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Author Details

Dylan Chivian
Lawrence Berkeley National Laboratory
2001
34
23
PMIDPaper TitleJournal TitlePublished Year
36376589Metagenome-assembled genome extraction and analysis from microbiomes using KBase.Nat Protoc2023
36451056Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase.Nat Protoc2023
33208936Publisher Correction: A genomic catalog of Earth's microbiomes.Nat Biotechnol2021
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
25767232High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.Genome Announc2015
25954269Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.Front Microbiol2015
24984213Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry.ACS Chem Biol2014
23203984MetaMicrobesOnline: phylogenomic analysis of microbial communities.Nucleic Acids Res2013
24019987Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.Stand Genomic Sci2013
22645145Tracing determinants of dual substrate specificity in glycoside hydrolase family 5.J Biol Chem2012
22694848Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli.Microb Cell Fact2012
21624891GLAMM: Genome-Linked Application for Metabolic Maps.Nucleic Acids Res2011
22180812Complete genome sequence of "Enterobacter lignolyticus" SCF1.Stand Genomic Sci2011
21810477Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases.Metab Eng2011
19906701MicrobesOnline: an integrated portal for comparative and functional genomics.Nucleic Acids Res2010
19737303Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.Environ Microbiol2009
18845759Environmental genomics reveals a single-species ecosystem deep within Earth.Science2008
17373854Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.PLoS Biol2007
17894356Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.Proteins2007
17631633In vivo oligomerization of the F conjugative coupling protein TraD.J Bacteriol2007
17680686Assessment of predictions submitted for the CASP7 domain prediction category.Proteins2007
16567638Physically realistic homology models built with ROSETTA can be more accurate than their templates.Proc Natl Acad Sci U S A2006
16971460Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection.Nucleic Acids Res2006
16650754Genomics for environmental microbiology.Curr Opin Biotechnol2006
16187354Free modeling with Rosetta in CASP6.Proteins2005
16187362Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.Proteins2005
16187358Prediction of CASP6 structures using automated Robetta protocols.Proteins2005
15103629Modeling structurally variable regions in homologous proteins with rosetta.Proteins2004
15215442Protein structure prediction and analysis using the Robetta server.Nucleic Acids Res2004
12647404Ab initio methods.Methods Biochem Anal2003
14579342Automated prediction of CASP-5 structures using the Robetta server.Proteins2003
14579334Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.Proteins2003
12215415De novo prediction of three-dimensional structures for major protein families.J Mol Biol2002
11835488Rosetta in CASP4: progress in ab initio protein structure prediction.Proteins2001
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Collaborators

Adam P Arkin
Lawrence Berkeley National Laboratory
Co-authored papers 15
David Baker
University of Washington
Co-authored papers 15
Paramvir S Dehal
Lawrence Berkeley National Laboratory
Co-authored papers 9
Terry C Hazen
University of Tennessee
Co-authored papers 5
Richard Bonneau
Center for Computational Biology (CCB), Flatiron Institute, Simons Foundation
Co-authored papers 5
Blake A Simmons
Joint BioEnergy Institute, USA Lawrence Berkeley National Laboratory
Co-authored papers 4
Miriam Land
Oak Ridge National Laboratory
Co-authored papers 4
Christopher S Henry
Argonne National Laboratory
Co-authored papers 4
Gregory D Friedland
Joint BioEnergy Institute
Co-authored papers 4
Jay D Keasling
University of California berkeley
Co-authored papers 3
Roman A Sutormin
Lawrence Berkeley National Laboratory
Co-authored papers 3
William J Riehl
Lawrence Berkeley National Laboratory
Co-authored papers 3
Robert W Cottingham
Oak Ridge National Laboratory
Co-authored papers 3
Paul D Adams
Lawrence Berkeley National Laboratory
Co-authored papers 3
Michael W Sneddon
Lawrence Berkeley National Laboratory
Co-authored papers 3
Swapnil R Chhabra
Lawrence Berkeley National Laboratory
Co-authored papers 3
Tanja Woyke
Co-authored papers 3
Elisha M Wood-Charlson
Lawrence Berkeley National Laboratory
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Patrik D'haeseleer
Lawrence Livermore National Laboratory
Co-authored papers 3
Nikos C Kyrpides
Co-authored papers 3
Benjamin H Allen
Oak Ridge National Laboratory
Co-authored papers 3
Kristen M DeAngelis
University of Massachusetts
Co-authored papers 2
Konstantinos Mavromatis
Celgene Corporation
Co-authored papers 2
Pavel S Novichkov
Lawrence Berkeley National Laboratory
Co-authored papers 2
Inna Dubchak
Lawrence Berkeley National Laboratory
Co-authored papers 2
Janaka N Edirisinghe
Computation Institute, University of Chicago
Co-authored papers 2
Christopher J Petzold
Joint BioEnergy Institute
Co-authored papers 2
John T Bates
University of Mississippi Medical Center
Co-authored papers 2
Eric J Alm
Massachusetts Institute of Technology 21 Ames St. Cambridge
Co-authored papers 2
Keith Keller
Co-authored papers 2
Release 1.2