{"id":5933,"date":"2025-01-02T16:46:18","date_gmt":"2025-01-02T15:46:18","guid":{"rendered":"https:\/\/crcm-marseille.fr\/our-technology-platforms\/integrative-bioinformatics-platform\/"},"modified":"2025-11-18T10:32:27","modified_gmt":"2025-11-18T09:32:27","slug":"integrative-bioinformatics","status":"publish","type":"page","link":"https:\/\/crcm-marseille.fr\/en\/our-technology-platforms\/integrative-bioinformatics\/","title":{"rendered":"Integrative Bioinformatics"},"content":{"rendered":"\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/en\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2024\/10\/logo-centre-de-recherche-en-cancerologie-de-marseille-crcm.webp#847\" alt=\"Logo Marseille Cancer Research Center\"\/><\/a><\/figure>\n\n<ul id=\"menu-menu-principal\" class=\"wp-block-list\">\n<li><a href=\"https:\/\/crcm-marseille.fr\/en\/\">Home<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/crcm-marseille.fr\/en\/our-technology-platforms\/integrative-bioinformatics\/#\">Our center<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/crcm-marseille.fr\/en\/our-technology-platforms\/integrative-bioinformatics\/#\">Our research<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/crcm-marseille.fr\/en\/our-technology-platforms\/integrative-bioinformatics\/#\">For students<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/crcm-marseille.fr\/en\/our-technology-platforms\/integrative-bioinformatics\/#\">For scientists<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/crcm-marseille.fr\/en\/our-technology-platforms\/integrative-bioinformatics\/#\">Research teams<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/crcm-marseille.fr\/en\/our-technology-platforms\/integrative-bioinformatics\/#\"><\/a><\/li>\n<\/ul>\n\n<h1 class=\"wp-block-heading\">Integrative Bioinformatics<\/h1>\n\n<p>Paoli Calmettes Institute<\/p>\n\n<figure class=\"wp-block-image\"><a class=\"\" href=\"https:\/\/crcm-marseille.fr\/nos-plateformes-technologiques\/plateforme-bioinformatique\/#\" target=\"_blank\" rel=\"noreferrer noopener\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2024\/09\/logo-x-equipe-crcm.png\" alt=\"\"\/><\/a><\/figure>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/ghislain-bidaut\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/bidaut_ghislain_crcm_2-1.jpg\" alt=\"Bidaut Ghilsain - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/ghislain-bidaut\/\">Ghislain Bidaut<\/a><\/p>\n\n<p>Platform Manager<\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/samuel-granjeaud\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2024\/12\/samuel-granjeaud_crcm.jpg\" alt=\"\"\/><\/a><\/figure>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/samuel-granjeaud\/\">Samuel Granjeaud<\/a><\/p>\n\n<p>Platform Manager<\/p>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/julien-vernerey\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/julien-vernerey\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/vernerey_julien_crcm.jpg\" alt=\"Vernerey Julien - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Julien Vernerey<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/paraskevi-kousteridou\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/paraskevi-kousteridou\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/kousteridou_paraskevi_crcm.jpg\" alt=\"Kousteridou Parakesvi - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Paraskevi Kousteridou<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/pierre-bertrand\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/pierre-bertrand\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2024\/12\/bertrand_pierre_crcm.webp\" alt=\"Pierre Bertrand CRCM - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Pierre Bertrand<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/benoit-goutorbe\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/benoit-goutorbe\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/goutorbe_benoit_crcm.jpg\" alt=\"Goutorbe Beno&#xEE;t - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Benoit Goutorbe<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/bertrand-llorente\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/bertrand-llorente\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/llorente_bertrand_crcm_3.jpg\" alt=\"Llorente Bertrand - Marseille Cancer Research Center - Genome Dynamics and Recombination Team - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Bertrand Llorente<\/h2>\n\n<h4 class=\"wp-block-heading\">Team leader \/ Researcher<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/eugenie-lohmann\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/eugenie-lohmann\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/lohmann_eugenie_crcm.jpg\" alt=\"Lohmann Eug&#xE9;nie - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Eug\u00e9nie Lohmann<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/julien-vernerey\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/julien-vernerey\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/vernerey_julien_crcm.jpg\" alt=\"Vernerey Julien - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Julien Vernerey<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/paraskevi-kousteridou\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/paraskevi-kousteridou\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/kousteridou_paraskevi_crcm.jpg\" alt=\"Kousteridou Parakesvi - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Paraskevi Kousteridou<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/pierre-bertrand\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/pierre-bertrand\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2024\/12\/bertrand_pierre_crcm.webp\" alt=\"Pierre Bertrand CRCM - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Pierre Bertrand<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/benoit-goutorbe\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/benoit-goutorbe\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/goutorbe_benoit_crcm.jpg\" alt=\"Goutorbe Beno&#xEE;t - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Benoit Goutorbe<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/bertrand-llorente\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/bertrand-llorente\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/llorente_bertrand_crcm_3.jpg\" alt=\"Llorente Bertrand - Marseille Cancer Research Center - Genome Dynamics and Recombination Team - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Bertrand Llorente<\/h2>\n\n<h4 class=\"wp-block-heading\">Team leader \/ Researcher<\/h4>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/team\/eugenie-lohmann\/\"><\/a><\/p>\n\n<figure class=\"wp-block-image\"><a href=\"https:\/\/crcm-marseille.fr\/team\/eugenie-lohmann\/\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/lohmann_eugenie_crcm.jpg\" alt=\"Lohmann Eug&#xE9;nie - Marseille Cancer Research Center - Integrative Bioinformatics Platform\"\/><\/a><\/figure>\n\n<h2 class=\"wp-block-heading\">Eug\u00e9nie Lohmann<\/h2>\n\n<h4 class=\"wp-block-heading\">Engineer<\/h4>\n\n<p>The Cibi platform offers a wide range of expertise and services in bioinformatics (data integration, development of customized biological analyses) and develops cutting-edge bioinformatics pipelines. Our engineers also develop biological databases for data storage and management. <\/p>\n\n<p>The Cibi platform offers the following services:<\/p>\n\n<ul class=\"wp-block-list\">\n<li>&#8211; <strong>Analysis and integration of NGS data <\/strong>(Next Generation Sequencing: ChIP-Seq, RNA-Seq, single cell RNA-Seq, analysis of genetic variants for research and diagnostic purposes)<\/li>\n\n\n\n<li><strong>&#8211; Analysis of flow cytometry and mass cytometry data<\/strong><\/li>\n\n\n\n<li><strong>&#8211; Proteomics data analysis<\/strong><\/li>\n\n\n\n<li>\u00a0<\/li>\n<\/ul>\n\n<p>Our expertise also extends to software development:<\/p>\n\n<ul class=\"wp-block-list\">\n<li>&#8211; <strong>Development of bioinformatics pipelines and databases<\/strong><em>(Python, R, Bioconductor, RShiny, Django, PostgreSQL, etc.<\/em>)<\/li>\n\n\n\n<li>&#8211; <strong>Project collaboration<\/strong><em>(INCa, ANR, ARC, etc.<\/em>)<\/li>\n<\/ul>\n\n<h2 class=\"wp-block-heading\">Our Pipelines<\/h2>\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/pipelines-bioinfo.gif\" alt=\"Bioinformatics pipelines - Centre de recherche en canc&#xE9;rologie de Marseille - Platform\"\/><\/figure>\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2024\/12\/forme-orange-plateforme-left-crcm.png\" alt=\"Form orange platform publications Marseille Cancer Research Center\"\/><\/figure>\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2024\/12\/forme-orange-plateforme-right-crcm.png\" alt=\"Form orange platform publications Marseille Cancer Research Center\"\/><\/figure>\n\n<h2 class=\"wp-block-heading\">front-page publications<\/h2>\n\n<p>09\/2024<\/p>\n\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38954834\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Genetic deletion of JAM-C in preleukemic cells rewires leukemic stem cell gene expression program in AML.<\/strong><\/a><\/p>\n\n<p>Grenier JMP , Testut C, Bal M, Bardin F, De Grandis M, Gelsi-Boyer V, Vernerey J, Delahaye M, Granjeaud S, Zemmour C, Spinella JF, Chavakis T, Mancini SJC, Boher JM, H\u00e9bert J, Sauvageau G, Vey N, Schwaller J, Hospital MA, Fauriat C, Aurrand-Lions M.<\/p>\n\n<p>01\/2024<\/p>\n\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38249340\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>DIAgui: a Shiny application to process the output from DIA-NN.<\/strong><\/a><\/p>\n\n<p>Gerault MA, Camoin L, Granjeaud S.<\/p>\n\n<p>08\/2022<\/p>\n\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35983031\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Gut microbiota in systemic lupus erythematosus patients and lupus mouse model: a cross species comparative analysis for biomarker discovery.<\/strong><\/a><\/p>\n\n<p>Toumi E, Goutorbe B, Plauzolles A, Bonnet M, Mezouar S, Militello M, Mege JL, Chiche L, Halfon P .<\/p>\n\n<p>10\/2024<\/p>\n\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39471249\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>CXCR4 signaling determines the fate of hematopoietic multipotent progenitors by stimulating mTOR activity and mitochondrial metabolism.<\/strong><\/a><\/p>\n\n<p>Rondeau V, Kalogeraki M, Roland L, Nader ZA, Gourhand V, Bonaud A, Lemos J, Khamyath M, Moulin C, Schell B, Delord M, Bidaut G, Lecourt S, Freitas C, Anginot A, Mazure N, McDermott DH, Parietti V, Setterblad N, Dulphy N, Bachelerie F, Aurrand-Lions M, Stockholm D, Lobry C, Murphy PM, Esp\u00e9li M, Mancini SJC, Balabanian K.<\/p>\n\n<p>04\/2022<\/p>\n\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35393954\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>TET2 regulates immune tolerance in chronically activated mast cells.<\/strong><\/a><\/p>\n\n<p>Rigo R, Chelbi R, Agopian J, Letard S, Griffon A, Ghamlouch H, Vernerey J, Ladopoulos V, Voisset E, De Sepulveda P , Guittard G, Nun\u00e8s JA, Bidaut G, G\u00f6ttgens B, Weber M, Bernard OA, Dubreuil P , Soucie E<\/p>\n\n<p>01\/2024<\/p>\n\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38167013\/\" target=\"_blank\" rel=\"noreferrer noopener\"><strong>Macrophages reprogramming driven by cancer-associated fibroblasts under FOLFIRINOX treatment correlates with shorter survival in pancreatic cancer.<\/strong><\/a><\/p>\n\n<p>Hussain Z, Bertran T, Finetti P , Lohmann E, Mamessier E, Bidaut G, Bertucci F, Rego M, Tomasini R.<\/p>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/wp-content\/uploads\/2025\/01\/Bioinformatique-Integrative-Cibi-publications.pdf\" target=\"_blank\" rel=\"noreferrer noopener\">All our publications<\/a><\/p>\n\n<h2 class=\"wp-block-heading\">Labels, Funding and Partners<\/h2>\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/www.institutpaolicalmettes.fr\/\" target=\"_blank\" rel=\"noreferrer noopener\"><\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.univ-amu.fr\/\" target=\"_blank\" rel=\"noreferrer noopener\"><\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.e-cancer.fr\/\" target=\"_blank\" rel=\"noreferrer noopener\"><\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.inserm.fr\/\" target=\"_blank\" rel=\"noreferrer noopener\"><\/a><\/li>\n<\/ul>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/en\/\">Intranet connection<\/a><br\/><a href=\"https:\/\/crcm-marseille.fr\/en\/directory\/\">Directory<\/a><br\/><a href=\"https:\/\/crcm-marseille.fr\/en\/\">About IPC<\/a><br\/><a href=\"https:\/\/crcm-marseille.fr\/en\/news\/\">News<\/a><br\/><a href=\"https:\/\/crcm-marseille.fr\/evenements\/\">Events<\/a><br\/><a href=\"https:\/\/crcm-marseille.fr\/en\/\">Legal notice<\/a><br\/><a href=\"https:\/\/crcm-marseille.fr\/en\/\">Privacy policy<\/a><\/p>\n\n<h3 class=\"wp-block-heading\">Marseille Cancer Research Center<\/h3>\n\n<p>27 Bd Le\u00ef Roure, CS 30059<br\/>13273 Marseille Cedex 09<\/p>\n\n<p>Tel: 04 86 97 72 00<\/p>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/en\/\">Contact us<br\/>How to get here<\/a><\/p>\n\n<p>Follow us<\/p>\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/x.com\/crcm_marseille\" target=\"_blank\" rel=\"noreferrer noopener\">X<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.youtube.com\/@CRCM-marseille\" target=\"_blank\" rel=\"noreferrer noopener\">YouTube<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/www.linkedin.com\/company\/crcm-marseille\/\" target=\"_blank\" rel=\"noreferrer noopener\">LinkedIn<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/bsky.app\/profile\/crcm.bsky.social\" target=\"_blank\" rel=\"noreferrer noopener\">Bluesky<\/a><\/li>\n<\/ul>\n\n<p><a href=\"https:\/\/crcm-marseille.fr\/en\/our-technology-platforms\/integrative-bioinformatics-platform\/\"><\/a><\/p>\n\n<p>www.crcm-marseille.fr \u00a92024 | All rights reserved &#8211; Created by <a href=\"https:\/\/yesss-communication.fr\/\" target=\"_blank\" rel=\"noreferrer noopener\">Yesss 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[\u2026]<\/span><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":5925,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_tec_requires_first_save":true,"_EventAllDay":false,"_EventTimezone":"","_EventStartDate":"","_EventEndDate":"","_EventStartDateUTC":"","_EventEndDateUTC":"","_EventShowMap":false,"_EventShowMapLink":false,"_EventURL":"","_EventCost":"","_EventCostDescription":"","_EventCurrencySymbol":"","_EventCurrencyCode":"","_EventCurrencyPosition":"","_EventDateTimeSeparator":"","_EventTimeRangeSeparator":"","_EventOrganizerID":[],"_EventVenueID":[],"_OrganizerEmail":"","_OrganizerPhone":"","_OrganizerWebsite":"","_VenueAddress":"","_VenueCity":"","_VenueCountry":"","_VenueProvince":"","_VenueState":"","_VenueZip":"","_VenuePhone":"","_VenueURL":"","_VenueStateProvince":"","_VenueLat":"","_VenueLng":"","_VenueShowMap":false,"_VenueShowMapLink":false,"_tribe_blocks_recurrence_rules":"","_tribe_blocks_recurrence_description":"","_tribe_blocks_recurrence_exclusions":"","footnotes":""},"class_list":["post-5933","page","type-page","status-publish","hentry"],"yoast_head":"<!-- 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