Dongying Wu


Project Scientist
UC Davis Genome Center

Research Interest

  • Endosymbiosis
  • Bioinformatics
  • Metagenomics


  • Project Scientist, the Genome Center of U.C. Davis, Davis, California, July 2010 – current
  • Associate Project Scientist, the Genome Center of U.C. Davis, Davis, California, June 2006 – June 2010
  • Bioinformatics Engineer, the Institute for Genomic Research, Rockville, Maryland, January 2003 – June 2006
  • Bioinformatics Scientist, AxCell Biosciences Corporation, Newtown, PA, June 2001 – September 2002


  • Ph.D., October 1999, Interdepartmental Genetics Program, Iowa State University, Ames, Iowa
  • Bachelor of Science, July 1990, Department of Genetics, Fudan University, Shanghai, China

Conferences and Presentations

Genomics of Energy & Environment 8th Annual DOE Joint Genome Institute User Meeting, Poster, Phylogenetic tree based taxonomic classification. Walnut Creek, California, Mar 26-28, 2013

Genomics of Energy & Environment 7th Annual DOE Joint Genome Institute User Meeting, Poster, Independent Contrast Based Phylogenetic Profiling. Walnut Creek, California, Mar 20-22, 2012

Keystone Symposia: Microbial Communities as Drivers of Ecosystem Complexity (C8), Poster, Identify gene markers for different taxonomic groups in Archaea and Bacteria Genomes. Breckenridge, Colorado Mar 25-29, 2011

Genomics of Energy & Environment 5th Annual DOE Joint Genome Institute User Meeting, Poster, Identify Novel Phylogenetic Markers for the Archaea and Bacteria Genomes. Walnut Creek, California, Mar 24-26, 2010

The symposium on the diversity and genomic analysis of the microbial symbionts in animal gastrointestinal tracts, Speaker, Three-Way Symbiosis in The glassy-winged sharpshooters. Taipei, Taiwan, Apr 15-22, 2009

Genomics of Energy & Environment 4th Annual DOE Joint Genome Institute User Meeting, Poster, Phylogenetic Diversity Contributions of the Genomic Encyclopedia for Bacteria and Archaea Pilot Project, Walnut Creek, California, Mar 25-27, 2009


Serve as reviewer for Plos Genetics, Aquatic Microbial Ecology, Nature Methods. Plos computational biology, Nucleic Acid Research, Plos ONE


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 Genet. 2014 Nov 13;10(11):e1004784.

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, 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 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol. 2014 Sep 19;9(9):2082-91.

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. 2014 Oct 23;15:924.

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. 2013 Oct 17;8(10):e77033.

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. Nat Commun. 2013;4:2120.

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, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA. Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.
Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):1053-8.

Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA (2012) Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics 13:264.

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 (2011) Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon. BMC Genomics12:242.

Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (2011) Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One6(3):e18011.

Hou L, Chen M, Jiang B, Wu D, Ng J, Hurley CK (2010) Thirty allele-level haplotypes centered around KIR2DL5 define the diversity in an African American population.Immunogenetics. DOI 10.1007/s00251-010-0458-8

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 (2010) One bacterial cell, one complete genome. PLoS One.5(4):e10314.

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, D’haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature462(7276):1056-60.

Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. (2009) Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet.5(2):e1000362.

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.(2009) Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.PLoS ONE. 4(1):e4207.

Wu D, Hartman A, Ward N, Eisen JA (2008) An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP).PLoS ONE.3(7):e2566.

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, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol. 5(3):e77.

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, Eisen JA, Cavanaugh CM. (2007) The Calyptogena magnifica chemoautotrophic symbiont genome.Science. 315(5814):998-1000.

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, et al. (2006) Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLoS Biol 4(9): e286

Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, et al. (2006) Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters. PLoS Biol 4(6): e188

Penn K, Wu D, Eisen JA, Ward N.(2006) Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Appl Environ Microbiol. 2006 Feb;72(2):1680-3

Haas BJ, Wortman JR, Ronning CM, Hannick LI, Smith RK Jr, Maiti R, Chan AP, Yu C, Farzad M, Wu D, White O, Town CD. (2005)Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC Biology 3:7

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, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO.(2004) Environmental Genome Shotgun Sequencing of the Sargasso Sea. Science. Vol 304(5667):66-74

Hu H, Columbus J, Zhang Y, Wu D, Lian L, Yang S, Goodwin J, Luczak C, Carter M, Chen L, James M, Davis R, Sudol M, Rodwell J, Herrero JJ.(2004) A map of WW domain family interactions.PROTEOMICS Vol 4(3)

Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, Dodson RJ, Madupu R, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Gwinn M, Kolonay JF, Sullivan SA, Haft DH, Selengut J, Davidsen TM, Zafar N, White O, Tran B, Romero C, Forberger HA, Weidman J, Khouri H, Feldblyum TV, Utterback TR, Van Aken SE, Lovley DR, Fraser CM.(2003)Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.Science. Vol 302(5652):1967-9

Yin Y, Wu D, Chory J. (2002)Plant receptor kinases: Systemin receptor identified.PNAS Vol 99:9090-9092

Chory J, Wu D. (2001)Weaving the Complex Web of Signal Transduction.Plant Physiology Vol125:77-80

Theologis A, Ecker JR,.. Wu D …, Venter JC, Davis RW. (2000) Sequence and Analysis of Chromosome 1 of the Plant Arabidopsis thaliana. Nature Vol 408(6814): 816-820

Kaul S, Town CD, …Wu D,…White O, Venter JC, Fraser CM. (2000) Sequence and Analysis of Chromosome 3 of the Plant Arabidopsis thaliana. Nature Vol 408(6814): 820-823

Mayer K, White O,…,Wu D,…Salzberg SL, Mewes H. (2000) Analysis of the Genome Sequence of the Flowering Plant Arabidopsis thaliana. Nature Vol 408(6814): 796-815

Wu D, Wright DA, Wetzel C, Voytas DF, Rodermel SR.(1999) The Arabidopsis Immutans Variegation Mutant Identifies a Novel Alternative Oxidase Homologue Necessary for Chloroplast. Plant Cell Vol 11:1-14

Wright DA, Park SK, Wu D, Phillips GJ, Rodermel SR, Voytas DF.(1997) Recovery of YAC-end Sequences Through Complementation of an Escherichia Coli pyrF Mutation. Nuclear Acids Res 25(13):2679-2680


An apoptosis network involving a growth factor and a transmembrane anchor protein. Dongying Wu, Hai Hu, 2002 (provisional patent application)

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