| Franklin, Alan B. | 2015 | "When fur and feather occur together: Interclass transmission of avian influenza A virus from mammals to birds through common resources" in Nature | 
              
                      | Franklin, Alan B. | 2015 | "Keeping Wildlife Out of Your Food: Mitigation and Control Strategies to Reduce the Transmission Risk of Food-Borne Pathogens" in Food Safety Risks from Wildlife | 
              
                      | Franklin, Alan B. | 2016 | "The effects of habitat, climate, and Barred Owls on long-term demography of Northern Spotted Owls" in Ornithological Applications | 
              
                      | Franklin, Alan B. | 2017 | "Transmission of H6N2 wild bird-origin influenza A virus among multiple bird species in a stacked-cage setting" in Archives of Virology | 
              
                      | Franklin, Alan B. | 2017 | "Differential Impacts of Wildfire on the Population Dynamics of an Old-Forest Species" in Ecology | 
              
                      | Franklin, Alan B. | 2017 | "Impact of body condition on influenza A virus infection dynamics in mallards following a secondary exposure" in PLoS ONE | 
              
                      | Franklin, Alan B. | 2017 | "A Method for the Improved Detection of Aerosolized Influenza Viruses and the Male-specific (F+) RNA Coliphage MS2" in Journal of Virological Methods | 
              
                      | Franklin, Alan B. | 2018 | "Variation in inbreeding rates across the range of Northern Spotted Owls ( Strix occidentalis caurina ): Insights from over 30 years of monitoring data" in Ornithology | 
              
                      | Franklin, Alan B. | 2018 | "Detection of Viruses from Bioaerosols Using Anion Exchange Resin" in Journal of Visualized Experiments | 
              
                      | Franklin, Alan B. | 2018 | "Spillover of Swine Coronaviruses, United States" in Emerging Infectious Diseases | 
              
                      | Franklin, Alan B. | 2018 | "Grass is not always greener: Rodenticide exposure of a threatened species near marijuana growing operations" in BMC Research Notes | 
              
                      | Franklin, Alan B. | 2019 | "Experimental infections of Norway rats with avian-derived low-pathogenic influenza A viruses" in Archives of Virology | 
              
                      | Franklin, Alan B. | 2019 | "Predicting the initial spread of novel Asian origin influenza A viruses in the continental United States by wild waterfowl" in Transboundary and Emerging Diseases | 
              
                      | Franklin, Alan B. | 2019 | "The conundrum of agenda-driven science in conservation" in Frontiers in Ecology and the Environment | 
              
                      | Franklin, Alan B. | 2019 | "Reinforcing the concept of agenda‐driven science: a response to Rohlf" in Frontiers in Ecology and the Environment | 
              
                      | Franklin, Alan B. | 2019 | "The past and future roles of competition and habitat in the range‐wide occupancy dynamics of Northern Spotted Owls" in Ecological Applications | 
              
                      | Franklin, Alan B. | 2020 | "Spillover of SARS-CoV-2 into novel wild hosts in North America: A conceptual model for perpetuation of the pathogen" in The Science of the Total Environment | 
              
                      | Franklin, Alan B. | 2020 | "Continental‐scale dynamics of avian influenza in U.S. waterfowl are driven by demography, migration, and temperature" in Ecological Applications | 
              
                      | Franklin, Alan B. | 2020 | "Gulls as Sources of Environmental Contamination by Colistin-resistant Bacteria" in Nature | 
              
                      | Franklin, Alan B. | 2020 | "Validation of a screening method for the detection of colistin-resistant E. coli containing mcr-1 in feral swine feces" in Journal of Microbiological Methods | 
              
                      | Franklin, Alan B. | 2020 | "Spotted owls and forest fire: Comment" in Ecosphere | 
              
                      | Franklin, Alan B. | 2021 | "Range-wide declines of northern spotted owl populations in the Pacific Northwest: A meta-analysis" in Biological Conservation | 
              
                      | Franklin, Alan B. | 2021 | "A Perspective on the Journal of Wildlife Management" in Journal of Wildlife Management | 
              
                      | Franklin, Alan B. | 2021 | "Pathogens from Wild Birds at the Wildlife–Agriculture Interface" in Infectious disease ecology of wild birds | 
              
                      | Franklin, Alan B. | 2021 | "Invader removal triggers competitive release in a threatened avian predator" in Proceedings of the National Academy of Sciences |