1. Yang F, Labani-Motlagh A, Ansari D, Garzon JAB, Moreira JD, Patel S, Spagnolo F, Florence J, Vankayalapati A, Vankayalapati R, Dennehy JJ, Samten B, and Yi G. 2023. Bacteriophage therapy for the treatment of Mycobacterium tuberculosis infections in humanized mice. Biorxiv.

  2. Qasmieh S, Robertson M, Teasdale C, Kulkarni S, Larsen D, Dennehy JJ, McNairy M, Jones H, Borrell L, & Nash D. 2023. The prevalence of SARS-CoV-2 infection and other public health outcomes during the BA.2/BA.2.12.1 surge, New York City, April-May 2022. MedRxiv.

  3. Gregory DA, Trujillo M, Rushford C, Fleury A, Kannoly S, San K, Lyfoung D, Wiseman RW, Bromert K, Zhou M-Y, Kesler E, Bivens N, Hoskins J, Lin C-H, O’Connor DH, Wieberg C, Wenzel J, Kantor RS, Dennehy JJ & Johnson MC. 2022. Genetic diversity and evolutionary convergence of cryptic SARS-CoV-2 lineages detected via wastewater sequencing. PLoS Pathogens.

  4. Kannoly S, Oken G, Shadan J, Musheyev D, Singh K, Singh A & Dennehy JJ. 2022. A single-cell approach reveals variation in cellular phage-producing capacities. Microbiology Spectrum.

  5. Kannoly S, Singh A & Dennehy JJ. 2022. An optimal lysis time maximizes bacteriophage fitness in quasi-continuous culture. mBio.

  6. Hoar C, Chauvin F, Katehis D, Clare A, McGibbon H, Castro E, Patinella S, Dennehy JJ, Trujillo M, Smyth DS, Silverman A. 2022. Monitoring SARS-CoV-2 in wastewater during New York City’s second wave of COVID-19: Sewershed-level trends and relationships to publicly available clinical testing data. Environmental Science: Water Research & Technology.

  7. Skanata A, Spagnolo F, Metz M, Smyth DS & Dennehy JJ. 2022. Humidity reduces rapid and distant airborne travel of viable viral particles in classroom settings. Environmental Science & Technology Letters.

  8. Kirby AE, Welsh R, Marsh Z, Yu AT, Vugia DJ, Boehm AB, Wolfe MK, White BJ, Matzinger S, Wheeler A, Bankers L, Andresen K, Slatas C, New York City Department of Environmental Protection, Gregory DA, Johnson MC, Trujillo M, Kannoly S, Smyth DS, Dennehy JJ, Hopkins L, Stadler L, Ensor K, Penn R, Brown P & Treangen T. 2022. Early evidence of the SARS-CoV-2 B.1.1.529 (Omicron) variant in community wastewater — United States, November–December 2021. Morbidity and Mortality Weekly Report.

  9. Burkhardt R, Dennehy JJ, Poon LLM, Saif LW, & Enquist LJ. 2022. Are COVID-19 vaccine boosters needed: the science behind boosters. Journal of Virology.

  10. Smyth DS, Trujillo M, Gregory DA, Cheung K, Gao A, Graham M, Guan Y, Hoxie I, Kannoly S, Kubota N, Lyddon TD, Markman M, Rushford C, San K, Sompanya G, Spagnolo F, Suarez R, Daniels M, Johnson MC & Dennehy JJ. 2022. Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nature Communications.

  11. Spagnolo F, Trujillo M & Dennehy JJ. 2021. Why do antibiotics exist? mBio.

  12. Hoxie I & Dennehy JJ. 2021. Rotavirus A genome segments show distinct segregation and codon usage patterns. Viruses.

  13. Trujillo M, Cheung K, Gao A, Hoxie I, Kannoly S, Kubota N, San KM, Smyth DS & Dennehy JJ. 2021. Protocol for safe, affordable, and reproducible isolation and quantitation of SARS-CoV-2 RNA from wastewater. PLoSONE

  14. 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.

  15. 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.

  16. Kannoly S, Gao T, Dey S, Wang I-N, Singh A, & Dennehy JJ. 2020. Optimum threshold minimizes noise in timing of intracellular events. iScience.

  17. Hoxie I & Dennehy JJ. 2020. Intragenic recombination influences rotavirus diversity and evolution. Virus Evolution.

  18. 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.

  19. Ghusinga KR, Dennehy JJ & Singh A. 2017. Controlling noise in the timing of intracellular events: A first-passage time approach. PNAS. PDF

  20. Dennehy, JJ. 2016. Evolutionary ecology of virus emergence. Annals of the New York Academy of Sciences.

  21. 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.

  22. 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.

  23. 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

  24. 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 Bacteriophage phi6 Host Range Mutations. PLoS ONE.

  25. Dennehy JJ. 2014. What ecologists can tell virologists. Annual Review of Microbiology.

  26. Singh, A & Dennehy JJ. 2014. Stochastic holin expression can account for lysis time variation in the bacteriophage λ. Journal of the Royal Society Interface.

  27. 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.

  28. Dennehy JJ, Duffy S, O'Keefe KJ, Edwards SV, & Turner PE. 2013. Frequent coinfection reduces RNA virus population genetic diversity. Journal of Heredity.

  29. Dennehy JJ. 2012. What can bacteriophages tell us about host-parasite coevolution? International Journal of Evolutionary Biology.

  30. 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.

  31. Ching J, Musheyev SA, Chowdhury D, Kim JA, Choi Y & Dennehy JJ. 2012. Migration enhances adaptation in bacteriophage populations evolving in ecological sinks. Evolution.

  32. Li J & Dennehy JJ. 2011. Differential bacteriophage mortality on exposure to copper. Applied and Environmental Microbiology, 77:6878-6883. PDF

  33. Dennehy JJ & Wang I-N. 2011. Factors influencing lysis time stochasticity in bacteriophage λ. BMC Microbiology.

  34. 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.

  35. Katchikian CE, Dennehy JJ, Vitek CJ & Livdahl TP. 2010. Environmental effects on bet hedging in Aedes mosquito egg hatch. Evolutionary Ecology.

  36. Dennehy JJ. 2009. Bacteriophages as model organisms for virus emergence research. Trends in Microbiology.

  37. 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.

  38. Dennehy JJ, Abedon ST & Turner PE. 2007. Host density impacts relative fitness of bacteriophage φ6 genotypes in structured habitats. Evolution.

  39. Dennehy JJ, Friedenberg N, Yang Y & Turner, PE. 2007. Virus population extinction via ecological traps. Ecology Letters. (Reported in the New York Times and the New Scientist).

  40. Monello RJ, Dennehy JJ, Murray D & Wirsing AJ. 2006. Growth and behavioral responses of tadpoles of two native frogs to an exotic competitor, Rana catesbeiana Journal of Herpetology.

  41. 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.

  42. Dennehy JJ, Friedenberg N, Holt RD & Turner PE. 2006. Viral ecology and the maintenance of novel host use. The American Naturalist.

  43. Evans MEK and Dennehy JJ. 2005. Germ Banking: Bet hedging and variable release from egg and seed dormancy. Quarterly Review of Biology.

  44. Dennehy JJ & Turner PE. 2004. Reduced fecundity is the cost of cheating in RNA virus φ6. Proceedings of the Royal Society: Biological Sciences.

  45. Dennehy JJ & Livdahl T. 2004. Polymorphic foraging behavior among Caenorhabditis elegans: Frequency- and density-dependent selection. Journal of Nematology.

  46. Dennehy JJ, Robakiewicz P & Livdahl T. 2001. Larval rearing conditions affect kin-mediated cannibalism in a treehole mosquito. Oikos.

  47. Dennehy JJ. 2001. Influence of social dominance rank on diet quality of pronghorn females. Behavioral Ecology.

  48. Dennehy JJ & Livdahl T. 1999. First record of Toxorhynchites rutilus (Diptera: culicidae) in Massachusetts. Journal of the American Mosquito Control Association.

    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.