Search Results - "Smith, P. L"

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

“…The cattle rumen has a diverse microbial ecosystem that is essential for the host to digest plant material. Extremes in body weight (BW) gain in mice and…”
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Development and Characterization of a High Density SNP Genotyping Assay for Cattle by 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

“…The success of genome-wide association (GWA) studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use…”
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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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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C by 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.

“…Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best…”
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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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Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data by Beiki, H, Liu, H, Huang, J, Manchanda, N, Nonneman, D, Smith, T P L, Reecy, J M, Tuggle, C K

“…Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule…”
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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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Repeat and single dose administration of gadodiamide to rats to investigate concentration and location of gadolinium and the cell ultrastructure by Davies, Julie, Marino, Michael, Smith, Adrian P. L., Crowder, Janell M., Larsen, Michael, Lowery, Lisa, Castle, Jason, Hibberd, Mark G., Evans, Paul M.

“…Gadolinium based contrast agents (GBCA) are used to image patients using magnetic resonance (MR) imaging. In recent years, there has been controversy around…”
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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 by 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

“…The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as…”
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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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Long read isoform sequencing reveals hidden transcriptional complexity between cattle subspecies by Ren, Yan, Tseng, Elizabeth, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L, Low, Wai Yee

“…The Iso-Seq method of full-length cDNA sequencing is suitable to quantify differentially expressed genes (DEGs), transcripts (DETs) and transcript usage (DTU)…”
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Peripheral myeloid cells contribute to brain injury in male neonatal mice by Smith, Peter L P, Mottahedin, Amin, Svedin, Pernilla, Mohn, Carl-Johan, Hagberg, Henrik, Ek, Joakim, Mallard, Carina

“…Neonatal brain injury is increasingly understood to be linked to inflammatory processes that involve specialised CNS and peripheral immune interactions…”
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Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle by 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

“…The intestinal microbiota of beef cattle are important for animal health, food safety, and methane emissions. This full-length sequencing survey of 11,171 16S…”
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Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species by Liu, Ruijie, Tearle, Rick, Low, Wai Yee, Chen, Tong, Thomsen, Dana, Smith, Timothy P L, Hiendleder, Stefan, Williams, John L

“…There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two…”
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Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content by 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.

“…Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. Here, we assemble complete and gapless telomere to…”
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Changes in waist circumference relative to body mass index in Chinese adults, 1993–2009 by Stern, D, Smith, L P, Zhang, B, Gordon-Larsen, P, Popkin, B M

“…Background: Although body mass index (BMI) and waist circumference (WC) are correlated, the relationship between WC and BMI may have changed over time…”
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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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Prospective Study of the Performance of Vibrational Spectroscopies for Rapid Identification of Bacterial and Fungal Pathogens Recovered from Blood Cultures by 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

“…Article Usage Stats Services JCM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Raman spectroscopy with an integrated arrayed-waveguide grating by Ismail, N, Choo-Smith, L-P, Wörhoff, K, Driessen, A, Baclig, A C, Caspers, P J, Puppels, G J, de Ridder, R M, Pollnau, M

“…An integrated arrayed-waveguide grating fabricated in silicon-oxynitride technology is applied to Raman spectroscopy. After its validation by reproducing the…”
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Identification of medically relevant microorganisms by vibrational spectroscopy by Maquelin, K, Kirschner, C, Choo-Smith, L.-P, van den Braak, N, Endtz, H.Ph, Naumann, D, Puppels, G.J

“…In the recent years, vibrational spectroscopies (infrared and Raman spectroscopy) have been developed for all sorts of analyses in microbiology. Important…”
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