Research

Papers/Articles – Conference Presentations – Preprints/Reports

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

Papers/Articles

Scalable Epidemic Simulation using FAVITES-Lite

Moshiri N (2024). "Scalable Epidemic Simulation using FAVITES-Lite." Computational Virology (Methods in Molecular Biology). Book Chapter. In Press.

Hidden evolutionary constraints dictate the retention of coronavirus accessory genes

Goldstein SA, Feeley TM, Babler KM, Hilbert ZA, Downhour DM, Moshiri N, Elde NC (2024). "Hidden evolutionary constraints dictate the retention of coronavirus accessory genes." Current Biology. In Press. doi:10.1016/j.cub.2024.10.050

HDBind: Encoding of Molecular Structure with Hyperdimensional Binary Representations

Jones D, Zhang X, Bennion BJ, Pinge S, Xu W, Kang J, Khaleghi B, Moshiri N, Allen JE, Rosing TS (2024). "HDBind: Encoding of Molecular Structure with Hyperdimensional Binary Representations." Scientific Reports. 14:29025. doi:10.1038/s41598-024-80009-w

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

HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors

Xu W, Hsu PK, Moshiri N, Yu S, Rosing T (2024). "HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors." Bioinformatics. 40(7):btae452. doi:10.1093/bioinformatics/btae452

SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering

Pinge S, Xu W, Kang J, Zhang T, Moshiri N, Bittremieux W, Rosing T (2024). "SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering." IEEE/ACM Design Automation and Test in Europe Conference (DATE) 2024. doi:10.23919/DATE58400.2024.10546776

DRAM-based Acceleration of Open Modification Search for Mass Spectrometry-based Proteomics

Kang J, Xu W, Bittremieux W, Moshiri N, Rosing T (2024). "DRAM-based Acceleration of Open Modification Search for Mass Spectrometry-based Proteomics." IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 43(9):2592–2605. doi:10.1109/TCAD.2024.3382842

Leveraging social networks for identification of people living with HIV who are virally unsuppressed

Cummins B, Johnson K, Schneider JA, Del Vecchio N, Moshiri N, Wertheim JO, Goyal R, Skaathun B (2024). "Leveraging social networks for identification of people living with HIV who are virally unsuppressed." AIDS. 38(2):245–254. doi:10.1097/QAD.0000000000003767

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

ViralWasm: a client-side user-friendly web application suite for viral genomics

Ji D, Aboukhalil R, Moshiri N (2024). "ViralWasm: a client-side user-friendly web application suite for viral genomics." Bioinformatics. 40(1):btae018. doi:10.1093/bioinformatics/btae018

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

GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences

Zhang T, González A, DeReus J, Armstrong G, Shaffer J, Sfigoli I, McDonald D, Moshiri N, Knight R, Rosing T (2023). "GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences." IEEE Biomedical Circuits and Systems Conference (BioCAS) 2023. doi:10.1109/BioCAS58349.2023.10388531

Accelerating Open Modification Spectral Library Searching on Tensor Core in Hyperdimensional Space

Kang J, Xu W, Bittremieux W, Moshiri N, Rosing T (2023). "Accelerating Open Modification Spectral Library Searching on Tensor Core in Hyperdimensional Space." Bioinformatics. 39(7):btad404. doi:10.1093/bioinformatics/btad404

ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data

Moshiri N (2023). "ViralConsensus: A fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data." Bioinformatics. 39(5):btad317. doi:10.1093/bioinformatics/btad317

HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space

Xu W, Kang J, Bittremieux W, Moshiri N, Rosing T (2023). "HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space." Journal of Proteome Research. 22(6):1639–1648. doi:10.1021/acs.jproteome.2c00612

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

RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment

Xu W, Gupta S, Moshiri N, Rosing T (2023). "RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment." IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. 42(10):3275–3288. doi:10.1109/TCAD.2023.3239537

SALIENT: Ultra-Fast FPGA-based Short Read Alignment

Khaleghi B, Zhang T, Martino 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. doi:10.1109/ICFPT56656.2022.9974548

FAST: FPGA-based Acceleration of Genomic Sequence Trimming

Khaleghi B, Zhang T, Shao N, Akel A, Curewitz K, Eno J, Eilert S, Moshiri N, Rosing T (2022). "FAST: FPGA-based Acceleration of Genomic Sequence Trimming." IEEE Biomedical Circuits and Systems Conference (BioCAS) 2022. doi:10.1109/BioCAS54905.2022.9948621

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

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

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

Jones D, Allen J, Yang Y, Bennett WF, Gokhale M, Moshiri N, Rosing T (2022). "Accelerators for Classical Molecular Dynamics Simulations of Biomolecules." Journal of Chemical Theory and Computation. 18(7):4047–4069. doi:10.1021/acs.jctc.1c01214

A scalable approach for detecting exam similarity in CS courses

Moshiri N (2022). "A scalable approach for detecting exam similarity in CS courses." Journal of Computing Sciences in Colleges. 37(10):8–16. doi:10.5555/3533760.3533761

An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology

Young C, Meng S, Moshiri N (2022). "An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology." Viruses. 14(4):774. doi:10.3390/v14040774

The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction

Moshiri N, Fisch KM, Birmingham A, DeHoff P, Yeo GW, Jepsen K, Laurent LC, Knight R (2022). "The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction." Scientific Reports. 12:5077. doi:10.1038/s41598-022-09035-w

Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases

Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, Dereus J, Zhu Q, Roush D, McDonald D, Gonzalez A, Shaffer J, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford A, Moshiri N, Rosing T, Knight R (2022). "Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases." mSystems. 7(2):e01378-21. doi:10.1128/msystems.01378-21

NiemaGraphGen: A memory-efficient global-scale contact network simulation toolkit

Moshiri N (2022). "NiemaGraphGen: A memory-efficient global-scale contact network simulation toolkit." Gigabyte. doi:10.46471/gigabyte.37

FPGA Acceleration of Pairwise Distance Calculation for Viral Transmission Clustering

Salamat S, Moshiri N, Rosing T (2021). "FPGA Acceleration of Pairwise Distance Calculation for Viral Transmission Clustering." IEEE Biomedical Circuits and Systems Conference (BioCAS) 2021. PDF.

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

Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing

Zhou M, Wu L, Li M, Moshiri N, Skadron K, Rosing T (2021). "Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing." International Conference on Parallel Architectures and Compilation Techniques (PACT) 2021. doi:10.1109/PACT52795.2021.00022

Ten simple rules for attending your first conference

Leininger E, Shaw K, Moshiri N, Neiles K, Onsongo G, Ritz A (2021). "Ten simple rules for attending your first conference." PLOS Computational Biology. 17(7):e1009133. doi:10.1371/journal.pcbi.1009133

SEPIA: simulation-based evaluation of prioritization algorithms

Almaraz K, Jang T, Lewis M, Ngo T, Song M, Moshiri N (2021). "SEPIA: simulation-based evaluation of prioritization algorithms." BMC Medical Informatics and Decision Making. 21:177. doi:10.1186/s12911-021-01536-4

Timing the SARS-CoV-2 index case in Hubei province

Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO (2021). "Timing the SARS-CoV-2 index case in Hubei province." Science. 372(6540):412–417. doi:10.1126/science.abf8003

HIV Care Prioritization Using Phylogenetic Branch Length

Moshiri N, Smith DM, Mirarab S (2021). "HIV Care Prioritization Using Phylogenetic Branch Length." Journal of Acquired Immune Deficiency Syndromes. 86(5):626–637. doi:10.1097/QAI.0000000000002612

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Moshiri N (2021). "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." Bioinformatics. 37(5):714–716. doi:10.1093/bioinformatics/btaa743

FPGA Acceleration of Protein Back-Translation and Alignment

Salamat S, Kang J, Kim Y, Imani M, Moshiri N, Rosing T (2021). "FPGA Acceleration of Protein Back-Translation and Alignment." IEEE/ACM Design Automation and Test in Europe Conference (DATE) 2021. doi:10.23919/DATE51398.2021.9474103

GenieHD: Efficient DNA Pattern Matching Accelerator Using Hyperdimensional Computing

Kim Y, Imani M, Moshiri N, Rosing T (2020). "GenieHD: Efficient DNA Pattern Matching Accelerator Using Hyperdimensional Computing." IEEE/ACM Design Automation and Test in Europe Conference (DATE) 2020. doi:10.23919/DATE48585.2020.9116397

TreeSwift: A massively scalable Python tree package

Moshiri N (2020). "TreeSwift: A massively scalable Python tree package." SoftwareX. 11:100436. doi:10.1016/j.softx.2020.100436

TreeCluster: Clustering biological sequences using phylogenetic trees

Balaban M, Moshiri N, Mai U, Jia X, Mirarab S (2019). "TreeCluster: Clustering biological sequences using phylogenetic trees." PLoS ONE. 14(8):e0221068. doi:10.1371/journal.pone.0221068

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks

Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, Knight R, Moshiri N, Nguyen M, Rosenthal SB, Perez F, Rose P (2019). "Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks." PLoS Computational Biology. 15(7):e1007007. doi:10.1371/journal.pcbi.1007007

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences

Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S (2019). "FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences." Bioinformatics. 35(11):1852–1861 doi:10.1093/bioinformatics/bty921

A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition

Moshiri N, Mirarab S (2018). "A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition." Systematic Biology. 67(3):475–489. doi:10.1093/sysbio/syx088

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Conference Presentations

Hidden evolutionary constraints dictate the retention of coronavirus accessory genes

Goldstein S, Feeley T, Babler K, Hilbert Z, Downhour D, Moshiri N, Elde N (2024). "Hidden evolutionary constraints dictate the retention of coronavirus accessory genes." 31st International Dynamics & Evolution of Human Viruses. Poster.

ViralWasm: a client-side user-friendly web application suite for viral genomics

Ji D, Aboukhalil R, Moshiri N (2024). "ViralWasm: a client-side user-friendly web application suite for viral genomics." Workshop on Emerging Computer Systems Challenges and Applications in Biomedicine (BioSys) 2024. Talk.

Hyflex Course Design: Student Experiences of Equity-centered Technology Enhanced Curriculum

Hadjipieris P, Moshiri N (2023). "Hyflex Course Design: Student Experiences of Equity-centered Technology Enhanced Curriculum." Professional and Organizational Development (POD) 2023. Talk.

Leveraging social networks for identification of people living with HIV and high transmission potential

Cummins B, Johnson K, Schneider JA, Del Vecchio N, Moshiri N, Wertheim JO, Goyal R, Skaathun B (2023). "Leveraging social networks for identification of people living with HIV and high transmission potential." International AIDS Society (IAS) 2023. Poster.

Simulacres et Simulation: Using GAMA to debug a real-world genetic-epidemiology outbreak simulator

Mkandawire W, Butler K, Varilly P, Moshiri N, Colubri A (2022). "Simulacres et Simulation: Using GAMA to debug a real-world genetic-epidemiology outbreak simulator." GAMA Days 2022. Talk.

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Moshiri N (2022). "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." San Diego Epidemiology Research Exchange Conference 2022. Talk.

A scalable approach for detecting exam similarity in CS courses

Moshiri N (2022). "A scalable approach for detecting exam similarity in CS courses." Consortium for Computing Sciences in Colleges, Southwest (CCSC-SW) 2022. Talk.

FPGA Acceleration of Pairwise Distance Calculation for Viral Transmission Clustering

Salamat S, Moshiri N, Rosing T (2021). "FPGA Acceleration of Pairwise Distance Calculation for Viral Transmission Clustering." 28th International Dynamics & Evolution of Human Viruses. Poster.

An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology

Young C, Meng S, Moshiri N (2021). "An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology." 28th International Dynamics & Evolution of Human Viruses. Poster.

Optimizing high-performance cloud computing to enable real-time high-throughput SARS-CoV-2 whole genome sequence analysis

Moshiri N (2021). "Optimizing high-performance cloud computing to enable real-time high-throughput SARS-CoV-2 whole genome sequence analysis." 28th International Dynamics & Evolution of Human Viruses. Poster.

A GPU-Powered Phylogenetic Analysis for Large-scale Genomic Sequences

Kang J, Young C, Morris J, Akel A, Eilert S, Eno J, Curewitz K, Moshiri N, Rosing T (2021). "A GPU-Powered Phylogenetic Analysis for Large-scale Genomic Sequences." 28th International Dynamics & Evolution of Human Viruses. Poster.

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.

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Moshiri N (2020). "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." Cold Spring Harbor Laboratory (CSHL) Biological Data Science Meeting 2020. Poster.

RAPIDx: A ReRAM Processing in-Memory Architecture for DNA Short Read Alignment

Gupta S, Imani M, Khaleghi B, Moshiri N, Rosing T (2020). "RAPIDx: A ReRAM Processing in-Memory Architecture for DNA Short Read Alignment." American Society of Human Genetics (ASHG) 2020. Poster.

FPGA Acceleration of Protein Back-Translation and Alignment

Salamat S, Kang J, Kim Y, Imani M, Moshiri N, Rosing T (2020). "FPGA Acceleration of Protein Back-Translation and Alignment." American Society of Human Genetics (ASHG) 2020. Poster.

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Moshiri N (2020). "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." COVID-19 Dynamics & Evolution. Talk.

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Moshiri N (2020). "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." Computing Research Association (CRA) Virtual Conference 2020. Talk.

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes

Moshiri N (2020). "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." Bioinformatics Community Conference (BCC) 2020. Poster.

SEPIA: simulation-based evaluation of prioritization algorithms

Almaraz K, Jang T, Lewis M, Ngo T, Song M, Moshiri N (2020). "SEPIA: simulation-based evaluation of prioritization algorithms." 27th International HIV Dynamics & Evolution. Talk.

Automated plagiarism detection in programming courses: a graph theoretical approach using MOSS

Lewis M, Moshiri N (2020). "Automated plagiarism detection in programming courses: a graph theoretical approach using MOSS." Consortium for Computing Sciences in Colleges, Southwest (CCSC-SW) 2020. Poster.

What to do after AP CS? A case study on short technical modules for post-AP-exam high school students

Mansuri S, Zhou H, Battu H, Fong A, Ho T, Xiao E, Moshiri N (2020). "What to do after AP CS? A case study on short technical modules for post-AP-exam high school students." Consortium for Computing Sciences in Colleges, Southwest (CCSC-SW) 2020. Poster.

Flipping computational courses using Massive Adaptive Interactive Texts

Moshiri N, Pevzner P (2018). "Flipping computational courses using Massive Adaptive Interactive Texts." Cold Spring Harbor Laboratory (CSHL) Biological Data Science Meeting 2018. Talk.

Open Computational Problems in HIV Epidemiology

Moshiri N (2018). "Open Computational Problems in HIV Epidemiology." Workshop on the Future of Algorithms in Biology (FAB) 2018. Talk.

Challenges and Guidelines for Reproducible Research with Jupyter Notebook

Huang SC, Moshiri N, Reich M, Rose P (2018). "Challenges and Guidelines for Reproducible Research with Jupyter Notebook." JupyterCon 2018. Poster.

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences

Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S (2018). "FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences." International AIDS Conference 2018. Poster.

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences

Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S (2018). "FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences." Society for Molecular Biology and Evolution (SMBE) 2018. Poster.

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences

Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S (2018). "FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences." 25th International HIV Dynamics & Evolution. Talk.

Using Online Classes to Flip Bioinformatics Classrooms

Moshiri N (2017). "Using Online Classes to Flip Bioinformatics Classrooms." International Society for Computational Biology (ISMB) 2017. Talk.

A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition

Moshiri N, Mirarab S (2017). "A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition." Society for Molecular Biology and Evolution (SMBE) 2017. Poster.

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Preprints/Reports

RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing

Pinge S, Xu W, Bittremieux W, Moshiri N, Jun S, Rosing T (2024). "RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing." arXiv:2409.13361

CompactTree: A lightweight header-only C++ library for ultra-large phylogenetics

Moshiri N (2024). "CompactTree: A lightweight header-only C++ library for ultra-large phylogenetics." bioRxiv. doi:10.1101/2024.07.15.603593

Improved user-friendliness in the design and analysis of FAVITES-Lite simulations

Stadler K, Phillips K, Moshiri N (2024). "Improved user-friendliness in the design and analysis of FAVITES-Lite simulations." medRxiv. doi:10.1101/2024.06.10.24308702

Single-linkage molecular clustering of viral pathogens

Soto Miranda M, Narváez Romo R, Moshiri N (2023). "Single-linkage molecular clustering of viral pathogens." bioRxiv. doi:10.1101/2023.08.03.551813

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

ViReaDB: A user-friendly database for compactly storing viral sequence data and rapidly computing consensus genome sequences

Moshiri N (2022). "ViReaDB: A user-friendly database for compactly storing viral sequence data and rapidly computing consensus genome sequences." bioRxiv. doi:10.1101/2022.10.21.513318

Niema Moshiri

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