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A whole-genome assembly of the domestic cow, Bos taurus
Aleksey V Zimin, Arthur L Delcher, Liliana Florea, David R Kelley, Michael C Schatz, Daniela Puiu, Finnian Hanrahan, Geo Pertea, Curtis P Van Tassell, Tad S Sonstegard, Guillaume Marçais, Michael Roberts, Poorani Subramanian, James A Yorke, Steven L Salzberg
Genome Biol. 2009; 10(4): R42. Published online 2009 April 24. doi: 10.1186/gb-2009-10-4-r42
PMCID:
PMC2688933
Abstract Full Text PDF–454K Supplementary Material

Is Cited by the Following 35 Articles in this Archive:

Identification of QTL for UV-Protective Eye Area Pigmentation in Cattle by Progeny Phenotyping and Genome-Wide Association Analysis
Hubert Pausch, Xiaolong Wang, Simone Jung, Dieter Krogmeier, Christian Edel, Reiner Emmerling, Kay-Uwe Götz, Ruedi Fries
PLoS One. 2012; 7(5): e36346. Published online 2012 May 2. doi: 10.1371/journal.pone.0036346
PMCID:
PMC3342244
Abstract Full Text PDF–371K Supplementary Material
Agouti Revisited: Transcript Quantification of the ASIP Gene in Bovine Tissues Related to Protein Expression and Localization
Elke Albrecht, Katrin Komolka, Judith Kuzinski, Steffen Maak
PLoS One. 2012; 7(4): e35282. Published online 2012 April 17. doi: 10.1371/journal.pone.0035282
PMCID:
PMC3328439
Abstract Full Text PDF–2.6M Supplementary Material
Copy number variation of individual cattle genomes using next-generation sequencing
Derek M. Bickhart, Yali Hou, Steven G. Schroeder, Can Alkan, Maria Francesca Cardone, Lakshmi K. Matukumalli, Jiuzhou Song, Robert D. Schnabel, Mario Ventura, Jeremy F. Taylor, Jose Fernando Garcia, Curtis P. Van Tassell, Tad S. Sonstegard, Evan E. Eichler, George E. Liu
Genome Res. 2012 April; 22(4): 778–790. doi: 10.1101/gr.133967.111
PMCID:
PMC3317159
Free in PMC on 2012/10/01
Evaluation of Bovine chemerin (RARRES2) Gene Variation on Beef Cattle Production Traits
Amanda K. Lindholm-Perry, Larry A. Kuehn, Lea A. Rempel, Timothy P. L. Smith, Robert A. Cushman, Tara G. McDaneld, Tommy L. Wheeler, Steven D. Shackelford, David A. King, Harvey C. Freetly
Front Genet. 2012; 3: 39. Published online 2012 March 29. doi: 10.3389/fgene.2012.00039
PMCID:
PMC3314841
Abstract Full Text PDF–289K
Genomic Position Mapping Discrepancies of Commercial SNP Chips
João Fadista, Christian Bendixen
PLoS One. 2012; 7(2): e31025. Published online 2012 February 17. doi: 10.1371/journal.pone.0031025
PMCID:
PMC3281913
Abstract Full Text PDF–217K Supplementary Material
Refinement of Bos taurus sequence assembly based on BAC-FISH experiments
Giulia Partipilo, Pietro D'Addabbo, Giovanni M Lacalandra, George E Liu, Mariano Rocchi
BMC Genomics. 2011; 12: 639. Published online 2011 December 30. doi: 10.1186/1471-2164-12-639
PMCID:
PMC3268123
Abstract Full Text PDF–1013K Supplementary Material
Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery
Paul Stothard, Jung-Woo Choi, Urmila Basu, Jennifer M Sumner-Thomson, Yan Meng, Xiaoping Liao, Stephen S Moore
BMC Genomics. 2011; 12: 559. Published online 2011 November 15. doi: 10.1186/1471-2164-12-559
PMCID:
PMC3229636
Abstract Full Text PDF–509K Supplementary Material
The UCSC Genome Browser database: extensions and updates 2011
Timothy R. Dreszer, Donna Karolchik, Ann S. Zweig, Angie S. Hinrichs, Brian J. Raney, Robert M. Kuhn, Laurence R. Meyer, Mathew Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke Rhead, Andy Pohl, Venkat S. Malladi, Chin H. Li, Katrina Learned, Vanessa Kirkup, Fan Hsu, Rachel A. Harte, Luvina Guruvadoo, Mary Goldman, Belinda M. Giardine, Pauline A. Fujita, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent
Nucleic Acids Res. 2012 January; 40(D1): D918–D923. Published online 2011 November 15. doi: 10.1093/nar/gkr1055
PMCID:
PMC3245018
Abstract Full Text PDF–3.0M
Association of an ACSL1 gene variant with polyunsaturated fatty acids in bovine skeletal muscle
Philipp Widmann, Karin Nuernberg, Christa Kuehn, Rosemarie Weikard
BMC Genet. 2011; 12: 96. Published online 2011 November 11. doi: 10.1186/1471-2156-12-96
PMCID:
PMC3260110
Abstract Full Text PDF–615K
diArk 2.0 provides detailed analyses of the ever increasing eukaryotic genome sequencing data
Björn Hammesfahr, Florian Odronitz, Marcel Hellkamp, Martin Kollmar
BMC Res Notes. 2011; 4: 338. Published online 2011 September 9. doi: 10.1186/1756-0500-4-338
PMCID:
PMC3180467
Abstract Full Text PDF–2.3M Supplementary Material
Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows
John B Cole, George R Wiggans, Li Ma, Tad S Sonstegard, Thomas J Lawlor, Jr, Brian A Crooker, Curtis P Van Tassell, Jing Yang, Shengwen Wang, Lakshmi K Matukumalli, Yang Da
BMC Genomics. 2011; 12: 408. Published online 2011 August 11. doi: 10.1186/1471-2164-12-408
PMCID:
PMC3176260
Abstract Full Text PDF–615K Supplementary Material
Computational Exploration of Structural Hypotheses for an Additional Sequence in a Mammalian Mitochondrial Protein
Aymen S. Yassin, Rajendra K. Agrawal, Nilesh K. Banavali
PLoS One. 2011; 6(7): e21871. Published online 2011 July 11. doi: 10.1371/journal.pone.0021871
PMCID:
PMC3136923
Abstract Full Text PDF–1.2M
Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies
Liliana Florea, Alexander Souvorov, Theodore S. Kalbfleisch, Steven L. Salzberg
PLoS One. 2011; 6(6): e21400. Published online 2011 June 22. doi: 10.1371/journal.pone.0021400
PMCID:
PMC3120881
Abstract Full Text PDF–524K
Assessment of genome integrity with array CGH in cattle transgenic cell lines produced by homologous recombination and somatic cell cloning
George E Liu, Yali Hou, James M Robl, Yoshimi Kuroiwa, Zhongde Wang
Genome Integr. 2011; 2: 6. Published online 2011 May 23. doi: 10.1186/2041-9414-2-6
PMCID:
PMC3123262
Abstract Full Text PDF–361K
Genome-wide association of milk fatty acids in Dutch dairy cattle
Aniek C Bouwman, Henk Bovenhuis, Marleen HPW Visker, Johan AM van Arendonk
BMC Genet. 2011; 12: 43. Published online 2011 May 11. doi: 10.1186/1471-2156-12-43
PMCID:
PMC3120725
Abstract Full Text PDF–562K
Tracing Cattle Breeds with Principal Components Analysis Ancestry Informative SNPs
Jamey Lewis, Zafiris Abas, Christos Dadousis, Dimitrios Lykidis, Peristera Paschou, Petros Drineas
PLoS One. 2011; 6(4): e18007. Published online 2011 April 7. doi: 10.1371/journal.pone.0018007
PMCID:
PMC3072384
Abstract Full Text PDF–744K Supplementary Material
Genomic characteristics of cattle copy number variations
Yali Hou, George E Liu, Derek M Bickhart, Maria Francesca Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard, Curt P Van Tassell
BMC Genomics. 2011; 12: 127. Published online 2011 February 23. doi: 10.1186/1471-2164-12-127
PMCID:
PMC3053260
Abstract Full Text PDF–540K Supplementary Material
Recent and historical recombination in the admixed Norwegian Red cattle breed
Marte Sodeland, Matthew Kent, Ben J Hayes, Harald Grove, Sigbjørn Lien
BMC Genomics. 2011; 12: 33. Published online 2011 January 14. doi: 10.1186/1471-2164-12-33
PMCID:
PMC3030550
Abstract Full Text PDF–507K Supplementary Material
Genome-Wide Association Study Identifies Two Major Loci Affecting Calving Ease and Growth-Related Traits in Cattle
Hubert Pausch, Krzysztof Flisikowski, Simone Jung, Reiner Emmerling, Christian Edel, Kay-Uwe Götz, Ruedi Fries
Genetics. 2011 January; 187(1): 289–297. doi: 10.1534/genetics.110.124057
PMCID:
PMC3018322
Abstract Full Text PDF–2.7M
A Global View of 54,001 Single Nucleotide Polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and Their Transferability to Water Buffalo
Vanessa N. Michelizzi, Xiaolin Wu, Michael V. Dodson, Jennifer J. Michal, Jorge Zambrano-Varon, Derek J. McLean, Zhihua Jiang
Int J Biol Sci. 2011; 7(1): 18–27. Published online 2010 December 30.
PMCID:
PMC3014552
Abstract Full Text PDF–2.2M Supplementary Material
Bovine Genome Database: integrated tools for genome annotation and discovery
Christopher P. Childers, Justin T. Reese, Jaideep P. Sundaram, Donald C. Vile, C. Michael Dickens, Kevin L. Childs, Hanni Salih, Anna K. Bennett, Darren E. Hagen, David L. Adelson, Christine G. Elsik
Nucleic Acids Res. 2011 January; 39(Database issue): D830–D834. Published online 2010 December 1. doi: 10.1093/nar/gkq1235
PMCID:
PMC3013744
Abstract Full Text PDF–84K
A Novel Mutation in the Maternally Imprinted PEG3 Domain Results in a Loss of MIMT1 Expression and Causes Abortions and Stillbirths in Cattle (Bos taurus)
Krzysztof Flisikowski, Heli Venhoranta, Joanna Nowacka-Woszuk, Stephanie D. McKay, Antti Flyckt, Juhani Taponen, Robert Schnabel, Hermann Schwarzenbacher, Izabela Szczerbal, Hannes Lohi, Ruedi Fries, Jeremy F. Taylor, Marek Switonski, Magnus Andersson
PLoS One. 2010; 5(11): e15116. Published online 2010 November 30. doi: 10.1371/journal.pone.0015116
PMCID:
PMC2994898
Abstract Full Text PDF–998K Supplementary Material
Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome
Justin T Reese, Christopher P Childers, Jaideep P Sundaram, C Michael Dickens, Kevin L Childs, Donald C Vile, Christine G Elsik
BMC Genomics. 2010; 11: 645. Published online 2010 November 19. doi: 10.1186/1471-2164-11-645
PMCID:
PMC3012608
Abstract Full Text PDF–1.4M
An initial comparative map of copy number variations in the goat (Capra hircus) genome
Luca Fontanesi, Pier Luigi Martelli, Francesca Beretti, Valentina Riggio, Stefania Dall'Olio, Michela Colombo, Rita Casadio, Vincenzo Russo, Baldassare Portolano
BMC Genomics. 2010; 11: 639. Published online 2010 November 17. doi: 10.1186/1471-2164-11-639
PMCID:
PMC3011854
Abstract Full Text PDF–847K Supplementary Material
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation
Gregory P Harhay, Timothy PL Smith, Leeson J Alexander, Christian D Haudenschild, John W Keele, Lakshmi K Matukumalli, Steven G Schroeder, Curtis P Van Tassell, Cathy R Gresham, Susan M Bridges, Shane C Burgess, Tad S Sonstegard
Genome Biol. 2010; 11(10): R102. Published online 2010 October 20. doi: 10.1186/gb-2010-11-10-r102
PMCID:
PMC3218658
Abstract Full Text PDF–2.2M Supplementary Material
Genes and genomes, an imperfect world: comparison of gene annotations of two Bos taurus draft assemblies
Liliana Florea, Alexander Souvorov, Steven L Salzberg
Genome Biol. 2010; 11(Suppl 1): P13. Published online 2010 October 11. doi: 10.1186/gb-2010-11-s1-p13
PMCID:
PMC3026241
Full Text PDF–171K
The bovine chemokine receptors and their mRNA abundance in mononuclear phagocytes
Stephanie Widdison, Nazneen Siddiqui, Victoria Easton, Freya Lawrence, George Ashley, Dirk Werling, Michael Watson, Tracey J Coffey
BMC Genomics. 2010; 11: 439. Published online 2010 July 19. doi: 10.1186/1471-2164-11-439
PMCID:
PMC3091636
Abstract Full Text PDF–1.1M Supplementary Material
Characteristics of linkage disequilibrium in North American Holsteins
Jarmila Bohmanova, Mehdi Sargolzaei, Flavio S Schenkel
BMC Genomics. 2010; 11: 421. Published online 2010 July 8. doi: 10.1186/1471-2164-11-421
PMCID:
PMC2996949
Abstract Full Text PDF–1.8M Supplementary Material
Analysis of copy number variations among diverse cattle breeds
George E. Liu, Yali Hou, Bin Zhu, Maria Francesca Cardone, Lu Jiang, Angelo Cellamare, Apratim Mitra, Leeson J. Alexander, Luiz L. Coutinho, Maria Elena Dell'Aquila, Lou C. Gasbarre, Gianni Lacalandra, Robert W. Li, Lakshmi K. Matukumalli, Dan Nonneman, Luciana C. de A. Regitano, Tim P.L. Smith, Jiuzhou Song, Tad S. Sonstegard, Curt P. Van Tassell, Mario Ventura, Evan E. Eichler, Tara G. McDaneld, John W. Keele
Genome Res. 2010 May; 20(5): 693–703. doi: 10.1101/gr.105403.110
PMCID:
PMC2860171
Abstract Full Text PDF–765K
Detection and correction of false segmental duplications caused by genome mis-assembly
David R Kelley, Steven L Salzberg
Genome Biol. 2010; 11(3): R28. Published online 2010 March 10. doi: 10.1186/gb-2010-11-3-r28
PMCID:
PMC2864568
Abstract Full Text PDF–1.2M Supplementary Material
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