015}, date = {2015-01-01}, journal = {Journal of Cryptographic Engineering}, volume = {5}, number = {4}, pages = {255-267}, note = {DOI: 10.1007/s13389-015-0106-1}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Abdulkarim, Baroj; Nicolino, Marc; Esteve, Mariana Igoillo; Daures, Mathilde; Romero, Sophie; Philippi, Anne; Senée, Valérie; Lopes, Miguel; Cunha, Daniel Andrade Da; Harding, Heather P; Derbois, Céline; Bendelac, Nathalie; Hattersley, Andrew T; Eizirik, Decio; Ron, David; Cnop, Miriam; Julier, Cécile A Missense Mutation in PPP1R15B Causes a Syndrome Including Diabetes, Short Stature, and Microcephaly. Journal Article In: Diabetes (New York, N.Y.), 64 (11), pp. 3951-3962, 2015, (DOI: 10.2337/db15-0477). @article{info:hdl:2013/222110, title = {A Missense Mutation in PPP1R15B Causes a Syndrome Including Diabetes, Short Stature, and Microcephaly.}, author = {Baroj Abdulkarim and Marc Nicolino and Mariana Igoillo Esteve and Mathilde Daures and Sophie Romero and Anne Philippi and Valérie Senée and Miguel Lopes and Daniel Andrade Da Cunha and Heather P Harding and Céline Derbois and Nathalie Bendelac and Andrew T Hattersley and Decio Eizirik and David Ron and Miriam Cnop and Cécile Julier}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/222110}, year = {2015}, date = {2015-01-01}, journal = {Diabetes (New York, N.Y.)}, volume = {64}, number = {11}, pages = {3951-3962}, note = {DOI: 10.2337/db15-0477}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
de la de Ryhove, Laurence Kethulle; Ansseau, Eugénie; Nachtegael, Charlotte; Pieters, Karlien; Vanderplanck, Céline; Geens, Marcel; Sermon, Karen; Wilton, Stephen B; Coppee, Frédérique; Lagneaux, Laurence; Belayew, Alexandra The Role of D4Z4-Encoded Proteins in the Osteogenic Differentiation of Mesenchymal Stromal Cells Isolated from Bone Marrow. Journal Article In: Stem cells and development, 24 (22), pp. 2674-2686, 2015, (DOI: 10.1089/scd.2014.0575). @article{info:hdl:2013/220558, title = {The Role of D4Z4-Encoded Proteins in the Osteogenic Differentiation of Mesenchymal Stromal Cells Isolated from Bone Marrow.}, author = {Laurence de la Kethulle de Ryhove and Eugénie Ansseau and Charlotte Nachtegael and Karlien Pieters and Céline Vanderplanck and Marcel Geens and Karen Sermon and Stephen B Wilton and Frédérique Coppee and Laurence Lagneaux and Alexandra Belayew}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220558}, year = {2015}, date = {2015-01-01}, journal = {Stem cells and development}, volume = {24}, number = {22}, pages = {2674-2686}, note = {DOI: 10.1089/scd.2014.0575}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gazzo, Andrea; Daneels, Dorien; Cilia, Elisa; Bonduelle, Maryse; Abramowicz, Marc; Dooren, Sonia Van; Smits, Guillaume; Lenaerts, Tom DIDA: A curated and annotated digenic diseases database. Journal Article In: Nucleic acids research, 2015, (DOI: 10.1093/nar/gkv1068). @article{info:hdl:2013/220549b, title = {DIDA: A curated and annotated digenic diseases database.}, author = {Andrea Gazzo and Dorien Daneels and Elisa Cilia and Maryse Bonduelle and Marc Abramowicz and Sonia Van Dooren and Guillaume Smits and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220549}, year = {2015}, date = {2015-01-01}, journal = {Nucleic acids research}, note = {DOI: 10.1093/nar/gkv1068}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Han, The Anh T A H; Pereira, Luís Moniz; Santos, Francisco C; Lenaerts, Tom Emergence of cooperation via intention recognition, commitment and apology-A research summary Journal Article In: AI communications, 28 (4), pp. 709-715, 2015, (DOI: 10.3233/AIC-150672). @article{info:hdl:2013/220724b, title = {Emergence of cooperation via intention recognition, commitment and apology-A research summary}, author = {The Anh T A H Han and Luís Moniz Pereira and Francisco C Santos and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220724}, year = {2015}, date = {2015-01-01}, journal = {AI communications}, volume = {28}, number = {4}, pages = {709-715}, note = {DOI: 10.3233/AIC-150672}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bellot, Pau; Olsen, Catharina; Salembier, Philippe; Oliveras-Vergés, Albert; Meyer, Patrick E NetBenchmark: A bioconductor package for reproducible benchmarks of gene regulatory network inference Journal Article In: BMC bioinformatics, 16 (1), 2015, (DOI: 10.1186/s12859-015-0728-4). @article{info:hdl:2013/220688, title = {NetBenchmark: A bioconductor package for reproducible benchmarks of gene regulatory network inference}, author = {Pau Bellot and Catharina Olsen and Philippe Salembier and Albert Oliveras-Vergés and Patrick E Meyer}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220688}, year = {2015}, date = {2015-01-01}, journal = {BMC bioinformatics}, volume = {16}, number = {1}, note = {DOI: 10.1186/s12859-015-0728-4}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Delatte, Benjamin; Jeschke, Jana; Defrance, Matthieu; Bachman, Martin; Creppe, Catherine; Calonne, Emilie; Bizet, Martin; Deplus, Rachel; Marroquí, Laura; Libin, Myriam; Ravichandran, Mirunalini; cc, Fran; Eizirik, Decio L; Murrell, Adele; Jurkowski, Tomasz Piotr; cc, Fran Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress. Journal Article In: Scientific reports, 5 , pp. 12714, 2015, (DOI: 10.1038/srep12714). @article{info:hdl:2013/265293, title = {Genome-wide hydroxymethylcytosine pattern changes in response to oxidative stress.}, author = {Benjamin Delatte and Jana Jeschke and Matthieu Defrance and Martin Bachman and Catherine Creppe and Emilie Calonne and Martin Bizet and Rachel Deplus and Laura Marroquí and Myriam Libin and Mirunalini Ravichandran and Fran{cc}oise Mascart and Decio L Eizirik and Adele Murrell and Tomasz Piotr Jurkowski and Fran{cc}ois Fuks}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/265293}, year = {2015}, date = {2015-01-01}, journal = {Scientific reports}, volume = {5}, pages = {12714}, note = {DOI: 10.1038/srep12714}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lerman, Liran; Poussier, Romain; Bontempi, Gianluca; Markowitch, Olivier; cc, Fran Template attacks vs Machine Learning Revisited Journal Article In: Lecture notes in computer science, 9064 , pp. 20-33, 2015, (Language of publication: en). @article{info:hdl:2013/223764b, title = {Template attacks vs Machine Learning Revisited}, author = {Liran Lerman and Romain Poussier and Gianluca Bontempi and Olivier Markowitch and Fran{cc}ois-Xavier Standaert}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/223764}, year = {2015}, date = {2015-01-01}, journal = {Lecture notes in computer science}, volume = {9064}, pages = {20-33}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Larsimont, Jean-Christophe; Kass, Youssef Khalil; Danes, Adriana Sanchez; Sukumaran, Vijayakumar; Defrance, Matthieu; Delatte, Benjamin; Liagre, Mélanie; Baatsen, Pieter; Marine, Jean-Christophe; Lippens, Saskia; Guerin, Christopher; Marmol, Véronique Del; Vanderwinden, Jean-Marie; cc, Fran; Blanpain, Cédric Sox9 Controls Self-Renewal of Oncogene Targeted Cells and Links Tumor Initiation and Invasion. Journal Article In: Cell stem cell, 17 (1), pp. 60-73, 2015, (DOI: 10.1016/j.stem.2015.05.008). @article{info:hdl:2013/262159, title = {Sox9 Controls Self-Renewal of Oncogene Targeted Cells and Links Tumor Initiation and Invasion.}, author = {Jean-Christophe Larsimont and Youssef Khalil Kass and Adriana Sanchez Danes and Vijayakumar Sukumaran and Matthieu Defrance and Benjamin Delatte and Mélanie Liagre and Pieter Baatsen and Jean-Christophe Marine and Saskia Lippens and Christopher Guerin and Véronique Del Marmol and Jean-Marie Vanderwinden and Fran{cc}ois Fuks and Cédric Blanpain}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262159}, year = {2015}, date = {2015-01-01}, journal = {Cell stem cell}, volume = {17}, number = {1}, pages = {60-73}, note = {DOI: 10.1016/j.stem.2015.05.008}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Raimondi, Daniele; Orlando, Gabriele; Vranken, Wim An evolutionary view on Disulfide bond connectivities prediction using phylogenetic trees and a simple cysteine mutation model Journal Article In: PloS one, 10 (7), 2015, (DOI: 10.1371/journal.pone.0131792). @article{info:hdl:2013/218119, title = {An evolutionary view on Disulfide bond connectivities prediction using phylogenetic trees and a simple cysteine mutation model}, author = {Daniele Raimondi and Gabriele Orlando and Wim Vranken}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/218119}, year = {2015}, date = {2015-01-01}, journal = {PloS one}, volume = {10}, number = {7}, note = {DOI: 10.1371/journal.pone.0131792}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Martinez-Vaquero, Luis L A; Han, The Anh T A H; Pereira, Luís Marcelo; Lenaerts, Tom Apology and forgiveness evolve to resolve failures in cooperative agreements Journal Article In: Scientific reports, 5 , 2015, (DOI: 10.1038/srep10639). @article{info:hdl:2013/205370b, title = {Apology and forgiveness evolve to resolve failures in cooperative agreements}, author = {Luis L A Martinez-Vaquero and The Anh T A H Han and Luís Marcelo Pereira and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/205370}, year = {2015}, date = {2015-01-01}, journal = {Scientific reports}, volume = {5}, note = {DOI: 10.1038/srep10639}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Olsen, Catharina; Fleming, Kathleen; Prendergast, Niall; Rubio, Renee; Emmert-Streib, Frank; Bontempi, Gianluca; Quackenbush, John; Haibe-Kains, Benjamin Using shRNA experiments to validate gene regulatory networks Journal Article In: Genomics Data, 4 , pp. 123-126, 2015, (DOI: 10.1016/j.gdata.2015.03.011). @article{info:hdl:2013/205439b, title = {Using shRNA experiments to validate gene regulatory networks}, author = {Catharina Olsen and Kathleen Fleming and Niall Prendergast and Renee Rubio and Frank Emmert-Streib and Gianluca Bontempi and John Quackenbush and Benjamin Haibe-Kains}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/205439}, year = {2015}, date = {2015-01-01}, journal = {Genomics Data}, volume = {4}, pages = {123-126}, note = {DOI: 10.1016/j.gdata.2015.03.011}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lerman, Liran; Bontempi, Gianluca; Markowitch, Olivier A machine learning approach against a masked AES: Reaching the limit of side-channel attacks with a learning model Journal Article In: Journal of Cryptographic Engineering, 5 (2), pp. 123-139, 2015, (DOI: 10.1007/s13389-014-0089-3). @article{info:hdl:2013/205371b, title = {A machine learning approach against a masked AES: Reaching the limit of side-channel attacks with a learning model}, author = {Liran Lerman and Gianluca Bontempi and Olivier Markowitch}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/205371}, year = {2015}, date = {2015-01-01}, journal = {Journal of Cryptographic Engineering}, volume = {5}, number = {2}, pages = {123-139}, note = {DOI: 10.1007/s13389-014-0089-3}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Brozzi, Flora; Nardelli, Tarlliza R; Lopes, Miguel; Millard, Isabelle; Barthson, Jenny; Esteve, Mariana Igoillo; Grieco, Fabio Arturo; Villate, Olatz; Oliveira, Joana Moitinho Oitinho J M; Casimir, Marina; Bugliani, Marco; Engin, Feyza; Hotamisligil, Gökhan S; Marchetti, Piero; Eizirik, Decio L Cytokines induce endoplasmic reticulum stress in human, rat and mouse beta cells via different mechanisms Journal Article In: Diabetologia, 58 (10), pp. 2307-2316, 2015, (DOI: 10.1007/s00125-015-3669-6). @article{info:hdl:2013/227347, title = {Cytokines induce endoplasmic reticulum stress in human, rat and mouse beta cells via different mechanisms}, author = {Flora Brozzi and Tarlliza R Nardelli and Miguel Lopes and Isabelle Millard and Jenny Barthson and Mariana Igoillo Esteve and Fabio Arturo Grieco and Olatz Villate and Joana Moitinho Oitinho J M Oliveira and Marina Casimir and Marco Bugliani and Feyza Engin and Gökhan S Hotamisligil and Piero Marchetti and Decio L Eizirik}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/227347}, year = {2015}, date = {2015-01-01}, journal = {Diabetologia}, volume = {58}, number = {10}, pages = {2307-2316}, note = {DOI: 10.1007/s00125-015-3669-6}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mendez, Gipsi Lima; Faust, Karoline; Henry, Lynn N; Decelle, Johan; Colin, Simon; Carcillo, Fabrizio; Chaffron, Samuel; Ignacio-Espinosa, Cesar JC; Roux, Simon; Vincent, Flora; Bittner, Lucie; Darzi, Youssef; Wang, Jun; Audic, Stéphane; Berline, Léo; Bontempi, Gianluca; Cabello, Ana AM; Coppola, Laurent; Cornejo-Castillo, Francisco FM; d'Ovidio, Francesco; Meester, Luc De; Ferrera, Isabel; Garet-Delmas, Marie-José; Guidi, Lionel; Lara, Elena; Pesant, Stéphane; Royo-Llonch, Marta; Salazar, Guillem; Sanchez, Paloma; Sebastian, Marta; Souffreau, Caroline; Dimier, Céline; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; coordinators, Tara Oceans; Gorsky, Gabriel; Not, Fabrice; Ogata, Hiroyuki; Speich, Sabrina; Stemmann, Lars; Weissenbach, Jean; Wincker, Patrick; Acinas, Silvia SG; Sunagawa, Shinichi; Bork, Peer; Sullivan, Matthew B; Karsenti, Eric; Bowler, Chris; de Vargas, Colomban; Raes, Jeroen JR Ocean plankton. Determinants of community structure in the global plankton interactome. Journal Article In: Science, 348 (6237), pp. 1262073, 2015, (DOI: 10.1126/science.1262073). @article{info:hdl:2013/200950b, title = {Ocean plankton. Determinants of community structure in the global plankton interactome.}, author = {Gipsi Lima Mendez and Karoline Faust and Lynn N Henry and Johan Decelle and Simon Colin and Fabrizio Carcillo and Samuel Chaffron and Cesar JC Ignacio-Espinosa and Simon Roux and Flora Vincent and Lucie Bittner and Youssef Darzi and Jun Wang and Stéphane Audic and Léo Berline and Gianluca Bontempi and Ana AM Cabello and Laurent Coppola and Francisco FM Cornejo-Castillo and Francesco d'Ovidio and Luc De Meester and Isabel Ferrera and Marie-José Garet-Delmas and Lionel Guidi and Elena Lara and Stéphane Pesant and Marta Royo-Llonch and Guillem Salazar and Paloma Sanchez and Marta Sebastian and Caroline Souffreau and Céline Dimier and Marc Picheral and Sarah Searson and Stefanie Kandels-Lewis and Tara Oceans coordinators and Gabriel Gorsky and Fabrice Not and Hiroyuki Ogata and Sabrina Speich and Lars Stemmann and Jean Weissenbach and Patrick Wincker and Silvia SG Acinas and Shinichi Sunagawa and Peer Bork and Matthew B Sullivan and Eric Karsenti and Chris Bowler and Colomban de Vargas and Jeroen JR Raes}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/200950}, year = {2015}, date = {2015-01-01}, journal = {Science}, volume = {348}, number = {6237}, pages = {1262073}, note = {DOI: 10.1126/science.1262073}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Uribe-Lewis, Santiago; Stark, Rory; Carroll, Thomas; Dunning, Mark J; Bachman, Martin; Ito, Yoko; Stojic, Lovorka; Halim, Silvia; Vowler, Sarah L; Lynch, Andy G; Delatte, Benjamin; de Bony, Eric James; Colin, Laurence; Defrance, Matthieu; Krueger, Felix; Silva, Ana Luisa; ten Hoopen, Rogier; Ibrahim, Ashraf Ek; Murrell, Adele; cc, Fran 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer. Journal Article In: Genome biology, 16 , pp. 69, 2015, (DOI: 10.1186/s13059-015-0605-5). @article{info:hdl:2013/262160, title = {5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer.}, author = {Santiago Uribe-Lewis and Rory Stark and Thomas Carroll and Mark J Dunning and Martin Bachman and Yoko Ito and Lovorka Stojic and Silvia Halim and Sarah L Vowler and Andy G Lynch and Benjamin Delatte and Eric James de Bony and Laurence Colin and Matthieu Defrance and Felix Krueger and Ana Luisa Silva and Rogier ten Hoopen and Ashraf Ek Ibrahim and Adele Murrell and Fran{cc}ois Fuks}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262160}, year = {2015}, date = {2015-01-01}, journal = {Genome biology}, volume = {16}, pages = {69}, note = {DOI: 10.1186/s13059-015-0605-5}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Raimondi, Daniele; Orlando, Gabriele; Vranken, Wim Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements Journal Article In: Bioinformatics, 31 (8), pp. 1219-1225, 2015, (DOI: 10.1093/bioinformatics/btu794). @article{info:hdl:2013/207593, title = {Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements}, author = {Daniele Raimondi and Gabriele Orlando and Wim Vranken}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/207593}, year = {2015}, date = {2015-01-01}, journal = {Bioinformatics}, volume = {31}, number = {8}, pages = {1219-1225}, note = {DOI: 10.1093/bioinformatics/btu794}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
cc, Fran; Jeschke, Jana; Defrance, Matthieu; Desmedt, Christine; Bizet, Martin; Sotiriou, Christos BREAST CANCER EPIGENETIC MARKERS USEFUL IN ANTHRACYCLINE TREATMENT PROGNOSIS Miscellaneous 2015, (Language of publication: fr). @misc{info:hdl:2013/272725, title = {BREAST CANCER EPIGENETIC MARKERS USEFUL IN ANTHRACYCLINE TREATMENT PROGNOSIS}, author = {Fran{cc}ois Fuks and Jana Jeschke and Matthieu Defrance and Christine Desmedt and Martin Bizet and Christos Sotiriou}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/272725}, year = {2015}, date = {2015-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
Han, The Anh T A H; Santos, Francisco C; Lenaerts, Tom; Pereira, Luís Marcelo Synergy between intention recognition and commitments in cooperation dilemmas Journal Article In: Scientific Reports, 5 , 2015, (DOI: 10.1038/srep09312). @article{info:hdl:2013/197743b, title = {Synergy between intention recognition and commitments in cooperation dilemmas}, author = {The Anh T A H Han and Francisco C Santos and Tom Lenaerts and Luís Marcelo Pereira}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/197743}, year = {2015}, date = {2015-01-01}, journal = {Scientific Reports}, volume = {5}, note = {DOI: 10.1038/srep09312}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Han, The Anh T A H; Pereira, Luís Moniz; Lenaerts, Tom Avoiding or restricting defectors in public goods games? Journal Article In: Journal of the Royal Society interface, 12 (103), pp. 20141203, 2015, (DOI: 10.1098/rsif.2014.1203). @article{info:hdl:2013/205981b, title = {Avoiding or restricting defectors in public goods games?}, author = {The Anh T A H Han and Luís Moniz Pereira and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/205981}, year = {2015}, date = {2015-01-01}, journal = {Journal of the Royal Society interface}, volume = {12}, number = {103}, pages = {20141203}, note = {DOI: 10.1098/rsif.2014.1203}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sekara, Mateusz; Kowalski, Michael; Byrski, Aleksander; Indurkhya, Bipin; Kisiel-Dorohinicki, Marek; Samson, Dana; Lenaerts, Tom Multi-pheromone ant Colony Optimization for Socio-cognitive Simulation Purposes Journal Article In: Procedia Computer Science, 51 , pp. 954-963, 2015, (DOI: 10.1016/j.procs.2015.05.234). @article{info:hdl:2013/206321b, title = {Multi-pheromone ant Colony Optimization for Socio-cognitive Simulation Purposes}, author = {Mateusz Sekara and Michael Kowalski and Aleksander Byrski and Bipin Indurkhya and Marek Kisiel-Dorohinicki and Dana Samson and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/206321}, year = {2015}, date = {2015-01-01}, journal = {Procedia Computer Science}, volume = {51}, pages = {954-963}, note = {DOI: 10.1016/j.procs.2015.05.234}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Han, The Anh T A H; Lenaerts, Tom The efficient interaction of costly punishment and commitment Journal Article In: Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS, 3 , pp. 1657-1658, 2015, (Language of publication: en). @article{info:hdl:2013/220750b, title = {The efficient interaction of costly punishment and commitment}, author = {The Anh T A H Han and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/220750}, year = {2015}, date = {2015-01-01}, journal = {Proceedings of the International Joint Conference on Autonomous Agents and Multiagent Systems, AAMAS}, volume = {3}, pages = {1657-1658}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Zisis, Ioannis; Guida, Sibilla Di; Han, The Anh T A H; Kirchsteiger, Georg; Lenaerts, Tom Generosity motivated by acceptance - evolutionary analysis of an anticipation game. Journal Article In: Scientific reports, 5 , pp. 18076, 2015, (DOI: 10.1038/srep18076). @article{info:hdl:2013/227987b, title = {Generosity motivated by acceptance - evolutionary analysis of an anticipation game.}, author = {Ioannis Zisis and Sibilla Di Guida and The Anh T A H Han and Georg Kirchsteiger and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/227987}, year = {2015}, date = {2015-01-01}, journal = {Scientific reports}, volume = {5}, pages = {18076}, note = {DOI: 10.1038/srep18076}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Faust, Karoline; Mendez, Gipsi Lima; Lerat, Jean-Sébastien; Sathirapongsasuti, Jarupon Fah; Knight, Rob; Huttenhower, Curtis; Lenaerts, Tom; Raes, Jeroen JR Cross-biome comparison of microbial association networks Journal Article In: Frontiers in microbiology, 6 (OCT), 2015, (DOI: 10.3389/fmicb.2015.01200). @article{info:hdl:2013/226810b, title = {Cross-biome comparison of microbial association networks}, author = {Karoline Faust and Gipsi Lima Mendez and Jean-Sébastien Lerat and Jarupon Fah Sathirapongsasuti and Rob Knight and Curtis Huttenhower and Tom Lenaerts and Jeroen JR Raes}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/226810}, year = {2015}, date = {2015-01-01}, journal = {Frontiers in microbiology}, volume = {6}, number = {OCT}, note = {DOI: 10.3389/fmicb.2015.01200}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Colaprico, Antonio; Cava, Claudia; Bertoli, Gloria; Bontempi, Gianluca; Castiglioni, Isabella Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer Journal Article In: BioMed Research International, 2015 , 2015, (DOI: 10.1155/2015/831314). @article{info:hdl:2013/217546b, title = {Integrative Analysis with Monte Carlo Cross-Validation Reveals miRNAs Regulating Pathways Cross-Talk in Aggressive Breast Cancer}, author = {Antonio Colaprico and Claudia Cava and Gloria Bertoli and Gianluca Bontempi and Isabella Castiglioni}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/217546}, year = {2015}, date = {2015-01-01}, journal = {BioMed Research International}, volume = {2015}, note = {DOI: 10.1155/2015/831314}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lopes, Miguel Inference of gene networks from time series expression data and application to type 1 Diabetes PhD Thesis 2015, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/216729c, title = {Inference of gene networks from time series expression data and application to type 1 Diabetes}, author = {Miguel Lopes}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/216729}, year = {2015}, date = {2015-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Bontempi, Gianluca; Flauder, Maxime From dependency to causality: a machine learning approach Journal Article In: Journal of machine learning research, 2015, (Language of publication: en). @article{info:hdl:2013/222900b, title = {From dependency to causality: a machine learning approach}, author = {Gianluca Bontempi and Maxime Flauder}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/222900}, year = {2015}, date = {2015-01-01}, journal = {Journal of machine learning research}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hoffman, Anthony; Lenaerts, Tom Live migration of virtual machines in the cloud computing. Informatique Masters Thesis 2015, (Language of publication: fr). @mastersthesis{info:hdl:2013/243958b, title = {Live migration of virtual machines in the cloud computing. Informatique}, author = {Anthony Hoffman and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243958}, year = {2015}, date = {2015-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Lerman, Liran; Poussier, Romain; Bontempi, Gianluca; Markowitch, Olivier; cc, Fran Template attacks vs. Machine learning revisited (and the curse of dimensionality in side-channel analysis) Journal Article In: Lecture notes in computer science, 9064 , pp. 20-33, 2015, (DOI: 10.1007/978-3-319-21476-4_2). @article{info:hdl:2013/226800b, title = {Template attacks vs. Machine learning revisited (and the curse of dimensionality in side-channel analysis)}, author = {Liran Lerman and Romain Poussier and Gianluca Bontempi and Olivier Markowitch and Fran{cc}ois-Xavier Standaert}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/226800}, year = {2015}, date = {2015-01-01}, journal = {Lecture notes in computer science}, volume = {9064}, pages = {20-33}, note = {DOI: 10.1007/978-3-319-21476-4_2}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pozzolo, Andrea Dal; Caelen, Olivier; Bontempi, Gianluca When is undersampling effective in unbalanced classification tasks? Journal Article In: Lecture notes in computer science, 9284 , pp. 200-215, 2015, (DOI: 10.1007/978-3-319-23528-8_13). @article{info:hdl:2013/237086b, title = {When is undersampling effective in unbalanced classification tasks?}, author = {Andrea Dal Pozzolo and Olivier Caelen and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/237086}, year = {2015}, date = {2015-01-01}, journal = {Lecture notes in computer science}, volume = {9284}, pages = {200-215}, note = {DOI: 10.1007/978-3-319-23528-8_13}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2014 |
Dedeurwaerder, Sarah; Defrance, Matthieu; Bizet, Martin; Calonne, Emilie; Bontempi, Gianluca; cc, Fran A comprehensive overview of Infinium Human Methylation450 data processing Journal Article In: Briefings in bioinformatics, 15 (6), pp. 929-941, 2014, (DOI: 0.1093/bib/bbt054). @article{info:hdl:2013/186990b, title = {A comprehensive overview of Infinium Human Methylation450 data processing}, author = {Sarah Dedeurwaerder and Matthieu Defrance and Martin Bizet and Emilie Calonne and Gianluca Bontempi and Fran{cc}ois Fuks}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/186990}, year = {2014}, date = {2014-01-01}, journal = {Briefings in bioinformatics}, volume = {15}, number = {6}, pages = {929-941}, note = {DOI: 0.1093/bib/bbt054}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Cilia, Elisa; Teso, Stefano; Ammendola, Sergio; Lenaerts, Tom; Passerini, Andrea Predicting virus mutations through statistical relational learning. Journal Article In: BMC bioinformatics, 15 , pp. 309, 2014, (DOI: 10.1186/1471-2105-15-309). @article{info:hdl:2013/186411b, title = {Predicting virus mutations through statistical relational learning.}, author = {Elisa Cilia and Stefano Teso and Sergio Ammendola and Tom Lenaerts and Andrea Passerini}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/186411}, year = {2014}, date = {2014-01-01}, journal = {BMC bioinformatics}, volume = {15}, pages = {309}, note = {DOI: 10.1186/1471-2105-15-309}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Deplus, Rachel; "i, Lo; Rajavelu, Arumugam; Boukaba, Abdel Halim; Defrance, Matthieu; Luciani, Judith; cc, Fran; Dedeurwaerder, Sarah; `e, Hél; Brinkman, Arie B; Simmer, Femke; Müller, Fabian; Bertin, Benjamin; Berdasco, Maria; Putmans, Pascale; Calonne, Emilie; Litchfield, David DW; Launoit, Yvan De; Jurkowski, Tomasz Piotr; Stunnenberg, Hendrik HG; Bock, Christoph; Sotiriou, Christos; Fraga, Mario F; Esteller, Manel; Jeltsch, Albert; cc, Fran Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a. Journal Article In: Cell reports, 8 (3), pp. 743-753, 2014, (DOI: 10.1016/j.celrep.2014.06.048). @article{info:hdl:2013/178545, title = {Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a.}, author = {Rachel Deplus and Lo{"i}c Blanchon and Arumugam Rajavelu and Abdel Halim Boukaba and Matthieu Defrance and Judith Luciani and Fran{cc}oise Rothé and Sarah Dedeurwaerder and Hél{`e}ne Denis and Arie B Brinkman and Femke Simmer and Fabian Müller and Benjamin Bertin and Maria Berdasco and Pascale Putmans and Emilie Calonne and David DW Litchfield and Yvan De Launoit and Tomasz Piotr Jurkowski and Hendrik HG Stunnenberg and Christoph Bock and Christos Sotiriou and Mario F Fraga and Manel Esteller and Albert Jeltsch and Fran{cc}ois Fuks}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/178545}, year = {2014}, date = {2014-01-01}, journal = {Cell reports}, volume = {8}, number = {3}, pages = {743-753}, note = {DOI: 10.1016/j.celrep.2014.06.048}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rubio, Lucia; Huculeci, Radu; Buts, Lieven; Vanwetswinkel, Sophie; Lenaerts, Tom; van Nuland, Nico A J (1)H, (13)C, and (15)N backbone and side-chain chemical shift assignments of the free and bound forms of the human PTPN11 second SH2 domain. Journal Article In: Biomolecular N M R Assignments, 8 , 2014, (DOI: 10.1007/s12104-013-9504-4). @article{info:hdl:2013/155960b, title = {(1)H, (13)C, and (15)N backbone and side-chain chemical shift assignments of the free and bound forms of the human PTPN11 second SH2 domain.}, author = {Lucia Rubio and Radu Huculeci and Lieven Buts and Sophie Vanwetswinkel and Tom Lenaerts and Nico A J van Nuland}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/155960}, year = {2014}, date = {2014-01-01}, journal = {Biomolecular N M R Assignments}, volume = {8}, note = {DOI: 10.1007/s12104-013-9504-4}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lerman, Liran; Medeiros, Stéphane Fernandes; Bontempi, Gianluca; Markowitch, Olivier A Machine Learning Approach Against a Masked AES Journal Article In: Lecture notes in computer science, 8419 , pp. 61-75, 2014, (Language of publication: en). @article{info:hdl:2013/223763b, title = {A Machine Learning Approach Against a Masked AES}, author = {Liran Lerman and Stéphane Fernandes Medeiros and Gianluca Bontempi and Olivier Markowitch}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/223763}, year = {2014}, date = {2014-01-01}, journal = {Lecture notes in computer science}, volume = {8419}, pages = {61-75}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Trepo, Eric; Nahon, Pierre; Bontempi, Gianluca; Valenti, Luca; Falleti, Edmondo; Nischalke, Hans Dieter; Hamza, Samia; Corradini, Stefano Ginanni; Burza, Maria Antonella; Guyot, Erwan; Donati, Benedetta; Spengler, Ulrich; Hillon, Patrick; Toniutto, Pierluigi; Henrion, Jean; Franchimont, Denis; `e, Jacques Devi; Mathurin, Philippe; Moreno, Christophe; Romeo, Stefano; Deltenre, Pierre In: Hepatology, 59 (6), pp. 2170-2177, 2014, (DOI: 10.1002/hep.26767). @article{info:hdl:2013/196264b, title = {Association between the PNPLA3 (rs738409 C>G) variant and hepatocellular carcinoma: Evidence from a meta-analysis of individual participant data.}, author = {Eric Trepo and Pierre Nahon and Gianluca Bontempi and Luca Valenti and Edmondo Falleti and Hans Dieter Nischalke and Samia Hamza and Stefano Ginanni Corradini and Maria Antonella Burza and Erwan Guyot and Benedetta Donati and Ulrich Spengler and Patrick Hillon and Pierluigi Toniutto and Jean Henrion and Denis Franchimont and Jacques Devi{`e}re and Philippe Mathurin and Christophe Moreno and Stefano Romeo and Pierre Deltenre}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/196264}, year = {2014}, date = {2014-01-01}, journal = {Hepatology}, volume = {59}, number = {6}, pages = {2170-2177}, note = {DOI: 10.1002/hep.26767}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim The DynaMine webserver: predicting protein dynamics from sequence. Journal Article In: Nucleic acids research, 42 , pp. W264-W270, 2014, (DOI: 10.1093/nar/gku270). @article{info:hdl:2013/186420b, title = {The DynaMine webserver: predicting protein dynamics from sequence.}, author = {Elisa Cilia and Rita Pancsa and Peter Tompa and Tom Lenaerts and Wim Vranken}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/186420}, year = {2014}, date = {2014-01-01}, journal = {Nucleic acids research}, volume = {42}, pages = {W264-W270}, note = {DOI: 10.1093/nar/gku270}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jansen, Maarten Information criteria for variable selection under sparsity Journal Article In: Biometrika, 101 (1), pp. 37-55, 2014, (DOI: 10.1093/biomet/ast055). @article{info:hdl:2013/133291, title = {Information criteria for variable selection under sparsity}, author = {Maarten Jansen}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/133291}, year = {2014}, date = {2014-01-01}, journal = {Biometrika}, volume = {101}, number = {1}, pages = {37-55}, note = {DOI: 10.1093/biomet/ast055}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lenaerts, Tom; Giacobini, Mario; Bersini, Hugues; Bourgine, Paul; Dorigo, Marco; Doursat, René Special issue for the 20th anniversary of the European conference on artificial life (ECAL 2011): Editorial Journal Article In: Artificial life, 20 (1), pp. 1-3, 2014, (DOI: 10.1162/ARTL-a-00093). @article{info:hdl:2013/204002b, title = {Special issue for the 20th anniversary of the European conference on artificial life (ECAL 2011): Editorial}, author = {Tom Lenaerts and Mario Giacobini and Hugues Bersini and Paul Bourgine and Marco Dorigo and René Doursat}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/204002}, year = {2014}, date = {2014-01-01}, journal = {Artificial life}, volume = {20}, number = {1}, pages = {1-3}, note = {DOI: 10.1162/ARTL-a-00093}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gagliolo, Matteo; Lenaerts, Tom; Jacobs, Dirk Politics Matters: Dynamics of Inter-organizational Networks among Immigrant Associations Journal Article In: Studies in Computational Intelligence, 549 , pp. 47-55, 2014, (DOI: 10.1007/978-3-319-05401-8_5). @article{info:hdl:2013/264842b, title = {Politics Matters: Dynamics of Inter-organizational Networks among Immigrant Associations}, author = {Matteo Gagliolo and Tom Lenaerts and Dirk Jacobs}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/264842}, year = {2014}, date = {2014-01-01}, journal = {Studies in Computational Intelligence}, volume = {549}, pages = {47-55}, note = {DOI: 10.1007/978-3-319-05401-8_5}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Olsen, Catharina; Fleming, Kathleen; Prendergast, Niall; Rubio, Renee; Emmert-Streib, Frank; Bontempi, Gianluca; Haibe-Kains, Benjamin; Quackenbush, John Inference and validation of predictive gene networks from biomedical literature and gene expression data Journal Article In: Genomics, 103 , pp. 329-336, 2014, (DOI: 10.1016/j.ygeno.2014.03.004). @article{info:hdl:2013/172095b, title = {Inference and validation of predictive gene networks from biomedical literature and gene expression data}, author = {Catharina Olsen and Kathleen Fleming and Niall Prendergast and Renee Rubio and Frank Emmert-Streib and Gianluca Bontempi and Benjamin Haibe-Kains and John Quackenbush}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/172095}, year = {2014}, date = {2014-01-01}, journal = {Genomics}, volume = {103}, pages = {329-336}, note = {DOI: 10.1016/j.ygeno.2014.03.004}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Olsen, Catharina; Bontempi, Gianluca; Emmert-Streib, Frank; Quackenbush, John; Haibe-Kains, Benjamin Relevance of different prior knowledge sources for inferring gene interaction networks Journal Article In: Frontiers in Genetics, 5 (177), 2014, (DOI: 10.3389/fgene.2014.00177). @article{info:hdl:2013/172097b, title = {Relevance of different prior knowledge sources for inferring gene interaction networks}, author = {Catharina Olsen and Gianluca Bontempi and Frank Emmert-Streib and John Quackenbush and Benjamin Haibe-Kains}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/172097}, year = {2014}, date = {2014-01-01}, journal = {Frontiers in Genetics}, volume = {5}, number = {177}, note = {DOI: 10.3389/fgene.2014.00177}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lopes, Miguel; Kutlu, Burak; Miani, MICHELA; Bang-Berthelsen, Claus H; Størling, Joachim; Pociot, Flemming; Goodman, Nathan; Hood, Lee; Welsh, Nils; Bontempi, Gianluca; Eizirik, Decio L Temporal profiling of cytokine-induced genes in pancreatic beta-cells by meta-analysis and network inference. Journal Article In: Genomics, 2014, (DOI: 10.1016/j.ygeno.2013.12.007). @article{info:hdl:2013/163447b, title = {Temporal profiling of cytokine-induced genes in pancreatic beta-cells by meta-analysis and network inference.}, author = {Miguel Lopes and Burak Kutlu and MICHELA Miani and Claus H Bang-Berthelsen and Joachim Størling and Flemming Pociot and Nathan Goodman and Lee Hood and Nils Welsh and Gianluca Bontempi and Decio L Eizirik}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/163447}, year = {2014}, date = {2014-01-01}, journal = {Genomics}, note = {DOI: 10.1016/j.ygeno.2013.12.007}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lerman, Liran; Bontempi, Gianluca; Markowitch, Olivier Power analysis attack: an approach based on machine learning Journal Article In: International Journal of Applied Cryptography, 3 (2), pp. 97-115, 2014, (DOI: 10.1504/IJACT.2014.062722). @article{info:hdl:2013/163770b, title = {Power analysis attack: an approach based on machine learning}, author = {Liran Lerman and Gianluca Bontempi and Olivier Markowitch}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/163770}, year = {2014}, date = {2014-01-01}, journal = {International Journal of Applied Cryptography}, volume = {3}, number = {2}, pages = {97-115}, note = {DOI: 10.1504/IJACT.2014.062722}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lopes, Miguel; Bontempi, Gianluca On the null distribution of the precision and recall curve Journal Article In: Lecture notes in computer science, 8725 LNAI (PART 2), pp. 322-337, 2014, (DOI: 10.1007/978-3-662-44851-9_21). @article{info:hdl:2013/187934b, title = {On the null distribution of the precision and recall curve}, author = {Miguel Lopes and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/187934}, year = {2014}, date = {2014-01-01}, journal = {Lecture notes in computer science}, volume = {8725 LNAI}, number = {PART 2}, pages = {322-337}, note = {DOI: 10.1007/978-3-662-44851-9_21}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Kidzinski, Lukasz Inference for stationary functional time series: dimension reduction and regression PhD Thesis 2014, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/209226, title = {Inference for stationary functional time series: dimension reduction and regression}, author = {Lukasz Kidzinski}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209226}, year = {2014}, date = {2014-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Pozzolo, Andrea Dal; "e, Yann-A; Bontempi, Gianluca; Caelen, Olivier; Waterschoot, Serge Learned lessons in credit card fraud detection from a practitioner perspective Journal Article In: Expert systems with applications, 41 (10), pp. 4915-4928, 2014, (DOI: 10.1016/j.eswa.2014.02.026). @article{info:hdl:2013/183504b, title = {Learned lessons in credit card fraud detection from a practitioner perspective}, author = {Andrea Dal Pozzolo and Yann-A{"e}l Le Borgne and Gianluca Bontempi and Olivier Caelen and Serge Waterschoot}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/183504}, year = {2014}, date = {2014-01-01}, journal = {Expert systems with applications}, volume = {41}, number = {10}, pages = {4915-4928}, note = {DOI: 10.1016/j.eswa.2014.02.026}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Taieb, Souhaib Ben Machine learning strategies for multi-step-ahead time series forecasting PhD Thesis 2014, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/209234c, title = {Machine learning strategies for multi-step-ahead time series forecasting}, author = {Souhaib Ben Taieb}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209234}, year = {2014}, date = {2014-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Milenkovic, Dragan; Berghe, Wim Vanden; Boby, Céline; Leroux, Christine; Declerck, Ken; vel Szic, Katarzyna Szarc; Heyninck, Karen; Laukens, Kris; Bizet, Martin; Defrance, Matthieu; Dedeurwaerder, Sarah; Calonne, Emilie; cc, Fran; Haegeman, Guy; Haenen, Guido R M M G R M M; Bast, Aalt; Weseler, Antje R Dietary flavanols modulate the transcription of genes associated with cardiovascular pathology without changes in their DNA methylation state. Journal Article In: PloS one, 9 (4), pp. e95527, 2014, (DOI: 10.1371/journal.pone.0095527). @article{info:hdl:2013/262156, title = {Dietary flavanols modulate the transcription of genes associated with cardiovascular pathology without changes in their DNA methylation state.}, author = {Dragan Milenkovic and Wim Vanden Berghe and Céline Boby and Christine Leroux and Ken Declerck and Katarzyna Szarc vel Szic and Karen Heyninck and Kris Laukens and Martin Bizet and Matthieu Defrance and Sarah Dedeurwaerder and Emilie Calonne and Fran{cc}ois Fuks and Guy Haegeman and Guido R M M G R M M Haenen and Aalt Bast and Antje R Weseler}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/262156}, year = {2014}, date = {2014-01-01}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e95527}, note = {DOI: 10.1371/journal.pone.0095527}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ampe, Eva; Hestir, Erin E L; Bresciani, Mariano; Salvadore, Elga; Brando, Vittorio V E; Dekker, Arnold; Malthus, Tim T J; Jansen, Maarten; Triest, Ludwig; Batelaan, Okke A wavelet approach for estimating chlorophyll-A from inland waters with reflectance spectroscopy Journal Article In: IEEE geoscience and remote sensing letters, 11 (1), pp. 89-93, 2014, (DOI: 10.1109/LGRS.2013.2247021). @article{info:hdl:2013/168155, title = {A wavelet approach for estimating chlorophyll-A from inland waters with reflectance spectroscopy}, author = {Eva Ampe and Erin E L Hestir and Mariano Bresciani and Elga Salvadore and Vittorio V E Brando and Arnold Dekker and Tim T J Malthus and Maarten Jansen and Ludwig Triest and Okke Batelaan}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/168155}, year = {2014}, date = {2014-01-01}, journal = {IEEE geoscience and remote sensing letters}, volume = {11}, number = {1}, pages = {89-93}, note = {DOI: 10.1109/LGRS.2013.2247021}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jansen, Maarten Multiscale local polynomial models for estimation and testing Journal Article In: Springer Proceedings in Mathematics and Statistics, 74 , pp. 155-166, 2014, (DOI: 10.1007/978-1-4939-0569-0_14). @article{info:hdl:2013/192340, title = {Multiscale local polynomial models for estimation and testing}, author = {Maarten Jansen}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/192340}, year = {2014}, date = {2014-01-01}, journal = {Springer Proceedings in Mathematics and Statistics}, volume = {74}, pages = {155-166}, note = {DOI: 10.1007/978-1-4939-0569-0_14}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jansen, Maarten Nonseparable laplacian pyramids with multiscale local polynomials for scattered data Journal Article In: International Conference on Systems, Signals, and Image Processing, pp. 115-118, 2014, (Language of publication: en). @article{info:hdl:2013/204291, title = {Nonseparable laplacian pyramids with multiscale local polynomials for scattered data}, author = {Maarten Jansen}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/204291}, year = {2014}, date = {2014-01-01}, journal = {International Conference on Systems, Signals, and Image Processing}, pages = {115-118}, note = {Language of publication: en}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Boes, Olivier; Lenaerts, Tom Improving the Needleman-Wunsch algorithm with the Dynamine predictor. Informatique Masters Thesis 2014, (Language of publication: fr). @mastersthesis{info:hdl:2013/243957, title = {Improving the Needleman-Wunsch algorithm with the Dynamine predictor. Informatique}, author = {Olivier Boes and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243957}, year = {2014}, date = {2014-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Wintjens, Florian; Lenaerts, Tom Machine Learning: Coalition-based naive bayesian classification. Informatique Masters Thesis 2014, (Language of publication: fr). @mastersthesis{info:hdl:2013/243955, title = {Machine Learning: Coalition-based naive bayesian classification. Informatique}, author = {Florian Wintjens and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243955}, year = {2014}, date = {2014-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Estievenart, Quentin; Lenaerts, Tom Predicting secondary structure with dynamine. Informatique Masters Thesis 2014, (Language of publication: fr). @mastersthesis{info:hdl:2013/243956, title = {Predicting secondary structure with dynamine. Informatique}, author = {Quentin Estievenart and Tom Lenaerts}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/243956}, year = {2014}, date = {2014-01-01}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {mastersthesis} } |
Reggiani, Claudio; "e, Yann-A; Pozzolo, Andrea Dal; Olsen, Catharina; Bontempi, Gianluca Minimum Redundancy Maximum Relevance: MapReduce implementation using Apache Hadoop Miscellaneous 2014, (Conference: Benelearn 2014). @misc{info:hdl:2013/184925, title = {Minimum Redundancy Maximum Relevance: MapReduce implementation using Apache Hadoop}, author = {Claudio Reggiani and Yann-A{"e}l Le Borgne and Andrea Dal Pozzolo and Catharina Olsen and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/184925}, year = {2014}, date = {2014-01-01}, note = {Conference: Benelearn 2014}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |
"i, Lo Blind inverse imaging with positivity constraints PhD Thesis 2014, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/209240, title = {Blind inverse imaging with positivity constraints}, author = {Lo{"i}c Lecharlier}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209240}, year = {2014}, date = {2014-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
2013 |
Olsen, Catharina Causal inference and prior integration in bioinformatics using information theory PhD Thesis 2013, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/209401, title = {Causal inference and prior integration in bioinformatics using information theory}, author = {Catharina Olsen}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/209401/1/ba9583ce-51e9-4718-b438-fb816d60aea4.txt}, year = {2013}, date = {2013-01-01}, abstract = {An important problem in bioinformatics is the reconstruction of gene regulatory networks from expression data. The analysis of genomic data stemming from high- throughput technologies such as microarray experiments or RNA-sequencing faces several difficulties. The first major issue is the high variable to sample ratio which is due to a number of factors: a single experiment captures all genes while the number of experiments is restricted by the experiment’s cost, time and patient cohort size. The second problem is that these data sets typically exhibit high amounts of noise. Another important problem in bioinformatics is the question of how the inferred networks’ quality can be evaluated. The current best practice is a two step procedure. In the first step, the highest scoring interactions are compared to known interactions stored in biological databases. The inferred networks passes this quality assessment if there is a large overlap with the known interactions. In this case, a second step is carried out in which unknown but high scoring and thus promising new interactions are validated ’by hand’ via laboratory experiments. Unfortunately when integrating prior knowledge in the inference procedure, this validation procedure would be biased by using the same information in both the inference and the validation. Therefore, it would no longer allow an independent validation of the resulting network. The main contribution of this thesis is a complete computational framework that uses experimental knock down data in a cross-validation scheme to both infer and validate directed networks. Its components are i) a method that integrates genomic data and prior knowledge to infer directed networks, ii) its implementation in an R/Bioconductor package and iii) a web application to retrieve prior knowledge from PubMed abstracts and biological databases. To infer directed networks from genomic data and prior knowledge, we propose a two step procedure: First, we adapt the pairwise feature selection strategy mRMR to integrate prior knowledge in order to obtain the network’s skeleton. Then for the subsequent orientation phase of the algorithm, we extend a criterion based on interaction information to include prior knowledge. The implementation of this method is available both as part of the prior retrieval tool Predictive Networks and as a stand-alone R/Bioconductor package named predictionet. Furthermore, we propose a fully data-driven quantitative validation of such directed networks using experimental knock-down data: We start by identifying the set of genes that was truly affected by the perturbation experiment. The rationale of our validation procedure is that these truly affected genes should also be part of the perturbed gene’s childhood in the inferred network. Consequently, we can compute a performance score}, An important problem in bioinformatics is the reconstruction of gene regulatory networks from expression data. The analysis of genomic data stemming from high- throughput technologies such as microarray experiments or RNA-sequencing faces several difficulties. The first major issue is the high variable to sample ratio which is due to a number of factors: a single experiment captures all genes while the number of experiments is restricted by the experiment’s cost, time and patient cohort size. The second problem is that these data sets typically exhibit high amounts of noise.<p><p>Another important problem in bioinformatics is the question of how the inferred networks’ quality can be evaluated. The current best practice is a two step procedure. In the first step, the highest scoring interactions are compared to known interactions stored in biological databases. The inferred networks passes this quality assessment if there is a large overlap with the known interactions. In this case, a second step is carried out in which unknown but high scoring and thus promising new interactions are validated ’by hand’ via laboratory experiments. Unfortunately when integrating prior knowledge in the inference procedure, this validation procedure would be biased by using the same information in both the inference and the validation. Therefore, it would no longer allow an independent validation of the resulting network.<p><p>The main contribution of this thesis is a complete computational framework that uses experimental knock down data in a cross-validation scheme to both infer and validate directed networks. Its components are i) a method that integrates genomic data and prior knowledge to infer directed networks, ii) its implementation in an R/Bioconductor package and iii) a web application to retrieve prior knowledge from PubMed abstracts and biological databases. To infer directed networks from genomic data and prior knowledge, we propose a two step procedure: First, we adapt the pairwise feature selection strategy mRMR to integrate prior knowledge in order to obtain the network’s skeleton. Then for the subsequent orientation phase of the algorithm, we extend a criterion based on interaction information to include prior knowledge. The implementation of this method is available both as part of the prior retrieval tool Predictive Networks and as a stand-alone R/Bioconductor package named predictionet.<p><p>Furthermore, we propose a fully data-driven quantitative validation of such directed networks using experimental knock-down data: We start by identifying the set of genes that was truly affected by the perturbation experiment. The rationale of our validation procedure is that these truly affected genes should also be part of the perturbed gene’s childhood in the inferred network. Consequently, we can compute a performance score |
Bontempi, Gianluca; Taieb, Souhaib Ben Statistical foundations of machine learning Book Otexts, Online Books, 2013, (Language of publication: fr). @book{info:hdl:2013/223362, title = {Statistical foundations of machine learning}, author = {Gianluca Bontempi and Souhaib Ben Taieb}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/223362}, year = {2013}, date = {2013-01-01}, publisher = {Otexts, Online Books}, series = {Otexts}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Govorun, Maria Pension and health insurance, phase-type modeling PhD Thesis 2013, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/209447b, title = {Pension and health insurance, phase-type modeling}, author = {Maria Govorun}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209447}, year = {2013}, date = {2013-01-01}, note = {Funder: Universite Libre de Bruxelles}, keywords = {}, pubstate = {published}, tppubtype = {phdthesis} } |
Olsen, Catharina; Haibe-Kains, Benjamin; Quackenbush, John; Bontempi, Gianluca On the Integration of Prior Knowledge in the Inference of Regulatory Networks. Book Chapter In: World Scientific, 2013, (Language of publication: fr). @inbook{info:hdl:2013/223360, title = {On the Integration of Prior Knowledge in the Inference of Regulatory Networks.}, author = {Catharina Olsen and Benjamin Haibe-Kains and John Quackenbush and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/223360}, year = {2013}, date = {2013-01-01}, publisher = {World Scientific}, series = {Biological Data Mining and Its Applications in Healthcare}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } |
Olsen, Catharina Causal inference and prior integration in bioinformatics using information theory PhD Thesis 2013, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/209401b, title = {Causal inference and prior integration in bioinformatics using information theory}, author = {Catharina Olsen}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/209401/1/ba9583ce-51e9-4718-b438-fb816d60aea4.txt}, year = {2013}, date = {2013-01-01}, abstract = {An important problem in bioinformatics is the reconstruction of gene regulatory networks from expression data. The analysis of genomic data stemming from high- throughput technologies such as microarray experiments or RNA-sequencing faces several difficulties. The first major issue is the high variable to sample ratio which is due to a number of factors: a single experiment captures all genes while the number of experiments is restricted by the experiment’s cost, time and patient cohort size. The second problem is that these data sets typically exhibit high amounts of noise. Another important problem in bioinformatics is the question of how the inferred networks’ quality can be evaluated. The current best practice is a two step procedure. In the first step, the highest scoring interactions are compared to known interactions stored in biological databases. The inferred networks passes this quality assessment if there is a large overlap with the known interactions. In this case, a second step is carried out in which unknown but high scoring and thus promising new interactions are validated ’by hand’ via laboratory experiments. Unfortunately when integrating prior knowledge in the inference procedure, this validation procedure would be biased by using the same information in both the inference and the validation. Therefore, it would no longer allow an independent validation of the resulting network. The main contribution of this thesis is a complete computational framework that uses experimental knock down data in a cross-validation scheme to both infer and validate directed networks. Its components are i) a method that integrates genomic data and prior knowledge to infer directed networks, ii) its implementation in an R/Bioconductor package and iii) a web application to retrieve prior knowledge from PubMed abstracts and biological databases. To infer directed networks from genomic data and prior knowledge, we propose a two step procedure: First, we adapt the pairwise feature selection strategy mRMR to integrate prior knowledge in order to obtain the network’s skeleton. Then for the subsequent orientation phase of the algorithm, we extend a criterion based on interaction information to include prior knowledge. The implementation of this method is available both as part of the prior retrieval tool Predictive Networks and as a stand-alone R/Bioconductor package named predictionet. Furthermore, we propose a fully data-driven quantitative validation of such directed networks using experimental knock-down data: We start by identifying the set of genes that was truly affected by the perturbation experiment. The rationale of our validation procedure is that these truly affected genes should also be part of the perturbed gene’s childhood in the inferred network. Consequently, we can compute a performance score}, An important problem in bioinformatics is the reconstruction of gene regulatory networks from expression data. The analysis of genomic data stemming from high- throughput technologies such as microarray experiments or RNA-sequencing faces several difficulties. The first major issue is the high variable to sample ratio which is due to a number of factors: a single experiment captures all genes while the number of experiments is restricted by the experiment’s cost, time and patient cohort size. The second problem is that these data sets typically exhibit high amounts of noise.<p><p>Another important problem in bioinformatics is the question of how the inferred networks’ quality can be evaluated. The current best practice is a two step procedure. In the first step, the highest scoring interactions are compared to known interactions stored in biological databases. The inferred networks passes this quality assessment if there is a large overlap with the known interactions. In this case, a second step is carried out in which unknown but high scoring and thus promising new interactions are validated ’by hand’ via laboratory experiments. Unfortunately when integrating prior knowledge in the inference procedure, this validation procedure would be biased by using the same information in both the inference and the validation. Therefore, it would no longer allow an independent validation of the resulting network.<p><p>The main contribution of this thesis is a complete computational framework that uses experimental knock down data in a cross-validation scheme to both infer and validate directed networks. Its components are i) a method that integrates genomic data and prior knowledge to infer directed networks, ii) its implementation in an R/Bioconductor package and iii) a web application to retrieve prior knowledge from PubMed abstracts and biological databases. To infer directed networks from genomic data and prior knowledge, we propose a two step procedure: First, we adapt the pairwise feature selection strategy mRMR to integrate prior knowledge in order to obtain the network’s skeleton. Then for the subsequent orientation phase of the algorithm, we extend a criterion based on interaction information to include prior knowledge. The implementation of this method is available both as part of the prior retrieval tool Predictive Networks and as a stand-alone R/Bioconductor package named predictionet.<p><p>Furthermore, we propose a fully data-driven quantitative validation of such directed networks using experimental knock-down data: We start by identifying the set of genes that was truly affected by the perturbation experiment. The rationale of our validation procedure is that these truly affected genes should also be part of the perturbed gene’s childhood in the inferred network. Consequently, we can compute a performance score |
Govorun, Maria Pension and health insurance, phase-type modeling PhD Thesis 2013, (Funder: Universite Libre de Bruxelles). @phdthesis{info:hdl:2013/209447, title = {Pension and health insurance, phase-type modeling}, author = {Maria Govorun}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/209447/1/ffb25fee-0dd2-47b6-85b3-5b9db8df6d5a.txt}, year = {2013}, date = {2013-01-01}, abstract = {Depuis longtemps les mod`eles de type phase sont utilisés dans plusieurs domaines scientifiques pour décrire des syst`emes qui peuvent ^etre caractérisés par différents états. Les mod`eles sont bien connus en théorie des files d’attentes, en économie et en assurance. La th`ese est focalisée sur différentes applications des mod`eles de type phase en assurance et montre leurs avantages. En particulier, le mod`ele de Lin et Liu en 2007 est intéressant, parce qu’il décrit le processus de vieillissement de l’organisme humain. La durée de vie d’un individu suit une loi de type phase et les états de ce mod`ele représentent des états de santé. Le fait que le mod`ele prévoit la connexion entre les états de santé et l’^age de l’individu le rend tr`es utile en assurance. Les résultats principaux de la th`ese sont des nouveaux mod`eles et méthodes en assurance pension et en assurance santé qui utilisent l’hypoth`ese de la loi de type phase pour décrire la durée de vie d’un individu. En assurance pension le but d’estimer la profitabilité d’un fonds de pension. Pour cette raison, on construit un mod`ele « profit-test » qui demande la modélisation de plusieurs caractéristiques. On décrit l’évolution des participants du fonds en adaptant le mod`ele du vieillissement aux causes multiples de sortie. L’estimation des profits futurs exige qu’on détermine les valeurs des cotisations pour chaque état de santé, ainsi que l’ancienneté et l’état de santé initial pour chaque participant. Cela nous permet d’obtenir la distribution de profits futurs et de développer des méthodes pour estimer les risques de longevité et de changements de marché. De plus, on suppose que la diminution des taux de mortalité pour les pensionnés influence les profits futurs plus que pour les participants actifs. C’est pourquoi, pour évaluer l’impact de changement de santé sur la profitabilité, on modélise séparément les profits venant des pensionnés. En assurance santé, on utilise le mod`ele de type phase pour calculer la distribution de la valeur actualisée des co^uts futurs de santé. On développe des algorithmes récursifs qui permettent d’évaluer la distribution au cours d’une période courte, en utilisant des mod`eles fluides en temps continu, et pendant toute la durée de vie de l’individu, en construisant des mod`eles en temps discret. Les trois mod`eles en temps discret correspondent `a des hypoth`eses différentes qu’on fait pour les co^uts: dans le premier mod`ele on suppose que les co^uts de santé sont indépendants et identiquement distribués et ne dépendent pas du vieillissement de l’individu; dans les deux autres mod`eles on suppose que les co^uts dépendent de son état de santé. }, Depuis longtemps les mod`eles de type phase sont utilisés dans plusieurs domaines scientifiques pour décrire des syst`emes qui peuvent ^etre caractérisés par différents états. Les mod`eles sont bien connus en théorie des files d’attentes, en économie et en assurance.<p><p>La th`ese est focalisée sur différentes applications des mod`eles de type phase en assurance et montre leurs avantages. En particulier, le mod`ele de Lin et Liu en 2007 est intéressant, parce qu’il décrit le processus de vieillissement de l’organisme humain. La durée de vie d’un individu suit une loi de type phase et les états de ce mod`ele représentent des états de santé. Le fait que le mod`ele prévoit la connexion entre les états de santé et l’^age de l’individu le rend tr`es utile en assurance.<p><p>Les résultats principaux de la th`ese sont des nouveaux mod`eles et méthodes en assurance pension et en assurance santé qui utilisent l’hypoth`ese de la loi de type phase pour décrire la durée de vie d’un individu.<p><p>En assurance pension le but d’estimer la profitabilité d’un fonds de pension. Pour cette raison, on construit un mod`ele « profit-test » qui demande la modélisation de plusieurs caractéristiques. On décrit l’évolution des participants du fonds en adaptant le mod`ele du vieillissement aux causes multiples de sortie. L’estimation des profits futurs exige qu’on détermine les valeurs des cotisations pour chaque état de santé, ainsi que l’ancienneté et l’état de santé initial pour chaque participant. Cela nous permet d’obtenir la distribution de profits futurs et de développer des méthodes pour estimer les risques de longevité et de changements de marché. De plus, on suppose que la diminution des taux de mortalité pour les pensionnés influence les profits futurs plus que pour les participants actifs. C’est pourquoi, pour évaluer l’impact de changement de santé sur la profitabilité, on modélise séparément les profits venant des pensionnés.<p><p>En assurance santé, on utilise le mod`ele de type phase pour calculer la distribution de la valeur actualisée des co^uts futurs de santé. On développe des algorithmes récursifs qui permettent d’évaluer la distribution au cours d’une période courte, en utilisant des mod`eles fluides en temps continu, et pendant toute la durée de vie de l’individu, en construisant des mod`eles en temps discret. Les trois mod`eles en temps discret correspondent `a des hypoth`eses différentes qu’on fait pour les co^uts: dans le premier mod`ele on suppose que les co^uts de santé sont indépendants et identiquement distribués et ne dépendent pas du vieillissement de l’individu; dans les deux autres mod`eles on suppose que les co^uts dépendent de son état de santé.<p> |
Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim From protein sequence to dynamics and disorder with DynaMine. Journal Article In: Nature communications, 4 , pp. 2741, 2013, (DOI: 10.1038/ncomms3741). @article{info:hdl:2013/186425, title = {From protein sequence to dynamics and disorder with DynaMine.}, author = {Elisa Cilia and Rita Pancsa and Peter Tompa and Tom Lenaerts and Wim Vranken}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/186425}, year = {2013}, date = {2013-01-01}, journal = {Nature communications}, volume = {4}, pages = {2741}, abstract = {Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.}, note = {DOI: 10.1038/ncomms3741}, keywords = {}, pubstate = {published}, tppubtype = {article} } Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5. |
Bontempi, Gianluca; Taieb, Souhaib Ben Statistical foundations of machine learning Book Otexts, Online Books, 2013, (Language of publication: fr). @book{info:hdl:2013/223362b, title = {Statistical foundations of machine learning}, author = {Gianluca Bontempi and Souhaib Ben Taieb}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/223362}, year = {2013}, date = {2013-01-01}, publisher = {Otexts, Online Books}, series = {Otexts}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Traulsen, Arne; Lenaerts, Tom; Pacheco, Jorge M J M; Dingli, David On the dynamics of neutral mutations in a mathematical model for a homogeneous stem cell population. Journal Article In: Journal of the Royal Society, Interface / the Royal Society, 10 (79), pp. 20120810, 2013, (DOI: 10.1098/rsif.2012.0810). @article{info:hdl:2013/138049, title = {On the dynamics of neutral mutations in a mathematical model for a homogeneous stem cell population.}, author = {Arne Traulsen and Tom Lenaerts and Jorge M J M Pacheco and David Dingli}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/138049}, year = {2013}, date = {2013-01-01}, journal = {Journal of the Royal Society, Interface / the Royal Society}, volume = {10}, number = {79}, pages = {20120810}, abstract = {The theory of the clonal origin of cancer states that a tumour arises from one cell that acquires mutation(s) leading to the malignant phenotype. It is the current belief that many of these mutations give a fitness advantage to the mutant population allowing it to expand, eventually leading to disease. However, mutations that lead to such a clonal expansion need not give a fitness advantage and may in fact be neutral-or almost neutral-with respect to fitness. Such mutant clones can be eliminated or expand stochastically, leading to a malignant phenotype (disease). Mutations in haematopoietic stem cells give rise to diseases such as chronic myeloid leukaemia (CML) and paroxysmal nocturnal haemoglobinuria (PNH). Although neutral drift often leads to clonal extinction, disease is still possible, and in this case, it has important implications both for the incidence of disease and for therapy, as it may be more difficult to eliminate neutral mutations with therapy. We illustrate the consequences of such dynamics, using CML and PNH as examples. These considerations have implications for many other tumours as well.}, note = {DOI: 10.1098/rsif.2012.0810}, keywords = {}, pubstate = {published}, tppubtype = {article} } The theory of the clonal origin of cancer states that a tumour arises from one cell that acquires mutation(s) leading to the malignant phenotype. It is the current belief that many of these mutations give a fitness advantage to the mutant population allowing it to expand, eventually leading to disease. However, mutations that lead to such a clonal expansion need not give a fitness advantage and may in fact be neutral-or almost neutral-with respect to fitness. Such mutant clones can be eliminated or expand stochastically, leading to a malignant phenotype (disease). Mutations in haematopoietic stem cells give rise to diseases such as chronic myeloid leukaemia (CML) and paroxysmal nocturnal haemoglobinuria (PNH). Although neutral drift often leads to clonal extinction, disease is still possible, and in this case, it has important implications both for the incidence of disease and for therapy, as it may be more difficult to eliminate neutral mutations with therapy. We illustrate the consequences of such dynamics, using CML and PNH as examples. These considerations have implications for many other tumours as well. |
Han, The Anh T A H; Pereira, Luís Moniz; Santos, Francisco C; Lenaerts, Tom Good agreements make good friends. Journal Article In: Scientific reports, 3 , pp. 2695, 2013, (DOI: 10.1038/srep02695). @article{info:hdl:2013/155962, title = {Good agreements make good friends.}, author = {The Anh T A H Han and Luís Moniz Pereira and Francisco C Santos and Tom Lenaerts}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/155962/1/PMC3776200.pdf}, year = {2013}, date = {2013-01-01}, journal = {Scientific reports}, volume = {3}, pages = {2695}, abstract = {When starting a new collaborative endeavor, it pays to establish upfront how strongly your partner commits to the common goal and what compensation can be expected in case the collaboration is violated. Diverse examples in biological and social contexts have demonstrated the pervasiveness of making prior agreements on posterior compensations, suggesting that this behavior could have been shaped by natural selection. Here, we analyze the evolutionary relevance of such a commitment strategy and relate it to the costly punishment strategy, where no prior agreements are made. We show that when the cost of arranging a commitment deal lies within certain limits, substantial levels of cooperation can be achieved. Moreover, these levels are higher than that achieved by simple costly punishment, especially when one insists on sharing the arrangement cost. Not only do we show that good agreements make good friends, agreements based on shared costs result in even better outcomes.}, note = {DOI: 10.1038/srep02695}, keywords = {}, pubstate = {published}, tppubtype = {article} } When starting a new collaborative endeavor, it pays to establish upfront how strongly your partner commits to the common goal and what compensation can be expected in case the collaboration is violated. Diverse examples in biological and social contexts have demonstrated the pervasiveness of making prior agreements on posterior compensations, suggesting that this behavior could have been shaped by natural selection. Here, we analyze the evolutionary relevance of such a commitment strategy and relate it to the costly punishment strategy, where no prior agreements are made. We show that when the cost of arranging a commitment deal lies within certain limits, substantial levels of cooperation can be achieved. Moreover, these levels are higher than that achieved by simple costly punishment, especially when one insists on sharing the arrangement cost. Not only do we show that good agreements make good friends, agreements based on shared costs result in even better outcomes. |
Haibe-Kains, Benjamin; Desmedt, Christine; Leo, Angelo Di; Azambuja, Evandro; Larsimont, Denis; Selleslags, Jean; Delaloge, Suzette; Duhem, Caroline; Kains, Jean-Pierre; Carly, Birgit; Maerevoet, Marie; Vindevoghel, Anita; Rouas, Ghizlane; cc, Fran; Durbecq, Virginie; Cardoso, Fatima; Salgado, Roberto; Rovere, Rodrigo Kraft; Bontempi, Gianluca; Michiels, Stefan; Buyse, Marc; Nogaret, Jean-Marie; Qi, Yuan; Symmans, William Fraser; Pusztai, Lajos; D'Hondt, Veronique; Piccart-Gebhart, Martine; Sotiriou, Christos Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients Journal Article In: Genomics Data, 1 , pp. 7-10, 2013, (DOI: 10.1016/j.gdata.2013.09.001). @article{info:hdl:2013/177704, title = {Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients}, author = {Benjamin Haibe-Kains and Christine Desmedt and Angelo Di Leo and Evandro Azambuja and Denis Larsimont and Jean Selleslags and Suzette Delaloge and Caroline Duhem and Jean-Pierre Kains and Birgit Carly and Marie Maerevoet and Anita Vindevoghel and Ghizlane Rouas and Fran{cc}oise Lallemand and Virginie Durbecq and Fatima Cardoso and Roberto Salgado and Rodrigo Kraft Rovere and Gianluca Bontempi and Stefan Michiels and Marc Buyse and Jean-Marie Nogaret and Yuan Qi and William Fraser Symmans and Lajos Pusztai and Veronique D'Hondt and Martine Piccart-Gebhart and Christos Sotiriou}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/177704/1/Elsevier_161331.pdf}, year = {2013}, date = {2013-01-01}, journal = {Genomics Data}, volume = {1}, pages = {7-10}, abstract = {Validated biomarkers predictive of response/resistance to anthracyclines in breast cancer are currently lacking. The neoadjuvant Trial of Principle (TOP) study, in which patients with estrogen receptor (ER)-negative tumors were treated with anthracycline (epirubicin) monotherapy, was specifically designed to evaluate the predictive value of topoisomerase II-alpha (TOP2A) and develop a gene expression signature to identify those patients who do not benefit from anthracyclines. Here we describe in details the contents and quality controls for the gene expression and clinical data associated with the study published by Desmedt and colleagues in the Journal of Clinical Oncology in 2011 (Desmedt et al., 2011). We also provide R code to easily access the data and perform the quality controls and basic analyses relevant to this dataset. © 2013 The Authors.}, note = {DOI: 10.1016/j.gdata.2013.09.001}, keywords = {}, pubstate = {published}, tppubtype = {article} } Validated biomarkers predictive of response/resistance to anthracyclines in breast cancer are currently lacking. The neoadjuvant Trial of Principle (TOP) study, in which patients with estrogen receptor (ER)-negative tumors were treated with anthracycline (epirubicin) monotherapy, was specifically designed to evaluate the predictive value of topoisomerase II-alpha (TOP2A) and develop a gene expression signature to identify those patients who do not benefit from anthracyclines. Here we describe in details the contents and quality controls for the gene expression and clinical data associated with the study published by Desmedt and colleagues in the Journal of Clinical Oncology in 2011 (Desmedt et al., 2011). We also provide R code to easily access the data and perform the quality controls and basic analyses relevant to this dataset. © 2013 The Authors. |
Bonnechere, Bruno; Wermenbol, Vanessa; Dan, Bernard; Salvia, Patrick; "e, Yann-A; Bontempi, Gianluca; Vansummeren, Stijn; Sholukha, Victor; Moiseev, Fedor; Jansen, Bart; Rooze, Marcel; Jan, Serge Van Sint Management and interpretation of medical data related to cerebral pasly: the ICT4 Rehab project Journal Article In: European journal of paediatric neurology, 17 (1), pp. 32, 2013, (Language of publication: na). @article{info:hdl:2013/151908, title = {Management and interpretation of medical data related to cerebral pasly: the ICT4 Rehab project}, author = {Bruno Bonnechere and Vanessa Wermenbol and Bernard Dan and Patrick Salvia and Yann-A{"e}l Le Borgne and Gianluca Bontempi and Stijn Vansummeren and Victor Sholukha and Fedor Moiseev and Bart Jansen and Marcel Rooze and Serge Van Sint Jan}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/151908}, year = {2013}, date = {2013-01-01}, journal = {European journal of paediatric neurology}, volume = {17}, number = {1}, pages = {32}, note = {Language of publication: na}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dedeurwaerder, Sarah; Defrance, Matthieu; Bizet, Martin; Calonne, Emilie; Bontempi, Gianluca; cc, Fran A comprehensive overview of Infinium Human Methylation450 data processing Journal Article In: Briefings in bioinformatics, 15 (6), pp. 929-941, 2013, (DOI: 0.1093/bib/bbt054). @article{info:hdl:2013/186990, title = {A comprehensive overview of Infinium Human Methylation450 data processing}, author = {Sarah Dedeurwaerder and Matthieu Defrance and Martin Bizet and Emilie Calonne and Gianluca Bontempi and Fran{cc}ois Fuks}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/186990}, year = {2013}, date = {2013-01-01}, journal = {Briefings in bioinformatics}, volume = {15}, number = {6}, pages = {929-941}, abstract = {Infinium HumanMethylation450 beadarray is a popular technology to explore DNA methylomes in health and disease, and there is a current explosion in the use of this technique. Despite experience acquired from gene expression microarrays, analyzing Infinium Methylation arrays appeared more complex than initially thought and several difficulties have been encountered, as those arrays display specific features that need to be taken into consideration during data processing. Here, we review several issues that have been highlighted by the scientific community, and we present an overview of the general data processing scheme and an evaluation of the different normalization methods available to date to guide the 450K users in their analysis and data interpretation.}, note = {DOI: 0.1093/bib/bbt054}, keywords = {}, pubstate = {published}, tppubtype = {article} } Infinium HumanMethylation450 beadarray is a popular technology to explore DNA methylomes in health and disease, and there is a current explosion in the use of this technique. Despite experience acquired from gene expression microarrays, analyzing Infinium Methylation arrays appeared more complex than initially thought and several difficulties have been encountered, as those arrays display specific features that need to be taken into consideration during data processing. Here, we review several issues that have been highlighted by the scientific community, and we present an overview of the general data processing scheme and an evaluation of the different normalization methods available to date to guide the 450K users in their analysis and data interpretation. |
Papillon-Cavanagh, Simon; Jay, Nicolas De; Hachem, Nehme; Olsen, Catharina; Bontempi, Gianluca; Aerts, Hugo J W L; Quackenbush, John; Haibe-Kains, Benjamin Comparison and validation of genomic predictors for anticancer drug sensitivity. Journal Article In: Journal of the American Medical Informatics Association, 20 (4), pp. 597-602, 2013, (DOI: 10.1136/amiajnl-2012-001442). @article{info:hdl:2013/145203, title = {Comparison and validation of genomic predictors for anticancer drug sensitivity.}, author = {Simon Papillon-Cavanagh and Nicolas De Jay and Nehme Hachem and Catharina Olsen and Gianluca Bontempi and Hugo J W L Aerts and John Quackenbush and Benjamin Haibe-Kains}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/145203}, year = {2013}, date = {2013-01-01}, journal = {Journal of the American Medical Informatics Association}, volume = {20}, number = {4}, pages = {597-602}, abstract = {An enduring challenge in personalized medicine lies in selecting the right drug for each individual patient. While testing of drugs on patients in large trials is the only way to assess their clinical efficacy and toxicity, we dramatically lack resources to test the hundreds of drugs currently under development. Therefore the use of preclinical model systems has been intensively investigated as this approach enables response to hundreds of drugs to be tested in multiple cell lines in parallel.}, note = {DOI: 10.1136/amiajnl-2012-001442}, keywords = {}, pubstate = {published}, tppubtype = {article} } An enduring challenge in personalized medicine lies in selecting the right drug for each individual patient. While testing of drugs on patients in large trials is the only way to assess their clinical efficacy and toxicity, we dramatically lack resources to test the hundreds of drugs currently under development. Therefore the use of preclinical model systems has been intensively investigated as this approach enables response to hundreds of drugs to be tested in multiple cell lines in parallel. |
Lerman, Liran; Medeiros, Stéphane Fernandes; Veshchikov, Nikita; Meuter, Cédric; Bontempi, Gianluca; Markowitch, Olivier Semi-Supervised Template Attack Journal Article In: Lecture Notes in Computer Science, 7864 , pp. 184-199, 2013, (DOI: 10.1007/978-3-642-40026-1_12). @article{info:hdl:2013/147304, title = {Semi-Supervised Template Attack}, author = {Liran Lerman and Stéphane Fernandes Medeiros and Nikita Veshchikov and Cédric Meuter and Gianluca Bontempi and Olivier Markowitch}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/147304}, year = {2013}, date = {2013-01-01}, journal = {Lecture Notes in Computer Science}, volume = {7864}, pages = {184-199}, abstract = {Side channel attacks take advantage of information leakagesin cryptographic devices. Template attacks form a family of side channelattacks which is reputed to be extremely effective. This kind of attacksassumes that the attacker fully controls a cryptographic device before at-tacking a similar one. In this paper, we propose to relax this assumption bygeneralizing the template attack using a method based on a semi-supervisedlearning strategy. The effectiveness of our proposal is confirmed by softwaresimulations, by experiments on a 8-bit microcontroller and by a comparisonto a template attack as well as to two supervised machine learning methods.}, note = {DOI: 10.1007/978-3-642-40026-1_12}, keywords = {}, pubstate = {published}, tppubtype = {article} } Side channel attacks take advantage of information leakagesin cryptographic devices. Template attacks form a family of side channelattacks which is reputed to be extremely effective. This kind of attacksassumes that the attacker fully controls a cryptographic device before at-tacking a similar one. In this paper, we propose to relax this assumption bygeneralizing the template attack using a method based on a semi-supervisedlearning strategy. The effectiveness of our proposal is confirmed by softwaresimulations, by experiments on a 8-bit microcontroller and by a comparisonto a template attack as well as to two supervised machine learning methods. |
Jay, Nicolas De; Papillon-Cavanagh, Simon; Olsen, Catharina; El-Hachem, N; Bontempi, Gianluca; Haibe-Kains, Benjamin mRMRe: an R package for parallelized mRMR ensemble feature selection Journal Article In: Bioinformatics, 2013, (DOI: 10.1093/bioinformatics/btt383). @article{info:hdl:2013/155448, title = {mRMRe: an R package for parallelized mRMR ensemble feature selection}, author = {Nicolas De Jay and Simon Papillon-Cavanagh and Catharina Olsen and N El-Hachem and Gianluca Bontempi and Benjamin Haibe-Kains}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/155448}, year = {2013}, date = {2013-01-01}, journal = {Bioinformatics}, abstract = {Motivation: Feature selection is one of the main challenges in analyzing high-throughput genomic data. Minimum redundancy maximum relevance (mRMR) is a particularly fast feature selection method for finding a set of both relevant and complementary features. Here we describe the mRMRe R package, in which the mRMR technique is extended by using an ensemble approach in order to better explore the feature space and build more robust predictors. To deal with the computational complexity of the ensemble approach the main functions of the package are implemented and parallelized in C using the openMP API.Results: Our ensemble mRMR implementations outperform the classical mRMR approach in terms of prediction accuracy. They identify genes more relevant to the biological context and may lead to richer biological interpretations. The parallelized functions included in the package show significant gains in terms of run-time speed when compared to previously released packages.Availability: The R package mRMRe is available on CRAN and is provided open source under the Artistic-2.0 License. The code used to generate all the results reported in this application note is available from Supplementary File 1.Contact: bhaibeka@ircm.qc.caSupplementary Information: Supplementary information is available at Bioinformatics online.}, note = {DOI: 10.1093/bioinformatics/btt383}, keywords = {}, pubstate = {published}, tppubtype = {article} } Motivation: Feature selection is one of the main challenges in analyzing high-throughput genomic data. Minimum redundancy maximum relevance (mRMR) is a particularly fast feature selection method for finding a set of both relevant and complementary features. Here we describe the mRMRe R package, in which the mRMR technique is extended by using an ensemble approach in order to better explore the feature space and build more robust predictors. To deal with the computational complexity of the ensemble approach the main functions of the package are implemented and parallelized in C using the openMP API.Results: Our ensemble mRMR implementations outperform the classical mRMR approach in terms of prediction accuracy. They identify genes more relevant to the biological context and may lead to richer biological interpretations. The parallelized functions included in the package show significant gains in terms of run-time speed when compared to previously released packages.Availability: The R package mRMRe is available on CRAN and is provided open source under the Artistic-2.0 License. The code used to generate all the results reported in this application note is available from Supplementary File 1.Contact: bhaibeka@ircm.qc.caSupplementary Information: Supplementary information is available at Bioinformatics online. |
Bontempi, Gianluca; Taieb, Souhaib Ben; "e, Yann-A Machine learning strategies for time series forecasting Journal Article In: Lecture Notes in Business Information Processing, 138 LNBIP , pp. 62-77, 2013, (DOI: 10.1007/978-3-642-36318-4_3). @article{info:hdl:2013/167761, title = {Machine learning strategies for time series forecasting}, author = {Gianluca Bontempi and Souhaib Ben Taieb and Yann-A{"e}l Le Borgne}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/167761}, year = {2013}, date = {2013-01-01}, journal = {Lecture Notes in Business Information Processing}, volume = {138 LNBIP}, pages = {62-77}, abstract = {The increasing availability of large amounts of historical data and the need of performing accurate forecasting of future behavior in several scientific and applied domains demands the definition of robust and efficient techniques able to infer from observations the stochastic dependency between past and future. The forecasting domain has been influenced, from the 1960s on, by linear statistical methods such as ARIMA models. More recently, machine learning models have drawn attention and have established themselves as serious contenders to classical statistical models in the forecasting community. This chapter presents an overview of machine learning techniques in time series forecasting by focusing on three aspects: the formalization of one-step forecasting problems as supervised learning tasks, the discussion of local learning techniques as an effective tool for dealing with temporal data and the role of the forecasting strategy when we move from one-step to multiple-step forecasting. © 2013 Springer-Verlag.}, note = {DOI: 10.1007/978-3-642-36318-4_3}, keywords = {}, pubstate = {published}, tppubtype = {article} } The increasing availability of large amounts of historical data and the need of performing accurate forecasting of future behavior in several scientific and applied domains demands the definition of robust and efficient techniques able to infer from observations the stochastic dependency between past and future. The forecasting domain has been influenced, from the 1960s on, by linear statistical methods such as ARIMA models. More recently, machine learning models have drawn attention and have established themselves as serious contenders to classical statistical models in the forecasting community. This chapter presents an overview of machine learning techniques in time series forecasting by focusing on three aspects: the formalization of one-step forecasting problems as supervised learning tasks, the discussion of local learning techniques as an effective tool for dealing with temporal data and the role of the forecasting strategy when we move from one-step to multiple-step forecasting. © 2013 Springer-Verlag. |
Lopes, Miguel; Bontempi, Gianluca Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data Journal Article In: Frontiers in Genetics, 4 (DEC), 2013, (DOI: 10.3389/fgene.2013.00303). @article{info:hdl:2013/168524, title = {Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data}, author = {Miguel Lopes and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/168524}, year = {2013}, date = {2013-01-01}, journal = {Frontiers in Genetics}, volume = {4}, number = {DEC}, abstract = {Accurate inference of causal gene regulatory networks from gene expression data is an open bioinformatics challenge. Gene interactions are dynamical processes and consequently we can expect that the effect of any regulation action occurs after a certain temporal lag. However such lag is unknown a priori and temporal aspects require specific inference algorithms. In this paper we aim to assess the impact of taking into consideration temporal aspects on the final accuracy of the inference procedure. In particular we will compare the accuracy of static algorithms, where no dynamic aspect is considered, to that of fixed lag and adaptive lag algorithms in three inference tasks from microarray expression data. Experimental results show that network inference algorithms that take dynamics into account perform consistently better than static ones, once the considered lags are properly chosen. However, no individual algorithm stands out in all three inference tasks, and the challenging nature of network inference tasks is evidenced, as a large number of the assessed algorithms does not perform better than random. © 2013 Lopes and Bontempi.}, note = {DOI: 10.3389/fgene.2013.00303}, keywords = {}, pubstate = {published}, tppubtype = {article} } Accurate inference of causal gene regulatory networks from gene expression data is an open bioinformatics challenge. Gene interactions are dynamical processes and consequently we can expect that the effect of any regulation action occurs after a certain temporal lag. However such lag is unknown a priori and temporal aspects require specific inference algorithms. In this paper we aim to assess the impact of taking into consideration temporal aspects on the final accuracy of the inference procedure. In particular we will compare the accuracy of static algorithms, where no dynamic aspect is considered, to that of fixed lag and adaptive lag algorithms in three inference tasks from microarray expression data. Experimental results show that network inference algorithms that take dynamics into account perform consistently better than static ones, once the considered lags are properly chosen. However, no individual algorithm stands out in all three inference tasks, and the challenging nature of network inference tasks is evidenced, as a large number of the assessed algorithms does not perform better than random. © 2013 Lopes and Bontempi. |
Olsen, Catharina; Haibe-Kains, Benjamin; Quackenbush, John; Bontempi, Gianluca On the Integration of Prior Knowledge in the Inference of Regulatory Networks. Book Chapter In: World Scientific, 2013, (Language of publication: fr). @inbook{info:hdl:2013/223360b, title = {On the Integration of Prior Knowledge in the Inference of Regulatory Networks.}, author = {Catharina Olsen and Benjamin Haibe-Kains and John Quackenbush and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/223360}, year = {2013}, date = {2013-01-01}, publisher = {World Scientific}, series = {Biological Data Mining and Its Applications in Healthcare}, note = {Language of publication: fr}, keywords = {}, pubstate = {published}, tppubtype = {inbook} } |
Lerman, Liran; Markowitch, Olivier; Bontempi, Gianluca; Taieb, Souhaib Ben A time series approach for profiling attack Journal Article In: Lecture notes in computer science, 8204 , pp. 75-94, 2013, (DOI: 10.1007/978-3-642-41224-0_7). @article{info:hdl:2013/183221, title = {A time series approach for profiling attack}, author = {Liran Lerman and Olivier Markowitch and Gianluca Bontempi and Souhaib Ben Taieb}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/183221}, year = {2013}, date = {2013-01-01}, journal = {Lecture notes in computer science}, volume = {8204}, pages = {75-94}, abstract = {The goal of a profiling attack is to challenge the security of a cryptographic device in the worst case scenario. Though template attack is reputed as the strongest power analysis attack, they effectiveness is strongly dependent on the validity of the Gaussian assumption. This led recently to the appearance of nonparametric approaches, often based on machine learning strategies. Though these approaches outperform template attack, they tend to neglect the potential source of information available in the temporal dependencies between power values. In this paper, we propose an original multi-class profiling attack that takes into account the temporal dependence of power traces. The experimental study shows that the time series analysis approach is competitive and often better than static classification alternatives. © 2013 Springer-Verlag.}, note = {DOI: 10.1007/978-3-642-41224-0_7}, keywords = {}, pubstate = {published}, tppubtype = {article} } The goal of a profiling attack is to challenge the security of a cryptographic device in the worst case scenario. Though template attack is reputed as the strongest power analysis attack, they effectiveness is strongly dependent on the validity of the Gaussian assumption. This led recently to the appearance of nonparametric approaches, often based on machine learning strategies. Though these approaches outperform template attack, they tend to neglect the potential source of information available in the temporal dependencies between power values. In this paper, we propose an original multi-class profiling attack that takes into account the temporal dependence of power traces. The experimental study shows that the time series analysis approach is competitive and often better than static classification alternatives. © 2013 Springer-Verlag. |
Pozzolo, Andrea Dal; Caelen, Olivier; Waterschoot, Serge; Bontempi, Gianluca Racing for unbalanced methods selection Journal Article In: Lecture notes in computer science, 8206 LNCS , pp. 24-31, 2013, (DOI: 10.1007/978-3-642-41278-3_4). @article{info:hdl:2013/168898, title = {Racing for unbalanced methods selection}, author = {Andrea Dal Pozzolo and Olivier Caelen and Serge Waterschoot and Gianluca Bontempi}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/168898}, year = {2013}, date = {2013-01-01}, journal = {Lecture notes in computer science}, volume = {8206 LNCS}, pages = {24-31}, abstract = {State-of-the-art classification algorithms suffer when the data is skewed towards one class. This led to the development of a number of techniques to cope with unbalanced data. However, as confirmed by our experimental comparison, no technique appears to work consistently better in all conditions. We propose to use a racing method to select adaptively the most appropriate strategy for a given unbalanced task. The results show that racing is able to adapt the choice of the strategy to the specific nature of the unbalanced problem and to select rapidly the most appropriate strategy without compromising the accuracy. © 2013 Springer-Verlag.}, note = {DOI: 10.1007/978-3-642-41278-3_4}, keywords = {}, pubstate = {published}, tppubtype = {article} } State-of-the-art classification algorithms suffer when the data is skewed towards one class. This led to the development of a number of techniques to cope with unbalanced data. However, as confirmed by our experimental comparison, no technique appears to work consistently better in all conditions. We propose to use a racing method to select adaptively the most appropriate strategy for a given unbalanced task. The results show that racing is able to adapt the choice of the strategy to the specific nature of the unbalanced problem and to select rapidly the most appropriate strategy without compromising the accuracy. © 2013 Springer-Verlag. |
Jan, Serge Van Sint; Wermenbol, Vanessa; Bogaert, Patrick Van; Desloovere, Kaat; Degelaen, Marc; Dan, Bernard; Salvia, P; Bonnechere, Bruno; "e, Yann-A; Bontempi, Gianluca; Vansummeren, Stijn; Sholukha, Victor; Moiseev, Fedor; Rooze, Marcel In: Médecine, 29 (5), pp. 529-536, 2013, (Language of publication: na). @article{info:hdl:2013/185849, title = {Recherche intégrée relative `a l’appareil musculosquelettique : application `a la prise en charge clinique de l’infirmité motrice cérébrale (IMC) – le projet ICT4Rehab}, author = {Serge Van Sint Jan and Vanessa Wermenbol and Patrick Van Bogaert and Kaat Desloovere and Marc Degelaen and Bernard Dan and P Salvia and Bruno Bonnechere and Yann-A{"e}l Leborgne and Gianluca Bontempi and Stijn Vansummeren and Victor Sholukha and Fedor Moiseev and Marcel Rooze}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/185849}, year = {2013}, date = {2013-01-01}, journal = {Médecine}, volume = {29}, number = {5}, pages = {529-536}, note = {Language of publication: na}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Olsen, Catharina; Bontempi, Gianluca; Quackenbush, John; Haibe-Kains, Benjamin Data-driven validation of gene regulatory networks using knock-down data Miscellaneous 2013, (Conference: 8th Benelux Bioinformatics Conference (BBC13)). @misc{info:hdl:2013/155454b, title = {Data-driven validation of gene regulatory networks using knock-down data}, author = {Catharina Olsen and Gianluca Bontempi and John Quackenbush and Benjamin Haibe-Kains}, url = {http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/155454}, year = {2013}, date = {2013-01-01}, note = {Conference: 8th Benelux Bioinformatics Conference (BBC13)}, keywords = {}, pubstate = {published}, tppubtype = {misc} } |