P. Peterlongo

发表

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

Philip D. Blood, Daniel A. Cuevas, Matthew Z. DeMaere, 2017, Nature Methods.

Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea

O. Jaillon, P. Wincker, P. Peterlongo, 2019, Molecular ecology resources.

Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Tom O. Delmont, P. Bork, S. Sunagawa, 2019, bioRxiv.

Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

C. Pineau, P. Peterlongo, A. Viari, 2019, BMC Genomics.

De novo clustering of long reads by gene from transcriptomics data

Pierre Peterlongo, Jacques Nicolas, Lolita Lecompte, 2018, Nucleic acids research.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Dominique Lavenier, Alexander Sczyrba, Mihai Pop, 2017, bioRxiv.

Investigating population‐scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866)

P. Wincker, P. Peterlongo, E. Petit, 2020, Ecology and evolution.

Investigating Population-scale Allele Specific Expression in Wild Populations of Oithona similis (Cyclopoida, Claus 1866)

P. Wincker, P. Peterlongo, E. Petit, 2020 .

Linking Allele-Specific Expression And Natural Selection In Wild Populations

P. Wincker, P. Peterlongo, E. Petit, 2019, bioRxiv.

DiscoSnp-RAD: de novo detection of small variants for RAD-Seq population genomics

C. Lemaitre, P. Peterlongo, Tomasz Suchan, 2020, PeerJ.

DiscoSnp-RAD: de novo detection of small variants for population genomics

C. Lemaitre, P. Peterlongo, Tomasz Suchan, 2017, bioRxiv.

Fast and scalable minimal perfect hashing for massive key sets

Rayan Chikhi, Guillaume Rizk, Pierre Peterlongo, 2017, SEA.

A de novo approach to disentangle partner identity and function in holobiont systems

E. Pelletier, P. Wincker, P. Peterlongo, 2017, Microbiome.

A de novo approach to disentangle partner identity and function in holobiont systems

E. Pelletier, P. Wincker, P. Peterlongo, 2017, bioRxiv.

A highly scalable data structure for read similarity computation and its application to marine plankton holobionts

P. Peterlongo, F. Not, E. Corre, 2017 .

SVJedi: Genotyping structural variations with long reads.

D. Lavenier, C. Lemaitre, P. Peterlongo, 2020, Bioinformatics.

Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of single nucleotide polymorphisms

P. Peterlongo, O. Quenez, O. Plantard, 2014, Molecular ecology resources.

Filters and seeds approaches for fast homology searches in large datasets

Nadia Pisanti, Pierre Peterlongo, Mathieu Giraud, 2010 .

Local and Maximal Repeats

A. Siegel, C. Rousseau, P. Peterlongo, 2022 .

De novo Clustering Nanopore Long Reads of Transcriptomics Data by Gene

Corinne Da Silva, P. Peterlongo, J. Aury, 2017 .

fimpera: drastic improvement of Approximate Membership Query data-structures with counts

P. Peterlongo, Lucas Robidou, 2022, bioRxiv.

Simka: large scale de novo comparative metagenomics

S. Schbath, M. Mariadassou, D. Lavenier, 2017 .

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras, G. Sacomoto, Eric Rivals, 2016, GigaScience.

Pattern matching under DTW distance

A. Driemel, P. Peterlongo, Garance Gourdel, 2022, 2208.14669.

Lossless Filter for Long Multiple Repetitions with Edit Distance

Alair Pereira do Lago, M. Sagot, P. Peterlongo, 2006 .

Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

Y. Le Loir, M. Mariadassou, H. Falentin, 2015, BMC Genomics.

fimpera: drastic improvement of Approximate Membership Query data-structures with counts

P. Peterlongo, Lucas Robidou, 2022, bioRxiv.

Computational pan-genomics: status, promises and challenges

Ying Zhang, Eleazar Eskin, Knut Reinert, 2016, bioRxiv.

metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics

P. Peterlongo, C. Ambroise, Mohammed-Amin Madoui, 2020, bioRxiv.

Clustering de Novo by Gene of Long Reads from Transcriptomics Data

Pierre Peterlongo, Jacques Nicolas, Lolita Lecompte, 2018, bioRxiv.

De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets

Pierre Peterlongo, Jacques Nicolas, Lolita Lecompte, 2017, RECOMB 2018.

kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections

R. Chikhi, P. Peterlongo, P. Medvedev, 2021, bioRxiv.

Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

J. Mosser, M. Aubry, P. Peterlongo, 2020, Molecular Cancer.

Finding and Characterizing Repeats in Plant Genomes.

Pierre Peterlongo, Jacques Nicolas, Sébastien Tempel, 2016, Methods in molecular biology.

SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population

P. Peterlongo, O. Bouchez, Susete Alves Carvalho, 2016, BMC Genomics.

Multiple comparative metagenomics using multiset k-mer counting

Dominique Lavenier, Pierre Peterlongo, Sophie Schbath, 2016, PeerJ Comput. Sci..

SVJedi: Genotyping structural variations with long reads

Dominique Lavenier, Lolita Lecompte, Claire Lemaitre, 2019, bioRxiv.

Genotyping Structural Variations using Long Read Data

Dominique Lavenier, Lolita Lecompte, Claire Lemaitre, 2019 .

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

Rayan Chikhi, Pierre Peterlongo, R. Chikhi, 2012, BMC Bioinformatics.

StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs

Mathieu Almeida, N. Pons, P. Peterlongo, 2021, bioRxiv.

Theme: Computational Biology and Bioinformatics Computational Sciences for Biology, Medicine and the Environment

Marie-France Sagot, Rayan Chikhi, Pierre Peterlongo, 2012 .

Critical Assessment of Metagenome Interpretation: the second round of challenges

K. Reinert, E. Eskin, F. Beghini, 2021, Nature Methods.

DiscoSnp++: de novo detection of small variants from raw unassembled read set(s)

Pierre Peterlongo, Claire Lemaitre, Erwan Drezen, 2017, bioRxiv.

Compareads: comparing huge metagenomic experiments

Dominique Lavenier, Rayan Chikhi, Pierre Peterlongo, 2012, BMC Bioinformatics.

Commet: Comparing and combining multiple metagenomic datasets

Dominique Lavenier, Guillaume Collet, Pierre Peterlongo, 2014, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

fimpera: drastic improvement of Approximate Membership Query data-structures with counts

P. Peterlongo, Lucas Robidou, 2023, bioRxiv.

GATB: Genome Assembly & Analysis Tool Box

Dominique Lavenier, Rayan Chikhi, Guillaume Rizk, 2014, Bioinform..

ELECTOR: evaluator for long reads correction methods

Arnaud Lefebvre, Pierre Peterlongo, Lolita Lecompte, 2019, bioRxiv.

Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii

Y. Le Loir, M. Mariadassou, H. Falentin, 2015, BMC Genomics.

Dominique Lavenier, Julien Jacques, Gregory Kucherov, 2007, PPAM.

Toward perfect reads

Pierre Peterlongo, Antoine Limasset, Jean-François Flot, 2017, Bioinform..

Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs

Pierre Peterlongo, Antoine Limasset, Jean-François Flot, 2017, bioRxiv.

c-GAMMA: Comparative Genome Analysis of Molecular Markers

Dominique Lavenier, Pierre Peterlongo, Jacques Nicolas, 2009, PRIB.

Read Mapping on de Bruijn graph pdf

Pierre Peterlongo, Antoine Limasset, P. Peterlongo, 2015, ArXiv.

Read mapping on de Bruijn graphs

Pierre Peterlongo, Antoine Limasset, Eric Rivals, 2015, BMC Bioinformatics.

Read mapping on de Bruijn graphs

Eric Rivals, P. Peterlongo, Bastien Cazaux, 2015, BMC Bioinformatics.

Rime: Repeat identification

Marie-France Sagot, Nadia Pisanti, Pierre Peterlongo, 2014, Discret. Appl. Math..

Finding Long and Multiple Repeats with Edit Distance

Marie-France Sagot, Nadia Pisanti, Pierre Peterlongo, 2011, Stringology.

Lossless filter for multiple repetitions with Hamming distance

Alair Pereira do Lago, Frédéric Boyer, Marie-France Sagot, 2008, J. Discrete Algorithms.

Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array

Frédéric Boyer, Marie-France Sagot, Nadia Pisanti, 2005, SPIRE.

ELECTOR: evaluator for long reads correction methods

Pierre Peterlongo, Lolita Lecompte, Camille Marchet, 2019, bioRxiv.

New Results - NGS methodology

Guillaume Rizk, Pierre Peterlongo, Dominique Lavenier, 2014 .

New Results - Parallelism and optimization

Dominique Lavenier, Guillaume Collet, Stéphane Rubini, 2006 .

Approximate Hashing for Bioinformatics

Shmuel Tomi Klein, Dana Shapira, Pierre Peterlongo, 2021, Data Compression Conference.

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

Pierre Peterlongo, Antoine Limasset, Jean-François Flot, 2019, Bioinformatics.

Proceedings of the 2004 Prague Stringology Conference (PSC'04)

James A. M. McHugh, Wojciech Rytter, Costas S. Iliopoulos, 2004 .

From genomics to metagenomics: benchmark of variation graphs

Pierre Peterlongo, Nicolas Pons, Magali Berland, 2019 .

findere: fast and precise approximate membership query

Pierre Peterlongo, Lucas Robidou, P. Peterlongo, 2021, bioRxiv.

Proceedings of the 1st International Conference on Language and Automata Theory and Applications (LATA'07)

Costas S. Iliopoulos, Max Crochemore, Pierre Peterlongo, 2007 .

New Software and Platforms - Next Generation Sequencing

Dominique Lavenier, Guillaume Rizk, Pierre Peterlongo, 2014 .

New Results - Data representation

Pierre Peterlongo, Antoine Limasset, P. Peterlongo, 2016 .

New Results - Optimized Algorithms on Parallel Specialized Architectures

Dominique Lavenier, Julien Jacques, Guillaume Rizk, 2008 .

New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data

Vincent Miele, Rayan Chikhi, Pierre Peterlongo, 2013 .

In-Place Update of Suffix Array while Recoding Words

Pierre Peterlongo, Matthias Gallé, François Coste, 2008, Int. J. Found. Comput. Sci..

The K-mer File Format: a standardized and compact disk representation of sets of k-mers

R. Chikhi, P. Peterlongo, S. Deorowicz, 2022, Bioinform..

Cytosine methylation of mature microRNAs inhibits their functions and is associated with poor prognosis in glioblastoma multiforme

J. Mosser, M. Aubry, P. Peterlongo, 2020, Molecular Cancer.

k mdiff, large-scale and user-friendly differential k-mer analyses

R. Chikhi, P. Peterlongo, T. Lemane, 2022, Bioinform..

Reference-free detection of isolated SNPs

Rayan Chikhi, Guillaume Rizk, Pierre Peterlongo, 2014, Nucleic acids research.

fimpera: drastic improvement of Approximate Membership Query data-structures with counts

P. Peterlongo, Lucas Robidou, 2023, bioRxiv.

kmindex and ORA: indexing and real-time user-friendly queries in terabytes-sized complex genomic datasets

R. Chikhi, P. Peterlongo, M. Lescot, 2023, bioRxiv.

findere: fast and precise approximate membership query

P. Peterlongo, Lucas Robidou, 2021, bioRxiv.

Finding all maximal perfect haplotype blocks in linear time

Jens Stoye, Pierre Peterlongo, Jarno Alanko, 2019, Algorithms for Molecular Biology.

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

Pierre Peterlongo, Liviu Ciortuz, Claire Lemaitre, 2014, AlCoB.

SVJedi : Structural variation genotyping using long reads

D. Lavenier, C. Lemaitre, P. Peterlongo, 2019 .

Identifying SNPs without a Reference Genome by Comparing Raw Reads

Marie-France Sagot, Nadia Pisanti, Pierre Peterlongo, 2010, SPIRE.

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

R. Chikhi, G. Sacomoto, M. Sagot, 2012, BMC Bioinformatics.

A resource-frugal probabilistic dictionary and applications in bioinformatics

Pierre Peterlongo, Lolita Lecompte, Camille Marchet, 2017, Discret. Appl. Math..

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

P. Peterlongo, Jean‐François Flot, A. Limasset, 2017, Bioinform..

Genomic evidence for global ocean plankton biogeography shaped 1 by large-scale current systems 2

S. Sunagawa, J. Poulain, O. Jaillon, 2019 .

Optimal neighborhood indexing for protein similarity search

Dominique Lavenier, Gregory Kucherov, Pierre Peterlongo, 2008, BMC Bioinformatics.

Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics

T. Lecroq, G. Fertin, R. Chikhi, 2021 .

Toward perfect reads

P. Peterlongo, Jean‐François Flot, A. Limasset, 2017, Bioinform..

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

Dongwan D. Kang, Philip D. Blood, Daniel A. Cuevas, 2017, bioRxiv.

A first approach to finding common motifs with gaps

James A. M. McHugh, Wojciech Rytter, Costas S. Iliopoulos, 2005, Int. J. Found. Comput. Sci..

An optimized filter for finding multiple repeats in DNA sequences

Nadia Pisanti, Pierre Peterlongo, Maria Federico, 2010, ACS/IEEE International Conference on Computer Systems and Applications - AICCSA 2010.

Clustering de Novo by Gene of Long Reads from Transcriptomics Data

P. Peterlongo, J. Aury, C. Cruaud, 2017, bioRxiv.

Linking Allele-Specific Expression And Natural 1 Selection In Wild Populations 2

P. Wincker, P. Peterlongo, E. Petit, 2019 .