Dylan C. Chivian, Ph.D. - Publications

University of Washington, Seattle, Seattle, WA 
protein structure prediction

29 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Labonté JM, Field EK, Lau M, Chivian D, Van Heerden E, Wommack KE, Kieft TL, Onstott TC, Stepanauskas R. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population. Frontiers in Microbiology. 6: 349. PMID 25954269 DOI: 10.3389/Fmicb.2015.00349  0.68
2014 Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, et al. Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. Acs Chemical Biology. 9: 2082-91. PMID 24984213 DOI: 10.1021/Cb500244V  0.68
2013 Deangelis KM, D'Haeseleer P, Chivian D, Simmons B, Arkin AP, Mavromatis K, Malfatti S, Tringe S, Hazen TC. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Standards in Genomic Sciences. 7: 382-98. PMID 24019987 DOI: 10.4056/Sigs.3377516  0.68
2013 Chivian D, Dehal PS, Keller K, Arkin AP. MetaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Research. 41: D648-54. PMID 23203984 DOI: 10.1093/Nar/Gks1202  0.68
2013 DeAngelis KM, Chivian D, Fortney JL, Arkin AP, Simmons B, Hazen TC, Silver WL. Changes in microbial dynamics during long-term decomposition in tropical forests Soil Biology and Biochemistry. 66: 60-68. DOI: 10.1016/J.Soilbio.2013.06.010  0.68
2012 McKee AE, Rutherford BJ, Chivian DC, Baidoo EK, Juminaga D, Kuo D, Benke PI, Dietrich JA, Ma SM, Arkin AP, Petzold CJ, Adams PD, Keasling JD, Chhabra SR. Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli. Microbial Cell Factories. 11: 79. PMID 22694848 DOI: 10.1186/1475-2859-11-79  0.68
2012 Chen Z, Friedland GD, Pereira JH, Reveco SA, Chan R, Park JI, Thelen MP, Adams PD, Arkin AP, Keasling JD, Blanch HW, Simmons BA, Sale KL, Chivian D, Chhabra SR. Tracing determinants of dual substrate specificity in glycoside hydrolase family 5. The Journal of Biological Chemistry. 287: 25335-43. PMID 22645145 DOI: 10.1074/Jbc.M112.362640  0.68
2011 Deangelis KM, D'Haeseleer P, Chivian D, Fortney JL, Khudyakov J, Simmons B, Woo H, Arkin AP, Davenport KW, Goodwin L, Chen A, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, et al. Complete genome sequence of "Enterobacter lignolyticus" SCF1. Standards in Genomic Sciences. 5: 69-85. PMID 22180812 DOI: 10.4056/Sigs.2104875  0.68
2011 Ma SM, Garcia DE, Redding-Johanson AM, Friedland GD, Chan R, Batth TS, Haliburton JR, Chivian D, Keasling JD, Petzold CJ, Lee TS, Chhabra SR. Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases. Metabolic Engineering. 13: 588-97. PMID 21810477 DOI: 10.1016/J.Ymben.2011.07.001  0.68
2011 Bates JT, Chivian D, Arkin AP. GLAMM: Genome-Linked Application for Metabolic Maps. Nucleic Acids Research. 39: W400-5. PMID 21624891 DOI: 10.1093/Nar/Gkr433  0.68
2010 Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research. 38: D396-400. PMID 19906701 DOI: 10.1093/Nar/Gkp919  0.68
2009 Walker CB, Stolyar S, Chivian D, Pinel N, Gabster JA, Dehal PS, He Z, Yang ZK, Yen HC, Zhou J, Wall JD, Hazen TC, Arkin AP, Stahl DA. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity. Environmental Microbiology. 11: 2244-52. PMID 19737303 DOI: 10.1111/J.1462-2920.2009.01946.X  0.68
2008 Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, et al. Environmental genomics reveals a single-species ecosystem deep within Earth. Science (New York, N.Y.). 322: 275-8. PMID 18845759 DOI: 10.1126/Science.1155495  0.68
2007 Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69: 118-28. PMID 17894356 DOI: 10.1002/Prot.21636  0.68
2007 Tress M, Cheng J, Baldi P, Joo K, Lee J, Seo JH, Lee J, Baker D, Chivian D, Kim D, Ezkurdia I. Assessment of predictions submitted for the CASP7 domain prediction category. Proteins. 69: 137-51. PMID 17680686 DOI: 10.1002/Prot.21675  0.68
2007 Malmström L, Riffle M, Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker D. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology Plos Biology. 5. PMID 17373854 DOI: 10.1371/Journal.Pbio.0050076  0.68
2006 Chivian D, Baker D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection Nucleic Acids Research. 34. PMID 16971460 DOI: 10.1093/Nar/Gkl480  0.8
2006 Deutschbauer AM, Chivian D, Arkin AP. Genomics for environmental microbiology. Current Opinion in Biotechnology. 17: 229-35. PMID 16650754 DOI: 10.1016/J.Copbio.2006.04.003  0.68
2006 Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proceedings of the National Academy of Sciences of the United States of America. 103: 5361-6. PMID 16567638 DOI: 10.1073/Pnas.0509355103  0.68
2005 Kim DE, Chivian D, Malmström L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 61: 193-200. PMID 16187362 DOI: 10.1002/Prot.20737  0.8
2005 Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D. Prediction of CASP6 structures using automated Robetta protocols. Proteins. 61: 157-66. PMID 16187358 DOI: 10.1002/Prot.20733  0.68
2005 Bradley P, Malmström L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D. Free modeling with Rosetta in CASP6. Proteins. 61: 128-34. PMID 16187354 DOI: 10.1002/Prot.20729  0.68
2004 Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Research. 32: W526-31. PMID 15215442 DOI: 10.1093/Nar/Gkh468  0.4
2004 Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins. 55: 656-77. PMID 15103629 DOI: 10.1002/Prot.10629  0.68
2003 Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53: 524-33. PMID 14579342 DOI: 10.1002/Prot.10529  0.68
2003 Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss CE, Baker D. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins. 53: 457-68. PMID 14579334 DOI: 10.1002/Prot.10552  0.68
2003 Chivian D, Robertson T, Bonneau R, Baker D. Ab initio methods Methods of Biochemical Analysis. 44: 547-557. PMID 12647404 DOI: 10.1002/0471721204.Ch27  0.68
2002 Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. Journal of Molecular Biology. 322: 65-78. PMID 12215415 DOI: 10.1016/S0022-2836(02)00698-8  0.68
2001 Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. 119-26. PMID 11835488 DOI: 10.1002/Prot.1170  0.68
Show low-probability matches.