Publications

1. Empowering bioinformatics communities with Nextflow and nf-core. Bjorn E. Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Krishna Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip A. Ewels, Sonia Eynard, James A. Fellows Yates, Daniel Fischer, Evan W. Floden, Sylvain Foissac, Gisela Gabernet, Maxime U. Garcia, Gareth Gillard, Manu Kumar Gundappa, Cervin Guyomar, Christopher Hakkaart, Friederike Hanssen, Peter W. Harrison, Matthias Hortenhuber, Cyril Kurylo, Christa Kuhn, Sandrine Lagarrigue, Delphine Lallias, Daniel J. Macqueen, Edmund Miller, Julia Mir-Pedrol, Gabriel Costa Monteiro Moreira, Sven Nahnsen, Harshil Patel, Alexander Peltzer, Frederique Pitel, Yuliaxis Ramayo-Caldas, Marcel da Camara Ribeiro-Dantas, Dominique Rocha, Mazdak Salavati, Alexey Sokolov, Jose Espinosa-Carrasco, and Cedric Notredame. bioRxiv, 2024. Link (doi) Article (pdf)
   
2. Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues. Fabien Degalez, Mathieu Charles, Sylvain Foissac, Haijuan Zhou, Dailu Guan, Lingzhao Fang, Christophe Klopp, Coralie Allain, Laetitia Lagoutte, Frédéric Lecerf, and Sandrine Lagarrigue. Scientific Reports, 14 (1): 6588, 2024. Link (doi) Article (pdf)
   
3. A two-sample tree-based test for hierarchically organized genomic signals. Pierre Neuvial, Nathanaël Randriamihamison, Marie Chavent, Sylvain Foissac, and Nathalie Vialaneix. Journal of the Royal Statistical Society Series C: Applied Statistics, 2024. Link (doi) Article (pdf)
   
4. Cell specification and functional interactions in the pig blastocyst inferred from single-cell transcriptomics and uterine fluids proteomics. Adrien Dufour, Cyril Kurylo, Jan B. Stöckl, Denis Laloë, Yoann Bailly, Patrick Manceau, Frédéric Martins, Ali G. Turhan, Stéphane Ferchaud, Bertrand Pain, Thomas Fröhlich, Sylvain Foissac, Jérôme Artus, and Hervé Acloque. Genomics, 116 (2): 110780, 2024. Link (doi) Article (pdf)
   
5. TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data. Cyril Kurylo, Cervin Guyomar, Sylvain Foissac, and Sarah Djebali. NAR Genomics And Bioinformatics, 5 (4): lqad089, 2023. Link (doi) Article (pdf)
   
6. Enhancer/gene relationships: need for more reliable genome-wide reference sets. Tristan Hoellinger, Camille Mestre, Hugues Aschard, Wilfried Le Goff, Sylvain Foissac, Thomas Faraut, and Sarah Djebali. Frontiers in Bioinformatics, 3: 1092853, 2023. Link (doi) Article (pdf)
   
7. Comprendre l’organisation spatiale de l’ADN à l’aide de la statistique. Pierre Neuvial, Sylvain Foissac, and Nathalie Vialaneix. L’Interdisciplinarité, 1: 172-179, 2023. Link (doi) Article (pdf)
   
8. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species. Frédéric Jehl, Fabien Degalez, Maria Bernard, Frédéric Lecerf, Laetitia Lagoutte, Colette Désert, Manon Coulée, Olivier Bouchez, Sophie Leroux, Behnam Abasht, Michèle Tixier-Boichard, Bertrand Bed’hom, Thierry Burlot, David Gourichon, Philippe Bardou, Hervé Acloque, Sylvain Foissac, Sarah Djebali, Elisabetta Giuffra, Tatiana Zerjal, Frédérique Pitel, Christophe Klopp, and Sandrine Lagarrigue. Frontiers in Genetics, 12: 1104, 2021. Link (doi) Article (pdf)
   
9. Major Reorganization of Chromosome Conformation During Muscle Development in Pig. Maria Marti-Marimon, Nathalie Vialaneix, Yvette Lahbib-Mansais, Matthias Zytnicki, Sylvie Camut, David Robelin, Martine Yerle-Bouissou, and Sylvain Foissac. Frontiers in Genetics, 12: 1895, 2021. Link (doi) Article (pdf)
   
10. An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Frédéric Jehl, Kévin Muret, Maria Bernard, Morgane Boutin, Laetitia Lagoutte, Colette Désert, Patrice Dehais, Diane Esquerré, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, Frédérique Pitel, Tatiana Zerjal, Christophe Klopp, and Sandrine Lagarrigue. Scientific Reports, 10 (1): 1–17, 2020. Link (doi) Article (pdf)
    
11. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Elisabetta Giuffra, Christopher K. Tuggle, and the FAANG Consortium. Annual Review of Animal Biosciences, 7: 65–88, 2019. Link (doi) Article (pdf)
    
12. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, Kevin Muret, Diane Esquerré, Matthias Zytnicki, Thomas Derrien, Philippe Bardou, Fany Blanc, Cédric Cabau, Elisa Crisci, Sophie Dhorne-Pollet, Françoise Drouet, Thomas Faraut, Ignacio Gonzalez, Adeline Goubil, Sonia Lacroix-Lamandé, Fabrice Laurent, Sylvain Marthey, Maria Marti-Marimon, Raphaelle Momal-Leisenring, Florence Mompart, Pascale Quéré, David Robelin, Magali San Cristobal, Gwenola Tosser-Klopp, Silvia Vincent-Naulleau, Stéphane Fabre, Marie Hélène Pinard Van Der Laan, Christophe Klopp, Michèle Tixier-Boichard, Hervé Acloque, Sandrine Lagarrigue, and Elisabetta Giuffra. BMC Biology, 17 (1): 1–25, 2019. Link (doi) Article (pdf)
    
13. Bioinformatics pipeline for transcriptome sequencing analysis. Sarah Djebali, Valentin Wucher, Sylvain Foissac, Christophe Hitte, Evan Corre, and Thomas Derrien. Methods in Molecular Biology, 1468: 201–219, 2017. Link (doi)
14. 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. Katia Fève, Sylvain Foissac, Alain Pinton, Florence Mompart, Diane Esquerré, Thomas Faraut, Martine Yerle, and Juliette Riquet. PLoS ONE, 12 (11): 1–17, 2017. Link (doi) Article (pdf)
    
15. Genome-wide epigenetic studies in chicken: A review. Sarah Anne David, Marjorie Mersch, Sylvain Foissac, Anne Collin, Frédérique Pitel, and Vincent Coustham. Epigenomes, 1 (3): 20, 2017. Link (doi) Article (pdf)
    
16. Long noncoding RNA repertoire in chicken liver and adipose tissue. Kévin Muret, Christophe Klopp, Valentin Wucher, Diane Esquerré, Fabrice Legeai, Frédéric Lecerf, Colette Désert, Morgane Boutin, Frédéric Jehl, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, and Sandrine Lagarrigue. Genetics Selection Evolution, 49 (1): 1–17, 2017. Link (doi) Article (pdf)
    
17. Analysis of alternative splicing events in custom gene datasets by AStalavista. Sylvain Foissac, and Michael Sammeth. Methods in Molecular Biology, 1269: 379–392, 2015. Link (doi) Article (pdf)
    
18. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Leif Andersson, Alan L. Archibald, Cynthia D. Bottema, Rudiger Brauning, Shane C. Burgess, Dave W. Burt, Eduardo Casas, Hans H. Cheng, Laura Clarke, Christine Couldrey, Brian P. Dalrymple, Christine G. Elsik, Sylvain Foissac, Elisabetta Giuffra, Martien A. Groenen, Ben J. Hayes, Lu Sheng S. Huang, Hassan Khatib, James W. Kijas, Heebal Kim, Joan K. Lunney, Fiona M. McCarthy, John C. McEwan, Stephen Moore, Bindu Nanduri, Cedric Notredame, Yniv Palti, Graham S. Plastow, James M. Reecy, Gary A. Rohrer, Elena Sarropoulou, Carl J. Schmidt, Jeffrey Silverstein, Ross L. Tellam, Michele Tixier-Boichard, Gwenola Tosser-Klopp, Christopher K. Tuggle, Johanna Vilkki, Stephen N. White, Shuhong Zhao, and Huaijun Zhou. Genome Biology, 16 (1): 1–6, 2015. Link (doi) Article (pdf)
    
19. 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. Karinna Rubio-Peña, Laura Fontrodona, David Aristizábal-Corrales, Silvia Torres, Eric Cornes, Francisco J. García-Rodríguez, Xènia Serrat, David González-Knowles, Sylvain Foissac, Montserrat Porta-De-La-Riva, and Julián Cerón. RNA, 21 (12): 2119–2131, 2015. Link (doi) Article (pdf)
    
20. An overview of gene expression dynamics during early ovarian folliculogenesis: Specificity of follicular compartments and bi-directional dialog. Agnes Bonnet, Cedric Cabau, Olivier Bouchez, Julien Sarry, Nathalie Marsaud, Sylvain Foissac, Florent Woloszyn, Philippe Mulsant, and Beatrice Mandon-Pepin. BMC Genomics, 14 (1): 1–19, 2013. Link (doi) Article (pdf)
    
21. Landscape of transcription in human cells. Sarah Djebali, Carrie A. Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger, Chenghai Xue, Georgi K. Marinov, Jainab Khatun, Brian A. Williams, Chris Zaleski, Joel Rozowsky, Maik Röder, Felix Kokocinski, Rehab F. Abdelhamid, Tyler Alioto, Igor Antoshechkin, Michael T. Baer, Nadav S. Bar, Philippe Batut, Kimberly Bell, Ian Bell, Sudipto Chakrabortty, Xian Chen, Jacqueline Chrast, Joao Curado, Thomas Derrien, Jorg Drenkow, Erica Dumais, Jacqueline Dumais, Radha Duttagupta, Emilie Falconnet, Meagan Fastuca, Kata Fejes-Toth, Pedro Ferreira, Sylvain Foissac, Melissa J. Fullwood, Hui Gao, David Gonzalez, Assaf Gordon, Harsha Gunawardena, Cedric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Oscar J. Luo, Eddie Park, Kimberly Persaud, Jonathan B. Preall, Paolo Ribeca, Brian Risk, Daniel Robyr, Michael Sammeth, Lorian Schaffer, Lei-Hoon See, Atif Shahab, Jorgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, John Wrobel, Yanbao Yu, Xiaoan Ruan, Yoshihide Hayashizaki, Jennifer Harrow, Mark Gerstein, Tim Hubbard, Alexandre Reymond, Stylianos E. Antonarakis, Gregory Hannon, Morgan C. Giddings, Yijun Ruan, Barbara Wold, Piero Carninci, Roderic Guigó, and Thomas R. Gingeras. Nature, 489 (7414): 101–108, 2012. Link (doi) Article (pdf)
    
22. Evidence for transcript networks composed of chimeric rnas in human cells. Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge, Cédric Howald, Sylvain Foissac, Catherine Ucla, Jacqueline Chrast, Paolo Ribeca, David Martin, Ryan R. Murray, Xinping Yang, Lila Ghamsari, Chenwei Lin, Ian Bell, Erica Dumais, Jorg Drenkow, Michael L. Tress, Josep Lluís Gelpí, Modesto Orozco, Alfonso Valencia, Nynke L. Berkum, Bryan R. Lajoie, Marc Vidal, John Stamatoyannopoulos, Philippe Batut, Alex Dobin, Jennifer Harrow, Tim Hubbard, Job Dekker, Adam Frankish, Kourosh Salehi-Ashtiani, Alexandre Reymond, Stylianos E. Antonarakis, Roderic Guigó, and Thomas R. Gingeras. PLoS ONE, 7 (1): e28213, 2012. Link (doi) Article (pdf)
    
23. An integrated encyclopedia of DNA elements in the human genome. The ENCODE Project Consortium. Nature, 489 (7414): 57–74, 2012. Link (doi) Article (pdf)
    
24. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Fatih Ozsolak, Philipp Kapranov, Sylvain Foissac, Sang Woo Kim, Elane Fishilevich, A. Paula Monaghan, Bino John, and Patrice M. Milos. Cell, 143 (6): 1018–1029, 2010. Link (doi) Article (pdf)
    
25. New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Philipp Kapranov, Fatih Ozsolak, Sang Woo Kim, Sylvain Foissac, Doron Lipson, Chris Hart, Steve Roels, Christelle Borel, Stylianos E. Antonarakis, A. Paula Monaghan, Bino John, and Patrice M. Milos. Nature, 466 (7306): 642–646, 2010. Link (doi) Article (pdf)
    
26. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Katalin Fejes-Toth, Vihra Sotirova, Ravi Sachidanandam, Gordon Assaf, Gregory J. Hannon, Philipp Kapranov, Sylvain Foissac, Aarron T. Willingham, Radha Duttagupta, Erica Dumais, and Thomas R. Gingeras. Nature, 457 (7232): 1028–1032, 2009. Link (doi) Article (pdf)
    
27. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Sarah Djebali, Philipp Kapranov, Sylvain Foissac, Julien Lagarde, Alexandre Reymond, Catherine Ucla, Carine Wyss, Jorg Drenkow, Erica Dumais, Ryan R. Murray, Chenwei Lin, David Szeto, France Denoeud, Miquel Calvo, Adam Frankish, Jennifer Harrow, Periklis Makrythanasis, Marc Vidal, Kourosh Salehi-Ashtiani, Stylianos E. Antonarakis, Thomas R. Gingeras, and Roderic Guigó. Nature Methods, 5 (7): 629–635, 2008. Link (doi) Article (pdf)
    
28. A Combinatorial Code for CPE-Mediated Translational Control. Maria Piqué, José Manuel López, Sylvain Foissac, Roderic Guigó, and Raúl Méndez. Cell, 132 (3): 434–448, 2008. Link (doi) Article (pdf)
    
29. A general definition and nomenclature for alternative splicing events. Michael Sammeth, Sylvain Foissac, and Roderic Guigó. PLoS Computational Biology, 4 (8): e1000147, 2008. Link (doi) Article (pdf)
    
30. Genome Annotation in Plants and Fungi: EuGene as a Model Platform. Sylvain Foissac, Jerome Gouzy, Stephane Rombauts, Catherine Mathe, Joelle Amselem, Lieven Sterck, Yves Peer, Pierre Rouze, and Thomas Schiex. Current Bioinformatics, 3 (2): 87–97, 2008. Link (doi) Article (pdf)
    
31. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Sylvain Foissac, and Michael Sammeth. Nucleic acids research, 35 (suppl_2): W297–W299, 2007. Link (doi) Article (pdf)
    
32. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. The ENCODE Project Consortium. Nature, 447 (7146): 799–816, 2007. Link (doi) Article (pdf)
    
33. Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. France Denoeud, Philipp Kapranov, Catherine Ucla, Adam Frankish, Robert Castelo, Jorg Drenkow, Julien Lagarde, Tyler Alioto, Caroline Manzano, Jacqueline Chrast, Sujit Dike, Carine Wyss, Charlotte N. Henrichsen, Nancy Holroyd, Mark C. Dickson, Ruth Taylor, Zahra Hance, Sylvain Foissac, Richard M. Myers, Jane Rogers, Tim Hubbard, Jennifer Harrow, Roderic Guigó, Thomas R. Gingeras, Stylianos E. Antonarakis, and Alexandre Reymond. Genome Research, 17 (6): 746–759, 2007. Link (doi) Article (pdf)
    
34. Integrating alternative splicing detection into gene prediction. Sylvain Foissac, and Thomas Schiex. BMC Bioinformatics, 6 (1): 1–10, 2005. Link (doi) Article (pdf)
    
35. EUGÈNE’HOM: A generic similarity-based gene finder using multiple homologous sequences. Sylvain Foissac, Philippe Bardou, Annick Moisan, Marie Josée Cros, and Thomas Schiex. Nucleic Acids Research, 31 (13): 3742–3745, 2003. Link (doi) Article (pdf)