Journal Articles

Ait-hamlat, A., Polit L., Richard* H., and Laine* E. The Impact of Alternative Splicing Evolution on Protein Structure and Conformational Dynamics: The JNK Family as a Case Study. Submitted.

Krakau, S., Richard* H., and Marsico* A.. PureCLIP: Capturing Target-Specific protein-RNA Interaction Footprints from Single-Nucleotide CLIP-Seq Data. Accepted (Genome Biology).

Shrestha, Anish MS, Asai, K., Frith, M., and Richard H. A New Framework for the Identification of Genomic Structural Variant Using Joint Alignment of Reads. Accepted (Nucleic Acids Research).

Weese, D., Schulz MH, and Richard H. 2017 DNA-Seq Error Correction Based on Substring Indices.In Algorithms for Next-Generations Sequencing Data: Techniques, Approaches and Applications.

Gillet-Markowska, A., Richard, H., Fischer, G. & Lafontaine, I. 2015 Ulysses: Accurate detection of low-frequency structural variations in large insert-size sequencing libraries. Bioinformatics 31, 801–808. (doi:10.1093/bioinformatics/btu730)

Hu, H., Haas, S. A., Chelly, J., Van Esch, H., Raynaud, M., Brouwer, A. P. M. de, Weinert, S., Froyen, G., Frints, S. G. M., Laumonnier, F., Zemojtel, T., Love, M. I., Richard, H. ., Chen, W., Ropers, H. H. & Kalscheuer, V. M. 2015 X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Molecular Psychiatry aop. (doi:10.1038/mp.2014.193)

Rogato*, A., Richard*, H., Voss, B., Sarazin, A., Navarro, S. C., Navarro, L., Carbone, A., Hess, W. R. & Falciatore, A. 2014 The diversity of small non coding rNA populations in the diatom phaeodactylum tricornotum. BMC Genomics 15, 698. (doi:10.1186/1471-2164-15-698)

Mirauta, B., Nicolas*, P. & Richard*, H. 2014 Parseq: Reconstruction of microbial transcription landscape from rNA-seq read counts using state-space models. Bioinformatics 30, 1409–1416. (doi:10.1093/bioinformatics/btu042)

Schulz*, M. H., Weese*, D., Holtgrewe*, M., Dimitrova, V., Niu, S., Reinert, K. & Richard*, H. 2014 Fiona: A parallel and automatic strategy for read error correction. Bioinformatics 30, i356–i363. (doi:10.1093/bioinformatics/btu440)

Mirauta, B., Nicolas*, P. & Richard*, H. 2013 Pardiff: Inference of differential expression at base-pair level from rNA-seq experiments. In ICIAP international workshops, naples, italy, september 9-13, 2013. proceedings (eds A. Petrosino L. Maddalena & P. Pala), pp. 418–427. Springer. (doi:10.1007/978-3-642-41190-8_45)

Steijger, T., Abril, J., Engstr, Kokocinski, F., The RGASP Consortium: 58 authors including Richard H., Hubbard, T., Guigo, Harrow, J. & Bertone, P. 2013 Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods 10, 1177–1184. (doi:10.1038/nmeth.2714)

Mäder, U., Nicolas, P., Richard, H., Bessières, P. & Aymerich, S. 2011 Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Current Opinion in Biotechnology 22, 32–41. (doi:10.1016/j.copbio.2010.10.003)

Richard*, H., Schulz*, M. H., Sultan*, M., Nurnberger, A., Schrinner, S., Balzereit, D., Dagand, E., Rasche, A., Lehrach, H., Vingron, M., Haas, S. A. & Yaspo, M.-L. 2010 Prediction of alternative isoforms from exon expression levels in rNA-seq experiments. Nucleic Acids Research (doi:10.1093/nar/gkq041)

Warren*, W. C., Clayton*, D. F., Ellegren*, H., Arnold*, A. P.,... (65 authors), Richard, H.,... (12 authors) & Wilson, R. K. 2010 The genome of a songbird. Nature 464, 757–762. (doi:10.1038/nature08819)

Hu, H., Wrogemann, K., Kalscheuer, V., Tzschach, A., Richard, H., Haas, S. A., Menzel, C., Bienek, M., Froyen, G., Raynaud, M., Bokhoven, H., Chelly, J., Ropers, H. & Chen, W. 2010 Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing. The HUGO Journal (doi:10.1007/s11568-010-9137-y)

Sultan*, M., Schulz*, 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. & Yaspo, M.-L. 2008 A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321, 956–960. (doi:10.1126/science.1160342)

Miele, V., Bourguignon, P.-Y., Robelin, D., Nuel, G. & Richard, H. 2005 Seq++: Analyzing biological sequences with a range of markov-related models. Bioinformatics 21, 2783–2784. (doi:10.1093/bioinformatics/bti389)

Richard, H. & Nuel, G. 2003 SPA: Simple web tool to assess statistical significance of dNA patterns. Nucleic Acids Research 31, 3679–3681. (doi:10.1093/nar/gkg613)

Robelin, D., Richard, H. & Prum, B. 2003 SIC: A tool to detect short inverted segments in a biological sequence. Nucleic Acids Research 31, 3669–3671. (doi:10.1093/nar/gkg596)

Robin, S., Daudin, J. J., Richard, H., Sagot, M.-F. & Schbath, S. 2002 Occurrence probability of structured motifs in random sequences. J. of Comp. Biol. 9, 761–773. (doi:10.1089/10665270260518254)

Selected Communications

list coming soon, available on my curriculum