Hybrid assembly with long and short reads improves discovery of gene family expansions

Autor: Jason R. Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P. Walenz, Junqi Liu, Robert M. Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G. Maron, Susan R. McCouch, W. Richard McCombie, Michael C. Schatz, Peter Tiffin, Nevin D. Young, Kevin A. T. Silverstein

Publikováno v: BMC Genomics, Vol 18, Iss 1, Pp 1-12 (2017)

Abstract Background Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. Methods We developed a

Externí odkaz: https://doaj.org/article/b23de4c2a6eb4c85ae3cd5ab8f841e47

KBase: The United States Department of Energy Systems Biology Knowledgebase

Autor: Shinjae Yoo, Matthew L. Henderson, Sarah S. Poon, Pavel S. Novichkov, Mark Mills, Roy T. Kamimura, Adam P. Arkin, Rick Stevens, Holly L. Haun, Shinnosuke Kondo, Meghan M Drake, Aaron A. Best, José P. Faria, Fernando Perez, Matthew DeJongh, Gang Fang, Thomas Brettin, Sergei Maslov, Janaka N. Edirisinghe, Folker Meyer, Jer Ming Chia, Scott Devoid, Doreen Ware, Steven E. Brenner, Paul M. Frybarger, Miriam Land, Dan Gunter, Fei He, John-Marc Chandonia, Hyunseung Yoo, Marcin P. Joachimiak, Dantong Yu, Christopher S. Henry, Mark Gerstein, Christopher Bun, Michael W. Sneddon, Samuel M. D. Seaver, Rashmi Jain, Stephen Y. Chan, Robert W. Cottingham, James J. Davis, Annette Greiner, Inna Dubchak, Vivek Kumar, Priya Ranjan, Daifeng Wang, Neal Conrad, James Thomason, Fangfang Xia, Maulik Shukla, Gavin Price, Nathan L. Tintle, Gary J. Olsen, Shiran Pasternak, Shane Canon, Roman A. Sutormin, William J. Riehl, Nomi L. Harris, Dan Murphy-Olson, Jason K. Baumohl, Wolfgang Gerlach, Benjamin H. Allen, Pamela C. Ronald, Michael C. Schatz, Mustafa H Syed, Brian H. Davison, Taeyun Oh, Dylan Chivian, Elizabeth M. Glass, R. L. Colasanti, Erik Pearson, David J. Weston, Sunita Kumari, Kevin P. Keegan, Emily M. Dietrich, Robert Olson, Srividya Ramakrishnan, James Gurtowski, Benjamin P. Bowen, Paramvir S. Dehal, Bruce Parrello

Publikováno v: Nature biotechnology, vol 36, iss 7
Nature Biotechnology
Arkin, AP; Cottingham, RW; Henry, CS; Harris, NL; Stevens, RL; Maslov, S; et al.(2018). KBase: The United States department of energy systems biology knowledgebase. Nature Biotechnology, 36(7), 566-569. doi: 10.1038/nbt.4163. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/7p39r37f

Author(s): Arkin, Adam P; Cottingham, Robert W; Henry, Christopher S; Harris, Nomi L; Stevens, Rick L; Maslov, Sergei; Dehal, Paramvir; Ware, Doreen; Perez, Fernando; Canon, Shane; Sneddon, Michael W; Henderson, Matthew L; Riehl, William J; Murphy-Ol

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c789b3716f923398ce5518911fb65ab7
https://doi.org/10.1038/nbt.4163

Antibiotic pressure on the acquisition and loss of antibiotic resistance genes in Klebsiella pneumoniae

Autor: James Gurtowski, Pranita D. Tamma, Patricia J. Simner, Michael C. Schatz, Karen C. Carroll, Clare Rock, Tsigereda Tekle, Winston Timp, Belita N. A. Opene, Annukka A.R. Antar, Stephanie Hao

OBJECTIVES: In this study, we characterize a concurrent disseminated infection with a virulent hypermucoviscous (HMV) Klebsiella pneumoniae and an OXA-181-producing XDR K. pneumoniae from a patient with recent hospitalization in India. During exposur

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::57965c271af3bab68e433fd7f27bdcf9
https://europepmc.org/articles/PMC6005101/

Hybrid assembly with long and short reads improves discovery of gene family expansions

Autor: Roxanne Denny, Hayan Lee, Li Song, Peter Tiffin, Junqi Liu, James Gurtowski, W. Richard McCombie, Michael C. Schatz, Jason R. Miller, Kevin A. T. Silverstein, Lyza G. Maron, Robert M. Stupar, Namrata Singh, Joann Mudge, Susan R. McCouch, Nevin D. Young, Peng Zhou, Brian P. Walenz, Thiruvarangan Ramaraj

Publikováno v: BMC Genomics, Vol 18, Iss 1, Pp 1-12 (2017)
BMC Genomics

Background Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. Methods We developed a hybrid a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0b58b2099e4d7b931ced186b514d0277
https://doi.org/10.1186/s12864-017-3927-8

Third-generation sequencing and the future of genomics

Autor: Sara Goodwin, James Gurtowski, Hayan Lee, Maria Nattestad, Shinjae Yoo, Michael C. Schatz, Richard McCombie W, Shoshana Marcus

Third-generation long-range DNA sequencing and mapping technologies are creating a renaissance in high-quality genome sequencing. Unlike second-generation sequencing, which produces short reads a few hundred base-pairs long, third-generation single-m

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f7686dd242681d137766fe01041b5b0