D. Chivian

发表

Physically realistic homology models built with ROSETTA can be more accurate than their templates.

David E. Kim, K. Misura, D. Baker, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Rosetta in CASP4: Progress in ab initio protein structure prediction

Richard Bonneau, D. Baker, C. Strauss, 2001, Proteins.

Modeling structurally variable regions in homologous proteins with rosetta

D. Baker, C. Strauss, C. Rohl, 2004, Proteins.

Free modeling with Rosetta in CASP6

David E. Kim, P. Bradley, K. Misura, 2005, Proteins.

De novo prediction of three-dimensional structures for major protein families.

Richard Bonneau, D. Baker, C. Strauss, 2002, Journal of molecular biology.

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

D. Baker, D. Chivian, D. Baker, 2006, Nucleic acids research.

Protein structure prediction and analysis using the Robetta server

David Baker, Dylan Chivian, David E. Kim, 2004, Nucleic Acids Res..

GLAMM: Genome-Linked Application for Metabolic Maps

Adam P. Arkin, John T. Bates, Dylan Chivian, 2011, Nucleic Acids Res..

KBase: The United States Department of Energy Systems Biology Knowledgebase

Rick L. Stevens, James J. Davis, Kevin P. Keegan, 2018, Nature Biotechnology.

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

Richard Bonneau, D. Baker, C. Strauss, 2007, PLoS biology.

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

R. Stepanauskas, K. Wommack, D. Chivian, 2015, Front. Microbiol..

Ab initio methods.

David Baker, Richard Bonneau, Dylan Chivian, 2003, Methods of biochemical analysis.

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

John R. Haliburton, J. Keasling, G. Friedland, 2011, Metabolic engineering.

A genomic catalog of Earth’s microbiomes

Vincent J. Denef, Natalia N. Ivanova, Paramvir S. Dehal, 2020, Nature Biotechnology.

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

A. Arkin, W. Silver, B. Simmons, 2013 .

Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity.

Paramvir S. Dehal, A. Arkin, Jizhong Zhou, 2009, Environmental microbiology.

Knowledgebase and Computing for Systems Biology 220 KBase : An Integrated Knowledgebase for Predictive Biology and Environmental Research

Rick L. Stevens, Paramvir S. Dehal, B. Davison, 2012 .

Publisher Correction: A genomic catalog of Earth’s microbiomes

Natalia N. Ivanova, Paramvir S. Dehal, José P. Faria, 2020, Nature biotechnology.

In Vivo Oligomerization of the F Conjugative Coupling Protein TraD

D. Chivian, L. Toussaint, B. Traxler, 2007, Journal of bacteriology.

Metagenome-assembled genome extraction and analysis from microbiomes using KBase

Paramvir S. Dehal, William J. Riehl, Michael W. Sneddon, 2022, Nature Protocols.

Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

Dylan Chivian, Alla Lapidus, Eoin L Brodie, 2008, Science.

Automated prediction of CASP‐5 structures using the Robetta server

Lars Malmström, David Baker, Timothy Robertson, 2003, Proteins.

metaMicrobesOnline: phylogenomic analysis of microbial communities

Adam P. Arkin, Dylan Chivian, Paramvir S. Dehal, 2012, Nucleic Acids Res..

The DOE Systems Biology Knowledgebase (KBase)

Fangfang Xia, Rick Stevens, Mark Gerstein, 2016, bioRxiv.

Author Correction: A genomic catalog of Earth’s microbiomes

Natalia N. Ivanova, Paramvir S. Dehal, José P. Faria, 2021, Nature biotechnology.

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

Jens Meiler, David Baker, Dylan Chivian, 2003, Proteins.

MicrobesOnline: an integrated portal for comparative and functional genomics

Inna Dubchak, Adam P. Arkin, Katherine H. Huang, 2009, Nucleic Acids Res..

The Virtual Institute of Microbial Stress and Survival : An Overview of the Environmental Stress Pathway Project

Yinjie J. Tang, Katherine H. Huang, Sharon, 2007 .

Genomics for environmental microbiology.

Dylan Chivian, Adam P Arkin, A. Arkin, 2006, Current opinion in biotechnology.

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

Lars Malmström, David Baker, Dylan Chivian, 2007, Proteins.

PROTEINS: Structure, Function, and Bioinformatics Suppl 7:193–200 (2005) Automated Prediction of Domain Boundaries in CASP6 Targets Using Ginzu and RosettaDOM

Lars Malmström, David Baker, Dylan Chivian, 2022 .

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

J. Keasling, A. Arkin, P. Adams, 2012, Microbial Cell Factories.

Complete genome sequence of “Enterobacter lignolyticus” SCF1

Natalia N. Ivanova, Hannah L. Woo, A. Arkin, 2011, Standards in genomic sciences.

Tracing Determinants of Dual Substrate Specificity in Glycoside Hydrolase Family 5*

Dylan Chivian, Jay D Keasling, Paul D Adams, 2012, The Journal of Biological Chemistry.

Complete genome sequence of “ Enterobacter lignolyticus ” SCF 1

Natalia N. Ivanova, Jane, Hannah L. Woo, 2018 .

Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron

S. Tringe, A. Arkin, P. D’haeseleer, 2013, Standards in genomic sciences.

Classification and general features of “ Enterobacter lignolyticus ” SCF 1 MIGS ID Property Term Evidence code Current classification Domain Bacteria

Natalia N. Ivanova, Hannah L. Woo, A. Arkin, 2011 .

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

Natalia N. Ivanova, Paramvir S. Dehal, Hannah L. Woo, 2015, Genome Announcements.

Prediction of CASP6 structures using automated robetta protocols

Lars Malmström, David Baker, Dylan Chivian, 2005, Proteins.

Assessment of predictions submitted for the CASP7 domain prediction category

David Kim, Keehyoung Joo, Jinwoo Lee, 2007, Proteins.

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

M. Bendall, P. D’haeseleer, S. Deutsch, 2014, ACS chemical biology.

MicroCOSM: Microbial Clade-Oriented Sequence Markers for Phylogenetic Classification of Metagenomic Data

Paramvir S. Dehal, A. Arkin, D. Chivian, 2007 .

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

Andrew M Wollacott, David E. Kim, Chu Wang, 2007, Proteins.

PROTEINS: Structure, Function, and Bioinformatics Suppl 7:157–166 (2005) Prediction of CASP6 Structures Using Automated Robetta Protocols

C. Rohl, D. Chivian, Jack Schonbrun, 2022 .

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

M. Bendall, P. D’haeseleer, B. Simmons, 2014, ACS chemical biology.

MicroCOSM: Microbial Clade-Oriented Sequence Markers for Phylogenetic Classification of Metagenomic Data

Paramvir S. Dehal, A. Arkin, D. Chivian, 2007 .

Assessment of predictions submitted for the CASP7 domain prediction category

M. Tress, K. Joo, D. Chivian, 2007, Proteins.

Modeling structurally variable regions in homologous proteins with rosetta

C. Rohl, D. Chivian, Charles E.M. Strauss, 2004, Proteins.