Tristan Bitard-Feildel

My name is Tristan and I am a French Postdoc working in Evolutionary Bioinformatics

Email: tristan [you know what] bitardfeildel.fr
Email: tristan.bitard-feildel [you know what] impmc.upmc.fr

Some keywords: Protein Evolution; Protein domain; Python; Evolutionary Biology; Computational Biology



Projects


My main research concerns the evolution of proteins. How new proteins arise, where do old proteins come from, and how they evolved are some general questions that I am interested in.

Currently, I develop tools in collaboration with Isabelle Callebaut group's based on the analysis of the hydrophobic pattern of protein sequences. We want to understand what are the physico-chemical properties of recent protein domains and the genomic mechanisms leading to the creation of these new domains.

In a transversal axis, I am working with various Biologists to help them annotate protein sequences for which no information are available. I use and develop dedicated tools to detect and analyse orphan protein domains on these sequences.

The evolution of proteins can also be studied in comparative genomic analyses. During my previous postdoc in Pr. Erich Bornberg-Bauer's group , I studied the evolution of proteins and protein domains in Arthropoda/Insecta species. I performed protein domain and protein domain arrangement comparisons taking into account the phylogenetic tree of the species annotated and the functional annotations of the proteins.
Using, for example, Dollo parsimony, I reconstructed ancestral states and link the presence of major functional innovations with the emergence of new proteins. The domain and functional annotations, using GO terms, bring understanding on the reuse of protein domains by species to adapt and to evolve new functions.

Most of my research involves the development of new softwares and new methodologies linked to protein evolution. I am particularly interested in projects requiring optimization and/or machine-learning approaches.
I am a Python fanboy and an experienced user of its computational libraries. But when needed I can easily switch to my second and third favorite languages: C and C++. My statistical analyses are either done using Python or the specialized libraries of R/Bioconductor.

Publications


Journals

Conferences

  • Tristan Bitard-Feildel, Steffen Klasberg, Magdalena Heberlein, Isabelle Callebaut, Erich Bornberg-Bauer.
    Detection and Evolution of orphan protein domains.
    Talk - SMBE 2015. Young Investigator Travel Award.
  • Tristan Bitard-Feildel, Antoine Vigneron, Jean-François Gibrat.
    Density based clustering algorithms for near native protein conformation search..
    Talk - Miage Seminar 2011.
  • Tristan Bitard-Feildel, Antoine Vigneron, Jean-François Gibrat.
    Ab initio prediction of protein structures.
    Poster - JOBIM 2011.
  • Tristan Bitard-Feildel, Antoine Vigneron, Jean-François Gibrat.
    Heterogeneous coarse-grained model for protein structure predictions.
    Poster - GGMM 2011.
  • Tristan Bitard-Feildel, Antoine Vigneron, Jean-François Gibrat.
    Statistical potential and coarse-grained model for protein structure predictions.
    Poster - JOBIM 2010.

Research and Teaching Experience


Research Experience

  • 2015-2016: Post-doctoral Research. CNRS - IMPMC, Université Pierre et Marie Curie, France
  • 2013-2015: Post-doctoral Research. IEB, WWU Münster, Germany
  • 2009-2012: Doctoral Research. INRA Jouy-en-Josas, France
  • 2009 (6 month): Internship, IRISA Rennes, France.
  • 2007 (5 month): Internship, INRIA Montpellier, France.

Student Supervision

  • 2015 (3 month): Forschungsmodul - Lukas Kremer.
    Protein domains analyze in Mammalian orthologous proteins
  • 2015 (on going): PhD student - Steffen Klasberg (unofficial supervision).
    Protein domains emergence and evolution linked to innovation in Arthropoda.
  • 2014 (2+3 month): Forschungsmodul+BSc - Lukas Kremer.
    Protein domains and RNA-seq analyses of the Human and Oposum species.
  • 2013 (2 month): Forschungsmodul - Lukas Vaut.
    Evolution of the Protein Domain Universe Graph (PDUG) in different lineages.

Teaching Experience

  • 20{14,15}: Coordination of the MSc module Biocomputing for beginner and advanced student in Python.
    WWU Münster, Germany.
  • 20{13,14,15}: Contribution to the BSc module Bioinformatik II.
    WWU Münster, Germany.
  • 2013: Contribution to the MSc module Computational and statistical sequence analysis.
    WWU Münster, Germany.
  • 2011: Coordination of the course Introduction to Python during the Migale platform training days.
    Public : researchers in biology without programming background
    MIG INRA, Jouy-en-Josas.
  • 2010: Contribution to the BSc module Learning C programming (biology).
    University of Evry, France
  • 2010: Coordination of the BSc module Algorithmic in C (mathematics/computer science).
    University of Evry, France
  • 2010: Contribution to the BSc module Java for biocomputing.
    University of Evry, France

Education


  • 2009-2012: PhD, Ab initio prediction of protein structures
    Antoine Vigneron, Jean-François Gibrat. INRA MIG Jouy-en-Josas (Paris area), France.
  • 2007-2009: Master of Science in Biological System Modelling.
    University of Rennes 1, Rennes, France.
  • 2004-2007: Bachelor of Science in Biology (minor Computer Science).
    University of Rennes 1, Rennes, France.