Niema Moshiri • UCSD Profiles (original) (raw)

  1. Epigenetic motifs distinguishing endogenous from exogenous retroviral integrants. J Virol. 2025 Oct 23; 99(10):e0077525. LaMere S, Xiong H, Wang W, LaMere B, Moshiri N. PMID: 41025794; PMCID: PMC12548410.
    View in: PubMed Mentions: Fields:
    Translation:HumansAnimalsCells
  2. Epigenetic motifs distinguishing endogenous from exogenous retroviral integrants. bioRxiv. 2025 Aug 14. LaMere S, Xiong H, Wang W, LaMere B, Moshiri N. PMID: 40832249; PMCID: PMC12363823.
    View in: PubMed Mentions:
  3. Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residences. EBioMedicine. 2025 Jun; 116:105729. Wertheim JO, Vasylyeva TI, Wood RJ, Cantrell K, Contreras SP, Feldheim A, Goyal R, Havens JL, Knight R, Laurent LC, Moshiri N, Neuhard R, Sathe S, Satterlund A, Scioscia A, Song AY, SEARCH Alliance, Schooley RT, Anderson CM, Martin NK. PMID: 40347833; PMCID: PMC12139431.
    View in: PubMed Mentions: Fields:
    Translation:HumansCells
  4. CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics. GigaByte. 2025; 2025:gigabyte152. Moshiri N. PMID: 40110034; PMCID: PMC11921128.
    View in: PubMed Mentions: 1
  5. Recently reported SARS-CoV-2 genomes suggested to be intermediate between the two early main lineages are instead likely derived. Virus Evol. 2025; 11(1):veaf008. Pekar JE, Moshiri N, Lemey P, Crits-Christoph A, Débarre F, Goldstein SA, Hensel Z, Rambaut A, Worobey M, Holmes EC, Wertheim JO. PMID: 40040925; PMCID: PMC11878783.
    View in: PubMed Mentions: 1
  6. Scalable Epidemic Simulation Using FAVITES-Lite. Methods Mol Biol. 2025; 2927:173-193. Moshiri N. PMID: 40455158.
    View in: PubMed Mentions: 1 Fields:
    Translation:HumansPHPublic Health
  7. HDBind: encoding of molecular structure with hyperdimensional binary representations. Sci Rep. 2024 Nov 23; 14(1):29025. Jones D, Zhang X, Bennion BJ, Pinge S, Xu W, Kang J, Khaleghi B, Moshiri N, Allen JE, Rosing TS. PMID: 39578580; PMCID: PMC11584749.
    View in: PubMed Mentions: 3 Fields:
  8. Hidden evolutionary constraints dictate the retention of coronavirus accessory genes. Curr Biol. 2024 Dec 16; 34(24):5685-5696.e3. Goldstein SA, Feeley TM, Babler KM, Hilbert ZA, Downhour DM, Moshiri N, Elde NC. PMID: 39566499; PMCID: PMC11652222.
    View in: PubMed Mentions: Fields:
    Translation:AnimalsCells
  9. Hidden evolutionary constraints dictate the retention of coronavirus accessory genes. bioRxiv. 2024 Oct 09. Goldstein SA, Feeley TM, Babler KM, Hilbert ZA, Downhour DM, Moshiri N, Elde NC. PMID: 37873270; PMCID: PMC10592793.
    View in: PubMed Mentions:
  10. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. Cell. 2024 Sep 19; 187(19):5468-5482.e11. 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. PMID: 39303692; PMCID: PMC11427129.
    View in: PubMed Mentions: 35 Fields:
    Translation:HumansAnimalsCellsPHPublic Health
  11. HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors. Bioinformatics. 2024 Jul 16. Xu W, Hsu PK, Moshiri N, Yu S, Rosing T. PMID: 39012512; PMCID: PMC11281827.
    View in: PubMed Mentions: 3 Fields:
  12. Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting. Clin Infect Dis. 2024 05 15; 78(5):1204-1213. 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. PMID: 38227643; PMCID: PMC11093679.
    View in: PubMed Mentions: 2 Fields:
    Translation:HumansCellsPHPublic Health
  13. ViralWasm: a client-side user-friendly web application suite for viral genomics. Bioinformatics. 2024 01 02; 40(1). Ji D, Aboukhalil R, Moshiri N. PMID: 38200583; PMCID: PMC10809900.
    View in: PubMed Mentions: 4 Fields:
    Translation:Humans
  14. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell. 2023 12 21; 186(26):5690-5704.e20. 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-Alavez 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, King AJ, 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. PMID: 38101407; PMCID: PMC10795731.
    View in: PubMed Mentions: 5 Fields:
    Translation:HumansCellsPHPublic Health
  15. Leveraging social networks for identification of people with HIV who are virally unsuppressed. AIDS. 2024 02 01; 38(2):245-254. Cummins B, Johnson K, Schneider JA, Del Vecchio N, Moshiri N, Wertheim JO, Goyal R, Skaathun B. PMID: 37890471; PMCID: PMC10843229.
    View in: PubMed Mentions: Fields:
    Translation:HumansPHPublic Health
  16. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. bioRxiv. 2023 Sep 14. 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, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. PMID: 37745602; PMCID: PMC10515900.
    View in: PubMed Mentions: 1
  17. Accelerating open modification spectral library searching on tensor core in high-dimensional space. Bioinformatics. 2023 07 01; 39(7). Kang J, Xu W, Bittremieux W, Moshiri N, Rosing T. PMID: 37369033; PMCID: PMC10323168.
    View in: PubMed Mentions: 3 Fields:
    Translation:Cells
  18. HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space. J Proteome Res. 2023 06 02; 22(6):1639-1648. Xu W, Kang J, Bittremieux W, Moshiri N, Rosing T. PMID: 37166120; PMCID: PMC10243109.
    View in: PubMed Mentions: 5 Fields:
  19. ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data. Bioinformatics. 2023 05 04; 39(5). Moshiri N. PMID: 37171896; PMCID: PMC10212278.
    View in: PubMed Mentions: 12 Fields:
  20. Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schools. Lancet Reg Health Am. 2023 Mar; 19:100449. 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. PMID: 36844610; PMCID: PMC9939935.
    View in: PubMed Mentions: 23
  21. Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project. medRxiv. 2023 Jan 25. 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. PMID: 34704096; PMCID: PMC8547528.
    View in: PubMed Mentions: 1
  22. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science. 2022 08 26; 377(6609):960-966. 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. PMID: 35881005; PMCID: PMC9348752.
  23. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature. 2022 09; 609(7925):101-108. 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, 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. PMID: 35798029; PMCID: PMC9433318.
    View in: PubMed Mentions: 211 Fields:
    Translation:HumansCellsPHPublic Health
  24. Accelerators for Classical Molecular Dynamics Simulations of Biomolecules. J Chem Theory Comput. 2022 Jul 12; 18(7):4047-4069. Jones D, Allen JE, Yang Y, Drew Bennett WF, Gokhale M, Moshiri N, Rosing TS. PMID: 35710099; PMCID: PMC9281402.
    View in: PubMed Mentions: 23 Fields:
    Translation:Cells
  25. An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology. Viruses. 2022 04 08; 14(4). Young C, Meng S, Moshiri N. PMID: 35458504; PMCID: PMC9032411.
    View in: PubMed Mentions: 3 Fields:
    Translation:Humans
  26. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv. 2022 Apr 04. 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, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. PMID: 35411350; PMCID: PMC8996633.
    View in: PubMed Mentions:
  27. The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction. Sci Rep. 2022 03 24; 12(1):5077. Moshiri N, Fisch KM, Birmingham A, DeHoff P, Yeo GW, Jepsen K, Laurent LC, Knight R. PMID: 35332213; PMCID: PMC8943356.
    View in: PubMed Mentions: 8 Fields:
    Translation:HumansCellsPHPublic Health
  28. Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases. mSystems. 2022 04 26; 7(2):e0137821. Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R. PMID: 35293792; PMCID: PMC9040843.
    View in: PubMed Mentions: 11 Fields:
  29. NiemaGraphGen: A memory-efficient global-scale contact network simulation toolkit. GigaByte. 2022; 2022:gigabyte37. Moshiri N. PMID: 36968795; PMCID: PMC10038133.
    View in: PubMed Mentions: 2
  30. Ten simple rules for attending your first conference. PLoS Comput Biol. 2021 07; 17(7):e1009133. Leininger E, Shaw K, Moshiri N, Neiles K, Onsongo G, Ritz A. PMID: 34264934; PMCID: PMC8282073.
    View in: PubMed Mentions: Fields:
    Translation:Humans
  31. SEPIA: simulation-based evaluation of prioritization algorithms. BMC Med Inform Decis Mak. 2021 06 03; 21(1):177. Almaraz K, Jang T, Lewis M, Ngo T, Song M, Moshiri N. PMID: 34082739; PMCID: PMC8173910.
    View in: PubMed Mentions: 1 Fields:
    Translation:HumansAnimals
  32. ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes. Bioinformatics. 2021 05 05; 37(5):714-716. Moshiri N. PMID: 32814953.
    View in: PubMed Mentions: 50 Fields:
  33. HIV Care Prioritization Using Phylogenetic Branch Length. J Acquir Immune Defic Syndr. 2021 04 15; 86(5):626-637. Moshiri N, Smith DM, Mirarab S. PMID: 33394616; PMCID: PMC7933099.
    View in: PubMed Mentions: 7 Fields:
    Translation:HumansCells
  34. Timing the SARS-CoV-2 index case in Hubei province. Science. 2021 04 23; 372(6540):412-417. Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. PMID: 33737402; PMCID: PMC8139421.
    View in: PubMed Mentions: 86 Fields:
    Translation:HumansAnimalsCellsPHPublic Health
  35. Timing the SARS-CoV-2 Index Case in Hubei Province. bioRxiv. 2020 Nov 24. Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. PMID: 33269353; PMCID: PMC7709179.
    View in: PubMed Mentions:
  36. TreeCluster: Clustering biological sequences using phylogenetic trees. PLoS One. 2019; 14(8):e0221068. Balaban M, Moshiri N, Mai U, Jia X, Mirarab S. PMID: 31437182; PMCID: PMC6705769.
    View in: PubMed Mentions: 92 Fields:
    Translation:HumansCells
  37. Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLoS Comput Biol. 2019 07; 15(7):e1007007. Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, Knight R, Moshiri N, Nguyen MH, Rosenthal SB, Pérez F, Rose PW. PMID: 31344036; PMCID: PMC6657818.
    View in: PubMed Mentions: 52 Fields:
    Translation:Humans
  38. FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinformatics. 2019 06 01; 35(11):1852-1861. Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. PMID: 30395173; PMCID: PMC6931354.
    View in: PubMed Mentions: 33 Fields:
    Translation:Humans
  39. A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition. Syst Biol. 2018 May 01; 67(3):475-489. Moshiri N, Mirarab S. PMID: 29165679; PMCID: PMC5920319.
    View in: PubMed Mentions: 4 Fields:
    Translation:HumansCells

Start with: newest oldestInclude: line numbers double spacing all authors publication IDs