- M. Régnier, E. Furletova, M. Roytberg and V. Yakovlev.Pattern occurrences Pvalues, Hidden Markov Models and Overlap Graphs. submitted.2013 .http://hal.inria.fr/hal-00858701
- M. Régnier, Z. Kirakossian, E. Furletova, M. Roytberg. A Word Counting Graph, in
“London Algorithmics 2008: Theory and Practice (Texts in Algorithmics)”, J. CHAN, J. W. DAYKIN, M.
SOHEL RAHMAN (editors), London College Publications, 06 2009, p. 10–43, http://hal.archivesouvertes.
fr/inria- 00437147/en/AMRU. - Boeva V, Clément J, Régnier M, Roytberg MA, Makeev VJ. Exact p-value calculation for heterotypic
clusters of regulatory motifs and its application in computational annotation of cis-regulatory
modules. Algorithms Mol Biol. (2007) Oct 10;2:13. PubMed PMID: 17927813; PubMed Central
PMCID: PMC2174486. - Boeva, J. Clément, M. Régnier, and M. Vandenbogaert. Assessing the significance of sets of words. In
Combinatorial Pattern Matching 05, volume 3537 of Lecture Notes in Computer Science, page
358370. Springer Verlag, 2005. In Proceedings CPM’05, Jeju Island, Korea. - Boeva, V. Makeev, D. Papatsenko, and M. R egnier. Short fuzzy tandem repeats in genomic
sequences, identification, and possible role in regulation of gene expression. Bioinformatics,
22(6):676–684, 2006. - Vandenbogaert (M.) and Makeev (V.). – Analysis of bacterial RM-systems through genome-scale
analysis and related taxonomic issues. In Silico Biology, vol. 12, n°3, 2003, pages 127–143. –
Special Issues of Volume 3: Bioinformatics on Genome Regulation and Structure (BGRS 2002,
Novossibirsk), Published as online journal by Bioinformation Systems e.V - Dmitri A. Papatsenko, Vsevolod J. Makeev, Alex P. Lifanov, Mireille R egnier, Anna G. Nazina, and
Claude Desplan. Extraction of functional binding sites from unique regulatory regions: The
drosophila early develop- mental enhancers. Genome Research, 12(3):470–481, 2002. - M. R égnier, A. Lifanov, and V. Makeev. Three variations on word counting. In GCB’00, pages 75–82.
Logos-Verlag, 2000. Proceedings German Conference on Bioinformatics, Heidelberg.
-
Short communications :
- M. Régnier, E. Furletova, M. Roytberg and V. Yakovlev.Pattern occurrences Pvalues, Hidden Markov Models and Overlap Graphs. Presentation at SeqBio13.
- V. Boeva, J. Clément, M. Régnier, M.A. Roytberg, V.J. Makeev.Exact P-value calculation for clusters of TFBSs. Application in Computational Annotation of Regulatory Sites. The 12th International Conference on Research in Computational and Molecular Biology (RECOMB 2008),
2008, Singapore - A. Boeva, J. Clément, M. Régnier, M.A. Roytberg , V.J. Makeev.P-value Approach in Computational Annotation of Regulatory Sites. V. The 15ème International Conference on Intelligence Systems in Molecular Biology (ISMB) and the 6th European Conference on Computational Biology (ECCB 2007), 2007, Vienna, Austria.