Author

Monjura Afrin Rumi

Virginia TechORCID 0009-0002-7353-8058Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 3 Research Focus:database / resource· 3 Assay:metagenomics· 3 Approach:statistical model· 2 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Approach:large language model· 1

Frequent Co-Authors

Amy J. PrudeniD· 3 shared Peter J. VikeslandiD· 3 shared Connor BrowniD· 2 shared Joung Min ChoiiD· 2 shared Liqing ZhangiD· 2 shared Adheesh Sunil Juvekar· 1 shared Ahmad Khan· 1 shared Ali Raza ButtiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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3 shared papersBioinformatics

Amy J. PrudenORCID

Mutual co-authors in cluster

Author profile →

4 papers

Recent·Most cited

GEO-BERT: A Retrieval augmented LLM Framework for Intelligent Dataset Retrieval from the Gene Expression Omnibus

Maruf Islam Shuvo, Monjura Afrin Rumi, Naznin Akter, Ewy A. Mathé, Shafiul Alam, Mahfuza Sharmin

GEO-BERT improves dataset retrieval from GEO by using a retrieval-augmented LLM framework with a hierarchical hybrid field-aware system, enhancing semantic search and traditional search performance.

bioRxiv · Oct 21, 2026 · PreprintBioinformatics

ARGfore: A multivariate framework for forecasting antibiotic resistance gene abundances using time-series metagenomic datasets

Joung Min Choi, Monjura Afrin Rumi, Connor L. Brown, Peter J. Vikesland, Amy J. Pruden, L. Zhang

ARGfore forecasts antibiotic resistance gene abundances from time-series metagenomic data, outperforming standard methods with lower error and better efficiency.

IEEE Access · Jan 1, 2026Peer-reviewedBioinformatics

MetaCompare 2.0: Differential ranking of ecological and human health resistome risks

Monjura Afrin Rumi, Min Oh, Benjamin C. Davis, Connor Brown, Adheesh Sunil Juvekar, Peter J. Vikesland, Amy J. Pruden, Liqing Zhang

MetaCompare 2.0 differentiates human health and ecological resistome risks using metagenomic data, showing higher risk scores for human-contaminated environments.

FEMS Microbiology Ecology · Nov 8, 2024Peer-reviewedBioinformatics

CIWARS: a web server for waterborne antibiotic resistance surveillance using longitudinal metagenomic data

Muhit Islam Emon, Yat Fei Cheung, James Stoll, Monjura Afrin Rumi, Connor Brown, Joung Min Choi, Nazifa Ahmed Moumi, Shafayat Ahmed, Haoqiu Song, Justin Sein, Shunyu Yao, Ahmad Khan, Suraj Gupta, Rutwik Kulkarni, Ali Raza Butt, , Liqing Zhang

CIWARS is a web server for analyzing longitudinal metagenomic data to detect antibiotic resistance genes and assess AR risks in environmental samples.

bioRxiv · Oct 30, 2024 · PreprintBioinformatics