Year |
Citation |
Score |
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 |
0.302 |
|
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 |
0.562 |
|
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 |
0.515 |
|
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 |
0.734 |
|
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 |
0.581 |
|
2007 |
Haft RJ, Gachelet EG, Nguyen T, Toussaint L, Chivian D, Traxler B. In vivo oligomerization of the F conjugative coupling protein TraD. Journal of Bacteriology. 189: 6626-34. PMID 17631633 DOI: 10.1128/Jb.00513-07 |
0.349 |
|
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 |
0.79 |
|
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 |
0.572 |
|
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 |
0.789 |
|
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 |
0.665 |
|
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 |
0.822 |
|
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 |
0.821 |
|
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 |
0.731 |
|
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 |
0.829 |
|
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 |
0.821 |
|
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 |
0.746 |
|
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 |
0.704 |
|
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 |
0.842 |
|
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 |
0.852 |
|
Low-probability matches (unlikely to be authored by this person) |
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 |
0.29 |
|
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 |
0.284 |
|
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 |
0.276 |
|
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 |
0.268 |
|
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 |
0.265 |
|
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 |
0.252 |
|
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 |
0.252 |
|
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 |
0.244 |
|
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 |
0.239 |
|
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 |
0.234 |
|
2015 |
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, ... ... Chivian D, et al. 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 Announcements. 3. PMID 25767232 DOI: 10.1128/Genomea.00092-15 |
0.234 |
|
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 |
0.212 |
|
2018 |
Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, ... ... Chivian D, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 36: 566-569. PMID 29979655 DOI: 10.1038/Nbt.4163 |
0.178 |
|
2022 |
Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, et al. Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nature Protocols. PMID 36376589 DOI: 10.1038/s41596-022-00747-x |
0.177 |
|
2020 |
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, ... ... Chivian D, et al. A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33169036 DOI: 10.1038/s41587-020-0718-6 |
0.143 |
|
2010 |
Singer SW, Gladden JM, D'Haeseleer P, Allgaier M, Chivian DC, Hazen TC, Vandergheynst JS, Hugenholtz P, Simmons BA. Targeted discovery of enzymes from enriched microbial consortia for high temperature saccharification of ionic-liquid pre-treated biomass 10aiche - 2010 Aiche Annual Meeting, Conference Proceedings. |
0.095 |
|
2020 |
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, ... ... Chivian D, et al. Publisher Correction: A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33208936 DOI: 10.1038/s41587-020-00769-4 |
0.091 |
|
2022 |
Chivian D, Jungbluth SP, Dehal PS, Wood-Charlson EM, Canon RS, Allen BH, Clark MM, Gu T, Land ML, Price GA, Riehl WJ, Sneddon MW, Sutormin R, Zhang Q, Cottingham RW, et al. Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nature Protocols. PMID 36451056 DOI: 10.1038/s41596-022-00794-4 |
0.085 |
|
2021 |
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, ... ... Chivian D, et al. Author Correction: A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33795890 DOI: 10.1038/s41587-021-00898-4 |
0.076 |
|
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