Chivian, Dylan

TitleCompl Biologist Res Sci/Engr
InstitutionLawrence Berkeley National Lab
DepartmentEnviron Genomics & Systems Bio
Address1 Cyclotron Road
Berkeley CA 94720
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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. Front Microbiol. 2015; 6:349. PMID: 25954269; PMCID: PMC4406082.
    2. Ramsay BD, Hwang C, Woo HL, Carroll SL, Lucas S, Han J, Lapidus AL, Cheng JF, Goodwin LA, Pitluck S, Peters L, Chertkov O, Held B, Detter JC, Han CS, Tapia R, Land ML, Hauser LJ, Kyrpides NC, Ivanova NN, Mikhailova N, Pagani I, Woyke T, Arkin AP, Dehal P, Chivian D, Criddle CS, Wu W, Chakraborty R, Hazen TC, Fields MW. 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 Announc. 2015 Mar 12; 3(2). PMID: 25767232; PMCID: PMC4357754.
    3. Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian D, Datta S, Friedland GD, D'Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. Phylogenomically guided identification of industrially relevant GH1 ß-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol. 2014 Sep 19; 9(9):2082-91. PMID: 24984213; PMCID: PMC4168791.
    4. 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. Stand Genomic Sci. 2013; 7(3):382-98. PMID: 24019987; PMCID: PMC3764933.
    5. Chivian D, Dehal PS, Keller K, Arkin AP. MetaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Res. 2013 Jan; 41(Database issue):D648-54. PMID: 23203984; PMCID: PMC3531168.
    6. McKee AE, Rutherford BJ, Chivian D, 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. Microb Cell Fact. 2012 Jun 13; 11:79. PMID: 22694848; PMCID: PMC3460784.
    7. 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. J Biol Chem. 2012 Jul 20; 287(30):25335-43. PMID: 22645145; PMCID: PMC3408205.
    8. 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, Hazen TC. Complete genome sequence of "Enterobacter lignolyticus" SCF1. Stand Genomic Sci. 2011 Oct 15; 5(1):69-85. PMID: 22180812; PMCID: PMC3236048.
    9. 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. Metab Eng. 2011 Sep; 13(5):588-97. PMID: 21810477.
      View in: PubMed
    10. Bates JT, Chivian D, Arkin AP. GLAMM: Genome-Linked Application for Metabolic Maps. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W400-5. PMID: 21624891; PMCID: PMC3125797.
    11. 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 Res. 2010 Jan; 38(Database issue):D396-400. PMID: 19906701; PMCID: PMC2808868.
    12. 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. Environ Microbiol. 2009 Sep; 11(9):2244-52. PMID: 19737303.
      View in: PubMed
    13. 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, Andersen GL, Hazen TC, Brockman FJ, Arkin AP, Onstott TC. Environmental genomics reveals a single-species ecosystem deep within Earth. Science. 2008 Oct 10; 322(5899):275-8. PMID: 18845759.
      View in: PubMed
    14. Haft RJ, Gachelet EG, Nguyen T, Toussaint L, Chivian D, Traxler B. In vivo oligomerization of the F conjugative coupling protein TraD. J Bacteriol. 2007 Sep; 189(18):6626-34. PMID: 17631633; PMCID: PMC2045173.
    15. Malmström L, Riffle M, Strauss CE, Chivian D, Davis TN, Bonneau R, Baker D. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol. 2007 Apr; 5(4):e76. PMID: 17373854; PMCID: PMC1828141.
    16. 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. 2007; 69 Suppl 8:137-51. PMID: 17680686.
      View in: PubMed
    17. 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, Andre I, Baker D. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 2007; 69 Suppl 8:118-28. PMID: 17894356.
      View in: PubMed
    18. Chivian D, Baker D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res. 2006; 34(17):e112. PMID: 16971460; PMCID: PMC1635247.
    19. Deutschbauer AM, Chivian D, Arkin AP. Genomics for environmental microbiology. Curr Opin Biotechnol. 2006 Jun; 17(3):229-35. PMID: 16650754.
      View in: PubMed
    20. Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci U S A. 2006 Apr 04; 103(14):5361-6. PMID: 16567638; PMCID: PMC1459360.
    21. Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D. Prediction of CASP6 structures using automated Robetta protocols. Proteins. 2005; 61 Suppl 7:157-66. PMID: 16187358.
      View in: PubMed
    22. Kim DE, Chivian D, Malmström L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 2005; 61 Suppl 7:193-200. PMID: 16187362.
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    23. 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. 2005; 61 Suppl 7:128-34. PMID: 16187354.
      View in: PubMed
    24. Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res. 2004 Jul 01; 32(Web Server issue):W526-31. PMID: 15215442; PMCID: PMC441606.
    25. Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins. 2004 May 15; 55(3):656-77. PMID: 15103629.
      View in: PubMed
    26. Chivian D, Robertson T, Bonneau R, Baker D. Ab initio methods. Methods Biochem Anal. 2003; 44:547-57. PMID: 12647404.
      View in: PubMed
    27. 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. 2003; 53 Suppl 6:457-68. PMID: 14579334.
      View in: PubMed
    28. 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. 2003; 53 Suppl 6:524-33. PMID: 14579342.
      View in: PubMed
    29. 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. J Mol Biol. 2002 Sep 06; 322(1):65-78. PMID: 12215415.
      View in: PubMed
    30. 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. 2001; Suppl 5:119-26. PMID: 11835488.
      View in: PubMed

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