Development and Characterization of a High Density SNP Genotyping Assay for Cattle von 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

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Rumen microbiome from steers differing in feed efficiency von Myer, Phillip R, Smith, Timothy P L, Wells, James E, Kuehn, Larry A, Freetly, Harvey C

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Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity von 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.

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Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies von 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

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C von 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.

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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 von 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

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Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle von 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

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Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data von Beiki, H, Liu, H, Huang, J, Manchanda, N, Nonneman, D, Smith, T P L, Reecy, J M, Tuggle, C K

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Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies von Ren, Yan, Tseng, Elizabeth, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L, Low, Wai Yee

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Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology von Ramos, Antonio M, Crooijmans, Richard P M A, Affara, Nabeel A, Amaral, Andreia J, Archibald, Alan L, Beever, Jonathan E, Bendixen, Christian, Churcher, Carol, Clark, Richard, Dehais, Patrick, Hansen, Mark S, Hedegaard, Jakob, Hu, Zhi-Liang, Kerstens, Hindrik H, Law, Andy S, Megens, Hendrik-Jan, Milan, Denis, Nonneman, Danny J, Rohrer, Gary A, Rothschild, Max F, Smith, Tim P L, Schnabel, Robert D, Van Tassell, Curt P, Taylor, Jeremy F, Wiedmann, Ralph T, Schook, Lawrence B, Groenen, Martien A M

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Repeat and single dose administration of gadodiamide to rats to investigate concentration and location of gadolinium and the cell ultrastructure von Davies, Julie, Marino, Michael, Smith, Adrian P. L., Crowder, Janell M., Larsen, Michael, Lowery, Lisa, Castle, Jason, Hibberd, Mark G., Evans, Paul M.

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Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content von 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.

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The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species von 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

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Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species von Liu, Ruijie, Tearle, Rick, Low, Wai Yee, Chen, Tong, Thomsen, Dana, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L

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metaFlye: scalable long-read metagenome assembly using repeat graphs von 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.

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Peripheral myeloid cells contribute to brain injury in male neonatal mice von Smith, Peter L P, Mottahedin, Amin, Svedin, Pernilla, Mohn, Carl-Johan, Hagberg, Henrik, Ek, Joakim, Mallard, Carina

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Changes in waist circumference relative to body mass index in Chinese adults, 1993–2009 von Stern, D, Smith, L P, Zhang, B, Gordon-Larsen, P, Popkin, B M

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Prospective Study of the Performance of Vibrational Spectroscopies for Rapid Identification of Bacterial and Fungal Pathogens Recovered from Blood Cultures von MAQUELIN, K, KIRSCHNER, C, CHOO-SMITH, L.-P, NGO-THI, N. A, VAN VREESWIJK, T, STÄMMLER, M, ENDTZ, H. P, BRUINING, H. A, NAUMANN, D, PUPPETS, G. J

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New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes von 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

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Classification of 16S rRNA reads is improved using a niche-specific database constructed by near-full length sequencing von 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

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