Pierre Peterlongo

According to our database, Pierre Peterlongo authored at least 45 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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

Back to sequences: Find the origin of k-mers.

Anthony Baire, Pierre Marijon, Francesco Andreace, Pierre Peterlongo

J. Open Source Softw., 2024

Cdbgtricks: Strategies to update a compacted de Bruijn graph.

Khodor Hannoush, Camille Marchet, Pierre Peterlongo

Proceedings of the Prague Stringology Conference 2024, 2024

2023

<tt>fimpera</tt>: drastic improvement of Approximate Membership Query data-structures with counts.

Lucas Robidou, Pierre Peterlongo

Bioinform., May, 2023

2022

<tt>k</tt> <tt>mdiff</tt>, large-scale and user-friendly differential <i>k</i>-mer analyses.

Téo Lemane, Rayan Chikhi, Pierre Peterlongo

Bioinform., December, 2022

The K-mer File Format: a standardized and compact disk representation of sets of <i>k</i>-mers.

Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi

Bioinform., 2022

Pattern Matching Under DTW Distance.

Garance Gourdel, Anne Driemel, Pierre Peterlongo, Tatiana Starikovskaya

Proceedings of the String Processing and Information Retrieval, 2022

2021

Approximate Hashing for Bioinformatics.

Guy Arbitman, Shmuel T. Klein, Pierre Peterlongo, Dana Shapira

Proceedings of the Implementation and Application of Automata, 2021

findere: Fast and Precise Approximate Membership Query.

Lucas Robidou, Pierre Peterlongo

Proceedings of the String Processing and Information Retrieval, 2021

2020

A resource-frugal probabilistic dictionary and applications in bioinformatics.

Camille Marchet, Lolita Lecompte, Antoine Limasset, Lucie Bittner, Pierre Peterlongo

Discret. Appl. Math., 2020

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.

Antoine Limasset, Jean-François Flot, Pierre Peterlongo

Bioinform., 2020

SVJedi: genotyping structural variations with long reads.

Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre

Bioinform., 2020

SimkaMin: fast and resource frugal de novo comparative metagenomics.

Gaëtan Benoit, Mahendra Mariadassou, Stéphane Robin, Sophie Schbath, Pierre Peterlongo, Claire Lemaitre

Bioinform., 2020

2019

Finding All Maximal Perfect Haplotype Blocks in Linear Time.

Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye

Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

2017

Toward perfect reads.

Antoine Limasset, Jean-François Flot, Pierre Peterlongo

CoRR, 2017

Fast and Scalable Minimal Perfect Hashing for Massive Key Sets.

Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo

Proceedings of the 16th International Symposium on Experimental Algorithms, 2017

2016

Multiple comparative metagenomics using multiset <i>k</i>-mer counting.

Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, Claire Lemaitre

PeerJ Comput. Sci., 2016

Read mapping on de Bruijn graphs.

Antoine Limasset, Bastien Cazaux, Eric Rivals, Pierre Peterlongo

BMC Bioinform., 2016

A Resource-frugal Probabilistic Dictionary and Applications in (Meta)Genomics.

Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo

Proceedings of the Prague Stringology Conference 2016, 2016

Lire les lectures: analyse de données de séquençage.

Pierre Peterlongo

, 2016

2015

Read Mapping on de Bruijn graph.

Antoine Limasset, Pierre Peterlongo

CoRR, 2015

2014

Rime: Repeat identification.

Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot

Discret. Appl. Math., 2014

GATB: Genome Assembly & Analysis Tool Box.

Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier

Bioinform., 2014

Commet: Comparing and combining multiple metagenomic datasets.

Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads.

Claire Lemaitre, Liviu Ciortuz, Pierre Peterlongo

Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

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

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.

Pierre Peterlongo, Rayan Chikhi

BMC Bioinform., 2012

Compareads: comparing huge metagenomic experiments.

Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo

BMC Bioinform., 2012

BlastGraph: Intensive Approximate Pattern Matching in Sequence Graphs and de-Bruijn Graphs.

Guillaume Holley, Pierre Peterlongo

Proceedings of the Prague Stringology Conference 2012, 2012

2011

Finding Long and Multiple Repeats with Edit Distance.

Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot

Proceedings of the Prague Stringology Conference 2011, 2011

2010

Identifying SNPs without a Reference Genome by Comparing Raw Reads.

Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix

Proceedings of the String Processing and Information Retrieval, 2010

An optimized filter for finding multiple repeats in DNA sequences.

Maria Federico, Pierre Peterlongo, Nadia Pisanti

Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications, 2010

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

c-GAMMA: Comparative Genome Analysis of Molecular Markers.

Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'h, Joël Querellou

Proceedings of the Pattern Recognition in Bioinformatics, 2009

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

Indexing Gapped-Factors Using a Tree.

Pierre Peterlongo, Julien Allali, Marie-France Sagot

Int. J. Found. Comput. Sci., 2008

Optimal neighborhood indexing for protein similarity search.

Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud

BMC Bioinform., 2008

In-place Update of Suffix Array while Recoding Words.

Matthias Gallé, Pierre Peterlongo, François Coste

Proceedings of the Prague Stringology Conference 2008, Prague, Czech Republic, 2008

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

Proceedings of the Parallel Processing and Applied Mathematics, 2007

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

Proceedings of the LATA 2007. Proceedings of the 1st International Conference on Language and Automata Theory and Applications., 2007

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

PhD thesis, 2006

Finding Common Motifs with Gaps Using Finite Automata.

Pavlos Antoniou, Jan Holub, Costas S. Iliopoulos, Borivoj Melichar, Pierre Peterlongo

Proceedings of the Implementation and Application of Automata, 2006

The gapped-factor tree.

Pierre Peterlongo, Julien Allali, Marie-France Sagot

Proceedings of the Prague Stringology Conference, 2006

2005

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

Proceedings of the String Processing and Information Retrieval, 2005

2004

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

Proceedings of the Prague Stringology Conference 2004, Prague, Czech Republic, August 30, 2004