Shapiro, Jason W. and Catherine Putonti (2021). Rephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies. PeerJ. link to article (OA)
Shapiro, Jason W. and Catherine Putonti (2020). UPɸ phages, a new group of filamentous phages found in several members of Enterobacteriales. Virus Evolution. link to article (OA)
Putonti, Catherine, Jason W. Shapiro, Adriana Ene, Oleksandra Tsibiere, and Alan J. Wolfe (2020). Comparative genomic study of Lactobacillus jensenii and the newly defined Lactobacillus mulieris species identifies species-specific functionality. mSphere. link to article (OA)
Miller-Ensminger, Taylor, Rita Mormando, Laura Maskeri, Jason W. Shapiro, Alan J. Wolfe, and Catherine Putonti (2020). Introducing Lu-1, a novel Lactobacillus jensenii phage abundant in the urogenital tract. PLoS ONE. link to article (OA)
Andrea Garretto et al. [including Jason W. Shapiro] (2020). Genomic survey of E. coli from the bladders of women with and without lower urinary tract symptoms. Frontiers in Microbiology. link to article (OA)
Shapiro, Jason W. and Catherine Putonti (2018). Gene co-occurrence networks reflect bacteriophage ecology and evolution. mBio. link to article (OA)
Shapiro, Jason W. and Paul E. Turner (2018). Evolution of mutualism from parasitism in experimental virus populations. Evolution. link to article
Malki, Kema, Jason W. Shapiro, Travis K. Price, Evann E. Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Gina Kuffel, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti (2016). Genomes of Gardnerella strains reveal an abundance of prophages within the bladder microbiome. PLoS ONE. link to article (OA)
Shapiro, Jason W., Elizabeth S.C.P. Williams, and Paul E. Turner (2016). Evolution of parasitism and mutualism between filamentous phage M13 and Escherichia coli. PeerJ. link to article (OA)
Bruder, Katherine, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhain C. Watkins, and Catherine Putonti (2016). Freshwater metaviromics and bacteriophages: a current assessment of the state of the art in relation to bioinformatics challenges. Evolutionary Bioinformatics. link to article (OA)
Harcombe, William R., Alex Betts, Jason W. Shapiro, and Christopher J. Marx (2016). Adding biotic complexity alters the metabolic benefits of mutualism. Evolution. link to article
Shapiro, Jason W. and Paul E. Turner (2014). The impact of transmission mode on the evolution of benefits provided by microbial symbionts. Ecology and Evolution. link to article (OA)
Shapiro, Jason W. and Catherine Putonti (2020). UPɸ phages, a new group of filamentous phages found in several members of Enterobacteriales. Virus Evolution. link to article (OA)
Putonti, Catherine, Jason W. Shapiro, Adriana Ene, Oleksandra Tsibiere, and Alan J. Wolfe (2020). Comparative genomic study of Lactobacillus jensenii and the newly defined Lactobacillus mulieris species identifies species-specific functionality. mSphere. link to article (OA)
Miller-Ensminger, Taylor, Rita Mormando, Laura Maskeri, Jason W. Shapiro, Alan J. Wolfe, and Catherine Putonti (2020). Introducing Lu-1, a novel Lactobacillus jensenii phage abundant in the urogenital tract. PLoS ONE. link to article (OA)
Andrea Garretto et al. [including Jason W. Shapiro] (2020). Genomic survey of E. coli from the bladders of women with and without lower urinary tract symptoms. Frontiers in Microbiology. link to article (OA)
Shapiro, Jason W. and Catherine Putonti (2018). Gene co-occurrence networks reflect bacteriophage ecology and evolution. mBio. link to article (OA)
Shapiro, Jason W. and Paul E. Turner (2018). Evolution of mutualism from parasitism in experimental virus populations. Evolution. link to article
Malki, Kema, Jason W. Shapiro, Travis K. Price, Evann E. Hilt, Krystal Thomas-White, Trina Sircar, Amy B. Rosenfeld, Gina Kuffel, Michael J. Zilliox, Alan J. Wolfe, Catherine Putonti (2016). Genomes of Gardnerella strains reveal an abundance of prophages within the bladder microbiome. PLoS ONE. link to article (OA)
Shapiro, Jason W., Elizabeth S.C.P. Williams, and Paul E. Turner (2016). Evolution of parasitism and mutualism between filamentous phage M13 and Escherichia coli. PeerJ. link to article (OA)
Bruder, Katherine, Kema Malki, Alexandria Cooper, Emily Sible, Jason W. Shapiro, Siobhain C. Watkins, and Catherine Putonti (2016). Freshwater metaviromics and bacteriophages: a current assessment of the state of the art in relation to bioinformatics challenges. Evolutionary Bioinformatics. link to article (OA)
Harcombe, William R., Alex Betts, Jason W. Shapiro, and Christopher J. Marx (2016). Adding biotic complexity alters the metabolic benefits of mutualism. Evolution. link to article
Shapiro, Jason W. and Paul E. Turner (2014). The impact of transmission mode on the evolution of benefits provided by microbial symbionts. Ecology and Evolution. link to article (OA)
