Elisabetta Giuffra

Documents

Publications

	Tissue resources for the functional annotation of animal genomes Michèle Tixier-Boichard , Stéphane Fabre , Sophie Dhorne-Pollet , Adeline Goubil , Hervé Acloque Frontiers in Genetics, 2021, 12, ⟨10.3389/fgene.2021.666265⟩ Article dans une revue hal-03353872v1
	Intestinal organoids in farm animals Martin Beaumont , Fany Blanc , Claire Cherbuy , Giorgia Egidy , Elisabetta Giuffra Veterinary Research, 2021, 52 (1), 15 p. ⟨10.1186/s13567-021-00909-x⟩ Article dans une revue hal-03154463v1
	Editorial: Functional Annotation of Animal Genomes Amanda Jane Chamberlain , Hans H Cheng , Elisabetta Giuffra , Christa Kuehn , Christopher K Tuggle Frontiers in Genetics, 2021, 12, pp.768626. ⟨10.3389/fgene.2021.768626⟩ Article dans une revue hal-03379984v1
	RNA-Seq Data for Reliable SNP Detection and Genotype Calling Frédéric Jehl , Fabien Degalez , Frédéric Lecerf , Maria Bernard , Laetitia Lagoutte Frontiers in Genetics, 2021, 12, pp.655707. ⟨10.3389/fgene.2021.655707⟩ Article dans une revue hal-03276149v1
	From FAANG to fork: application of highly annotated genomes to improve farmed animal production Emily Clark , Alan Archibald , Hans Daetwyler , Martien Groenen , Peter Harrison Genome Biology, 2020, 21 (1), ⟨10.1186/s13059-020-02197-8⟩ Article dans une revue hal-03056514v1
	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 Scientific Reports, 2020, 10 (1), pp.1-17. ⟨10.1038/s41598-020-77586-x⟩ Article dans une revue hal-03039897v1
	The mirna-targeted transcriptome of porcine alveolar macrophages upon infection with porcine reproductive and respiratory syndrome virus Sophie Dhorne-Pollet , Elisa Crisci , Núria Mach , Patricia Renson , Florence Jaffrezic Scientific Reports, 2019, 9 (1), pp.3160. ⟨10.1038/s41598-019-39220-3⟩ Article dans une revue hal-02573144v1
	Multi-species annotation of transcriptome and chromatin structure in domesticated animals Sylvain Foissac , Sarah Djebali , Kylie Munyard , Nathalie Vialaneix , Andrea Rau BMC Biology, 2019, 17 (1), 25 p. ⟨10.1186/s12915-019-0726-5⟩ Article dans une revue hal-02437599v1
	Functional Annotation of Animal Genomes (FAANG) : Current Achievements and Roadmap Elisabetta Giuffra , Christopher K. Tuggle , A.L. Archibald , Hervé Acloque , Amanda J. Chamberlain Annual Review of Animal Biosciences, 2019, 7 (1), pp.65-88. ⟨10.1146/annurev-animal-020518-114913⟩ Article dans une revue hal-02626183v1
	Macrophage-B Cell Interactions in the Inverted Porcine Lymph Node and Their Response to Porcine Reproductive and Respiratory Syndrome Virus Elise Bordet , Maxence Fretaud , Elisa Crisci , Edwige Bouguyon , Stephane Rault Frontiers in Immunology, 2019, 10, pp.953. ⟨10.3389/fimmu.2019.00953⟩ Article dans une revue hal-02164040v1
	Porcine Reproductive and Respiratory Syndrome Virus Type 1.3 Lena Triggers Conventional Dendritic Cells 1 Activation and T Helper 1 Immune Response Without Infecting Dendritic Cells Elise Bordet , Fany Blanc , Mathieu Tiret , Elisa Crisci , Edwige Bouguyon Frontiers in Immunology, 2018, 9, pp.2299. ⟨10.3389/fimmu.2018.02299⟩ Article dans une revue hal-02176497v1
	RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae Bouabid Badaoui , Andre Fougeroux , Fabien Petit , Anna Anselmo , Chiara Gorni PLoS ONE, 2017, 12 (3), ⟨10.1371/journal.pone.0173438⟩ Article dans une revue hal-01604257v1
	Long noncoding RNA repertoire in chicken liver and adipose tissue Kévin Muret , Christophe C. Klopp , Valentin Wucher , Diane Esquerré , Fabrice Legeai Genetics Selection Evolution, 2017, 49 (1), pp.6. ⟨10.1186/s12711-016-0275-0⟩ Article dans une revue hal-01431420v1
	GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes Christopher K Tuggle , Elisabetta Giuffra , Stephen W White , Laura Clarke , Huaijun Zhou Animal Genetics, 2016, 47 (5), pp.528-533. ⟨10.1111/age.12466⟩ Article dans une revue hal-02912035v1
	A 2.5-kilobase deletion containing a cluster of cine microRNAs in the latency-associated-transcript locus of the pseudorabies virus affects the host response of porcine trigeminal ganglia during established latency Nada Mahjoub , Sophie Dhorne-Pollet , Walter Fuchs , Marie-Laure M.-L. Endale Ahanda , Elke Lange Journal of Virology, 2015, 89 (1), pp.428-442. ⟨10.1128/JVI.02181-14⟩ Article dans une revue hal-02631711v1
	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 Genome Biology, 2015, 16 (1), pp.57. ⟨10.1186/s13059-015-0622-4⟩ Article dans une revue hal-01194102v1
	Impact of the genetic background on the composition of the chicken plasma MiRNome in response to a stress Marie-Laure Endale Ahanda , Tatiana Zerjal , Sophie Pollet , Andrea Rau , Amanda Cooksey PLoS ONE, 2014, 9 (12), pp.1-26. ⟨10.1371/journal.pone.0114598⟩ Article dans une revue hal-01194096v1
	Structural and functional annotation of the porcine immunome Harry D Dawson , Jane E Loveland , Géraldine Pascal , James G R Gilbert , Hirohide Uenishi BMC Genomics, 2013, 14, online (may), Non paginé. ⟨10.1186/1471-2164-14-332⟩ Article dans une revue hal-01019897v1
	Prediction of Altered 3′- UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region Marie-Laure Endale Ahanda , Eric R. Fritz , Jordi Estellé , Zhi-Liang Hu , Ole Madsen PLoS ONE, 2012, 7, online (11), Non paginé. ⟨10.1371/journal.pone.0048607⟩ Article dans une revue hal-01019035v1
	Analyses of pig genomes provide insight into porcine demography and evolution Martien A. M. Groenen , Alan L. Archibald , Hirohide Uenishi , Christopher K. Tuggle , Yasuhiro Takeuchi Nature, 2012, 491 (7426), pp.393-398. ⟨10.1038/nature11622⟩ Article dans une revue cea-00880676v1
	Co-Expression of Host and Viral MicroRNAs in Porcine Dendritic Cells Infected by the Pseudorabies Virus Anna Anselmo , Laurence Flori , Florence Jaffrezic , Teresa Rutigliano , Maria Cecere PLoS ONE, 2011, 6 (3), ⟨10.1371/journal.pone.0017374⟩ Article dans une revue hal-01190510v1
	Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources Sem Genini , Bouabid Badaoui , Gert Sclep , Stephen Bishop , Dave Waddington BMC Genomics, 2011, 12 (1), pp.225. ⟨10.1186/1471-2164-12-225⟩ Article dans une revue inserm-00601542v1
	A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Elisabetta Giuffra , S. Marklund , E. Bongcam-Rudloff , Patrick Chardon , J.M.H. Kijas Mammalian Genome, 2002, 13, pp.569-577 Article dans une revue hal-02679569v1
	The origin of the domestic pig: independent domestication and subsequent introgression. Elisabetta Giuffra , J. M. Kijas , Valérie Amarger , O. Carlborg , J.T. Jeon Genetics, 2000, 154 (4), pp.1785-91 Article dans une revue hal-02699239v1
	Genetic diversity of eleven European pig breeds Guillaume Laval , N. Iannucelli , Christian Legault , Denis Milan , Martien A.M Groenen Genetics Selection Evolution, 2000, 32, pp.187-203 Article dans une revue hal-02683681v1
	Genetic diversity of eleven European pig breeds Guillaume Laval , Nathalie Iannuccelli , Christian Legault , Denis Milan , Martien Groenen Genetics Selection Evolution, 2000, 32 (2), pp.187-203. ⟨10.1051/gse:2000113⟩ Article dans une revue hal-00894306v1
	A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to the IGF2 locus. J. T. Jeon , O. Carlborg , A Törnsten , Elisabetta Giuffra , Valérie Amarger Nature Genetics, 1999, 21 (2), pp.157-158. ⟨10.1038/5938⟩ Article dans une revue hal-02695367v1
	Phylogenetic relationships and introgression patterns between incipient parapatric species of Italian brown trout (Salmo trutta L. complex) Elisabetta Giuffra , René R. Guyomard , G. Forneris Molecular Ecology, 1996, 5, pp.207-220 Article dans une revue hal-02687096v1
	Mitochondrial control region and protein coding genes sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy Elisabetta Giuffra , L. Bernatchez , René R. Guyomard Molecular Ecology, 1994, 3, pp.161-171 Article dans une revue hal-02712184v1

	RNA-seq data for detecting reliable SNPs & genotypes in livestock species: interest for coding variant characterization and cis-regulation analysis by allele-specific expression ! Frédéric Jehl , Fabien Degalez , Maria Bernard , Frédéric Lecerf , Laetitia Lagoutte World Poultry Congress (WPC) 2022, Aug 2022, Paris, France Communication dans un congrès hal-04258396v1
	The EU-H2020 Project GENE-Switch (The regulatory GENomE of SWine and CHicken: functional annotation during development) Elisabetta Giuffra The Plant and Animal Genome XXVII Conference (PAG), Jan 2020, San Diego, United States Communication dans un congrès hal-03364331v1
	FR-Agencode: An Update Elisabetta Giuffra , Sarah Djebali , Andrea Rau , Sandrine Lagarrigue , Hervé Acloque The Plant and Animal Genome XXVII Conference (PAG), Jan 2019, San Diego, United States Communication dans un congrès hal-03364351v1
	Introduction to functional annotation of animal genomes consortium Christopher Tuggle , Elisabetta Giuffra 2019 ASAS Midwest Meeting, American Society of Animal Science (ASAS); American Dairy Science Association (ADSA), Jul 2019, Inconnue, France. pp.17, ⟨10.1093/jas/skz122.031⟩ Communication dans un congrès hal-03178046v1
	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 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 ASAS/ASDS Midwest Joint Meeting, Mar 2019, Omaha, United States. ⟨10.1093/jas/skz122.028⟩ Communication dans un congrès hal-02735898v1
	An atlas of chicken long non-coding RNAs gathering multiple sources : gene models and expression across more than twenty tissues Frédéric Jehl , Kévin Muret , Maria Bernard , Diane Esquerré , Hervé Acloque PAG XXVII - Plant & Animal Genome Conference, Jan 2019, San Diego, United States Communication dans un congrès hal-02790912v1
	Chromatin accessibility conservation across four livestock species Sarah Djebali Quelen , Sylvain Foissac , Nathalie Vialaneix , Kylie Munyard , Andrea Rau Conference of the International Society for Animal Genetics (ISAG 2019), Jul 2019, Llieda, Spain Communication dans un congrès hal-02788732v1
	Generating 3D organoid-like structures from porcine induced pluripotent-like cells in vitro. Elisabetta Giuffra , Hervé Acloque , Giorgia Egidy , Nico Taverne , Anya Taverne-Thiele 11. Symposium of the French Domestic Animal Immunology Network,, Mar 2018, Tours, France Communication dans un congrès hal-02918626v1
	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 3. Journée de Séminaires du Département Phase sur l'Epigénétique EpiPhase, May 2017, Jouy-en-Josas, France Communication dans un congrès hal-01603057v1
	Functional Analysis of microRNAs:mRNA Interactions Between Pseudorabies Virus (PrV) and Its Natural Pig Host Sophie Pollet , Guillemette Marot , Jerôme Lecardonnel , Marco Moroldo , Florence Jaffrezic 24. Plant and Animal Genome Conference (PAG), Jan 2016, San Diego, United States Communication dans un congrès hal-01606998v1
	Perspective of FAANG (Functional Annotation of Animal Genomes) Elisabetta Giuffra AGRI Research workshops, Oct 2016, Bruxelles, Belgium Communication dans un congrès hal-01605576v1
	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 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 Nuclear Spatial Conformation of Livestock Genomes in Cell Lines and Liver Cells Sylvain Foissac , Hervé Acloque , Florence Mompart , Diane Esquerre , David Robelin PAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States. Non paginé Communication dans un congrès hal-01508146v1
	Chromatin Accessibility in Porcine Liver, Spleen and Circulating Immune Cells Sylvain Foissac , Kylie Munyard , Adeline Goubil , Silvia Vincent-Naulleau , Diane Esquerre XXIV PAG - Plant and Animal Genome Conference, Jan 2016, San Diego, United States Communication dans un congrès hal-01532588v1
	Investigating the nuclear spatial conformation of livestock genomes using Hi-C Sylvain Foissac , Hervé Acloque , Florence Mompart , Diane Esquerre , David Robelin NGS'16 Genome Annotation, Apr 2016, Barcelone, Spain Communication dans un congrès hal-01581540v1
	Chromatin accessibility in the liver and circulating immune cells of pigs, cattle, goats and chickens Elisabetta Giuffra , . Fr-Agencode Consortium Livestock Genomics Workshop, Sep 2016, Cambridge, United Kingdom Communication dans un congrès hal-01607950v1
	RNA silencing-targeted transcriptome of porcine alveolar macrophages upon infection with porcine reproductive and respiratory syndrome viruses (PRRSV) of different virulence Sophie Dhorne-Pollet , Patricia Renson , Florence Jaffrezic , Guillemette Marot , Marco M. Moroldo 35. Conference of the International Society for Animal Genetics (ISAG), Jul 2016, Salt Lake City, Utah, United States. 197 p Communication dans un congrès hal-02740229v1
	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
	Update on the Functional Annotation of ANimal Genomes (FAANG) initiative Elisabetta Giuffra Final RGB-Net Meeting and 6th Rabbit Biotechnology Meeting, Nov 2015, Lyon, France Communication dans un congrès hal-01602315v1
	Les microARN circulants : de nouveaux biomarqueurs pour des caractères économiquement importants chez les poules ? Tatiana Zerjal , Marie-Laure Endale Ahanda , Sophie Pollet , Andrea Rau , Elisabetta Giuffra 11. Journées de la Recherche Avicole et Palmipèdes à Foie Gras, Mar 2015, Tours, France. pp.1-5 Communication dans un congrès hal-01194121v1
	The Functional Annotation of Animal Genomes (FAANG) Initiative Elisabetta Giuffra , Sylvain Foissac , Ole Madsen , Martien Groenen , Richard Crooijmans Plant and Animal Genome (PAG), Jan 2015, San Diego, United States Communication dans un congrès hal-01194056v1
	Functional analysis of candidate interactions between miRNAs encoded by the pseudorabies virus (PrV) and pig genes. Nada Mahjoub , Sophie Pollet , Gail Sherba , Thomas Mettenleiter , Elisabetta Giuffra 34. International Society for Animal Genetics Conference (ISAG), Jul 2014, Xi'An, China Communication dans un congrès hal-01606096v1
	Impact of the genetic background on the composition of the chicken plasma miRNome in response to a stress Elisabetta Giuffra Livestock genomics workshop, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). GBR., Sep 2014, Cambridge, United Kingdom Communication dans un congrès hal-01602316v1
	MicroRNA technology, relevance and application Elisabetta Giuffra EADGENE-S final meeting, May 2013, Bruxelles, Belgium Communication dans un congrès hal-01602318v1
	MiRNA targeting in host-virus interaction: inter-strain comparison in Pseudorabies Virus (PrV) Marie-Laure Endale Ahanda , Thomas Letellier , Elisabetta Giuffra 33. Conference of the International Society of Animal Genetics, Cairns Conference. Cairns, AUS., Jul 2012, Cairns, Australia. 1 p Communication dans un congrès hal-01019836v1
	Functional genomics of Pseudorabies in pigs: a model for host-pathogen interaction studies Nada N. Mahjoub , Elisabetta Giuffra 15. Séminaire des Thésards du département Génétique Animale, Institut National de la Recherche Agronomique (INRA). Paris, FRA., Mar 2012, Ile d'Oléron, France. pp.1 Communication dans un congrès hal-01000389v1
	In silico prediction of microRNAs targeting alleles of the Swine Leukocyte Antigen complex Marie-Laure M.-L. Endale Ahanda , Zhi-Liang Hu , Jordi Estellé , Eric R. Fritz , Claire Rogel Gaillard ISAFG 2011, Oct 2011, Dublin, Ireland Communication dans un congrès hal-02803523v1
	microRNA target prediction and 3'UTR polymorphism in swine Marie-Laure M.-L. Endale Ahanda , Zhi-Liang Z.-L. Hu , Jordi Estellé , Eric R. E. R. Fritz , Claire Gaillard RNAi World Congress, Apr 2011, Boston, United States Communication dans un congrès hal-01000372v1
	Community annotation of immunity-related genes in the pig genome Christopher K. Tuggle , Claire Gaillard , Jane Loveland , Hirohide Uenishi , Harry Dawson 4. International Symposium on Animal Functional Genomics, Oct 2011, Dublin, Ireland Communication dans un congrès hal-01193966v1
	miRNA discovery in Sus scrofa and in the Pseudorabies virus through a deep sequencing approach Anna Anselmo , Laurence Flori , Naima Cortes-Perez , F. Lefevre , Claire Gaillard Pig Genome III Conference, A celebration for completing the pig genome sequence, 2009, Hinxton, United States Communication dans un congrès hal-01193416v1
	Towards a genomic platform for analysis of wild boar and suiforme diversity and evolution. R.P.M.A. Crooijmans , T. Baxter , S. Casu , K. Chen , A. Ducos 7th International Symposium on Wild Boar (Sus scrofa) and on Sub-order Suiformes, 2008, Sopron, pp.Inconnu Communication dans un congrès hal-02822635v1
	Exploring the host-virus miRNA regulation layer: pig dendritic cells (DCs) infected by PrV (pseudorabies virus) V. Mariani , Laurence Flori , Roberto Malinverni , F. Lefevre , Sem Genini Pig Genome II Conference, 2008, Ljubljana, Slovenia Communication dans un congrès hal-02814829v1
	Exploring the host-virus miRNAs regulation layer: pig dendritic cells (DCs) infected by PrV (Pseudorabies virus) Valentina Mariani , R. Malinverni , S. Genini , Naima G. Cortes-Perez , Laurence Flori EADGENE, Mar 2008, Liège, Belgium. n.p Communication dans un congrès hal-02812828v1

	Integrative analyses of chromosome conformation, chromatin accessibility and gene expression in human and livestock genomes Camille Mestre , Sarah Djebali Quelen , Thomas Faraut , Nathalie Vialaneix , Andrea Rau European Conference on Computational Biology (ECCB 2018), Sep 2018, Athènes, Greece. , 2018 Poster de conférence hal-02784857v1
	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 36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book Poster de conférence hal-01603033v1
	Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project] Sylvain Foissac , Sarah Djebali Quelen , Hervé Acloque , Philippe Bardou , Fany Blanc 36th International Society for Animal Genetics Conference, Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book Poster de conférence hal-01608449v1
	Long-non coding RNAs repertoires in liver and two T lymphocyte cell types in four livestock species Kévin Muret , Sarah Djebali Quelen , Thomas Derrien , Cédric Cabau , Christophe C. Klopp 36. Conference of the International Society for Animal Genetics (ISAG), Jul 2017, Dublin, Ireland. 2017, ISAG 2017 - Genomes to Phenomes - Abstract Book Poster de conférence hal-01621915v1
	Une nouvelle facette du génome de poule : les genes “longs non-codants" Kévin Muret , Christophe C. Klopp , Valentin Wucher , Diane Esquerre , Fabrice Legeai 12. Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, Apr 2017, Tours, France. ITAVI - Institut Technique de l'Aviculture, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, 2017, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras Poster de conférence hal-01605848v1
	Long-non coding RNAs repertoire in liver and adipose tissue in chicken Kévin Muret , Christophe C. Klopp , Valentin Wucher , Diane D. Esquerre , Fabrice Legeai XXIV International Plant & Animal Genome (Pag), Jan 2016, San Diego, United States. 2016 Poster de conférence hal-02799305v1
	Sampling tissue for FAANG: the example of cattle and chickens in France Michèle Tixier-Boichard , Stéphane Fabre , Sophie Dhorne-Pollet , Emmanuelle Rebours , Adeline Goubil GO-FAANG Workshop, Oct 2015, Washington DC, United States. , 1 p., 2015 Poster de conférence hal-02801142v1
	miRNA-mediated regulation: learning from Pseudorabies virus infected pigs Elisabetta Giuffra International Plant & Animal Genome XXII (PAG), Jan 2014, San Diego, United States. 2014 Poster de conférence hal-01602317v1
	Understanding the complex interaction between pseudorabies virus (PrV) and its natural host using RIP-Chip enrichment analysis Sophie Pollet , Jerôme Lecardonnel , Florence Jaffrezic , Marco Moroldo , Elisabetta Giuffra 34. International Society for Animal Genetics Conference (ISAG), Jul 2014, Xi'An, China. 2014, Proceedings of the 34th International Society for Animal Genetics Conference Poster de conférence hal-01603396v1
	Structural and functional annotation of immunity-related genes in the pig genome Chris Tuggle , Claire Rogel Gaillard , Jane E Loveland , Hirohide Uenishi , Harry D Dawson 20. Plant and Animal Genome Conference, Jan 2012, San Diego, United States. 2012 Poster de conférence hal-02745739v1
	Annotation of the immunity-related genes in the pig genome . Immune Response Annotation Group (irag) , Claire Rogel Gaillard , Christopher K. Tuggle , Jane Loveland , Jennifer Harrow 32nd Conference of the International Society of Animal Genetics (ISAG), Jul 2010, Edinburgh, United Kingdom. 2010 Poster de conférence hal-02821666v1

	Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig Sylvain Foissac , Sarah Djebali , Kylie Munyard , Nathalie Vialaneix , Andrea Rau 2018 Pré-publication, Document de travail hal-02791029v1

	Implementing a program of host genomics of key host-pathogen systems in livestock Elisabetta Giuffra Life Sciences [q-bio]. Université de Versailles Saint-Quentin-en-Yvelines, 2014 HDR tel-02797687v1

Elisabetta Giuffra

Publications

Tissue resources for the functional annotation of animal genomes

Intestinal organoids in farm animals

Editorial: Functional Annotation of Animal Genomes

RNA-Seq Data for Reliable SNP Detection and Genotype Calling

From FAANG to fork: application of highly annotated genomes to improve farmed animal production

An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

The mirna-targeted transcriptome of porcine alveolar macrophages upon infection with porcine reproductive and respiratory syndrome virus

Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Functional Annotation of Animal Genomes (FAANG) : Current Achievements and Roadmap

Macrophage-B Cell Interactions in the Inverted Porcine Lymph Node and Their Response to Porcine Reproductive and Respiratory Syndrome Virus

Porcine Reproductive and Respiratory Syndrome Virus Type 1.3 Lena Triggers Conventional Dendritic Cells 1 Activation and T Helper 1 Immune Response Without Infecting Dendritic Cells

RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae

Long noncoding RNA repertoire in chicken liver and adipose tissue

GO-FAANG meeting: a Gathering On Functional Annotation of Animal Genomes

A 2.5-kilobase deletion containing a cluster of cine microRNAs in the latency-associated-transcript locus of the pseudorabies virus affects the host response of porcine trigeminal ganglia during established latency

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.

Impact of the genetic background on the composition of the chicken plasma MiRNome in response to a stress

Structural and functional annotation of the porcine immunome

Prediction of Altered 3′- UTR miRNA-Binding Sites from RNA-Seq Data: The Swine Leukocyte Antigen Complex (SLA) as a Model Region

Analyses of pig genomes provide insight into porcine demography and evolution

Co-Expression of Host and Viral MicroRNAs in Porcine Dendritic Cells Infected by the Pseudorabies Virus

Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources

A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT.

The origin of the domestic pig: independent domestication and subsequent introgression.

Genetic diversity of eleven European pig breeds

Genetic diversity of eleven European pig breeds

A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to the IGF2 locus.

Phylogenetic relationships and introgression patterns between incipient parapatric species of Italian brown trout (Salmo trutta L. complex)

Mitochondrial control region and protein coding genes sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy

RNA-seq data for detecting reliable SNPs & genotypes in livestock species: interest for coding variant characterization and cis-regulation analysis by allele-specific expression !

The EU-H2020 Project GENE-Switch (The regulatory GENomE of SWine and CHicken: functional annotation during development)

FR-Agencode: An Update

Introduction to functional annotation of animal genomes consortium

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

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

An atlas of chicken long non-coding RNAs gathering multiple sources : gene models and expression across more than twenty tissues

Chromatin accessibility conservation across four livestock species

Generating 3D organoid-like structures from porcine induced pluripotent-like cells in vitro.

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

Functional Analysis of microRNAs:mRNA Interactions Between Pseudorabies Virus (PrV) and Its Natural Pig Host

Perspective of FAANG (Functional Annotation of Animal Genomes)

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

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

Chromatin Accessibility in Porcine Liver, Spleen and Circulating Immune Cells

Investigating the nuclear spatial conformation of livestock genomes using Hi-C

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

RNA silencing-targeted transcriptome of porcine alveolar macrophages upon infection with porcine reproductive and respiratory syndrome viruses (PRRSV) of different virulence

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

Update on the Functional Annotation of ANimal Genomes (FAANG) initiative

Les microARN circulants : de nouveaux biomarqueurs pour des caractères économiquement importants chez les poules ?

The Functional Annotation of Animal Genomes (FAANG) Initiative

Functional analysis of candidate interactions between miRNAs encoded by the pseudorabies virus (PrV) and pig genes.

Impact of the genetic background on the composition of the chicken plasma miRNome in response to a stress

MicroRNA technology, relevance and application

MiRNA targeting in host-virus interaction: inter-strain comparison in Pseudorabies Virus (PrV)

Functional genomics of Pseudorabies in pigs: a model for host-pathogen interaction studies

In silico prediction of microRNAs targeting alleles of the Swine Leukocyte Antigen complex

microRNA target prediction and 3'UTR polymorphism in swine

Community annotation of immunity-related genes in the pig genome

miRNA discovery in Sus scrofa and in the Pseudorabies virus through a deep sequencing approach

Towards a genomic platform for analysis of wild boar and suiforme diversity and evolution.

Exploring the host-virus miRNA regulation layer: pig dendritic cells (DCs) infected by PrV (pseudorabies virus)

Exploring the host-virus miRNAs regulation layer: pig dendritic cells (DCs) infected by PrV (Pseudorabies virus)

Integrative analyses of chromosome conformation, chromatin accessibility and gene expression in human and livestock genomes

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

Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Long-non coding RNAs repertoires in liver and two T lymphocyte cell types in four livestock species

Une nouvelle facette du génome de poule : les genes “longs non-codants"

Long-non coding RNAs repertoire in liver and adipose tissue in chicken

Sampling tissue for FAANG: the example of cattle and chickens in France

miRNA-mediated regulation: learning from Pseudorabies virus infected pigs

Understanding the complex interaction between pseudorabies virus (PrV) and its natural host using RIP-Chip enrichment analysis

Structural and functional annotation of immunity-related genes in the pig genome

Annotation of the immunity-related genes in the pig genome

Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig

Implementing a program of host genomics of key host-pathogen systems in livestock