Rumen microbiome from steers differing in feed efficiency
Myer, Phillip R, Smith, Timothy P L, Wells, James E, Kuehn, Larry A, Freetly, Harvey C
Published in PloS one (01.06.2015)
Published in PloS one (01.06.2015)
Get full text
Journal Article
Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity
Low, Wai Yee, Tearle, Rick, Bickhart, Derek M, Rosen, Benjamin D, Kingan, Sarah B, Swale, Thomas, Thibaud-Nissen, Françoise, Murphy, Terence D, Young, Rachel, Lefevre, Lucas, Hume, David A, Collins, Andrew, Ajmone-Marsan, Paolo, Smith, Timothy P L, Williams, John L
Published in Nature communications (16.01.2019)
Published in Nature communications (16.01.2019)
Get full text
Journal Article
Development and Characterization of a High Density SNP Genotyping Assay for Cattle
Matukumalli, Lakshmi K, Lawley, Cynthia T, Schnabel, Robert D, Taylor, Jeremy F, Allan, Mark F, Heaton, Michael P, O'Connell, Jeff, Moore, Stephen S, Smith, Timothy P.L, Sonstegard, Tad S, Van Tassell, Curtis P
Published in PloS one (24.04.2009)
Published in PloS one (24.04.2009)
Get full text
Journal Article
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
Kronenberg, Zev N, Rhie, Arang, Koren, Sergey, Concepcion, Gregory T, Peluso, Paul, Munson, Katherine M, Porubsky, David, Kuhn, Kristen, Mueller, Kathryn A, Low, Wai Yee, Hiendleder, Stefan, Fedrigo, Olivier, Liachko, Ivan, Hall, Richard J, Phillippy, Adam M, Eichler, Evan E, Williams, John L, Smith, Timothy P L, Jarvis, Erich D, Sullivan, Shawn T, Kingan, Sarah B
Published in Nature communications (28.04.2021)
Published in Nature communications (28.04.2021)
Get full text
Journal Article
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation
Bickhart, Derek M, Watson, Mick, Koren, Sergey, Panke-Buisse, Kevin, Cersosimo, Laura M, Press, Maximilian O, Van Tassell, Curtis P, Van Kessel, Jo Ann S, Haley, Bradd J, Kim, Seon Woo, Heiner, Cheryl, Suen, Garret, Bakshy, Kiranmayee, Liachko, Ivan, Sullivan, Shawn T, Myer, Phillip R, Ghurye, Jay, Pop, Mihai, Weimer, Paul J, Phillippy, Adam M, Smith, Timothy P L
Published in Genome Biology (02.08.2019)
Published in Genome Biology (02.08.2019)
Get full text
Journal Article
Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies
Leonard, Alexander S, Crysnanto, Danang, Fang, Zih-Hua, Heaton, Michael P, Vander Ley, Brian L, Herrera, Carolina, Bollwein, Heinrich, Bickhart, Derek M, Kuhn, Kristen L, Smith, Timothy P L, Rosen, Benjamin D, Pausch, Hubert
Published in Nature communications (31.05.2022)
Published in Nature communications (31.05.2022)
Get full text
Journal Article
The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species
Smith, Timothy P L, Bickhart, Derek M, Boichard, Didier, Chamberlain, Amanda J, Djikeng, Appolinaire, Jiang, Yu, Low, Wai Y, Pausch, Hubert, Demyda-Peyrás, Sebastian, Prendergast, James, Schnabel, Robert D, Rosen, Benjamin D
Published in Genome Biology (19.06.2023)
Published in Genome Biology (19.06.2023)
Get full text
Journal Article
Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies
Ren, Yan, Tseng, Elizabeth, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L, Low, Wai Yee
Published in BMC genomics (13.03.2023)
Published in BMC genomics (13.03.2023)
Get full text
Journal Article
Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle
Durso, Lisa M, Harhay, Gregory P, Smith, Timothy P.L, Bono, James L, DeSantis, Todd Z, Harhay, Dayna M, Andersen, Gary L, Keen, James E, Laegreid, William W, Clawson, Michael L
Published in Applied and Environmental Microbiology (01.07.2010)
Published in Applied and Environmental Microbiology (01.07.2010)
Get full text
Journal Article
Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species
Liu, Ruijie, Tearle, Rick, Low, Wai Yee, Chen, Tong, Thomsen, Dana, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L
Published in BMC genomics (03.06.2021)
Published in BMC genomics (03.06.2021)
Get full text
Journal Article
Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content
Olagunju, Temitayo A, Rosen, Benjamin D, Neibergs, Holly L, Becker, Gabrielle M, Davenport, Kimberly M, Elsik, Christine G, Hadfield, Tracy S, Koren, Sergey, Kuhn, Kristen L, Rhie, Arang, Shira, Katie A, Skibiel, Amy L, Stegemiller, Morgan R, Thorne, Jacob W, Villamediana, Patricia, Cockett, Noelle E, Murdoch, Brenda M, Smith, Timothy P L
Published in Nature communications (27.09.2024)
Published in Nature communications (27.09.2024)
Get full text
Journal Article
New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes
Liu, Ruijie, Low, Wai Yee, Tearle, Rick, Koren, Sergey, Ghurye, Jay, Rhie, Arang, Phillippy, Adam M, Rosen, Benjamin D, Bickhart, Derek M, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L
Published in BMC genomics (19.12.2019)
Published in BMC genomics (19.12.2019)
Get full text
Journal Article
Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing
Myer, Phillip R, McDaneld, Tara G, Kuehn, Larry A, Dedonder, Keith D, Apley, Michael D, Capik, Sarah F, Lubbers, Brian V, Harhay, Gregory P, Harhay, Dayna M, Keele, John W, Henniger, Madison T, Clemmons, Brooke A, Smith, Timothy P. L
Published in PloS one (13.07.2020)
Published in PloS one (13.07.2020)
Get full text
Journal Article
Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle
Low, Wai Yee, Rosen, Benjamin D, Ren, Yan, Bickhart, Derek M, To, Thu-Hien, Martin, Fergal J, Billis, Konstantinos, Sonstegard, Tad S, Sullivan, Shawn T, Hiendleder, Stefan, Williams, John L, Heaton, Michael P, Smith, Timothy P L
Published in BMC genomics (04.05.2022)
Published in BMC genomics (04.05.2022)
Get full text
Journal Article
metaFlye: scalable long-read metagenome assembly using repeat graphs
Kolmogorov, Mikhail, Bickhart, Derek M, Behsaz, Bahar, Gurevich, Alexey, Rayko, Mikhail, Shin, Sung Bong, Kuhn, Kristen, Yuan, Jeffrey, Polevikov, Evgeny, Smith, Timothy P L, Pevzner, Pavel A
Published in Nature methods (01.11.2020)
Published in Nature methods (01.11.2020)
Get full text
Journal Article
Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi
Anton, Brian P, Harhay, Gregory P, Smith, Timothy P L, Blom, Jochen, Roberts, Richard J
Published in PloS one (24.08.2016)
Published in PloS one (24.08.2016)
Get full text
Journal Article
Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library
Sánchez, Cecilia Castaño, Smith, Timothy P L, Wiedmann, Ralph T, Vallejo, Roger L, Salem, Mohamed, Yao, Jianbo, Rexroad, 3rd, Caird E
Published in BMC genomics (25.11.2009)
Published in BMC genomics (25.11.2009)
Get full text
Journal Article
Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica
Clawson, Michael L, Schuller, Gennie, Dickey, Aaron M, Bono, James L, Murray, Robert W, Sweeney, Michael T, Apley, Michael D, DeDonder, Keith D, Capik, Sarah F, Larson, Robert L, Lubbers, Brian V, White, Brad J, Blom, Jochen, Chitko-McKown, Carol G, Brichta-Harhay, Dayna M, Smith, Timothy P L
Published in BMC microbiology (12.08.2020)
Published in BMC microbiology (12.08.2020)
Get full text
Journal Article
MicroRNA transcriptome profiles during swine skeletal muscle development
McDaneld, Tara G, Smith, Timothy P L, Doumit, Matthew E, Miles, Jeremy R, Coutinho, Luiz L, Sonstegard, Tad S, Matukumalli, Lakshmi K, Nonneman, Dan J, Wiedmann, Ralph T
Published in BMC genomics (10.02.2009)
Published in BMC genomics (10.02.2009)
Get full text
Journal Article