De novo assembly of the cattle reference genome with single-molecule sequencing

Rosen, Benjamin D, Bickhart, Derek M, Schnabel, Robert D, Koren, Sergey, Elsik, Christine G, Tseng, Elizabeth, Rowan, Troy N, Low, Wai Y, Zimin, Aleksey, Couldrey, Christine, Hall, Richard, Li, Wenli, Rhie, Arang, Ghurye, Jay, McKay, Stephanie D, Thibaud-Nissen, Françoise, Hoffman, Jinna, Murdoch, Brenda M, Snelling, Warren M, McDaneld, Tara G, Hammond, John A, Schwartz, John C, Nandolo, Wilson, Hagen, Darren E, Dreischer, Christian, Schultheiss, Sebastian J, Schroeder, Steven G, Phillippy, Adam M, Cole, John B, Van Tassell, Curtis P, Liu, George, Smith, Timothy P L, Medrano, Juan F·2020·GigaScience
DOI 10.1093/gigascience/giaa021

Cited by (858)

Items 701–800 of 858

  1. Additional file 7 of Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds
    Juliane Friedrich, Richard I. Bailey, Andrea Talenti, Chaudhry, Umer, Ali, Qasim, Obishakin, Emmanuel F., Chukwunonso Ezeasor, Jessica Powell, Olivier Hanotte, Abdulfatai Tijjani et al. · 2024 · Figshare
  2. Additional file 3 of A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle
    Julien Corbeau, Grohs, Cécile, Jeanlin Jourdain, Boussaha, Mekki, F. Besnard, Anne Barbat, Vincent Plassard, Rivière, Julie, Christophe Hamelin, Jeremy Raphael Mortier et al. · 2024 · Figshare
  3. Additional file 9 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
    Henrique A. Mulim, Victor Breno Pedrosa, Luís Fernando Batista Pinto, Francesco Tiezzi, Christian Maltecca, Schenkel, Flavio S., Brito, Luiz F. · 2024 · Figshare
  4. Additional file 7 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
    Mackenzie A. Marrella, Fernando H. Biase · 2024 · Figshare
  5. Additional file 2 of Single-step genome-wide association analyses of claw horn lesions in Holstein cattle using linear and threshold models
    Bingjie Li, Matthew Barden, Vanessa Varvara Kapsona, Sánchez-Molano, Enrique, Alkiviadis Anagnostopoulos, Bethany Eloise Griffiths, Cherril Bedford, Xiaoxia Dai, Coffey, Mike, Androniki Psifidi et al. · 2023 · Figshare
  6. Additional file 4 of Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
    Pierce Rafter, Gormley, Isobel Claire, Deirdre C. Purfield, Parnell, Andrew C., Saeid Naderi, Berry, Donagh P. · 2021 · Figshare
  7. Additional file 3 of The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle
    Audald Lloret‐Villas, Hubert Pausch, Alexander S. Leonard · 2023 · Figshare
  8. Additional file 2 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
    Wong, Kim, Abascal, Federico, Latasha Ludwig, Heike Aupperle‐Lellbach, Julia Maria Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Romero, Laura P. et al. · 2023 · Figshare
  9. Additional file 8 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
    Wong, Kim, Abascal, Federico, Latasha Ludwig, Heike Aupperle‐Lellbach, Julia Maria Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Romero, Laura P. et al. · 2023 · Figshare
  10. Additional file 2 of Sequence-based GWAS meta-analyses for beef production traits
    Sanchez, Marie-Pierre, Thierry Tribout, Naveen Kumar Kadri, Praveen Chitneedi, Steffen Maak, Chris Hozé, Boussaha, Mekki, Pascal Croiseau, Romain Philippe, Mirjam Spengeler et al. · 2024 · Figshare
  11. Additional file 1 of Variants at the ASIP locus contribute to coat color darkening in Nellore cattle
    Beatriz Batista Trigo, Adam Taiti Harth Utsunomiya, Alvaro A. A. D. Fortunato, Milanesi, Marco, Rafaela Beatriz Pintor Torrecilha, Harrison J. Lamb, Loan T Nguyen, Elizabeth M. Ross, Ben J. Hayes, Rômulo C. M. Padula et al. · 2021 · Figshare
  12. Additional file 7 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
    Henrique A. Mulim, Victor Breno Pedrosa, Luís Fernando Batista Pinto, Francesco Tiezzi, Christian Maltecca, Schenkel, Flavio S., Brito, Luiz F. · 2024 · Figshare
  13. Additional file 6 of Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds
    Juliane Friedrich, Richard I. Bailey, Andrea Talenti, Chaudhry, Umer, Ali, Qasim, Obishakin, Emmanuel F., Chukwunonso Ezeasor, Jessica Powell, Olivier Hanotte, Abdulfatai Tijjani et al. · 2024 · Figshare
  14. Additional file 8 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
    Mackenzie A. Marrella, Fernando H. Biase · 2024 · Figshare
  15. Additional file 11 of Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle
    Lam, S., J. Zeidan, Miglior, F., Aroa Suárez‐Vega, Gómez-Redondo, I., Fonseca, P. A. S., Guan, L. L., Waters, S., Ángela Cánovas · 2020 · Figshare
  16. Additional file 1 of Relationship between the rumen microbiome and liver transcriptome in beef cattle divergent for feed efficiency
    Kate A. Keogh, Kenny, David A., Pâmela A. Alexandre, Waters, Sinead M., McGovern, Emily, McGee, Mark, Antônio Reverter · 2024 · Figshare
  17. Additional file 6 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
    Christin Schmidtmann, Anna A. Schönherz, Guldbrandtsen, Bernt, Jovana Marjanovic, Calus, Mario, Dirk Hinrichs, Thaller, Georg · 2021 · Figshare
  18. Additional file 3 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
    Christin Schmidtmann, Anna A. Schönherz, Guldbrandtsen, Bernt, Jovana Marjanovic, Calus, Mario, Dirk Hinrichs, Thaller, Georg · 2021 · Figshare
  19. Additional file 3 of Allele-specific binding variants causing ChIP-seq peak height of histone modification are not enriched in expression QTL annotations
    Ghoreishifar, Mohammad, Amanda Jane Chamberlain, Ruidong Xiang, Claire Prowse-Wilkins, Thomas Lopdell, Mathew D. Littlejohn, J.E. Pryce, Michael Edward Goddard · 2024 · Figshare
  20. Additional file 9 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
    Wong, Kim, Abascal, Federico, Latasha Ludwig, Heike Aupperle‐Lellbach, Julia Maria Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Romero, Laura P. et al. · 2023 · Figshare
  21. Additional file 3 of Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle
    Lam, S., J. Zeidan, Miglior, F., Aroa Suárez‐Vega, Gómez-Redondo, I., Fonseca, P. A. S., Guan, L. L., Waters, S., Ángela Cánovas · 2020 · Figshare
  22. Additional file 3 of Male recombination map of the autosomal genome in German Holstein
    Saber Qanbari, Dörte Wittenburg · 2020 · Figshare
  23. Additional file 6 of Male recombination map of the autosomal genome in German Holstein
    Saber Qanbari, Dörte Wittenburg · 2020 · Figshare
  24. Additional file 8 of Long-range linkage disequilibrium in French beef cattle breeds
    Abdelmajid El Hou, Dominique Rocha, Éric Venot, Véronique Blanquet, Romain Philippe · 2021 · Figshare
  25. Additional file 6 of Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
    Pierce Rafter, Gormley, Isobel Claire, Deirdre C. Purfield, Parnell, Andrew C., Saeid Naderi, Berry, Donagh P. · 2021 · Figshare
  26. Additional file 5 of A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle
    Julien Corbeau, Grohs, Cécile, Jeanlin Jourdain, Boussaha, Mekki, F. Besnard, Anne Barbat, Vincent Plassard, Rivière, Julie, Christophe Hamelin, Jeremy Raphael Mortier et al. · 2024 · Figshare
  27. Additional file 4 of Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome
    Ísis da Costa Hermisdorff, Raphael Bermal Costa, de Albuquerque, Lucia Galvão, Hubert Pausch, Naveen Kumar Kadri · 2020 · Figshare
  28. Additional file 6 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
    Wong, Kim, Abascal, Federico, Latasha Ludwig, Heike Aupperle‐Lellbach, Julia Maria Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Romero, Laura P. et al. · 2023 · Figshare
  29. Additional file 5 of Graph construction method impacts variation representation and analyses in a bovine super-pangenome
    Alexander S. Leonard, Danang Crysnanto, Xena Marie Mapel, Meenu Bhati, Hubert Pausch · 2024 · Figshare
  30. Additional file 4 of Male recombination map of the autosomal genome in German Holstein
    Saber Qanbari, Dörte Wittenburg · 2020 · Figshare
  31. Additional file 5 of Using expression data to fine map QTL associated with fertility in dairy cattle
    Irene van den Berg, Amanda Jane Chamberlain, Iona M. MacLeod, Nguyen, Tuan V., Michael Edward Goddard, Ruidong Xiang, Brett Mason, S. Meier, Claire V. C. Phyn, C.R. Burke et al. · 2024 · Figshare
  32. Additional file 2 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle
    Claire Prowse-Wilkins, Thomas Lopdell, Ruidong Xiang, Christy J. Vander-Jagt, Mathew D. Littlejohn, Amanda Jane Chamberlain, Michael Edward Goddard · 2023 · Figshare
  33. Additional file 1 of Whole genome sequencing of simmental cattle for SNP and CNV discovery
    Sun, Ting, Shengwei Pei, Liu, Yangkai, Quratulain Hanif, Xu, Haiyue, Chen, Ningbo, Lei, Chuzhao, Yue, Xiangpeng · 2024 · Figshare
  34. Additional file 8 of Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
    William Poisson, Julien Prunier, Alexandra Carrier, Isabelle Gilbert, Mastromonaco, Gabriela, Albert, Vicky, Joëlle Taillon, Vincent Bourret, Arnaud Droit, Steeve D. Côté et al. · 2023 · Figshare
  35. Additional file 2 of Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance
    Cai, Zexi, Terhi Iso‐Touru, Sanchez, Marie-Pierre, Naveen Kumar Kadri, A.C. Bouwman, Praveen Chitneedi, Iona M. MacLeod, Christy J. Vander-Jagt, Amanda Jane Chamberlain, Birgit Gredler et al. · 2024 · Figshare
  36. Additional file 9 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
    Elisa Somenzi, Erika Partel, Mario Barbato, Ana María Chero Osorio, Licia Colli, Niccolò Franceschi, Roberto Mantovani, Pilla, Fabio, M. Komjanc, Alessandro Achilli et al. · 2024 · Figshare
  37. Additional file 4 of Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle
    Lam, S., J. Zeidan, Miglior, F., Aroa Suárez‐Vega, Gómez-Redondo, I., Fonseca, P. A. S., Guan, L. L., Waters, S., Ángela Cánovas · 2020 · Figshare
  38. Additional file 7 of Long-range linkage disequilibrium in French beef cattle breeds
    Abdelmajid El Hou, Dominique Rocha, Éric Venot, Véronique Blanquet, Romain Philippe · 2021 · Figshare
  39. Additional file 4 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
    Elisa Somenzi, Erika Partel, Mario Barbato, Ana María Chero Osorio, Licia Colli, Niccolò Franceschi, Roberto Mantovani, Pilla, Fabio, M. Komjanc, Alessandro Achilli et al. · 2024 · Figshare
  40. Additional file 3 of Sequence-based GWAS meta-analyses for beef production traits
    Sanchez, Marie-Pierre, Thierry Tribout, Naveen Kumar Kadri, Praveen Chitneedi, Steffen Maak, Chris Hozé, Boussaha, Mekki, Pascal Croiseau, Romain Philippe, Mirjam Spengeler et al. · 2024 · Figshare
  41. Additional file 4 of Meta-analysis of six dairy cattle breeds reveals biologically relevant candidate genes for mastitis resistance
    Cai, Zexi, Terhi Iso‐Touru, Sanchez, Marie-Pierre, Naveen Kumar Kadri, A.C. Bouwman, Praveen Chitneedi, Iona M. MacLeod, Christy J. Vander-Jagt, Amanda Jane Chamberlain, Birgit Gredler et al. · 2024 · Figshare
  42. Additional file 2 of A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application
    Jason R. Grant, Emily K. Herman, Lael D. Barlow, F. Miglior, Flávio Schramm Schenkel, Christine F. Baes, Stothard, Paul · 2024 · Figshare
  43. Additional file 3 of Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle
    Lorena Ferreira Benfica, Brito, Luiz F., Ricardo Dutra do Bem, Henrique A. Mulim, Glessner, Joseph, Braga, Larissa G., Gloria, Leonardo S., Joslaine Noely dos Santos Gonçalves Cyrillo, Sarah Figueiredo Martins Bonilha, Maria Eugênia Zerlotti Mercadante · 2024 · Figshare
  44. Additional file 6 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
    Mackenzie A. Marrella, Fernando H. Biase · 2024 · Figshare
  45. Additional file 5 of Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds
    Juliane Friedrich, Richard I. Bailey, Andrea Talenti, Chaudhry, Umer, Ali, Qasim, Obishakin, Emmanuel F., Chukwunonso Ezeasor, Jessica Powell, Olivier Hanotte, Abdulfatai Tijjani et al. · 2024 · Figshare
  46. Additional file 1 of Using expression data to fine map QTL associated with fertility in dairy cattle
    Irene van den Berg, Amanda Jane Chamberlain, Iona M. MacLeod, Nguyen, Tuan V., Michael Edward Goddard, Ruidong Xiang, Brett Mason, S. Meier, Claire V. C. Phyn, C.R. Burke et al. · 2024 · Figshare
  47. Additional file 3 of Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals
    José Luis Gualdrón Duarte, Can Yuan, Gori, Ann-Stephan, Moreira, Gabriel C. M., Takeda, Haruko, Coppieters, Wouter, Carole Charlier, Michel Georges, Tom Druet · 2024 · Figshare
  48. Additional file 6 of Long-range linkage disequilibrium in French beef cattle breeds
    Abdelmajid El Hou, Dominique Rocha, Éric Venot, Véronique Blanquet, Romain Philippe · 2021 · Figshare
  49. Additional file 2 of An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle
    Kate A. Keogh, Kenny, D. A., Pâmela A. Alexandre, McGee, M., Reverter, A. · 2024 · Figshare
  50. Additional file 3 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
    Henrique A. Mulim, Victor Breno Pedrosa, Luís Fernando Batista Pinto, Francesco Tiezzi, Christian Maltecca, Flávio Schramm Schenkel, Brito, Luiz F. · 2024 · Figshare
  51. Additional file 1 of Confirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle
    Thierry Tribout, Pascal Croiseau, Rachel Lefebvre, Anne Barbat, Boussaha, Mekki, Sébastien Fritz, Boichard, Didier, Chris Hozé, Sanchez, Marie-Pierre · 2020 · Figshare
  52. Additional file 10 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
    Elisa Somenzi, Erika Partel, Mario Barbato, Ana María Chero Osorio, Licia Colli, Niccolò Franceschi, Roberto Mantovani, Pilla, Fabio, M. Komjanc, Alessandro Achilli et al. · 2024 · Figshare
  53. Additional file 1 of High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data
    Lee, Young-Lim, Mirte Bosse, Takeda, Haruko, Gabriel Costa Monteiro Moreira, Latifa Karim, Tom Druet, Claire Oget, Coppieters, Wouter, Veerkamp, Roel F., Martien A. M. Groenen et al. · 2023 · Figshare
  54. Additional file 18 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
    Wong, Kim, Abascal, Federico, Latasha Ludwig, Heike Aupperle‐Lellbach, Julia Maria Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Romero, Laura P. et al. · 2023 · Figshare
  55. Additional file 1 of Investigation of ancestral alleles in the Bovinae subfamily
    Maulana M. Naji, Yuri Tani Utsunomiya, Johann Sölkner, Benjamin D. Rosen, Mészáros, Gábor · 2021 · Figshare
  56. Additional file 3 of Using expression data to fine map QTL associated with fertility in dairy cattle
    Irene van den Berg, Chamberlain, Amanda J., Iona M. MacLeod, Nguyen, Tuan V., Michael Edward Goddard, Ruidong Xiang, Brett Mason, S. Meier, Claire V. C. Phyn, C.R. Burke et al. · 2024 · Figshare
  57. Additional file 5 of Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
    Pierce Rafter, Isobel Claire Gormley, Deirdre C. Purfield, Parnell, Andrew C., Saeid Naderi, Donagh Pearse Berry · 2021 · Figshare
  58. Additional file 3 of Congenital syndromic Chiari-like malformation (CSCM) in Holstein cattle: towards unravelling of possible genetic causes
    Joana G. P. Jacinto, Anna Letko, Irene M. Häfliger, Cord Drögemüller, Agerholm, Jørgen Steen · 2024 · Figshare
  59. Additional file 4 of A recurrent de novo missense mutation in COL1A1 causes osteogenesis imperfecta type II and preterm delivery in Normande cattle
    Julien Corbeau, Grohs, Cécile, Jeanlin Jourdain, Boussaha, Mekki, F. Besnard, Anne Barbat, Vincent Plassard, Julie Rivière, Christophe Hamelin, Jeremy Raphael Mortier et al. · 2024 · Figshare
  60. Additional file 1 of Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle
    Lam, S., J. Zeidan, Miglior, F., Suárez-Vega, A., Gómez-Redondo, I., Fonseca, P. A. S., Guan, L. L., Waters, S., Ángela Cánovas · 2020 · Figshare
  61. Additional file 2 of Long-range linkage disequilibrium in French beef cattle breeds
    Abdelmajid El Hou, Dominique Rocha, Éric Venot, Véronique Blanquet, Romain Philippe · 2021 · Figshare
  62. Additional file 1 of Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds
    Juliane Friedrich, Richard I. Bailey, Andrea Talenti, Chaudhry, Umer, Ali, Qasim, Obishakin, Emmanuel F., Chukwunonso Ezeasor, Jessica Powell, Olivier Hanotte, Abdulfatai Tijjani et al. · 2024 · Figshare
  63. Additional file 1 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
    Elisa Somenzi, Erika Partel, Mario Barbato, Ana María Chero Osorio, Licia Colli, Niccolò Franceschi, Roberto Mantovani, Pilla, Fabio, M. Komjanc, Alessandro Achilli et al. · 2024 · Figshare
  64. Additional file 14 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
    Wong, Kim, Abascal, Federico, Latasha Ludwig, Heike Aupperle‐Lellbach, Julia Maria Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Romero, Laura P. et al. · 2023 · Figshare
  65. Additional file 1 of Allele-specific binding variants causing ChIP-seq peak height of histone modification are not enriched in expression QTL annotations
    Ghoreishifar, Mohammad, Amanda Jane Chamberlain, Ruidong Xiang, Claire Prowse-Wilkins, Thomas Lopdell, Mathew D. Littlejohn, J.E. Pryce, Michael Edward Goddard · 2024 · Figshare
  66. Additional file 1 of Characterization of runs of homozygosity, heterozygosity-enriched regions, and population structure in cattle populations selected for different breeding goals
    Henrique A. Mulim, Brito, Luiz F., Luís Fernando Batista Pinto, Ferraz, José Bento Sterman, Laís Grigoletto, Márcio Ribeiro Silva, Victor Breno Pedrosa · 2022 · Figshare
  67. Additional file 7 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
    Elisa Somenzi, Erika Partel, Mario Barbato, Ana María Chero Osorio, Licia Colli, Niccolò Franceschi, Roberto Mantovani, Pilla, Fabio, M. Komjanc, Alessandro Achilli et al. · 2024 · Figshare
  68. Additional file 4 of Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
    Christin Schmidtmann, Anna A. Schönherz, Guldbrandtsen, Bernt, Jovana Marjanovic, Calus, Mario, Dirk Hinrichs, Thaller, Georg · 2021 · Figshare
  69. Additional file 5 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
    Mackenzie A. Marrella, Fernando H. Biase · 2024 · Figshare
  70. Additional file 8 of Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data
    Henrique A. Mulim, Victor Breno Pedrosa, Luís Fernando Batista Pinto, Francesco Tiezzi, Christian Maltecca, Schenkel, Flavio S., Brito, Luiz F. · 2024 · Figshare
  71. Additional file 4 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle
    Claire Prowse-Wilkins, Thomas Lopdell, Ruidong Xiang, Christy J. Vander-Jagt, Mathew D. Littlejohn, Amanda Jane Chamberlain, Michael Edward Goddard · 2023 · Figshare
  72. Additional file 4 of Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing
    Mackenzie A. Marrella, Fernando H. Biase · 2024 · Figshare
  73. Additional file 1 of Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment
    Xia, Xiaoting, Zhang, Fengwei, Li, Shuang, Luo, Xiaoyu, Peng, Lixin, Dong, Zheng, Hubert Pausch, Alexander S. Leonard, Danang Crysnanto, Shikang Wang et al. · 2023 · Figshare
  74. Additional file 7 of Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
    Pierce Rafter, Gormley, Isobel Claire, Deirdre C. Purfield, Parnell, Andrew C., Saeid Naderi, Berry, Donagh P. · 2021 · Figshare
  75. Additional file 2 of Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals
    José Luis Gualdrón Duarte, Can Yuan, Gori, Ann-Stephan, Moreira, Gabriel C. M., Takeda, Haruko, Coppieters, Wouter, Carole Charlier, Michel Georges, Tom Druet · 2024 · Figshare
  76. Additional file 3 of Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
    Pierce Rafter, Gormley, Isobel Claire, Deirdre C. Purfield, Parnell, Andrew C., Saeid Naderi, Berry, Donagh P. · 2021 · Figshare
  77. Additional file 3 of Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle
    Claire Prowse-Wilkins, Thomas Lopdell, Ruidong Xiang, Christy J. Vander-Jagt, Mathew D. Littlejohn, Amanda Jane Chamberlain, Michael Edward Goddard · 2023 · Figshare
  78. Additional file 5 of Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
    William Poisson, Julien Prunier, Alexandra Carrier, Isabelle Gilbert, Gabriela F. Mastromonaco, Albert, Vicky, Joëlle Taillon, Vincent Bourret, Arnaud Droit, Steeve D. Côté et al. · 2023 · Figshare
  79. Additional file 5 of A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application
    Jason R. Grant, Emily K. Herman, Lael D. Barlow, F. Miglior, Flávio Schramm Schenkel, Christine F. Baes, Stothard, Paul · 2024 · Figshare
  80. Additional file 2 of Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics
    Elisa Somenzi, Erika Partel, Mario Barbato, Ana María Chero Osorio, Licia Colli, Niccolò Franceschi, Mantovani, Roberto, Pilla, Fabio, M. Komjanc, Alessandro Achilli et al. · 2024 · Figshare
  81. Additional file 25 of Cross-species oncogenomics offers insight into human muscle-invasive bladder cancer
    Wong, Kim, Abascal, Federico, Latasha Ludwig, Heike Aupperle‐Lellbach, Julia Maria Grassinger, Colin W. Wright, Simon J. Allison, Emma Pinder, Roger M. Phillips, Romero, Laura P. et al. · 2023 · Figshare
  82. Additional file 1 of Long-range linkage disequilibrium in French beef cattle breeds
    Abdelmajid El Hou, Dominique Rocha, Éric Venot, Véronique Blanquet, Romain Philippe · 2021 · Figshare
  83. Additional file 2 of Congenital syndromic Chiari-like malformation (CSCM) in Holstein cattle: towards unravelling of possible genetic causes
    Jacinto, Joana Goncalves Pontes, Anna Letko, Irene M. Häfliger, Cord Drögemüller, Agerholm, Jørgen Steen · 2024 · Figshare
  84. Additional file 1 of Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle
    Lorena Ferreira Benfica, Brito, Luiz F., Ricardo Dutra do Bem, Henrique A. Mulim, Glessner, Joseph, Braga, Larissa G., Gloria, Leonardo S., Joslaine Noely dos Santos Gonçalves Cyrillo, Sarah Figueiredo Martins Bonilha, Maria Eugênia Zerlotti Mercadante · 2024 · Figshare
  85. Additional file 2 of Mapping restricted introgression across the genomes of admixed indigenous African cattle breeds
    Juliane Friedrich, Richard I. Bailey, Andrea Talenti, Chaudhry, Umer, Ali, Qasim, Obishakin, Emmanuel F., Chukwunonso Ezeasor, Jessica Powell, Olivier Hanotte, Abdulfatai Tijjani et al. · 2024 · Figshare
  86. Additional file 9 of Long-range linkage disequilibrium in French beef cattle breeds
    Abdelmajid El Hou, Dominique Rocha, Éric Venot, Véronique Blanquet, Romain Philippe · 2021 · Figshare
  87. Additional file 1 of Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals
    José Luis Gualdrón Duarte, Can Yuan, Gori, Ann-Stephan, Moreira, Gabriel C. M., Takeda, Haruko, Coppieters, Wouter, Carole Charlier, Michel Georges, Tom Druet · 2024 · Figshare
  88. Additional file 2 of Whole genome sequencing of simmental cattle for SNP and CNV discovery
    Sun, Ting, Shengwei Pei, Liu, Yangkai, Quratulain Hanif, Xu, Haiyue, Chen, Ningbo, Lei, Chuzhao, Yue, Xiangpeng · 2024 · Figshare
  89. Additional file 4 of Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery
    Danang Crysnanto, Hubert Pausch · 2020 · Figshare
  90. Additional file 4 of Profiling the immune epigenome across global cattle breeds
    Jessica Powell, Andrea Talenti, Andressa Fisch, Johanneke Dinie Hemmink, Edith A. Paxton, Philip G. Toye, Isabel Kinney Ferreira de Miranda Santos, Beatriz Rossetti Ferreira, Tim Connelley, Morrison, Liam J. et al. · 2024 · Figshare
  91. Additional file 4 of A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application
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