Emmanuel Barillot

Summary

Affiliation: Institut Curie
Country: France

Publications

  1. pmc CAPweb: a bioinformatics CGH array Analysis Platform
    Stéphane Liva
    Institut Curie, Service Bioinformatique 26 rue d Ulm, 75248 Paris Cedex 05, France
    Nucleic Acids Res 34:W477-81. 2006
  2. ncbi request reprint VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles
    Philippe La Rosa
    Institut Curie, Service Bioinformatique, 26 Rue d Ulm, Paris 75248 cedex 05, France
    Bioinformatics 22:2066-73. 2006
  3. doi request reprint ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays
    Guillem Rigaill
    Institut Curie, Service de Bioinformatique, INSERM, U900, CNRS UMR144, Institut Curie, Translational Research Department, 26 Rue d Ulm, Paris F 75248, France
    Bioinformatics 24:768-74. 2008
  4. doi request reprint Practical use of BiNoM: a biological network manager software
    Eric Bonnet
    Institut Curie, Paris, France
    Methods Mol Biol 1021:127-46. 2013
  5. pmc De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis
    Valentina Boeva
    Institut Curie, 26 Rue d Ulm, Paris, France
    Nucleic Acids Res 38:e126. 2010
  6. pmc TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer
    Virginie Maire
    Institut Curie, Research Center, Paris, France Breast Cancer Biology Group, Department of Translational Research, Paris, France
    PLoS ONE 8:e63712. 2013
  7. pmc Patient-derived xenografts recapitulate molecular features of human uveal melanomas
    Cecile Laurent
    Institut Curie, Paris, France
    Mol Oncol 7:625-36. 2013
  8. doi request reprint Genomic profiling and identification of high-risk uveal melanoma by array CGH analysis of primary tumors and liver metastases
    Julien Trolet
    Department of Bioinformatics, Institut Curie, Paris, France
    Invest Ophthalmol Vis Sci 50:2572-80. 2009
  9. doi request reprint Establishment and characterization of a panel of human uveal melanoma xenografts derived from primary and/or metastatic tumors
    Fariba Nemati
    Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
    Clin Cancer Res 16:2352-62. 2010
  10. pmc HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data
    Haitham Ashoor
    Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center CBRC, King Abdullah University of Science and Technology KAUST, Thuwal 23955 6900, Saudi Arabia, Institut Curie, 75248 Paris Cedex 05, France, INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Mines ParisTech, Fontainebleau 77300, France and UMR 144 CNRS, Subcellular Structure and Cellular Dynamics
    Bioinformatics 29:2979-86. 2013

Detail Information

Publications82

  1. pmc CAPweb: a bioinformatics CGH array Analysis Platform
    Stéphane Liva
    Institut Curie, Service Bioinformatique 26 rue d Ulm, 75248 Paris Cedex 05, France
    Nucleic Acids Res 34:W477-81. 2006
    ..CAPweb is accessible at http://bioinfo.curie.fr/CAPweb...
  2. ncbi request reprint VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles
    Philippe La Rosa
    Institut Curie, Service Bioinformatique, 26 Rue d Ulm, Paris 75248 cedex 05, France
    Bioinformatics 22:2066-73. 2006
    ..This step requires visualization of the data in a meaningful way to visualize the results and to perform first level analyses...
  3. doi request reprint ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays
    Guillem Rigaill
    Institut Curie, Service de Bioinformatique, INSERM, U900, CNRS UMR144, Institut Curie, Translational Research Department, 26 Rue d Ulm, Paris F 75248, France
    Bioinformatics 24:768-74. 2008
    ..e. true copy number), making it difficult to estimate non-relevant effects accurately without including the biologically relevant effect...
  4. doi request reprint Practical use of BiNoM: a biological network manager software
    Eric Bonnet
    Institut Curie, Paris, France
    Methods Mol Biol 1021:127-46. 2013
    ..In this tutorial, we present a detailed and practical case study of how to use BiNoM to analyze biological networks...
  5. pmc De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis
    Valentina Boeva
    Institut Curie, 26 Rue d Ulm, Paris, France
    Nucleic Acids Res 38:e126. 2010
    ..Furthermore, we observed that sites without microsatellites can also induce regulation of gene expression--positively as often as negatively--and at much larger distances (up to approximately 1 Mb)...
  6. pmc TTK/hMPS1 is an attractive therapeutic target for triple-negative breast cancer
    Virginie Maire
    Institut Curie, Research Center, Paris, France Breast Cancer Biology Group, Department of Translational Research, Paris, France
    PLoS ONE 8:e63712. 2013
    ..These results point out TTK as a protein kinase overexpressed in TNBC that may represent an attractive therapeutic target specifically for this poor prognosis associated subgroup of breast cancer...
  7. pmc Patient-derived xenografts recapitulate molecular features of human uveal melanomas
    Cecile Laurent
    Institut Curie, Paris, France
    Mol Oncol 7:625-36. 2013
    ..These models therefore constitute valuable preclinical tool for drug screening in UM...
  8. doi request reprint Genomic profiling and identification of high-risk uveal melanoma by array CGH analysis of primary tumors and liver metastases
    Julien Trolet
    Department of Bioinformatics, Institut Curie, Paris, France
    Invest Ophthalmol Vis Sci 50:2572-80. 2009
    ..The purpose of this study was to analyze genomic profiles in a large series of ocular tumors and liver metastases and design a genome-based classifier for metastatic risk assessment...
  9. doi request reprint Establishment and characterization of a panel of human uveal melanoma xenografts derived from primary and/or metastatic tumors
    Fariba Nemati
    Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
    Clin Cancer Res 16:2352-62. 2010
    ..The aim of this study was to develop and characterize a panel of human uveal melanoma xenografts transplanted into immunodeficient mice...
  10. pmc HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data
    Haitham Ashoor
    Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center CBRC, King Abdullah University of Science and Technology KAUST, Thuwal 23955 6900, Saudi Arabia, Institut Curie, 75248 Paris Cedex 05, France, INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Mines ParisTech, Fontainebleau 77300, France and UMR 144 CNRS, Subcellular Structure and Cellular Dynamics
    Bioinformatics 29:2979-86. 2013
    ....
  11. doi request reprint From a biological hypothesis to the construction of a mathematical model
    David Cohen
    Institut Curie, Paris, France
    Methods Mol Biol 1021:107-25. 2013
    ..This chapter aims at introducing modeling to experts in molecular biology that would like to convert their hypotheses into mathematical models...
  12. doi request reprint Polo-like kinase 1: a potential therapeutic option in combination with conventional chemotherapy for the management of patients with triple-negative breast cancer
    Virginie Maire
    Institut Curie, Centre de Recherche, Paris, France
    Cancer Res 73:813-23. 2013
    ..Altogether, our observations suggest PLK1 inhibition as an attractive therapeutic approach, in association with conventional chemotherapy, for the management of patients with TNBC...
  13. pmc Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia
    Maya Ridinger-Saison
    Institut Curie, Paris, F 75248, France
    Nucleic Acids Res 40:8927-41. 2012
    ..Thus, our work describes a new mechanism of gene activation through clustered site occupancy of Spi-1 particularly relevant in regard to the strong expression of Spi-1 in the erythroleukemic cells...
  14. pmc Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
    Valentina Boeva
    Institut Curie, Paris 75248, France
    Bioinformatics 28:423-5. 2012
    ..Control-FREEC is able to analyze overdiploid tumor samples and samples contaminated by normal cells. Low mappability regions can be excluded from the analysis using provided mappability tracks...
  15. pmc Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells
    Bérengère Marty
    Département de Transfert, Institut Curie, 26 Rue d Ulm, 75005 Paris, France
    Breast Cancer Res 10:R101. 2008
    ..In contrast to HER2+ carcinomas, no targeted therapy is currently available for the treatment of patients with BLCs. In order to discover potential therapeutic targets, we aimed to discover deregulated signalling pathways in human BLCs...
  16. pmc Asf1b, the necessary Asf1 isoform for proliferation, is predictive of outcome in breast cancer
    Armelle Corpet
    Institut Curie, UMR218, Nuclear Dynamics and Genome Plasticity, Paris, France
    EMBO J 30:480-93. 2011
    ..We discuss the implications of these results for breast cancer diagnosis and prognosis...
  17. doi request reprint [Biological network modelling and precision medicine in oncology]
    Laurence Calzone
    Institut Curie, 26 Rue d Ulm, 75248 Paris, France, INSERM U900, 75248 Paris, France, Mines ParisTech, 77300 Fontainebleau, France
    Bull Cancer 101:S18-21. 2014
    ....
  18. pmc Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
    Tatiana Popova
    Centre de Recherche, Institut Curie, 26 Rue d Ulm, Paris, 75248, France
    Genome Biol 10:R128. 2009
    ..Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes...
  19. pmc Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps
    Andrei Zinovyev
    Institut Curie, Paris, France
    PLoS Comput Biol 9:e1003016. 2013
    ..These observations extend the canonical interpretation of synthetic-lethal or synthetic-sick interactions with direct implications to reconstruct molecular pathways and improve therapeutic approaches to diseases such as cancer...
  20. pmc Spatial normalization of array-CGH data
    Pierre Neuvial
    Institut Curie, Service de Bioinformatique, 26, rue d Ulm, Paris, 75248 Cedex 05, France
    BMC Bioinformatics 7:264. 2006
    ..Local spatial bias affects a large proportion of arrays, and has not previously been considered in array-CGH experiments...
  21. doi request reprint Frequent genomic structural alterations at HPV insertion sites in cervical carcinoma
    Martine Peter
    Department of Tumour Biology, Institut Curie, F 75248 Paris, France
    J Pathol 221:320-30. 2010
    ..Structural alterations of the host genome are frequently observed at the integration site of HPV DNA in cervical cancer and may act in oncogenesis...
  22. doi request reprint ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data
    Chong Jian Chen
    Institut Curie, F 75248 Paris, France
    Bioinformatics 28:3147-9. 2012
    ..The ncPRO-seq pipeline can be used to analyze read and alignment data, based on any sequenced genome, including mammals and plants...
  23. pmc Deep-sequencing protocols influence the results obtained in small-RNA sequencing
    Joern Toedling
    Institut Curie, Paris, France
    PLoS ONE 7:e32724. 2012
    ..Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons...
  24. pmc Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
    Valentina Boeva
    Institut Curie, INSERM, U900, Paris, France
    Bioinformatics 27:268-9. 2011
    ..We demonstrate that for Illumina single-end, mate-pair or paired-end sequencing, GC-contentr normalization provides smooth profiles that can be further segmented and analyzed in order to predict CNAs...
  25. pmc HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
    Nicolas Servant
    Institut Curie, Paris, France
    Genome Biol 16:259. 2015
    ..We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro . ..
  26. pmc NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps
    Inna Kuperstein
    Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 5, France
    BMC Syst Biol 7:100. 2013
    ..It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them...
  27. doi request reprint Developmental dynamics and disease potential of random monoallelic gene expression
    Anne Valerie Gendrel
    Institut Curie, 26 Rue d Ulm, Paris 75248, France Genetics and Developmental Biology Unit, INSERM U934 CNRS UMR3215, Paris 75248, France
    Dev Cell 28:366-80. 2014
    ....
  28. pmc Systems biology of Ewing sarcoma: a network model of EWS-FLI1 effect on proliferation and apoptosis
    Gautier Stoll
    Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France, INSERM U900, Bioinformatique, biostatistique et épidémiologie d un système complexe, Paris, France, Mines ParisTech, Fontainebleau, France, INSERM U830, Unité de Génétique et Biologie des Cancers, Paris, France and Institut Curie, Unité de Génétique Somatique, Paris, France
    Nucleic Acids Res 41:8853-71. 2013
    ..Altogether, using an original methodology of data integration, we provide the first version of EWS-FLI1 network model of cell cycle and apoptosis regulation. ..
  29. pmc HiTC: exploration of high-throughput 'C' experiments
    Nicolas Servant
    Institut Curie, F 75248 Paris, France
    Bioinformatics 28:2843-4. 2012
    ..The package operates within the Bioconductor framework and thus offers new opportunities for future development in this field...
  30. ncbi request reprint Nebula--a web-server for advanced ChIP-seq data analysis
    Valentina Boeva
    Institut Curie, Paris 75248, France
    Bioinformatics 28:2517-9. 2012
    ..We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data...
  31. pmc Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma
    Loredana Martignetti
    Institut Curie, Paris, France
    PLoS ONE 7:e41770. 2012
    ..The procedure allows us to infer crucial miRNA regulators and their potential targets in Ewing's sarcoma disease. It can be considered as a valid statistical approach to discover new insights in the miRNA regulatory mechanisms...
  32. ncbi request reprint BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
    Andrei Zinovyev
    Institut Curie, Service de Bioinformatique, 26 Rue d Ulm, F 75248 Paris Cedex 05, France
    Bioinformatics 24:876-7. 2008
    ..BiNoM comes as a library and as a Cytoscape plugin which adds a rich set of operations to Cytoscape such as path and cycle analysis, clustering sub-networks, decomposition of network into modules, clipboard operations and others...
  33. doi request reprint High PTP4A3 phosphatase expression correlates with metastatic risk in uveal melanoma patients
    Cecile Laurent
    Institut Curie, Paris, France
    Cancer Res 71:666-74. 2011
    ..Our findings suggest that PTP4A3 or its cellular substrates could constitute attractive therapeutic targets to treat metastatic uveal melanomas...
  34. pmc SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data
    Bruno Zeitouni
    INSERM U900, Institut Curie, Paris, France
    Bioinformatics 26:1895-6. 2010
    ..g. large insertions-deletions, inversions, duplications and balanced or unbalanced inter-chromosomal translocations. SVDetect outputs predicted structural variants in various file formats for appropriate graphical visualization...
  35. pmc A comprehensive modular map of molecular interactions in RB/E2F pathway
    Laurence Calzone
    Institut Curie, Service Blolnforrnatique, Paris, France
    Mol Syst Biol 4:173. 2008
    ..The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway...
  36. pmc NaviCell Web Service for network-based data visualization
    Eric Bonnet
    Institut Curie, 26 Rue d Ulm, 75248 Paris, France INSERM, U900, 75248 Paris, France MINES ParisTech, 77300 Fontainebleau, France
    Nucleic Acids Res 43:W560-5. 2015
    ....
  37. pmc BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
    Eric Bonnet
    Institut Curie, 26 Rue d Ulm, Paris, F 75248, France
    BMC Syst Biol 7:18. 2013
    ..However, large-scale molecular maps are not always easy to mine and interpret...
  38. pmc NormaCurve: a SuperCurve-based method that simultaneously quantifies and normalizes reverse phase protein array data
    Sylvie Troncale
    Institut Curie, Paris, France
    PLoS ONE 7:e38686. 2012
    ..However, appropriate tools allowing the normalization of the data for external sources of variation are currently missing...
  39. doi request reprint Cell death and life in cancer: mathematical modeling of cell fate decisions
    Andrei Zinovyev
    U900 INSERM Institut Curie Ecole de Mines, Institut Curie, 26 Rue d Ulm, Paris 75005, France
    Adv Exp Med Biol 736:261-74. 2012
    ..Using an original parameter sensitivity analysis developed for discrete dynamic systems, we determine variables that appear to be critical in the cellular fate decision and discuss how they are exploited by existing cancer therapies...
  40. pmc EMA - A R package for Easy Microarray data analysis
    Nicolas Servant
    Institut Curie, Paris F 75248, France
    BMC Res Notes 3:277. 2010
    ..The increasing number of methodologies and tools currently available to analyse gene expression microarray data can be confusing for non specialist users...
  41. ncbi request reprint A robust algorithm for ratio estimation in two-color microarray experiments
    Eugene Novikov
    Service Bioinformatique Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France
    J Bioinform Comput Biol 3:1411-28. 2005
    ..The developed algorithms have been evaluated using simulated artificial images and experimental images of different designs. A demonstration version of the software can be downloaded from http://bioinfo.curie.fr/projects/maia/...
  42. doi request reprint [Systems biology of cancer]
    Emmanuel Barillot
    Institut Curie, 26, rue d Ulm, F 75248 Paris Cedex 05, INSERM, U900, F 75248 Paris, France
    Med Sci (Paris) 25:601-7. 2009
    ..These characteristics emphasize the important role of Systems Biology of Cancer in the future of biomedical research...
  43. doi request reprint Integrated genomic and transcriptomic analysis of ductal carcinoma in situ of the breast
    Anne Vincent-Salomon
    Institut Curie, Department of Tumor Biology, Paris, France
    Clin Cancer Res 14:1956-65. 2008
    ..To gain insight into genomic and transcriptomic subtypes of ductal carcinomas in situ of the breast (DCIS)...
  44. doi request reprint The shortest path is not the one you know: application of biological network resources in precision oncology research
    Inna Kuperstein
    Institut Curie, 26 Rue d Ulm, Paris F 75248, France, INSERM, U900, Paris F 75248, France, Mines ParisTech, Fontainebleau F 77300, France
    Mutagenesis 30:191-204. 2015
    ..Taking into account the information about biological signalling machinery in cells may help to better interpret molecular patterns of tumours and enable to put precision oncology into general clinical practice. ..
  45. doi request reprint OCSANA: optimal combinations of interventions from network analysis
    Paola Vera-Licona
    Institut Curie, Paris F 75248, France, INSERM, U900, Paris F 75248, France
    Bioinformatics 29:1571-3. 2013
    ..With the crucial ability to cope with very large networks, OCSANA includes an exact solution and a novel selective enumeration approach for the combinatorial interventions' problem...
  46. ncbi request reprint Urokinase-type plasminogen activator and plasminogen-activator-inhibitor type 1 predict metastases in good prognosis breast cancer patients
    Patricia De Cremoux
    Departement de Biologie des Tumeurs, Institut Curie, 26 Rue d Ulm, 75231 Paris Cedex, France
    Anticancer Res 29:1475-82. 2009
    ..This retrospective analysis was designed to confirm the predictive role of urokinase-type plasminogen activator (uPA) and plasminogen activator inhibitor type I (PAI-1) in the outcome of early stage, node-negative breast cancer patients...
  47. doi request reprint Beta-catenin status in paediatric medulloblastomas: correlation of immunohistochemical expression with mutational status, genetic profiles, and clinical characteristics
    Sarah Fattet
    INSERM U830, Laboratoire de Génétique et Biologie des Cancers, 75248 Paris Cedex 05, France
    J Pathol 218:86-94. 2009
    ..International consensus on the definition criteria of this distinct medulloblastoma subgroup should be achieved...
  48. doi request reprint Search for a gene expression signature of breast cancer local recurrence in young women
    Nicolas Servant
    Institut Curie, CNRS, Paris, France
    Clin Cancer Res 18:1704-15. 2012
    ..We evaluated this signature on both another platform and an independent series, compared its performance with other published gene-sets, and investigated the gene expression profile of a larger data set...
  49. doi request reprint Multiparametric analysis of cytokine-driven human Th17 differentiation reveals a differential regulation of IL-17 and IL-22 production
    Elisabetta Volpe
    Institut Curie, Laboratoire d Immunologie Clinique, Paris, France
    Blood 114:3610-4. 2009
    ..Thus, IL-17 and IL-22 are differentially regulated during cytokine-induced Th cell differentiation. This has important implications for the understanding and pharmacologic manipulation of Th17-associated pathologies...
  50. ncbi request reprint Software package for automatic microarray image analysis (MAIA)
    Eugene Novikov
    Service Bioinformatique, Institut Curie, 75248 Paris Cedex 05, France
    Bioinformatics 23:639-40. 2007
    ..The developed algorithms aim at making ratio estimates more resistant to array contamination and offer automatic tools to evaluate spot quality...
  51. pmc Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation
    Osamu Masui
    Institut Curie, Paris, France
    Cell 145:447-58. 2011
    ....
  52. pmc Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration
    David P A Cohen
    Institut Curie, Paris, France INSERM, U900, Paris, France MINES ParisTech, Fontainebleau, Paris, France
    PLoS Comput Biol 11:e1004571. 2015
    ..Furthermore, the model predicts new gene perturbations that affect the early steps of metastasis underlying potential intervention points for innovative therapeutic strategies in oncology. ..
  53. pmc Combinatorial code governing cellular responses to complex stimuli
    Antonio Cappuccio
    1 Department of Immunology, Institut Curie, Paris F 75248, France 2 INSERM U932, Paris F 75248, France
    Nat Commun 6:6847. 2015
    ..Our work defines an exhaustive map of interaction modes for cells integrating pairs of physiopathological and pharmacological stimuli. ..
  54. pmc Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
    Valentina Boeva
    INSERM, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche, 26 Rue d Ulm, Paris 75248, Mines ParisTech, Fontainebleau 77300, INSERM, U830, Genetics and Biology of Cancers, Paris 75248, France, Institut de Pathologie et de Génétique, Gosselies 6041, Belgium, Clinical Research Department, Department of Medical Oncology, Plateforme de Génomique, département de recherche translationnelle, Centre de Recherche, Next generation sequencing platform, Institut Curie, CNRS, UMR144, Subcellular Structure and Cellular Dynamics, Paris 75248, France and OncoDNA, Gosselies 6041, Belgium INSERM, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institut Curie, Centre de Recherche
    Bioinformatics 30:3443-50. 2014
    ..So far, there has been no proven method to extract the information on gene copy number aberrations based solely on amplicon sequencing...
  55. pmc Germline BAP1 mutations predispose to renal cell carcinomas
    Tatiana Popova
    Institut Curie, INSERM U830, Paris 75248, France
    Am J Hum Genet 92:974-80. 2013
    ..This strongly argues that RCC belongs to the BAP1 syndrome and that BAP1 is a RCC-predisposition gene...
  56. doi request reprint Identification of shortened 3' untranslated regions from expression arrays
    Loredana Martignetti
    Institut Curie, 26 Rue d Ulm, Paris, F 75248, France
    J Bioinform Comput Biol 10:1241001. 2012
    ..Selected gene sets are significantly enriched for annotated splice variant genes as well as genes involved in estrogen dependent cancer mechanisms, confirming the validity of the proposed procedure...
  57. pmc Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads
    Joern Toedling
    Institut Curie, 26 Rue d Ulm, F 75248 Paris, INSERM U900, F 75248 Paris, France
    Bioinformatics 26:2902-3. 2010
    ..Moreover, the package operates within and extends the ever-growing Bioconductor framework and thus enables users to leverage a multitude of methods for their data in order to answer specific research questions...
  58. doi request reprint Spi-1/PU.1 oncogene accelerates DNA replication fork elongation and promotes genetic instability in the absence of DNA breakage
    Pauline Rimmelé
    Institut Curie, INSERM U830, Paris, France
    Cancer Res 70:6757-66. 2010
    ..Thus, we propose that the hitherto unsuspected role for spi-1 oncogene in promoting replication elongation and genomic mutation promotes blastic progression during leukemic development...
  59. ncbi request reprint myProMS, a web server for management and validation of mass spectrometry-based proteomic data
    Patrick Poullet
    Institut Curie, Service de Bioinformatique, Paris, France
    Proteomics 7:2553-6. 2007
    ..A demo is accessible at http://bioinfo.curie.fr/myproms...
  60. ncbi request reprint LICORN: learning cooperative regulation networks from gene expression data
    Mohamed Elati
    LRI, CNRS UMR 8623, Bat 490, Universite Paris Sud, 91405 F Orsay, France
    Bioinformatics 23:2407-14. 2007
    ..DNA microarrays can be used to investigate relationships between regulators and their target genes, through simultaneous observations of their RNA levels...
  61. ncbi request reprint Analysis of array CGH data: from signal ratio to gain and loss of DNA regions
    Philippe Hupe
    Service Bioinformatique, UMR 144 CNRS Institut Curie, 26, rue d Ulm, Paris, 75248 Cedex 05, France
    Bioinformatics 20:3413-22. 2004
    ..The achievement of these goals requires a methodology for detecting the breakpoints delimiting altered regions in genomic patterns and assigning a status (normal, gained or lost) to each chromosomal region...
  62. pmc Classification of microarray data using gene networks
    Franck Rapaport
    lnstitut Curie, Service de Bioinformatique, 26 Rue d Ulm, F 75248 Paris Cedex 05, France
    BMC Bioinformatics 8:35. 2007
    ..However, integrating a priori knowledge of the gene networks could help in the statistical analysis of gene expression data and in their biological interpretation...
  63. pmc Classification of arrayCGH data using fused SVM
    Franck Rapaport
    Institut Curie, Centre de Recherche, INSERM, U900, Paris, F 75248 France
    Bioinformatics 24:i375-82. 2008
    ..This suggests that classical classification methods, often based on the selection of a small number of discriminative features, may not be the most accurate methods and may not produce easily interpretable prediction rules...
  64. ncbi request reprint High-resolution mapping of DNA breakpoints to define true recurrences among ipsilateral breast cancers
    Marc A Bollet
    Département d Oncologie Radiothérapie, Institut Curie, 26, rue d Ulm, 75248 Paris Cedex 05, France
    J Natl Cancer Inst 100:48-58. 2008
    ..To distinguish new primary breast cancers from true recurrences, pangenomic analyses of DNA copy number alterations (CNAs) using single-nucleotide polymorphism arrays have proven useful...
  65. ncbi request reprint Preferential occurrence of chromosome breakpoints within early replicating regions in neuroblastoma
    Isabelle Janoueix-Lerosey
    Laboratoire de Pathologie Moléculaire des Cancers, Institut Curie, Paris, France
    Cell Cycle 4:1842-6. 2005
    ..These results unambiguously establish a link between unbalanced translocations, whose most likely mechanism of occurrence relies on break-induced replication, and early replication of the genome...
  66. pmc Stability-based comparison of class discovery methods for DNA copy number profiles
    Isabel Brito
    Institut Curie, Paris, France INSERM, U900, Paris, France MINES ParisTech, Fontainebleau, France
    PLoS ONE 8:e81458. 2013
    ..Robustness of the resulting classes is a common requirement, but no stability-based comparison of class discovery methods for array-CGH profiles has ever been reported...
  67. pmc Genome-wide redistribution of meiotic double-strand breaks in Saccharomyces cerevisiae
    Nicolas Robine
    Institut Curie, Recombinaison et Instabilité Génétique, Centre de Recherche, UMR7147 CNRS Institut Curie Université P et M Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France
    Mol Cell Biol 27:1868-80. 2007
    ....
  68. doi request reprint Characterization of rearrangements involving the ALK gene reveals a novel truncated form associated with tumor aggressiveness in neuroblastoma
    Alex Cazes
    INSERM U830, Institut Curie, Centre de Recherche, Paris, France
    Cancer Res 73:195-204. 2013
    ..These results indicate that genomic rearrangements constitute an alternative mechanism to ALK point mutations resulting in receptor activation...
  69. pmc Spatial partitioning of the regulatory landscape of the X-inactivation centre
    Elphège P Nora
    Institut Curie, 26 Rue d Ulm, Paris F 75248, France
    Nature 485:381-5. 2012
    ..In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, our study sets the stage for the full genetic dissection of the X-inactivation centre...
  70. pmc Dynamical modeling of microRNA action on the protein translation process
    Andrei Zinovyev
    Institut Curie, Bioinformatics and Computational Systems Biology of Cancer, Paris, France
    BMC Syst Biol 4:13. 2010
    ..For their analysis they used two simple kinetic models of protein translation...
  71. doi request reprint LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation
    Jennifer C Chow
    Institut Curie, Paris F 75248, France
    Cell 141:956-69. 2010
    ....
  72. pmc ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis
    Adil Elfilali
    Institut Curie, Service Bioinformatique, 26 Rue d Ulm, Paris, 75248 Cedex 05, France
    Nucleic Acids Res 34:D613-6. 2006
    ..This added flexibility and the user-friendly web interface makes ITTACA especially useful for comparing personal results with the results in the existing literature. ITTACA is accessible online at http://bioinfo.curie.fr/ittaca...
  73. pmc The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function
    Noëlle Guillon
    Institut Curie, Paris, France
    PLoS ONE 4:e4932. 2009
    ..Put together, these results point out the likely contribution of microsatellite elements to long-distance transcription regulation and to oncogenesis...
  74. pmc Mathematical modelling of cell-fate decision in response to death receptor engagement
    Laurence Calzone
    Institut Curie, Paris, France
    PLoS Comput Biol 6:e1000702. 2010
    ..Moreover, our current model can be used to assess contradictory or controversial data from the literature. Ultimately, it constitutes a valuable reasoning tool to delineate novel experiments...
  75. doi request reprint Multiple-checkpoint inhibition of thymic stromal lymphopoietin-induced TH2 response by TH17-related cytokines
    Sofia I Bogiatzi
    Institut Curie, Laboratoire d Immunologie Clinique, Paris, France
    J Allergy Clin Immunol 130:233-40.e5. 2012
    ..However, recent studies suggest that IL-17 and related cytokines, which play a central role in autoimmunity, might also promote allergy...
  76. pmc Regulatory network reconstruction using an integral additive model with flexible kernel functions
    Eugene Novikov
    Service Bioinformatique, Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France
    BMC Syst Biol 2:8. 2008
    ....
  77. pmc An algorithm for automatic evaluation of the spot quality in two-color DNA microarray experiments
    Eugene Novikov
    Service Bioinformatique, Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France
    BMC Bioinformatics 6:293. 2005
    ..The problem is difficult to formalize due to the diversity of instrumental and biological factors that can influence the result...
  78. pmc Model selection in the reconstruction of regulatory networks from time-series data
    Eugene Novikov
    Service Bioinformatique, Institut Curie, 26 Rue d Ulm, 75248 Paris Cedex 05, France
    BMC Res Notes 2:68. 2009
    ..However, weak perturbations may not be informative enough to reveal network structures. Other approaches are based on specific models of gene regulation and therefore are of limited applicability...
  79. pmc GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics
    Delphine Samson
    Génoplante Info, Unité de Recherche Génomique Info, INRA, Infobiogen, 523 Place des Terrasses, F 91000 Evry, France
    Nucleic Acids Res 31:179-82. 2003
    ..This continuous flood of data and tools is regularly updated and will grow continuously during the coming two years. Access to the GPI databases and tools is available at http://genoplante-info.infobiogen.fr/...
  80. ncbi request reprint Selecting biomedical data sources according to user preferences
    Sarah Cohen Boulakia
    Laboratoire de Recherche en Informatique, CNRS UMR 8623, Universite Paris Sud, Orsay Cedex, France
    Bioinformatics 20:i86-93. 2004
    ..The selection of the sources to be considered is thus critically important...
  81. ncbi request reprint APC inactivation associates with abnormal mitosis completion and concomitant BUB1B/MAD2L1 up-regulation
    Miguel Abal
    Morphogenesis and intracellular signalling, UMR 144, Institut Curie CNRS, Paris, France
    Gastroenterology 132:2448-58. 2007
    ..Here, we tackled the genetic basis for the contribution of APC to chromosomal instability in familial adenomatous polyposis and sporadic colorectal cancer...
  82. pmc The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa)
    Emmanuelle Karsenty
    Infobiogen, 523 Place des Terrasses, F 91000 Evry, France
    Nucleic Acids Res 31:138-41. 2003
    ..Functional annotation of the mapped ESTs is also given when a significant similarity to cognate genes was established. The database is accessible for consultation via the Internet at http://www.infobiogen.fr/services/Genetpig/...