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Dongying Wu - Publications

Affiliations: 
University of California, Davis, Davis, CA 
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28 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
2025 Wu D, Seshadri R, Kyrpides NC, Ivanova NN. A metagenomic perspective on the microbial prokaryotic genome census. Science Advances. 11: eadq2166. PMID 39823337 DOI: 10.1126/sciadv.adq2166  0.563
2022 Seshadri R, Roux S, Huber KJ, Wu D, Yu S, Udwary D, Call L, Nayfach S, Hahnke RL, Pukall R, White JR, Varghese NJ, Webb C, Palaniappan K, Reimer LC, et al. Expanding the genomic encyclopedia of with 824 isolate reference genomes. Cell Genomics. 2: 100213. PMID 36778052 DOI: 10.1016/j.xgen.2022.100213  0.579
2022 Chen IA, Chu K, Palaniappan K, Ratner A, Huang J, Huntemann M, Hajek P, Ritter SJ, Webb C, Wu D, Varghese NJ, Reddy TBK, Mukherjee S, Ovchinnikova G, Nolan M, et al. The IMG/M data management and analysis system v.7: content updates and new features. Nucleic Acids Research. PMID 36382399 DOI: 10.1093/nar/gkac976  0.38
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, et al. Author Correction: A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33795890 DOI: 10.1038/s41587-021-00898-4  0.385
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, et al. Publisher Correction: A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33208936 DOI: 10.1038/s41587-020-00769-4  0.328
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, et al. A genomic catalog of Earth's microbiomes. Nature Biotechnology. PMID 33169036 DOI: 10.1038/s41587-020-0718-6  0.497
2014 Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, Wu D, Madern D, Eisen JA, Darling AE, Facciotti MT. Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. Plos Genetics. 10: e1004784. PMID 25393412 DOI: 10.1371/Journal.Pgen.1004784  0.755
2014 Dmytrenko O, Russell SL, Loo WT, Fontanez KM, Liao L, Roeselers G, Sharma R, Stewart FJ, Newton IL, Woyke T, Wu D, Lang JM, Eisen JA, Cavanaugh CM. The genome of the intracellular bacterium of the coastal bivalve, Solemya velum: a blueprint for thriving in and out of symbiosis. Bmc Genomics. 15: 924. PMID 25342549 DOI: 10.1186/1471-2164-15-924  0.748
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  0.39
2013 Wu D, Jospin G, Eisen JA. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. Plos One. 8: e77033. PMID 24146954 DOI: 10.1371/Journal.Pone.0077033  0.689
2013 Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, Tringe SG, Singer SW, Eisen JA, Banfield JF. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nature Communications. 4: 2120. PMID 23979677 DOI: 10.1038/Ncomms3120  0.608
2013 Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, et al. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences of the United States of America. 110: 1053-8. PMID 23277585 DOI: 10.1073/Pnas.1217107110  0.728
2012 Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. Bmc Bioinformatics. 13: 264. PMID 23061897 DOI: 10.1186/1471-2105-13-264  0.754
2011 Huang SW, Lin YY, You EM, Liu TT, Shu HY, Wu KM, Tsai SF, Lo CF, Kou GH, Ma GC, Chen M, Wu D, Aoki T, Hirono I, Yu HT. Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon Bmc Genomics. 12. PMID 21575266 DOI: 10.1186/1471-2164-12-242  0.583
2011 Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. Plos One. 6: e18011. PMID 21437252 DOI: 10.1371/Journal.Pone.0018011  0.755
2010 Roeselers G, Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, et al. Complete genome sequence of Candidatus Ruthia magnifica. Standards in Genomic Sciences. 3: 163-73. PMID 21304746 DOI: 10.4056/Sigs.1103048  0.719
2010 Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF. One bacterial cell, one complete genome. Plos One. 5: e10314. PMID 20428247 DOI: 10.1371/Journal.Pone.0010314  0.526
2009 Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 462: 1056-60. PMID 20033048 DOI: 10.1038/Nature08656  0.794
2009 Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. Plos Genetics. 5: e1000362. PMID 19197347 DOI: 10.1371/Journal.Pgen.1000362  0.607
2009 Wu D, Raymond J, Wu M, Chatterji S, Ren Q, Graham JE, Bryant DA, Robb F, Colman A, Tallon LJ, Badger JH, Madupu R, Ward NL, Eisen JA. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. Plos One. 4: e4207. PMID 19148287 DOI: 10.1371/Journal.Pone.0004207  0.755
2008 Wu D, Hartman A, Ward N, Eisen JA. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). Plos One. 3: e2566. PMID 18596968 DOI: 10.1371/Journal.Pone.0002566  0.757
2007 Hazen TH, Wu D, Eisen JA, Sobecky PA. Sequence characterization and comparative analysis of three plasmids isolated from environmental Vibrio spp. Applied and Environmental Microbiology. 73: 7703-10. PMID 17921277 DOI: 10.1128/Aem.01577-07  0.596
2007 Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. Plos Biology. 5: e77. PMID 17355176 DOI: 10.1371/Journal.Pbio.0050077  0.725
2006 Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Plos Biology. 4: e286. PMID 16933976 DOI: 10.1371/Journal.Pbio.0040286  0.774
2006 Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. Plos Biology. 4: e188. PMID 16729848 DOI: 10.1371/Journal.Pbio.0040188  0.655
2006 Penn K, Wu D, Eisen JA, Ward N. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology. 72: 1680-3. PMID 16461727 DOI: 10.1128/Aem.72.2.1680-1683.2006  0.435
2005 Haas BJ, Wortman JR, Ronning CM, Hannick LI, Smith RK, Maiti R, Chan AP, Yu C, Farzad M, Wu D, White O, Town CD. Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. Bmc Biology. 3: 7. PMID 15784138 DOI: 10.1186/1741-7007-3-7  0.485
2004 Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science (New York, N.Y.). 304: 66-74. PMID 15001713 DOI: 10.1126/Science.1093857  0.7
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