Sustainable data analysis with Snakemake F Mölder, KP Jablonski, B Letcher, MB Hall, CH Tomkins-Tinch, V Sochat, ... F1000Research 10, 2021 | 1282 | 2021 |
Bioconda: sustainable and comprehensive software distribution for the life sciences B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ... Nature methods 15 (7), 475-476, 2018 | 1241 | 2018 |
Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant L Yurkovetskiy, X Wang, KE Pascal, C Tomkins-Tinch, TP Nyalile, Y Wang, ... Cell 183 (3), 739-751. e8, 2020 | 1177 | 2020 |
Zika virus evolution and spread in the Americas HC Metsky, CB Matranga, S Wohl, SF Schaffner, CA Freije, SM Winnicki, ... Nature 546 (7658), 411-415, 2017 | 456 | 2017 |
Genomic epidemiology reveals multiple introductions of Zika virus into the United States ND Grubaugh, JT Ladner, MUG Kraemer, G Dudas, AL Tan, ... Nature 546 (7658), 401-405, 2017 | 387 | 2017 |
Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone DJ Park, G Dudas, S Wohl, A Goba, SLM Whitmer, KG Andersen, ... Cell 161 (7), 1516-1526, 2015 | 354 | 2015 |
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events JE Lemieux, KJ Siddle, BM Shaw, C Loreth, SF Schaffner, ... Science 371 (6529), eabe3261, 2021 | 314* | 2021 |
Comparative transmissibility of SARS-CoV-2 variants delta and alpha in New England, USA R Earnest, R Uddin, N Matluk, N Renzette, SE Turbett, KJ Siddle, C Loreth, ... Cell Reports Medicine 3 (4), 2022 | 199 | 2022 |
Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs S Weingarten-Gabbay, S Klaeger, S Sarkizova, LR Pearlman, DY Chen, ... Cell 184 (15), 3962-3980. e17, 2021 | 152* | 2021 |
Sustainable data analysis with Snakemake. F1000Res 10: 33 F Mölder, KP Jablonski, B Letcher, MB Hall, CH Tomkins-Tinch, V Sochat, ... | 74 | 2021 |
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak KJ Siddle, LA Krasilnikova, GK Moreno, SF Schaffner, J Vostok, ... Cell 185 (3), 485-492. e10, 2022 | 64* | 2022 |
Sensorpedia: Information sharing across incompatible sensor systems BL Gorman, DR Resseguie, C Tomkins-Tinch 2009 International Symposium on Collaborative Technologies and Systems, 448-454, 2009 | 49 | 2009 |
Powassan virus neuropathology and genomic diversity in patients with fatal encephalitis E Normandin, IH Solomon, S Zamirpour, J Lemieux, CA Freije, SS Mukerji, ... Open forum infectious diseases 7 (10), ofaa392, 2020 | 32 | 2020 |
Ebola virus epidemiology and evolution in Nigeria OA Folarin, D Ehichioya, SF Schaffner, SM Winnicki, S Wohl, P Eromon, ... The Journal of infectious diseases 214 (suppl_3), S102-S109, 2016 | 31 | 2016 |
Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018 A Gaye, T Ndiaye, M Sy, AB Deme, AB Thiaw, A Sene, C Ndiaye, ... Scientific Reports 11 (1), 10321, 2021 | 28 | 2021 |
Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework BA Petros, JS Paull, CH Tomkins-Tinch, BC Loftness, KC DeRuff, P Nair, ... Med 3 (12), 883-900. e13, 2022 | 27 | 2022 |
Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems KG Barnes, JI Levy, J Gauld, J Rigby, O Kanjerwa, CB Uzzell, ... Nature Communications 14 (1), 7883, 2023 | 15 | 2023 |
Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria JU Oguzie, BA Petros, PE Oluniyi, SB Mehta, PE Eromon, P Nair, ... Nature Communications 14 (1), 4693, 2023 | 14 | 2023 |
SARS-CoV-2 reinfection in a liver transplant recipient CH Tomkins-Tinch, JS Daly, A Gladden-Young, NM Theodoropoulos, ... Annals of Internal Medicine 174 (8), 1178-1180, 2021 | 13 | 2021 |
The origins and future of sentinel: an early-warning system for pandemic preemption and response Y Botti-Lodovico, P Nair, D Nosamiefan, M Stremlau, S Schaffner, ... Viruses 13 (8), 1605, 2021 | 11 | 2021 |