Livrables
Lists and maps of inter- and transgenerational paternally transmitted effects on the embryonic intermediate phenotype (transcriptome) and epigenetic characteristics and marks (T5.3)
Final report on BovReg data productionFinal report on BovReg data production (T3.4)
Genomic prediction for feed efficiency in single and multi-breed contextD7.4 Genomic prediction for feed efficiency in single and multi-breed context
Training course/hackathon on bioinformatics methodsReport on course/hackathon on bioinformatics methods at CRG premises (T9.2)
Reports on 3 dissemination workshopsReports on 3 dissemination workshops (T9.4)
Differentially expressed genes in bovine embryosLists of differentially expressed genes affected by different culture conditions temperature increased fatty acid concentrations in bovine embryos T52
Report on ontologies used across BovRegReport on ontologies used across BovReg (T3.3)
Report on promoting Democs game to specific target groupsReport on promoting Democs game to specific target groups (T9.3)
Spatial DNA-DNA interaction mapA spatial DNADNA interaction map of the bovine genome T23
Final version of the cow evolutionary annotationFinal version of the cow genome evolutionary annotation (T3.5)
List of antibodies for ChIP-seq on bovine tissuesList of antibodies suitable for ChIPSeq on bovine tissues T12
Map of open chromatin regions, 4 specific histone marks, CTCF binding sites across bovine cell-linesA map of open chromatin regions four specific histone marks of CTCF binding sites of the bovine genome across the five bovine celllines T22
Final report on cluster cooperation activitiesFinal report on cluster cooperation activities (T9.1)
Communication PlanCommunication Plan (T9.3)
Agreed Statutes of the EEABAgreed Statutes of the EEAB (T11.3)
Article on the societal context and ethical dimensionJournal article on societal context and ethical dimensions T81
Training on methodology for biology-driven selectionReport on course on methodology for biology-driven selection (T9.2)
Audit on required and available pipelinesAudit on required and available pipelines across the consortium (T3.1)
Genomic prediction for mastitis in Nordic breedsD7.5 Genomic prediction for mastitis in Nordic breeds
Demonstration of performance of the mastitis feature model in the Nordic cattle breeding programmeDemonstration of performance of the mastitis feature model in the Nordic cattle breeding program (T9.4)
Public report on ethical dimensions of innovations in livestock genomicsPublic Report on the ethical dimensions (T8.1)
Public report: on societal context of innovations in livestock genomicsPublic Report: Societal context of innovations in livestock genomics (T8.1)
Policy seminar for all relevant stakeholderPolicy seminar for all relevant stakeholders (T8.3)
BAM files for CAGE libraries144 BAM files for CAGE libraries (T2.1)
Project sessions at international conferences and final conferenceReports on 3 project sessions at international conferences and final conference (T9.3)
Mid project report on BovReg data productionMid project report on BovReg data production T34
First version of the cow evolutionary annotationFirst version of the cow genome evolutionary annotation T35
Bayesian multi-feature genomic prediction model with overlapping featuresDevelopment and evaluation of Bayesian multi-feature genomic prediction model with overlapping features (T7.1)
Training course on new laboratory methodsReport on course on new laboratory methods at UNLIM premises (T9.2)
Single-cell analysis results of key tissuesMaps of chromatin architecture in bovine embryos
Maps of culture conditionspecific chromatin architecture in bovine embryos T52
lncRNA-DNA interaction mapA map of features in the bovine genome interacting with selected long lncRNAs (T2.3)
First prototype of a normalized ENCODE pipelineFirst prototype of a normalized ENCODE pipeline (T3.2)
Map of open chromatin regions, 4 specific histone marks and CTCF binding sites for 24 tissuesA map of open chromatin regions four specific histone marks and CTCF binding sites of the bovine genome for 24 tissues across three breeds two sexes and two developmental stages T22
Communication tools, the website and communication packageCommunication tools, including the project website (concept, screenshots) and the project communication package (logo, flyer, poster) (T9.3)
A comprehensive functional annotation mapA comprehensive map of functional annotation of the bovine genome (T2.5)
Establishment of novel bovine cell linesEstablishment of novel bovine cell lines T11
6-monthly reports on BovReg data releases6-monthly reports on BovReg data releases (T10.2)
150 BAM files for ATAC-seq & ChIP-seq libraries150 BAM files for each of the ATACseq and ChIPseq H3K4me3 H3K4me1 H3K27me3 H3K27ac and CTCF libraries T22
Ontology improvementsD3.11 Ontology improvements updating and extending D3.3, the report on ontologies used across BovReg, in collaboration with the EuroFAANG cluster partnes
Framework to enable professionals to address societal dimensions of livestock breedingFramework to enable professionals to address societal dimensions of livestock breeding (T8.3)
Final report on normalized pipelinesFinal report on normalized pipelines (T3.2)
Plan to achieve synergies with cluster projectsCollaboration plan (T9.1)
Bayesian Variable Selection models with SNP- specific a-priori inclusion probabilitiesDevelopment and evaluation of Bayesian Variable Selection models with SNPspecific a priori inclusion probabilities T71
Contribution of annotations to heritabilityContribution of different functional annotations to the heritability of BovRegs key traits T44
A panel of tests at selected MGE insertionsA panel of tests for presence of copies of selected MGE insertions in the available breeds (T2.4)
Mid-term report on cluster cooperation activitiesMidterm report on cluster cooperation activities T91
Report of final GA meetingApproved Minutes of final GA meeting, including EEAB meeting (T11.2 &3)
Genomic prediction using functional annotations and QTL features in small dairy breedsD7.3 Genomic prediction using functional annotations and QTL features in small dairy breeds
Mid project report on normalized pipelinesMid project report on normalized consortium pipelines T32
List of genotypes at each MGE insertion siteA list of genotypes of whole-genome sequenced animals at each MGE insertion site (T2.4)
Deployment procedure for optimized pipelineCloud deployment procedure for normalized pipeline T32
Report on results of playing Democs gamesReport on results of playing Democs game in English and Finnish (T8.2)
Maps of tissue and cell line specific DNA methylationGenome wide maps of tissue and cell line specific DNA methylation T51
BAM files for PolyA+,Total and small RNA144 BAM files for RNA transcripts from PolyA Total and small RNA libraries T21
Genomic data of novel bovine cell linesGenomic data of novel bovine cell lines T11
Map of fully annotated bovine transcriptomesA map of fully annotated bovine transcriptome for 24 tissues across three breeds two sexes and two developmental stages T21
Catalogue of MGE insertion sitesA catalogue of MGE insertion sites across the cattle genome (T2.4)
Data management plan (T10.1)
A collection of pipelines registered in the main repository (T10.3)
Democs game, boxed and downloadable formsDemocs game in boxed and downloadable forms (T8.2)
Dedicated portal website to access and publish the BovReg metadata T102
Publications
Auteurs:
Young-Lim, Lee; Mirte, Bosse; Haruko, Takeda; Gabriel Costa Monteiro, Moreira; Latifa, Karim; Tom, Druet; Claire, Oget-Ebrad; Wouter, Coppieters; Roel F, Veerkamp; Martien A M, Groenen; Michel, Georges; Aniek C, Bouwman; Carole, Charlier
Publié dans:
BMC Genomics, Numéro 24, Article number: 225 (2023), 2023, ISSN 1471-2164
Éditeur:
BioMed Central
DOI:
10.1186/s12864-023-09259-8
Auteurs:
Annie Robic; Chloé Cerutti; Christa Kühn; Christa Kühn; Thomas Faraut
Publié dans:
Frontier Genetics, Numéro 4, 2021, ISSN 1664-8021
Éditeur:
Frontiers Media
DOI:
10.3389/fgene.2021.665153
Auteurs:
Audald Lloret-Villas, Hubert Pausch, Alexander S. Leonard
Publié dans:
Genetics Selection Evolution, Numéro 55, 2023, ISSN 1297-9686
Éditeur:
Springer Nature
DOI:
10.1186/s12711-023-00809-y
Auteurs:
Kramer, K.; Meijboom, F. L.B.; AISS Sustainable Animal Stewardship; dASS BW-2; LS Wijsgerige Ethiek; OFR - Ethics Institute
Publié dans:
Journal of Agricultural and Environmental Ethics, Numéro 34 (1), 2021, ISSN 1187-7863
Éditeur:
Kluwer Academic Publishers
DOI:
10.1007/s10806-021-09843-6
Auteurs:
Mapel, Kadri, et al.
Publié dans:
Nature Communications, Numéro 15, Article number: 674, 2024, ISSN 2041-1723
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41467-024-44935-7
Auteurs:
Marie-Pierre Sanchez; Thierry Tribout; Naveen K. Kadri; Praveen K. Chitneedi; Steffen Maak; Chris Hozé; Mekki Boussaha; Pascal Croiseau; Romain Philippe; Mirjam Spengeler; Christa Kühn; Yining Wang; Changxi Li; Graham Plastow; Hubert Pausch; Didier Boichard
Publié dans:
Genetics Selection Evolution, Numéro 55, Article number: 70 (2023), 2023, Page(s) Springer Nature, ISSN 1297-9686
Éditeur:
Springer
DOI:
10.1186/s12711-023-00848-5
Auteurs:
Joanna Stojak; Dominique Rocha; Caroline Mörke; Christa Kühn; Veronique Blanquet; Hiroaki Taniguchi
Publié dans:
Journal of Applied Genetics, Numéro Volume 65, 2024, ISSN 1234-1983
Éditeur:
Polska Akademia Nauk
DOI:
10.1007/s13353-024-00846-3
Auteurs:
Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Lea
Publié dans:
Nucleic Acids Research, Numéro 49/D1, 2020, Page(s) D884-D891, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkaa942
Auteurs:
Jiyuan Li, Robert Mukiibi, Yining Wang, Graham S. Plastow, Changxi Li
Publié dans:
BMC Genomics, Numéro 22, 2021, Page(s) 823, ISSN 1471-2164
Éditeur:
BioMed Central
DOI:
10.1186/s12864-021-08064-5#ack1
Auteurs:
Peter W Harrison; M Ridwan Amode; Olanrewaju Austine-Orimoloye; Andrey G Azov; Matthieu Barba; If Barnes; Arne Becker; Ruth Bennett; Andrew Berry; Jyothish Bhai; Simarpreet Kaur Bhurji; Sanjay Boddu; Paulo R Branco Lins; Lucy Brooks; Shashank Budhanuru Ramaraju; Lahcen I Campbell; Manuel Carbajo Martinez; Mehrnaz Charkhchi; Kapeel Chougule; Alexander Cockburn; Claire Davidson; Nishadi H De Silva;
Publié dans:
Nucleic Acids Research, Numéro Volume 52, Numéro D1, 2024, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkad1049
Auteurs:
Audald Lloret-Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries and Hubert Pausch
Publié dans:
BMC Genomics, Numéro 22, 2021, Page(s) 363, ISSN 1471-2164
Éditeur:
BioMed Central
DOI:
10.1186/s12864-021-07554-w
Auteurs:
Doreen Becker, Rosemarie Weikard, Frieder Hadlich, Christa Kühn
Publié dans:
Scientific Data, Numéro 8, 2022, ISSN 2052-4463
Éditeur:
Springer Nature
DOI:
10.1038/s41597-021-00972-1
Auteurs:
Mollandin, Fanny
Publié dans:
BMC Bioinformatics, Numéro 23, Article number: 365, 2022, ISSN 1471-2105
Éditeur:
BioMed Central
DOI:
10.1186/s12859-022-04914-5
Auteurs:
Peter W Harrison, Alisha Ahamed, Raheela Aslam, Blaise T F Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O’Cathail, Amir Pakseresht, Youngmi Park, Stephane Pesant, Nadim Rahm
Publié dans:
Nucleic Acids Research, Numéro 49/D1, 2020, Page(s) D82-D85, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkaa1028
Auteurs:
Fiona Cunningham, James E Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tama
Publié dans:
Nucleic Acids Research, Numéro Volume 50, Numéro D1, 2022, ISSN 1362-4962
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkab1049
Auteurs:
Wietje Nolte, Rosemarie Weikard, Elke Albrecht, Harald M.Hammon, Christa Kühn
Publié dans:
Genomics, Numéro Volume 114 Numéro 1, 2022, Page(s) Pages 202-214, ISSN 0888-7543
Éditeur:
Academic Press
DOI:
10.1016/j.ygeno.2021.12.004
Auteurs:
Emily L. Clark, Alan L. Archibald, Hans D. Daetwyler, Martien A. M. Groenen, Peter W. Harrison, Ross D. Houston, Christa Kühn, Sigbjørn Lien, Daniel J. Macqueen, James M. Reecy, Diego Robledo, Mick Watson, Christopher K. Tuggle, Elisabetta Giuffra
Publié dans:
Genome Biology, Numéro 21/1, 2020, ISSN 1474-760X
Éditeur:
Springer nature
DOI:
10.1186/s13059-020-02197-8
Auteurs:
Viktor Milkevych, Emre Karaman, Goutam Sahana, Luc Janss, Zexi Cai, Mogens Sandø Lund
Publié dans:
G3 Genes|Genomes|Genetics, Numéro 21601836, 2021, ISSN 2160-1836
Éditeur:
Genetics Society of America
DOI:
10.1093/g3journal/jkab133
Auteurs:
Kramer, K.; Meijboom, F. L.B.; dASS BW-2; AISS Sustainable Animal Stewardship; LS Wijsgerige Ethiek; OFR - Ethics Institute
Publié dans:
Journal of Agricultural and Environmental Ethics, Numéro Volume 35, Numéro 2, 2022, ISSN 1187-7863
Éditeur:
Kluwer Academic Publishers
DOI:
10.1007/s10806-022-09883-6
Auteurs:
Xena Marie Mapel; Maya Hiltpold; Naveen Kumar Kadri; Ulrich Witschi; Hubert Pausch
Publié dans:
JDS Communications, Numéro Vol 3, Iss 2, 2022, ISSN 2666-9102
Éditeur:
Elsevier
DOI:
10.3168/jdsc.2021-0164
Auteurs:
Jiyuan Li; Yining Wang; Robert Mukiibi; Brian Karisa; Graham S. Plastow; Changxi Li
Publié dans:
Scientific Reports, Numéro vol. 12 , no. 1, 2022, ISSN 2045-2322
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41598-022-06567-z
Auteurs:
M. Salavati; R. Clark; D. Becker; C. Kühn; G. Plastow; S. Dupont; G.C.M. Moreira; C. Charlier; E.L. Clark
Publié dans:
G3 Genes|Genomes|Genetics, Numéro Volume 13, Numéro 8, 2023, ISSN 2160-1836
Éditeur:
Genetics Society of America
DOI:
10.1093/g3journal/jkad108
Auteurs:
Naveen Kumar Kadri; Xena M. Mapel; Hubert Pausch
Publié dans:
Communications Biology, Numéro Vol 4, Numéro 1, 2021, Page(s) Pp 1-13, ISSN 2399-3642
Éditeur:
Springer Nature
DOI:
10.1038/s42003-021-02725-7
Auteurs:
Peter W. Harrison; Alexey Sokolov; Akshatha Nayak; Jun Fan; Daniel R. Zerbino; Guy Cochrane; Paul Flicek
Publié dans:
Frontiers in Genetics, Numéro Vol 12, 2021, ISSN 1664-8021
Éditeur:
Frontiers Media
DOI:
10.3389/fgene.2021.639238
Auteurs:
Andres S, Bartling B, Stiensmeier V, Starke A, Schmicke M.
Publié dans:
Frontiers in Veterinary Science, Numéro Volume 10 - 2023, 2023, ISSN 2297-1769
Éditeur:
Frontiers Media
DOI:
10.3389/fvets.2023.1211135
Auteurs:
Fanny Mollandin, Andrea Rau, Pascal Croiseau
Publié dans:
G3 Genes|Genomes|Genetics, Numéro Volume 11, Numéro 11, 2021, ISSN 2160-1836
Éditeur:
Genetics Society of America
DOI:
10.1093/g3journal/jkab225
Auteurs:
Fergal J Martin; M Ridwan Amode; Alisha Aneja; Olanrewaju Austine-Orimoloye; Andrey G Azov; If Barnes; Arne Becker; Ruth Bennett; Andrew Berry; Jyothish Bhai; Simarpreet Kaur Bhurji; Alexandra Bignell; Sanjay Boddu; Paulo R Branco Lins; Lucy Brooks; Shashank Budhanuru Ramaraju; Mehrnaz Charkhchi; Alexander Cockburn; Luca Da Rin Fiorretto; Claire Davidson; Kamalkumar Dodiya; Sarah Donaldson; Bilal
Publié dans:
Nucleic Acids Research, Numéro Volume 51, Numéro D1, 2022, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkac958
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