Search

Your search keyword '"Chow, William"' showing total 9 results
Start Over Author "Chow, William" Publisher oxford university press (oup)
9 results on '"Chow, William"'

1. A high-quality genome and comparison of short- versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Author

Mueller, Ralf C, primary, Ellström, Patrik, additional, Howe, Kerstin, additional, Uliano-Silva, Marcela, additional, Kuo, Richard I, additional, Miedzinska, Katarzyna, additional, Warr, Amanda, additional, Fedrigo, Olivier, additional, Haase, Bettina, additional, Mountcastle, Jacquelyn, additional, Chow, William, additional, Torrance, James, additional, Wood, Jonathan M D, additional, Järhult, Josef D, additional, Naguib, Mahmoud M, additional, Olsen, Björn, additional, Jarvis, Erich D, additional, Smith, Jacqueline, additional, Eöry, Lél, additional, and Kraus, Robert H S, additional

Published
2021
Full Text
View/download PDF

2. A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)

Author

Sætre, Camilla Lo Cascio, primary, Eroukhmanoff, Fabrice, additional, Rönkä, Katja, additional, Kluen, Edward, additional, Thorogood, Rose, additional, Torrance, James, additional, Tracey, Alan, additional, Chow, William, additional, Pelan, Sarah, additional, Howe, Kerstin, additional, Jakobsen, Kjetill S, additional, and Tørresen, Ole K, additional

Published
2021
Full Text
View/download PDF

3. A high-quality genome and comparison of short-versus long-read transcriptome of the palaearctic duck Aythya fuligula (tufted duck)

Author

Mueller, Ralf C., Ellström, Patrik, Howe, Kerstin, Uliano-Silva, Marcela, Kuo, Richard I., Miedzinska, Katarzyna, Warr, Amanda, Fedrigo, Olivier, Haase, Bettina, Mountcastle, Jacquelyn, Chow, William, Torrance, James, Wood, Jonathan M. D., Järhult, Josef D., Naguib, Mahmoud, Olsen, Björn, Jarvis, Erich D., Smith, Jacqueline, Eory, Lel, Kraus, Robert H. S., Mueller, Ralf C., Ellström, Patrik, Howe, Kerstin, Uliano-Silva, Marcela, Kuo, Richard I., Miedzinska, Katarzyna, Warr, Amanda, Fedrigo, Olivier, Haase, Bettina, Mountcastle, Jacquelyn, Chow, William, Torrance, James, Wood, Jonathan M. D., Järhult, Josef D., Naguib, Mahmoud, Olsen, Björn, Jarvis, Erich D., Smith, Jacqueline, Eory, Lel, and Kraus, Robert H. S.

Abstract

Background: The tufted duck is a non-model organism that experiences high mortality in highly pathogenic avian influenza outbreaks. It belongs to the same bird family (Anatidae) as the mallard, one of the best-studied natural hosts of low-pathogenic avian influenza viruses. Studies in non-model bird species are crucial to disentangle the role of the host response in avian influenza virus infection in the natural reservoir. Such endeavour requires a high-quality genome assembly and transcriptome. Findings: This study presents the first high-quality, chromosome-level reference genome assembly of the tufted duck using the Vertebrate Genomes Project pipeline. We sequenced RNA (complementary DNA) from brain, ileum, lung, ovary, spleen, and testis using Illumina short-read and Pacific Biosciences long-read sequencing platforms, which were used for annotation. We found 34 autosomes plus Z and W sex chromosomes in the curated genome assembly, with 99.6% of the sequence assigned to chromosomes. Functional annotation revealed 14,099 protein-coding genes that generate 111,934 transcripts, which implies a mean of 7.9 isoforms per gene. We also identified 246 small RNA families. Conclusions: This annotated genome contributes to continuing research into the host response in avian influenza virus infections in a natural reservoir. Our findings from a comparison between short-read and long -read reference transcriptomics contribute to a deeper understanding of these competing options. In this study, both technologies complemented each other. We expect this annotation to be a foundation for further comparative and evolutionary genomic studies, including many waterfowl relatives with differing susceptibilities to avian influenza viruses.

Published
2021
Full Text
View/download PDF

5. An improved pig reference genome sequence to enable pig genetics and genomics research

Author

Warr, Amanda, primary, Affara, Nabeel, primary, Aken, Bronwen, primary, Beiki, Hamid, primary, Bickhart, Derek M, primary, Billis, Konstantinos, primary, Chow, William, primary, Eory, Lel, primary, Finlayson, Heather A, primary, Flicek, Paul, primary, Girón, Carlos G, primary, Griffin, Darren K, primary, Hall, Richard, primary, Hannum, Greg, primary, Hourlier, Thibaut, primary, Howe, Kerstin, primary, Hume, David A, primary, Izuogu, Osagie, primary, Kim, Kristi, primary, Koren, Sergey, primary, Liu, Haibou, primary, Manchanda, Nancy, primary, Martin, Fergal J, primary, Nonneman, Dan J, primary, O'Connor, Rebecca E, primary, Phillippy, Adam M, primary, Rohrer, Gary A, primary, Rosen, Benjamin D, primary, Rund, Laurie A, primary, Sargent, Carole A, primary, Schook, Lawrence B, primary, Schroeder, Steven G, primary, Schwartz, Ariel S, primary, Skinner, Ben M, primary, Talbot, Richard, primary, Tseng, Elizabeth, primary, Tuggle, Christopher K, primary, Watson, Mick, primary, Smith, Timothy P L, primary, and Archibald, Alan L, primary

Published
2020
Full Text
View/download PDF

6. A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Author

Warren, Wesley C, primary, Hillier, LaDeana W, additional, Tomlinson, Chad, additional, Minx, Patrick, additional, Kremitzki, Milinn, additional, Graves, Tina, additional, Markovic, Chris, additional, Bouk, Nathan, additional, Pruitt, Kim D, additional, Thibaud-Nissen, Francoise, additional, Schneider, Valerie, additional, Mansour, Tamer A, additional, Brown, C Titus, additional, Zimin, Aleksey, additional, Hawken, Rachel, additional, Abrahamsen, Mitch, additional, Pyrkosz, Alexis B, additional, Morisson, Mireille, additional, Fillon, Valerie, additional, Vignal, Alain, additional, Chow, William, additional, Howe, Kerstin, additional, Fulton, Janet E, additional, Miller, Marcia M, additional, Lovell, Peter, additional, Mello, Claudio V, additional, Wirthlin, Morgan, additional, Mason, Andrew S, additional, Kuo, Richard, additional, Burt, David W, additional, Dodgson, Jerry B, additional, and Cheng, Hans H, additional

Published
2017
Full Text
View/download PDF

9. An improved pig reference genome sequence to enable pig genetics and genomics research

Author

Warr, Amanda, Affara, Nabeel, Aken, Bronwen, Beiki, Hamid, Bickhart, Derek M, Billis, Konstantinos, Chow, William, Eory, Lel, Finlayson, Heather A, Flicek, Paul, Girón, Carlos G, Griffin, Darren K, Hall, Richard, Hannum, Greg, Hourlier, Thibaut, Howe, Kerstin, Hume, David A, Izuogu, Osagie, Kim, Kristi, Koren, Sergey, Liu, Haibou, Manchanda, Nancy, Martin, Fergal J, Nonneman, Dan J, O'Connor, Rebecca E, Phillippy, Adam M, Rohrer, Gary A, Rosen, Benjamin D, Rund, Laurie A, Sargent, Carole A, Schook, Lawrence B, Schroeder, Steven G, Schwartz, Ariel S, Skinner, Ben M, Talbot, Richard, Tseng, Elizabeth, Tuggle, Christopher K, Watson, Mick, Smith, Timothy PL, and Archibald, Alan L

Subjects
2. Zero hunger, pig, reference assembly, Genome, genome annotation, Swine, Research, Sus scrofa, Computational Biology, Reproducibility of Results, Molecular Sequence Annotation, Genomics, Sequence Analysis, DNA, pig genomes, Animals
Abstract

BACKGROUND: The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. RESULTS: We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. CONCLUSIONS: These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

Catalog

Books, media, physical & digital resources
See catalog results