Niema Moshiri

Niema Moshiri

Associate Teaching Professor
Computer Science, UCSD

Research

Papers/Articles – Conference Presentations – Preprints/Reports

You can find a complete list of my collaborators in this Google Sheet.

Papers/Articles

  1. Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residences

    Wertheim JO, Vasylyeva TI, Wood RJ, Cantrell K, Piña Contreras S, Feldheim A, Goyal R, Havens JL, Knight R, Laurent LC, Moshiri N, Neuhard R, Sathe S, Satterlund A, Scioscia A, Song AY, Schooley RT, Anderson CM, Martin NK (2025). "Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residences." eBioMedicine. 116:105729. doi:10.1016/j.ebiom.2025.105729

  2. 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 (2024). "Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic." Cell. 187(19):5468–5482.e11. doi:10.1016/j.cell.2024.08.010

  3. Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 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, Aigner S, Andersen KG, Anderson C, Baer NA, Barber T, Bauk M, Beck JN, Belda-Ferre P, Betty M, Birmingham A, Castro-Martinez A, Cheung W, Fisch KM, Gangavarapu K, Gargano I, Hakim A, Harsono S, Henson B, Hobbs C, Holmes J, Jepsen K, Kurzban E, Marotz CA, Matteson NL, Moshiri N, Ngo TT, Ostrander TR, Perkins S, Plascencia A, Rivera An, Rivera Ar, Salido RA, Seaver P, Schwab M, Veder A, Zeller M, Lucas A, Pride D, Sathe S, Tran AR, Vasylyeva TI, Yeo G, Knight R, Wertheim JO, Torriani FJ (2024). "Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting." Clinical Infectious Diseases. ciad738. doi:10.1093/cid/ciad738

  4. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics

    Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alvarez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M (2023). "Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics." Cell. 186(26):5690–5704.e20. doi:10.1016/j.cell.2023.11.024

  5. Safer at School Early Alert: An observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools

    Fielding-Miller RK, 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 (2023). "Safer at School Early Alert: An observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools". The Lancet Regional Health - Americas. 19:100449. doi:10.1016/j.lana.2023.100449

  6. 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

  7. 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, 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, 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 R, 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, Murphy Schafer A, 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, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, 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

  8. 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/Reports

  1. Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control

    Crits-Christoph A, Gangavarapu K, Pekar JE, Moshiri N, Singh R, Levy JI, Goldstein SA, Suchard MA, Popescu S, Robertson DL, Lemey P, Wertheim JO, Garry RF, Rasmussen AL, Andersen KG, Holmes EC, Rambaut A, Worobey M, Débarre F (2023). "Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control." Zenodo. doi:10.5281/zenodo.7754298

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