1. Kannoly S, Singh A & Dennehy JJ. 2020. An optimal lysis time maximizes bacteriophage fitness inquasi-continuous culture. bioRxiv. (In revision at The American Naturalist).
  2. Pecson BM, Darby E, Haas CN, Amha Y, Bartolo M, Danielson R, Dearborn Y, Di Giovanni G, Ferguson C, Fevig S, Gaddis E, Gray D, Lukasik G, Mull B, Olivas L, Olivieri A, Qu Y, SARS-CoV-2 Interlaboratory Consortium. 2021. Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S. Environmental Science: Water Research & Technology  PDF
  3. Dunning Hotopp JC, Baltrus DA, Bruno VM, Dennehy JJ, Gill SR, Maresca JA, Matthijnssens J, Newton ILG, Putonti C, Rasko DA, Rokas A, Roux S, Stajich JE, Stedman KM, Stewart FJ, & Thrash JC. 2020. Best practices for successfully writing and publishing a genome announcement in Microbiology Resource Announcements. Microbiology Resource Announcements 2020 Sep 3; 9:e00763-20. PDF    
  4. Kannoly S, Gao T, Dey S, Wang I-N, Singh A, & Dennehy JJ. Optimum threshold minimizes noise in timing of intracellular events. iScience. 2020 May 21; 23(6): 101186. PDF   
  5. Hoxie I & Dennehy JJ. 2020. Intragenic recombination influences rotavirus diversity and evolution. Virus Evolution. PDF    
  6. Baltrus DA, Cuomo CA, Dennehy JJ, Dunning-Hotopp JC, Maresca JA, Newton ILG, Rasko D, RokasA, Roux S & Stajich JE. 2019. Future-proofing your Microbiology Resource Announcements genome assembly for reproducibility and clarity. Microbiology Resource Announcements, e00954-19. PDF
  7. Ghusinga KR, Dennehy JJ & Singh A. 2017. Controlling noise in the timing of intracellular events: A first-passage time approach. PNAS. PDF    
  8. Dennehy, JJ. 2016. Evolutionary ecology of virus emergence. Annals of the New York Academy of Sciences. PDF    
  9. Ahmadi M, Torshizi MAK, Rahimi S & Dennehy JJ. 2016. Prophylactic bacteriophage administration more effective than post-infection administration in reducing Salmonella enterica serovar enteritidis shedding in quail. Frontiers in Microbiology. PDF    
  10. Esposito LA, Gupta S, Streiter F, Prasad A and Dennehy JJ. 2016. Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias. Microbial Genomics. PDF       
  11. Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Cresawn SG, Jacobs WR Jr, Hendrix RW, Lawrence JG, Hatfull GF, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA PHAGES), Phage Hunters Integrating Research and Education (PHIRE), & Mycobacterial Genetics Course (MGC). 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife 4:e06416. PDF     
  12. Ford BE, Sun B, Carpino J, Chapler ES, Ching J, Yoon C, Jhun K, Kim JD, Lallos GG, Morgenstern R, Singh S, Theja S, Dennehy JJ. 2014. Frequency and Fitness Consequences of Bacteriophageφ6 Host Range Mutations. PLoS ONE 9(11): e113078. PDF     
  13. Dennehy JJ. 2014. What ecologists can tell virologists. Annual Review of Microbiology, 68:117-135. PDF     
  14. Singh, A & Dennehy JJ. 2014. Stochastic holin expression can account for lysis time variation in the bacteriophage λ. Journal of the Royal Society Interface, 6 June 2014 vol. 11 no. 95. PDF     
  15. Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, Dennehy JJ et al. 2014. A broadly implementable research course in phage discovery and genomics for first-year undergraduate students. mBio, 5:1, e01051-13. PDF     
  16. Dennehy JJ, Duffy S, O’Keefe KJ, Edwards SV, & Turner PE. 2013. Frequent coinfection reduces RNA virus population genetic diversity. Journal of Heredity, 104: 704 – 712. PDF 
  17. Dennehy JJ. 2012. What can bacteriophages tell us about host-parasite coevolution? International Journal of Evolutionary Biology, Article ID 396165. PDF     
  18. Hatfull GF, the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Program, the KwaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course Students, and the Phage Hunters Integrating Research and Education Program. 2012. The complete genome sequences of 138 mycobacteriophages. Journal of Virology, 86: 2382-2384. PDF     
  19. Ching J, Musheyev SA, Chowdhury D, Kim JA, Choi Y & Dennehy JJ. 2012. Intermediate dispersal rate maximizes adaptation in bacteriophage populations evolving in an ecological sink. Evolution, 67: 10–17. PDF     
  20. Li J & Dennehy JJ. 2011. Differential bacteriophage mortality on exposure to copper. Applied and Environmental Microbiology, 77:6878-6883. PDF     
  21. Dennehy JJ & Wang I-N. 2011. Factors influencing lysis time stochasticity in bacteriophage λ. BMC Microbiology, 11:174. PDF     
  22. Dennehy JJ, Friedenberg NA, McBride RC, Holt RD & Turner PE. 2010. Experimental evidence that source genetic variation drives pathogen emergence. Proceedings of the Royal Society B. 277: 3113-3121. PDF     
  23. Katchikian CE, Dennehy JJ, Vitek CJ & Livdahl TP. 2010. Environmental effects on bet hedging in Aedes mosquito egg hatch. Evolutionary Ecology, 24:1159–1169. PDF     
  24. Dennehy JJ. 2009. Bacteriophages as model organisms for virus emergence research. Trends in Microbiology, 17:450-457. PDF     
  25. Katchikian CE, Dennehy JJ, Vitek CJ & Livdahl TP. 2009. Climate and geographic trends in hatch delay of the treehole mosquito, Aedes triseriatus Say (Diptera: Culicidae). Journal of Vector Ecology 34: 119-128. PDF     
  26. Dennehy JJ, Abedon ST & Turner PE. 2007. Host density impacts relative fitness of bacteriophage φ6 genotypes in structured habitats. Evolution, 61: 2516-2527. PDF     
  27. Dennehy JJ, Friedenberg N, Yang Y & Turner, PE. 2007. Virus population extinction via ecological traps. Ecology Letters, 10: 230–240. (Reported in the New York Times and the New Scientist). PDF     
  28. Monello RJ, Dennehy JJ, Murray D & Wirsing AJ. 2006. Species differences among native ranids in coping with an exotic invader, the bullfrog Rana catesbeiana. Journal of Herpetology, 40: 403-407. PDF     
  29. Dennehy JJ, Yang Y, Friedenberg N & Turner PE. 2006. Bacteriophage migration via nematode vectors: host-parasite-consumer interactions in laboratory microcosms. Applied and Environmental Microbiology, 72: 1974-1979. PDF     
  30. Dennehy JJ, Friedenberg N, Holt RD & Turner PE. 2006. Viral ecology and the maintenance of novel host use. The American Naturalist, 167: 429-439. PDF     
  31. Evans MEK and Dennehy JJ. 2005. Germ Banking: Bet hedging and variable release from egg and seed dormancy. Quarterly Review of Biology, 80: 431-451. PDF     
  32. Dennehy JJ & Turner PE. 2004. Reduced fecundity is the cost of cheating in RNA virus φ6. Proceedings of the Royal Society: Biological Sciences, 271: 2275-2282. PDF     
  33. Dennehy JJ & Livdahl T. 2004. Polymorphic foraging behavior among Caenorhabditis elegans: Frequency- and density-dependent selection. Journal of Nematology, 36: 276-280. PDF     
  34. Dennehy JJ, Robakiewicz P & Livdahl T. 2001. Larval rearing conditions affect kin-mediated cannibalism in a treehole mosquito. Oikos, 95: 335-339. PDF     
  35. Dennehy JJ. 2001. Influence of social dominance rank on diet quality of pronghorn females. Behavioral Ecology, 12: 177-181. PDF     
  36. Dennehy JJ & Livdahl T. 1999. First record of Toxorhynchites rutilus (Diptera: culicidae) in Massachusetts. Journal of the American Mosquito Control Association, 15: 24-25. PDF     

Book Chapters

  1. Dennehy JJ, Abedon ST (2020) Adsorption: phage acquisition of bacteria. In Bacteriophages. Harper D, Abedon ST, Burrowes B, Mcconville M (eds). Springer, Cham. Chapter 1; p. 1-25. PDF    
  2. Dennehy JJ, Abedon ST (2020) Bacteriophage Ecology. In Bacteriophages. Harper D, Abedon ST, Burrowes B, Mcconville M (eds). Springer, Cham. Chapter 5; p. 1-44. PDF    
  3. Dennehy JJ, Abedon ST (2020) Phage Infection and Lysis. In Bacteriophages. Harper D, Abedon ST, Burrowes B, Mcconville M (eds). Springer, Cham. Chapter 31; p. 1-43. PDF    
  4. Ford BE, Baloh M, & Dennehy JJ. (2018) Evolutionary ecology of the viruses of microorganisms. In Viruses of Microorganisms. Hyman P & Abedon ST (eds.). Poole, UK: Caister Academic Press. Chapter 3; p. 53-76. vi + 374p. PDF    

Conference Proceedings (Peer Reviewed)

  1. Dey S, Kannoly S, Dennehy JJ & Singh A. 2020. The role of incoherent feedforward circuits in regulating precision of event timing. 18th International Conference on Computational Methods in Systems Biology. Konstanz, Germany.
  2. Blotnick JA, Vargas CA, Dennehy JJ, Zurakowski R & Singh A. 2017. The effect of multiplicity of infection on the temperateness of a bacteriophage: implications for viral fitness. 56th IEEE Conference on Decision and Control, Melbourne, Australia. DOI: 10.1109/CDC.2017.8263885.
  3. Conway, JE, Dennehy JJ & Singh A. 2016. Optimizing phage λ survival in a changing environment: stochastic model predictions. 55th IEEE Conference on Decision and Control, Las Vegas, NV. DOI: 10.1109/CDC.2016.7799174.
  4. DGhusinga KR, Dennehy JJ & Singh A. 2014. First passage time stochasticity in a gene network with feedback regulation. Northeast Bioengineering Conference (NEBEC), Boston, MA, 2014, pp. 1-2. DOI: 10.1109/NEBEC.2014.6972797.