Olivier LANGELLA

Olivier LANGELLA

 CNRS, Engineer

 olivier.langella@universite-paris-saclay.fr —   +33 (0)1 69 33 23 68 —  1214
 https://fosstodon.org/@olangella


 Plateforme d'Analyse Protéomique de Paris Sud-Ouest
 Bioinformatics and Informatics
 Bioinformatics, Open Science & Systems

 Publications       x

  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • IDEEV
  • 12 route 128
  • 91190 Gif-sur-Yvette

Position and Education

  • CNRS research engineer, GQE-Le Moulon (Gif-sur-Yvette, France), 2004-present
  • CNRS engineer, EGCE (Gif-sur-Yvette, France), 1996-2003
  • Bioinformatics post graduate degree (Université Pierre et Marie Curie, Paris VI), 1995

Research interests

I am interested in computational challenges raised by highthroughtput proteomics studies (data storage and intensive calculation). In charge of the bioinformatics developments of the PAPPSO team, I thus lead several projects :

  • i2MassChroQ (), for peptide identification, protein inference and quantification
  • MassChroQ (1), mass spectrometry based quantification software
  • PROTICdb (2), proteomic database to store, publish and query proteomics data

We have developped a complete solution using free softwares and common hardware to store 50Tbytes per year and offering high speed connection to an HPC cluster (based on ceph and Slurm).

I am also involved in the GQE Bioinformatics facility (ABI), in which I lead the ABI-SYS group (system).

Bibliography

  1. Valot B, Langella O, Nano E, Zivy M. (2011) MassChroQ: a versatile tool for mass spectrometry quantification. Proteomics, 17 (11) 3572-7
  2. Langella O, Valot B, Jacob D, Balliau T, Flores R, Hoogland C, Joets J, Zivy M. (2013) Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction. Proteomics, 9 (13) 1457-66

Publications

  • Balliau T., Frambourg A., Langella O. , Martin ML., Zivy M., Blein-Nicolas M.. (2025) MCQR : Enhancing the Processing and Analysis of Quantitative Proteomics Data by Incorporating Chromatography and Mass Spectrometry Information. J. Proteome Res., acs.jproteome.4c01119
  • Langella O. , Renne T., Balliau T., Davanture M., Brehmer S., Zivy M., Blein-Nicolas M., Rusconi F.. (2024) Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package. J. Proteome Res., 8 (23) 3353-3366
  • Voedts H., Anoyatis-Pelé C., Langella O. , Rusconi F., Hugonnet JE., Arthur M.. (2024) (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nat Microbiol, 3 (9) 647-656
  • Prunier G., Cherkaoui M., Lysiak A., Langella O. , Blein-Nicolas M., Lollier V., Benoist E., Jean G., Fertin G., Rogniaux H., Tessier D.. (2023) Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides. BMC Bioinformatics, 1 (24) 421
  • Henry C., Bassignani A., Berland M., Langella O. , Sokol H., Juste C.. (2022) Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerative Colitis Flare-Ups. Cells, 8 (11) 1340
  • Plancade S., Berland M., Blein-Nicolas M., Langella O. , Bassignani A., Juste C.. (2022) A combined test for feature selection on sparse metaproteomics data—an alternative to missing value imputation. PeerJ, (10) e13525
  • Bassignani A., Plancade S., Berland M., Blein-Nicolas M., Guillot A., Chevret D., Moritz C., Huet S., Rizkalla S., Clément K., Doré J., Langella O. , Juste C.. (2021) Benefits of Iterative Searches of Large Databases to Interpret Large Human Gut Metaproteomic Data Sets. J. Proteome Res.,
  • Langella O. , Rusconi F.. (2021) mineXpert2 : Full-Depth Visualization and Exploration of MS n Mass Spectrometry Data. J. Am. Soc. Mass Spectrom., 4 (32) 1138-1141
  • Plancade S., Berland M., Blein-Nicolas M., Langella O. , Bassignani A., Juste C.. (2021) A combined test for feature selection on sparse metaproteomics data - alternative to missing value imputation. bioRxiv, 2021.06.22.449387
  • Van Den Bossche T., Kunath BJ., Schallert K., Schäpe SS., Abraham PE., Armengaud J., Arntzen M., Bassignani A., Benndorf D., Fuchs S., Giannone RJ., Griffin TJ., Hagen LH., Halder R., Henry C., Hettich RL., Heyer R., Jagtap P., Jehmlich N., Jensen M., Juste C., Kleiner M., Langella O. , Lehmann T., Leith E., May P., Mesuere B., Miotello G., Peters SL., Pible O., Queiros PT., Reichl U., Renard BY., Schiebenhoefer H., Sczyrba A., Tanca A., Trappe K., Trezzi JP., Uzzau S., Verschaffelt P., Von Bergen M., Wilmes P., Wolf M., Martens L., Muth T.. (2021) Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun, 1 (12) 7305
  • Adenot P., Bansard S., Benaben D., Brunaud V., Caron C., Dehne Garcia A., Duperier C., Falce A., Filangi O., Giacomoni F., Granier F., Grevet P., Guilhot N., Hofstetter A., Joets J., Hotelier T., Langella O. , Legrand L., LOAEC M., Lollier V., Moreau P., Morin E., Quesneville H., Rabemanantsoa T., Salin G., Tessier D.. (2018) AgroDataRing: Une infrastructure partagée et mutualisée pour le stockage longue durée. Cahier des Techniques de l'INRA, 1-7
  • Langella O. , Valot B., Balliau T., Blein-Nicolas M., Bonhomme L., Zivy M.. (2017) X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. J. Proteome Res., 2 (16) 494-503
  • Dobrenel T., Mancera-Martínez E., Forzani C., Azzopardi M., Davanture M., Moreau M., Schepetilnikov M., Chicher J., Langella O. , Zivy M., Robaglia C., Ryabova LA., Hanson J., Meyer C.. (2016) The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6. Front Plant Sci, (7)
  • Sabarly V., Aubron C., Glodt J., Balliau T., Langella O. , Chevret D., Rigal O., Bourgais A., Picard B., de Vienne D., Denamur E., Bouvet O., Dillmann C.. (2016) Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates. Environmental microbiology, 1 (18) 100-17
  • Chaze T., Guillot A., Valot B., Langella O. , Chamot-Rooke J., Di Guilmi AM., Trieu-Cuot P., Dramsi S., Mistou MY.. (2014) O-Glycosylation of the N-terminal region of the serine-rich adhesin Srr1 of Streptococcus agalactiae explored by mass spectrometry. Molecular & cellular proteomics : MCP, 9 (13) 2168-82
  • Albertin W., Marullo P., Bely M., Aigle M., Bourgais A., Langella O. , Balliau T., Chevret D., Valot B., da Silva T., Dillmann C., de Vienne D., Sicard D.. (2013) Linking post-translational modifications and variation of phenotypic traits. Molecular & cellular proteomics : MCP, 3 (12) 720-35
  • Langella O. , Valot B., Jacob D., Balliau T., Flores R., Hoogland C., Joets J., Zivy M.. (2013) Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction. Proteomics, 9 (13) 1457-66
  • Valot B., Langella O. , Nano E., Zivy M.. (2011) MassChroQ: a versatile tool for mass spectrometry quantification. Proteomics, 17 (11) 3572-7
  • Albertin W., Langella O. , Joets J., Negroni L., Zivy M., Damerval C., Thiellement H.. (2009) Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus. Proteomics, 3 (9) 793-9
  • Langella O. , Zivy M.. (2008) A method based on bead flows for spot detection on 2-D gel images. Proteomics, 23-24 (8) 4914-8