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SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning

https://doi.org/10.1186/s13059-022-02695-x

Balaji, Advait ; Kille, Bryce ; Kappell, Anthony D. ; Godbold, Gene D. ; Diep, Madeline ; Elworth, R. A. Leo ; Qian, Zhiqin ; Albin, Dreycey ; Nasko, Daniel J. ; Shah, Nidhi ; et al ( June 2022 , Genome Biology)

Abstract
The COVID-19 pandemic has emphasized the importance of accurate detection of known and emerging pathogens. However, robust characterization of pathogenic sequences remains an open challenge. To address this need we developed SeqScreen, which accurately characterizes 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 synthetic DNA screening and pathogen characterization, available for download atwww.gitlab.com/treangenlab/seqscreen.

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Benchmarking of computational error-correction methods for next-generation sequencing data

https://doi.org/10.1186/s13059-020-01988-3

Mitchell, Keith ; Brito, Jaqueline J. ; Mandric, Igor ; Wu, Qiaozhen ; Knyazev, Sergey ; Chang, Sei ; Martin, Lana S. ; Karlsberg, Aaron ; Gerasimov, Ekaterina ; Littman, Russell ; et al ( December 2020 , Genome Biology)

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Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows

https://doi.org/10.1093/bioinformatics/bty833

Shah, Nidhi ; Nute, Michael G. ; Warnow, Tandy ; Pop, Mihai ; Hancock, ed., John ( September 2018 , Bioinformatics)
Pharmaceuticals, herbicides, and disinfectants in agricultural water sources

https://doi.org/10.1016/j.envres.2019.04.011

Panthi, Suraj ; Sapkota, Amy R. ; Raspanti, Greg ; Allard, Sarah M. ; Bui, Anthony ; Craddock, Hillary A. ; Murray, Rianna ; Zhu, Libin ; East, Cheryl ; Handy, Eric ; et al ( July 2019 , Environmental Research)
null (Ed.)
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Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study

https://doi.org/10.1021/acs.est.2c02281

Malayil, Leena ; Ramachandran, Padmini ; Chattopadhyay, Suhana ; Allard, Sarah M. ; Bui, Anthony ; Butron, Jicell ; Callahan, Mary Theresa ; Craddock, Hillary A. ; Murray, Rianna ; East, Cheryl ; et al ( October 2022 , Environmental Science & Technology)