Rezultaty
Report on course/hackathon on bioinformatics methods at CRG premises (T9.2)
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)
Spatial DNA-DNA interaction mapA spatial DNADNA interaction map of the bovine genome T23
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
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
Audit on required and available pipelinesAudit on required and available pipelines across the consortium (T3.1)
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)
BAM files for CAGE libraries144 BAM files for CAGE libraries (T2.1)
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)
Maps of chromatin architecture in bovine embryosMaps of culture conditionspecific chromatin architecture in bovine embryos T52
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)
Establishment of novel bovine cell linesEstablishment of novel bovine cell lines T11
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
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
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
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)
Dedicated portal website to access and publish the BovReg metadata T102
Democs game in boxed and downloadable forms (T8.2)
Publikacje
Autorzy:
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
Opublikowane w:
BMC Genomics, Numer 24, Article number: 225 (2023), 2023, ISSN 1471-2164
Wydawca:
BioMed Central
DOI:
10.1186/s12864-023-09259-8
Autorzy:
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
Opublikowane w:
BMC Genomics, Numer 24, Article number: 225 (2023), 2023, ISSN 1471-2164
Wydawca:
BioMed Central
DOI:
10.1186/s12864-023-09259-8
Autorzy:
Annie Robic; Chloé Cerutti; Christa Kühn; Christa Kühn; Thomas Faraut
Opublikowane w:
Frontier Genetics, Numer 4, 2021, ISSN 1664-8021
Wydawca:
Frontiers Media
DOI:
10.3389/fgene.2021.665153
Autorzy:
Kramer, K.; Meijboom, F. L.B.; AISS Sustainable Animal Stewardship; dASS BW-2; LS Wijsgerige Ethiek; OFR - Ethics Institute
Opublikowane w:
Journal of Agricultural and Environmental Ethics, Numer 34 (1), 2021, ISSN 1187-7863
Wydawca:
Kluwer Academic Publishers
DOI:
10.1007/s10806-021-09843-6
Autorzy:
Mapel, Kadri, et al.
Opublikowane w:
Nature Communications, Numer 15, Article number: 674, 2024, ISSN 2041-1723
Wydawca:
Nature Publishing Group
DOI:
10.1038/s41467-024-44935-7
Autorzy:
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
Opublikowane w:
Genetics Selection Evolution, Numer 55, Article number: 70 (2023), 2023, Strona(/y) Springer Nature, ISSN 1297-9686
Wydawca:
Springer
DOI:
10.1186/s12711-023-00848-5
Autorzy:
Joanna Stojak; Dominique Rocha; Caroline Mörke; Christa Kühn; Veronique Blanquet; Hiroaki Taniguchi
Opublikowane w:
Journal of Applied Genetics, Numer Volume 65, 2024, ISSN 1234-1983
Wydawca:
Polska Akademia Nauk
DOI:
10.1007/s13353-024-00846-3
Autorzy:
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
Opublikowane w:
Nucleic Acids Research, Numer 49/D1, 2020, Strona(/y) D884-D891, ISSN 0305-1048
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkaa942
Autorzy:
Jiyuan Li, Robert Mukiibi, Yining Wang, Graham S. Plastow, Changxi Li
Opublikowane w:
BMC Genomics, Numer 22, 2021, Strona(/y) 823, ISSN 1471-2164
Wydawca:
BioMed Central
DOI:
10.1186/s12864-021-08064-5#ack1
Autorzy:
Joanna Stojak; Dominique Rocha; Caroline Mörke; Christa Kühn; Veronique Blanquet; Hiroaki Taniguchi
Opublikowane w:
Journal of Applied Genetics, Numer Volume 65, 2024, ISSN 1234-1983
Wydawca:
Polska Akademia Nauk
DOI:
10.1007/s13353-024-00846-3
Autorzy:
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;
Opublikowane w:
Nucleic Acids Research, Numer Volume 52, Numer D1, 2024, ISSN 0305-1048
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkad1049
Autorzy:
Audald Lloret-Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries and Hubert Pausch
Opublikowane w:
BMC Genomics, Numer 22, 2021, Strona(/y) 363, ISSN 1471-2164
Wydawca:
BioMed Central
DOI:
10.1186/s12864-021-07554-w
Autorzy:
Mollandin, Fanny
Opublikowane w:
BMC Bioinformatics, Numer 23, Article number: 365, 2022, ISSN 1471-2105
Wydawca:
BioMed Central
DOI:
10.1186/s12859-022-04914-5
Autorzy:
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
Opublikowane w:
Nucleic Acids Research, Numer 49/D1, 2020, Strona(/y) D82-D85, ISSN 0305-1048
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkaa1028
Autorzy:
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
Opublikowane w:
Nucleic Acids Research, Numer Volume 50, Numer D1, 2022, ISSN 1362-4962
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkab1049
Autorzy:
Koen Kramer; Franck L. B. Meijboom
Opublikowane w:
Ethical Theory and Moral Practice, 2022, ISSN 1386-2820
Wydawca:
Kluwer Academic Publishers
DOI:
10.1007/s10677-022-10305-9
Autorzy:
Doreen Becker; Rosemarie Weikard; Frieder Hadlich; Christa Kühn; Christa Kühn
Opublikowane w:
Scientific Data, Numer 7, 2021, ISSN 2052-4463
Wydawca:
Springer Nature
DOI:
10.1038/s41597-021-00972-1
Autorzy:
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
Opublikowane w:
Genetics Selection Evolution, Numer 55, Article number: 70 (2023), 2023, ISSN 1297-9686
Wydawca:
Springer Nature
DOI:
10.1186/s12711-023-00848-5
Autorzy:
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; B
Opublikowane w:
Nucleic Acids Research, Numer Volume 51, Numer D1, 2022, ISSN 0305-1048
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkac958
Autorzy:
Wietje Nolte, Rosemarie Weikard, Elke Albrecht, Harald M.Hammon, Christa Kühn
Opublikowane w:
Genomics, Numer Volume 114 Numer 1, 2022, Strona(/y) Pages 202-214, ISSN 0888-7543
Wydawca:
Academic Press
DOI:
10.1016/j.ygeno.2021.12.004
Autorzy:
A. Lloret-Villas; H. Pausch; A.S. Leonard
Opublikowane w:
Genetics Selection Evolution, Numer 55, Article number: 33 (2023), 2023, ISSN 1297-9686
Wydawca:
Springer Nature
DOI:
10.1186/s12711-023-00809-y
Autorzy:
Kramer, K.; Meijboom, F. L.B.; AISS Sustainable Animal Stewardship; dASS BW-2; LS Wijsgerige Ethiek; OFR - Ethics Institute
Opublikowane w:
Journal of Agricultural and Environmental Ethics, Numer 34 (1), 2021, ISSN 1187-7863
Wydawca:
Kluwer Academic Publishers
DOI:
10.1007/s10806-021-09843-6
Autorzy:
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
Opublikowane w:
Genome Biology, Numer 21/1, 2020, ISSN 1474-760X
Wydawca:
Springer nature
DOI:
10.1186/s13059-020-02197-8
Autorzy:
Viktor Milkevych, Emre Karaman, Goutam Sahana, Luc Janss, Zexi Cai, Mogens Sandø Lund
Opublikowane w:
G3 Genes|Genomes|Genetics, Numer 21601836, 2021, ISSN 2160-1836
Wydawca:
Genetics Society of America
DOI:
10.1093/g3journal/jkab133
Autorzy:
Kramer, K.; Meijboom, F. L.B.; dASS BW-2; AISS Sustainable Animal Stewardship; LS Wijsgerige Ethiek; OFR - Ethics Institute
Opublikowane w:
Journal of Agricultural and Environmental Ethics, Numer Volume 35, Numer 2, 2022, ISSN 1187-7863
Wydawca:
Kluwer Academic Publishers
DOI:
10.1007/s10806-022-09883-6
Autorzy:
Xena Marie Mapel; Maya Hiltpold; Naveen Kumar Kadri; Ulrich Witschi; Hubert Pausch
Opublikowane w:
JDS Communications, Numer Vol 3, Iss 2, 2022, ISSN 2666-9102
Wydawca:
Elsevier
DOI:
10.3168/jdsc.2021-0164
Autorzy:
Fanny Mollandin, Andrea Rau, Pascal Croiseau
Opublikowane w:
G3 Genes|Genomes|Genetics, Numer Volume 11, Numer 11, 2021, ISSN 2160-1836
Wydawca:
Genetics Society of America
DOI:
10.1093/g3journal/jkab225
Autorzy:
Jiyuan Li; Yining Wang; Robert Mukiibi; Brian Karisa; Graham S. Plastow; Changxi Li
Opublikowane w:
Scientific Reports, Numer vol. 12 , no. 1, 2022, ISSN 2045-2322
Wydawca:
Nature Publishing Group
DOI:
10.1038/s41598-022-06567-z
Autorzy:
M. Salavati; R. Clark; D. Becker; C. Kühn; G. Plastow; S. Dupont; G.C.M. Moreira; C. Charlier; E.L. Clark
Opublikowane w:
G3 Genes|Genomes|Genetics, Numer Volume 13, Numer 8, 2023, ISSN 2160-1836
Wydawca:
Genetics Society of America
DOI:
10.1093/g3journal/jkad108
Autorzy:
Jiyuan Li; Yining Wang; Robert Mukiibi; Brian Karisa; Graham S. Plastow; Changxi Li
Opublikowane w:
Scientific Reports, Numer vol. 12 , no. 1, 2022, ISSN 2045-2322
Wydawca:
Nature Publishing Group
DOI:
10.1038/s41598-022-06567-z
Autorzy:
Naveen Kumar Kadri; Xena M. Mapel; Hubert Pausch
Opublikowane w:
Communications Biology, Numer Vol 4, Numer 1, 2021, Strona(/y) Pp 1-13, ISSN 2399-3642
Wydawca:
Springer Nature
DOI:
10.1038/s42003-021-02725-7
Autorzy:
Peter W. Harrison; Alexey Sokolov; Akshatha Nayak; Jun Fan; Daniel R. Zerbino; Guy Cochrane; Paul Flicek
Opublikowane w:
Frontiers in Genetics, Numer Vol 12, 2021, ISSN 1664-8021
Wydawca:
Frontiers Media
DOI:
10.3389/fgene.2021.639238
Autorzy:
Andres S, Bartling B, Stiensmeier V, Starke A, Schmicke M.
Opublikowane w:
Frontiers in Veterinary Science, Numer Volume 10 - 2023, 2023, ISSN 2297-1769
Wydawca:
Frontiers Media
DOI:
10.3389/fvets.2023.1211135
Autorzy:
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 S
Opublikowane w:
Nucleic Acids Research, Numer Volume 52, Numer D1, 2024, ISSN 0305-1048
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkad1049
Autorzy:
Kramer, K.; Meijboom, F. L.B.; dASS BW-2; AISS Sustainable Animal Stewardship; LS Wijsgerige Ethiek; OFR - Ethics Institute
Opublikowane w:
Journal of Agricultural and Environmental Ethics, Numer Volume 35, Numer 2, 2022, ISSN 1187-7863
Wydawca:
Kluwer Academic Publishers
DOI:
10.1007/s10806-022-09883-6
Autorzy:
Fanny Mollandin, Andrea Rau, Pascal Croiseau
Opublikowane w:
G3 Genes|Genomes|Genetics, Numer Volume 11, Numer 11, 2021, ISSN 2160-1836
Wydawca:
Genetics Society of America
DOI:
10.1093/g3journal/jkab225
Autorzy:
M. Salavati; R. Clark; D. Becker; C. Kühn; G. Plastow; S. Dupont; G.C.M. Moreira; C. Charlier; E.L. Clark
Opublikowane w:
G3 Genes|Genomes|Genetics, Numer Volume 13, Numer 8, 2023, ISSN 2160-1836
Wydawca:
Genetics Society of America
DOI:
10.1093/g3journal/jkad108
Autorzy:
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
Opublikowane w:
Nucleic Acids Research, Numer Volume 51, Numer D1, 2022, ISSN 0305-1048
Wydawca:
Oxford University Press
DOI:
10.1093/nar/gkac958
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