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Integrative and differential analysis of transcriptomes and chromatin accessibility regions reveals regulatory mechanisms involved in pig immune and metabolic functions

 Sarah Djebali Quelen , Kylie Munyard , Nathalie Villa-Vialaneix , Cédric Cabau , Andrea Rau , et al.
36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book
Poster de conférence hal-01603033v1
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Characterization of 3D genomic interactions in fetal pig muscle

 Maria Marti-Marimon , Hervé Acloque , Matthias Zytnicki , Sarah Djebali Quelen , Nathalie Villa-Vialaneix , et al.
36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book
Poster de conférence hal-01608046v1
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Evidence for transcript networks composed of chimeric RNAs in human cells

 Sarah Djebali , Julien Lagarde , Philipp Kapranov , Vincent Lacroix , Christelle Borel , et al.
PLoS ONE, 2012, 7 (1), Non paginé. ⟨10.1371/journal.pone.0028213⟩
Article dans une revue hal-01216248v2

3D nuclear positioning of IGF2 alleles and trans interactions with imprinted genes in pig fetal cells

 Yvette Lahbib Mansais , Maria Marti-Marimon , Valentin Voillet , Harmonie Barasc , Florence Mompart , et al.
22. International Colloquim on Animal Cytogenetics and Genomics (ICACG), Jul 2016, Toulouse, France. 116 p
Communication dans un congrès hal-02743243v1

Effects of balanced chromosome translocations on boar fertility and cell reprogramming

 Annabelle Congras , Harmonie Barasc , Valentine Marquet , Kamila Canale-Tabet , Emeline Lhuillier , et al.
22. International Colloquium on Animal Cytogenetics and Genomics (ICACG), Jul 2016, Toulouse, France. 116p
Communication dans un congrès hal-02738753v1

FR-AgENCODE: A Pilot Project to Improve the Functional Annotation of Livestock Genomes

 Sylvain Foissac , Elisabetta Giuffra
Plant and Animal Genome (PAG), Jan 2015, San Diego, United States
Communication dans un congrès hal-01194055v1
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An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog

 Agnès Bonnet , Cédric Cabau , Olivier Bouchez , Julien Sarry , Nathalie Marsaud , et al.
BMC Genomics, 2013, 14 (december), pp.1-19. ⟨10.1186/1471-2164-14-904⟩
Article dans une revue hal-01019557v1
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Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig

 Sylvain Foissac , Sarah Djebali , Kylie Munyard , Nathalie Vialaneix , Andrea Rau , et al.
2018
Pré-publication, Document de travail hal-02791029v1
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Landscape of transcription in human cells

 Sarah Djebali , Carrie A. Davis , Angelika Merkel , Alex Dobin , Timo Lassmann , et al.
Nature, 2012, 489 (7414), pp.101-108. ⟨10.1038/nature11233⟩
Article dans une revue hal-01216755v1
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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 Feve , Sylvain Foissac , Alain Pinton , Florence Mompart , Diane Esquerré , et al.
PLoS ONE, 2017, 12 (11), Non paginé. ⟨10.1371/journal.pone.0187617⟩
Article dans une revue hal-02622330v1

A lncRNA gene-enriched atlas for GRCg7b chicken genome using Ensembl, RefSeq and two FAANG databases

 Fabien Degalez , Mathieu Charles , Sylvain Foissac , Zhou Haijuan , Guan Dailu , et al.
74. Annual meeting of the european federation of animal science (EAAP), Aug 2023, Lyon, France. Wageningen Academic Publishers, Book of abstracts, 29, pp.932, 2023, Book of abstracts of the 74st annual meeting of the european federation of animal science
Poster de conférence hal-04217567v1
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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 , et al.
RNA, 2015, 21 (12), pp.2119-2131. ⟨10.1261/rna.053397.115⟩
Article dans une revue hal-02629774v1

Multi-level conservation of chromosome conformation across livestock species reveals evolutionary links between genome structure and function

 Sylvain Foissac , Sarah Djebali Quelen , Nathalie Vialaneix , Matthias Zytnicki , Andrea Rau , et al.
Conference of the International Society for Animal Genetics (ISAG 2019), Jul 2019, Lleida, Spain
Communication dans un congrès hal-02788476v1

Functional annotation of livestock genomes: chromatin structure and regulation of gene expression

 Sylvain Foissac , Sarah Djebali , Kylie Munyard , Nathalie Vialaneix , Andrea Rau , et al.
ASAS/ASDS Midwest Joint Meeting, Mar 2019, Omaha, United States. ⟨10.1093/jas/skz122.028⟩
Communication dans un congrès hal-02735898v1
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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 , et al.
Scientific Reports, 2020, 10 (1), pp.1-17. ⟨10.1038/s41598-020-77586-x⟩
Article dans une revue hal-03039897v1
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A lncRNA gene-enriched atlas for GRCg7b chicken genome and its functional annotation across 47 tissues

 Fabien Degalez , Mathieu Charles , Sylvain Foissac , Haijuan Zhou , Dailu Guan , et al.
39. Congress of the international society for animal genetics (ISAG), Jul 2023, Cape Town, South Africa. , pp.78, 2023, Abstracts
Poster de conférence hal-04217582v1

Chromatin accessibility in the liver and circulating immune cells of pigs, goats and chickens

 Elisabetta Giuffra , Kylie Munyard , Adeline Goubil , Silvia Vincent-Naulleau , Diane Esquerre , et al.
35. Conference of the International Society for Animal Genetics (ISAG), Jul 2016, Salt Lake City, United States. ⟨10.2134/jas2016.94supplement471a⟩
Communication dans un congrès hal-01533947v1

Profiling the landscape of transcription and chromatin conformation reveals regulatory mechanisms involved in immune and metabolic functions

 Sylvain Foissac , Sarah Djebali Quelen , Hervé Acloque , Marie-Hélène Pinard-van Der Laan , Sandrine Lagarrigue , et al.
3. Journée de Séminaires du Département Phase sur l'Epigénétique EpiPhase, May 2017, Jouy-en-Josas, France
Communication dans un congrès hal-01603057v1

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 , et al.
Genome Research, 2007, 17 (6), pp.746-759. ⟨10.1101/gr.5660607⟩
Article dans une revue hal-01425793v1
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A two-sample tree-based test for hierarchically organized genomic signals

 Pierre Neuvial , Nathanaël Randriamihamison , Marie Chavent , Sylvain Foissac , Nathalie Vialaneix
Journal of the Royal Statistical Society: Series C Applied Statistics, 2024, pp.qlae011. ⟨10.1093/jrsssc/qlae011⟩
Article dans une revue hal-04516167v1

Profiling the Nuclear Spatial Conformation of Livestock Genomes in Cell Lines and Liver Cells

 Sylvain Foissac , Hervé Acloque , Florence Mompart , Diane Esquerre , David Robelin , et al.
PAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States. Non paginé
Communication dans un congrès hal-01508146v1
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Cell specification and functional interactions in the pig blastocyst inferred from single cell transcriptomics

 Adrien Dufour , Cyril Kurilo , Jan B Stöckl , Denis Laloë , Yoann Bailly , et al.
2023
Pré-publication, Document de travail hal-04143106v1
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Characterization of 3D genomic interactions in fetal pig muscle

 Maria Eugenia Marti Marimon , Hervé Acloque , Matthias Zytnicki , David Robelin , Sarah Djebali Quelen , et al.
36. International Society for Animal Genetics Conference (ISAG), Jul 2017, Dublin, Ireland. pp.43
Communication dans un congrès hal-02868765v1
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Integrating alternative splicing detection into gene prediction

 Sylvain Foissac , Thomas Schiex
BMC Bioinformatics, 2005, 6, Non paginé. ⟨10.1186/1471-2105-6-25⟩
Article dans une revue hal-01417735v1

An integrated encyclopedia of DNA elements in the human genome

 Sylvain Foissac
Nature, 2012, 489 (7414), pp.57-74. ⟨10.1038/nature11247⟩
Article dans une revue hal-01217624v1
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A General Definition and Nomenclature for Alternative Splicing Events

 Michael Sammeth , Sylvain Foissac , Roderic Guigó
PLoS Computational Biology, 2008, 4 (8), Non paginé. ⟨10.1371/journal.pcbi.1000147⟩
Article dans une revue hal-01412838v1

nBioinformatics Pipeline for Transcriptome Sequencing Analysis

 Sarah Djebali , Valentin Wucher , Sylvain Foissac , Christophe Hitte , Erwan Corre , et al.
Enhancer RNAs : Methods and Protocols, 1468 (Chapter 14), Humana Press Inc., 2017, Methods in Molecular Biology, 978-1-4939-4033-2. ⟨10.1007/978-1-4939-4035-6_14⟩
Chapitre d'ouvrage hal-02788591v1

Organisation nucléaire et expression génique lors du développement chez le porc

 Yvette Lahbib Mansais , Maria Marti-Marimon , Nathalie Vialaneix , Sylvain Foissac , Martine Bouissou-Matet , et al.
5. Journée d'Animation Scientifique du réseau épiPhase, Jun 2019, Toulouse, France. 35 p
Communication dans un congrès hal-02736301v1
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RNA-Seq Data for Reliable SNP Detection and Genotype Calling

 Frédéric Jehl , Fabien Degalez , Frédéric Lecerf , Maria Bernard , Laetitia Lagoutte , et al.
Frontiers in Genetics, 2021, 12, pp.655707. ⟨10.3389/fgene.2021.655707⟩
Article dans une revue hal-03276149v1
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Major reorganization of chromosome conformation during muscle development in pig

 Maria Marti-Marimon , Nathalie Vialaneix , Yvette Lahbib Mansais , Matthias Zytnicki , Sylvie Camut , et al.
Frontiers in Genetics, 2021, 12, pp.19 P. ⟨10.3389/fgene.2021.748239⟩
Article dans une revue hal-03367056v1
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