Mélisande BLEIN-NICOLAS

Mélisande BLEIN-NICOLAS

     
  • Proteomics, mass spectrometry, systems biology, omics data integration, plant genetics

 INRAE, Research Engineer

 melisande.blein-nicolas@inrae.fr —   +33 (0)1 69 15 68 06 —  1219


 Plateforme d'Analyse Protéomique de Paris Sud-Ouest
 Biology and Adaptation, Systems in Evolution

 Publications      

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

Position and education

  • 2015-present: INRAE research engineer, UMR GQE-Le Moulon, Gif-sur-Yvette, France
  • 2010-2015: Post-doctoral fellow, INRAE, UMR GQE-Le Moulon, Gif-sur-Yvette, France
    • Analysis of heterosis for protein abundance under normal and drought conditions in sunflower
    • Genome wide association study for protein expression under normal and water deficit conditions in maize leaves
    • Analysis of heterosis for protein abundance in inter- and intra-specific yeast hybrids grown under grape must fermentation
  • 2008-2010: Postdoctoral fellow, CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite, Montpellier, France
    • Role of the CIGR1 gene in the resistance of rice to blast
  • 2004-2007: PhD student (MENRT fellowship), IGEPP (formely UMR Amélioration des Plantes et Biotechnologies Végétales), Rennes, France
    • Role of the Pch1 gene in the resistance of wheat to eyespot
  • 2004: Master of Science and Engineer degrees in Plants Genetics and Breeding, Agrocampus Ouest (formerly École Nationale Supérieure Agronomique de Rennes).

Responsabilities

  • 2022-present: Scientist-in-charge of the PAPPSO core facility
  • 2017-2023: member of the executive board of the French Proteomics Society (FPS)

Activities of research and development

I am interested in understanding how living organisms respond and adapt to environmental changes. My research focuses on identifying genes and molecular mechanisms responsible for variations in adaptive traits, such as plant resistance to pathogenic fungi, the ability of yeasts to complete grape juice fermentation, and drought tolerance in plants. During my PhD and first postdoctoral fellowship, I addressed these issues using functional genomics approaches. Since joining UMR GQE-Le Moulon, I have transitioned to systems approaches that integrate multi-omics data to elucidate the genotype-phenotype relationship. My current research is centered on the genetic control and plasticity of molecular networks involved in drought response in maize. As the scientist-in-charge of the PAPPSO facility, I am also developing high-throughput plant proteomics approaches to enhance the application of proteomics in research programs related to plant breeding and agroecology, which require the analysis of large cohorts of samples.

Teaching and training

  • Introduction to mass-spectrometry based proteomics (Licence 1 and Master 1 and 2 at Université Paris Saclay)
  • Proteomics Research School: “From Sample Preparation to Results Interpretation—Strategies and Practical Aspects” organized in the framework of the MassProt’INRAE network

Publications

  • Blein-Nicolas M. , Devijver E., Gallopin M., Perthame E.. (2024) Nonlinear network-based quantitative trait prediction from biological data. Journal of the Royal Statistical Society Series C: Applied Statistics, qlae012
  • 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,
  • Tarkowski Łukasz P., Clochard T., Blein-Nicolas M. , Zivy M., Baillau T., Abadie C., Morère-Le Paven MC., Limami AM., Tcherkez G., Montrichard F.. (2024) The nitrate transporter-sensor MtNPF6.8 regulates the branched chain amino acid/pantothenate metabolic pathway in barrel medic (Medicago truncatula Gaertn.) root tip. Plant Physiology and Biochemistry, (206) 108213
  • Chasseriaud L., Albertin W., Blein-Nicolas M. , Balliau T., Zivy M., Coulon J., Bely M.. (2023) Physical Contact between Torulaspora delbrueckii and Saccharomyces cerevisiae Alters Cell Growth and Molecular Interactions in Grape Must. Beverages, 3 (9) 81
  • Djabali Y., Rincent R., Martin ML., Blein-Nicolas M. . (2023) Plasticity QTLs specifically contribute to the genotype × water availability interaction in maize. Theor Appl Genet, 11 (136) 228
  • Djabali Yacine ., 2023-12-13, Exploitation des données multi-omiques pour élucider les bases génétiques et moléculaires de caractères complexes : une étude de génétique des systèmes de la réponse du maïs à la sécheresse, , Université Paris Saclay
  • Duruflé H., Balliau T., Blanchet N., Chaubet A., Duhnen A., Pouilly N., Blein-Nicolas M. , Mangin B., Maury P., Langlade NB., Zivy M.. (2023) Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules, 7 (13) 1110
  • Jamet E., Esquerré-Tugayé MT., Gallardo-Guerrero K., Rolland N., Zivy M., Blein-Nicolas M. , Vincent D., Gontero B., Rajjou L.. (2023) Obituary: Dominique Job (1947-2022). Front. Plant Sci., (14) 1188766
  • 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
  • Baudouin E., Puyaubert J., Meimoun P., Blein-Nicolas M. , Davanture M., Zivy M., Bailly C.. (2022) Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination. International Journal of Molecular Sciences, 13 (23) 7059
  • Millán-Oropeza A., Blein-Nicolas M. , Monnet V., Zivy M., Henry C.. (2022) Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes, 1 (10) 2
  • 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.,
  • 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
  • Urrutia M., Blein-Nicolas M. , Prigent S., Bernillon S., Deborde C., Balliau T., Maucourt M., Jacob D., Ballias P., Bénard C., Sellier H., Gibon Y., Giauffret C., Zivy M., Moing A.. (2021) Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis. Plant Cell Environ,
  • Belouah I., Bénard C., Denton A., Blein-Nicolas M. , Balliau T., Teyssier E., Gallusci P., Bouchez O., Usadel B., Zivy M., Gibon Y., Colombié S.. (2020) Transcriptomic and proteomic data in developing tomato fruit. Data in Brief, (28) 105015
  • Blein-Nicolas M. , Negro SS., Balliau T., Welcker C., Cabrera-Bosquet L., Nicolas SD., Charcosset A., Zivy M.. (2020) A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Res., 11 (30) 1593-1604
  • Belouah I., Nazaret C., Pétriacq P., Prigent S., Bénard C., Mengin V., Blein-Nicolas M. , Denton AK., Balliau T., Augé S., Bouchez O., Mazat JP., Stitt M., Usadel B., Zivy M., Beauvoit B., Gibon Y., Colombié S.. (2019) Modeling Protein Destiny in Developing Fruit. Plant Physiology, 3 (180) 1709-1724
  • Belouah I., Blein-Nicolas M. , Balliau T., Gibon Y., Zivy M., Colombié S.. (2019) Peptide filtering differently affects the performances of XIC-based quantification methods. J Proteomics, (193) 131-141
  • Henry C., Haller L., Blein-Nicolas M. , Zivy M., Canette A., Verbrugghe M., Mézange C., Boulay M., Gardan R., Samson S., Martin V., André-Leroux G., Monnet V.. (2019) Identification of Hanks-Type Kinase PknB-Specific Targets in the Streptococcus thermophilus Phosphoproteome. Front. Microbiol., (10) 1329
  • Balliau T., Blein-Nicolas M. , Zivy M.. (2018) Evaluation of Optimized Tube-Gel Methods of Sample Preparation for Large-Scale Plant Proteomics. Proteomes, 1 (6) 6
  • 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
  • Millan-Oropeza A., Henry C., Blein-Nicolas M. , Aubert-Frambourg A., Moussa F., Bleton J., Virolle MJ.. (2017) Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. J. Proteome Res., 7 (16) 2597-2613
  • Blein-Nicolas M. , Zivy M.. (2016) Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 8 (1864) 883-895
  • Blein-Nicolas M. , Albertin W., da Silva T., Valot B., Balliau T., Masneuf-Pomarède I., Bely M., Marullo P., Sicard D., Dillmann C., de Vienne D., Zivy M.. (2015) A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast. Mol. Cell Proteomics, 8 (14) 2056-2071
  • Blein-Nicolas M. , Albertin W., Valot B., Marullo P., Sicard D., Giraud C., Huet S., Bourgais A., Dillmann C., de Vienne D., Zivy M.. (2013) Yeast proteome variations reveal different adaptive responses to grape must fermentation. Molecular biology and evolution, 6 (30) 1368-83
  • Blein-Nicolas M. , Xu H., de Vienne D., Giraud C., Huet S., Zivy M.. (2012) Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics. Proteomics, 18 (12) 2797-801
  • Delteil A., Blein M., Faivre-Rampant O., Guellim A., Estevan J., Hirsch J., Bevitori R., Michel C., Morel JB.. (2012) Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence: A mutant resource for disease resistance analysis in rice. Molecular Plant Pathology, 1 (13) 72-82
  • Lorieux M., Blein M., Lozano J., Bouniol M., Droc G., Diévart A., Périn C., Mieulet D., Lanau N., Bès M., Rouvière C., Gay C., Piffanelli P., Larmande P., Michel C., Barnola I., Biderre-Petit C., Sallaud C., Perez P., Bourgis F., Ghesquière A., Gantet P., Tohme J., Morel JB., Guiderdoni E.. (2012) In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches: Characterization of a rice insertion library. Plant Biotechnology Journal, 5 (10) 555-568
  • Blein M., Levrel A., Lemoine J., Gautier V., Chevalier M., Barloy D.. (2009) Oculimacula yallundae lifestyle revisited: relationships between the timing of eyespot symptom appearance, the development of the pathogen and the responses of infected partially resistant wheat plants. Plant Pathology, 1 (58) 1-11
  • Cifuentes M., Blein M., Benavente E.. (2006) A cytomolecular approach to assess the potential of gene transfer from a crop (Triticum turgidum L.) to a wild relative (Aegilops geniculata Roth.). Theor Appl Genet, 4 (112) 657-664