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Employment (1)

Lawrence Berkeley National Laboratory: Berkeley, California, US

Employment
Source: Self-asserted source
Dylan Chivian

Education and qualifications (2)

University of Washington: Seattle, Washington, US

1999 to 2005 | PhD (Biochemistry and Biomolecular Structure & Design)
Education
Source: Self-asserted source
Dylan Chivian

University of California, Berkeley: Berkeley, California, US

1989 to 1994 | B.Eng. (Bioengineering)
Education
Source: Self-asserted source
Dylan Chivian

Works (38)

Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Nature Protocols
2023-02 | Journal article
DOI: 10.1038/s41596-022-00794-4
Contributors: 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 et al.
Source: check_circle
Crossref

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Nature Protocols
2023-01 | Journal article
DOI: 10.1038/s41596-022-00747-x
Contributors: 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 et al.
Source: check_circle
Crossref

A genomic catalog of Earth’s microbiomes

Nature Biotechnology
2021-04 | Journal article | Author
DOI: 10.1038/s41587-020-0718-6
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Contributors: Stephen Nayfach; Simon Roux; Rekha Seshadri; Daniel Udwary; Neha Varghese; Frederik Schulz; Dongying Wu; David Paez-Espino; I-Min Chen; Marcel Huntemann et al.
Source: Self-asserted source
Dylan Chivian

KBase: The United States Department of Energy Systems Biology Knowledgebase

Nature Biotechnology
2018-08 | Journal article
DOI: 10.1038/nbt.4163
Part of ISSN: 1087-0156
Part of ISSN: 1546-1696
Contributors: Dylan Chivian; Adam Arkin; Robert W Cottingham; Christopher S Henry; Nomi Harris; Rick L Stevens; Sergei Maslov; Paramvir Dehal; Doreen Ware; Fernando Pérez et al.
Source: Self-asserted source
Dylan Chivian

Glycoside hydrolases having multiple hydrolase activities

2017-08-08 | Patent
LENSID: 128-739-593-704-246
URI:

lens.org/128-739-593-704-246

PAT:

US 9725749 B2
Contributors: Chen Zhiwei; Friedland Gregory D; Chhabra Swapnil R; Chivian Dylan C; Simmons Blake A
Source: Self-asserted source
Dylan Chivian via The Lens

High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

Genome Announcements
2015-04-30 | Journal article
DOI: 10.1128/genomea.00092-15
Part of ISSN: 2169-8287
Contributors: Dylan Chivian; Bradley D. Ramsay; Chiachi Hwang; Hannah Woo; Sue L. Carroll; Susan Lucas; James Han; Alla L. Lapidus; Jan-Fang Cheng; Lynne A. Goodwin et al.
Source: Self-asserted source
Dylan Chivian

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

Frontiers in Microbiology
2015-04-22 | Journal article
DOI: 10.3389/fmicb.2015.00349
Part of ISSN: 1664-302X
Contributors: Dylan Chivian; Jessica M. Labonté; Erin K. Field; Maggie Lau; Dylan Chivian; Esta Van Heerden; K. Eric Wommack; Thomas L. Kieft; Tullis C. Onstott; Ramunas Stepanauskas
Source: Self-asserted source
Dylan Chivian

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

ACS Chemical Biology
2014-09-19 | Journal article
DOI: 10.1021/cb500244v
Part of ISSN: 1554-8929
Part of ISSN: 1554-8937
Contributors: Dylan Chivian; Richard A. Heins; Xiaoliang Cheng; Sangeeta Nath; Kai Deng; Benjamin P. Bowen; Dylan C. Chivian; Supratim Datta; Gregory D. Friedland; Patrik D’Haeseleer et al.
Source: Self-asserted source
Dylan Chivian

GLYCOSIDE HYDROLASES HAVING MULTIPLE HYDROLASE ACTIVITIES

2014-06-05 | Patent
LENSID: 131-416-792-936-105
URI:

lens.org/131-416-792-936-105

PAT:

US 2014/0154752 A1
Contributors: Chen Zhiwei; Friedland Gregory D; Chhabra Swapnil R; Chivian Dylan C; Simmons Blake A
Source: Self-asserted source
Dylan Chivian via The Lens

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

Soil Biology and Biochemistry
2013-11 | Journal article
DOI: 10.1016/j.soilbio.2013.06.010
Part of ISSN: 0038-0717
Contributors: Dylan Chivian; Kristen M. DeAngelis; Dylan Chivian; Julian L. Fortney; Adam P. Arkin; Blake Simmons; Terry C. Hazen; Whendee L. Silver
Source: Self-asserted source
Dylan Chivian

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

Microbial Cell Factories
2012-12 | Journal article
DOI: 10.1186/1475-2859-11-79
Part of ISSN: 1475-2859
Contributors: Dylan Chivian; Adrienne E McKee; Becky J Rutherford; Dylan C Chivian; Edward K Baidoo; Darmawi Juminaga; Dwight Kuo; Peter I Benke; Jeffrey A Dietrich; Suzanne M Ma et al.
Source: Self-asserted source
Dylan Chivian

metaMicrobesOnline: phylogenomic analysis of microbial communities

Nucleic Acids Research
2012-11-30 | Journal article
DOI: 10.1093/nar/gks1202
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Contributors: Dylan Chivian; Dylan Chivian; Paramvir S. Dehal; Keith Keller; Adam P. Arkin
Source: Self-asserted source
Dylan Chivian

GLYCOSIDE HYDROLASES HAVING MULTIPLE HYDROLASE ACTIVITIES

2012-11-08 | Patent
LENSID: 075-678-390-876-18X
URI:

lens.org/075-678-390-876-18X

PAT:

WO 2012/151214 A1
Contributors: Chen Zhiwei; Friedland Gregory D; Chhabra Swapnil R; Chivian Dylan C; Simmons Blake A
Source: Self-asserted source
Dylan Chivian via The Lens

Tracing Determinants of Dual Substrate Specificity in Glycoside Hydrolase Family 5

Journal of Biological Chemistry
2012-07 | Journal article
DOI: 10.1074/jbc.m112.362640
Part of ISSN: 0021-9258
Contributors: Dylan Chivian; Zhiwei Chen; Gregory D. Friedland; Jose H. Pereira; Sonia A. Reveco; Rosa Chan; Joshua I. Park; Michael P. Thelen; Paul D. Adams; Adam P. Arkin et al.
Source: Self-asserted source
Dylan Chivian

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

Metabolic Engineering
2011-09 | Journal article
DOI: 10.1016/j.ymben.2011.07.001
Part of ISSN: 1096-7176
Contributors: Dylan Chivian; Suzanne M. Ma; David E. Garcia; Alyssa M. Redding-Johanson; Gregory D. Friedland; Rossana Chan; Tanveer S. Batth; John R. Haliburton; Dylan Chivian; Jay D. Keasling et al.
Source: Self-asserted source
Dylan Chivian

Complete genome sequence of “Enterobacter lignolyticus” SCF1

Standards in Genomic Sciences
2011-09-23 | Journal article
DOI: 10.4056/sigs.2104875
Part of ISSN: 1944-3277
Contributors: Dylan Chivian; Kristen M. DeAngelis; Patrik D’Haeseleer; Dylan Chivian; Julian L. Fortney; Jane Khudyakov; Blake Simmons; Hannah Woo; Adam P. Arkin; Karen Walston Davenport et al.
Source: Self-asserted source
Dylan Chivian

GLAMM: Genome-Linked Application for Metabolic Maps

Nucleic Acids Research
2011-07-01 | Journal article
DOI: 10.1093/nar/gkr433
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Contributors: Dylan Chivian; J. T. Bates; D. Chivian; A. P. Arkin
Source: Self-asserted source
Dylan Chivian

MicrobesOnline: an integrated portal for comparative and functional genomics

Nucleic Acids Research
2010-01-01 | Journal article
DOI: 10.1093/nar/gkp919
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Contributors: Dylan Chivian; P. S. Dehal; M. P. Joachimiak; M. N. Price; J. T. Bates; J. K. Baumohl; D. Chivian; G. D. Friedland; K. H. Huang; K. Keller et al.
Source: Self-asserted source
Dylan Chivian

Contribution of mobile genetic elements to<i>Desulfovibrio vulgaris</i>genome plasticity

Environmental Microbiology
2009-09 | Journal article
DOI: 10.1111/j.1462-2920.2009.01946.x
Part of ISSN: 1462-2912
Part of ISSN: 1462-2920
Contributors: Dylan Chivian; Christopher B. Walker; Sergey Stolyar; Dylan Chivian; Nicolas Pinel; Jeffrey A. Gabster; Paramvir S. Dehal; Zhili He; Zamin Koo Yang; Huei-Che B. Yen et al.
Source: Self-asserted source
Dylan Chivian

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

Science
2008-10-10 | Journal article
DOI: 10.1126/science.1155495
Part of ISSN: 0036-8075
Contributors: Dylan Chivian; Eoin L. Brodie; Eric J. Alm; David E. Culley; Paramvir S. Dehal; Todd Z. DeSantis; Thomas M. Gihring; Alla Lapidus; Li-Hung Lin; Stephen R. Lowry et al.
Source: Self-asserted source
Dylan Chivian via Crossref Metadata Search

Assessment of predictions submitted for the CASP7 domain prediction category

Proteins: Structure, Function, and Bioinformatics
2007 | Journal article
DOI: 10.1002/prot.21675
Part of ISSN: 0887-3585
Part of ISSN: 1097-0134
Contributors: Dylan Chivian; Michael Tress; Jianlin Cheng; Pierre Baldi; Keehyoung Joo; Jinwoo Lee; Joo-Hyun Seo; Jooyoung Lee; David Baker; Dylan Chivian et al.
Source: Self-asserted source
Dylan Chivian

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

Proteins: Structure, Function, and Bioinformatics
2007 | Journal article
DOI: 10.1002/prot.21636
Part of ISSN: 0887-3585
Part of ISSN: 1097-0134
Contributors: Dylan Chivian; Rhiju Das; Bin Qian; Srivatsan Raman; Robert Vernon; James Thompson; Philip Bradley; Sagar Khare; Michael D. Tyka; Divya Bhat et al.
Source: Self-asserted source
Dylan Chivian

In Vivo Oligomerization of the F Conjugative Coupling Protein TraD

Journal of Bacteriology
2007-09-15 | Journal article
DOI: 10.1128/jb.00513-07
Part of ISSN: 0021-9193
Part of ISSN: 1098-5530
Contributors: Dylan Chivian; Rembrandt J. F. Haft; Eliora G. Gachelet; Tran Nguyen; Luttrell Toussaint; Dylan Chivian; Beth Traxler
Source: Self-asserted source
Dylan Chivian

Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology

PLoS Biology
2007-03-20 | Journal article
DOI: 10.1371/journal.pbio.0050076
Part of ISSN: 1545-7885
Contributors: Dylan Chivian; Lars Malmström; Michael Riffle; Charlie E. M Strauss; Dylan Chivian; Trisha N Davis; Richard Bonneau; David Baker
Source: Self-asserted source
Dylan Chivian

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

Nucleic Acids Research
2006-10 | Journal article
DOI: 10.1093/nar/gkl480
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Contributors: Dylan Chivian; Dylan Chivian; David Baker
Source: Self-asserted source
Dylan Chivian

Genomics for environmental microbiology

Current Opinion in Biotechnology
2006-06 | Journal article
DOI: 10.1016/j.copbio.2006.04.003
Part of ISSN: 0958-1669
Contributors: Dylan Chivian; Adam M Deutschbauer; Dylan Chivian; Adam P Arkin
Source: Self-asserted source
Dylan Chivian

Physically realistic homology models built with <scp>rosetta</scp> can be more accurate than their templates

Proceedings of the National Academy of Sciences
2006-04-04 | Journal article
DOI: 10.1073/pnas.0509355103
Part of ISSN: 0027-8424
Part of ISSN: 1091-6490
Contributors: Dylan Chivian; Kira M. S. Misura; Dylan Chivian; Carol A. Rohl; David E. Kim; David Baker
Source: Self-asserted source
Dylan Chivian

Application of information from homologous proteins for the prediction of protein structure

2005 | Dissertation or Thesis
Contributors: Dylan Chivian
Source: Self-asserted source
Dylan Chivian

Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM

Proteins: Structure, Function, and Bioinformatics
2005 | Journal article
DOI: 10.1002/prot.20737
Part of ISSN: 0887-3585
Part of ISSN: 1097-0134
Contributors: Dylan Chivian; David E. Kim; Dylan Chivian; Lars Malmström; David Baker
Source: Self-asserted source
Dylan Chivian

Free modeling with Rosetta in CASP6

Proteins: Structure, Function, and Bioinformatics
2005 | Journal article
DOI: 10.1002/prot.20729
Part of ISSN: 0887-3585
Part of ISSN: 1097-0134
Contributors: Dylan Chivian; Philip Bradley; Lars Malmström; Bin Qian; Jack Schonbrun; Dylan Chivian; David E. Kim; Jens Meiler; Kira M.S. Misura; David Baker
Source: Self-asserted source
Dylan Chivian

Prediction of CASP6 structures using automated robetta protocols

Proteins: Structure, Function, and Bioinformatics
2005 | Journal article
DOI: 10.1002/prot.20733
Part of ISSN: 0887-3585
Part of ISSN: 1097-0134
Contributors: Dylan Chivian; Dylan Chivian; David E. Kim; Lars Malmström; Jack Schonbrun; Carol A. Rohl; David Baker
Source: Self-asserted source
Dylan Chivian

<i>Ab Initio</i> Methods

Structural Bioinformatics
2005-01-28 | Book chapter
DOI: 10.1002/0471721204.ch27
Part of ISSN: 1934-4325
Contributors: Dylan Chivian; Dylan Chivian; Timothy Robertson; Richard Bonneau; David Baker
Source: Self-asserted source
Dylan Chivian

Protein structure prediction and analysis using the Robetta server

Nucleic Acids Research
2004-07-01 | Journal article
DOI: 10.1093/nar/gkh468
Part of ISSN: 0305-1048
Contributors: D. E. Kim; D. Chivian; D. Baker
Source: Self-asserted source
Dylan Chivian via Crossref Metadata Search

Modeling structurally variable regions in homologous proteins with rosetta

Proteins: Structure, Function, and Bioinformatics
2004-04-01 | Journal article
DOI: 10.1002/prot.10629
Part of ISSN: 0887-3585
Contributors: Dylan Chivian; Carol A. Rohl; Charlie E.M. Strauss; Dylan Chivian; David Baker
Source: Self-asserted source
Dylan Chivian

Automated prediction of CASP-5 structures using the Robetta server

Proteins: Structure, Function, and Genetics
2003 | Journal article
DOI: 10.1002/prot.10529
Part of ISSN: 0887-3585
Part of ISSN: 1097-0134
Contributors: Dylan Chivian; Dylan Chivian; David E. Kim; Lars Malmstr�m; Philip Bradley; Timothy Robertson; Paul Murphy; Charles E.M. Strauss; Richard Bonneau; Carol A. Rohl et al.
Source: Self-asserted source
Dylan Chivian

Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation

Proteins: Structure, Function, and Genetics
2003 | Journal article
DOI: 10.1002/prot.10552
Part of ISSN: 0887-3585
Part of ISSN: 1097-0134
Contributors: Dylan Chivian; Philip Bradley; Dylan Chivian; Jens Meiler; Kira M.S. Misura; Carol A. Rohl; William R. Schief; William J. Wedemeyer; Ora Schueler-Furman; Paul Murphy et al.
Source: Self-asserted source
Dylan Chivian

De Novo Prediction of Three-dimensional Structures for Major Protein Families

Journal of Molecular Biology
2002-09 | Journal article
DOI: 10.1016/s0022-2836(02)00698-8
Part of ISSN: 0022-2836
Contributors: Dylan Chivian; Richard Bonneau; Charlie E.M Strauss; Carol A Rohl; Dylan Chivian; Phillip Bradley; Lars Malmström; Tim Robertson; David Baker
Source: Self-asserted source
Dylan Chivian

Rosetta in CASP4: Progress in ab initio protein structure prediction

Proteins: Structure, Function, and Genetics
2001 | Journal article
DOI: 10.1002/prot.1170
Part of ISSN: 0887-3585
Part of ISSN: 1097-0134
Contributors: Dylan Chivian; Richard Bonneau; Jerry Tsai; Ingo Ruczinski; Dylan Chivian; Carol Rohl; Charlie E. M. Strauss; David Baker
Source: Self-asserted source
Dylan Chivian

Peer review (1 review for 1 publication/grant)

Review activity for Nature communications (1)
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