Publications by authors named "Todd Treangen"

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A class of benzofuranoindoline-bearing heptacyclic fungal RiPPs with anticancer activities.
Qiuyue Nie, Fanglong Zhao, Xuerong Yu, Mithun C Madhusudhanan, Caleb Chang, Todd Treangen

Nat Chem Biol· December 2025

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Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.
Rossie S Luo, Bryce Kille, Ellen E Vaughan, Justin R Clark, Anthony W Maresso, Todd J Treangen

bioRxiv· November 2025

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Seqwin: Ultrafast identification of signature sequences in microbial genomes.
Michael X Wang, Bryce Kille, Michael G Nute, Siyi Zhou, Lauren B Stadler, Todd J Treangen

bioRxiv· November 2025

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Reference-guided assembly of metagenomes with MetaCompass.
Tu Luan, Victoria P Cepeda-Espinoza, Bo Liu, Zac Bowen, Ujjwal Ayyangar, Todd J Treangen

Cell Rep Methods· October 2025

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Gut microbiome remodeling by antibiotics reduces neuroinflammation in traumatic brain injury.
Hannah Flinn, Austin Marshall, Morgan Holcomb, Marissa Burke, Leonardo Cruz-Pineda, Todd J Treangen

Res Sq· September 2025

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The Case for Limiting "Sequences of Concern" to Those with Demonstrated Pathogenic Function.
Gene D Godbold, Krista L Ternus, Kevin Flyangolts, Nicole Wheeler, Michael Parker, Todd Treangen

Appl Biosaf· August 2025

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Impact of Ventilation on Respiratory Virus Transmission in College Residence Hall Cohorts: Potential for Causal Inference About Mode of Transmission.
T Louis Gold, Kathleen M McPhaul, Huang Lin, Ryan Doughty, Irina Maljkovic Berry, Todd J Treangen

Influenza Other Respir Viruses· July 2025

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Inter-tool analysis of a NIST dataset for assessing baseline nucleic acid sequence screening.
Tyler S Laird, Kevin Flyangolts, Craig Bartling, Bryan T Gemler, Jacob Beal, Todd J Treangen

bioRxiv· June 2025

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A survey of computational approaches for characterizing microbial interactions in microbial mats.
Vanesa L Perillo, Michael Nute, Nicolae Sapoval, Kristen D Curry, Logan Golia, Todd J Treangen

Genome Biol· June 2025

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A Comparison of Methods for the Optimal Recovery of the Human Fecal Virome.
Loretta De Chiara, Ryan Doughty, Nuria Estévez-Gómez, Pilar Gallego-García, Pilar Alvariño, Todd J Treangen

medRxiv· May 2025

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Probiotic treatment induces sex-dependent neuroprotection and gut microbiome shifts after traumatic brain injury.
Morgan Holcomb, Austin G Marshall, Hannah Flinn, Mariana Lozano-Cavazos, Sirena Soriano, Todd J Treangen

J Neuroinflammation· April 2025

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Gut Microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients.
Paula L Scalzo, Austin G Marshall, Sirena Soriano, Kristen Curry, Mario Dulay, Todd J Treangen

J Transl Med· March 2025

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Probiotic therapy modulates the brain-gut-liver microbiota axis in a mouse model of traumatic brain injury.
Wellington Z Amaral, Natalie Kokroko, Todd J Treangen, Sonia Villapol, Fernando Gomez-Pinilla

Biochim Biophys Acta Mol Basis Dis· December 2024

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Multiplexed Detection, Partitioning, and Persistence of Wild-Type and Vaccine Strains of Measles, Mumps, and Rubella Viruses in Wastewater.
Jingjing Wu, Michael X Wang, Prashant Kalvapalle, Michael Nute, Todd J Treangen

Environ Sci Technol· December 2024

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A near-tight lower bound on the density of forward sampling schemes.
Bryce Kille, Ragnar Groot Koerkamp, Drake McAdams, Alan Liu, Todd J Treangen

Bioinformatics· December 2024

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Rapid whole genome characterization of antimicrobial-resistant pathogens using long-read sequencing to identify potential healthcare transmission.
Chin-Ting Wu, William C Shropshire, Micah M Bhatti, Sherry Cantu, Israel K Glover, Todd J Treangen

Infect Control Hosp Epidemiol· December 2024

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A near-tight lower bound on the density of forward sampling schemes.
Bryce Kille, Ragnar Groot Koerkamp, Drake McAdams, Alan Liu, Todd J Treangen

bioRxiv· November 2024

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Gut microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients: Microbiome dysbiosis linked to COVID-19 symptoms.
Paula L Scalzo, Austin Marshall, Sirena Soriano, Kristen Curry, Mario Dulay, Todd J Treangen

medRxiv· November 2024

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Graph-based self-supervised learning for repeat detection in metagenomic assembly.
Ali Azizpour, Advait Balaji, Todd J Treangen, Santiago Segarra

Genome Res· October 2024

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Rapid Whole Genome Characterization of High-Risk Pathogens Using Long-Read Sequencing to Identify Potential Healthcare Transmission.
Chin-Ting Wu, William C Shropshire, Micah M Bhatti, Sherry Cantu, Israel K Glover, Todd J Treangen

medRxiv· August 2024

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Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens.
Michael X Wang, Esther G Lou, Nicolae Sapoval, Eddie Kim, Prashant Kalvapalle, Todd J Treangen

Nat Commun· July 2024

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MethPhaser: methylation-based long-read haplotype phasing of human genomes.
Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J Treangen

Nat Commun· June 2024

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Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.
Kristen D Curry, Feiqiao Brian Yu, Summer E Vance, Santiago Segarra, Devaki Bhaya, Todd J Treangen

Bioinformatics· June 2024

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Antibiotic treatment induces microbiome dysbiosis and reduction of neuroinflammation following traumatic brain injury in mice.
Hannah Flinn, Austin Marshall, Morgan Holcomb, Leonardo Cruz, Sirena Soriano, Todd J Treangen

Res Sq· June 2024

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MetaCompass: Reference-guided Assembly of Metagenomes.
Tu Luan, Victoria Cepeda, Bo Liu, Zac Bowen, Ujjwal Ayyangar, Todd J Treangen

ArXiv· March 2024

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