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Textbooks

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Papers/Articles

  1. SALIENT: Ultra-Fast FPGA-based Short Read Alignment

    Khaleghi B, Zhang T, Martion C, Armstrong G, Akel A, Curewitz K, Eno J, Eilert S, Knight R, Moshiri N, Rosing T (2022). "SALIENT: Ultra-Fast FPGA-based Short Read Alignment." International Conference on Field Programmable Technology (FPT) 2022.

  2. 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, Tzer Pin Lin R, Mat Isa MN, Muhammad Noor Y, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO (2022). "The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2." Science. 377(6609):960–966. doi:10.1126/science.abp8337

  3. 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, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacon M, Cheung W, Crescini 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, 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, Murphy Schafer A, Gurfield N, Stous S, Fielding-Miller R, Gaines T, Garfein R, Anderson CAM, Martin NK, Schooley RT, Austin B, Kingsmore SF, Lee W, Shah S, McDonald E, Zeller M, Fisch KM, Laurent LC, Yeo GW, Andersen KG, Knight R (2022). "Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission." Nature. 609:101–108. doi:10.1038/s41586-022-05049-6

  4. Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce

    Keehner J, Horton LE, Binkin NJ, Laurent LC, Pride D, Longhurst CA, Abeles SR, Torriani FJ, SEARCH Alliance (Aigner S, Andersen KG, Anderson C, Baer NA, Barber T, Belda-Ferre P, Betty M, Birmingham A, Castro-Martinez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner ER, Fisch K, Vargas LF, Gangavarapu K, Hakim A, Henson B, Hobbs C, Humphrey G, Jepsen K, Kapadia BK, Knight R, Lastrella AL, Laurent LC, Lawrence ES, Machnicki M, Marotz CA, Matteson NL, Maunder DJ, Moshiri N, Ngo TT, Nouri A, Ostrander TR, Plascencia A, Ruiz CA, Salido RA, Sathe S, Seaver P, Smoot EW, Tsai R, Wu MY, Xia B, Yeo GW, Zeller M) (2021). "Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce." The New England Journal of Medicine. 385:1330–1332. doi:10.1056/NEJMc2112981

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Conference Presentations

  1. FPGA-based acceleration of primer trimming

    Khaleghi B, Akel A, Curewitz K, Eno J, Eilert S, Moshiri N, Rosing T (2021). "FPGA-based acceleration of primer trimming." 28th International Dynamics & Evolution of Human Viruses. Talk.

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Preprints

  1. Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project

    Fielding-Miller RK, Karthikeyan S, Gaines T, Garfein RS, Salido RA, Cantu V, Kohn L, Wijaya FC, Flores M, Omaleki V, Majnoonian A, Martin NK, Austin D, Laurent LC, Gonzalez-Zuniga P, Nguyen M, Vo AV, Le TT, Duong D, Hassani A, Tweeten S, Jepsen K, Henson B, Hakim A, Birmingham A, Mark AM, Nasamran CA, Rosenthal SB, Moshiri N, Fisch KM, Humphrey G, Farmer S, Tubb H, Valles T, Morris J, Kang J, Khaleghi B, Young C, Akel AD, Eilert S, Eno J, Curewitz K, Rosing T, Knight R (2021). "Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project". medRxiv. doi:10.1101/2021.10.19.21265226

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