Hugues Richard

Research Interests:

• Analysis of Alternative Splicing and Gene Expression by Sequencing (RNA-Seq)
• Statistical analysis of expression data (ESTs, microarrays,...)
• Genome resequencing
• gene regulation & tissue specificity
• Word probabilities
• Hidden Markov Models
• prediction of protein localization

Short Vita:

• since 2009:
  Assistant professor at the University Pierre and Marie Curie, affiliated to the interdisciplinary laboratory, Genomics of Microorganisms.
• 2006-2009:
  Postdoctorate research in Bioinformatics at the Computational Molecular Biology Group at the Max-Planck-Institute for Molecular Genetics.
• 2001-2005:
  PhD thesis (defended on 12-15-2005) and temporary assistant professor (ATER) at the Evry university under the direction of Bernard Prum, François Képès and Marie-Hélène Mucchielli-Giorgi.
  My thesis dealt with the prediction of protein subcellular localization within the cell. We focused on eukaryotic organisms with a number of compartments ranging from 9 to 12 (if you want to have a look, french version)
• 2000-2001:
  Master's Degree in Mathematics "Analysis and Stochastic Processes" Marne-la-Vallée university, France.

Publications and Abstracts:

• Warren, W.C., Clayton D.F, Ellegren H., Arnold H.P., ... (65 authors), Hugues Richard, ... (13 authors) :
  The genome of a songbird
  Nature, Vol. 454, 2010, p. 757-62. ( abstract )
• Richard, H.*, Schulz, M-H*, Sultan, M*, Nürnberger, A., Schrinner S., Balzereit D., Dagand E., Rasche A., Lehrach H., Vingron M., Haas S.A. and Yaspo M.-L.:
  Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments,
  Nucleic Acid Research, Advance Access published online on February 11, 2010 . The R package Solas can be downloaded here
• Sultan*, M., Schultz*, M. H., Richard*, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., Schmidt, D., O'Keeffe, S., Haas, S., Vingron, M., Lehrach, H., and Yaspo, M-L.:
  A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome,
  Science ,Vol. 321, n. 5891, 2008, p. 956-960. (published online July 3)
• Bekaert, M., Richard, H., Prum, B. and Rousset J.P. :
  Identification of programmed translationnal -1 frameshifting sites in the genome of Saccharomyces cerevisiae,
  Genome Research, vol. 15, 2005, p. 1411-1420.
• Miele, V., Bourguignon, P.Y., Robelin, D., Nuel, G., Richard, H. :
  seq++, analysing biological sequences with a range of Markov-related models (2004),
  Bioinformatics, vol. 21, n. 11, 2005, p. 2783-2784.
• Richard, H. et Nuel, G.:
  SPA: Simple web-tool to assess statistical significance of DNA patterns,
  Nucl. Acids. Res., vol. 31, n. 13, 2003, p.3679-3681.
• Robelin, D., Richard, H. et Prum, B:
  SIC: A tool to detect short inverted segments in a biological sequence,
  Nucl. Acids. Res., vol. 31, n. 13, 2003, p.3669-71.
• Robin, S., Daudin, J.-J., Richard, H., Sagot, M.-F. and Schbath, S. (2002).
  Occurrence probability of structured motifs in random sequences.
  J. Comp. Biol. 9 761-773., (ps).

*shared first authorship

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