Publications by authors named "Dylan Chivian"

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Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase.
Dylan Chivian, Sean P Jungbluth, Paramvir S Dehal, Elisha M Wood-Charlson, Richard S Canon

Nat Protoc· February 2023

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Metagenome-assembled genome extraction and analysis from microbiomes using KBase.
Dylan Chivian, Sean P Jungbluth, Paramvir S Dehal, Elisha M Wood-Charlson, Richard S Canon

Nat Protoc· January 2023

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A genomic catalog of Earth's microbiomes.
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Dylan Chivian

Nat Biotechnol· April 2021

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Publisher Correction: A genomic catalog of Earth's microbiomes.
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Dylan Chivian

Nat Biotechnol· April 2021

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Author Correction: A genomic catalog of Earth's microbiomes.
Stephen Nayfach, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Dylan Chivian

Nat Biotechnol· April 2021

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KBase: The United States Department of Energy Systems Biology Knowledgebase.
Adam P Arkin, Robert W Cottingham, Christopher S Henry, Nomi L Harris, Rick L Stevens, Dylan Chivian

Nat Biotechnol· July 2018

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Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.
Jessica M Labonté, Erin K Field, Maggie Lau, Dylan Chivian, Esta Van Heerden

Front Microbiol· May 2015

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High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.
Bradley D Ramsay, Chiachi Hwang, Hannah L Woo, Sue L Carroll, Susan Lucas, Dylan Chivian

Genome Announc· March 2015

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Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry.
Richard A Heins, Xiaoliang Cheng, Sangeeta Nath, Kai Deng, Benjamin P Bowen, Dylan C Chivian

ACS Chem Biol· September 2014

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Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron.
Kristen M Deangelis, Patrik D'Haeseleer, Dylan Chivian, Blake Simmons, Adam P Arkin

Stand Genomic Sci· September 2013

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MetaMicrobesOnline: phylogenomic analysis of microbial communities.
Dylan Chivian, Paramvir S Dehal, Keith Keller, Adam P Arkin

Nucleic Acids Res· January 2013

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Tracing determinants of dual substrate specificity in glycoside hydrolase family 5.
Zhiwei Chen, Gregory D Friedland, Jose H Pereira, Sonia A Reveco, Rosa Chan, Dylan Chivian

J Biol Chem· July 2012

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Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli.
Adrienne E McKee, Becky J Rutherford, Dylan C Chivian, Edward K Baidoo, Darmawi Juminaga

Microb Cell Fact· June 2012

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Complete genome sequence of "Enterobacter lignolyticus" SCF1.
Kristen M Deangelis, Patrik D'Haeseleer, Dylan Chivian, Julian L Fortney, Jane Khudyakov

Stand Genomic Sci· October 2011

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Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases.
Suzanne M Ma, David E Garcia, Alyssa M Redding-Johanson, Gregory D Friedland, Rossana Chan, Dylan Chivian

Metab Eng· September 2011

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GLAMM: Genome-Linked Application for Metabolic Maps.
John T Bates, Dylan Chivian, Adam P Arkin

Nucleic Acids Res· July 2011

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MicrobesOnline: an integrated portal for comparative and functional genomics.
Paramvir S Dehal, Marcin P Joachimiak, Morgan N Price, John T Bates, Jason K Baumohl, Dylan Chivian

Nucleic Acids Res· January 2010

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Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.
Christopher B Walker, Sergey Stolyar, Dylan Chivian, Nicolas Pinel, Jeffrey A Gabster

Environ Microbiol· September 2009

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Environmental genomics reveals a single-species ecosystem deep within Earth.
Dylan Chivian, Eoin L Brodie, Eric J Alm, David E Culley, Paramvir S Dehal

Science· October 2008

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Assessment of predictions submitted for the CASP7 domain prediction category.
Michael Tress, Jianlin Cheng, Pierre Baldi, Keehyoung Joo, Jinwoo Lee, Dylan Chivian

Proteins· January 2008

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Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.
Rhiju Das, Bin Qian, Srivatsan Raman, Robert Vernon, James Thompson, Dylan Chivian

Proteins· January 2008

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In vivo oligomerization of the F conjugative coupling protein TraD.
Rembrandt J F Haft, Eliora G Gachelet, Tran Nguyen, Luttrell Toussaint, Dylan Chivian

J Bacteriol· September 2007

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Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology.
Lars Malmström, Michael Riffle, Charlie E M Strauss, Dylan Chivian, Trisha N Davis

PLoS Biol· April 2007

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Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection.
Dylan Chivian, David Baker

Nucleic Acids Res· November 2006

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Genomics for environmental microbiology.
Adam M Deutschbauer, Dylan Chivian, Adam P Arkin

Curr Opin Biotechnol· June 2006

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