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UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive" UCB Lyon 1 - Bât. Grégor Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex
- +Research Interests -Research Interests
I have broad interests in computational biology. I have been working in two main areas so far: the structural analysis of metabolic networks and the analysis of alternative splicing through the use of RNA-seq data.
- +Projects -Projects
Current Projects
Colib’Read: Models and Algorithms for the analysis of NGS data using De Bruijn Graphs
Exomic: Alternative Splicing and Cancer
ABS4NGS: Analyis of NGS data in Human
Past Projects
Alcovna : Algorithms for NGS of non-model species
NEMO : Statistics of motif-based analysis of biological networks
MIRI : Mathematical investigation of symbiosis
- +Software -Software
Next Generation Sequencing:
KisSplice: De novo calling of alternative splicing events from RNA-seq data (developped mainly by Gustavo Sacomoto, Pierre Peterlongo, Rayan Chikhi)
KisSNP: Identification of SNPs without a reference genome (developped by Pierre Peterlongo)
GEM : Mapping and Split-mapping of short reads against a reference genome, mappability of a genome (developped by Paolo Ribeca)
Networks:
MOTUS: Coloured motif search and inference in vertex coloured graphs
- +Training -Training
2001-2004: I received a mixed training of both biology and computer science at the INSA de Lyon, Biosciences department
2004-2007: PhD in the Baobab team under the supervision of Marie-France Sagot. This team belongs to the LBBE (CNRS) and the Bamboo Project (INRIA).
Subject: Motif identification in metabolic networks.
[manuscript] (18Mb, french)
[slides of the defense]2008-2009: Post-doc in the group of Roderic Guigo, at the Centre de Regulacio Genomica, Barcelona
Subject: The possibilities of Next-Generation Sequencing (NGS) for the analysis of splicing
+Publications -Publications
article :
Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A (2013)
ChiTaRS: a database of human mouse and fruit fly chimeric transcripts and RNA-sequencing data, Nucleic Acids Research, vol. 41 pp.D142-51, DOI.
Acuna V, Birmelé E, Cottret L, Crescenzi P, Jourdan F, Lacroix V, Marchetti-Spaccamela A, Marino A, Vieira Milreu P, Sagot M-F, Stougie L (2012)
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets, Theoretical Computer Science, vol. 457 pp.1-9.
Coimbra Klein C, Cottret L, Keilbassa J, Charles H, Gautier C, Ribeiro de Vasconcelos AT, Lacroix V, Sagot MF (2012)
Exploration of the core metabolism of symbiotic bacteria, BMC Genomics, vol. 13 pp.438-438, DOI.
Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge J M, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray R R, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress M L, Gelpi J L, Orozco M, Valencia A, van Berkum N L, Lajoie B R, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis S E, Guigo R, Gingeras T R (2012)
Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells, PLoS one, vol. 7 pp.1-22.
Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, del Pozo A, Tress M, Johnson R, Guigo R, Valencia A (2012)
Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts, Genome Res, vol. pp.1-13.
Griebel T, Zacher B, Ribera P, Raineri E, Lacroix V, Guigo R, Sammeth M (2012)
Modelling and simulating generic RNA-Seq experiments with the flux simulator, Nucleic Acids Research, vol. pp.1-11.
Sacomoto G, Kielbassa J, Chikhi R, Uricaru R, Antoniou P, Sagot M-F, Peterlongo P, Lacroix V (2012)
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data, BMC Bioinformatics, vol. 13 pp.1-12.
Veron AS, Lemaitre C, Gautier C, Lacroix V, Sagot M-F (2011)
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny, BMC Genomics, vol. 12(1) pp.1-38.
Schbath S, Lacroix V, Sagot M-F (2009)
Assessing the exceptionality of coloured motifs in networks, Eurasip Journal on Bioinformatics and Systems Biology, vol. 2009 pp.1-9.
Acuña V, Chierichetti F, Lacroix V, Marchetti-Spaccamela A, Sagot M-F, Stougie L (2008)
Modes and Cuts in Metabolic Networks:Complexity and Algorithms, BioSystems, vol. 95 - n°1 pp.51-60.
Lacroix V, Cottret L, Thébault P, Sagot M-F (2008)
An Introduction to Metabolic Networks and Their Structural Analysis, IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 5 - n°4 pp.1-24, DOI.
Bourqui R, Cottret L, Lacroix V, Auber D, Mary P, Sagot M-F, Jourdan F (2007)
Metabolic network visualization eliminating node redundance and preserving metabolic pathways, BMC Systems Biology, vol. 1 - n°29 pp.1-19.
Lacroix V, Fernandes CG, Sagot M-F (2006)
Motif search in graphs: application to metabolic networks., IEEE-ACM Transactions on Computational Biology and Bioinformatics, vol. 3 - n°4 pp.360-368.
book :
Lacroix V (2008)
Identification de motifs dans les réseaux métaboliques, Edilivre, 2008.
inbook :
Ribeca P, Lacroix V, Sammeth M, Guigo R (2012)
Analysis of RNA Transcripts by High-Throughput RNA Sequencing, , vol. pp.544-554, DOI.
inproceedings :
Bourqui R, Auber D, Lacroix V, Jourdan F (2011)
Metabolic network visualization using constraint planar graph drawing algorithm, 10th conf. on Information Visualization, IEEE Computer Society pp.489-496.
Peterlongo P, Schnel N, Pisanti N, Sagot M-F, Lacroix V (2009)
Identifying SNPs without a Reference Genome by Comparing Raw Reads, SPIRE, Springer, Lecture Notes in Computer Science, vol. 6393 pp.147-158.
Lacroix V, Fernandes CG, Sagot M-F (2008)
Reaction motifs in metabolic networks, Proceedings of WABI `05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3692 pp.178-191.
Lacroix V, Sammeth M, Guigo R, Bergeron A (2006)
Exact Transcriptome Reconstruction from Short Sequence Reads, Proceeding of WABI`08, Springer Verlag, Lecture Notes in Bioinformatics, vol. 5251 pp.50-63.
Freire AS, Acuna V, Crescenzi P, Ferreira CE, Lacroix V, Milreu PV, Moreno E, Sagot M-F (2003)
Minimum ratio cover of matrix colums by extreme rays of its induced cone, International Symposium on Combinatorial Optimization, pp.1-12.
Vieira-Milreu P, Acuña V, Birmelé E, Crescenzi P, Marchetti-Spaccamela A, Sagot M-F, Stougie L, Lacroix V (2000)
Enumerating Chemical Organisations in consistent metabolic networks: complexity and algorithms, WABI` 2010, Springer-Verlag Berlin, Lecture notes in computer science, vol. 6293 pp.226-237.
misc :
Sacomoto G, Kielbassa J, Chikhi R, Uricaru R, Antoniou P, Sagot M-F, Peterlongo P, Lacroix V (2012)
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data, , vol. 13 Suppl 6 pp.S5-S5.
phdthesis :
Lacroix V (2007)
Identification de motifs dans les réseaux métaboliques Définitions algorithmes et application au métabolisme d’Escherichia coli .
