Vincent Lacroix

Documents

Publications

	Navigating in a Sea of Repeats in RNA-seq without Drowning Gustavo Sacomoto , Blerina Sinaimeri , Camille Marchet , Vincent Miele , Marie-France Sagot WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics, Sep 2014, Wroclaw, Poland. pp.82-96, ⟨10.1007/978-3-662-44753-6_7⟩ Conference papers hal-01079947v1
	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 Conference papers cea-00876659v1
	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 Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2013, Toulouse, France Conference papers hal-02069363v1
	Telling Stories Fast Michele Borassi , Pierluigi Crescenzi , Vincent Lacroix , Andrea Marino , Marie-France Sagot 12th International Symposium Experimental Algorithms (SEA), Jun 2013, Rome, Italy. pp.200-211 Conference papers hal-00835201v1
	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 Conference papers hal-00842982v1
	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 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⟩ Conference papers hal-00763453v1
	Efficient Bubble Enumeration in Directed Graphs Etienne E. Birmelé , Pierluigi Crescenzi , Rui Ferreira , Roberto Grossi , Vincent Lacroix String Processing and Information Retrieval (SPIRE), Oct 2012, Cartagena, Colombia. pp.118-129, ⟨10.1007/978-3-642-34109-0_13⟩ Conference papers hal-00738927v1
	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 Conference papers hal-00748612v1
	Metabolic network comparison of bacteria in the context of symbiosis Cecilia C. Klein , Ludovic Cottret , Hubert Charles , Christian Gautier , Ana T Vasconcelos Otto Warburg International Summer School and Research Symposium on Evolutionary Genomics, 2011, Berlin, Germany Conference papers hal-00748784v1
	Telling Stories Vicente Acuña , Etienne Birmele , Ludovic Cottret , Pierluigi Crescenzi , Fabien Jourdan ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA), 2011, Zurich, Switzerland. ⟨10.1016/j.tcs.2012.07.023⟩ Conference papers hal-00748788v1
	NGS without a reference genome, comparison and visualisation of non assembled data Vincent Lacroix Statistical Methods for Post-Genomic Data (SMPGD), 2011, Paris, France Conference papers 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 Vasconcelos 6. Meeting GDRE-RA Comparative genomics, Nov 2011, Lyon, France. 33 diapositives Conference papers hal-02806316v1
	Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms Paulo Vieira Milreu , Vicente Acuña , Etienne E. Birmelé , Pierluigi Crescenzi , Alberto Marchetti-Spaccamela Workshop on Algorithms in Bioinformatics (WABI), Sep 2010, Liverpool, United Kingdom. pp.226-237, ⟨10.1007/978-3-642-15294-8_19⟩ Conference papers 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⟩ Conference papers 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⟩ Conference papers 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 Conference papers 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 Conference papers 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⟩ Conference papers hal-00427769v1

	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 Nucleic Acids Research, 2022, ⟨10.1093/nar/gkac1182⟩ Journal articles hal-03913654v1
	Influenza virus infection induces widespread alterations of host cell splicing Usama Ashraf , Clara Benoit-Pilven , Vincent Navratil , Cécile Ligneau , Guillaume Fournier NAR Genomics and Bioinformatics, 2020, 2 (4), ⟨10.1093/nargab/lqaa095⟩ Journal articles hal-03021806v1
	Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene Clara Benoit-Pilven , Alicia Besson , Audrey Putoux , Claire Benetollo , Clément Saccaro PLoS ONE, 2020, 15 (7), pp.e0235655. ⟨10.1371/journal.pone.0235655⟩ Journal articles 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⟩ Journal articles hal-01964983v1
	Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules Camille Sessegolo , Corinne Cruaud , Corinne da Silva , Audric Cologne , Marion Dubarry Scientific Reports, 2019, 9 (1), pp.14908. ⟨10.1038/s41598-019-51470-9⟩ Journal articles hal-02335574v1
	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 RNA, 2019, pp.1-21. ⟨10.1261/rna.071423.119⟩ Journal articles hal-02305628v1
	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 PLoS Genetics, 2018, 14 (11), pp.1-28. ⟨10.1371/journal.pgen.1007758⟩ Journal articles hal-01920359v1
	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 Scientific Reports, 2018, 8 (1), ⟨10.1038/s41598-018-21770-7⟩ Journal articles hal-01924204v1
	Identification of misexpressed genetic elements in hybrids between Drosophila-related species Hélène Lopez-Maestre , Elias Alberto Gutierrez Carnelossi , Vincent Lacroix , Nelly Burlet , Bruno Mugat Scientific Reports, 2017, 7, pp.40618. ⟨10.1038/srep40618⟩ Journal articles hal-01524879v2
	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 Algorithms for Molecular Biology, 2017, 12 (1), pp.2. ⟨10.1186/s13015-017-0091-2⟩ Journal articles hal-01474524v1
	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 GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩ Journal articles 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 Bastien Nucleic Acids Research, 2016, ⟨10.1093/nar/gkw655⟩ Journal articles hal-01352586v1
	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 Nature Communications, 2016, 7, pp.11067. ⟨10.1038/ncomms11067⟩ Journal articles hal-01301863v1
	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⟩ Journal articles hal-01170399v1
	Reference-free detection of isolated SNPs Raluca Uricaru , Guillaume Rizk , Vincent Lacroix , Elsa Quillery , Olivier Plantard Nucleic Acids Research, 2014, 43 (2), pp.e11. ⟨10.1093/nar/gku1187⟩ Journal articles 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. Birmelé Bioinformatics, 2014, 30 (1), pp.61-70. ⟨10.1093/bioinformatics/btt597⟩ Journal articles 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⟩ Journal articles hal-00834426v1
	Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Milana Frenkel-Morgenstern , Vincent Lacroix , Iakes Ezkurdia , Yishai Levin , Alexandra Gabashvili Genome Research, 2012, 22 (7), pp.1231-1242. ⟨10.1101/gr.130062.111⟩ Journal articles hal-00744761v1
	Exploration of the core metabolism of symbiotic bacteria Cecilia Coimbra Klein , Ludovic Cottret , Janice Kielbassa , Hubert Charles , Christian Gautier BMC Genomics, 2012, 13 (1), pp.438. ⟨10.1186/1471-2164-13-438⟩ Journal articles hal-00784396v1
	Evidence for transcript networks composed of chimeric RNAs in human cells Sarah Djebali , Julien Lagarde , Philipp Kapranov , Vincent Lacroix , Christelle Borel PLoS ONE, 2012, 7 (1), Non paginé. ⟨10.1371/journal.pone.0028213⟩ Journal articles hal-01216248v2
	Modelling and simulating generic RNA-Seq experiments with the flux simulator. Thasso Griebel , Benedikt Zacher , Paolo Ribeca , Emanuele Raineri , Vincent Lacroix Nucleic Acids Research, 2012, 40 (20), pp.10073-10083. ⟨10.1093/nar/gks666⟩ Journal articles hal-00744755v1
	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 Ibanez Nucleic Acids Research, 2012, 41 (D1), pp.D142-D151. ⟨10.1093/nar/gks1041⟩ Journal articles hal-00756097v1
	KISSPLICE: de-novo calling alternative splicing events from RNA-seq data Gustavo Sacomoto , Janice Kielbassa , Rayan Chikhi , Raluca Uricaru , Pavlos Antoniou BMC Bioinformatics, 2012, 13 (Suppl 6), pp.S5. ⟨10.1186/1471-2105-13-S6-S5⟩ Journal articles hal-00784407v1
	Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets Vicente Acuña , Etienne Birmelé , Ludovic Cottret , Pierluigi Crescenzi , Fabien Jourdan Theoretical Computer Science, 2012, 457, pp.1--9. ⟨10.1016/j.tcs.2012.07.023⟩ Journal articles hal-00764025v1
	Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells Sarah Djebali , Julien Lagarde , Philipp Kapranov , Vincent Lacroix , Christelle Borel PLoS ONE, 2012, 7, pp.1-22 Journal articles hal-00698428v1
	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⟩ Journal articles 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⟩ Journal articles hal-02656035v1
	Identification de motifs dans les réseaux métaboliques Vincent Lacroix incollection, 2008, --, pp.D1-D5 Journal articles hal-00428083v1
	Modes and Cuts in Metabolic Networks:Complexity and Algorithms Vicente Acuna , F. Chierichetti , Vincent Lacroix , A. Marchetti-Spaccamela , M.-F. Sagot BioSystems, 2008, 95 - n°1, pp.51-60 Journal articles hal-00428239v1
	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⟩ Journal articles hal-00355497v1
	Metabolic network visualization eliminating node redundance and preserving metabolic pathways Romain Bourqui , L. Cottret , Vincent Lacroix , D. Auber , P. Mary BMC Biology, 2007, 1 - n°29, pp.1-19. ⟨10.1186/1752-0509-1-29⟩ Journal articles hal-00434765v1
	Metabolic network visualization using constraint planar graph drawing algorithm Romain Bourqui , D. Auber , Vincent Lacroix , F. Jourdan incollection, 2006, --, pp.489-496 Journal articles hal-00427907v1
	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 Journal articles hal-00427984v1
	Uncovering structure in biological networks J.J. Daudin , Vincent Lacroix , M. Mariadassou , V. Miele , Franck Picard incollection, 2006, --, pp.471-483 Journal articles hal-00427936v1

	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⟩ Book sections hal-00850866v1

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

	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 2017 Preprints, Working Papers, ... hal-01643169v1

	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 Books hal-00434732v1

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

	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 Habilitation à diriger des recherches tel-04662714v1

Vincent Lacroix

Publications

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

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

Telling Stories Fast

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

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

Efficient Bubble Enumeration in Directed Graphs

RNA-seq without a reference genome: a comparison of the mapping and the assembly approaches

Metabolic network comparison of bacteria in the context of symbiosis

Telling Stories

NGS without a reference genome, comparison and visualisation of non assembled data

Absence of a core metabolic network common to symbiotic bacteria

Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms

Identifying SNPs without a reference genome by comparing raw reads

Exact Transcriptome Reconstruction from Short Sequence Reads

Metabolic network visualization using constraint planar graph drawing Algorithm

Un Algorithme Contraint de Dessin de Graphe Planaire pour la Visualisation de Réseaux Métaboliques

Reaction motifs in metabolic networks

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

Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

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

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

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

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

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

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

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

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

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

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

Short and long-term genome stability analysis of prokaryotic genomes

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Exploration of the core metabolism of symbiotic bacteria

Evidence for transcript networks composed of chimeric RNAs in human cells

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

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

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

Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Assessing the exceptionality of coloured motifs in networks

Identification de motifs dans les réseaux métaboliques

Modes and Cuts in Metabolic Networks:Complexity and Algorithms

An introduction to metabolic networks and their structural analysis.

Metabolic network visualization eliminating node redundance and preserving metabolic pathways

Metabolic network visualization using constraint planar graph drawing algorithm

Motif search in graphs: application to metabolic networks.

Uncovering structure in biological networks

Analysis of RNA Transcripts by High-Throughput RNA Sequencing

kisSplice, détection d'évènements d'épissages alternatifs dans les données RNA-seq

Reaction Motifs in Metabolic Networks

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

Identification de motifs dans les réseaux métaboliques : définitions algorithmes et application au métabolisme d’Escherichia coli

Identification de motifs dans les réseaux métaboliques

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