Genome biologyBioinformaticsPeer-reviewed journal article
SeqScreen: Accurate and Sensitive Functional Screening of Pathogenic Sequences via Ensemble Learning
Advait BalajiiD, Bryce L. KilleiD, Anthony D. KappelliD, Gene D. GodboldiD, Madeline M. DiepiD, Ryan A. Leo ElworthiD, Zhiqin Qian, Dreycey AlbiniD, Daniel J. NaskoiD, Nidhi Shah, Mihai PopiD, Santiago SegarraiD, Krista L. TernusiD, Todd J. TreangeniD
Abstract
The COVID-19 pandemic has emphasized the importance of detecting known and emerging pathogens from clinical and environmental samples. However, robust characterization of pathogenic sequences remains an open challenge. To this end, we developed SeqScreen, which can accurately characterize short nucleotide sequences using taxonomic and functional labels, and a customized set of curated Functions of Sequences of Concern (FunSoCs) specific to microbial pathogenesis. We show our ensemble machine learning model can label protein-coding sequences with FunSoCs with high recall and precision. SeqScreen is a step towards a novel paradigm of functionally informed pathogen characterization and is available for download at: www.gitlab.com/treangenlab/seqscreen
- assay: DNA methylation
- assay: whole-genome sequencing
- assay: whole-exome sequencing
- research focus: variant effect prediction
- research focus: variant calling
- research focus: software / tool
- approach: machine learning (classical)
- Citations
- 42
- FWCI
- 2.12
- Field percentile
- top 11%
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens.
Advait Balaji, Yunxi Liu, … Todd J. Treangen·bioRxiv·Feb 10, 2023
- Deep learning-based real-time detection of novel pathogens during sequencing
Jakub M. Bartoszewicz, Ulrich Genske, Bernhard Y. Renard·Briefings in BioinformaticsPeer-reviewed·Jun 24, 2021
- TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection
Brian B. Merritt, Jeremy D. Ratcliff, … Peter Thielen·BioinformaticsPeer-reviewed·Mar 31, 2026
- Developing a Standard Definition for Sequences of Concern
Tessa Alexanian, Jacob Beal, … Nicole E. Wheeler·Frontiers in Bioengineering and BiotechnologyPeer-reviewed·Jun 4, 2026
- Tiled Amplicon Sequencing Enables Culture-free Whole-Genome Sequencing of Pathogenic Bacteria From Clinical Specimens
Chaney C. Kalinich, Freddy L. Gonzalez, … Seth N. Redmond·bioRxiv·Dec 19, 2024
- 16S rRNA sequence captures microbial functional potential
Jia Liu, M. Clara De Paolis Kaluza, Yana Bromberg·bioRxiv·Apr 20, 2026