Oltean HN, Lipton B, Black A, Snekvik K, Haman K, Buswell M, Baines AE, Rabinowitz PM, Russell SL, Shadomy S, Ghai RR, Rekant S, Lindquist S, Baseman JG. (2025). Developing a one health data integration framework focused on real-time pathogen surveillance and applied genomic epidemiology. One health outlook, 7(1)
Tran-Kiem C, Paredes MI, Perofsky AC, Frisbie LA, Xie H, Kong K, Weixler A, Greninger AL, Roychoudhury P, Peterson JM, Delgado A, Halstead H, MacKellar D, Dykema P, Gamboa L, Frazar CD, Ryke E, Stone J, Reinhart D, Starita L, Thibodeau A, Yun C, Aragona F, Black A, Viboud C, Bedford T. (2025). Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences. Nature
Tran-Kiem C, Paredes MI, Perofsky AC, Frisbie LA, Xie H, Kong K, Weixler A, Greninger AL, Roychoudhury P, Peterson JM, Delgado A, Halstead H, MacKellar D, Dykema P, Gamboa L, Frazar CD, Ryke E, Stone J, Reinhart D, Starita L, Thibodeau A, Yun C, Aragona F, Black A, Viboud C, Bedford T. (2024). Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences. medRxiv : the preprint server for health sciences
Oltean HN, Black A, Lunn SM, Smith N, Templeton A, Bevers E, Kibiger L, Sixberry M, Bickel JB, Hughes JP, Lindquist S, Baseman JG, Bedford T. (2024). Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020-2022 pandemic, Washington State. BMC public health, 24(1)
Rich SN, Richards V, Mavian C, Rife Magalis B, Grubaugh N, Rasmussen SA, Dellicour S, Vrancken B, Carrington C, Fisk-Hoffman R, Danso-Odei D, Chacreton D, Shapiro J, Seraphin MN, Hepp C, Black A, Dennis A, Trovão NS, Vandamme AM, Rasmussen A, Lauzardo M, Dean N, Salemi M, Prosperi M. (2023). Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions. JMIR formative research, (7)
Mwakibete L, Takahashi S, Ahyong V, Black A, Rek J, Ssewanyana I, Kamya M, Dorsey G, Jagannathan P, Rodríguez-Barraquer I, Tato CM, Greenhouse B. (2023). Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda. PLOS global public health, 3(5)
Griffiths EJ, Timme RE, Mendes CI, Page AJ, Alikhan NF, Fornika D, Maguire F, Campos J, Park D, Olawoye IB, Oluniyi PE, Anderson D, Christoffels A, da Silva AG, Cameron R, Dooley D, Katz LS, Black A, Karsch-Mizrachi I, Barrett T, Johnston A, Connor TR, Nicholls SM, Witney AA, Tyson GH, Tausch SH, Raphenya AR, Alcock B, Aanensen DM, Hodcroft E, Hsiao WWL, Vasconcelos ATR, MacCannell DR. (2022). Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package. GigaScience, (11)
Mbala-Kingebeni P, Pratt C, Mutafali-Ruffin M, Pauthner MG, Bile F, Nkuba-Ndaye A, Black A, Kinganda-Lusamaki E, Faye M, Aziza A, Diagne MM, Mukadi D, White B, Hadfield J, Gangavarapu K, Bisento N, Kazadi D, Nsunda B, Akonga M, Tshiani O, Misasi J, Ploquin A, Epaso V, Sana-Paka E, N'kasar YTT, Mambu F, Edidi F, Matondo M, Bula Bula J, Diallo B, Keita M, Belizaire MRD, Fall IS, Yam A, Mulangu S, Rimion AW, Salfati E, Torkamani A, Suchard MA, Crozier I, Hensley L, Rambaut A, Faye O, Sall A, Sullivan NJ, Bedford T, Andersen KG, Wiley MR, Ahuka-Mundeke S, Muyembe Tamfum JJ. (2021). Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease. The New England journal of medicine, 384(13)
Moncla LH, Black A, DeBolt C, Lang M, Graff NR, Pérez-Osorio AC, Müller NF, Haselow D, Lindquist S, Bedford T. (2021). Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State. eLife, (10)
Kinganda-Lusamaki E, Black A, Mukadi DB, Hadfield J, Mbala-Kingebeni P, Pratt CB, Aziza A, Diagne MM, White B, Bisento N, Nsunda B, Akonga M, Faye M, Faye O, Edidi-Atani F, Matondo-Kuamfumu M, Mambu-Mbika F, Bulabula J, Di Paola N, Pauthner MG, Andersen KG, Palacios G, Delaporte E, Sall AA, Peeters M, Wiley MR, Ahuka-Mundeke S, Bedford T, Tamfum JM. (2021). Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo. Nature medicine
Black A, MacCannell DR, Sibley TR, Bedford T. (2020). Ten recommendations for supporting open pathogen genomic analysis in public health. Nature medicine
Hilton SK, Huddleston J, Black A, North K, Dingens AS, Bedford T, Bloom JD. (2020). dms-view: Interactive visualization tool for deep mutational scanning data. Journal of open source software, 5(52)
Black A, Moncla LH, Laiton-Donato K, Potter B, Pardo L, Rico A, Tovar C, Rojas DP, Longini IM, Halloran ME, Peláez-Carvajal D, Ramírez JD, Mercado-Reyes M, Bedford T. (2019). Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia. BMC infectious diseases, 19(1)
Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr., Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ. (2017). Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature protocols, 12(6)
Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr., Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG. (2017). Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature, 546(7658)
Rouet F, Nouhin J, Zheng DP, Roche B, Black A, Prak S, Leoz M, Gaudy-Graffin C, Ferradini L, Mom C, Mam S, Gautier C, Lesage G, Ken S, Phon K, Kerleguer A, Yang C, Killam W, Fujita M, Mean C, Fontenille D, Barin F, Plantier JC, Bedford T, Ramos A, Saphonn V. (2018). Massive Iatrogenic Outbreak of Human Immunodeficiency Virus Type 1 in Rural Cambodia, 2014-2015. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 66(11)
Black A, Breyta R, Bedford T, Kurath G. (2016). Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus. Virus evolution, 2(2)
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