Occurrence Probability of Structured Motifs in Random Sequences. - Stéphane Robin; Jean-Jacques Daudin; Hugues Richard; Marie-France Sagot; Sophie Schbath (J. Comput. Biol., 2002)

SPA: simple web tool to assess statistical significance of DNA patterns. - Hugues Richard; Grégory Nuel (Nucleic Acids Res., 2003)

SIC: a tool to detect short inverted segments in a biological sequence. - David Robelin; Hugues Richard; Bernard Prum (Nucleic Acids Res., 2003)

seq++: analyzing biological sequences with a range of Markov-related models. - Vincent Miele; Pierre-Yves Bourguignon; David Robelin; Grégory Nuel; Hugues Richard (Bioinform., 2005)

Pardiff: Inference of Differential Expression at Base-Pair Level from RNA-Seq Experiments. - Bogdan Mirauta; Pierre Nicolas; Hugues Richard (ICIAP Workshops, 2013)

Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models. - Bogdan Mirauta; Pierre Nicolas; Hugues Richard (Bioinform., 2014)

Fiona: a parallel and automatic strategy for read error correction. - Marcel H. Schulz; David Weese; Manuel Holtgrewe; Viktoria Dimitrova; Sijia Niu; Knut Reinert; Hugues Richard (Bioinform., 2014)

Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries. - Alexandre Gillet-Markowska; Hugues Richard; Gilles Fischer; Ingrid Lafontaine (Bioinform., 2015)

DNA-Seq Error Correction Based on Substring Indices. - David Weese; Marcel H. Schulz; Hugues Richard (Algorithms for Next-Generation Sequencing Data, 2017)

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data. - Chadi Saad; Laurent Noé; Hugues Richard; Julie Leclerc; Marie-Pierre Buisine; Hélène Touzet; Martin Figeac (BMC Bioinform., 2018)

Meet-U: Educating through research immersion. - Nika Abdollahi; Alexandre Albani; Éric Anthony; Agnes Baud; Mélissa Cardon; Robert Clerc; Dariusz Czernecki; Romain Conte; Laurent David; Agathe Delaune; Samia Djerroud; Pauline Fourgoux; et al. (PLoS Comput. Biol., 2018)

Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A. - Laurent David; Riccardo Vicedomini; Hugues Richard; Alessandra Carbone (Bioinform., 2020)

Statistical methods for analysing high throughput sequencing data. (Méthodes statistiques pour l'analyse des données de séquençage à haut débit). - Hugues Richard (2022)

CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance. - Alice Wittig; Fábio Miranda 002; Martin Hölzer; Tom Altenburg; Jakub M. Bartoszewicz; Sebastian Beyvers; Marius A. Dieckmann; Ulrich Genske; Sven H. Giese; Melania Nowicka; Hugues Richard; Henning Schiebenhoefer; et al. (Bioinform., 2022)

ASES: visualizing evolutionary conservation of alternative splicing in proteins. - Diego Javier Zea; Hugues Richard; Elodie Laine (Bioinform., 2022)