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580 results on '"Ussery, David W"'

1. Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing

Author

Jenjaroenpun, Piroon, Wanchai, Visanu, Ono-Moore, Kikumi D, Laudadio, Jennifer, James, Laura P, Adams, Sean H, Prior, Fred, Nookaew, Intawat, Ussery, David W, and Wongsurawat, Thidathip

Subjects
Vaccine Related, Genetics, Pneumonia & Influenza, Lung, Bioengineering, Pneumonia, Nanotechnology, Human Genome, Biotechnology, Prevention, Good Health and Well Being
Abstract

Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples from two patients in Arkansas, in the southeastern corner of the United States. The viral genome was obtained using the ARTIC Network protocol and Oxford Nanopore Technologies sequencing.

Published
2021

2. Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing.

Author

Jenjaroenpun, Piroon, Wanchai, Visanu, Ono-Moore, Kikumi D, Laudadio, Jennifer, James, Laura P, Adams, Sean H, Prior, Fred, Nookaew, Intawat, Ussery, David W, and Wongsurawat, Thidathip

Subjects
Genetics, Human Genome, Prevention, Lung, Biotechnology, Nanotechnology, Pneumonia & Influenza, Bioengineering, Pneumonia, Vaccine Related
Abstract

Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples from two patients in Arkansas, in the southeastern corner of the United States. The viral genome was obtained using the ARTIC Network protocol and Oxford Nanopore Technologies sequencing.

Published
2020

3. Toward unrestricted use of public genomic data

Author

Amann, Rudolf I, Baichoo, Shakuntala, Blencowe, Benjamin J, Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick SG, Colwell, Rita R, Daffonchio, Daniele G, Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C, Finn, Robert D, Fraser, Claire M, Gilbert, Jack A, Hallam, Steven J, Hugenholtz, Philip, Ioannidis, John PA, Jansson, Janet K, Kim, Jihyun F, Klenk, Hans-Peter, Klotz, Martin G, Knight, Rob, Konstantinidis, Konstantinos T, Kyrpides, Nikos C, Mason, Christopher E, McHardy, Alice C, Meyer, Folker, Ouzounis, Christos A, Patrinos, Aristides AN, Podar, Mircea, Pollard, Katherine S, Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J, Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D, Schriml, Lynn M, Setubal, João C, Sorek, Rotem, Stevens, Rick L, Tiedje, James M, Turjanski, Adrian, Tyson, Gene W, Ussery, David W, Weinstock, George M, White, Owen, Whitman, William B, and Xenarios, Ioannis

Subjects
Information and Computing Sciences, Law and Legal Studies, Library and Information Studies, Access to Information, Databases, Genetic, Genome, Human, Genomics, Humans, Information Dissemination, General Science & Technology
Abstract

Publication interests should not limit access to public data

Published
2019

5. Response

Author

Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., K. Jansson, Janet, Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., C. McHardy, Alice, Meyer, Folker, Ouzounis, Christos A., Patrinos, Aristides A. N., Podar, Mircea, Pollard, Katherine S., Ravel, Jacques, Muñoz, Alejandro Reyes, Roberts, Richard J., Rosselló-Móra, Ramon, Sansone, Susanna-Assunta, Schloss, Patrick D., Schriml, Lynn M., Setubal, João C., Sorek, Rotem, Stevens, Rick L., Tiedje, James M., Turjanski, Adrian, Tyson, Gene W., Ussery, David W., Weinstock, George M., White, Owen, Whitman, William B., and Xenarios, Ioannis

Published
2019

8. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

Author

Timm, Collin M, Campbell, Alisha G, Utturkar, Sagar M, Jun, Se-Ran, Parales, Rebecca E, Tan, Watumesa A, Robeson, Michael S, Lu, Tse-Yuan S, Jawdy, Sara, Brown, Steven D, Ussery, David W, Schadt, Christopher W, Tuskan, Gerald A, Doktycz, Mitchel J, Weston, David J, and Pelletier, Dale A

Subjects
Microbiology, Plant Biology, Biological Sciences, microbiome, Populus, metabolism, endosphere, rhizosphere, metabolic modeling, Environmental Science and Management, Soil Sciences, Medical microbiology
Abstract

The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.

Published
2015

13. The Genomic Standards Consortium.

Author

Field, Dawn, Amaral-Zettler, Linda, Cochrane, Guy, Cole, James R, Dawyndt, Peter, Garrity, George M, Gilbert, Jack, Glöckner, Frank Oliver, Hirschman, Lynette, Karsch-Mizrachi, Ilene, Klenk, Hans-Peter, Knight, Rob, Kottmann, Renzo, Kyrpides, Nikos, Meyer, Folker, San Gil, Inigo, Sansone, Susanna-Assunta, Schriml, Lynn M, Sterk, Peter, Tatusova, Tatiana, Ussery, David W, White, Owen, and Wooley, John

Subjects
Genomics, International Cooperation, Databases, Genetic, Metagenome, Human Genome, Genetics, Generic health relevance, Developmental Biology, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences
Abstract

A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.

Published
2011

16. Case of Microcephaly after Congenital Infection with Asian Lineage Zika Virus, Thailand

Author

Wongsurawat, Thidathip, Athipanyasilp, Niracha, Jenjaroenpun, Piroon, Jun, Se- Ran, Kaewnapan, Bualan, Wassenaar, Trudy M., Leelahakorn, Nattawat, Angkasekwinai, Nasikarn, Kantakamalakul, Wannee, Ussery, David W., Sutthent, Ruengpung, Nookaew, Intawat, and Horthongkham, Navin

Subjects
Zika virus -- Health aspects, Infection -- Health aspects, Genomes -- Health aspects, Genomics -- Health aspects, Pregnant women -- Health aspects, Health
Abstract

Although Zika virus has circulated in Asia longer than in the Americas, only 3 confirmed cases of congenital Zika virus infection with microcephaly have been reported in Asia (2 Thailand, [...]

Published
2018
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18. Evolution of Microbial Communities; or, On the Origins of Bacterial Species

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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19. Transcriptomics: Translated and Untranslated RNA

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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20. Microbial Communities: Core and Pan-Genomics

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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21. Metagenomics of Microbial Communities

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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22. Of Proteins, Genomes, and Proteomes

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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23. Expression of Genes and Proteins

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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24. Word Frequencies and Repeats

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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25. Genomic Properties: Length, Base Composition and DNA Structures

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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26. Methods to Compare Genomes The First Examples

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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27. Microbial Genome Sequences: A New Era in Microbiology

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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28. The Challenges of Programming: A Brief Introduction

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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29. An Overview of Genome Databases

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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30. Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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31. Bioinformatics for Microbiologists: An Introduction

Author

Ussery, David W., Wassenaar, Trudy M., Borini, Stefano, Grippen, Gordon, editor, Felsenstein, Joe, editor, Gusfield, Dan, editor, Istrail, Sorin, editor, Karlin, Samuel, editor, Lengauer, Thomas, editor, McClure, Marcella, editor, Nowak, Martin, editor, Sankoff, David, editor, Shamir, Ron, editor, Steel, Mike, editor, Stormo, Gary, editor, Tavaré, Simon, editor, Warnow, Tandy, editor, Myers, Gene, editor, Giegerich, Robert, editor, Fitch, Walter M., editor, Pevzner, Pavel, editor, Vingron, Martin, editor, Ussery, David W., editor, Wassenaar, Trudy M., editor, and Borini, Stefano, editor

Published
2009
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33. Severe Acute Respiratory Syndrome Coronavirus-2 Lambda Variant Collected from a Child from Arkansas and Sequenced

Author

Wong, Lori, primary, Randolph, Christopher, additional, Kanwischer, Emily, additional, Ingold, Ashton, additional, Boyanton, Bobby L., additional, Taylor, Jay, additional, Frenner, Rachel A., additional, Harley, Susan E., additional, Bird, Jordan T., additional, Thurman, Timothy J., additional, Kandel, Sangam, additional, Ussery, David W., additional, Byrum, Stephanie D., additional, Dinwiddie, Darrell, additional, Domman, Daryl, additional, Chalwadi, Uday K., additional, and Kennedy, Joshua, additional

Published
2023
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34. Comparative Genomics

Author

Ozen, Asli Ismihan, Vesth, Tammi, Ussery, David W., Rosenberg, Eugene, editor, DeLong, Edward F., editor, Lory, Stephen, editor, Stackebrandt, Erko, editor, and Thompson, Fabiano, editor

Published
2013
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38. The Genome Atlas Resource

Author

Qureshi, Matloob, Rotenberg, Eva, Stærfeldt, Hans-Henrik, Hansson, Lena, Ussery, David W., Chan, Jonathan H., editor, Ong, Yew-Soon, editor, and Cho, Sung-Bae, editor

Published
2010
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46. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

Author

Kröger, Carsten, Dillon, Shane C., Cameron, Andrew D. S., Papenfort, Kai, Sivasankaran, Sathesh K., Hokamp, Karsten, Chao, Yanjie, Sittka, Alexandra, Hébrard, Magali, Händler, Kristian, Colgan, Aoife, Leekitcharoenphon, Pimlapas, Langridge, Gemma C., Lohan, Amanda J., Loftus, Brendan, Lucchini, Sacha, Ussery, David W., Dorman, Charles J., Thomson, Nicholas R., Vogel, Jörg, and Hinton, Jay C. D.

Published
2012

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