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ORCIDPierre Peterlongo
Person information
- affiliation: Inria, France
- affiliation: Rennes University, France
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Books and Theses
- 2016
[b2]Pierre Peterlongo:
Lire les lectures: analyse de données de séquençage. University of Rennes 1, France, 2016- 2006
- [b1]Pierre Peterlongo:
Filtrage de séquences d'ADN pour la recherche de longues répétitions multiples. (DNA sequence filtration for the problem of finding long multiple repetitions). University of Marne-la-Vallée, Marne la Vallée, France, 2006
Journal Articles
- 2024
- [j23]Téo Lemane
, Nolan Lezzoche, Julien Lecubin, Eric Pelletier, Magali Lescot, Rayan Chikhi, Pierre Peterlongo:
Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA. Nat. Comput. Sci. 4(2): 104-109 (2024) - 2023
- [j22]Lucas Robidou, Pierre Peterlongo:
fimpera: drastic improvement of Approximate Membership Query data-structures with counts. Bioinform. 39(5) (2023) - 2022
- [j21]Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi:
The K-mer File Format: a standardized and compact disk representation of sets of k-mers. Bioinform. 38(18): 4423-4425 (2022) - [j20]Téo Lemane, Rayan Chikhi, Pierre Peterlongo:
k mdiff, large-scale and user-friendly differential k-mer analyses. Bioinform. 38(24): 5443-5445 (2022) - 2020
- [j19]Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye:
Finding all maximal perfect haplotype blocks in linear time. Algorithms Mol. Biol. 15(1): 2 (2020) - [j18]Antoine Limasset, Jean-François Flot, Pierre Peterlongo:
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinform. 36(2): 651 (2020) - [j17]Gaëtan Benoit, Mahendra Mariadassou, Stéphane Robin, Sophie Schbath, Pierre Peterlongo, Claire Lemaitre:
SimkaMin: fast and resource frugal de novo comparative metagenomics. Bioinform. 36(4): 1275-1276 (2020) - [j16]Antoine Limasset, Jean-François Flot, Pierre Peterlongo:
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinform. 36(5): 1374-1381 (2020) - [j15]Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre:
SVJedi: genotyping structural variations with long reads. Bioinform. 36(17): 4568-4575 (2020) - [j14]Camille Marchet, Lolita Lecompte, Antoine Limasset, Lucie Bittner, Pierre Peterlongo:
A resource-frugal probabilistic dictionary and applications in bioinformatics. Discret. Appl. Math. 274: 92-102 (2020) - 2016
- [j13]Antoine Limasset, Bastien Cazaux, Eric Rivals, Pierre Peterlongo:
Read mapping on de Bruijn graphs. BMC Bioinform. 17: 237 (2016) - [j12]Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, Dominique Lavenier, Claire Lemaitre:
Multiple comparative metagenomics using multiset k-mer counting. PeerJ Comput. Sci. 2: e94 (2016) - 2014
- [j11]Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, Pierre Peterlongo, Dominique Lavenier:
GATB: Genome Assembly & Analysis Tool Box. Bioinform. 30(20): 2959-2961 (2014) - [j10]Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot:
Rime: Repeat identification. Discret. Appl. Math. 163: 275-286 (2014) - 2012
- [j9]Pierre Peterlongo, Rayan Chikhi:
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC Bioinform. 13: 48 (2012) - [j8]Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo:
Compareads: comparing huge metagenomic experiments. BMC Bioinform. 13(S-19): S10 (2012) - [j7]Gustavo Akio Tominaga Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix:
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinform. 13(S-6): S5 (2012) - 2009
- [j6]Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira do Lago, Nadia Pisanti, Marie-France Sagot:
Lossless filter for multiple repeats with bounded edit distance. Algorithms Mol. Biol. 4 (2009) - [j5]Matthias Gallé, Pierre Peterlongo, François Coste:
In-Place Update of Suffix Array while Recoding Words. Int. J. Found. Comput. Sci. 20(6): 1025-1045 (2009) - 2008
- [j4]Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud:
Optimal neighborhood indexing for protein similarity search. BMC Bioinform. 9 (2008) - [j3]Pierre Peterlongo, Julien Allali, Marie-France Sagot:
Indexing Gapped-Factors Using a Tree. Int. J. Found. Comput. Sci. 19(1): 71-87 (2008) - [j2]Pierre Peterlongo, Nadia Pisanti, Frédéric Boyer, Alair Pereira do Lago, Marie-France Sagot:
Lossless filter for multiple repetitions with Hamming distance. J. Discrete Algorithms 6(3): 497-509 (2008) - 2005
- [j1]Costas S. Iliopoulos, James A. M. McHugh, Pierre Peterlongo, Nadia Pisanti, Wojciech Rytter, Marie-France Sagot:
A first approach to finding common motifs with gaps. Int. J. Found. Comput. Sci. 16(6): 1145-1154 (2005)
Conference and Workshop Papers
- 2022
- [c21]Garance Gourdel, Anne Driemel, Pierre Peterlongo, Tatiana Starikovskaya:
Pattern Matching Under DTW Distance. SPIRE 2022: 315-330 - 2021
- [c20]Guy Arbitman, Shmuel T. Klein, Pierre Peterlongo, Dana Shapira:
Approximate Hashing for Bioinformatics. DCC 2021: 337 - [c19]Lucas Robidou, Pierre Peterlongo:
findere: Fast and Precise Approximate Membership Query. SPIRE 2021: 151-163 - [c18]Guy Arbitman, Shmuel T. Klein, Pierre Peterlongo, Dana Shapira:
Approximate Hashing for Bioinformatics. CIAA 2021: 178-189 - 2019
- [c17]Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye:
Finding All Maximal Perfect Haplotype Blocks in Linear Time. WABI 2019: 8:1-8:9 - 2017
- [c16]Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo:
Fast and Scalable Minimal Perfect Hashing for Massive Key Sets. SEA 2017: 25:1-25:16 - 2016
- [c15]Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo:
A Resource-frugal Probabilistic Dictionary and Applications in (Meta)Genomics. Stringology 2016: 85-97 - 2014
- [c14]Claire Lemaitre, Liviu Ciortuz, Pierre Peterlongo:
Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads. AlCoB 2014: 119-130 - [c13]Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo:
Commet: Comparing and combining multiple metagenomic datasets. BIBM 2014: 94-98 - 2012
- [c12]Guillaume Holley, Pierre Peterlongo:
BlastGraph: Intensive Approximate Pattern Matching in Sequence Graphs and de-Bruijn Graphs. Stringology 2012: 53-63 - 2011
- [c11]Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot:
Finding Long and Multiple Repeats with Edit Distance. Stringology 2011: 83-97 - 2010
- [c10]Maria Federico, Pierre Peterlongo, Nadia Pisanti:
An optimized filter for finding multiple repeats in DNA sequences. AICCSA 2010: 1-8 - [c9]Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix:
Identifying SNPs without a Reference Genome by Comparing Raw Reads. SPIRE 2010: 147-158 - 2009
- [c8]Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'h, Joël Querellou:
c-GAMMA: Comparative Genome Analysis of Molecular Markers. PRIB 2009: 255-269 - 2008
- [c7]Matthias Gallé, Pierre Peterlongo, François Coste:
In-place Update of Suffix Array while Recoding Words. Stringology 2008: 54-67 - 2007
- [c6]Pavlos Antoniou, Maxime Crochemore, Costas S. Iliopoulos, Pierre Peterlongo:
Application of suffix trees for the acquisition of common motifs with gaps in a set of strings. LATA 2007: 57-66 - [c5]Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, Gregory Kucherov, Mathieu Giraud:
Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware. PPAM 2007: 1240-1248 - 2006
- [c4]Pierre Peterlongo, Julien Allali, Marie-France Sagot:
The gapped-factor tree. Stringology 2006: 182-196 - [c3]Pavlos Antoniou, Jan Holub, Costas S. Iliopoulos, Borivoj Melichar, Pierre Peterlongo:
Finding Common Motifs with Gaps Using Finite Automata. CIAA 2006: 69-77 - 2005
- [c2]Pierre Peterlongo, Nadia Pisanti, Frédéric Boyer, Marie-France Sagot:
Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array. SPIRE 2005: 179-190 - 2004
- [c1]Costas S. Iliopoulos, James A. M. McHugh, Pierre Peterlongo, Nadia Pisanti, Wojciech Rytter, Marie-France Sagot:
A First Approach to Finding Common Motifs With Gaps. Stringology 2004: 88-97
Informal and Other Publications
- 2022
- [i6]Garance Gourdel, Anne Driemel, Pierre Peterlongo, Tatiana Starikovskaya:
Pattern matching under DTW distance. CoRR abs/2208.14669 (2022) - 2017
- [i5]Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo:
Fast and scalable minimal perfect hashing for massive key sets. CoRR abs/1702.03154 (2017) - [i4]Camille Marchet, Lolita Lecompte, Antoine Limasset, Lucie Bittner, Pierre Peterlongo:
A resource-frugal probabilistic dictionary and applications in bioinformatics. CoRR abs/1703.00667 (2017) - [i3]Antoine Limasset, Jean-François Flot, Pierre Peterlongo:
Toward perfect reads. CoRR abs/1711.03336 (2017) - 2016
- [i2]Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo:
A resource-frugal probabilistic dictionary and applications in (meta)genomics. CoRR abs/1605.08319 (2016) - 2015
- [i1]Antoine Limasset, Pierre Peterlongo:
Read Mapping on de Bruijn graph. CoRR abs/1505.04911 (2015)
Coauthor Index
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