Mathilde Carpentier


Atelier de BioInformatique
45, rue Buffon
75005 Paris

Tel: +33-1-40-79-57-68


Interests in Biology


  • Protein Structure Evolution, Protein Alignment Algorithm, Structural Bioinformatics, Virus, Metaviromics, Computational biology, evolution, bioinformatics".

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.



I teach algorithms, programming languages  and bioinformatics at l' UFR d’Ingénierie

Actual courses
  • Programmation et structures de données en C ( 2i001)
  • Algorithmique appliquée et structures de données ( 2i006)
  • Modélisation, algorithmique et programmation pour la biologie ( 3V687)
  • Introduction à la biologie et aux algorithmes sur les arbres et les graphes en bioinformatique (AAGB, 4I700)
  • Python ( ISUP)

Where and when

  • 2016-now : Assistant professor, ISYEB UMR 7205, Sorbonne University, Museum d’Histoire Naturelle (Paris, France)..
  • 2010-16 Assistant professor, IMPMC UMR 7590, University Pierre and Marie Curie (Paris, France).
  • 2007 Invited scholar at M. Levitt Team (CBS, Stanford, CA)
  • 2006-2010: Assistant professor, Analytical Genomics laboratory, University Paris 6 (UPMC).
  • 2005-2006: postdoc laboratory Modeling in integrated Biology, University D. Diderot (Paris 7).
  • 2002-2005: PhD with Joël Pothier & Pierre Netter (UPMC ; ABI).


  • Data of Carpentier, M., and Chomilier, J. (2018). Protein Multiple Alignments: Sequence-based vs Structure-based Programs. BioRxiv. 10.1101/413369: