Niema Moshiri

According to our database, Niema Moshiri authored at least 22 papers between 2018 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

DRAM-Based Acceleration of Open Modification Search in Hyperdimensional Space.

Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Simunic Rosing

IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., September, 2024

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

Daniel Ji, Robert Aboukhalil, Niema Moshiri

Bioinform., January, 2024

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

Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo Jun, Tajana Rosing

CoRR, 2024

SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering.

Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing

Proceedings of the Design, Automation & Test in Europe Conference & Exhibition, 2024

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., October, 2023

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

Niema Moshiri

Bioinform., May, 2023

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations.

Derek Jones, Jonathan E. Allen, Xiaohua Zhang, Behnam Khaleghi, Jaeyoung Kang, Weihong Xu, Niema Moshiri, Tajana Simunic Rosing

CoRR, 2023

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

Tianqi Zhang, Antonio González, Niema Moshiri, Rob Knight, Tajana Rosing

Proceedings of the IEEE Biomedical Circuits and Systems Conference, 2023

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, Niema Moshiri, Tajana Rosing

Proceedings of the International Conference on Field-Programmable Technology, 2022

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

Proceedings of the IEEE Biomedical Circuits and Systems Conference, 2022

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

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

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

Niema Moshiri

Bioinform., 2021

FPGA Acceleration of Protein Back-Translation and Alignment.

Sahand Salamat, Jaeyoung Kang, Yeseong Kim, Mohsen Imani, Niema Moshiri, Tajana Rosing

Proceedings of the Design, Automation & Test in Europe Conference & Exhibition, 2021

MethylDrift: A Software Package for Calculating Age-related Epigenetic Drift in Human Tissues Using DNA Methylation Data.

McKenna Lewis, Niema Moshiri, Kit Curtius

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

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

Minxuan Zhou, Lingxi Wu, Muzhou Li, Niema Moshiri, Kevin Skadron, Tajana Rosing

Proceedings of the 30th International Conference on Parallel Architectures and Compilation Techniques, 2021

2020

TreeSwift: A massively scalable Python tree package.

Niema Moshiri

SoftwareX, 2020

GenieHD: Efficient DNA Pattern Matching Accelerator Using Hyperdimensional Computing.

Yeseong Kim, Mohsen Imani, Niema Moshiri, Tajana Rosing

Proceedings of the 2020 Design, Automation & Test in Europe Conference & Exhibition, 2020

2019

Mathematical Modeling of Viral Evolution and Epidemiology.

Niema Moshiri

PhD thesis, 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, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose

PLoS Comput. Biol., 2019

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

Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab

Bioinform., 2019

2018

Ten Simple Rules for Reproducible Research in Jupyter Notebooks.

Adam Rule, Amanda Birmingham, Cristal Zuñiga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose

CoRR, 2018