The transformation distance: A dissimilarity measure based an movements of segments. - Jean-Stéphane Varré; Jean-Paul Delahaye; Eric Rivals (German Conference on Bioinformatics, 1998)

Transformation distances: a family of dissimilarity measures based on movements of segments. - Jean-Stéphane Varré; Jean-Paul Delahaye; Eric Rivals (Bioinform., 1999)

Sorting by Reversals with Common Intervals. - Martin Figeac; Jean-Stéphane Varré (WABI, 2004)

Large Scale Matching for Position Weight Matrices. - Aude Liefooghe; Hélène Touzet; Jean-Stéphane Varré (CPM, 2006)

Efficient and accurate P-value computation for Position Weight Matrices. - Hélène Touzet; Jean-Stéphane Varré (Algorithms Mol. Biol., 2007)

Algorithmes pour la comparaison de génomes et la recherche de signaux cis-régulateurs. - Jean-Stéphane Varré (2008)

Self-overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching. - Aude Liefooghe; Hélène Touzet; Jean-Stéphane Varré (LATA, 2009)

TFM-Explorer: mining cis-regulatory regions in genomes. - Laurie Tonon; Hélène Touzet; Jean-Stéphane Varré (Nucleic Acids Res., 2010)

Bit-Parallel Multiple Pattern Matching. - Tuan Tu Tran; Mathieu Giraud; Jean-Stéphane Varré (PPAM (2), 2011)

Genome dedoubling by DCJ and reversal. - Antoine Thomas; Jean-Stéphane Varré; Aïda Ouangraoua (BMC Bioinform., 2011)

Parallel Position Weight Matrices algorithms. - Mathieu Giraud; Jean-Stéphane Varré (Parallel Comput., 2011)

Genome Halving by Block Interchange. - Antoine Thomas; Aïda Ouangraoua; Jean-Stéphane Varré (BIOINFORMATICS, 2012)

Single Tandem Halving by Block Interchange. - Antoine Thomas; Aïda Ouangraoua; Jean-Stéphane Varré (BIOSTEC (Selected Papers), 2012)

Tandem Halving Problems by DCJ. - Antoine Thomas; Aïda Ouangraoua; Jean-Stéphane Varré (WABI, 2012)

Perfect Hashing Structures for Parallel Similarity Searches. - Tuan Tu Tran; Mathieu Giraud; Jean-Stéphane Varré (IPDPS Workshops, 2015)

Graph analysis of fragmented long-read bacterial genome assemblies. - Pierre Marijon; Rayan Chikhi; Jean-Stéphane Varré (Bioinform., 2019)

yacrd and fpa: upstream tools for long-read genome assembly. - Pierre Marijon; Rayan Chikhi; Jean-Stéphane Varré (Bioinform., 2020)