Publications

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93 documents

Articles dans une revue

  • Romuald Laso-Jadart, Christophe Ambroise, Pierre Peterlongo, Mohammed-Amin Madoui. metaVaR: introducing metavariant species models for reference-free metagenomic-based population genomics. PLoS ONE, Public Library of Science, 2020, ⟨10.1371/journal.pone.0244637⟩. ⟨hal-02464983⟩
  • Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. SVJedi: genotyping structural variations with long reads. Bioinformatics, Oxford University Press (OUP), 2020, 36 (17), pp.4568-4575. ⟨10.1093/bioinformatics/btaa527⟩. ⟨hal-03032737⟩
  • Romuald Laso‐jadart, Kevin Sugier, Emmanuelle Petit, Karine Labadie, Pierre Peterlongo, et al.. Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866). Ecology and Evolution, Wiley Open Access, 2020, 10 (16), pp.8894-8905. ⟨10.1002/ece3.6588⟩. ⟨hal-02999798⟩
  • Jérémy Gauthier, Charlotte Mouden, Tomasz Suchan, Nadir Alvarez, Nils Arrigo, et al.. DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics. PeerJ, PeerJ, 2020, pp.1-20. ⟨10.7717/peerj.9291⟩. ⟨hal-01634232v4⟩
  • Camille Marchet, Lolita Lecompte, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in bioinformatics. Discrete Applied Mathematics, Elsevier, 2020, 92-102 (Volume 274), ⟨10.1016/j.dam.2018.03.035⟩. ⟨hal-01322440⟩
  • Camille Marchet, Pierre Morisse, Lolita Lecompte, Arnaud Lefebvre, Thierry Lecroq, et al.. ELECTOR: evaluator for long reads correction methods. NAR Genomics and Bioinformatics, Oxford University Press, 2020, 2 (1), pp.1-12. ⟨10.1093/nargab/lqz015⟩. ⟨hal-02371117⟩
  • Gaëtan Benoit, Mahendra Mariadassou, Stéphane Robin, Sophie Schbath, Pierre Peterlongo, et al.. SimkaMin: fast and resource frugal de novo comparative metagenomics. Bioinformatics, Oxford University Press (OUP), 2020, 36 (4), pp.1-2. ⟨10.1093/bioinformatics/btz685⟩. ⟨hal-02308101⟩
  • Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye. Finding all maximal perfect haplotype blocks in linear time. Algorithms for Molecular Biology, BioMed Central, 2020, pp.1-9. ⟨10.1186/s13015-020-0163-6⟩. ⟨hal-02187246⟩
  • Mathilde Cheray, Amandine Etcheverry, Camille Jacques, Romain Pacaud, Gwenola Bougras-Cartron, et al.. Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme. Molecular Cancer, BioMed Central, 2020, 19 (1), pp.1-36. ⟨10.1186/s12943-020-01155-z⟩. ⟨hal-02500622⟩
  • Antoine Limasset, Jean-François Flot, Pierre Peterlongo. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/btz102⟩. ⟨hal-02407243⟩
  • Laetitia Guillot, Ludovic Delage, Alain Viari, Yves Vandenbrouck, Emmanuelle Com, et al.. Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes. BMC Genomics, BioMed Central, 2019, 20 (1), pp.56. ⟨10.1186/s12864-019-5431-9⟩. ⟨hal-01987197⟩
  • Majda Arif, Jérémy Gauthier, Kevin Sugier, Daniele Iudicone, Olivier Jaillon, et al.. Discovering Millions of Plankton Genomic Markers from the Atlantic Ocean and the Mediterranean Sea. Molecular Ecology Resources, Wiley/Blackwell, 2018, pp.1-24. ⟨10.1111/1755-0998.12985⟩. ⟨hal-01987200⟩
  • Arnaud Meng, Camille Marchet, Erwan Corre, Pierre Peterlongo, Adriana Alberti, et al.. A de novo approach to disentangle partner identity and function in holobiont systems. Microbiome, BioMed Central, 2018, pp.1-35. ⟨10.1101/221424⟩. ⟨hal-01643153v2⟩
  • Camille Marchet, Lolita Lecompte, Corinne da Silva, Corinne Cruaud, Jean-Marc Aury, et al.. De Novo Clustering of Long Reads by Gene from Transcriptomics Data. Nucleic Acids Research, Oxford University Press, In press, pp.1-12. ⟨10.1093/nar/gky834⟩. ⟨hal-01643156v2⟩
  • Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra, Bas E. Dutilh, et al.. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, Oxford University Press (OUP), 2018, 19 (1), pp.118-135. ⟨10.1093/bib/bbw089⟩. ⟨hal-01390478⟩
  • Antoine Limasset, Bastien Cazaux, Eric Rivals, Pierre Peterlongo. Read mapping on de Bruijn graphs. BMC Bioinformatics, BioMed Central, 2016, 17 (1), ⟨10.1186/s12859-016-1103-9⟩. ⟨hal-01349636⟩
  • Gilles Boutet, Susete Alves Carvalho, Matthieu Falque, Pierre Peterlongo, Emeline Lhuillier, et al.. SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. BMC Genomics, BioMed Central, 2016, 17 (1), pp.121. ⟨10.1186/s12864-016-2447-2⟩. ⟨hal-01275696⟩
  • Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, et al.. Multiple comparative metagenomics using multiset k -mer counting. PeerJ Computer Science, PeerJ, 2016, 2 (14), 25 p. ⟨10.7717/peerj-cs.94⟩. ⟨hal-01397150⟩
  • Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, et al.. Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. GigaScience, BioMed Central, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩. ⟨hal-01280238⟩
  • Valentin Loux, Mahendra Mariadassou, Sintia Almeida, Hélène Chiapello, Amal Hammani, et al.. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. BMC Genomics, BioMed Central, 2015, 16 (1), pp.35. ⟨10.1186/s12864-015-1467-7⟩. ⟨hal-01142363⟩
  • Raluca Uricaru, Guillaume Rizk, Vincent Lacroix, Elsa Quillery, Olivier Plantard, et al.. Reference-free detection of isolated SNPs. Nucleic Acids Research, Oxford University Press, 2014, 43 (2), pp.e11. ⟨10.1093/nar/gku1187⟩. ⟨hal-01083715⟩
  • Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, et al.. GATB: Genome Assembly & Analysis Tool Box. Bioinformatics, Oxford University Press (OUP), 2014, 30, pp.2959 - 2961. ⟨10.1093/bioinformatics/btu406⟩. ⟨hal-01088571⟩
  • Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot. Rime: Repeat identification. Discrete Applied Mathematics, Elsevier, 2014, 163 (3), pp.275-286. ⟨10.1016/j.dam.2013.02.016⟩. ⟨hal-00802023⟩
  • Elsa Quillery, Olivier Quenez, Pierre Peterlongo, Olivier Plantard. Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms. Molecular Ecology Resources, Wiley/Blackwell, 2013, 14 (2), pp.393-400. ⟨10.1111/1755-0998.12179⟩. ⟨hal-00880072⟩
  • Gustavo Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, et al.. KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinformatics, BioMed Central, 2012, 13 (Suppl 6), pp.S5. ⟨10.1186/1471-2105-13-S6-S5⟩. ⟨hal-00784407⟩
  • Pierre Peterlongo, Rayan Chikhi. Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC Bioinformatics, BioMed Central, 2012, 13 (1), pp.48. ⟨10.1186/1471-2105-13-48⟩. ⟨hal-00784408⟩
  • Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo. Compareads: comparing huge metagenomic experiments. BMC Bioinformatics, BioMed Central, 2012, 13 (Suppl 19), pp.S10. ⟨10.1186/1471-2105-13-S19-S10⟩. ⟨hal-00784394⟩
  • Matthias Gallé, Pierre Peterlongo, François Coste. In-place update of suffix array while recoding words. International Journal of Foundations of Computer Science, World Scientific Publishing, 2009, 20 (6), pp.1025-1045. ⟨10.1142/S0129054109007029⟩. ⟨inria-00471599⟩
  • Pierre Peterlongo, Gustavo Sacomoto, Alair Do Lago, Nadia Pisanti, Marie-France Sagot. Lossless filter for multiple repeats with bounded edit distance. Algorithms for Molecular Biology, BioMed Central, 2009, 4 (1), pp.3. ⟨10.1186/1748-7188-4-3⟩. ⟨hal-00784457⟩
  • Pierre Peterlongo, Laurent Noé, Dominique Lavenier, van Hoa Nguyen, Gregory Kucherov, et al.. Optimal neighborhood indexing for protein similarity search. BMC Bioinformatics, BioMed Central, 2008, 9 (534), ⟨10.1186/1471-2105-9-534⟩. ⟨inria-00340510⟩
  • Pierre Peterlongo, Nadia Pisanti, Frédéric Boyer, Alair Pereira Do Lago, Marie-France Sagot. Lossless filter for multiple repetitions with Hamming distance. Journal of Discrete Algorithms, Elsevier, 2008, 6 (3), pp.497-509. ⟨10.1016/j.jda.2007.03.003⟩. ⟨inria-00179731⟩
  • Pierre Peterlongo, Julien Allali, Marie-France Sagot. Indexing gapped-factors using a tree. International Journal of Foundations of Computer Science, World Scientific Publishing, 2008, 19 (1), pp.71-87. ⟨10.1142/S0129054108005541⟩. ⟨inria-00179719⟩
  • Costas Iliopoulos, J. Mchugh, Pierre Peterlongo, Nadia Pisanti, W. Rytter, et al.. A first approach to finding common motifs with gaps,. International Journal of Foundations of Computer Science, World Scientific Publishing, 2005, 16 (6), pp.1145--1155. ⟨inria-00328042⟩

Communications dans un congrès

  • Guy Arbitman, Shmuel Klein, Pierre Peterlongo, Dana Shapira. Approximate Hashing for Bioinformatics. CIAA 2021 - 25th International Conference on Implementation and Application of Automata, Jul 2021, Bremen, Germany. pp.1-12. ⟨hal-03219482⟩
  • Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. Genotyping Structural Variations using Long Read Data. HiTSeq 2019 - Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland. pp.1-3. ⟨hal-02289484⟩
  • Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. Genotyping Structural Variations using Long Read data. JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1-8. ⟨hal-02288091⟩
  • Camille Marchet, Lolita Lecompte, Corinne da Silva, Corinne Cruaud, Jean-Marc Aury, et al.. CARNAC-LR : Clustering coefficient-based Acquisition of RNA Communities in Long Reads. JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-3. ⟨hal-01930211⟩
  • Antoine Limasset, Jean-François Flot, Pierre Peterlongo. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. RECOMB 2018, Apr 2018, Paris, France. ⟨hal-01644163⟩
  • Antoine Limasset, Guillaume Rizk, Rayan Chikhi, Pierre Peterlongo. Fast and scalable minimal perfect hashing for massive key sets. 16th International Symposium on Experimental Algorithms, Jun 2017, London, United Kingdom. pp.1 - 11. ⟨hal-01566246⟩
  • Arnaud Meng, Erwan Corre, Pierre Peterlongo, Camille Marchet, Adriana Alberti, et al.. A transcriptomic approach to study marine plankton holobionts . International Conference on Holobionts, Apr 2017, Paris, France. ⟨hal-01575069⟩
  • Camille Marchet, Antoine Limasset, Lucie Bittner, Pierre Peterlongo. A resource-frugal probabilistic dictionary and applications in (meta)genomics. Prageu Stringology Conference , Aug 2016, Prague, Czech Republic. ⟨hal-01386744⟩
  • François Coste, Pierre Peterlongo, Olivier Plantard. De la bioinformatique aux tiques. Data Science Symposium, Nov 2015, Rennes, France. pp.1. ⟨hal-02797229⟩
  • Nicolas Maillet, Guillaume Collet, Thomas Vannier, Dominique Lavenier, Pierre Peterlongo. COMMET: comparing and combining multiple metagenomic datasets. IEEE BIBM 2014, Nov 2014, Belfast, United Kingdom. ⟨hal-01080050⟩
  • Claire Lemaitre, Liviu Ciortuz, Pierre Peterlongo. Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads. Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. pp.119-130, ⟨10.1007/978-3-319-07953-0_10⟩. ⟨hal-01063157v3⟩
  • Alice Julien-Laferriere, Gustavo Sacomoto, Rayan Chikhi, Erwan Scaon, David P. Parsons, et al.. New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2013, Toulouse, France. ⟨hal-02069363⟩
  • Christian Diot, Magalie Houee, Olivier Demeure, Elisabeth Baéza, Alain Vignal, et al.. Analyse de transcriptomes de foies de canards par séquençage d’ARN (RNA-Seq). 10. Journées de la Recherche Avicole et Palmipèdes à Foie Gras, La Rochelle., Mar 2013, La Rochelle, France. ⟨hal-01210404⟩
  • Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo. Compareads: comparing huge metagenomic experiments. RECOMB Comparative Genomics 2012, Oct 2012, Niterói, Brazil. ⟨hal-00720951⟩
  • Guillaume Holley, Pierre Peterlongo. BlastGraph: intensive approximate pattern matching in string graphs and de-Bruijn graphs. PSC 2012, Aug 2012, Prague, Czech Republic. ⟨hal-00711911⟩
  • Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot. Finding Long and Multiple Repeats with Edit Distance. The Prague Stringology Conference 2011, Aug 2011, Prague, Czech Republic. ⟨inria-00608208⟩
  • Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix. Identifying SNPs without a reference genome by comparing raw reads. String Processing and Information Retrieval, Oct 2010, Los Cabos, Mexico. pp.147-158, ⟨10.1007/978-3-642-16321-0_14⟩. ⟨inria-00514887⟩
  • Maria Federico, Pierre Peterlongo, Nadia Pisanti. An optimized filter for finding multiple repeats in DNA sequences. 2010 ACS/IEEE International Conference on Computer Systems and Applications, May 2010, HAMMAMET, Tunisia. ⟨inria-00480001⟩
  • Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'H, Joël Querellou. c-GAMMA: Comparative Genome Analysis of Molecular Markers. Pattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. pp.255-269, ⟨10.1007/978-3-642-04031-3_23⟩. ⟨inria-00425373⟩
  • Matthias Gallé, Pierre Peterlongo, François Coste. In-place Update of Suffix Array while Recoding Words. Prague Stringology Conference 2008, Sep 2008, Prague, Czech Republic. pp.54--67. ⟨inria-00327582⟩
  • Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, et al.. Protein similarity search with subset seeds on a dedicated reconfigurable hardware. Parallel Bio-Computing, Sep 2007, Gdansk,, Poland. ⟨inria-00178325⟩
  • François Coste, Pierre Peterlongo, Matthias Gallé. Mise à jour incrémentale de tableau des suffxes en cours de recodage. Algorithmique, combinatoire du texte et applications en bio-informatique, Sep 2007, Chessy, France. ⟨inria-00186352⟩
  • Pavlos Antoniou, Maxime Crochemore, Costas Iliopoulos, Pierre Peterlongo. Application of suffix trees for the acquisition of common motifs with gaps in a set of strings. International Conference on Language and Automata Theory and Applications, Mar 2007, Tarragona, Spain. ⟨inria-00328081⟩
  • Pavlos Antoniou, Jan Holub, Costas Iliopoulos, Borijov Melichar, Pierre Peterlongo. Finding Common Motifs with Gaps Using Finite Automata. Implementation and Application of Automata, Aug 2006, Taipei, Taiwan. pp.69-77, ⟨10.1007/11812128_8⟩. ⟨inria-00328124⟩
  • Pierre Peterlongo, Julien Allali, Marie-France Sagot. The Gapped-Factor Tree. Prague Stringology Conference 2006, 2006, Prague, Czech Republic. pp.182--196. ⟨hal-00306572⟩
  • Pierre Peterlongo, Nadia Pisanti, Frederique Boyer, Marie-France Sagot. Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array. String Processing and Information Retrieval, 12th International Conference, SPIRE 2005, Nov 2005, Buenos Aires, Argentina. pp.179-190, ⟨10.1007/11575832⟩. ⟨inria-00328129⟩
  • Costas S. Iliopoulos, James Mchugh, Pierre Peterlongo, Nadia Pisanti, Wojciech Rytter, et al.. A first approach to finding common motifs with Gaps. Prague Stringology Conference 2004, Sep 2004, Czech Republic. pp.88-97. ⟨hal-00620030⟩

Posters

  • Guy Arbitman, Shmuel Klein, Pierre Peterlongo, Dana Shapira. Approximate Hashing for Bioinformatics. DCC 2021 - Data Compression Conference, Mar 2021, Virtual, United States. ⟨hal-03166000⟩
  • Lolita Lecompte, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. SVJedi : Structural variation genotyping using long reads. HiTSeq 2019 - Conference on High Throughput Sequencing, Jul 2019, Basel, Switzerland. ⟨hal-02290884⟩
  • Kévin da Silva, Nicolas Pons, Magali Berland, Florian Plaza Oñate, Mathieu Almeida, et al.. From genomics to metagenomics: benchmark of variation graphs. JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. ⟨hal-02284559⟩
  • Lolita Lecompte, Camille Marchet, Pierre Morisse, Antoine Limasset, Pierre Peterlongo, et al.. ELECTOR: EvaLuation of Error Correction Tools for lOng Reads. JOBIM 2018 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. pp.1-2. ⟨hal-01929900⟩
  • Camille Marchet, Lolita Lecompte, Corinne da Silva, Corinne Cruaud, Jean-Marc Aury, et al.. CARNAC-LR: De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets. RECOMB-seq 2018 - Eighth RECOMB Satellite Workshop on Massively Parallel Sequencing, Apr 2018, Paris, France. pp.1-2. ⟨hal-01929963⟩
  • Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, et al.. Simka: large scale de novo comparative metagenomics. JOBIM 2017 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2017, Lille, France. pp.234, 2017, JOBIM 2017 LILLE. ⟨hal-01595071⟩
  • Christian Diot, Frédéric Herault, Julien Navarro, Laure Le Calvez, Elisabeth Baéza, et al.. Genome specific expression in the liver of mule and hinny duck hybrids. 10. European Symposium on Poultry Genetics (ESPG), Jun 2017, Saint-Malo, France. pp.1, 2017, Proceedings of the 10th European symposium on poultry genetics. ⟨hal-01594559⟩
  • Antoine Limasset, Camille Marchet, Pierre Peterlongo, Lucie Bittner. Minimal perfect hash functions in large scale bioinformatics Problem. JOBIM 2016, Jun 2016, Lyon, France. ⟨hal-01341718⟩
  • Valentin Loux, Mahendra Mariadassou, Sintia Almeida da Silva, Helene Chiapello, Amal Hammami, et al.. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of [i]Propionibacterium freudenreichii[/i]. JOBIM 16.Journées Ouvertes de Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015. ⟨hal-01209851⟩
  • Antoine Limasset, Pierre Peterlongo. BGREAT: A De Bruijn graph read mapping tool. JOBIM 2015, Jul 2015, Clermont ferrant, France. ⟨hal-01192857⟩
  • Gaëtan Benoit, Pierre Peterlongo, Dominique Lavenier, Claire Lemaitre. Simka: fast kmer-based method for estimating the similarity between numerous metagenomic datasets. JOBIM 2015, Jul 2015, Clermont-Ferrand, France. ⟨10.1093/Bioinforma-cs/btu406⟩. ⟨hal-01180603⟩
  • Chloé Riou, Claire Lemaitre, Pierre Peterlongo. VCF$\_$creator: Mapping and VCF Creation features in DiscoSnp++. JOBIM 2015, Jul 2015, Clermont-Ferrand, France. ⟨hal-01176492⟩
  • Valentin Loux, Mahendra Mariadassou, Sintia Almeida da Silva, Hélène Chiapello, Amal Hammami, et al.. Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii. 20. Colloque du Club des Bactéries Lactiques, Jun 2015, Lille, France. 2015. ⟨hal-01170054⟩
  • Susete Alves Carvalho, Raluca Uricaru, Jorge Duarte, Claire Lemaitre, Nathalie Rivière, et al.. Reference-free high-throughput SNP detection in pea: an example of discoSnp usage for a non-model complex genome. ECCB 2014, Sep 2014, Strasbourg, France. ⟨hal-01091184⟩
  • Gilles Boutet, J. Duarte, Susete Alves Carvalho, Clément Lavaud, Raluca Uricaru, et al.. SNP discovery in pea: a powerful tool for academic research and breeding. 6. International Food Legumes Research Conference (IFLRC VI), Jul 2014, Saskatook, Canada. 2014. ⟨hal-01208702⟩
  • Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, et al.. Speeding up NGS software development. Sequencing, Finishing and Analysis in the Future Meeting, May 2014, Santa Fé, United States. ⟨hal-01088683⟩
  • Erwan Drezen, Guillaume Rizk, Rayan Chikhi, Charles Deltel, Claire Lemaitre, et al.. GATB: a software toolbox for genome assembly and analysis. Bio-IT World Conference, Apr 2014, Boston, United States. ⟨hal-01088641⟩
  • Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo. Compareads: comparing huge metagenomic experiments. 13e édition des Journées Ouvertes en Biologie, Informatique et Mathématiques - JOBIM 2012, Jul 2012, Rennes, France. 2012. ⟨hal-00760332⟩

Chapitres d'ouvrage

  • Jacques Nicolas, Pierre Peterlongo, Sébastien Tempel. Finding and Characterizing Repeats in Plant Genomes. David Edwards. Plant Bioinformatics: Methods and Protocols, Humana Press - Springer Science+Business Media, pp.365, 2015, Methods in Molecular Biology, 978-1-4939-3166-8. ⟨10.1007/978-1-4939-3167-5_17⟩. ⟨hal-01228488⟩
  • Nadia Pisanti, Mathieu Giraud, Pierre Peterlongo. Filters and seeds approaches for fast homology searches in large datasets. Mourad Elloumi and Albert Y. Zomaya. Algorithms in computational molecular biology, John Wiley & sons, 2010. ⟨inria-00425370⟩

Pré-publications, Documents de travail

  • Lucas Robidou, Pierre Peterlongo. findere: fast and precise approximate membership query. 2021. ⟨hal-03243791⟩
  • Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo. kmtricks: Efficient construction of Bloom filters for large sequencing data collections. 2021. ⟨hal-03166007⟩
  • Kévin da Silva, Nicolas Pons, Magali Berland, Florian Plaza Oñate, Mathieu Almeida, et al.. StrainFLAIR: Strain-level profiling of metagenomic samples using variation graphs. 2021. ⟨hal-03141144⟩
  • Daniel Richter, Romain Watteaux, Thomas Vannier, Jade Leconte, Paul Frémont, et al.. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. 2020. ⟨hal-02399723⟩
  • Romuald Laso-Jadart, Kevin Sugier, Emmanuelle Petit, Karine Labadie, Pierre Peterlongo, et al.. Linking Allele-Specific Expression And Natural Selection In Wild Populations. 2019. ⟨hal-02275928⟩
  • Gaëtan Benoit, Pierre Peterlongo, Mahendra Mariadassou, Erwan Drezen, Sophie Schbath, et al.. Multiple Comparative Metagenomics using Multiset k-mer Counting. 2016. ⟨hal-01300485⟩

Rapports

  • Antoine Rousseau, Aurélie Darnaud, Brice Goglin, Céline Acharian, Christine Leininger, et al.. Médiation Scientifique : une facette de nos métiers de la recherche. [Interne] none. 2013, pp.34. ⟨hal-00804915⟩
  • Gustavo Akio Tominaga Sacomoto, J. Kielbassa, Pavlos Antoniou, Rayan Chikhi, Raluca Uricaru, et al.. kisSplice, détection d'évènements d'épissages alternatifs dans les données RNA-seq. [Research Report] RR-7852, INRIA. 2011, pp.12. ⟨hal-00654249v2⟩
  • Pierre Peterlongo, Rayan Chikhi. Mapsembler, targeted assembly of larges genomes on a desktop computer. [Research Report] RR-7565, INRIA. 2011, pp.17. ⟨inria-00577218⟩
  • Jacques Nicolas, Christine Rousseau, Anne Siegel, Pierre Peterlongo, François Coste, et al.. Modeling local repeats on genomic sequences. [Research Report] RR-6802, INRIA. 2008, pp.43. ⟨inria-00353690⟩
  • Pierre Peterlongo, Nadia Pisanti, Alair Peirera Do Lago, Marie-France Sagot. Lossless Filter for Long Multiple Repetitions with Edit Distance. 2006. ⟨hal-00627831⟩

Thèses

  • Pierre Peterlongo. Filtrage de séquences d'ADN pour la recherche de longues répétitions multiples. Interface homme-machine [cs.HC]. Université de Marne la Vallée, 2006. Français. ⟨tel-00132300⟩

Habilitations à diriger des recherches

  • Pierre Peterlongo. Lire les lectures : analyse de données de séquençage. Bio-informatique [q-bio.QM]. Université rennes1, 2016. ⟨tel-01278275⟩

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