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Supervision
Postdocs:
Anne Lopes, ATER UPMC, 2010-2012: structural bioinformatics and coevolution
Yann Ponty, INSERM and CNRS, projet Decrypthon, 2008:
bioinformatics
Stefan Engelen, INSERM, projet Decrypthon, 2007-08: bioinformatics
Annelies Gerber, UPMC, Holcim Foundation, 2005-07: logic
and geometry
Sophie Sacquin-Mora, INSERM, projet Decrypthon, 2005-06:
bioinformatics
Andrey Zinovyev, IHES, France, 2001-2003: bioinformatics
Richard Madden, IHES, France, 2001-2003: bioinformatics
Erika Balog, IHES, France, 2001-2003: bioinformatics.
Doctoral students:
Raphael Champeimont, Université Pierre et Marie
Curie. Bioinformatics: sequence evolution and models of coevolution to identify genetic mutations;
beginning october 2011.
Juliana Bernardes, Université Pierre et Marie Curie and Universidade Federal de Rio de Janeiro, Bresil. Bioinformatics: remote homology, september 2009-expected january 2012. (Co-advisor with Gerson Zaverucha)
Guénola Drillon, Université Pierre et Marie
Curie. Bioinformatics: genome rearrangements and evolution;
october 2008-expected july 2012. (Co-advisor with Gilles Fischer)
Linda Dib, Université Pierre et Marie Curie. Bioinformatics:
protein coevolution and motif search for detection of
weakly homologous proteins; january 2008-November 2011.
Anthony Mathelier, Université Pierre et Marie Curie.
Bioinformatics: algorithms for the detection of new microRNA
and their targets and applications; september
2006-september 2010. Current position: postdoctoral position in Wyeth Wasserman Lab, Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, Canada.
Julie Baussand, Université Pierre et Marie Curie. Bioinformatics
: alignment of distantly related proteins, and coevolution
of amino-acids in proteins; september 2004 - march 2008.
Current position: EMBO fellow at theDivision of Mathematical Biology, National Institute for Medical Research, London, UK.
Stefano Borgo, Department of Mathematics of Indiana University
at Bloomington (USA) and Department of Computer Science
of the Université de Paris 12. Logic, complexity and parallelism;
co-direction with Prof.Daniel Leivant.
Current position: Research Fellow, CNR, Bolzano, Italy.
Master Students Interships:
Students come from several different backgrounds at
the interface with mathematics, physics, computer science
and molecular biology.
Computer Science and bioinformatics: Tamara Front, Université
de Paris 12, 2001. Alexis Darrasse, Linda Dib, Pierre
Franquin, Anthony Mathelier, UPMC. 2006.
Victoria Dimitrova and Sijia Niu, UPMC, 2011.
Computer Science and logic: Nicola Piccinini, University
of Verona (Italy) in the framework of the european exchange
program ERASMUS-SOCRATES. Co-advised with Prof. Gianluigi
Bellin, 2000.
Bioinformatics: Stephane Peugeot, Université de Paris
7, 2008; Gaëtan Poncelin de Raucourt, ENS and Université
de Paris 7, 2006 ; Julie Baussand, Université de Paris
7, 2004.
Biomathematics: Ladislas Trojan, UPMC,
2005 et 2006.
Mathematics and Computer Science applied to Biology: Anissa
Sadik, Université d'Evry, 2005.
Biophysics and Biochemistry: Cyril Deremble, ESPCI and
Université de Paris 6. 2003.
Undergraduates in Computer Science:
15 interships. Subjects: computer graphics, formal languages
and computer graphics, cellular automata, coding theory
and symbolic dynamics, the language XSL, computational
models based on DNA, manipulation of genomic sequences,
secondary structures of RNA and transcriptomic and proteomic
levels in yeast, algorithms for phylogenetic trees reconstruction
and comparison, algorithms for multiple alignmentof distantly
related proteins.
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