Peer-reviewed journal articles:

  1. Abdul Rahman, N et al. (2015) A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes. Microbiome. doi:10.1186/s40168-015-0067-8
  2. Costello, ME et al. (2014) Intestinal dysbiosis in ankylosing spondylitis. Arthritis & Rheumatology. doi: 10.1002/art.38967
  3. Willner, D et al. (2014) Single clinical isolates from acute uncomplicated urinary tract infections are representative of dominant in situ populations. Mbio.doi:10.1128/mBio.01064-13
  4. Jiang, L, et al. (2014) Novel risk loci for rheumatoid arthritis in han chinese and congruence with risk variants in europeans. Arthritis and Rheumatology. doi: 10.1002/art.38353. [Epub ahead of print]
  5. Braff, W, Willner, D, Hugenholtz, P, Rabaey, K, Buie, C. (2013) Dielectrophoresis-based discrimination of bacteria at the strain level based on their surface properties. PLoS ONE.
  6. Willner, D and Hugenholtz, P. (2013) From deep sequencing to viral tagging: recent advances in viral metagenomics. Bioessays. 35(5): 436-442.
  7. Willner, D et al. (2013) Re-establishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome. American Journal of Respiratory and Critical Care Medicine. 187(6): 640-647.
  8. Jiang, L et al. (2013) Comparison of the performance of two commerical genome wide association study genotyping platforms in Han Chinese samples. G3: Genes, Genomes, Genetics. 3(1): 23-29.
  9. Willner, D and Hugenholtz, P. (2013) Metagenomics and community profiling: culture-independent techniques in the clinical laboratory. Clinical Microbiology Newsletter. 35(1):1-9.
  10. Cassman, N et al. (2012) Oxygen minimum zones harbor novel viral communities with low diversity. Environmental Microbiology: 14(11):3043-65.
  11. Lim, YW et al. (2012) Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities. Journal of Cystic Fibrosis. DOI:10.1016/j.jcf.2012.07.009.
  12. Willner, D et al.(2012)Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS ONE.
  13. Estrada K et al. (2012) Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nature Genetics. 44(5):491-501. 
  14. Angly, F et al. (2012) Grinder: a versatile amplicon and shotgun sequence simulator.Nucleic Acids Research: 40(12): e94.
  15. Willner, D et al. (2012) Spatial distribution of microbial communities in the cystic fibrosis lung. ISME Journal: 6(2):471-4.
  16. Willner, D et al. (2012) Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am J Respir Cell Mol Biol: 46(2):127-31.
  17. Kelly, L et al. (2012) Black reefs: iron induced phase shifts on coral reefs. ISME Journal: 6: 638-649.
  18. Ng, TFF et al. (2011) Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes. PLoS ONE. 6(6):e20579.
  19. Rodriguez-Mueller, B et al. (2010) Viral and microbial community dynamics in four aquatic environments. ISME Journal. 4(6):739-51.
  20. Willner, D et al.(2011) Metagenomic detection of phage-encoded platelet binding factors in the human oral cavity. PNAS. 108 (Supplement 1): 4547-4553.
  21. Willner, D and Furlan, M. (2010) Deciphering the role of phage in the CF airway. Virulence. 1(4):309-13.
  22. Su, L, Willner, D, Segall, A. (2010) A peptide that targets DNA repair intermediates in vitro inhibits Salmonella growth within murine macrophages. Antimicrobial Agents and Chemotherapy 54(5):1888-99.
  23. Willner D et al. (2009) Metagenomic analysis of respiratory tract viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS ONE. 4(10):e7370. 18.
  24. Willner D, Thurber RV, Rohwer F (2009) Metagenomic signatures of 86 microbial and viral metagenomes. Environmental Microbiology. 11(7):1752-66.
  25. Angly, F et al. (2009) The GAAS metagenomic tool and its application to the estimation of viral and microbial average genome size in four biomes.PLoS Computational Biology. 5(12): e1000593.
  26. Allen, B et al. (2009) Top-down control of microbial biomass and activity in an Arctic ecosystem. Environmental Microbiology. 12(3):642-8.
  27. Thurber RV et al. (2009) Metagenomic analysis of stressed coral holobionts. Environmental Microbiology. 11(8):2148-63.
  28. Dinsdale EA et al. (2008) Microbial ecology of four coral atolls in the northern line islands. PloS ONE. 3(2):e1584.
  29. Desnues C et al. (2008) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature. 452(7185):340-3.
  30. Vega Thurber RL et al. (2008) Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. PNAS. 105:18413-18418.
  31. Dinsdale EA et al.(2008) Functional metagenomic profiling of nine biomes. Nature. 452(7187):629-32.

Book chapter:

  1. Willner D, Desnues, C, Rohwer, F. Viral metagenomics: from fish slime to the world. (2011) Chapter in “Metagenomics and its applications in agriculture, biomedicine, and environmental studies”. Nova Scientific Publishers.

Press releases and media:

  6. Carl Zimmer’s book A Planet of Viruses


  1. Willner, D and Chambers, D (2014) Exploring the respiratory mycobiome. ISHLT Links Newsletter. 5(10).
  2. Willner, D (2012) Unlocking microbial diversity with metagenomics. ISHLT Links Newsletter. 4(5).
  3. Willner, D et al. (2013) Longitudinal holistic profiling of the lung transplant microbiome. The Journal of Heart and Lung Transplantation. 32 (4, Supplement):S10.
  4. Willner, D et al. (2012) Distinct microbial signatures of healthy and failing lung allografts. The Journal of Heart and Lung Transplantation. 31(4, Supplement):S32.