Scientific Publications

2022

  • The Ethics of Innovations in Genomic Selection: On How to Broaden the Scope of Discussion

Kramer, K., Meijboom, F.L.B. The Ethics of Innovations in Genomic Selection: On How to Broaden the Scope of Discussion. J Agric Environ Ethics 357 (2022). DOI: 10.1007/s10806-022-09883-6

  • Metabogenomic analysis to functionally annotate the regulatory role of long non-coding RNAs in the liver of cows with different nutrient partitioning phenotype

Nolte, W., Weikard, R., Albrecht, E., Hammon H. M. & Kühn, C. Metabogenomic analysis to functionally annotate the regulatory role of long non-coding RNAs in the liver of cows with different nutrient partitioning phenotype, Genomics, Volume 114, Issue 1, (2022). DOI: 10.1016/j.ygeno.2021.12.004

2021

  • Ensembl 2022 

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, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N Ogeh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, José G Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Brandon Walts, Natalie Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish, Stefano Giorgetti, Leanne Haggerty, Sarah E Hunt, Garth R IIsley, Jane E Loveland, Fergal J Martin, Benjamin Moore, Jonathan M Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J Trevanion, Sarah Dyer, Peter W Harrison, Kevin L Howe, Andrew D Yates, Daniel R Zerbino, Paul Flicek, Ensembl 2022, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D988–D995, https://DOI.org/10.1093/nar/gkab1049

  • The FAANG Data Portal: Global, Open-Access, “FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes

Harrison PW, Sokolov A, Nayak A, Fan J, Zerbino D, Cochrane G and Flicek P (2021) The FAANG Data Portal: Global, Open-Access, “FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes. Front. Genet. 12:639238. DOI: 10.3389/fgene.2021.639238

  • Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

Li, J., Mukiibi, R., Wang, Y. et al. Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle. BMC Genomics 22, 823 (2021). DOI: 10.1186/s12864-021-08064-5

  • Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

Lloret-Villas, A., Bhati, M., Kadri, N.K. et al. Investigating the impact of reference assembly choice on genomic analyses in a cattle breed. BMC Genomics 22, 363 (2021). DOI: 10.1186/s12864-021-07554-w

  • Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species

Robic, A., Cerutti, C., Kühn, C. and Faraut, T. Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species. Front. Genet. (2021). DOI: 10.3389/fgene.2021.665153

  • Single-cell RNA sequencing of freshly isolated bovine milk cells and cultured primary mammary epithelial cells

Becker, D., Weikard, R., Hadlich, F. & Kühn, C. Single-cell RNA sequencing of freshly isolated bovine milk cells and cultured primary mammary epithelial cells. Sci Data 8, 177 (2021). DOI: 10.1038/s41597-021-00972-1

  • The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome

Kadri, N.K., Mapel, X.M. & Pausch, H. The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome. Commun Biol 41206 (2021). DOI: 10.1038/s42003-021-02725-7

  • Ensembl 2021 

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, Leanne Haggerty, Anmol Hemrom, Thibaut Hourlier, Osagie G Izuogu, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, José Carlos Marugán, Thomas Maurel, Aoife C McMahon, Shamika Mohanan, Benjamin Moore, Matthieu Muffato, Denye N Oheh, Dimitrios Paraschas, Anne Parker, Andrew Parton, Irina Prosovetskaia, Manoj P Sakthivel, Ahamed I Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Emily Steed, Michal Szpak, Marek Szuba, Kieron Taylor, Anja Thormann, Glen Threadgold, Brandon Walts, Andrea Winterbottom, Marc Chakiachvili, Ameya Chaubal, Nishadi De Silva, Bethany Flint, Adam Frankish, Sarah E Hunt, Garth R IIsley, Nick Langridge, Jane E Loveland, Fergal J Martin, Jonathan M Mudge, Joanella Morales, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J Trevanion, Fiona Cunningham, Andrew D Yates, Daniel R Zerbino, Paul Flicek. Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D884–D891. DOI: 10.1093/nar/gkaa942

2020

  • The European Nucleotide Archive in 2020

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 Rahman, Jeena Rajan, Alexey Sokolov, Senthilnathan Vijayaraja, Zahra Waheed, Ahmad Zyoud, Tony Burdett, Guy Cochrane. Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D82–D85. DOI: 10.1093/nar/gkaa1028

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

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. Genome Biology, Volume 21, Article number: 285 (2020). DOI: 10.1186/s13059-020-02197-8

File(s) uploaded.