Publications

Found 23 results
Filters: Author is Foissac, Sylvain  [Clear All Filters]
2023
Hoellinger T, Mestre C, Aschard H, et al. Enhancer/gene relationships: Need for more reliable genome-wide reference sets. Front Bioinform. 2023;3:1092853. doi:10.3389/fbinf.2023.1092853.
2021
Jehl F, Muret K, Bernard M, et al. Author Correction: An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Sci Rep. 2021;11(1):9463. doi:10.1038/s41598-021-89158-8.
Jehl F, Degalez F, Bernard M, et al. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and -Regulation Analysis by Allele-Specific Expression in Livestock Species. Front Genet. 2021;12:655707. doi:10.3389/fgene.2021.655707.
2020
Jehl F, Muret K, Bernard M, et al. An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Sci Rep. 2020;10(1):20457. doi:10.1038/s41598-020-77586-x.
2017
Djebali S, Wucher V, Foissac S, Hitte C, Corre E, Derrien T. Bioinformatics Pipeline for Transcriptome Sequencing Analysis. Methods Mol Biol. 2017;1468:201-19. doi:10.1007/978-1-4939-4035-6_14.
Djebali S, Wucher V, Foissac S, Hitte C, Corre E, Derrien T. Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis. Methods Mol Biol. 2017;1468:E1. doi:10.1007/978-1-4939-4035-6_17.
Feve K, Foissac S, Pinton A, et al. Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing. PLoS One. 2017;12(11):e0187617. doi:10.1371/journal.pone.0187617.
Muret K, Klopp C, Wucher V, et al. Long noncoding RNA repertoire in chicken liver and adipose tissue. Genet Sel Evol. 2017;49(1):6. doi:10.1186/s12711-016-0275-0.
2015
Foissac S, Sammeth M. Analysis of alternative splicing events in custom gene datasets by AStalavista. Methods Mol Biol. 2015;1269:379-92. doi:10.1007/978-1-4939-2291-8_24.
Andersson L, Archibald AL, Bottema CD, et al. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol. 2015;16:57. doi:10.1186/s13059-015-0622-4.
Rubio-Peña K, Fontrodona L, Aristizábal-Corrales D, et al. Modeling of autosomal-dominant retinitis pigmentosa in Caenorhabditis elegans uncovers a nexus between global impaired functioning of certain splicing factors and cell type-specific apoptosis. RNA. 2015;21(12):2119-31. doi:10.1261/rna.053397.115.
2013
Bonnet A, Cabau C, Bouchez O, et al. An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog. BMC Genomics. 2013;14:904. doi:10.1186/1471-2164-14-904.
2012
Djebali-Quelen S, Lagarde J, Kapranov P, et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012;7(1):e28213. doi:10.1371/journal.pone.0028213.
Djebali-Quelen S, Davis CA, Merkel A, et al. Landscape of transcription in human cells. Nature. 2012;489(7414):101-8. doi:10.1038/nature11233.
2010
Ozsolak F, Kapranov P, Foissac S, et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell. 2010;143(6):1018-29. doi:10.1016/j.cell.2010.11.020.
Kapranov P, Ozsolak F, Kim SWoo, et al. New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature. 2010;466(7306):642-6. doi:10.1038/nature09190.
2008
Piqué M, López JManuel, Foissac S, Guigó R, Méndez R. A combinatorial code for CPE-mediated translational control. Cell. 2008;132(3):434-48. doi:10.1016/j.cell.2007.12.038.
Djebali-Quelen S, Kapranov P, Foissac S, et al. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods. 2008;5(7):629-35. doi:10.1038/nmeth.1216.
Sammeth M, Foissac S, Guigó R. A general definition and nomenclature for alternative splicing events. PLoS Comput Biol. 2008;4(8):e1000147. doi:10.1371/journal.pcbi.1000147.
2007
Foissac S, Sammeth M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res. 2007;35(Web Server issue):W297-9. doi:10.1093/nar/gkm311.
Denoeud F, Kapranov P, Ucla C, et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007;17(6):746-59. doi:10.1101/gr.5660607.
2005
Foissac S, Schiex T. Integrating alternative splicing detection into gene prediction. BMC Bioinformatics. 2005;6:25. doi:10.1186/1471-2105-6-25.
2003
Foissac S, Bardou P, Moisan A, Cros M-J, Schiex T. EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. Nucleic Acids Res. 2003;31(13):3742-5.