Business address :

Ecole normale Supérieure
46, rue d'Ulm
FR-75230 Paris,
France

Personal Address:

104, rue Balard
75015 Paris,
France

Degrees:

• Ph.D. (March 2004), Computer Science, University of Bordeaux I, France.

  Algorithmes et Mesures Statistiques pour la Recherche de Signaux Fonctionnels dans les Zones de Régulation (Promotors: Dr. M. Régnier, Prof. Dr. S. Dulucq)
  Mention: Très honorable.
  
  Accomplished in:

  • the Laboratoire bordelais de Recherche en Informatique (LaBri, Bordeaux, France) and in

  • the Institut National de Recherche en Informatique et Automatique (Inria Rocquencourt, France).

• M.S. (Juin 2000), Biochemistry, University of Ghent, Belgium

End of scholarship's thesis in the laboratory of Biochemistry, Microbiology and Physiology:

Klonering en expressie van het Chlorobium limicola forma thiosulfatophylum cytochroom c-551 gen, deel uitmakend van een thiosulfaatverbruikend gencluster (Promotors: Prof. Dr. J. Van Beeumen, Dr. F. Verté).

• B.S. (Juin 1997), Biology, University of Ghent, Belgium
  
  

Experience:

• May 2005 -- now: Post-doc Position Ecole Normale Supérieure, Paris, France.

• May 2004 -- May 2005: Post-doc Position University Basel, Switzerland.

• January -- April 2000: Course of Computer-science in Biology (Cours d'Informatique en Biologie).
  Pasteur Institute, Paris, France. Different biological algorithms were analysed and implemented in Scheme (a Lisp dialect) and Java.

• April 2001 & April 2003: Collaboration with the Engelhardt Institute of Molecular Biology (Dr. M. Gelfand, Dr. V. Makeev) & French-Russian Lyapunov Institute, Moscow, Russia. Topics related to the current PhD study: word-counting in biological sequences and related phylogenetics -- tree construction through clustering problems.
  
  

Computer related skills:

• UNIX power tools:

• MAPLE symbolic computing,

• C, C++, Java, Perl, Awk, Lisp (Scheme),

• Html web design: Javascript, php, mysql,

• TCP/IP knowledge basics,

• Bases Statistical environment: R.

• October 2002 -- January 2003: Teaching Assistant, Department of Computer Science, University of Marne la Vallée (first years' students -- practical work in computer science: UNIX power tools, Html web design, MAPLE and MuPAD symbolic computing).
  
  

• April 2002 & April 2003:Teaching Assistant, Department of Computer Science, Ecole Centrale de Paris:
  Statistics and probability frameworks used in bioinformatics. (Blast, Fasta, and SW - alignment and lookup tools,
  analysis of genomic signals with different software like RSAT, QuickScore, RegExpCount (Maple-based), AlignAce).
  Supplementary course in Protein Structure and Function, with software tools SwissPDB-Viewer, Rasmol, Chime,
  and comparison of protein secondary structure prediction algorithms. (Teaching and practical work given for 3rd years' students.)

Publications:

• Denise and M. Régnier and M. Vandenbogaert (2001) Assessing statistical significance of overrepresented oligonucleotides. In Proc. First Intern. Workshop on Algorithms in Bioinformatics, Aarhus, Denmark, August 2001; Journal version in preperation. WABI'01 85--97.

• M. Vandenbogaert and Makeev V. (2002). Analysis of bacterial RM-systems through genome-scale analysis and related taxonomic issues. Preliminary version at BGRS'02, Novossibirsk, Russia; Published in In Silico Biology vol. 12, no.3, 2003. - Special Issues of Volume 3: Bioinformatics on Genome Regulation and Structure (BGRS 2002, Novossibirsk), Published as online journal by Bioinformation Systems e.V. Available online at http://www.bioinfo.de/isb/2003/03/0012/.

• Tompa M., Li N., Bailey T.L., Church G.M., De Moor B., Eskin E., Favorov A.V., Frith M.C., Fu Y., Kent J.W., Makeev V.J., Mironov A.A., Noble W.S., Pavesi G., Pesole G., Régnier M., Simonis N., Sinha S., Thijs G., van Helden J., Vandenbogaert M., Weng Z., Workman C., Ye C. & Zhu Z. - An Assessment of Computational Tools for the Discovery of Transcription Factor Binding Sites. Nature Biotechnology, vol. 23, no. 1, January 2005, 137 - 144.

• C. Banderier and M. Vandenbogaert, A Markovian generalization of Feller's coin tossing constants, unpublished note (2000).

• Boeva (V.), Clément (J.), Régnier (M.), and Vandenbogaert (M.). - Assessing the significance of Sets of Words. In Combinatorial Pattern Matching 05. Lecture Notes in Computer Science, vol. 3537, pages 358--370. - Springer Verlag, 2005. In Proceedings CPM'05, Jeju Island, Korea.

• Régnier (M.) and Vandenbogaert (M.). - Comparison of statistical significance criteria. Journal of Bioinformatics and Computational Biology, To appear. - 12 pages. In press.

• Planned publications on phylogenetics of restriction enzymatic systems, and on oligomer analysis in bacterial genomes
  
  

Presentations:

• Laboratoire Bordelais de Recherche Informatique (LaBRI)in Bordeaux, PhD study onset with Ms. M. Régnier at I.N.R.I.A. and Mr. S. Dulucq at LaBRI (Thursday 05/04/2000).

• INRIA Rocquencourt Colloque Junior, subject "Bioinformatics, its objectives and its constraints" (Tuesday 10/04/01).

• WABI 2001, 1st Workshop on Algorithms in BioInformatics, BRICS, University of Aarhus, Denmark, August 28-31, 2001. The stress was laid on the algorithms addressed to significant problems in molecular biology, and bringing effective solutions having been implemented and having been tested by simulations on real data.

• AMASIG: Approches Multicritères pour l'Analyse in SIlico des Génomes, LRI, Orsay, November 15, 2001. Title: ``Comptage de mots et recherche de signaux de régulation dans le génome.''

• BBC'02: 3rd Belgian Bioinformatics Conference: oral contribution to be presented at the Université de Namur, 12 April 2002.

• JOBIM'02 poster presentation entitled ``Statistical measurements applied to bacterial RM-systems through genome-scale analysis.'' February 15, 2002 Saint-Malo, France.

• BGRS'2002: The Third International Conference on Bioinformatics of Genome Regulation and Structure. Oral contribution presented, entitled ``Analysis of Bacterial RM-Systems through genome-scale analysis and related Taxonomic issues.''

• Bioinformatics at LaBRI, Rapport de travail de thèse, entitled ``Analyse de systèmes de restriction-modification bacteriens par le caractère exceptionnel de leur site de reconnaissance, et inférences taxonomiques.'', 14 Novembre 2002.

• RECOMB 2003 Poster presentation, entitled ``Bacterial RMS revisited using degenerate pattern consensi.'' Berlin, Germany. 10-14 april 2003.

• MCCMB 2003 Poster presentation, entitled ``Bacterial RMS revisited using degenerate pattern consensi, with its underlying protein phylogeny.'' Moscow, Russia. July 22-25, 2003.
  

• RECOMB Satellite Workshop on Systems Biology and Regulatory Genomics 2-4 dec. 2005 UCSD La Jolla CA
  
  
  

Phd Study:

Subject Title: Extraction of functional signals in regulationally important genomic regions, and assessment of their statistical relevance. The PhD study is involved in the development of procedures aimed to search for signals located in upstream regions of coregulated genes. These regions are known to regulate the expression of these genes. In this context, the so-called structured motifs, as well as a word and his neighbors that share a common structure typical of a family are of particular interest. These signals (words), appear to be either overrepresented or avoided in specific genomes. Within this particular framework recent statistical and computational approaches are being handled with. This work will find applications in the determination of the secondary and tertiary structures of RNA molecules and proteines, as well in the determination of the relatedness of different species, according to the word usages in the genomic texts. This work has been the subject of various collaborations. M. Régnier and A. Denise (University of Orsay) are involved with the effective establishment of the formulas, for various structures of sets of words. A function library called QuickScore is currently under development, and will be containing the concepts of the approach. The studies on the relatedness of different bacterial species based on the current word-counting, statistical assesment and phylogenetics inference methods is a joint work with Dr. V. Makeev, and is supervised by Dr. M. Gelfand. This work, as well as the results obtained by Ms. M. Régnier and Mr. A. Denise in the statistical large deviations domain, which allow a very precise computation of probabilities on words, when exact calculations are very expensive or numerically unstable, have been applied in the search of functional signals in the zones of regulation (search for motifs applied to genomics).
Comments: The effective calculation of the general explicit formulas for the assessment of the pertinence of genomic signals is simplified when the sets of words are structured. From a formal point of view, one is interested in particular in regular expressions and the approximate motifs which appear in many molecular biology problems. Within this particular framework, recent statistical calculations were applied to signals of regulation in the genomes of Bacillus subtilis, Arabidopsis thaliana and of Saccharomyces cerevisiae, as well as poly-adenylation signals in the human genome. The latter motifs were the subject of a statistical method that was presented making it possible to separate the artifacts words, e.g. neighbouring words with random composition, that are close to the required motifs. This approach makes it possible to obtain a concise list of high quality motifs, that is consistent enough to explain the over-representation of the motifs in the sequence. This work will also finds applications in the determination of secondary and tertiary structures of RNA and proteins.

Language Knowledge:

• French--Dutch--English: spoken--written

• 1997--98: Course in English for Scientific purposes at the University of Ghent (Talencentrum).

• German: easy learner.

• Russian: beginning learner.

• Spanish: Notions.
  First level in a Spanish Course at the University of Ghent (Talencentrum). Further autodidactic learning.

References :