Niema Moshiri

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 22

Top Topics

Software Package

Sequence Alignment

Genome Sequences

Top Venues

Publications

Daniel Ji, Robert Aboukhalil, Niema Moshiri
ViralWasm: a client-side user-friendly web application suite for viral genomics. Bioinform. 40 (1) (2024)
Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing
SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering. DATE (2024)
Derek Jones, Jonathan E. Allen, Xiaohua Zhang, Behnam Khaleghi, Jaeyoung Kang, Weihong Xu, Niema Moshiri, Tajana Simunic Rosing
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations. CoRR (2023)
Niema Moshiri
ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data. Bioinform. 39 (5) (2023)
Tianqi Zhang, Antonio González, Niema Moshiri, Rob Knight, Tajana Rosing
GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences. BioCAS (2023)
Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing
SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering. CoRR (2023)
Weihong Xu, Saransh Gupta, Niema Moshiri, Tajana Simunic Rosing
RAPIDx: High-Performance ReRAM Processing In-Memory Accelerator for Sequence Alignment. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 42 (10) (2023)
Weihong Xu, Saransh Gupta, Niema Moshiri, Tajana Rosing
RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment. CoRR (2022)
Behnam Khaleghi, Tianqi Zhang, Cameron Martino, George Armstrong, Ameen Akel, Ken Curewitz, Justin Eno, Sean Eilert, Rob Knight, Niema Moshiri, Tajana Rosing
SALIENT: Ultra-Fast FPGA-based Short Read Alignment. FPT (2022)
Behnam Khaleghi, Tianqi Zhang, Niya Shao, Ameen Akel, Ken Curewitz, Justin Eno, Sean Eilert, Niema Moshiri, Tajana Rosing
FAST: FPGA-based Acceleration of Genomic Sequence Trimming. BioCAS (2022)
Kimberly Almaraz, Tyler Jang, McKenna Lewis, Titan Ngo, Miranda Song, Niema Moshiri
SEPIA: simulation-based evaluation of prioritization algorithms. BMC Medical Informatics Decis. Mak. 21 (1) (2021)
Minxuan Zhou, Lingxi Wu, Muzhou Li, Niema Moshiri, Kevin Skadron, Tajana Rosing
Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing. PACT (2021)
McKenna Lewis, Niema Moshiri, Kit Curtius
MethylDrift: A Software Package for Calculating Age-related Epigenetic Drift in Human Tissues Using DNA Methylation Data. AMIA (2021)
Niema Moshiri
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes. Bioinform. 37 (5) (2021)
Elizabeth Leininger, Kelly Shaw, Niema Moshiri, Kelly Neiles, Getiria Onsongo, Anna M. Ritz
Ten Simple Rules for Attending Your First Conference. CoRR (2021)
Sahand Salamat, Jaeyoung Kang, Yeseong Kim, Mohsen Imani, Niema Moshiri, Tajana Rosing
FPGA Acceleration of Protein Back-Translation and Alignment. DATE (2021)
Elizabeth Leininger, Kelly Shaw, Niema Moshiri, Kelly Neiles, Getiria Onsongo, Anna M. Ritz
Ten simple rules for attending your first conference. PLoS Comput. Biol. 17 (7) (2021)
Yeseong Kim, Mohsen Imani, Niema Moshiri, Tajana Rosing
GenieHD: Efficient DNA Pattern Matching Accelerator Using Hyperdimensional Computing. DATE (2020)
Niema Moshiri
TreeSwift: A massively scalable Python tree package. SoftwareX 11 (2020)
Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLoS Comput. Biol. 15 (7) (2019)
Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences. Bioinform. 35 (11) (2019)
Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
Ten Simple Rules for Reproducible Research in Jupyter Notebooks. CoRR (2018)