Reseach area
My general research area is Theoretical Computer Science. Current research subjects include:
- Probabilistic data structures, sketching
- Algorithms on words and trees, pattern matching, indexes for sequential data
- Combinatorial algorithms and their applications to computational molecular biology
Formerly, I worked on the following subjects:
- Abstract data types theory (I was doing this in the 80s)
- Automated deduction, term rewriting systems (in the middle 80s - early 90s)
- Formal language theory, tree languages (till the middle 90s)
Background and short bio
My background is applied mathematics. I graduated in 1982 from the Institute of Electrical Engineering in Novosibirsk in Russia, now renamed to Novosibirsk State Technical University. Then I went to work to what is now called the A.P.Ershov Institute of Informatics Systems, located in Akademgorodok - a satellite "scientific town" near Novosibirsk built in 50s. I did there my PhD thesis, that I defended in 1988, on a quite theoretical topic: Abstract data type specification and term rewriting systems (no electronic version, sorry, it was typed on a typewriter machine!).In 1991 I moved to Nancy, France, and joined the Loria lab (at that time called CRIN: Centre de Recherche en Informatique de Nancy. In 1993 I joined INRIA and worked, until 2005, in several successive (and successful ;) INRIA project-teams: Euréca, Polka, Adage. In 2005 I joined CNRS and moved to Lille, to the LIFL Lab. In 2006, we created the SEQUOIA project-team of Inria that I headed until 2008. In 2008-2010, I made a two-years leave to the French-Russian J.-V.Poncelet Lab in Moscow. From 2011, I joined the Laboratoire d'Informatique Gaspard-Monge at Marne-la-Vallée...
Publications
Please consult my publication pagePhD students
- Yoshihiro Shibuya (2018 - 2022)
- Kamil Salikhov (2013-2017, co-tutelle)
- Karel Brinda (2013-2016)
- Tatiana Starikovskaya (2009-2012, co-supervision)
- Marta Girdea (2007-2010, co-supervised with Laurent Noé)
- Ségolène Caboche (2006-2009, co-supervised with Philippe Jacques, Maude Pupin and Valérie Leclère)
- Fabrice Touzain (2003-2007, co-supervised with Pierre Leblond)
- Laurent Noé (2002-2005)
- Vladimir Grebinski (1995-1998)
Software
ProPhyle: phylogeny-based metagenomic classification of whole genome sequencing dataRNFtools: a naming format for simulated NGS reads and associated toolbox
Norine: a database for nonribosomal peptides
YASS: local alignment of DNA sequences
path: pairwise alignment of protein sequences based on back-translation
ReBLOSUM: rectangular BLOSUM matrices
mreps: a package for finding tandem repeats in DNA sequences
grappe : a pattern matching program. You can have a look at README.
Designer : a C++ program for constructing combinatorial 2-designs (covering of a set by subsets such that every pair of elements belongs to exactly one subset)