Scientific Publications

Scientific peer-reviewed publications

2023

  • Ensembl 2024

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, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Dionysios Grigoriadis, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Tatiana A Gurbich, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Disha Lodha, Diego Marques-Coelho, Gareth Maslen, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Daniel Poppleton, Irina Prosovetskaia, Shriya Raj, José G Pérez-Silva, Ahamed Imran Abdul Salam, Shradha Saraf, Nuno Saraiva-Agostinho, Dan Sheppard, Swati Sinha, Botond Sipos, Vasily Sitnik, William Stark, Emily Steed, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Doreen Ware, Elizabeth Wass, Natalie L Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jon Keatley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, Guy Naamati, John Tate, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Fiona Cunningham, Sarah Dyer, Robert D Finn, Fergal J Martin, Andrew D Yates. Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D891–D899, DOI: 10.1093/nar/gkad1049 11 November 2023.

  • Sequence-based GWAS meta-analyses for beef production traits

Sanchez, MP., Tribout, T., Kadri, N.K. et al. Genet Sel Evol 55, 70 (2023). DOI: 10.1186/s12711-023-00848-5 12 October 2023.

  • Comparative cryopreservation of bovine and porcine primary hepatocytes

Andres S, Bartling B, Stiensmeier V, Starke A, Schmicke M. Front Vet Sci. 2023 Aug 8;10:1211135. DOI: 10.3389/fvets.2023.1211135. 08 August 2023.

  • Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing
Salavati M, Clark R, Becker D, et al. G3 (Bethesda, Md.). DOI: 10.1093/g3journal/jkad108 .01 August 2023.
  • The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle

Lloret-Villas, A., Pausch, H. & Leonard, A.S. Genet Sel Evol 55, 33 (2023). DOI: 10.1186/s12711-023-00809-y 11 May 2023

  • High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data

Lee YL, Bosse M, Takeda H, et al. BMC Genomics. 2023 May;24(1):225. DOI: 10.1186/s12864-023-09259-8. 01 May 2023

2022

  • Ensembl 2023

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 El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, José G Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Brandon Walts, Elizabeth Wass, Natalie Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, John Tate, David Thybert, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D Finn, Kevin L Howe, Peter W Harrison, Andrew D Yates, Paul Flicek Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D933–D941, DOI: 10.1093/nar/gkac958 01 November 2022

  • Accounting for overlapping annotations in genomic prediction models of complex traits

Mollandin F., Gilbert H., Croiseau P. , Rau A. BMC Bioinformatics. (2022). DOI: 10.1186/s12859-022-04914-5 06 September 2022

  • How Do Technologies Affect How We See and Treat Animals? Extending Technological Mediation Theory to Human-animal Relations

Kramer, K., Meijboom, F.L.B. Ethic Theory Moral Prac (2022). DOI: 10.1007/s10677-022-10305-9 22 June 2022

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

Kramer, K., Meijboom, F.L.B. J Agric Environ Ethics 357 (2022). DOI: 10.1007/s10806-022-09883-6 22 April 2022

  • Integrative analyses of genomic and metabolomic data reveal genetic mechanisms associated with carcass merit traits in beef cattle

Li, J., Wang, Y., Mukiibi, R. et al. Sci Rep 12, 3389 (2022). DOI: 10.1038/s41598-022-06567-z 1 March 2022

  • Bull fertility and semen quality are not correlated with dairy and production traits in Brown Swiss cattle

Mapel X.M., Hiltpold M., Kadri N.K., Witschi U., Pausch H. JDS Commun, 3(2):120-125. DOI: 10.3168/jdsc.2021-0164 10 January 2022

  • 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., Genomics, Volume 114, Issue 1, (2022). DOI: 10.1016/j.ygeno.2021.12.004 16 December 2021

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, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D988–D995, DOI: 10.1093/nar/gkab1049 17 November 2021

  • 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. BMC Genomics 22,823 (2021). DOI: 10.1186/s12864-021-08064-5 15 November 2021

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

Kadri, N.K., Mapel, X.M. & Pausch, H. Commun Biol 41206 (2021). DOI: 10.1038/s42003-021-02725-7 21 October 2021

Lee YL, Takeda H, Costa Monteiro Moreira G, et al. Plos Genetics. 2021 DOI: 10.1371/journal.pgen.1009331. 21 July 2021
  • Single-cell RNA sequencing of freshly isolated bovine milk cells and cultured primary mammary epithelial cells

Becker, D., Weikard, R., Hadlich, F. & Kühn, C. Sci Data 8, 177 (2021). DOI: 10.1038/s41597-021-00972-1 15 July 2021

  • MeSCoT: the tool for quantitative trait simulation through the mechanistic modeling of genes’ regulatory interactions

Viktor Milkevych, Emre Karaman, Goutam Sahana, Luc Janss, Zexi Cai, Mogens Sandø Lund. G3 Genes|Genomes|Genetics, Volume 11, Issue 7. DOI: 10.1093/g3journal/jkab133 7 July 2021

  • An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction

Fanny Mollandin, Andrea Rau, Pascal Croiseau, G3 Genes|Genomes|Genetics, Volume 11, Issue 11, November 2021, jkab225,  DOI.org/10.1093/g3journal/jkab225  7 July 2021

  • 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). Front. Genet. 12:639238. DOI: 10.3389/fgene.2021.639238 17 June 2021

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

Lloret-Villas, A., Bhati, M., Kadri, N.K. et al. BMC Genomics 22, 363 (2021). DOI: 10.1186/s12864-021-07554-w 19 May 2021

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

Robic, A., Cerutti, C., Kühn, C. and Faraut, T. Front. Genet. (2021). DOI: 10.3389/fgene.2021.665153 10 May 2021

  • Using Breeding Technologies to Improve Farm Animal Welfare: What is the Ethical Relevance of Telos?

Kramer, K., Meijboom, F.L.B. J Agric Environ Ethics 34, 2 (2021). DOI: 10.1007/s10806-021-09843-6 9 February 2021

  • 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 02 November 2020

2020

  • 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 24 November 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 11 November 2020

Scientific no peer-reviewed publications

2021

  • Editorial: Functional Annotation of Animal Genomes

Amanda Chamberlain, Hans Cheng, Elisabetta Giuffra, Christa Kuehn, Christopher Tuggle, et al. Frontiers in Genetics, Frontiers, 2021, 12, pp.768626. 10.3389/fgene.2021.768626. hal-03379984 15 October 2021

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