Olivier LANGELLA

Olivier LANGELLA

 dernières mises à jour 19/07/2024 -   01 69 33 23 68 -  1214
 olivier.langella@universite-paris-saclay.fr
 https://fosstodon.org/@olangella
 Plateforme d'Analyse Protéomique de Paris Sud-Ouest
 CNRS, Ingénieur de Recherche
 publications - orcid  - HAL

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   (1), for peptide identification, protein inference and quantification
  • MassChroQ   (2), mass spectrometry based quantification software
  • PROTICdb   (3), 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 ( ), in which I lead the group (system).

Bibliographie

  1. 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. Journal of Proteome Research,
  2. Valot B., Langella O. , Nano E., Zivy M.. (2011) MassChroQ: a versatile tool for mass spectrometry quantification. Proteomics, 17 (11) 3572-7
  3. 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

  • 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. Journal of Proteome Research,
  • 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
  • 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
  • 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
  • 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