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Allison Black

PhD Candidate

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Papers

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)

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

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)

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). : 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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