Lacroix Vincent

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Rita Rebollo, Pierre Gerenton, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet...

DOI: 10.1101/2023.05.27.542554

2024

Preprint

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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Rita Rebollo, Pierre Gerenton, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet...

Peer Community Journal . 4 ( e89 )

DOI: 10.24072/pcjournal.457

2024

Journal article

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De novo analysis of splicing from RNA-seq data: models, algorithms and applications

Vincent Lacroix

2023

HDR

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Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex

Fatimat Almentina Ramos Shidi, Audric Cologne, Marion Delous, Alicia Besson, Audrey Putoux, Anne-Louise Leutenegger...

Nucleic Acids Research .

DOI: 10.1093/nar/gkac1182

2022

Journal article

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Influenza virus infection induces widespread alterations of host cell splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Navratil, Cécile Ligneau, Guillaume Fournier, Sandie Munier...

NAR Genomics and Bioinformatics . 2 ( 4 )

DOI: 10.1093/nargab/lqaa095

2020

Journal article

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Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene

Clara Benoit-Pilven, Alicia Besson, Audrey Putoux, Claire Benetollo, Clément Saccaro, Justine Guguin...

PLoS ONE . 15 ( 7 ) : e0235655

DOI: 10.1371/journal.pone.0235655

2020

Journal article

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New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients

Audric Cologne, Clara Benoit-Pilven, Alicia Besson, Audrey Putoux, Amandine Campan-Fournier, Michael B Bober...

RNA . : 1-21

DOI: 10.1261/rna.071423.119

2019

Journal article

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Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Lacroix, Vincent Navratil, Nadia Naffakh

Trends in Microbiology . 27 ( 3 ) : 268-281

DOI: 10.1016/j.tim.2018.11.004

2019

Journal article

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Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Camille Sessegolo, Corinne Cruaud, Corinne da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien...

Scientific Reports . 9 ( 1 ) : 14908

DOI: 10.1038/s41598-019-51470-9

2019

Journal article

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Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto...

Scientific Reports . 8 ( 1 )

DOI: 10.1038/s41598-018-21770-7

2018

Journal article

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A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix...

PLoS Genetics . 14 ( 11 ) : 1-28

DOI: 10.1371/journal.pgen.1007758

2018

Journal article

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Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto...

DOI: 10.1101/074807

2017

Preprint

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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele...

Algorithms for Molecular Biology . 12 ( 1 ) : 2

DOI: 10.1186/s13015-017-0091-2

2017

Journal article

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Identification of misexpressed genetic elements in hybrids between Drosophila-related species

Hélène Lopez-Maestre, Elias Alberto Gutierrez Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron...

Scientific Reports . 7 : 40618

DOI: 10.1038/srep40618

2017

Journal article

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

Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, Claire Lemaitre...

GigaScience . 5 ( 1 )

DOI: 10.1186/s13742-015-0105-2

2016

Journal article

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Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy

Fernande Freyermuth, Frédérique Rau, Yosuke Kokunai, Thomas Linke, Chantal Sellier, Masayuki Nakamori...

Nature Communications . 7 : 11067

DOI: 10.1038/ncomms11067

2016

Journal article

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny...

Nucleic Acids Research .

DOI: 10.1093/nar/gkw655

2016

Journal article

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A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

Gustavo Sacomoto, Vincent Lacroix, Marie‑france Sagot

Algorithms for Molecular Biology . : 10

DOI: 10.1186/s13015-015-0046-4

2015

Journal article

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Reference-free detection of isolated SNPs

Raluca Uricaru, Guillaume Rizk, Vincent Lacroix, Elsa Quillery, Olivier Plantard, Rayan Chikhi...

Nucleic Acids Research . 43 ( 2 ) : e11

DOI: 10.1093/nar/gku1187

2014

Journal article

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Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne E. Birmelé, Michele Borassi...

Bioinformatics . 30 ( 1 ) : 61-70

DOI: 10.1093/bioinformatics/btt597

2014

Journal article

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Navigating in a Sea of Repeats in RNA-seq without Drowning

Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix

WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96

DOI: 10.1007/978-3-662-44753-6_7

2014

Conference paper

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A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

Gustavo Akio Tominaga Sacomoto, Vincent Lacroix, Marie-France Sagot

Workshop on Algorithms in Bioinformatics (WABI) .

2013

Conference paper

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Telling Stories Fast

Michele Borassi, Pierluigi Crescenzi, Vincent Lacroix, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu

12th International Symposium Experimental Algorithms (SEA) . 7933 : 200-211

2013

Conference paper

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Procédé de fabrication de Gaz Naturel de Synthèse par couplage d'une méthanation avec une électrolyse de vapeur d'eau à haute température

Myriam de Saint Jean, Vincent Lacroix, Pierre Baurens, Chakib Bouallou

XIVeme congrès SFGP . 104 : 2012214

2013

Conference paper

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

Alice Julien-Laferriere, Gustavo Sacomoto, Rayan Chikhi, Erwan Scaon, David P. Parsons, Marie-France Sagot...

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) .

2013

Conference paper

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Short and long-term genome stability analysis of prokaryotic genomes

Matteo Brilli, Pietro Liò, Vincent Lacroix, Marie-France Sagot

BMC Genomics . 14 ( 1 ) : 309

DOI: 10.1186/1471-2164-14-309

2013

Journal article

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Modelling and simulating generic RNA-Seq experiments with the flux simulator.

Thasso Griebel, Benedikt Zacher, Paolo Ribeca, Emanuele Raineri, Vincent Lacroix, Roderic Guigó...

Nucleic Acids Research . 40 ( 20 ) : 10073-10083

DOI: 10.1093/nar/gks666

2012

Journal article

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Efficient Bubble Enumeration in Directed Graphs

Etienne E. Birmelé, Pierluigi Crescenzi, Rui Ferreira, Roberto Grossi, Vincent Lacroix, Andrea Marino...

String Processing and Information Retrieval (SPIRE) . 7608 : 118-129

DOI: 10.1007/978-3-642-34109-0_13

2012

Conference paper

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Minimum ratio cover of matrix columns by extreme rays of its induced cone

Alexandre da Silva Freire, Vicente Acuña, Pierluigi Crescenzi, Carlos Eduardo Ferreira, Vincent Lacroix, Paulo Vieira Milreu...

Proceedings of the Second international Symposium on Combinatorial Optimization (ISCO) . 7422 : 165--177

DOI: 10.1007/978-3-642-32147-4_16

2012

Conference paper

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

Gustavo Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot...

BMC Bioinformatics . 13 ( Suppl 6 ) : S5

DOI: 10.1186/1471-2105-13-S6-S5

2012

Journal article

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Publications

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

De novo analysis of splicing from RNA-seq data: models, algorithms and applications

Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex

Influenza virus infection induces widespread alterations of host cell splicing

Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene

New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients

Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

Identification of misexpressed genetic elements in hybrids between Drosophila-related species

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

Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

Reference-free detection of isolated SNPs

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

Navigating in a Sea of Repeats in RNA-seq without Drowning

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

Telling Stories Fast

Procédé de fabrication de Gaz Naturel de Synthèse par couplage d'une méthanation avec une électrolyse de vapeur d'eau à haute température

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

Short and long-term genome stability analysis of prokaryotic genomes

Modelling and simulating generic RNA-Seq experiments with the flux simulator.

Efficient Bubble Enumeration in Directed Graphs

Minimum ratio cover of matrix columns by extreme rays of its induced cone

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