Dylan Chivian - Publications, H-index & Citations

Dylan Chivian

united states department of energy (doe)

29H指数

48论文数

8.5K被引数

收录论文 29

发表时间

KBase: Open-source platform for collaborative biological data analysis and publication

Journal of Molecular Biology

IF4.5

2026-02-05

OAAI

Elisha M. Wood-Charlson; Christopher Henry; Paramvir Dehal; Gazi Mahmud; Ben Allen; Kathleen Bielsmith; D.Dakota Blair; Shane Canon; Mikaela Cashman; Dylan Chivian; Robert Cottingham; Zach Crocket; Ellen Dow; Meghan Drake; Janaka N. Edirisinghe; José P. Faria; Andrew Freiburger; Tianhao Gu; Prachi Gupta; AJ Ireland

Metagenome-assembled genome extraction and analysis from microbiomes using KBase (vol 1350, pg 32, 2022)

NATURE PROTOCOLS

IF16

2022-11-30

OAAI

Chivian, Dylan; Jungbluth, Sean P.; Dehal, Paramvir S.; Wood-Charlson, Elisha M.; Canon, Richard S.; Allen, Benjamin H.; Clark, Mikayla M.; Gu, Tianhao; Land, Miriam L.; Price, Gavin A.; Riehl, William J.; Sneddon, Michael W.; Sutormin, Roman; Zhang, Qizhi; Cottingham, Robert W.; Henry, Chris S.; Arkin, Adam P.

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

NATURE PROTOCOLS

IF16

2022-11-14

OAAI

A genomic catalog of Earth's microbiomes (Nov, 10.1038/s41587-020-0718-6, 2020)地球微生物组的基因组目录 (11月，10.1038/s41587-020-0718-6，2020)

NATURE BIOTECHNOLOGY

IF41.7

2021-04-01

OAAI

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I- Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, Jose P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.

A genomic catalog of Earth's microbiomes (November, 10.1038/s41587-020-0718-6, 2020)地球微生物组的基因组目录 (11月，10.1038/s41587-020-0718-6，2020)

NATURE BIOTECHNOLOGY

IF41.7

2020-11-18

OAAI

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, Jose P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.

A genomic catalog of Earth's microbiomes 地球微生物组的基因组目录

NATURE BIOTECHNOLOGY

IF41.7

2020-11-09

458

OAAI

Nayfach, Stephen; Roux, Simon; Seshadri, Rekha; Udwary, Daniel; Varghese, Neha; Schulz, Frederik; Wu, Dongying; Paez-Espino, David; Chen, I-Min; Huntemann, Marcel; Palaniappan, Krishna; Ladau, Joshua; Mukherjee, Supratim; Reddy, T. B. K.; Nielsen, Torben; Kirton, Edward; Faria, Jose P.; Edirisinghe, Janaka N.; Henry, Christopher S.; Jungbluth, Sean P.; Chivian, Dylan; Dehal, Paramvir; Wood-Charlson, Elisha M.; Arkin, Adam P.; Tringe, Susannah G.; Visel, Axel; Woyke, Tanja; Mouncey, Nigel J.; Ivanova, Natalia N.; Kyrpides, Nikos C.; Eloe-Fadrosh, Emiley A.

KBase: The United States Department of Energy Systems Biology Knowledgebase

NATURE BIOTECHNOLOGY

IF41.7

2018-07-06

928

OAAI

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

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

FRONTIERS IN MICROBIOLOGY

IF4.5

2015-04-22

OAAI

Labonte, Jessica M.; Field, Erin K.; Lau, Maggie; Chivian, Dylan; Van Heerden, Esta; Wommace, K. Eric; Kieft, Thomas L.; Onstott, Tullis C.; Stepanauskas, Ramunas

Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry

ACS CHEMICAL BIOLOGY

IF3.8

2014-07-17

OAAI

Heins, Richard A.; Cheng, Xiaoliang; Nath, Sangeeta; Deng, Kai; Bowen, Benjamin P.; Chivian, Dylan C.; Datta, Supratim; Friedland, Gregory D.; D'Haeseleer, Patrik; Wu, Dongying; Tran-Gyamfi, Mary; Scullin, Chessa S.; Singh, Seema; Shi, Weibing; Hamilton, Matthew G.; Bendall, Matthew L.; Sczyrba, Alexander; Thompson, John; Feldman, Taya; Guenther, Joel M.; Gladden, John M.; Cheng, Jan-Fang; Adams, Paul D.; Rubin, Edward M.; Simmons, Blake A.; Sale, Kenneth L.; Northen, Trent R.; Deutsch, Samuel

Changes in microbial dynamics during long-term decomposition in tropical forests

SOIL BIOLOGY & BIOCHEMISTRY

IF10.3

2013-11-01

PREAI

DeAngelis, Kristen M.; Chivian, Dylan; Fortney, Julian L.; Arkin, Adam P.; Simmons, Blake; Hazen, Terry C.; Silver, Whendee L.

metaMicrobesOnline: phylogenomic analysis of microbial communities

NUCLEIC ACIDS RESEARCH

IF13.1

2012-11-30

OAAI

Chivian, Dylan; Dehal, Paramvir S.; Keller, Keith; Arkin, Adam P.

Tracing Determinants of Dual Substrate Specificity in Glycoside Hydrolase Family 5

JOURNAL OF BIOLOGICAL CHEMISTRY

IF3.9

2012-07-01

OAAI

Chen, Zhiwei; Friedland, Gregory D.; Pereira, Jose H.; Reveco, Sonia A.; Chan, Rosa; Park, Joshua I.; Thelen, Michael P.; Adams, Paul D.; Arkin, Adam P.; Keasling, Jay D.; Blanch, Harvey W.; Simmons, Blake A.; Sale, Kenneth L.; Chivian, Dylan; Chhabra, Swapnil R.

Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli

MICROBIAL CELL FACTORIES

IF4.9

2012-06-13

OAAI

McKee, Adrienne E.; Rutherford, Becky J.; Chivian, Dylan C.; Baidoo, Edward K.; Juminaga, Darmawi; Kuo, Dwight; Benke, Peter I.; Dietrich, Jeffrey A.; Ma, Suzanne M.; Arkin, Adam P.; Petzold, Christopher J.; Adams, Paul D.; Keasling, Jay D.; Chhabra, Swapnil R.

Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases

METABOLIC ENGINEERING

IF6.8

2011-09-01

162

PREAI

Ma, Suzanne M.; Garcia, David E.; Redding-Johanson, Alyssa M.; Friedland, Gregory D.; Chan, Rossana; Batth, Tanveer S.; Haliburton, John R.; Chivian, Dylan; Keasling, Jay D.; Petzold, Christopher J.; Lee, Taek Soon; Chhabra, Swapnil R.

GLAMM: Genome-Linked Application for Metabolic Maps

NUCLEIC ACIDS RESEARCH

IF13.1

2011-05-29

OAAI

Bates, John T.; Chivian, Dylan; Arkin, Adam P.

MicrobesOnline: an integrated portal for comparative and functional genomics

NUCLEIC ACIDS RESEARCH

IF13.1

2009-11-11

407

OAAI

Dehal, Paramvir S.; Joachimiak, Marcin P.; Price, Morgan N.; Bates, John T.; Baumohl, Jason K.; Chivian, Dylan; Friedland, Greg D.; Huang, Katherine H.; Keller, Keith; Novichkov, Pavel S.; Dubchak, Inna L.; Alm, Eric J.; Arkin, Adam P.

Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity

ENVIRONMENTAL MICROBIOLOGY

IF4

2009-09-04

294

OAAI

Walker, Christopher B.; Stolyar, Sergey; Chivian, Dylan; Pinel, Nicolas; Gabster, Jeffrey A.; Dehal, Paramvir S.; He, Zhili; Yang, Zamin Koo; Yen, Huei-Che B.; Zhou, Jizhong; Wall, Judy D.; Hazen, Terry C.; Arkin, Adam P.; Stahl, David A.

Assessment of predictions submitted for the CASP7 domain prediction category

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

IF2.8

2007-01-01

PREAI

Tress, Michael; Cheng, Jianlin; Baldi, Pierre; Joo, Keehyoung; Lee, Jinwoo; Seo, Joo-Hyun; Lee, Jooyoung; Baker, David; Chivian, Dylan; Kim, David; Ezkurdia, Lakes

Structure prediction for CABP7 targets using extensive all-atom refinement with Rosetta@home

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

IF2.8

2007-01-01

198

PREAI

Das, Rhiju; Bin Qian; Raman, Srivatsan; Vernon, Robert; Thompson, James; Bradley, Philip; Khare, Sagar; Tyka, Michael D.; Bhat, Divya; Chivian, Dylan; Kim, David E.; Sheffler, William H.; Malmstrom, Lars; Wollacott, Andrew M.; Wang, Chu; Andre, Ingemar; Baker, David

Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection

NUCLEIC ACIDS RESEARCH

IF13.1

2006-08-13

106

OAAI

Chivian, Dylan; Baker, David

研究方向