AlgoB :: Algorithmics for Bioinformatics

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Members of AlgoB

Laurent Bulteau
- Currently a CNRS researcher at LIGM (since 2015)
- In 2013, he defended his PhD thesis entitled "Algorithmic aspects of genome rearrangements". After postdocs at TU Berlin from 2013 to 2014 and at Université Lyon 1 from 2014 to 2015, he joined the CNRS and LIGM in October 2015.
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Maxime Crochemore
- Currently an emeritus researcher at LIGM (since 2007)
- In 1978, he defended a PhD thesis on the following topic : "Standardization of formal series and minimization of automata". In 1983, he defended a thesis on : "Avoidable Regularities". From 1971 to 1985, he has been an assistant professor at University of Rouen. From 1985 to 1989, he was a professor at University Paris-Nord. He then became a professor at University of Marne-la-Vallée.
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Isabelle Fagnot
- Currently an associate professor of LIGM/Université Paris 7 (since 2002)
- In 1995, she defended a Thesis on : "Subword equivalence. Formal series diagonals". Since 1996 an associate professor of Paris 7 and since 2002 also member of LIGM.
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Philippe Gambette
- Currently an associate professor at LIGM (since 2011)
- From September 2007 to November 2010, he has been preparing a thesis in Bioinformatics on the following topic : "Combinatorial methods for phylogenetic network reconstruction" at LIRMM in Montpellier. He defended this thesis on November 30th, 2010, and is interested in graph algorithms for bioinformatics or natural language processing. He joined LIGM and Université Paris-Est Marne-la-Vallée in 2011.
- Philippe is also in charge of the open repository of the University.
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Gregory Kucherov
- Currently a CNRS senior researcher at LIGM (since 2011)
- In 1988, he defended his thesis on : "Abstract data type specification and term rewriting systems". He moved to the LORIA in Nancy in 1991, and worked as an INRIA researcher from 1993 to 2005, when he became a CNRS researcher at the LIFL in Lille. After a two-year leave to the French-Russian J.-V.Poncelet Lab in Moscow in 2008-2010, he joined LIGM in 2011.
- Gregory is also the local coordinator of the bioinformatics project ABS4NGS at UPEM.
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Anthony Labarre
- Currently an associate professor at LIGM (since 2012)
- In 2008, he defended his thesis in Bioinformatics on the following topic : "Combinatorial aspects of genome rearrangements and haplotype networks" at Université Libre de Bruxelles, in Belgium. His research interests include genome rearrangements, data compression, DNA computing, and lie more generally in the application of combinatorial and algorithmic techniques to all kinds of problems.
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Yoshihiro Shibuya
- Currently a PhD candidate at LIGM (since 2018)
- In 2017, he obtained his Master's Degree in Computer Science at Università degli Studi di Padova. He joined LIGM and Université Paris-Est in 2018 for a PhD on locality-sensitive hashing of DNA sequences and applications, supervised by Gregory Kucherov.
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Stéphane Vialette
- Currently a CNRS senior researcher at LIGM (since 2011)
- In 2001, he defended a Thesis on the following topic : "Algorithmic aspects of RNA secondary structure prediction". From 2002 to September 2007, he has been an associate professor in the Bioinformatic team of the Laboratoire de Recherche en Informatique of Paris-Sud. He then became a CNRS researcher at the LIGM.
- Stéphane is also the head of the Models and Algorithms team of LIGM.
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Mathias Weller
- Currently a CNRS researcher at LIGM (since 2017)
- In 2012, he defended his PhD thesis entitled "Aspects of preprocessing applied to combinatorial graph problems" at TU Berlin. After postdocs at LIRMM in Montpellier Berlin from 2013 to 2017, he joined the CNRS and LIGM in October 2017.
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Former members of AlgoB

Guillaume Blin
- Currently a professor at LABRI / Université de Bordeaux (since 2014)
- From October 2002 to November 2005, he has been preparing a thesis in Bioinformatics on the following topic : "Combinatorics and Bioinformatics : Comparaison of RNA structures and computation of intergenomic distances". He defended this thesis on November 17th, 2005, was hired as an associate professor at LIGM in 2006, and defended his habilitation on June 18th, 2012.
- Besides his teaching and research activities, he also started the open repository of the University.
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Karel Břinda
- Currently a postdoctoral researcher at Harvard University (since 2016)
- In 2013, he obtained his Master's Degree in Software Engineering and Mathematical Informatics at Czech Technical University in Prague. He joined LIGM and Université Paris-Est in 2013 for a PhD supervised by Gregory Kucherov on algorithmic, bioinformatic and software solutions for the analysis of Next Generation Sequencing data, in the ABS4NGS project. He was involved in the development of OCOCO, an online consensus caller for dynamic read mapping; RNF tools, a toolkit for read simulation and mapper evaluation, DyMaS, a dynamic mapping simulator, Seed-Kraken, a modification of the taxonomic sequence classification system Kraken and ProPhyle, a memory efficient metagenomic classifier. On November 28th, 2016, he defended his PhD thesis entitled "Novel computational techniques for mapping and classifying Next-Generation Sequencing data".
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Mathieu Chapelle
- Currently an engineer at Sopa Steria in Orléans (since 2015), after a postdoc at Université Libre de Bruxelles in Belgium (since 2013)
- In 2012-2013, he was an assistant professor (ATER) at Université Paris-Est Marne-la-Vallée and LIGM. In 2011, he defended in Orleans a PhD thesis on the following topic : "Graph decompositions: some limits and obstructions". He is interested in computational and parameterized complexity theory as well as graph algorithms.
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Carlo Comin
- Currently a PhD candidate at LIGM and at University Trento (since 2013)
- In 2011, he obtained his Master's Degree in Computer Science at University of Milano. He joined LIGM and Université Paris-Est in 2013 for a joint PhD with University of Trento on Computational Mathematics and Biology.
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Paul Morel
- Currently a software engineer at Ion Beam Applications S.A. in Louvain-la-Neuve, Belgium (since 2014)
- In 2010, he obtained his Master's Degree in Electronics, telecommunications, computer sciences at Ecole supérieure de Chimie Physique Electronique de Lyon. He joined LIGM in 2011 for a PhD on algorithmic aspects of radiotherapy, supervised by Guillaume Blin, Stéphane Vialette and Xiaodong Wu (University of Iowa), where he developed the MSPT software. On November 17th, 2014, he defended his PhD thesis entitled "MSPT: Motion Simulator for Proton Therapy"
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Both Emerite Neou
- Currently a big data consultant at Alten (since 2018)
- In 2013, he obtained his Master's Degree in Computer Science at Université Paris-Est Marne-la-Vallée. He joined LIGM and Université Paris-Est in 2013 for a PhD on algorithmics of transposition switches, supervised by Stéphane Vialette. On December 18th, 2017, he defended his PhD thesis entitled "Permutation Pattern Matching"
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Christiane Rayssiguier
- In 1978, she defended a Thesis on : "Multiple infection reactivation of T4 bacteriophages inactivated by exposure to ultraviolet radiation". From 1973 to 1999, she has been an assistant professor, an associate professor at University of Paris XI. She then became a professor at University of Marne-la-Vallée. She was then involved in the "Service de la Recherche Universitaire" at the "Direction Générale de l'Enseignement Supérieur" as a specialist in molecular biology, and she retired in 2014.
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Kamil Salikhov
- Currently a PhD candidate at LIGM (since 2013)
- Before 2013, he was a student at Lomonosov Moscow State University. He joined LIGM and Université Paris-Est in 2013 for a joint PhD on algorithmic, bioinformatic and software solutions for the analysis of Next Generation Sequencing data, supervised by Gregory Kucherov.
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Florian Sikora
- Currently an associate professor at LAMSADE / Université Paris-Daupine (since 2012)
- Supervised by Stéphane Vialette and Guillaume Blin, he defended on September 30, 2011, his thesis on "Algorithmic aspects of biological element comparison". After a one-year postdoc at Friedrich-Schiller-Universität Jena, he became an associate professor at Université Paris-Dauphine (LAMSADE).
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Maciek Sykulski
- Currently a ‎adiunct at Medical University of Warsaw (2016)
- In 2014-2015, he was a postdoc at Université Paris-Est Marne-la-Vallée and LIGM, working with Gregory Kucherov. He defended his PhD in bioinformatics entitled "Data analysis and modeling in human genomics" at University of Warsaw in 2014, where he was in the Computational and Systems Biology Group at the Faculty of Mathematics, Informatics and Mechanics.
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