Team List
Handles creating, reading and updating teams.
GET /api/team/?format=api&ordering=lat
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Le laboratoire comprend une installation de séquençage (TGML, membre de France Génomique) et une solide équipe de bio-informaticiens qui développent et donnent accès au public à des ressources bio-informatiques (outils logiciels et bases de données) dans des domaines allant de l'analyse de protéines individuelles et de séquences d'ADN à l'analyse à grande échelle et à l'intégration de données omiques, avec un accent particulier sur les variations du génome, la régulation génétique et épigénétique, et l'analyse de réseaux.", "expertise": [], "expertise_description": "coming soon", "linkCovid19": "", "homepage": "https://tagc.univ-amu.fr", "unitId": "", "address": "163 avenue de Luminy\r\nParc Scientifique de Luminy case 928", "city": "Marseille", "country": "France", "communities": [], "projects": [], "affiliatedWith": [ { "id": 56, "name": "INSERM", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/INSERM/?format=api" } ], "publications": [ "" ], "certifications": [], "fundedBy": [ { "id": 56, "name": "INSERM", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/INSERM/?format=api" } ], "keywords": [ "Biostatistics", "Analysis of RNAseq data", "Systems Biology", "Genome analysis", "Transcript and transcript variant analysis", "Protein/protein interaction modelisation", "Single-Cell Analysis", "Workflow development", "Databases and information systems" ], "fields": [ "Biologie", "Biomédical" ], "orgid": null, "tools": [ "ledpred", "metamorf", "MoonDB", "ocg", "inserm-remap", "rsat" ], "services": [], "leaders": [], "deputies": [], "scientificLeaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/846/?format=api" ], "technicalLeaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/639/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/83/?format=api" ], "members": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/639/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/844/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/845/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/624/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/28/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/46/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/83/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/260/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/393/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/512/?format=api" ], "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/639/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/83/?format=api" ], "ifbMembership": "Associated Team", "platforms": [], "is_active": true, "closing_date": null, "lat": "43.231496", "lng": "5.441888", "updated_at": "2025-12-08T15:37:46.500141Z" }, { "id": 45, "name": "CENTURI-MEP", "logo_url": "https://centuri-livingsystems.org/wp-content/uploads/2025/12/logo_mep_2025.jpg", "description": "La Plateforme Multi-Ingénierie pour les Systèmes Vivants (AMU/CNRS UAR 2027 / INSERM US 60) rassemble des ingénieurs experts en bioinformatique, analyse d’images, mécatronique et développement logiciel.\r\nSes ingénieurs accompagnent et conseillent les chercheurs dans leurs questions d’ingénierie et d’analyse de données, et participent à des projets de recherche sur le long terme dans le cadre de collaborations scientifiques. En complément de ses activités de service, la plateforme développe une offre de formation et d’accompagnement à destination des chercheurs et des doctorants.", "expertise": [ "http://edamontology.org/topic_3391", "http://edamontology.org/topic_3387", "http://edamontology.org/topic_3382", "http://edamontology.org/topic_3941", "http://edamontology.org/topic_0203", "http://edamontology.org/topic_3174", "http://edamontology.org/topic_3308", "http://edamontology.org/topic_0622", "http://edamontology.org/topic_2269", "http://edamontology.org/topic_0080", "http://edamontology.org/topic_3372", "http://edamontology.org/topic_0091" ], "expertise_description": "Conception d’instruments pour l’acquisition des données, imagerie (segmentation, tracking, analyse quantitative), bioinformatique (données omiques, biostatistique, intégration), et développement logiciel (Java, R, Python) pour pipelines et outils sur mesure. Les ingénieurs accompagnent les projets de la conception à la publication en garantissant reproductibilité et valorisation des résultats.", "linkCovid19": "", "homepage": "https://centuri-livingsystems.org/multi-engineering-platform/", "unitId": "", "address": "Étage 0 – Bâtiment TPR2-AMU\r\nCampus de Luminy\r\n13288 MARSEILLE Cedex 09 \r\nFrance", "city": "Marseille", "country": "France", "communities": [], "projects": [], "affiliatedWith": [ { "id": 109, "name": "Aix Marseille Univ", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/Aix%20Marseille%20Univ/?format=api" }, { "id": 56, "name": "INSERM", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/INSERM/?format=api" }, { "id": 52, "name": "CNRS", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/CNRS/?format=api" } ], "publications": [ "", "10.1039/d4lc00901k", "10.1002/lol2.10380", "10.1016/j.devcel.2023.07.017", "10.1073/pnas.2300095120", "10.1101/2022.04.15.488452", "10.1016/j.isci.2023.106910", "10.1038/s41467-023-35965-8", "10.7554/eLife.75906", "10.1038/s41598-023-40959-z", "10.1113/JP282536", "10.1016/j.nupar.2021.12.012", "10.15252/embj.2021107982", "10.1016/j.bpj.2021.03.037", "10.3389/fbioe.2021.625366", "10.3791/61823" ], "certifications": [ "label Plateforme Aix-Marseille" ], "fundedBy": [ { "id": 98, "name": "CENTURI", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/CENTURI/?format=api" } ], "keywords": [ "Biostatistics", "Programming Languages & Computer Sciences", "NGS Data Analysis", "Metagenomics", "Analysis of RNAseq data", "Image analysis", "Bioinformatics", "Single-Cell Analysis", "Metabarcoding", "Workflow development" ], "fields": [ "Biologie", "Informatique" ], "orgid": null, "tools": [], "services": [], "leaders": [], "deputies": [], "scientificLeaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/860/?format=api" ], "technicalLeaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/859/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/863/?format=api" ], "members": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/859/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/860/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/861/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/862/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/863/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/864/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/831/?format=api" ], "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/859/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/831/?format=api" ], "ifbMembership": "Associated Team", "platforms": [], "is_active": true, "closing_date": null, "lat": "43.231558", "lng": "5.439244", "updated_at": "2025-12-17T16:20:18.454329Z" }, { "id": 23, "name": "PACA-Bioinfo", "logo_url": "https://www.igs.cnrs-mrs.fr/wp-content/uploads/2025/12/LOGO_PACA_VECTO_WhiteBG-nomargin.png", "description": "PACA Bioinfo's services focus on microbial genomics, metagenomics, comparative genomics, and molecular phylogenetics. It provides the community with various free online tools that can be accessed without prior registration, such as phylogeny.fr and ACDtools. The platform collaborates on genomics and metagenomics projects, providing the main bioinformatics support, particularly for teams at the \"Institut Méditerranéen de Microbiologie de Marseille\". With expertise in analyzing all types of genomes, it focuses in giant viruses.", "expertise": [ "http://edamontology.org/topic_3174", "http://edamontology.org/topic_0196", "http://edamontology.org/topic_3170", "http://edamontology.org/topic_0797", "http://edamontology.org/topic_0622", "http://edamontology.org/topic_0080", "http://edamontology.org/topic_0082", "http://edamontology.org/topic_0781" ], "expertise_description": "PACA Bioinfo's services focus on microbial genomics, metagenomics, comparative genomics, molecular phylogenetics and structural bioinformatics. With expertise in analyzing all types of genomes, it focuses in giant viruses.", "linkCovid19": "", "homepage": "https://www.igs.cnrs-mrs.fr/paca-bioinfo/", "unitId": "UMR7256", "address": "163 Avenue de Luminy\r\nCase 934", "city": "Marseille", "country": "France", "communities": [], "projects": [], "affiliatedWith": [ { "id": 52, "name": "CNRS", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/CNRS/?format=api" }, { "id": 38, "name": "IGS - Laboratoire Information Génomique et Structurale", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/IGS%20-%20Laboratoire%20Information%20G%C3%A9nomique%20et%20Structurale/?format=api" } ], "publications": [ "10.1093/bioinformatics/bty640", "10.1093/bioadv/vbab034", "10.1093/femsml/uqac003", "10.1128/JVI.01997-19", "10.3389/fmicb.2019.00430", "10.1186/s12864-018-4715-9", "10.1080/23802359.2017.1285210", "10.1128/JVI.00230-17", "10.1038/ncomms15087", "10.1038/ismej.2015.192", "10.1111/mec.13621", "10.1073/pnas.1506469112", "10.1371/journal.pone.0090988", "10.1371/journal.pone.0090989", "10.1186/1471-2164-14-158", "10.1111/mec.12108", "10.1038/ismej.2013.116", "10.1074/jbc.M111.314559", "10.1371/journal.pgen.1003122", "10.1186/gb-2012-13-5-r39", "10.1371/journal.pone.0018528", "10.1186/1743-422X-8-99", "10.1105/tpc.110.076406", "10.1186/gb-2009-10-10-r114", "10.1186/1743-422X-6-178", "10.1101/gr.091686.109", "10.1016/j.jip.2009.03.011", "10.1101/gr.091561.109", "10.1186/1471-2164-10-352", "", "10.1093/nar/gkn180" ], "certifications": [ "CATI - CTAI", "RIO", "label Plateforme Aix-Marseille" ], "fundedBy": [ { "id": 52, "name": "CNRS", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/CNRS/?format=api" } ], "keywords": [ "Virology", "NGS Data Analysis", "Metagenomics", "Evolution and Phylogeny", "metatranscriptomics", "Sequence analysis", "proteomics", "Comparative genomics", "Structural Bioinformatics" ], "fields": [ "Biomédical", "Environnement", "Biotechnologie" ], "orgid": "05v0fms67", "tools": [ "acdtool", "phylogeny.fr" ], "services": [], "leaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/557/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/372/?format=api" ], "deputies": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/557/?format=api" ], "scientificLeaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/372/?format=api" ], "technicalLeaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/557/?format=api" ], "members": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/741/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/557/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/129/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/372/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/502/?format=api" ], "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/557/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/372/?format=api" ], "ifbMembership": "Associated Team", "platforms": [], "is_active": true, "closing_date": null, "lat": "43.239127", "lng": "5.436787", "updated_at": "2025-12-12T08:59:53.115922Z" }, { "id": 32, "name": "MMG-GBIT", "logo_url": "https://www.ifb-elixir.fr/wp-content/uploads/2025/11/Equipe_IFB-Core_Generique-7.webp", "description": "Our team has been involved for years in different topics. The analysis of the many variations identified during the sequencing process of genes. In order to identify causative mutations, especially if they are missense mutations or null substitutions that only impact mRNA, we developed two tools: UMD-Predictor® to predict the pathogenicity of missense mutations, and the Human Splicing Finder® (HSF) to identify splicing signals and evaluate the impact of mutations on splicing.\r\n Locus Specific Databases (LSDBs). Since 1994, our team developed the Universal Mutation Database system (UMD®) an international reference system for the creation of Locus Specific Databases (LSDBs).\r\nPatient registries. We also developed through years, patient registries for neuromuscular rare diseases and others.", "expertise": [], "expertise_description": "The analysis of the many variations identified during the sequencing process of genes. In order to identify causative mutations, especially if they are missense mutations or null substitutions that only impact mRNA", "linkCovid19": "", "homepage": "https://geneticsandbioinformatics.eu/", "unitId": "", "address": "Faculté de Médecine de la Timone, \r\n27 Bd Jean Moulin", "city": "Marseille", "country": "France", "communities": [], "projects": [], "affiliatedWith": [ { "id": 56, "name": "INSERM", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/INSERM/?format=api" }, { "id": 47, "name": "MMG - Marseille Medical Genetics", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/MMG%20-%20Marseille%20Medical%20Genetics/?format=api" } ], "publications": [ "" ], "certifications": [], "fundedBy": [ { "id": 56, "name": "INSERM", "url": "https://catalogue.france-bioinformatique.fr/api/organisation/INSERM/?format=api" } ], "keywords": [ "NGS Data Analysis" ], "fields": [ "Biologie", "Biomédical", "Biotechnologie" ], "orgid": null, "tools": [ "varaft" ], "services": [], "leaders": [], "deputies": [], "scientificLeaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/48/?format=api" ], "technicalLeaders": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/49/?format=api" ], "members": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/48/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/49/?format=api", "https://catalogue.france-bioinformatique.fr/api/userprofile/180/?format=api" ], "maintainers": [ "https://catalogue.france-bioinformatique.fr/api/userprofile/48/?format=api" ], "ifbMembership": "Contributing platform", "platforms": [], "is_active": true, "closing_date": null, "lat": "43.288900", "lng": "5.402160", "updated_at": "2026-01-13T13:40:47.509859Z" }, { "id": 37, "name": "Systems Biomedicine", "logo_url": "https://www.marseille-medical-genetics.org/fileadmin/templates/mmg/imgs/mmg_logo.png", "description": "The advances in high-throughput technologies are providing unprecedented opportunities to better understand human diseases. Recent years have in this context witnessed the accumulation of omics approaches and datasets. Biomedicine is further transitioning from multiomics to multimodal datasets: data are not only available at the molecular omics level, as we now have access to signals and images, but also to various datasets related to disease phenotypes, health databases, or drug chemical similarities. The bottleneck now lies in the analysis and integration of these complex, large-scale and heterogeneous datasets. 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Dans le domaine des services la spécificité de la PF est la bioinformatique structurale (Modélisation moléculaire, prédiction de structure) introduite sur Lyon dès 1986 (il y a 25 ans avant même que le mot n'existe...). Dans ce domaine, l’activité proposée par le PRABI-Gerland s’appuie sur les expertises suivantes:\r\n Prédiction de structure de protéines [G. Deléage]\r\n Modélisation moléculaire [E. Bettler, G. Deléage, R. Terreux]\r\n Intégration de méthodes et serveurs Web [C. Combet, G Deléage]\r\n Serveur Web 3D [E. Bettler, G. Deléage]\r\n Drug design et QSAR (R. Terreux, J.A. Chemelle)\r\n \r\nMots clefs: Bioinformatique structurale, Prédiction de structure, Base de données structurales, Analyse de séquences, Modélisation moléculaire, docking moléculaire.\r\n \r\nPrincipaux sites web: https://prabi.ibcp.fr (site en cours de refonte)\r\n https://geno3d-prabi.ibcp.fr/\r\n https://npsa-prabi.ibcp.fr/\r\n http://sumo-pbil.ibcp.fr\r\n http://espript.ibcp.fr\r\n http://endscript.ibcp.fr\r\nMéthodes de prédiction des structures secondaires de protéines.\r\nPlusieurs méthodes originales ont été développées, Self Optimized Prediction Method (SOPM), génère automatiquement à partir de cette base de donnée, une \"sous-base\" rassemblant les 60 à 80 protéines les plus homologues ou appartenant à la même classe structurale que la protéine\r\nétudiée. En effet, des protéines homologues ont généralement une structure assez proche (30% d'identité indique une architecture semblable). Après une phase d'apprentissage automatique sur cette \"sous-base\", en particulier d'optimisation des paramètres, la prédiction de la structure de la protéine est réalisée. La version SOPMA tire bénéfice des alignements multiples. La méthode MLRC combine les réseaux de neurones avec la méthode SOPMA.\r\n [SOPMA] Self optimised Prediction Method (1995)\r\n [SOPM] Self optimised Prediction Method (1994)\r\n [DPM] Double prediction Method (1987)\r\n [MLRC] Multivariate Linear Regression Combination (1999)\r\n [AMPHIPASEEK] Prediction of membrane anchor helical peptides (2006)\r\n \r\nIntégration de methodes- WebicielsServeur NPS@\r\nLe PRABI Gerland a développé le premier serveur de mail Français pour la prédiction de structures secondaires de protéines (80 000 prédictions en tout). Ensuite ces méthodes ont été intégrées dans [NPS@ 2000]. Le serveur est actuellement dans sa version 3. Dans le cadre de RENABI-IFB, ce serveur généraliste de séquences couplé aux prédictions de structures sera mis à jour en termes d’ergonomie, d’interface et de conception. Mise à disposition d’outils et de services en ligne correspondant aux domaines d’expertise du laboratoire d’accueil de la PF.\r\n \r\nServeur Web ESPript/ENDscript\r\nA partir d’une protéine de structure connue (code ou fichier PDB), le serveur ENDscript produit, en quelques secondes et de manière automatisée, plusieurs illustrations téléchargeables dans des formats usuels (PostScript, PDF, PNG et TIFF) :\r\n1/ Une première figure, générée par le logiciel ESPript, présente la séquence de la protéine d’intérêt agrémentée de ses éléments de structure secondaire, de l’accessibilité au solvant et de l’hydropathie par résidu. Si disponibles, sont aussi représentés les contacts cristallographiques et non-cristallographiques protéine/protéine et/ou protéine/ligand ainsi que les résidus impliqués dans des ponts disulfures.\r\n2/ Une seconde figure ESPript montre, en plus des informations précédentes, un alignement multiple de séquences des protéines homologues coloré en fonction de la conservation des résidus et agrémenté des éléments de structure secondaire de ces dernières si leurs structures sont connues. \r\n3/ Deux représentations 3D interactives visualisables par le logiciel PyMOL : a) une représentation en ruban, colorée en fonction de la conservation de séquence. b) une représentation en tube dont le diamètre est proportionnel à la déviation structurale (rmsd) entre la protéine d’intérêt et les protéines homologues de structure connue. De plus, si disponible, peuvent être affichés : l’assemblage de l’unité biologique, les modèles RMN multiples, les ligands et les résidus en contact avec ces derniers.\r\nLe serveur ESPript permet, en complément d’ENDscript ou de manière autonome, de représenter des alignements multiples de séquences avec la possibilité d’ajouter des marqueurs définis par l’utilisateur de manière à produire des figures facilitant l’analyse ou dédiées aux communications scientifiques.\r\n \r\nModélisation moléculaire\r\nUn serveur Web de modélisation moléculaire automatique de structure 3D de protéines appelé geno3D est disponible depsuis 2002 qui permet aux biologistes et biochimistes d'obtenir un modèle 3D de qualité si la séquence \"query\" présente plus de 35% d'identité avec une protéine de structure 3D connue. Le principe de cette modélisation consiste à appliquer les techniques de modélisation sous contraintes à la protéine à modéliser (de type RMN) à partir d'un jeu de contraintes calculées sur l'empreinte structurale. Plusieurs empreintes sont utilisables, le ligand (si présent) est replacé dans les modèles, 10 modèles sont générés. Les résultats sont proposés sous la forme d’une archive récupérable et les résultats sont conservés 8 jours sur le serveur. Ce serveur génère 100 modèles/mois. Un système intégré de modélisation moléculaire (MAGOS ) à grande échelle de protéomes entiers a été utilisé pour des protéomes de virus (modeome3D) et de plantes (arabidome3D).\r\n \r\nDocking et sites 3D- chemo-informatique\r\nUne méthode bioinformatique SUMO a été développée permettant de détecter des sites 3D fonctionnels communs à plusieurs protéines. 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