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Author Details

Niema Moshiri
Bonita Vista High School, University of California San Diego, University of California, San Diego
0000-0003-2209-8128
2018
25
9
PMIDPaper TitleJournal TitlePublished Year
37873270Hidden evolutionary constraints dictate the retention of coronavirus accessory genes.bioRxiv2024
37890471Leveraging social networks for identification of people with HIV who are virally unsuppressed.AIDS2024
37166120HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space.J Proteome Res2023
37745602Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.bioRxiv2023
37171896ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data.Bioinformatics2023
37369033Accelerating open modification spectral library searching on tensor core in high-dimensional space.Bioinformatics2023
35293792Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases.mSystems2022
35710099Accelerators for Classical Molecular Dynamics Simulations of Biomolecules.J Chem Theory Comput2022
35411350Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.medRxiv2022
35798029Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission.Nature2022
35458504An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology.Viruses2022
36968795NiemaGraphGen: A memory-efficient global-scale contact network simulation toolkit.GigaByte2022
35881005The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.Science2022
35332213The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.Sci Rep2022
32814953ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes.Bioinformatics2021
33737402Timing the SARS-CoV-2 index case in Hubei province.Science2021
34264934Ten simple rules for attending your first conference.PLoS Comput Biol2021
34082739SEPIA: simulation-based evaluation of prioritization algorithms.BMC Med Inform Decis Mak2021
33394616HIV Care Prioritization Using Phylogenetic Branch Length.J Acquir Immune Defic Syndr2021
33269353Timing the SARS-CoV-2 Index Case in Hubei Province.bioRxiv2020
35903557TreeSwift: A massively scalable Python tree package.SoftwareX2020
30395173FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences.Bioinformatics2019
31437182TreeCluster: Clustering biological sequences using phylogenetic trees.PLoS One2019
31344036Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.PLoS Comput Biol2019
29165679A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition.Syst Biol2018
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Collaborators

Joel O Wertheim
University of California
Co-authored papers 6
Michael Worobey
University of Arizona
Co-authored papers 4
Siavash Mirarab
University of California San Diego
Co-authored papers 4
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Center for Computational Biology & Bioinformatics , University of California
Co-authored papers 4
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Co-authored papers 4
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University of California San Diego
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Co-authored papers 3
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The Scripps Research Institute
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University of California San Diego
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Alexandre Bolze
The Rockefeller University
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Clarisse Marotz
University of California San Diego
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Ian McHardy
University of California, Davis Center for Valley Fever
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Adam Buckley
Imperial College London Diabetes Centre
Co-authored papers 2
David T Pride
University of California San Diego
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Stephen F Kingsmore
Rady Children's Institute for Genomic Medicine
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Angela L Scioscia
University of California San Diego
Co-authored papers 2
David Dimmock
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Alison Sanders
University of California San Diego
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Steven L Gonias
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Smruthi Karthikeyan
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Release 1.2