Niema Moshiri

30 papers A 3B 1Misc 1Journal 20Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
SurGBSA: Learning Representations From Molecular Dynamics Simulations.
CoRR
Derek Jones, Yue Yang, Felice C. Lightstone, Niema Moshiri, Jonathan E. Allen, Tajana Simunic Rosing
2024 J jnl
DRAM-Based Acceleration of Open Modification Search in Hyperdimensional Space.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst.
Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Simunic Rosing
2024 J jnl
HyperGen: compact and efficient genome sketching using hyperdimensional vectors.
Bioinform.
Weihong Xu, Po-Kai Hsu, Niema Moshiri, Shimeng Yu, Tajana Rosing
2024 — conf
RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing.
BioCAS
Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo Jun, Tajana Rosing
2024 J jnl
RapidOMS: FPGA-based Open Modification Spectral Library Searching with HD Computing.
CoRR
Sumukh Pinge, Weihong Xu, Wout Bittremieux, Niema Moshiri, Sang-Woo Jun, Tajana Rosing
2024 A conf
SpecHD: Hyperdimensional Computing Framework for FPGA-Based Mass Spectrometry Clustering.
DATE
Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing
2024 J jnl
ViralWasm: a client-side user-friendly web application suite for viral genomics.
Bioinform.
Daniel Ji, Robert Aboukhalil, Niema Moshiri
2023 J jnl
Accelerating open modification spectral library searching on tensor core in high-dimensional space.
Bioinform.
Jaeyoung Kang, Weihong Xu, Wout Bittremieux, Niema Moshiri, Tajana Rosing
2023 — conf
GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences.
BioCAS
Tianqi Zhang, Antonio González, Niema Moshiri, Rob Knight, Tajana Rosing
2023 J jnl
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations.
CoRR
Derek Jones, Jonathan E. Allen, Xiaohua Zhang, Behnam Khaleghi, Jaeyoung Kang, Weihong Xu, Niema Moshiri, Tajana Simunic Rosing
2023 J jnl
RAPIDx: High-Performance ReRAM Processing In-Memory Accelerator for Sequence Alignment.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst.
Weihong Xu, Saransh Gupta, Niema Moshiri, Tajana Simunic Rosing
2023 J jnl
SpecHD: Hyperdimensional Computing Framework for FPGA-based Mass Spectrometry Clustering.
CoRR
Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Tianqi Zhang, Niema Moshiri, Wout Bittremieux, Tajana Rosing
2023 J jnl
ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data.
Bioinform.
Niema Moshiri
2022 J jnl
A scalable approach for detecting exam similarity in CS courses.
J. Comput. Sci. Coll.
Niema Moshiri
2022 — conf
FAST: FPGA-based Acceleration of Genomic Sequence Trimming.
BioCAS
Behnam Khaleghi, Tianqi Zhang, Niya Shao, Ameen Akel, Ken Curewitz, Justin Eno, Sean Eilert, Niema Moshiri, Tajana Rosing
2022 J jnl
RAPIDx: High-performance ReRAM Processing in-Memory Accelerator for Sequence Alignment.
CoRR
Weihong Xu, Saransh Gupta, Niema Moshiri, Tajana Rosing
2022 — conf
SALIENT: Ultra-Fast FPGA-based Short Read Alignment.
FPT
Behnam Khaleghi, Tianqi Zhang, Cameron Martino, George Armstrong, Ameen Akel, Ken Curewitz, Justin Eno, Sean Eilert, Rob Knight, Niema Moshiri, Tajana Rosing
2021 A conf
FPGA Acceleration of Protein Back-Translation and Alignment.
DATE
Sahand Salamat, Jaeyoung Kang, Yeseong Kim, Mohsen Imani, Niema Moshiri, Tajana Rosing
2021 Misc conf
MethylDrift: A Software Package for Calculating Age-related Epigenetic Drift in Human Tissues Using DNA Methylation Data.
AMIA
McKenna Lewis, Niema Moshiri, Kit Curtius
2021 J jnl
SEPIA: simulation-based evaluation of prioritization algorithms.
BMC Medical Informatics Decis. Mak.
Kimberly Almaraz, Tyler Jang, McKenna Lewis, Titan Ngo, Miranda Song, Niema Moshiri
2021 J jnl
Ten Simple Rules for Attending Your First Conference.
CoRR
Elizabeth Leininger, Kelly Shaw, Niema Moshiri, Kelly Neiles, Getiria Onsongo, Anna M. Ritz
2021 J jnl
Ten simple rules for attending your first conference.
PLoS Comput. Biol.
Elizabeth Leininger, Kelly Shaw, Niema Moshiri, Kelly Neiles, Getiria Onsongo, Anna M. Ritz
2021 B conf
Ultra Efficient Acceleration for De Novo Genome Assembly via Near-Memory Computing.
PACT
Minxuan Zhou, Lingxi Wu, Muzhou Li, Niema Moshiri, Kevin Skadron, Tajana Rosing
2021 J jnl
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes.
Bioinform.
Niema Moshiri
2020 A conf
GenieHD: Efficient DNA Pattern Matching Accelerator Using Hyperdimensional Computing.
DATE
Yeseong Kim, Mohsen Imani, Niema Moshiri, Tajana Rosing
2020 J jnl
TreeSwift: A massively scalable Python tree package.
SoftwareX
Niema Moshiri
2019 J jnl
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences.
Bioinform.
Niema Moshiri, Manon Ragonnet-Cronin, Joel O. Wertheim, Siavash Mirarab
2019 — —
Mathematical Modeling of Viral Evolution and Epidemiology.
Niema Moshiri
2019 J jnl
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.
PLoS Comput. Biol.
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
2018 J jnl
Ten Simple Rules for Reproducible Research in Jupyter Notebooks.
CoRR
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