Ten Simple Rules for Reproducible Research in Jupyter Notebooks. - Adam Rule; Amanda Birmingham; Cristal Zuñiga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight 001; Niema Moshiri; Mai H. Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W. Rose (CoRR, 2018)

FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. - Niema Moshiri; Manon Ragonnet-Cronin; Joel O. Wertheim; Siavash Mirarab (Bioinform., 2019)

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. - Adam Rule; Amanda Birmingham; Cristal Zuñiga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight 001; Niema Moshiri; Mai H. Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W. Rose (PLoS Comput. Biol., 2019)

Mathematical Modeling of Viral Evolution and Epidemiology. - Niema Moshiri (2019)

GenieHD: Efficient DNA Pattern Matching Accelerator Using Hyperdimensional Computing. - Yeseong Kim; Mohsen Imani; Niema Moshiri; Tajana Rosing (DATE, 2020)

TreeSwift: A massively scalable Python tree package. - Niema Moshiri (SoftwareX, 2020)

Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing. - Minxuan Zhou; Lingxi Wu; Muzhou Li; Niema Moshiri; Kevin Skadron; Tajana Rosing (PACT, 2021)

MethylDrift: A Software Package for Calculating Age-related Epigenetic Drift in Human Tissues Using DNA Methylation Data. - McKenna Lewis; Niema Moshiri; Kit Curtius (AMIA, 2021)

FPGA Acceleration of Protein Back-Translation and Alignment. - Sahand Salamat; Jaeyoung Kang 001; Yeseong Kim; Mohsen Imani; Niema Moshiri; Tajana Rosing (DATE, 2021)

ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes. - Niema Moshiri (Bioinform., 2021)

SEPIA: simulation-based evaluation of prioritization algorithms. - Kimberly Almaraz; Tyler Jang; McKenna Lewis; Titan Ngo; Miranda Song; Niema Moshiri (BMC Medical Informatics Decis. Mak., 2021)

Ten simple rules for attending your first conference. - Elizabeth Leininger; Kelly Shaw; Niema Moshiri; Kelly Neiles; Getiria Onsongo; Anna M. Ritz (PLoS Comput. Biol., 2021)

FAST: FPGA-based Acceleration of Genomic Sequence Trimming. - Behnam Khaleghi; Tianqi Zhang; Niya Shao; Ameen Akel; Ken Curewitz; Justin Eno; Sean Eilert; Niema Moshiri; Tajana Rosing (BioCAS, 2022)

SALIENT: Ultra-Fast FPGA-based Short Read Alignment. - Behnam Khaleghi; Tianqi Zhang; Cameron Martino; George Armstrong; Ameen Akel; Ken Curewitz; Justin Eno; Sean Eilert; Rob Knight 001; Niema Moshiri; Tajana Rosing (FPT, 2022)

A scalable approach for detecting exam similarity in CS courses. - Niema Moshiri (J. Comput. Sci. Coll., 2022)

GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences. - Tianqi Zhang; Antonio González; Niema Moshiri; Rob Knight 001; Tajana Rosing (BioCAS, 2023)

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations. - Derek Jones; Jonathan E. Allen; Xiaohua Zhang; Behnam Khaleghi; Jaeyoung Kang 001; Weihong Xu; Niema Moshiri; Tajana Simunic Rosing (CoRR, 2023)

ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data. - Niema Moshiri (Bioinform., 2023)

RAPIDx: High-Performance ReRAM Processing In-Memory Accelerator for Sequence Alignment. - Weihong Xu; Saransh Gupta; Niema Moshiri; Tajana Simunic Rosing (IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2023)

RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing. - Sumukh Pinge; Weihong Xu; Wout Bittremieux; Niema Moshiri; Sang-Woo Jun; Tajana Rosing (BioCAS, 2024)

SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering. - Sumukh Pinge; Weihong Xu; Jaeyoung Kang 001; Tianqi Zhang; Niema Moshiri; Wout Bittremieux; Tajana Rosing (DATE, 2024)

ViralWasm: a client-side user-friendly web application suite for viral genomics. - Daniel Ji; Robert Aboukhalil; Niema Moshiri (Bioinform., 2024)

DRAM-Based Acceleration of Open Modification Search in Hyperdimensional Space. - Jaeyoung Kang 001; Weihong Xu; Wout Bittremieux; Niema Moshiri; Tajana Simunic Rosing (IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2024)