Mathilde Carpentier

Présentation

After a PhD in bioinformatics on protein structural comparison and classification (2001-2005) at Université Pierre and Marie Curie (UPMC, Paris), I have developed skills in viral metagenomics during my post-doctoral fellowship (ATER, 2005-2006) at Université Denis Diderot (Paris). Since I have been recruted at UPMC (2006), and I have divided my time between teaching algorithmic, programming languages and bioinformatics to students in computer science and students in biology, while performing research in various fields of bioinformatics. I have spent 6 months in 2007 in Stanford (California, USA) as invited researcher at Michael Levitt Lab, working on protein structural classification in order to build a database for fold recognition. I have been the principal investigator of a grant for preliminary studies (PEPS BMI 2013 and 2014) for oceanic metaviromics annotation and analyses presented in a conference and resulted in a publication. I have published several major articles on protein structure analyses as well.

Publications

Article dans une revue (12)

On the Variation of Structural Divergence Among Residues in Enzyme Evolution Julian Echave,Mathilde Carpentier Proteins - Structure, Function and Bioinformatics, 2025, ⟨10.1002/prot.70103⟩ Article dans une revue mnhn-05418947v1
Origins and Functional Significance of Eukaryotic Protein Folds Martin Romei,Mathilde Carpentier,Jacques Chomilier,Guillaume Lecointre Journal of Molecular Evolution, 2023, 91 (6), pp.854-864. ⟨10.1007/s00239-023-10136-x⟩ Article dans une revue hal-04379543v1
Protein folds as synapomorphies of the tree of life Martin Romei,Guillaume Sapriel,Pierre Imbert,Théo Jamay,Jacques Chomilieret al. Evolution - International Journal of Organic Evolution, 2022, 76 (8), pp.1706-1719. ⟨10.1111/evo.14550⟩ Article dans une revue hal-03775795v1
Analyses of displacements resulting from a point mutation in proteins Mathilde Carpentier,Jacques Chomilier Journal of Structural Biology, 2020, 211 (2), pp.107543. ⟨10.1016/j.jsb.2020.107543⟩ Article dans une revue hal-02799788v1
Identification of a Novel Elastin-Degrading Enzyme from the Fish Pathogen Flavobacterium psychrophilum Tatiana Rochat,D. Pérez-Pascual,H. Nilsen,M. Carpentier,S. Bridelet al. Applied and Environmental Microbiology, 2019, 85 (6), pp.e02535-18. ⟨10.1128/AEM.02535-18⟩ Article dans une revue hal-02311311v1
Protein Multiple Alignments: Sequence-based versus Structure-based Programs Jacques Chomilier,Mathilde Carpentier Bioinformatics, 2019, Bioinformatics, 35 (20), pp.3970-3980. ⟨10.1093/bioinformatics/btz236⟩ Article dans une revue hal-02133485v1
Structural effects of point mutations in proteins Suvethigaa Shanthirabalan,Jacques Chomilier,Mathilde Carpentier Proteins - Structure, Function and Bioinformatics, 2018, 86 (8), pp.853-867. ⟨10.1002/prot.25499⟩ Article dans une revue hal-01909365v1
Contribution to the Prediction of the Fold Code: Application to Immunoglobulin and Flavodoxin Cases Mateusz Banach,Nicolas Prudhomme,Mathilde Carpentier,Élodie Duprat,Nikolaos Papandreouet al. PLoS ONE, 2015 Article dans une revue hal-02105843v1
Contribution to the Prediction of the Fold Code: Application to Immunoglobulin and Flavodoxin Cases Mateusz Banach,Nicolas Prudhomme,Mathilde Carpentier,Elodie Duprat,Nikolaos Papandreouet al. PLoS ONE, 2015, 10 (4), pp.e0125098. ⟨10.1371/journal.pone.0125098⟩ Article dans une revue hal-01230861v1
Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937. Jeremy D. Glasner,Ching-Hong Yang,Sylvie Reverchon,Nicole Hugouvieux-Cotte-Pattat,Guy Condemineet al. Journal of Bacteriology, 2011, 193 (8), pp.2076-7. ⟨10.1128/JB.01513-10⟩ Article dans une revue hal-00750360v1
A Relational Extension of the Notion of Motifs : Application to the Protein Common 3D Substructures Searching Problem Nadia Pisanti,Henry Soldano,Mathilde Carpentier,Joël Pothier Journal of Computational Biology, 2009, 16 (12), pp.1635-1660 Article dans une revue hal-00618073v1
RPBS: a web resource for structural bioinformatics Cynthia Alland,François Moreews,D. Boens,Mathilde Carpentier,Sylvain Chiusaet al. Nucleic Acids Research, 2005, 33 (2), pp.W44-W49. ⟨10.1093/nar/gki477⟩ Article dans une revue hal-04712180v1

HDR (1)

La structure des protéines et son évolution Mathilde Carpentier Bio-informatique [q-bio.QM]. Sorbonne Université, 2023 HDR tel-04076823v1

Poster de conférence (2)

PPalign: optimal alignment of Potts models representing proteins with direct coupling information Hugo Talibart,François Coste,Mathilde Carpentier ISMB 2022 - 30th Conference on Intelligent Systems for Molecular Biology, Jul 2022, Madison, United States. pp.1-1 Poster de conférence hal-03926272v1
Are protein folds reliable phylogenetic markers? Guillaume Sapriel,Pierre Imbert,Mathilde Carpentier,Jacques Chomilier,Guillaume Lecointreet al. Mathematical and Computational Evolutionary Biology, Jun 2022, Château d'Oex, Switzerland Poster de conférence hal-03959674v1

Chapitre d'ouvrage (2)

Impact of a Point Mutation in a Protein Structure Mathilde Carpentier,Jacques Chomilier Philippe Grandcolas; Marie-Christine Maurel. Systematics and the Exploration of Life, 1, Wiley, 2021, 9781119476870. ⟨10.1002/9781119476870.ch2⟩ Chapitre d'ouvrage mnhn-03959542v1
Implicit and Explicit Representation of Approximated Motifs Nadia Pisanti,Henry Soldano,Mathilde Carpentier,Joël Pothier C. S. Iliopoulos and K. Park and K. Steinhoefel. Algorithms in Bioinformatics, College Press, pp.1-15, 2006 Chapitre d'ouvrage hal-00087010v1

Communication dans un congrès (2)

Identifying distant homologous viral sequences in metagenomes using protein structure information Martine Boccara,Mathilde Carpentier,Jacques Chomilier,François Coste,Clovis Galiezet al. ECCB'14 Workshop on Recent Computational Advances in Metagenomics, Sep 2014, Strasbourg, France Communication dans un congrès hal-01090987v1
Incremental Inference of Relational Motifs with a Degenerate Alphabet Nadia Pisanti,Henry Soldano,Mathilde Carpentier 2005, pp.229 - 240 Communication dans un congrès hal-00077380v1

Thèse (1)

Méthodes de détection des similarités structurales : caractérisation des motifs conservés dans les familles de structures pour l'annotation des génomes Mathilde Carpentier Bio-informatique [q-bio.QM]. Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 2005. Français. ⟨NNT : ⟩ Thèse tel-03959695v1