Author

Haoqiu Song

Virginia TechORCID 0000-0001-5733-4085Unclaimed 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· 2 Research Focus:database / resource· 2 Assay:metagenomics· 2 Organism:bacteria (other)· 1 Approach:deep learning· 1 Approach:experimental assay· 1 Research Focus:gene regulatory network inference· 1 Approach:statistical model· 1

Frequent Co-Authors

Liqing ZhangiD· 3 shared Amy J. PrudeniD· 2 shared Connor BrowniD· 2 shared Peter J. VikeslandiD· 2 shared Yat Fei Cheung· 2 shared Ahmad Khan· 1 shared Ali Raza ButtiD· 1 shared Delaney SneadiD· 1 shared

Activity by Year

2023-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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3 shared papersBioinformatics

Liqing ZhangORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

BioinformaticsbioRxivPreprintOct 30, 2024

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

Muhit Islam Emon, Yat Fei Cheung, James Stoll…·Liqing Zhang

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

1 citation

metagenomicsexperimental assay

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BioinformaticsbioRxivPreprintJun 18, 2024

PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation Model

Sajib Acharjee Dip, Uddip Acharjee Shuvo, Tran Chau…·Liqing Zhang

PathoLM is a pathogen language model that improves pathogenicity identification in bacterial and viral sequences by leveraging pre-trained DNA models and minimal data, outperforming existing methods.

8 citations

bacteria (other)virus

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BioinformaticsbioRxivPreprintOct 24, 2023

Kairos infers in situ horizontal gene transfer in longitudinally sampled microbiomes through microdiversity-aware sequence analysis

Connor Brown, Yat Fei Cheung, Haoqiu Song…·Liqing Zhang

Kairos detects in situ horizontal gene transfer in microbiomes using time-series metagenomic data and competitive read alignment, improving detection of antibiotic resistance genes compared to MAG-based methods.

4 citations

metagenomicsstatistical model

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