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Page 1
Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.
Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P. Dellicour S, et al. Among authors: matteson nl. Nat Commun. 2020 Nov 6;11(1):5620. doi: 10.1038/s41467-020-19122-z. Nat Commun. 2020. PMID: 33159066 Free PMC article.
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG. Grubaugh ND, et al. Among authors: matteson nl. Genome Biol. 2019 Jan 8;20(1):8. doi: 10.1186/s13059-018-1618-7. Genome Biol. 2019. PMID: 30621750 Free PMC article.
Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic.
Grubaugh ND, Saraf S, Gangavarapu K, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW 4th, Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH; GeoSentinel Surveillance Network; Gardner LM, Perkins TA, Baele G, Khan K, Morrison A, Isern S, Michael SF, Andersen KG. Grubaugh ND, et al. Among authors: matteson nl. Cell. 2019 Aug 22;178(5):1057-1071.e11. doi: 10.1016/j.cell.2019.07.018. Cell. 2019. PMID: 31442400 Free PMC article.
Emergence of an early SARS-CoV-2 epidemic in the United States.
Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G Jr, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh N, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Zeller M, et al. Among authors: matteson nl. medRxiv [Preprint]. 2021 Feb 8:2021.02.05.21251235. doi: 10.1101/2021.02.05.21251235. medRxiv. 2021. PMID: 33564781 Free PMC article. Updated. Preprint.
Emergence of an early SARS-CoV-2 epidemic in the United States.
Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G Jr, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Zeller M, et al. Among authors: matteson nl. Cell. 2021 Sep 16;184(19):4939-4952.e15. doi: 10.1016/j.cell.2021.07.030. Epub 2021 Jul 27. Cell. 2021. PMID: 34508652 Free PMC article.
Wastewater sequencing reveals 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, Schiabor Barrett KM, 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, Sha… See abstract for full author list ➔ Karthikeyan S, et al. Among authors: matteson nl. Nature. 2022 Sep;609(7925):101-108. doi: 10.1038/s41586-022-05049-6. Epub 2022 Jul 7. Nature. 2022. PMID: 35798029 Free PMC article.
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.
Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching Zi Yan K, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO. Pekar JE, et al. Among authors: matteson nl. Science. 2022 Aug 26;377(6609):960-966. doi: 10.1126/science.abp8337. Epub 2022 Jul 26. Science. 2022. PMID: 35881005 Free PMC article.
Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions.
Parker E, Anderson C, Zeller M, Tibi A, Havens JL, Laroche G, Benlarbi M, Ariana A, Robles-Sikisaka R, Latif AA, Watts A, Awidi A, Jaradat SA, Gangavarapu K, Ramesh K, Kurzban E, Matteson NL, Han AX, Hughes LD, McGraw M, Spencer E, Nicholson L, Khan K, Suchard MA, Wertheim JO, Wohl S, Côté M, Abdelnour A, Andersen KG, Abu-Dayyeh I. Parker E, et al. Among authors: matteson nl. Nat Commun. 2022 Aug 15;13(1):4784. doi: 10.1038/s41467-022-32536-1. Nat Commun. 2022. PMID: 35970983 Free PMC article.
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.
Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S; GISAID Core and Curation Team; Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Gangavarapu K, et al. Among authors: matteson nl. Nat Methods. 2023 Apr;20(4):512-522. doi: 10.1038/s41592-023-01769-3. Epub 2023 Feb 23. Nat Methods. 2023. PMID: 36823332 Free PMC article.
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.
17 results