Zobrazeno 1 - 10
of 35
pro vyhledávání: '"Dylan Chivian"'
Autor:
Lars Malmström, Michael Riffle, Charlie E M Strauss, Dylan Chivian, Trisha N Davis, Richard Bonneau, David Baker
Publikováno v:
PLoS Biology, Vol 5, Iss 4, p e76 (2007)
Saccharomyces cerevisiae is one of the best-studied model organisms, yet the three-dimensional structure and molecular function of many yeast proteins remain unknown. Yeast proteins were parsed into 14,934 domains, and those lacking sequence similari
Externí odkaz:
https://doaj.org/article/3d2903ae1917477193ee6bb42bfab50a
Autor:
Dylan Chivian, Sean P. Jungbluth, Paramvir S. Dehal, Elisha M. Wood-Charlson, Richard S. Canon, Benjamin H. Allen, Mikayla M. Clark, Tianhao Gu, Miriam L. Land, Gavin A. Price, William J. Riehl, Michael W. Sneddon, Roman Sutormin, Qizhi Zhang, Robert W. Cottingham, Chris S. Henry, Adam P. Arkin
Publikováno v:
Nature Protocols.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ff4884c1371b3c44e75542abad4c1944
https://doi.org/10.1038/s41596-022-00794-4
https://doi.org/10.1038/s41596-022-00794-4
Autor:
Dylan, Chivian, Sean P, Jungbluth, Paramvir S, Dehal, Elisha M, Wood-Charlson, Richard S, Canon, Benjamin H, Allen, Mikayla M, Clark, Tianhao, Gu, Miriam L, Land, Gavin A, Price, William J, Riehl, Michael W, Sneddon, Roman, Sutormin, Qizhi, Zhang, Robert W, Cottingham, Chris S, Henry, Adam P, Arkin
Publikováno v:
Nature protocols.
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth's micr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::894d6877e8c1518ba141af01ebae2606
https://pubmed.ncbi.nlm.nih.gov/36451056
https://pubmed.ncbi.nlm.nih.gov/36451056
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
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
https://doi.org/10.1038/nbt.4163
Autor:
José P. Faria, Edward Kirton, Nikos C. Kyrpides, Joshua Ladau, Torben Nielsen, Stephen Nayfach, David Paez-Espino, Nigel J Mouncey, Tanja Woyke, Christopher S. Henry, T. B. K. Reddy, Rekha Seshadri, Neha Varghese, Susannah G. Tringe, Daniel W. Udwary, Sean P. Jungbluth, Axel Visel, Dongying Wu, Emiley A. Eloe-Fadrosh, Supratim Mukherjee, Krishna Palaniappan, I-Min Chen, Frederik Schulz, Adam P. Arkin, Natalia Ivanova, Simon Roux, Dylan Chivian, Elisha M. Wood-Charlson, Janaka N. Edirisinghe, Marcel Huntemann, Paramvir S. Dehal
Publikováno v:
Nature Biotechnology
In the version of this article initially published, four people were missing from the alphabetical list of IMG/M Data Consortium members: Lauren V. Alteio of the Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::34cabcac968347f4e23cbd2437d0622c
http://europepmc.org/articles/PMC8041622
http://europepmc.org/articles/PMC8041622
Autor:
Adam P. Arkin, Whendee L. Silver, Kristen M. DeAngelis, Terry C. Hazen, Dylan Chivian, Julian L. Fortney, Blake A. Simmons
Publikováno v:
Soil Biology and Biochemistry. 66:60-68
Humid tropical forest soils are characterized by low and fluctuating redox, conditions which are thought to inhibit organic matter degradation by microbes. However, evidence suggests that soil microbial communities are adapted to the redox conditions
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::de186c82c1530a47d05756e45606d500
https://doi.org/10.1016/j.soilbio.2013.06.010
https://doi.org/10.1016/j.soilbio.2013.06.010
Autor:
Seaver Smd, Erik Pearson, José P. Faria, Gary J. Olsen, Olson B, Sarah S. Poon, Jason K. Baumohl, Christopher Bun, Emily M. Dietrich, Pamela C. Ronald, Nathan L. Tintle, Fei He, Paramvir S. Dehal, Marcin P. Joachimiak, Benjamin H. Allen, Thomas Brettin, Benjamin P. Bowen, Folker Meyer, Steven E. Brenner, Holly L. Haun, Shinjae Yoo, Fernando Perez, Matthew DeJongh, R. L. Colasanti, Maulik Shukla, Wolfgang Gerlach, Kevin P. Keegan, Jer Ming Chia, Michael C. Schatz, Taeyun Oh, Dylan Chivian, James Thomason, Sergei Maslov, Roman A. Sutormin, John-Marc Chandonia, Nomi L. Harris, Dan Murphy-Olson, James J. Davis, Hyunseung Yoo, Matthew L. Henderson, Roy T. Kamimura, Shane Canon, Michael W. Sneddon, Christopher S. Henry, Stephen Y. Chan, Pavel S. Novichkov, Inna Dubchak, Mark Mills, Adam P. Arkin, Neal Conrad, Fangfang Xia, Gang Fang, Scott Devoid, Janaka N. Edirisinghe, Brian H. Davison, Bruce Parrello, Shinnosuke Kondo, William J. Riehl, Paul M. Frybarger, Doreen Ware, Miriam Land, Dan Gunter, Rashmi Jain, Rick Stevens, Meghan M Drake, Gavin Price, Shiran Pasternak, Mustafa H Syed, Mark Gerstein, David J. Weston, Sunita Kumari, Kumar, Robert W. Cottingham, Elizabeth M. Glass, James Gurtowski, Aaron A. Best, Daifeng Wang, Srividya Ramakrishnan, Priya Ranjan
The U.S. Department of Energy Systems Biology Knowledgebase (KBase) is an open-source software and data platform designed to meet the grand challenge of systems biology — predicting and designing biological function from the biomolecular (small sca
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a42f71091420946234b6e35b826e316f
https://escholarship.org/uc/item/4058b7v5
https://escholarship.org/uc/item/4058b7v5
Publikováno v:
Nucleic acids research, vol 41, iss Database issue
Nucleic Acids Research
Nucleic Acids Research
The metaMicrobesOnline database (freely available at http://meta.MicrobesOnline.org) offers phylogenetic analysis of genes from microbial genomes and metagenomes. Gene trees are constructed for canonical gene families such as COG and Pfam. Such gene
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::72317d860650926e04970769f670c91b
https://doi.org/10.1093/nar/gks1202
https://doi.org/10.1093/nar/gks1202
Autor:
Paul D. Adams, Zhiwei Chen, Sonia A. Reveco, Kenneth L. Sale, Blake A. Simmons, Dylan Chivian, Adam P. Arkin, Joshua I. Park, Rosa Chan, Gregory D. Friedland, Michael P. Thelen, Swapnil R. Chhabra, Jay D. Keasling, Harvey W. Blanch, Jose Henrique Pereira
Publikováno v:
Journal of Biological Chemistry. 287:25335-25343
Enzymes are traditionally viewed as having exquisite substrate specificity; however, recent evidence supports the notion that many enzymes have evolved activities against a range of substrates. The diversity of activities across glycoside hydrolase f
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5f46ca6a7ee25a493607c2144a427004
https://doi.org/10.1074/jbc.m112.362640
https://doi.org/10.1074/jbc.m112.362640
Autor:
Rossana Chan, Jay D. Keasling, Taek Soon Lee, Christopher J. Petzold, Dylan Chivian, John Haliburton, Tanveer S. Batth, David E. Garcia, Swapnil R. Chhabra, Alyssa M. Redding-Johanson, Gregory D. Friedland, Suzanne M. Ma
Publikováno v:
Metabolic Engineering. 13:588-597
Expression of foreign pathways often results in suboptimal performance due to unintended factors such as introduction of toxic metabolites, cofactor imbalances or poor expression of pathway components. In this study we report a 120% improvement in th
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5e02deb23c88f2b1c257cf58fccc2eba
https://doi.org/10.1016/j.ymben.2011.07.001
https://doi.org/10.1016/j.ymben.2011.07.001