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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.
Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R. Cantrell K, et al. Among authors: andersen kg. mSystems. 2021 Mar 16;6(2):e01216-20. doi: 10.1128/mSystems.01216-20. mSystems. 2021. PMID: 33727399 Free PMC article.
Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.
Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E… See abstract for full author list ➔ Karthikeyan S, et al. Among authors: andersen kg. medRxiv [Preprint]. 2022 Apr 4:2021.12.21.21268143. doi: 10.1101/2021.12.21.21268143. medRxiv. 2022. Update in: Nature. 2022 Sep;609(7925):101-108. doi: 10.1038/s41586-022-05049-6 PMID: 35411350 Free PMC article. Updated. Preprint.
Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting.
Keehner J, Abeles SR, Longhurst CA, Horton LE, Myers FE, Riggs-Rodriguez L, Ahmad M, Baxter S, Boussina A, Cantrell K, Cardenas P, De Hoff P, El-Kareh R, Holland J, Ikeda D, Kurashige K, Laurent LC; SEARCH Alliance; Lucas A, Pride D, Sathe S, Tran AR, Vasylyeva TI, Yeo G, Knight R, Wertheim JO, Torriani FJ. Keehner J, et al. Clin Infect Dis. 2024 May 15;78(5):1204-1213. doi: 10.1093/cid/ciad738. Clin Infect Dis. 2024. PMID: 38227643
Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools.
Fielding-Miller R, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu VJ, Kohn L, Martin NK, Wynn A, Wijaya C, Flores M, Omaleki V, Majnoonian A, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le T, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, De Hoff P, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb HM, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Laurent LC, Rosing T, Knight R; SEARCH. Fielding-Miller R, et al. Lancet Reg Health Am. 2023 Feb 20;19:100449. doi: 10.1016/j.lana.2023.100449. eCollection 2023 Mar. Lancet Reg Health Am. 2023. PMID: 36844610 Free PMC article.
Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.
Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Peacock TP, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Crits-Christoph A, et al. Among authors: andersen kg. Cell. 2024 Sep 19;187(19):5468-5482.e11. doi: 10.1016/j.cell.2024.08.010. Cell. 2024. PMID: 39303692
Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans.
Parker E, Omah IF, Varilly P, Magee A, Ayinla AO, Sijuwola AE, Ahmed MI, Ope-Ewe OO, Ogunsanya OA, Olono A, Eromon P, Tomkins-Tinch CH, Otieno JR, Akanbi O, Egwuenu A, Ehiakhamen O, Chukwu C, Suleiman K, Akinpelu A, Ahmad A, Imam KI, Ojedele R, Oripenaye V, Ikeata K, Adelakun S, Olajumoke B, Djuicy DD, Essengue LLM, Yifomnjou MHM, Zeller M, Gangavarapu K, O'Toole Á, Park DJ, Mboowa G, Tessema SK, Tebeje YK, Folarin O, Happi A, Lemey P, Suchard MA, Andersen KG, Sabeti P, Rambaut A, Njoum R, Ihekweazu C, Jide I, Adetifa I, Happi CT. Parker E, et al. Among authors: andersen kg. medRxiv [Preprint]. 2024 Jun 19:2024.06.18.24309104. doi: 10.1101/2024.06.18.24309104. medRxiv. 2024. PMID: 38947052 Free PMC article. Preprint.
Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa.
Djuicy DD, Omah IF, Parker E, Tomkins-Tinch CH, Otieno JR, Yifomnjou MHM, Essengue LLM, Ayinla AO, Sijuwola AE, Ahmed MI, Ope-Ewe OO, Ogunsanya OA, Olono A, Eromon P, Yonga MGW, Essima GD, Touoyem IP, Mounchili LJM, Eyangoh SI, Esso L, Nguidjol IME, Metomb SF, Chebo C, Agwe SM, Mossi HM, Bilounga CN, Etoundi AGM, Akanbi O, Egwuenu A, Ehiakhamen O, Chukwu C, Suleiman K, Akinpelu A, Ahmad A, Imam KI, Ojedele R, Oripenaye V, Ikeata K, Adelakun S, Olajumoke B, O'Toole Á, Magee A, Zeller M, Gangavarapu K, Varilly P, Park DJ, Mboowa G, Tessema SK, Tebeje YK, Folarin O, Happi A, Lemey P, Suchard MA, Andersen KG, Sabeti P, Rambaut A, Ihekweazu C, Jide I, Adetifa I, Njoum R, Happi CT. Djuicy DD, et al. Among authors: andersen kg. medRxiv [Preprint]. 2024 Jun 19:2024.06.18.24309115. doi: 10.1101/2024.06.18.24309115. medRxiv. 2024. PMID: 38947021 Free PMC article. Preprint.
157 results