Hugues Richard (on leave, RKI, Berlin)

David L, Vicedomini R, Richard H, Carbone A*. Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. Bioinformatics. (2020).

Ait-hamlat A, Zea DJavier, Labeeuw A, Polit L, Richard H, Laine E. Transcripts’ Evolutionary History and Structural Dynamics Give Mechanistic Insights into the Functional Diversity of the JNK Family. Journal of Molecular Biology. (2020).

Saad C, Noé L, Richard H, Leclerc J, Buisine M-P, Touzet H, Figeac M. DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data. 19(1), pp.223 (2018).

Shrestha AMS, Asai K, Frith M, Richard H. Jointly aligning a group of DNA reads improves accuracy of identifying large deletions. Nucleic Acids Research. 46(3), (2018).

Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A*, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes JS, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine E, Lopes* A. Meet-U: Educating through research immersion. PLOS Computational Biology. 14, pp.1-10 (2018).

Krakau S, Richard H, Marsico A. PureCLIP: Capturing Target-Specific protein-RNA Interaction Footprints from Single-Nucleotide CLIP-Seq Data. Genome Biology. 18(1), (2017).

MetaSUB International Consortium, Lafontaine I, Richard H. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome. 4(1), pp.24 (2016).

Gillet-Markowska A, Richard H, Fischer G, Lafontaine I. Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries. Bioinformatics. 31(6), pp.801-8 (2015).

Rogato A, Richard H, Sarazin A, Voss B, Cheminant Navarro S, Champeimont R, Navarro L, Carbone A*, Hess WR, Falciatore A. The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. BMC Genomics. 15, pp.698 (2014).

Schulz MH, Weese D, Holtgrewe M, Dimitrova V, Niu S, Reinert K, Richard H. Fiona: a parallel and automatic strategy for read error correction. Bioinformatics. 30(17), pp.i356-63 (2014).

Mirauta B, Nicolas P, Richard H. Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models. Bioinformatics. 30(10), pp.1409-16 (2014).

Mirauta B, Nicolas P, Richard H Pardiff: Inference of Differential Expression at Base-Pair Level from RNA-Seq Experiments. in IEEE International Conference on Image Analysis and Processing (ICIAP) 2013 Workshops, LNCS 8158. Springer. pp. 418–427 (2013)

Mäder U, Nicolas P, Richard H, Bessières P, Aymerich S. Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Curr Opin Biotechnol. 22(1), pp.32-41 (2011).

Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LDW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TAF, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin Y-C, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AFA, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang S-P, Li XC, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, et al.. The genome of a songbird. Nature. 464(7289), pp.757 - 762 (2010).

Richard H, Schulz MH, Sultan M, Nürnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, Haas SA, Yaspo M-L. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res. 38(10), pp.e112 (2010).

Hu H, Wrogemann K, Kalscheuer V, Tzschach A, Richard H, Haas SA, Menzel C, Bienek M, Froyen G, Raynaud M, Van Bokhoven H, Chelly J, Ropers H, Chen W. Erratum to: Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing. Hugo J. 3(1-4), pp.83 (2009).

Sultan M, Schulz MH, 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. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science. 321(5891), pp.956-60 (2008).

Miele V, Bourguignon P-Y, Robelin D, Nuel G, Richard H. seq++: analyzing biological sequences with a range of Markov-related models. Bioinformatics. 21, pp.2783-2784 (2005).

Robelin D, Richard H, Prum B. SIC: A tool to detect short inverted segments in a biological sequence. Nucleic Acids Res. 31(13), pp.3669-71 (2003).

Richard H, Nuel G. SPA: Simple web tool to assess statistical significance of DNA patterns. Nucleic Acids Res. 31(13), pp.3679-81 (2003).

Robin S, Daudin J-J, Richard H, Sagot M-F, Schbath S. Occurrence probability of structured motifs in random sequences. J Comput Biol. 9(6), pp.761-73 (2002).