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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
- +Initial Training -Initial Training
2001-2004 : I received a mixed training of both biology and
computer science at the INSA de Lyon, Biosciences department2004-2007 : 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
- +Projects -Projects
Current Projects :
ASTER : Algorithms and software for third generation RNA sequencing, funded by ANR 2016-2021, coordinator : Hélène Touzet
U4atac Brain : Role of minor splicing in embryonic development, funded by ANR 2018-2022, coordinator : Patrick EderyPast Projects :
Colib’Read : Méthodes d’extraction d’information biologique dans les données HTS non assemblées, funded by ANR 2013-2016, coordinator : Pierre Peterlongo
Exomic : Alternative Splicing and Cancer, funded by INSERM 2012-2015, coordinator : Didier Auboeuf
Alcovna : Algorithms for the analysis of variation from non-assembled data, funded by INRIA, 2009-2010, coordinator : Pierre PeterlongoABS4NGS : Algorithmic, Bioinformatic and Software solutions for the analysis of Next Generation Sequencing data, funded by ANR, coordinator : Emmanuel Barillot
NEMO : Network Motifs, funded by ANR 2009-2011, coordinator : Stéphane Robin
MIRI : Combinatorial exploration of the molecular landscape and evolution of intimate species relations, funded by ANR 2009-2013, coordinator : Marie-France Sagot
- +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.
+Publications -Publications
article :
Benoit-Pilven C, Marchet C, Chautard E, Lima L, Lambert MP, Sacomoto G, Rey A, Cologne A, Terrone S, Dulaurier L, Claude JB, Bourgeois CF, Auboeuf D, Lacroix V (2018)
Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data, Scientific reports, vol. 8 pp.4307-4307.
Jaillard M, Lima L, Tournoud M, Mahé P, van Belkum A, Lacroix V, Jacob L (2018)
A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events, PLoS genetics, vol. 14 pp.e1007758-e1007758.
Lima L, Sinaimeri B, Sacomoto G, Lopez-Maestre H, Marchet C, Miele V, Sagot MF, Lacroix V (2017)
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads, Algorithms for Molecular Biology, vol. 12 pp.2-2.
Lopez-Maestre H, Carnelossi EA, Lacroix V, Burlet N, Mugat B, Chambeyron S, Carareto CM, Vieira C (2017)
Identification of misexpressed genetic elements in hybrids between Drosophila-related species, Scientific reports, vol. 7 pp.40618-40618.
Freyermuth F, Rau F, Kokunai Y, Linke T, Sellier C, Nakamori M, Kino Y, Arandel L, Jollet A, Thibault C, Philipps M, Vicaire S, Jost B, Udd B, Day JW, Duboc D, Wahbi K, Matsumura T, Fujimura H, Mochizuki H, Deryckere F, Kimura T, Nukina N, Ishiura S, Lacroix V, Campan-Fournier A, Navratil V, Chautard E, Auboeuf D, Horie M, Imoto K, Lee KY, Swanson MS, Lopez de Munain A, Inada S, Itoh H, Nakazawa K, Ashihara T, Wang E, Zimmer T, Furling D, Takahashi MP, Charlet-Berguerand N (2016)
Splicing misregulation of SCN5A contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy, Nature communications, vol. 7 pp.11067-11067.
Le Bras Y, Collin O, Monjeaud C, Lacroix V, Rivals E, Lemaitre C, Miele V, Sacomoto G, Marchet C, Cazaux B, Zine El Aabidine A, Salmela L, Alves-Carvalho S, Andrieux A, Uricaru R, Peterlongo P (2016)
Colib`read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads, GigaScience, vol. 5 pp.9-9.
Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, El Filali A, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot MF, Lacroix V (2016)
SNP calling from RNA-seq data without a reference genome: identification quantification differential analysis and impact on the protein sequence, Nucleic Acids Research, vol. 44 pp.e148-e148.
Sacomoto G, Lacroix V, Sagot MF (2015)
A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs, Algorithms for Molecular Biology, vol. 10 pp.20-20.
Milreu PV, Klein C C, Cottret L, Acuna V, Birmele E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V, Sagot MF (2014)
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure, Bioinformatics, vol. 30 pp.61-70.
Sacomoto G, Sinaimeri B, Marchet C, Miele V, Sagot MF, Lacroix V (2014)
Navigating in a Sea of Repeats in RNA-seq without Drowning, Lecture Notes in Computer Science, vol. 8701 pp.82-96.
Uricaru R, Rizk G, Lacroix V, Quillery E, Plantard O, Chikhi R, Lemaitre C, Peterlongo P (2014)
Reference-free detection of isolated SNPs, Nucleic Acids Research, vol. 43 pp.e11-e11.
Brilli M, Lio P, Lacroix V, Sagot MF (2013)
Short and long-term genome stability analysis of prokaryotic genomes, BMC Genomics, vol. 14 pp.309-309.
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.
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.
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.e28213-e28213.
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 Research, vol. 22 pp.1231-1242.
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. 40 pp.10073-10083.
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.S5-S5.
Veron AS, Lemaitre C, Gautier C, Lacroix V, Sagot MF (2011)
Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny, BMC Genomics, vol. 12 pp.303-303.
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.619234-619234.
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.
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
in: Alternative pre-mRNA Splicing, Wiley-VCH Verlag GmbH & Co. KGaA, pp.544-554.
inproceedings :
Julien-Laferrière A, Sacomoto G, Chikhi R, Scaon E, Parsons D , Sagot MF, Peterlongo P, Miele V, Lacroix V (2013)
New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data, JOBIM, pp.1-6.
Birmelé E, Crescenzi P, Ferreira R, Grossi R, Lacroix V, Marino A, Pisanti N, Sacomoto G, Sagot MF (2012)
Efficient Bubble Enumeration in Directed Graphs, SPIRE 2012, pp.1505-1515.
Freire AS, Acuna V, Crescenzi P, Ferreira CE, Lacroix V, Milreu PV, Moreno E, Sagot M-F (2012)
Minimum ratio cover of matrix colums by extreme rays of its induced cone, International Symposium on Combinatorial Optimization, pp.1-12.
Peterlongo P, Schnel N, Pisanti N, Sagot M-F, Lacroix V (2010)
Identifying SNPs without a Reference Genome by Comparing Raw Reads, SPIRE, Springer, Lecture Notes in Computer Science, vol. 6393 pp.147-158.
Vieira-Milreu P, Acuña V, Birmelé E, Crescenzi P, Marchetti-Spaccamela A, Sagot M-F, Stougie L, Lacroix V (2010)
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.
Lacroix V, Sammeth M, Guigo R, Bergeron A (2008)
Exact Transcriptome Reconstruction from Short Sequence Reads, Proceeding of WABI`08, Springer Verlag, Lecture Notes in Bioinformatics, vol. 5251 pp.50-63.
Bourqui R, Auber D, Lacroix V, Jourdan F (2006)
Metabolic network visualization using constraint planar graph drawing algorithm, 10th conf. on Information Visualization, IEEE Computer Society pp.489-496.
Lacroix V, Fernandes CG, Sagot MF (2005)
Reaction motifs in metabolic networks, Proceedings of WABI `05, Springer-Verlag, Lecture Notes in Computer Science, vol. 3692 pp.178-191.
phdthesis :
Lacroix V (2007)
Identification de motifs dans les réseaux métaboliques Définitions algorithmes et application au métabolisme d’Escherichia coli .
