Vincent Lacroix

Publications

Poster de conférence (1)

Models and Algorithms for Managing Repeats in the De Novo Assembly of Transcriptomes Models and Algorithms for Managing Repeats in the De Novo Assembly of Transcriptomes Sasha Darmon,Arnaud Mary,Vincent Lacroix JOBIM 2025, Jul 2025, Talence (Université de Bordeaux 1), France. 2025 Poster de conférence hal-05214723v1

Pré-publication, Document de travail (3)

Metabolic resistance of the tiger mosquito to pyrethroid insecticides in La Réunion Island likely results from local adaptation Tiphaine Bacot,Jean-Marc Bonneville,Vincent Lacroix,Pascal Oberbach,Thierry Gaudeet al. 2025 Pré-publication, Document de travail hal-05379188v1
Identification and quantification of transposable element transcripts using Long-Read RNA-seq in &lt;i&gt;Drosophila&lt;/i&gt; germline tissues Rita Rebollo,Pierre Gerenton,Eric Cumunel,Arnaud Mary,François Sabotet al. 2024 Pré-publication, Document de travail hal-04791876v1
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 Lambertet al. 2017 Pré-publication, Document de travail (preprint/prepublication) hal-01643169v1

Article dans une revue (35)

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 Sabotet al. Peer Community Journal, 2024, 4 (e89), ⟨10.24072/pcjournal.457⟩ Article dans une revue hal-04285238v1
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 Putouxet al. Nucleic Acids Research, 2022, ⟨10.1093/nar/gkac1182⟩ Article dans une revue hal-03913654v1
Influenza virus infection induces widespread alterations of host cell splicing Usama Ashraf,Clara Benoit-Pilven,Vincent Navratil,Cécile Ligneau,Guillaume Fournieret al. NAR Genomics and Bioinformatics, 2020, 2 (4), ⟨10.1093/nargab/lqaa095⟩ Article dans une revue hal-03021806v1
Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene Clara Benoit-Pilven,Alicia Besson,Audrey Putoux,Claire Benetollo,Clément Saccaroet al. PLoS ONE, 2020, 15 (7), pp.e0235655. ⟨10.1371/journal.pone.0235655⟩ Article dans une revue inserm-02915106v1
Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing Usama Ashraf,Clara Benoit-Pilven,Vincent Lacroix,Vincent Navratil,Nadia Naffakh Trends in Microbiology, 2019, 27 (3), pp.268-281. ⟨10.1016/j.tim.2018.11.004⟩ Article dans une revue hal-01964983v1
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-Fournieret al. RNA, 2019, pp.1-21. ⟨10.1261/rna.071423.119⟩ Article dans une revue hal-02305628v1
Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules Camille Sessegolo,Corinne Cruaud,Corinne da Silva,Audric Cologne,Marion Dubarryet al. Scientific Reports, 2019, 9 (1), pp.14908. ⟨10.1038/s41598-019-51470-9⟩ Article dans une revue hal-02335574v1
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 Lambertet al. Scientific Reports, 2018, 8 (1), ⟨10.1038/s41598-018-21770-7⟩ Article dans une revue hal-01924204v1
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 Belkumet al. PLoS Genetics, 2018, 14 (11), pp.1-28. ⟨10.1371/journal.pgen.1007758⟩ Article dans une revue hal-01920359v1
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 Marchetet al. Algorithms for Molecular Biology, 2017, 12 (1), pp.2. ⟨10.1186/s13015-017-0091-2⟩ Article dans une revue hal-01474524v1
Identification of misexpressed genetic elements in hybrids between Drosophila-related species Hélène Lopez-Maestre,Elias Alberto Gutierrez Carnelossi,Vincent Lacroix,Nelly Burlet,Bruno Mugatet al. Scientific Reports, 2017, 7, pp.40618. ⟨10.1038/srep40618⟩ Article dans une revue hal-01524879v2
Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy Fernande Freyermuth,Frédérique Rau,Yosuke Kokunai,Thomas Linke,Chantal Sellieret al. Nature Communications, 2016, 7, pp.11067. ⟨10.1038/ncomms11067⟩ Article dans une revue hal-01301863v1
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 Rivalset al. GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩ Article dans une revue hal-01280238v1
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 Bastienet al. Nucleic Acids Research, 2016, ⟨10.1093/nar/gkw655⟩ Article dans une revue hal-01352586v1
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, 2015, pp.10. ⟨10.1186/s13015-015-0046-4⟩ Article dans une revue hal-01170399v1
Reference-free detection of isolated SNPs Raluca Uricaru,Guillaume Rizk,Vincent Lacroix,Elsa Quillery,Olivier Plantardet al. Nucleic Acids Research, 2014, 43 (2), pp.e11. ⟨10.1093/nar/gku1187⟩ Article dans une revue hal-01083715v1
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. Birmeléet al. Bioinformatics, 2014, 30 (1), pp.61-70. ⟨10.1093/bioinformatics/btt597⟩ Article dans une revue hal-00922567v1
Short and long-term genome stability analysis of prokaryotic genomes Matteo Brilli,Pietro Liò,Vincent Lacroix,Marie-France Sagot BMC Genomics, 2013, 14 (1), pp.309. ⟨10.1186/1471-2164-14-309⟩ Article dans une revue hal-00834426v1
Evidence for transcript networks composed of chimeric RNAs in human cells Sarah Djebali,Julien Lagarde,Philipp Kapranov,Vincent Lacroix,Christelle Borelet al. PLoS ONE, 2012, 7 (1), Non paginé. ⟨10.1371/journal.pone.0028213⟩ Article dans une revue hal-01216248v2
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets Vicente Acuña,Etienne Birmelé,Ludovic Cottret,Pierluigi Crescenzi,Fabien Jourdanet al. Theoretical Computer Science, 2012, 457, pp.1--9. ⟨10.1016/j.tcs.2012.07.023⟩ Article dans une revue istex hal-00764025v1
Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells Sarah Djebali,Julien Lagarde,Philipp Kapranov,Vincent Lacroix,Christelle Borelet al. PLoS ONE, 2012, 7, pp.1-22 Article dans une revue hal-00698428v1
Exploration of the core metabolism of symbiotic bacteria Cecilia Coimbra Klein,Ludovic Cottret,Janice Kielbassa,Hubert Charles,Christian Gautieret al. BMC Genomics, 2012, 13 (1), pp.438. ⟨10.1186/1471-2164-13-438⟩ Article dans une revue hal-00784396v1
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Milana Frenkel-Morgenstern,Vincent Lacroix,Iakes Ezkurdia,Yishai Levin,Alexandra Gabashviliet al. Genome Research, 2012, 22 (7), pp.1231-1242. ⟨10.1101/gr.130062.111⟩ Article dans une revue hal-00744761v1
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Milana Frenkel-Morgenstern,Alessandro Gorohovski,Vincent Lacroix,Mark Rogers,Kristina Ibanezet al. Nucleic Acids Research, 2012, 41 (D1), pp.D142-D151. ⟨10.1093/nar/gks1041⟩ Article dans une revue hal-00756097v1
Modelling and simulating generic RNA-Seq experiments with the flux simulator. Thasso Griebel,Benedikt Zacher,Paolo Ribeca,Emanuele Raineri,Vincent Lacroixet al. Nucleic Acids Research, 2012, 40 (20), pp.10073-10083. ⟨10.1093/nar/gks666⟩ Article dans une revue hal-00744755v1
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data Gustavo Sacomoto,Janice Kielbassa,Rayan Chikhi,Raluca Uricaru,Pavlos Antoniouet al. BMC Bioinformatics, 2012, 13 (Suppl 6), pp.S5. ⟨10.1186/1471-2105-13-S6-S5⟩ Article dans une revue hal-00784407v1
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny Amélie Véron,Claire Lemaitre,Christian Gautier,Vincent Lacroix,Marie-France Sagot BMC Genomics, 2011, 12 (1), pp.303. ⟨10.1186/1471-2164-12-303⟩ Article dans une revue hal-00784423v1
Assessing the exceptionality of coloured motifs in networks Sophie S. Schbath,Vincent Lacroix,Marie-France Sagot EURASIP Journal on Bioinformatics and Systems Biology, 2009, 2009, 9 p. on line. ⟨10.1155/2009/616234⟩ Article dans une revue hal-02656035v1
Identification de motifs dans les réseaux métaboliques Vincent Lacroix incollection, 2008, --, pp.D1-D5 Article dans une revue hal-00428083v1
An introduction to metabolic networks and their structural analysis. Vincent Lacroix,Ludovic Cottret,Patricia Thebault,Marie-France Sagot IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008, 5 (4), pp.594-617. ⟨10.1109/TCBB.2008.79⟩ Article dans une revue hal-00355497v1
Modes and Cuts in Metabolic Networks:Complexity and Algorithms Vicente Acuna,F. Chierichetti,Vincent Lacroix,A. Marchetti-Spaccamela,M.-F. Sagotet al. BioSystems, 2008, 95 - n°1, pp.51-60 Article dans une revue hal-00428239v1
Metabolic network visualization eliminating node redundance and preserving metabolic pathways Romain Bourqui,L. Cottret,Vincent Lacroix,D. Auber,P. Maryet al. BMC Biology, 2007, 1 - n°29, pp.1-19. ⟨10.1186/1752-0509-1-29⟩ Article dans une revue hal-00434765v1
Motif search in graphs: application to metabolic networks. Vincent Lacroix,C.G. Fernandes,M.-F. Sagot IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2006, 3 - n°4, pp.360-368 Article dans une revue hal-00427984v1
Metabolic network visualization using constraint planar graph drawing algorithm Romain Bourqui,D. Auber,Vincent Lacroix,F. Jourdan incollection, 2006, --, pp.489-496 Article dans une revue hal-00427907v1
Uncovering structure in biological networks J.J. Daudin,Vincent Lacroix,M. Mariadassou,V. Miele,Franck Picardet al. incollection, 2006, --, pp.471-483 Article dans une revue hal-00427936v1

HDR (1)

De novo analysis of splicing from RNA-seq data: models, algorithms and applications Vincent Lacroix Bioinformatics [q-bio.QM]. Université Claude Bernard Lyon 1, 2023 HDR tel-04662714v1

Communication dans un congrès (18)

Navigating in a Sea of Repeats in RNA-seq without Drowning Gustavo Sacomoto,Blerina Sinaimeri,Camille Marchet,Vincent Miele,Marie-France Sagotet al. WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics, Sep 2014, Wroclaw, Poland. pp.82-96, ⟨10.1007/978-3-662-44753-6_7⟩ Communication dans un congrès hal-01079947v1
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), Sep 2013, Nice, France Communication dans un congrès hal-00842982v1
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. Parsonset al. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2013, Toulouse, France Communication dans un congrès hal-02069363v1
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, Oct 2013, Lyon, France. pp.2012214 Communication dans un congrès cea-00876659v1
Telling Stories Fast Michele Borassi,Pierluigi Crescenzi,Vincent Lacroix,Andrea Marino,Marie-France Sagotet al. 12th International Symposium Experimental Algorithms (SEA), Jun 2013, Rome, Italy. pp.200-211 Communication dans un congrès hal-00835201v1
Efficient Bubble Enumeration in Directed Graphs Etienne E. Birmelé,Pierluigi Crescenzi,Rui Ferreira,Roberto Grossi,Vincent Lacroixet al. String Processing and Information Retrieval (SPIRE), Oct 2012, Cartagena, Colombia. pp.118-129, ⟨10.1007/978-3-642-34109-0_13⟩ Communication dans un congrès hal-00738927v1
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 Lacroixet al. Proceedings of the Second international Symposium on Combinatorial Optimization (ISCO), Apr 2012, Athens, Greece. pp.165--177, ⟨10.1007/978-3-642-32147-4_16⟩ Communication dans un congrès hal-00763453v1
RNA-seq without a reference genome: a comparison of the mapping and the assembly approaches M.-C. Carpentier,J. Charif,Vincent Lacroix,Marie-France Sagot,Fabrice Vavre JOBIM, 2011, Paris, France Communication dans un congrès hal-00748612v1
NGS without a reference genome, comparison and visualisation of non assembled data Vincent Lacroix Statistical Methods for Post-Genomic Data (SMPGD), 2011, Paris, France Communication dans un congrès hal-00748787v1
Absence of a core metabolic network common to symbiotic bacteria Cecilia Coimbra Klein,Ludovic Cottret,Hubert Charles,Christian Gautier,Ana Tereza Ribeiro de Vasconceloset al. 6. Meeting GDRE-RA Comparative genomics, Nov 2011, Lyon, France. 33 diapositives Communication dans un congrès hal-02806316v1
Metabolic network comparison of bacteria in the context of symbiosis Cecilia C. Klein,Ludovic Cottret,Hubert Charles,Christian Gautier,Ana T Vasconceloset al. Otto Warburg International Summer School and Research Symposium on Evolutionary Genomics, 2011, Berlin, Germany Communication dans un congrès hal-00748784v1
Telling Stories Vicente Acuña,Etienne Birmele,Ludovic Cottret,Pierluigi Crescenzi,Fabien Jourdanet al. ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA), 2011, Zurich, Switzerland. ⟨10.1016/j.tcs.2012.07.023⟩ Communication dans un congrès istex hal-00748788v1
Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms Paulo Vieira Milreu,Vicente Acuña,Etienne E. Birmelé,Pierluigi Crescenzi,Alberto Marchetti-Spaccamelaet al. Workshop on Algorithms in Bioinformatics (WABI), Sep 2010, Liverpool, United Kingdom. pp.226-237, ⟨10.1007/978-3-642-15294-8_19⟩ Communication dans un congrès hal-00751339v1
Identifying SNPs without a reference genome by comparing raw reads Pierre Peterlongo,Nicolas Schnel,Nadia Pisanti,Marie-France Sagot,Vincent Lacroix String Processing and Information Retrieval, Oct 2010, Los Cabos, Mexico. pp.147-158, ⟨10.1007/978-3-642-16321-0_14⟩ Communication dans un congrès inria-00514887v1
Exact Transcriptome Reconstruction from Short Sequence Reads Vincent Lacroix,M. Sammeth,R. Guigo,A. Bergeron International Workshop on Algorithms in Bioinformatics (WABI), Sep 2008, Karlsruhe, Germany. pp.50-63, ⟨10.1007/978-3-540-87361-7_5⟩ Communication dans un congrès istex hal-00428220v1
Metabolic network visualization using constraint planar graph drawing Algorithm Romain Bourqui,David Auber,Vincent Lacroix,Fabien Jourdan IV 06: Proceedings of the 10 International Conference on Information Visualisation (IV06), 2006, United States. pp.489 - 496 Communication dans un congrès hal-00306676v1
Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques Romain Bourqui,David Auber,Vincent Lacroix,Fabien Jourdan Quatrième édition du congrés francophone de doctorants en STIC, MajecSTIC, 2006, France. pp.électronique Communication dans un congrès hal-00306673v1
Reaction motifs in metabolic networks Vincent Lacroix,C.G. Fernandes,M.-F. Sagot International Workshop on Algorithms in Bioinformatics (WABI), Oct 2005, Mallorca, Spain. pp.178-191, ⟨10.1007/11557067_15⟩ Communication dans un congrès istex hal-00427769v1

Chapitre d'ouvrage (1)

Analysis of RNA Transcripts by High-Throughput RNA Sequencing Paolo Ribeca,Vincent Lacroix,Michael Sammeth,Roderic Guigó Stefan Stamm, Christopher W. J. Smith, Reinhard Lührmann. Alternative pre-mRNA Splicing: Theory and Protocols, Wiley-VCH Verlag GmbH & Co. KGaA, 2012, 9783527636778. ⟨10.1002/9783527636778.ch50⟩ Chapitre d'ouvrage hal-00850866v1

Rapport (2)

kisSplice, détection d'évènements d'épissages alternatifs dans les données RNA-seq Gustavo Akio Tominaga Sacomoto,J. Kielbassa,Pavlos Antoniou,Rayan Chikhi,Raluca Uricaruet al. [Research Report] RR-7852, INRIA. 2011, pp.12 Rapport (rapport de recherche) hal-00654249v2
Reaction Motifs in Metabolic Networks Vincent Lacroix,Cristina Gomes Fernandes,Marie-France Sagot RR-5563, INRIA. 2005, pp.14 Rapport inria-00070443v1

Ouvrages (1)

Identification de motifs dans les réseaux métaboliques : définitions algorithmes et application au métabolisme d’Escherichia coli Vincent Lacroix Edilivre. 2008, 978-2-35607-642-7 Ouvrages hal-00434732v1

Thèse (1)

Identification de motifs dans les réseaux métaboliques Vincent Lacroix Autre [cs.OH]. Université Claude Bernard - Lyon I, 2007. Français. ⟨NNT : ⟩ Thèse tel-00195401v1