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Supervision
Postdocs and Research Engineers:
Léon Faure, ANR, 2025: protein design and antibiotic resistance
Niccolo' Righetti (RE), ANR, 2024: ancient genomes and gene copy number variation
Mustafa Tekpinar, ANR, 2022-2023: mutational landscapes of proteins
Lélia Polit, ANR, 2021-2023: archaic genomes, modern populations and human adaptation
Edoardo Sarti, ANR, 2020-21: coevolution of SARS-Cov-2 proteins and design of peptides
Léopold Carron, ANR, 2019-22: 3D chromosomal structure in plants and gene regulation
Beatriz Seoane Bartolomé, ISCD-SU, 2018-20: RNA-protein interactions and protein disorder
Flavia Corsi, ISCD-SU, apr 2019-sept 2019: DNA-protein interactions
Elin Teppa, ANRS, 2017-20: coevolution of viral genomes
Tristan Bitard-Feildel, ISCD-SU, 2017-19: molecular modeling, mutations and evolution
Riccardo Vicedomini, ISCD-SU, 2015-19: genome and metagenome annotation
Raffaele Raucci, UPMC, 2014-2016: molecular modeling and protein binding affinity
Francesca Nadalin, MAPPING-UPMC, 2014-17: protein interactions and coevolution
Juliana Bernardes, UPMC, 2014: genome annotation
Shuang-Wei Hu, MAPPING-UPMC, 2013: protein interactions
Guenola Drillon, ATER UPMC, 2011-2013: genome rearrangements
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:
Alessandro Bianchi, Sorbonne Université. Deep Learning and Computational Biology: Deep Learning and Protein Functional classification; Jan 2025.
Chujun Lyu, Sorbonne Université. Deep Learning and Computational Biology: Machine learning and protein annotation; nov 2024. Co-advised with Chris Bowler.
Sara Rescalli, Sorbonne Université. Deep Learning and Computational Biology: Deep Learning and protein interactions in neuroscience; sept 2024-.
Vinh-Son Pho, Sorbonne Université. Deep Learning and Computational Biology: Deep Learning and functional classification of proteins; nov 2023-. Co-advised with Chris Bowler.
Gianluca Lombardi, Sorbonne Université. Deep Learning and Computational Biology: Machine Learning approaches for the estimation of effects of mutations in protein interactions; sept 2022-.
Konstantin Volzhenin, Sorbonne Université. Deep Learning and Computational Biology: deep learning approaches to PPI predictions in metagenomics and implications in ecosystems; sept 2021-2024. (Co-advised with Lucie Bittner)
Shadi Shafighi, Sorbonne Université and University of Warsaw. Bioinformatics: computational oncology; sept 2021. (Co-advised with Ewa Szczurek) Following position: postdoc at Cancer Research UK (CRUK) and University of Cambridge.
Yasser Mohseni, Sorbonne Université. Bioinformatics: protein-protein interaction and deep learning; sept 2019-sept 2022. (Co-advised with Elodie Laine) Following position: data scientist.
Laurent David, Sorbonne Université. Bioinformatics: metagenomics, assembly, annotation and deep learning; sept 2017-dec 2021. (Co-advised with Hugues Richard)
Flavia Corsi, Université Pierre et Marie Curie. Bioinformatics: Protein and DNA/RNA/small molecules interaction; jan 2016-feb 2019. (Co-advised with Elodie Laine) Following position: postdoc at the Austrian Academy of Science, Institute of Molecular Biotechnology.
Chloé Dekequer, Université Pierre et Marie Curie. Bioinformatics: geometrical models of protein-protein interactions; sept 2015- sept 2018. (Co-advised with Elodie Laine) Following position: data scientist.
Adel Ait-hamlat, Université Pierre et Marie Curie. Bioinformatics: development of a mathematical model explaining the interactions between hematopoietic stem cells and their microenvironment; beginning september 2014. (Co-advised with Thierry Jaffredo) Following position: data scientist.
Yasaman Karami, Université Pierre et Marie Curie. Bioinformatics: molecular modeling and sequence analysis approaches to coevolution; september 2013 - november 2016. (Co-advised with Elodie Laine) Following position: postdoc at Molécules Thérapeutique in silico lab, Université Paris Diderot, Paris, France. Now: Permanent Researcher at INRIA, France.
Ari Ugarte, Université Pierre et Marie
Curie. Bioinformatics: protein domain prediction in metagenomic sequences and applications to marine metagenomics;
october 2012 - december 2016. (Co-advisor with A.Falciatore) Following position: engineer at the Institute Cardiometabolism and Nutrition (ICAN), UPMC, Paris, France.
Raphael Champeimont, Université Pierre et Marie
Curie. Bioinformatics: sequence evolution and models of coevolution to identify genetic mutations; october 2011- december 2014. Following position: engineer at the Observatoire des Sciences et des Techniques, Paris, France.
Juliana Bernardes, Université Pierre et Marie Curie and Universidade Federal de Rio de Janeiro, Bresil. Bioinformatics: remote homology, september 2009-March 2012. (Co-advisor with Gerson Zaverucha). Following position: postdoc at the Department of Electrical Engineering, Machine Learning Laboratory, Universidade Federal de Rio de Janeiro, Bresil. Now: Associate professor at Sorbonne Université.
Guénola Drillon, Université Pierre et Marie
Curie. Bioinformatics: genome rearrangements and evolution;
october 2008-february 2013. (Co-advisor with Gilles Fischer) Following position: postdoc at ENS Lyon, Laboratoire Joliot-Curie, France
Linda Dib, Université Pierre et Marie Curie. Bioinformatics:
protein coevolution and motif search for detection of
weakly homologous proteins; january 2008-March 2012. Following position: postdoctoral position in Nicolas Salamin Lab, Department of Ecology and Evolution, Université de Lausanne, Switzerland.
Anthony Mathelier, Université Pierre et Marie Curie.
Bioinformatics: algorithms for the detection of new microRNA
and their targets and applications; september
2006-september 2010. Following position: postdoctoral position in Wyeth Wasserman Lab, Center for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, Canada. Now: Associate Director of the Centre for Molecular Medicine Norway, and University of Oslo, Norway.
Julie Baussand, Université Pierre et Marie Curie. Bioinformatics
: alignment of distantly related proteins, and coevolution
of amino-acids in proteins; september 2004 - march 2008.
Following position: EMBO fellow at theDivision of Mathematical Biology, National Institute for Medical Research, London, UK. Now: Projects Director at Health Innovation.
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: Permanent Researcher, 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, computer science and logic, bioinformatics, biomathematics, mathematics and computer science applied to biology, biophysics and biochemistry.
Undergraduates in Computer Science:
Various interships: 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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