MARTIN WU

  • Assistant Professor of Biology
  • Email:    mw4yv@virginia.edu
  • Office:    (434)-924-4518
  • Lab:       (434) 982-5478
  • Office:    404 PLSB

Laboratory Website

EDUCATION

  • B.S., Wuhan University, 1992
  • Ph.D., The Johns Hopkins University, 2000

RESEARCH INTERESTS

We are interested in studying how microbes evolve, adapt and diversify at the molecular, organismal and community levels. To gain insights into the fundamental mechanisms underlying these processes, we use an interdisciplinary approach that draws upon the fields of genomics, evolutionary biology, computational biology, and ecology. In particular, a large portion of our work will employ phylogenomics -- the synergistic integration of evolutionary and genomic analyses -- to investigate these questions. Research opportunities are available. See my lab homepage for details.

REPRESENTATIVE PUBLICATIONS 

2012 

  1. ✤Ren T, Glatt DU, Nguyen TN, Allen EK, Early SV, Sale M, Winther B, Wu M. 16S rRNA survey revealed complex bacterial communities and evidence of bacterial interference on human adenoids. Environmental Microbiology (in press)

  2. ✤Kembel SW, Wu M, Eisen JA, Green JL. Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance. PLoS Computational Biology. (in press).

  3. ✤Kolling GL, Wu M, Alcantara-Warren C, Durmaz E, Klaenhammer TR, Guerrant RL. Lactic acid production by Streptococcus thermophilus alters Clostridium difficile infection and in vitro Toxin A production. Gut Microbes 2012, 3:6,1-7. doi:10.4161/gutmicrobes.21757.

  4. ✤Lu HP, Wang YB, Huang SW, Lin CY, Wu M, Hsieh CH, Yu HT. Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). BMC Genomics. 2012,13:466. doi:10.1186/1471-2164-13-466.

  5. ✤Kolling G, Wu M, Guerrant RL. Enteric Pathogens Through Life Stages. Frontiers in Cellular and Infection Microbiology. 2012, 2:114. doi:10.3389/fcimb.2012.00114.

  6. ✤Koeppel AF and Wu M. Lineage-dependent ecological coherence in bacteria. FEMS Microbiology Ecology. 2012, doi: 10.1111/j.1574-6941.2012.01387.x. Download 10.1111_j.1574-6941.2012.01387.x.pdf.

  7. ✤Sloan DB, Alverson AJ, Wu M, Palmer JD, Taylor DR. Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus silene.Genome Biol Evol. 2012, Jan;4(3):294-306. Epub 2012 Jan 12.

  8. ✤Wu M and Scott AJ. Phylogenomic Analysis of Bacterial and Archaeal Sequences with AMPHORA2. Bioinformatics 2012, doi: 10.1093/bioinformatics/bts079. Download AMPHORA2.pdf

  9. ✤Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. 2012 Jan;10(1):e1001241. Epub 2012 Jan 17.

  10. ✤Wu M, Chatterji S, Eisen JA. Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 2012, 7(1): e30288. doi:10.1371/journal.pone.0030288


2011

  1. ✤Coyne RS, Hannick L, Shanmugam D, Hostetler JB, Brami D, Joardar VS, Johnson J, Radune D, Singh I, Kumar U, Saier M, Wang Y, Cai H, Gu J, Mather MW, Vaidya AB, Wilkes DE, Rajagopalan V, Asai DJ, Pearson CG, Findly RC, Dickerson HW, Badger JH, Wu M, Martens C, Van de Peer Y, Roos DS, Cassidy-Hanley DM, Clark TG. Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control. Genome Biol 2011 Oct 17;12(10):R100.

  2. ✤Wang Z, Kadouri DE and Wu M. Genomic Insights into An Obligate Epibiotic Bacterial Predator: Micavibrio aeruginosavorus ARL-13. BMC Genomics 2011, 12:453. doi:10.1186/1471-2164-12-453[highly accessed]

  3. ✤Wu M and Eisen JA. Towards Automated Phylogenomic Inference in Bruijn, F.J.d., Handbook of molecular microbial ecology I : metagenomics and complementary approaches. 2011, Hoboken, N.J.: Wiley-Blackwell.

  4. ✤Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC and Eisen JA. Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS One 2011 6(3): e18011. doi:10.1371/journal.pone.0018011.