A secondary and tertiary structure editor for nucleic acids. - Robert Cedergren; Daniel Gautheret; Guy Lapalme; François Major (Comput. Appl. Biosci., 1988)

Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA. - Daniel Gautheret; François Major; Robert Cedergren (Comput. Appl. Biosci., 1990)

An RNA pattern matching program with enhanced performance and portability. - A. Laferriere; Daniel Gautheret; Robert Cedergren (Comput. Appl. Biosci., 1994)

The ERPIN server: an interface to profile-based RNA motif identification. - André Lambert; Jean-Fred Fontaine; Matthieu Legendre; Fabrice Leclerc; Emmanuelle Permal; François Major; Harald Putzer; Olivier Delfour; Bernard Michot; Daniel Gautheret (Nucleic Acids Res., 2004)

Profile-based detection of microRNA precursors in animal genomes. - Matthieu Legendre; André Lambert; Daniel Gautheret (Bioinform., 2005)

Computing expectation values for RNA motifs using discrete convolutions. - André Lambert; Matthieu Legendre; Jean-Fred Fontaine; Daniel Gautheret (BMC Bioinform., 2005)

AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. - Vincent Le Texier; Jean-Jack M. Riethoven; Vasudev Kumanduri; Chellappa Gopalakrishnan; Fabrice Lopez; Daniel Gautheret; Thangavel Alphonse Thanaraj (BMC Bioinform., 2006)

Differential Repression of Alternative Transcripts: A Screen for miRNA Targets. - Matthieu Legendre; William Ritchie; Fabrice Lopez; Daniel Gautheret (PLoS Comput. Biol., 2006)

Mireval: a web tool for simple microRNA prediction in genome sequences. - William Ritchie; François-Xavier Théodule; Daniel Gautheret (Bioinform., 2008)

Entropy Measures Quantify Global Splicing Disorders in Cancer. - William Ritchie; Samuel Granjeaud; Denis Puthier; Daniel Gautheret (PLoS Comput. Biol., 2008)

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. - Julien Allali; Cédric Saule; Cédric Chauve; Yves D'Aubenton-Carafa; Alain Denise; Christine Drevet; Pascal Ferraro; Daniel Gautheret; Claire Herrbach; Fabrice Leclerc; Antoine de Monte; Aïda Ouangraoua; et al. (Adv. Bioinformatics, 2012)

NAPP: the Nucleic Acid Phylogenetic Profile Database. - Alban Ott; Anouar Idali; Antonin Marchais; Daniel Gautheret (Nucleic Acids Res., 2012)

A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events. - Jia Li 007; Marie-Anne Poursat; Damien Drubay; Arnaud Motz; Zohra Saci; Antonin Morillon; Stefan Michiels; Daniel Gautheret (PLoS Comput. Biol., 2015)

A benchmark study of scoring methods for non-coding mutations. - Damien Drubay; Daniel Gautheret; Stefan Michiels (Bioinform., 2018)

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. - David Couvin; Aude Bernheim; Claire Toffano-Nioche; Marie Touchon; Juraj Michalik; Bertrand Néron; Eduardo P. C. Rocha; Gilles Vergnaud; Daniel Gautheret; Christine Pourcel (Nucleic Acids Res., 2018)

REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets. - Camille Marchet; Zamin Iqbal; Daniel Gautheret; Mikaël Salson; Rayan Chikhi (Bioinform., 2020)

2-kupl: mapping-free variant detection from DNA-seq data of matched samples. - Yunfeng Wang; Haoliang Xue; Christine Pourcel; Yang Du 004; Daniel Gautheret (BMC Bioinform., 2021)

Rfam 14: expanded coverage of metagenomic, viral and microRNA families. - Ioanna Kalvari; Eric P. Nawrocki; Nancy Ontiveros-Palacios; Joanna Argasinska; Kevin Lamkiewicz; Manja Marz; Sam Griffiths-Jones; Claire Toffano-Nioche; Daniel Gautheret; Zasha Weinberg; Elena Rivas; Sean R. Eddy; et al. (Nucleic Acids Res., 2021)

KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction. - Haoliang Xue; Mélina Gallopin; Camille Marchet; Ha N. Nguyen; Yunfeng Wang; Antoine Lainé; Chloé Bessiere; Daniel Gautheret (Bioinform., 2024)