Search Results - "Bickhart, Derek M."

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome by Bickhart, Derek M, Rosen, Benjamin D, Koren, Sergey, Sayre, Brian L, Hastie, Alex R, Chan, Saki, Lee, Joyce, Lam, Ernest T, Liachko, Ivan, Sullivan, Shawn T, Burton, Joshua N, Huson, Heather J, Nystrom, John C, Kelley, Christy M, Hutchison, Jana L, Zhou, Yang, Sun, Jiajie, Crisà, Alessandra, Ponce de León, F Abel, Schwartz, John C, Hammond, John A, Waldbieser, Geoffrey C, Schroeder, Steven G, Liu, George E, Dunham, Maitreya J, Shendure, Jay, Sonstegard, Tad S, Phillippy, Adam M, Van Tassell, Curtis P, Smith, Timothy P L

“…Adam Phillippy, Curtis Van Tassell, Timothy Smith and colleagues present a new reference genome assembly for the domestic goat using a pipeline that improves…”
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Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis by Ma, Li, O'Connell, Jeffrey R, VanRaden, Paul M, Shen, Botong, Padhi, Abinash, Sun, Chuanyu, Bickhart, Derek M, Cole, John B, Null, Daniel J, Liu, George E, Da, Yang, Wiggans, George R

“…Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a…”
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Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity by 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.

“…Rapid innovation in sequencing technologies and improvement in assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we…”
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The challenges and importance of structural variation detection in livestock by Bickhart, Derek M, Liu, George E

“…Recent studies in humans and other model organisms have demonstrated that structural variants (SVs) comprise a substantial proportion of variation among…”
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Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle by Low, Wai Yee, Tearle, Rick, Liu, Ruijie, Koren, Sergey, Rhie, Arang, Bickhart, Derek M., Rosen, Benjamin D., Kronenberg, Zev N., Kingan, Sarah B., Tseng, Elizabeth, Thibaud-Nissen, Françoise, Martin, Fergal J., Billis, Konstantinos, Ghurye, Jay, Hastie, Alex R., Lee, Joyce, Pang, Andy W. C., Heaton, Michael P., Phillippy, Adam M., Hiendleder, Stefan, Smith, Timothy P. L., Williams, John L.

“…Inbred animals were historically chosen for genome analysis to circumvent assembly issues caused by haplotype variation but this resulted in a composite of the…”
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Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation by 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

“…We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a…”
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Copy number variation of individual cattle genomes using next-generation sequencing by Bickhart, Derek M, Hou, Yali, Schroeder, Steven G, Alkan, Can, Cardone, Maria Francesca, Matukumalli, Lakshmi K, Song, Jiuzhou, Schnabel, Robert D, Ventura, Mario, Taylor, Jeremy F, Garcia, Jose Fernando, Van Tassell, Curtis P, Sonstegard, Tad S, Eichler, Evan E, Liu, George E

“…Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a…”
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Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies by 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

“…Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform…”
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Genomic characteristics of cattle copy number variations by Hou, Yali, Liu, George E, Bickhart, Derek M, Cardone, Maria Francesca, Wang, Kai, Kim, Eui-Soo, Matukumalli, Lakshmi K, Ventura, Mario, Song, Jiuzhou, VanRaden, Paul M, Sonstegard, Tad S, Van Tassell, Curt P

“…Copy number variation (CNV) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP…”
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The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species by 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

“…The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation…”
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Truncation of IFT80 causes early embryonic loss in Holstein cattle associated with Holstein haplotype 2 by Ortega, M. Sofía, Bickhart, Derek M., Lockhart, Kelsey N., Null, Daniel J., Hutchison, Jana L., McClure, Jennifer C., Cole, John B.

“…Recessive alleles represent genetic risk in populations that have undergone bottleneck events. We present a comprehensive framework for identification and…”
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Population-genetic properties of differentiated copy number variations in cattle by Xu, Lingyang, Hou, Yali, Bickhart, Derek M., Zhou, Yang, Hay, El Hamidi abdel, Song, Jiuzhou, Sonstegard, Tad S., Van Tassell, Curtis P., Liu, George E.

“…While single nucleotide polymorphism (SNP) is typically the variant of choice for population genetics, copy number variation (CNV) which comprises insertion,…”
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Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping by Porto-Neto, Laercio R, Sonstegard, Tad S, Liu, George E, Bickhart, Derek M, Da Silva, Marcos V B, Machado, Marco A, Utsunomiya, Yuri T, Garcia, Jose F, Gondro, Cedric, Van Tassell, Curtis P

“…Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types of…”
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New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes by 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

“…Mammalian X chromosomes are mainly euchromatic with a similar size and structure among species whereas Y chromosomes are smaller, have undergone substantial…”
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Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach by Young, Juliana, Skarlupka, Joseph H., Cox, Madison S., Resende, Rafael Tassinari, Fischer, Amelie, Kalscheur, Kenneth F., McClure, Jennifer C., Cole, John B., Suen, Garret, Bickhart, Derek M.

“…The gastrointestinal tracts of ruminants harbor a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health,…”
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On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales by Zhaxybayeva, Olga, Swithers, Kristen S, Lapierre, Pascal, Fournier, Gregory P, Bickhart, Derek M, DeBoy, Robert T, Nelson, Karen E, Nesbø, Camilla L, Doolittle, W. Ford, Gogarten, J. Peter, Noll, Kenneth M

“…Since publication of the first Thermotogales genome, Thermotoga maritima strain MSB8, single- and multi-gene analyses have disagreed on the phylogenetic…”
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Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle by 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

“…The gaur (Bos gaurus) is the largest extant wild bovine species, native to South and Southeast Asia, with unique traits, and is listed as vulnerable by the…”
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Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color by Skarlupka, Joseph H, Cox, Madison S, Steinberger, Andrew J, Sbardellati, Dino L, McClure, Jennifer C, Bickhart, Derek M, Scheftgen, Andrew J, Zuniga-Chaves, Ibrahim, Wolfe, Luke A, Paget, Eric, Skadron, Charles, Attipetty, Nithya, Suen, Garret

“…Using oral swabs to collect the remnants of stomach content regurgitation during rumination in dairy cows can replicate up to 70% of the ruminal bacterial…”
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Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array by Hou, Yali, Bickhart, Derek M, Hvinden, Miranda L, Li, Congjun, Song, Jiuzhou, Boichard, Didier A, Fritz, Sébastien, Eggen, André, DeNise, Sue, Wiggans, George R, Sonstegard, Tad S, Van Tassell, Curtis P, Liu, George E

“…Btau_4.0 and UMD3.1 are two distinct cattle reference genome assemblies. In our previous study using the low density BovineSNP50 array, we reported a copy…”
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Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities by Bickhart, Derek M., Kolmogorov, Mikhail, Tseng, Elizabeth, Portik, Daniel M., Korobeynikov, Anton, Tolstoganov, Ivan, Uritskiy, Gherman, Liachko, Ivan, Sullivan, Shawn T., Shin, Sung Bong, Zorea, Alvah, Andreu, Victòria Pascal, Panke-Buisse, Kevin, Medema, Marnix H., Mizrahi, Itzhak, Pevzner, Pavel A., Smith, Timothy P. L.

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