Chhabra, Preeti; Tully, Damien C; Mans, Janet; Niendorf, Sandra; Barclay, Leslie; Cannon, Jennifer L; Montmayeur, Anna M; Pan, Chao-Yang; Page, Nicola; Williams, Rachel; +14 more... Tutill, Helena; Roy, Sunando; Celma, Cristina; Beard, Stuart; Mallory, Michael L; Manouana, Gédéon Prince; Velavan, Thirumalaisamy P; Adegnika, Ayola Akim; Kremsner, Peter G; Lindesmith, Lisa C; Hué, Stéphane; Baric, Ralph S; Breuer, Judith; Vinjé, Jan; (2024) Emergence of Novel Norovirus GII.4 Variant. Emerging infectious diseases, 30 (1). pp. 163-167. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid3001.231003

Baxter, James; Langhorne, Sarah; Shi, Ting; Tully, Damien C; Villabona-Arenas, Ch Julián; Hué, Stéphane; Albert, Jan; Leigh Brown, Andrew; Atkins, Katherine E; (2023) Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis. Lancet Microbe, 4 (2). e102-e112. ISSN 2666-5247 DOI: https://doi.org/10.1016/S2666-5247(22)00327-5

Tully, Damien C; (2022) Leveraging genomic surveillance to enhance elimination strategies for hepatitis C virus. The Lancet Microbe, 3 (12). e893-e894. ISSN 2666-5247 DOI: https://doi.org/10.1016/S2666-5247(22)00204-X

Davies, Nicholas G; Abbott, Sam; Barnard, Rosanna C; Jarvis, Christopher I; Kucharski, Adam J; Munday, James D; Pearson, Carl AB; Russell, Timothy W; Tully, Damien C; Washburne, Alex D; +15 more... Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry LM; van Zandvoort, Kevin; Silverman, Justin D; CMMID COVID-19 Working Group; COVID-19 Genomics UK (COG-UK) Consortium; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M; Funk, Sebastian; Jit, Mark; Atkins, Katherine E; Edmunds, W John; (2021) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (New York, N.Y.), 372 (6538). 149-+. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.abg3055

Hochstatter, Karli R; Tully, Damien C; Power, Karen A; Koepke, Ruth; Akhtar, Wajiha Z; Prieve, Audrey F; Whyte, Thomas; Bean, David J; Seal, David W; Allen, Todd M; +1 more... Westergaard, Ryan P; (2021) Hepatitis C Virus Transmission Clusters in Public Health and Correctional Settings, Wisconsin, USA, 2016-20171. Emerging Infectious Diseases, 27 (2). pp. 480-489. ISSN 1080-6040 DOI: https://doi.org/10.3201/eid2702.202957

Tully, Damien C; Hahn, Judith A; Bean, David J; Evans, Jennifer L; Morris, Meghan D; Page, Kimberly; Allen, Todd M; (2021) Identification of Genetically Related HCV Infections Among Self-Described Injecting Partnerships. Clinical infectious diseases, 74 (6). pp. 993-1003. ISSN 1058-4838 DOI: https://doi.org/10.1093/cid/ciab596

Davies, Nicholas G; Abbott, Sam; Barnard, Rosanna C; Jarvis, Christopher I; Kucharski, Adam J; Munday, James D; Pearson, Carl AB; Russell, Timothy W; Tully, Damien C; Washburne, Alex D; +13 more... Wenseleers, Tom; Gimma, Amy; Waites, William; Wong, Kerry LM; van Zandvoort, Kevin; Silverman, Justin D; Diaz-Ordaz, Karla; Keogh, Ruth; Eggo, Rosalind M; Funk, Sebastian; Jit, Mark; Atkins, Katherine E; Edmunds, W John; (2020) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. MedRxiv. DOI: https://doi.org/10.1101/2020.12.24.20248822 Item availability may be restricted.

Villabona-Arenas, Ch Julián; Hanage, William P; Tully, Damien C; (2020) Phylogenetic interpretation during outbreaks requires caution. NATURE MICROBIOLOGY, 5 (7). pp. 876-877. DOI: https://doi.org/10.1038/s41564-020-0738-5

Euler, Zelda; VAN DEN Kerkhof, Tom L; Kouyos, Roger D; Tully, Damien C; Allen, Todd M; Trkola, Alexandra; Sanders, Rogier W; Schuitemaker, Hanneke; VAN Gils, Marit J; (2019) Lower Broadly Neutralizing Antibody Responses in Female Versus Male HIV-1 Infected Injecting Drug Users. Viruses, 11 (4). p. 384. ISSN 1999-4915 DOI: https://doi.org/10.3390/v11040384

Hahn, Judith A; Tully, Damien C; Evans, Jennifer L; Morris, Meghan D; Briceno, Alya; Bean, David J; Allen, Todd M; Page, Kimberly; (2019) Role of HCV Viremia in Corroborated HCV Transmission Events Within Young Adult Injecting Partnerships. Open forum infectious diseases, 6 (4). ofz125-. ISSN 2328-8957 DOI: https://doi.org/10.1093/ofid/ofz125

Metsky, Hayden C; Siddle, Katherine J; Gladden-Young, Adrianne; Qu, James; Yang, David K; Brehio, Patrick; Goldfarb, Andrew; Piantadosi, Anne; Wohl, Shirlee; Carter, Amber; +38 more... Lin, Aaron E; Barnes, Kayla G; Tully, Damien C; Corleis, Bjӧrn; Hennigan, Scott; Barbosa-Lima, Giselle; Vieira, Yasmine R; Paul, Lauren M; Tan, Amanda L; Garcia, Kimberly F; Parham, Leda A; Odia, Ikponmwosa; Eromon, Philomena; Folarin, Onikepe A; Goba, Augustine; Viral Hemorrhagic Fever Consortium; Simon-Lorière, Etienne; Hensley, Lisa; Balmaseda, Angel; Harris, Eva; Kwon, Douglas S; Allen, Todd M; Runstadler, Jonathan A; Smole, Sandra; Bozza, Fernando A; Souza, Thiago ML; Isern, Sharon; Michael, Scott F; Lorenzana, Ivette; Gehrke, Lee; Bosch, Irene; Ebel, Gregory; Grant, Donald S; Happi, Christian T; Park, Daniel J; Gnirke, Andreas; Sabeti, Pardis C; Matranga, Christian B; (2019) Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nature biotechnology, 37 (2). pp. 160-168. ISSN 1087-0156 DOI: https://doi.org/10.1038/s41587-018-0006-x

Yuan, Huangbo; Liu, Zhenqiu; Wu, Xuefu; Wu, Mingshan; Fang, Qiwen; Tully, Damien C; Zhang, Tiejun; (2019) Evolutionary characteristics and genetic transmission patterns of predominant HIV-1 subtypes among men who have sex with men in China. International journal of infectious diseases, 90. pp. 125-131. ISSN 1201-9712 DOI: https://doi.org/10.1016/j.ijid.2019.10.035

Martins, Mauricio A; Tully, Damien C; Pedreño-Lopez, Núria; von Bredow, Benjamin; Pauthner, Matthias G; Shin, Young C; Yuan, Maoli; Lima, Noemia S; Bean, David J; Gonzalez-Nieto, Lucas; +19 more... Domingues, Aline; Gutman, Martin J; Maxwell, Helen S; Magnani, Diogo M; Ricciardi, Michael J; Bailey, Varian K; Altman, John D; Burton, Dennis R; Ejima, Keisuke; Allison, David B; Evans, David T; Rakasz, Eva G; Parks, Christopher L; Bonaldo, Myrna C; Capuano, Saverio; Lifson, Jeffrey D; Desrosiers, Ronald C; Allen, Todd M; Watkins, David I; (2018) Mamu-B*17+ Rhesus Macaques Vaccinated with env, vif, and nef Manifest Early Control of SIVmac239 Replication. JOURNAL OF VIROLOGY, 92 (16). ISSN 0022-538X DOI: https://doi.org/10.1128/JVI.00690-18

Piantadosi, Anne; Freije, Catherine A; Gosmann, Christina; Ye, Simon; Park, Daniel; Schaffner, Stephen F; Tully, Damien C; Allen, Todd M; Dong, Krista L; Sabeti, Pardis C; +1 more... Kwon, Douglas S; (2018) Metagenomic Sequencing of HIV-1 in the Blood and Female Genital Tract Reveals Little Quasispecies Diversity during Acute Infection. Journal of Virology, 93 (2). ISSN 0022-538X DOI: https://doi.org/10.1128/JVI.00804-18

Hedegaard, Ditte L; Tully, Damien C; Rowe, Ian A; Reynolds, Gary M; Bean, David J; Hu, Ke; Davis, Christopher; Wilhelm, Annika; Ogilvie, Colin B; Power, Karen A; +5 more... Tarr, Alexander W; Kelly, Deirdre; Allen, Todd M; Balfe, Peter; McKeating, Jane A; (2017) High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease. Journal of hepatology, 66 (1). pp. 28-38. ISSN 0168-8278 DOI: https://doi.org/10.1016/j.jhep.2016.07.048

Martins, Mauricio A; Tully, Damien C; Shin, Young C; Gonzalez-Nieto, Lucas; Weisgrau, Kim L; Bean, David J; Gadgil, Rujuta; Gutman, Martin J; Domingues, Aline; Maxwell, Helen S; +16 more... Magnani, Diogo M; Ricciardi, Michael; Pedreño-Lopez, Nuria; Bailey, Varian; Cruz, Michael A; Lima, Noemia S; Bonaldo, Myrna C; Altman, John D; Rakasz, Eva; Capuano, Saverio; Reimann, Keith A; Piatak, Michael; Lifson, Jeffrey D; Desrosiers, Ronald C; Allen, Todd M; Watkins, David I; (2017) Rare Control of SIVmac239 Infection in a Vaccinated Rhesus Macaque. AIDS research and human retroviruses, 33 (8). pp. 843-858. ISSN 0889-2229 DOI: https://doi.org/10.1089/AID.2017.0046

Tully, Damien C; Claiborne, Daniel T; Allen, Todd M; (2017) Interferon-I: The Pièce de Résistance of HIV-1 Transmission? Trends in microbiology, 25 (5). pp. 332-334. ISSN 0966-842X DOI: https://doi.org/10.1016/j.tim.2017.02.010

Wolski, David; Foote, Peter K; Chen, Diana Y; Lewis-Ximenez, Lia L; Fauvelle, Catherine; Aneja, Jasneet; Walker, Andreas; Tonnerre, Pierre; Torres-Cornejo, Almudena; Kvistad, Daniel; +10 more... Imam, Sabrina; Waring, Michael T; Tully, Damien C; Allen, Todd M; Chung, Raymond T; Timm, Jörg; Haining, W Nicholas; Kim, Arthur Y; Baumert, Thomas F; Lauer, Georg M; (2017) Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8+ T Cells in Chronic versus Acute Infection. IMMUNITY, 47 (4). 648-663.e8. ISSN 1074-7613 DOI: https://doi.org/10.1016/j.immuni.2017.09.006

Salazar-Gonzalez, Jesus F; Salazar, Maria G; Tully, Damien C; Ogilvie, Colin B; Learn, Gerald H; Allen, Todd M; Heath, Sonya L; Goepfert, Paul; Bar, Katharine J; (2016) Use of Dried Blood Spots to Elucidate Full-Length Transmitted/Founder HIV-1 Genomes. Pathogens & immunity, 1 (1). pp. 129-153. ISSN 2469-2964 DOI: https://doi.org/10.20411/pai.v1i1.116

Sen, Debattama R; Kaminski, James; Barnitz, R Anthony; Kurachi, Makoto; Gerdemann, Ulrike; Yates, Kathleen B; Tsao, Hsiao-Wei; Godec, Jernej; LaFleur, Martin W; Brown, Flavian D; +9 more... Tonnerre, Pierre; Chung, Raymond T; Tully, Damien C; Allen, Todd M; Frahm, Nicole; Lauer, Georg M; Wherry, E John; Yosef, Nir; Haining, W Nicholas; (2016) The epigenetic landscape of T cell exhaustion. SCIENCE, 354 (6316). pp. 1165-1169. ISSN 0036-8075 DOI: https://doi.org/10.1126/science.aae0491

Tully, Damien C; Ogilvie, Colin B; Batorsky, Rebecca E; Bean, David J; Power, Karen A; Ghebremichael, Musie; Bedard, Hunter E; Gladden, Adrianne D; Seese, Aaron M; Amero, Molly A; +16 more... Lane, Kimberly; McGrath, Graham; Bazner, Suzane B; Tinsley, Jake; Lennon, Niall J; Henn, Matthew R; Brumme, Zabrina L; Norris, Philip J; Rosenberg, Eric S; Mayer, Kenneth H; Jessen, Heiko; Kosakovsky Pond, Sergei L; Walker, Bruce D; Altfeld, Marcus; Carlson, Jonathan M; Allen, Todd M; (2016) Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. PLoS pathogens, 12 (5). e1005619-. ISSN 1553-7366 DOI: https://doi.org/10.1371/journal.ppat.1005619