Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array. - Pierre Peterlongo; Nadia Pisanti; Frédéric Boyer; Marie-France Sagot (SPIRE, 2005)

A first approach to finding common motifs with gaps. - Costas S. Iliopoulos; James A. M. McHugh; Pierre Peterlongo; Nadia Pisanti; Wojciech Rytter; Marie-France Sagot (Int. J. Found. Comput. Sci., 2005)

The gapped-factor tree. - Pierre Peterlongo; Julien Allali; Marie-France Sagot (Stringology, 2006)

Finding Common Motifs with Gaps Using Finite Automata. - Pavlos Antoniou; Jan Holub 001; Costas S. Iliopoulos; Borivoj Melichar; Pierre Peterlongo (CIAA, 2006)

Filtrage de séquences d'ADN pour la recherche de longues répétitions multiples. (DNA sequence filtration for the problem of finding long multiple repetitions). - Pierre Peterlongo (2006)

Application of suffix trees for the acquisition of common motifs with gaps in a set of strings. - Pavlos Antoniou; Maxime Crochemore; Costas S. Iliopoulos; Pierre Peterlongo (LATA, 2007)

Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware. - Pierre Peterlongo; Laurent Noé; Dominique Lavenier; Gilles Georges; Julien Jacques; Gregory Kucherov; Mathieu Giraud (PPAM, 2007)

Optimal neighborhood indexing for protein similarity search. - Pierre Peterlongo; Laurent Noé; Dominique Lavenier; Van Hoa Nguyen; Gregory Kucherov; Mathieu Giraud (BMC Bioinform., 2008)

Indexing Gapped-Factors Using a Tree. - Pierre Peterlongo; Julien Allali; Marie-France Sagot (Int. J. Found. Comput. Sci., 2008)

Lossless filter for multiple repetitions with Hamming distance. - Pierre Peterlongo; Nadia Pisanti; Frédéric Boyer; Alair Pereira do Lago; Marie-France Sagot (J. Discrete Algorithms, 2008)

c-GAMMA: Comparative Genome Analysis of Molecular Markers. - Pierre Peterlongo; Jacques Nicolas; Dominique Lavenier; Raoul Vorc'h; Joël Querellou (PRIB, 2009)

Lossless filter for multiple repeats with bounded edit distance. - Pierre Peterlongo; Gustavo Akio Tominaga Sacomoto; Alair Pereira do Lago; Nadia Pisanti; Marie-France Sagot (Algorithms Mol. Biol., 2009)

In-Place Update of Suffix Array while Recoding Words. - Matthias Gallé; Pierre Peterlongo; François Coste (Int. J. Found. Comput. Sci., 2009)

An optimized filter for finding multiple repeats in DNA sequences. - Maria Federico; Pierre Peterlongo; Nadia Pisanti (AICCSA, 2010)

Identifying SNPs without a Reference Genome by Comparing Raw Reads. - Pierre Peterlongo; Nicolas Schnel; Nadia Pisanti; Marie-France Sagot; Vincent Lacroix (SPIRE, 2010)

Finding Long and Multiple Repeats with Edit Distance. - Maria Federico; Pierre Peterlongo; Nadia Pisanti; Marie-France Sagot (Stringology, 2011)

BlastGraph: Intensive Approximate Pattern Matching in Sequence Graphs and de-Bruijn Graphs. - Guillaume Holley; Pierre Peterlongo (Stringology, 2012)

Compareads: comparing huge metagenomic experiments. - Nicolas Maillet; Claire Lemaitre; Rayan Chikhi; Dominique Lavenier; Pierre Peterlongo (BMC Bioinform., 2012)

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. - Pierre Peterlongo; Rayan Chikhi (BMC Bioinform., 2012)

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. - Gustavo Akio Tominaga Sacomoto; Janice Kielbassa; Rayan Chikhi; Raluca Uricaru; Pavlos Antoniou; Marie-France Sagot; Pierre Peterlongo; Vincent Lacroix (BMC Bioinform., 2012)

Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads. - Claire Lemaitre; Liviu Ciortuz; Pierre Peterlongo (AlCoB, 2014)

Commet: Comparing and combining multiple metagenomic datasets. - Nicolas Maillet; Guillaume Collet; Thomas Vannier; Dominique Lavenier; Pierre Peterlongo (BIBM, 2014)

GATB: Genome Assembly & Analysis Tool Box. - Erwan Drezen; Guillaume Rizk; Rayan Chikhi; Charles Deltel; Claire Lemaitre; Pierre Peterlongo; Dominique Lavenier (Bioinform., 2014)

Rime: Repeat identification. - Maria Federico; Pierre Peterlongo; Nadia Pisanti; Marie-France Sagot (Discret. Appl. Math., 2014)

Read Mapping on de Bruijn graph. - Antoine Limasset; Pierre Peterlongo (CoRR, 2015)

Lire les lectures: analyse de données de séquençage. - Pierre Peterlongo (2016)

A Resource-frugal Probabilistic Dictionary and Applications in (Meta)Genomics. - Camille Marchet; Antoine Limasset; Lucie Bittner; Pierre Peterlongo (Stringology, 2016)

Read mapping on de Bruijn graphs. - Antoine Limasset; Bastien Cazaux; Eric Rivals; Pierre Peterlongo (BMC Bioinform., 2016)

Multiple comparative metagenomics using multiset k-mer counting. - Gaëtan Benoit; Pierre Peterlongo; Mahendra Mariadassou; Erwan Drezen; Sophie Schbath; Dominique Lavenier; Claire Lemaitre (PeerJ Comput. Sci., 2016)

Fast and Scalable Minimal Perfect Hashing for Massive Key Sets. - Antoine Limasset; Guillaume Rizk; Rayan Chikhi; Pierre Peterlongo (SEA, 2017)

Toward perfect reads. - Antoine Limasset; Jean-François Flot; Pierre Peterlongo (CoRR, 2017)

Finding all maximal perfect haplotype blocks in linear time. - Jarno Alanko; Hideo Bannai; Bastien Cazaux; Pierre Peterlongo; Jens Stoye (Algorithms Mol. Biol., 2020)

SimkaMin: fast and resource frugal de novo comparative metagenomics. - Gaëtan Benoit; Mahendra Mariadassou; Stéphane Robin; Sophie Schbath; Pierre Peterlongo; Claire Lemaitre (Bioinform., 2020)

SVJedi: genotyping structural variations with long reads. - Lolita Lecompte; Pierre Peterlongo; Dominique Lavenier; Claire Lemaitre (Bioinform., 2020)

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. - Antoine Limasset; Jean-François Flot; Pierre Peterlongo (Bioinform., 2020)

A resource-frugal probabilistic dictionary and applications in bioinformatics. - Camille Marchet; Lolita Lecompte; Antoine Limasset; Lucie Bittner; Pierre Peterlongo (Discret. Appl. Math., 2020)

Approximate Hashing for Bioinformatics. - Guy Arbitman; Shmuel T. Klein; Pierre Peterlongo; Dana Shapira (DCC, 2021)

findere: Fast and Precise Approximate Membership Query. - Lucas Robidou; Pierre Peterlongo (SPIRE, 2021)

Pattern Matching Under DTW Distance. - Garance Gourdel; Anne Driemel; Pierre Peterlongo; Tatiana Starikovskaya (SPIRE, 2022)

The K-mer File Format: a standardized and compact disk representation of sets of k-mers. - Yoann Dufresne; Téo Lemane; Pierre Marijon; Pierre Peterlongo; Amatur Rahman; Marek Kokot; Paul Medvedev; Sebastian Deorowicz; Rayan Chikhi (Bioinform., 2022)

k mdiff, large-scale and user-friendly differential k-mer analyses. - Téo Lemane; Rayan Chikhi; Pierre Peterlongo (Bioinform., 2022)

fimpera: drastic improvement of Approximate Membership Query data-structures with counts. - Lucas Robidou; Pierre Peterlongo (Bioinform., 2023)

Cdbgtricks: Strategies to update a compacted de Bruijn graph. - Khodor Hannoush; Camille Marchet; Pierre Peterlongo (PSC, 2024)

Back to sequences: Find the origin of k-mers. - Anthony Baire; Pierre Marijon; Francesco Andreace; Pierre Peterlongo (J. Open Source Softw., 2024)

Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA. - Téo Lemane; Nolan Lezzoche; Julien Lecubin; Eric Pelletier; Magali Lescot; Rayan Chikhi; Pierre Peterlongo (Nat. Comput. Sci., 2024)