IFB Core

Formation professionnelle

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Training time:
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IBI - 2

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Access conditions
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Internal publications
External publications
Guillaume Postic and Julien Marcoux and Victor Reys and Jessica Andreani and Yves Vandenbrouck and Marie-Pierre Bousquet and Emmanuelle Mouton-Barbosa and Sarah Cianférani and Odile Burlet-Schiltz and Raphael Guerois and Gilles Labesse and Pierre Tufféry; Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration, Journal of Proteome Research 2020; 19(7) doi: 10.1021/acs.jproteome.0c00066.
Yves Vandenbrouck and Charles Pineau and Lydie Lane; The Functionally Unannotated Proteome of Human Male Tissues: A Shared Resource to Uncover New Protein Functions Associated with Reproductive Biology, Journal of Proteome Research 2020; 19(12) doi: 10.1021/acs.jproteome.0c00516.
Citlalli Mejía-Almonte and Stephen J. W. Busby and Joseph T. Wade and Jacques van Helden and Adam P. Arkin and Gary D. Stormo and Karen Eilbeck and Bernhard O. Palsson and James E. Galagan and Julio Collado-Vides; Redefining fundamental concepts of transcription initiation in bacteria, Nature Reviews Genetics 2020; 21(11) doi: 10.1038/s41576-020-0254-8.
Marek Ostaszewski and Alexander Mazein and Marc E. Gillespie and Inna Kuperstein and Anna Niarakis and Henning Hermjakob and Alexander R. Pico and Egon L. Willighagen and Chris T. Evelo and Jan Hasenauer and Falk Schreiber and Andreas Dräger and Emek Demir and Olaf Wolkenhauer and Laura I. Furlong and Emmanuel Barillot and Joaquin Dopazo and Aurelio Orta-Resendiz and Francesco Messina and Alfonso Valencia and Akira Funahashi and Hiroaki Kitano and Charles Auffray and Rudi Balling and Reinhard Schneider; COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms, Scientific Data 2020; 7(1) doi: 10.1038/s41597-020-0477-8.
Franck Touret and Magali Gilles and Karine Barral and Antoine Nougairède and Jacques van Helden and Etienne Decroly and Xavier de Lamballerie and Bruno Coutard; In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication, Scientific Reports 2020; 10(1) doi: 10.1038/s41598-020-70143-6.
Matthieu Lagardère and Ingrid Chamma and Emmanuel Bouilhol and Macha Nikolski and Olivier Thoumine; FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins, Scientific Reports 2020; 10(1) doi: 10.1038/s41598-020-75814-y.
Erwan Sallard and José Halloy and Didier Casane and Jacques van Helden and Étienne Decroly; Retrouver les origines du SARS-CoV-2 dans les phylogénies de coronavirus, médecine/sciences 2020; 36(8-9) doi: 10.1051/medsci/2020123.
Franziska Hufsky and Kevin Lamkiewicz and Alexandre Almeida and Abdel Aouacheria and Cecilia Arighi and Alex Bateman and Jan Baumbach and Niko Beerenwinkel and Christian Brandt and Marco Cacciabue and Sara Chuguransky and Oliver Drechsel and Robert D Finn and Adrian Fritz and Stephan Fuchs and Georges Hattab and Anne-Christin Hauschild and Dominik Heider and Marie Hoffmann and Martin Hölzer and Stefan Hoops and Lars Kaderali and Ioanna Kalvari and Max von Kleist and Renó Kmiecinski and Denise Kühnert and Gorka Lasso and Pieter Libin and Markus List and Hannah F Löchel and Maria J Martin and Roman Martin and Julian Matschinske and Alice C McHardy and Pedro Mendes and Jaina Mistry and Vincent Navratil and Eric P Nawrocki and Áine Niamh O'Toole and Nancy Ontiveros-Palacios and Anton I Petrov and Guillermo Rangel-Pineros and Nicole Redaschi and Susanne Reimering and Knut Reinert and Alejandro Reyes and Lorna Richardson and David L Robertson and Sepideh Sadegh and Joshua B Singer and Kristof Theys and Chris Upton and Marius Welzel and Lowri Williams and Manja Marz; Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research, Briefings in Bioinformatics 2020; doi: 10.1093/bib/bbaa232.
Benjamin Linard and Nikolai Romashchenko and Fabio Pardi and Eric Rivals; PEWO: a collection of workflows to benchmark phylogenetic placement, Bioinformatics 2020; 36(21) doi: 10.1093/bioinformatics/btaa657.
Adelme Bazin and Guillaume Gautreau and Claudine Médigue and David Vallenet and Alexandra Calteau; panRGP: a pangenome-based method to predict genomic islands and explore their diversity, Bioinformatics 2020; 36(Supplement_2) doi: 10.1093/bioinformatics/btaa792.
Mehmet Tekman and Bérénice Batut and Alexander Ostrovsky and Christophe Antoniewski and Dave Clements and Fidel Ramirez and Graham J Etherington and Hans-Rudolf Hotz and Jelle Scholtalbers and Jonathan R Manning and Lea Bellenger and Maria A Doyle and Mohammad Heydarian and Ni Huang and Nicola Soranzo and Pablo Moreno and Stefan Mautner and Irene Papatheodorou and Anton Nekrutenko and James Taylor and Daniel Blankenberg and Rolf Backofen and Björn Grüning; A single-cell RNA-sequencing training and analysis suite using the Galaxy framework, GigaScience 2020; 9(10) doi: 10.1093/gigascience/giaa102.
Guignon Valentin and Toure Abdel and Droc Gaëtan and Dufayard Jean-François and Conte Matthieu and Rouard Mathieu; GreenPhylDB v5: a comparative pangenomic database for plant genomes, Nucleic Acids Research 2020; 49(D1) doi: 10.1093/nar/gkaa1068.
Fotis E. Psomopoulos and Jacques van Helden and Claudine Médigue and Anastasia Chasapi and Christos A. Ouzounis; Ancestral state reconstruction of metabolic pathways across pangenome ensembles, Microbial Genomics 2020; 6(11) doi: 10.1099/mgen.0.000429.
Vincent Navratil and Loïc Lionnard and Sonia Longhi and J. Marie Hardwick and Christophe Combet and Abdel Aouacheria; The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like sequence, Cold Spring Harbor Laboratory 2020; doi: 10.1101/2020.04.09.033522.
Jingwen Bai and Chakradhar Bandla and Jiaxin Guo and Roberto Vera Alvarez and Juan Antonio Vizcaíno and Mingze Bai and Pablo Moreno and Björn A. Grüning and Olivier Sallou and Yasset Perez-Riverol; BioContainers Registry: searching for bioinformatics tools, packages and containers, Cold Spring Harbor Laboratory 2020; doi: 10.1101/2020.07.21.187609.
Evangelia A. Papoutsoglou and Daniel Faria and Daniel Arend and Elizabeth Arnaud and Ioannis N. Athanasiadis and Inês Chaves and Frederik Coppens and Guillaume Cornut and Bruno V. Costa and Hanna Ćwiek-Kupczyńska and Bert Droesbeke and Richard Finkers and Kristina Gruden and Astrid Junker and Graham J. King and Paweł Krajewski and Matthias Lange and Marie-Angélique Laporte and Célia Michotey and Markus Oppermann and Richard Ostler and Hendrik Poorter and Ricardo Ramıŕez-Gonzalez and Živa Ramšak and Jochen C. Reif and Philippe Rocca-Serra and Susanna-Assunta Sansone and Uwe Scholz and François Tardieu and Cristobal Uauy and Björn Usadel and Richard G. F. Visser and Stephan Weise and Paul J. Kersey and Célia M. Miguel and Anne-Françoise Adam-Blondon and Cyril Pommier; Enabling reusability of plant phenomic datasets with MIAPPE 1.1, New Phytologist 2020; 227(1) doi: 10.1111/nph.16544.
Fabienne Soulet and Clement Bodineau and Katarzyna B. Hooks and Jean Descarpentrie and Isabel Alves and Marielle Dubreuil and Amandine Mouchard and Malaurie Eugenie and Jean-Luc Hoepffner and Jose J. López and Juan A. Rosado and Isabelle Soubeyran and Mercedes Tomé and Raúl V. Durán and Macha Nikolski and Bruno O. Villoutreix and Serge Evrard and Geraldine Siegfried and Abdel-Majid Khatib; ELA/APELA precursor cleaved by furin displays tumor suppressor function in renal cell carcinoma through mTORC1 activation, JCI Insight 2020; 5(14) doi: 10.1172/jci.insight.129070.
Philippe Cubry and Hélène Pidon and Kim Nhung Ta and Christine Tranchant-Dubreuil and Anne-Céline Thuillet and Maria Holzinger and Hélène Adam and Honoré Kam and Harold Chrestin and Alain Ghesquière and Olivier François and François Sabot and Yves Vigouroux and Laurence Albar and Stefan Jouannic; Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima, Rice 2020; 13(1) doi: 10.1186/s12284-020-00424-1.
Christian Jean Michel and Claudine Mayer and Olivier Poch and Julie Dawn Thompson; Characterization of accessory genes in coronavirus genomes, Virology Journal 2020; 17(1) doi: 10.1186/s12985-020-01402-1.
Hélène Badouin and Amandine Velt and François Gindraud and Timothée Flutre and Vincent Dumas and Sonia Vautrin and William Marande and Jonathan Corbi and Erika Sallet and Jérémy Ganofsky and Sylvain Santoni and Dominique Guyot and Eugenia Ricciardelli and Kristen Jepsen and Jos Käfer and Hélène Berges and Eric Duchêne and Franck Picard and Philippe Hugueney and Raquel Tavares and Roberto Bacilieri and Camille Rustenholz and Gabriel A. B. Marais; The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication, Genome Biology 2020; 21(1) doi: 10.1186/s13059-020-02131-y.
Hadi Quesneville; Twenty years of transposable element analysis in the Arabidopsis thaliana genome, Mobile DNA 2020; 11(1) doi: 10.1186/s13100-020-00223-x.
Frédéric Jarlier and Nicolas Joly and Nicolas Fedy and Thomas Magalhaes and Leonor Sirotti and Paul Paganiban and Firmin Martin and Michael McManus and Philippe Hupé; QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing, F1000Research 2020; 9 doi: 10.12688/f1000research.22954.3.
Taner Z. Sen and Mario Caccamo and David Edwards and Hadi Quesneville; Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS), F1000Research 2020; 9 doi: 10.12688/f1000research.23525.1.
Choumouss Kamoun and Julien Roméjon and Henri de Soyres and Apolline Gallois and Elodie Girard and Philippe Hupé; biogitflow: development workflow protocols for bioinformatics pipelines with git and GitLab, F1000Research 2021; 9 doi: 10.12688/f1000research.24714.3.
David Salgado and Irina M. Armean and Michael Baudis and Sergi Beltran and Salvador Capella-Gutierrez and Denise Carvalho-Silva and Victoria Dominguez Del Angel and Joaquin Dopazo and Laura I. Furlong and Bo Gao and Leyla Garcia and Dietlind Gerloff and Ivo Gut and Attila Gyenesei and Nina Habermann and John M. Hancock and Marc Hanauer and Eivind Hovig and Lennart F. Johansson and Thomas Keane and Jan Korbel and Katharina B. Lauer and Steve Laurie and Brane Leskošek and David Lloyd and Tomas Marques-Bonet and Hailiang Mei and Katalin Monostory and Janet Piñero and Krzysztof Poterlowicz and Ana Rath and Pubudu Samarakoon and Ferran Sanz and Gary Saunders and Daoud Sie and Morris A. Swertz and Kirill Tsukanov and Alfonso Valencia and Marko Vidak and Cristina Yenyxe González and Bauke Ylstra and Christophe Béroud; The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research, F1000Research 2020; 9 doi: 10.12688/f1000research.24887.1.
Guillaume Gautreau and Adelme Bazin and Mathieu Gachet and Rémi Planel and Laura Burlot and Mathieu Dubois and Amandine Perrin and Claudine Médigue and Alexandra Calteau and Stéphane Cruveiller and Catherine Matias and Christophe Ambroise and Eduardo P. C. Rocha and David Vallenet; PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph, PLOS Computational Biology 2020; 16(3) doi: 10.1371/journal.pcbi.1007732.
Leyla Garcia and Bérénice Batut and Melissa L. Burke and Mateusz Kuzak and Fotis Psomopoulos and Ricardo Arcila and Teresa K. Attwood and Niall Beard and Denise Carvalho-Silva and Alexandros C. Dimopoulos and Victoria Dominguez del Angel and Michel Dumontier and Kim T. Gurwitz and Roland Krause and Peter McQuilton and Loredana Le Pera and Sarah L. Morgan and Päivi Rauste and Allegra Via and Pascal Kahlem and Gabriella Rustici and Celia W. G. van Gelder and Patricia M. Palagi; Ten simple rules for making training materials FAIR, PLOS Computational Biology 2020; 16(5) doi: 10.1371/journal.pcbi.1007854.
Kim T. Gurwitz and Prakash Singh Gaur and Louisa J. Bellis and Lee Larcombe and Eva Alloza and Balint Laszlo Balint and Alexander Botzki and Jure Dimec and Victoria Dominguez del Angel and Pedro L. Fernandes and Eija Korpelainen and Roland Krause and Mateusz Kuzak and Loredana Le Pera and Brane Leskošek and Jessica M. Lindvall and Diana Marek and Paula A. Martinez and Tuur Muyldermans and Ståle Nygård and Patricia M. Palagi and Hedi Peterson and Fotis Psomopoulos and Vojtech Spiwok and Celia W. G. van Gelder and Allegra Via and Marko Vidak and Daniel Wibberg and Sarah L. Morgan and Gabriella Rustici; A framework to assess the quality and impact of bioinformatics training across ELIXIR, PLOS Computational Biology 2020; 16(7) doi: 10.1371/journal.pcbi.1007976.
Alban Gaignard and Hala Skaf-Molli and Khalid Belhajjame; Findable and reusable workflow data products: A genomic workflow case study, Semantic Web 2020; doi: 10.3233/sw-200374.
Romain De Oliveira and Hélène Rimbert and François Balfourier and Jonathan Kitt and Emeric Dynomant and Jan Vrána and Jaroslav Doležel and Federica Cattonaro and Etienne Paux and Frédéric Choulet; Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats, Frontiers in Genetics 2020; 11 doi: 10.3389/fgene.2020.00891.
Hermenegildo Taboada-Castro and Jaime Abraham Castro-Mondragón and Alejandro Aguilar-Vera and Alfredo José Hernández-Álvarez and Jacques van Helden and Sergio Encarnación-Guevara; RhizoBindingSites, a Database of DNA-Binding Motifs in Nitrogen-Fixing Bacteria Inferred Using a Footprint Discovery Approach, Frontiers in Microbiology 2020; 11 doi: 10.3389/fmicb.2020.567471.
Mourdas Mohamed and Nguyet Thi-Minh Dang and Yuki Ogyama and Nelly Burlet and Bruno Mugat and Matthieu Boulesteix and Vincent Mérel and Philippe Veber and Judit Salces-Ortiz and Dany Severac and Alain Pélisson and Cristina Vieira and François Sabot and Marie Fablet and Séverine Chambeyron; A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore, Cells 2020; 9(8) doi: 10.3390/cells9081776.
Publications with the hosting laboratory
Users distribution
25 %
25 %
25 %
Explanation about this distribution:

Descripion test

Platform's own projects

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National projets
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International and European projects
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Projets with industry
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Collaboration projects not founded through an external organism
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Provision of services not founded through an external organism
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Animations (Workshops, Work-groups, seminars, conferences ... )
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