Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.

by Todd J Treangen, Eduardo P C Rocha
Published 2011-01-01

Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome

by Todd J. Treangen, Justin Wagner, Mark P. Burns, Sonia Villapol
Published 2018-11-01

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

by Daniel J. Nasko, Sergey Koren, Adam M. Phillippy, Todd J. Treangen
Published 2018-10-01

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers.

by Michelle Davison, Todd J Treangen, Sergey Koren, Mihai Pop, Devaki Bhaya
Published 2016-01-01

Multiple genome alignment in the telomere-to-telomere assembly era

by Bryce Kille, Advait Balaji, Fritz J. Sedlazeck, Michael Nute, Todd J. Treangen
Published 2022-08-01

Fecal Microbiota Transplantation Derived from Alzheimer’s Disease Mice Worsens Brain Trauma Outcomes in Wild-Type Controls

by Sirena Soriano, Kristen Curry, Qi Wang, Elsbeth Chow, Todd J. Treangen, Sonia Villapol
Published 2022-04-01

PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment

by Qi Wang, Bryce Kille, Tian Rui Liu, R. A. Leo Elworth, Todd J. Treangen
Published 2021-02-01

Identification and Genomic Analysis of a Novel Group C Orthobunyavirus Isolated from a Mosquito Captured near Iquitos, Peru.

by Todd J Treangen, George Schoeler, Adam M Phillippy, Nicholas H Bergman, Michael J Turell
Published 2016-04-01

Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data

by Yunxi Liu, Joshua Kearney, Medhat Mahmoud, Bryce Kille, Fritz J. Sedlazeck, Todd J. Treangen
Published 2022-03-01

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee

by Yunxi Liu, R. A. Leo Elworth, Michael D. Jochum, Kjersti M. Aagaard, Todd J. Treangen
Published 2022-11-01

MethPhaser: methylation-based long-read haplotype phasing of human genomes

by Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J. Treangen, Fritz J. Sedlazeck
Published 2024-06-01

Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater

by Yunxi Liu, Nicolae Sapoval, Pilar Gallego-García, Laura Tomás, David Posada, Todd J. Treangen, Lauren B. Stadler
Published 2024-05-01

Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

by Nicolae Sapoval, Yunxi Liu, Esther G. Lou, Loren Hopkins, Katherine B. Ensor, Rebecca Schneider, Lauren B. Stadler, Todd J. Treangen
Published 2023-05-01

KOMB: K-core based de novo characterization of copy number variation in microbiomes

by Advait Balaji, Nicolae Sapoval, Charlie Seto, R.A. Leo Elworth, Yilei Fu, Michael G. Nute, Tor Savidge, Santiago Segarra, Todd J. Treangen
Published 2022-01-01

Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern

by Gene D. Godbold, F. Curtis Hewitt, Anthony D. Kappell, Matthew B. Scholz, Stacy L. Agar, Todd J. Treangen, Krista L. Ternus, Jonas B. Sandbrink, Gregory D. Koblentz
Published 2023-04-01

Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta

by Nidia S. Trovao, Vincent Pan, Chirag Goel, Pilar Gallego-García, Yunxi Liu, Christopher Barbara, Rebecca Borg, Mark Briffa, Chanelle Cilia, Laura Grech, Mario Vassallo, Todd J. Treangen, David Posada, Afshin Beheshti, Joseph Borg, Graziella Zahra
Published 2023-12-01

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

by Advait Balaji, Bryce Kille, Anthony D. Kappell, Gene D. Godbold, Madeline Diep, R. A. Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J. Nasko, Nidhi Shah, Mihai Pop, Santiago Segarra, Krista L. Ternus, Todd J. Treangen
Published 2022-06-01

Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

by Bo Liu, Lina L Faller, Niels Klitgord, Varun Mazumdar, Mohammad Ghodsi, Daniel D Sommer, Theodore R Gibbons, Todd J Treangen, Yi-Chien Chang, Shan Li, O Colin Stine, Hatice Hasturk, Simon Kasif, Daniel Segrè, Mihai Pop, Salomon Amar
Published 2012-01-01

Current progress and open challenges for applying deep learning across the biosciences

by Nicolae Sapoval, Amirali Aghazadeh, Michael G. Nute, Dinler A. Antunes, Advait Balaji, Richard Baraniuk, C. J. Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, R. A. Leo Elworth, Bryce Kille, Anastasios Kyrillidis, Luay Nakhleh, Cameron R. Wolfe, Zhi Yan, Vicky Yao, Todd J. Treangen
Published 2022-04-01

Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College P...

by Jacquelyn S. Meisel, Daniel J. Nasko, Brian Brubach, Victoria Cepeda-Espinoza, Jessica Chopyk, Héctor Corrada-Bravo, Marcus Fedarko, Jay Ghurye, Kiran Javkar, Nathan D. Olson, Nidhi Shah, Sarah M. Allard, Adam L. Bazinet, Nicholas H. Bergman, Alexis Brown, J. Gregory Caporaso, Sean Conlan, Jocelyne DiRuggiero, Samuel P. Forry, Nur A. Hasan, Jason Kralj, Paul M. Luethy, Donald K. Milton, Brian D. Ondov, Sarah Preheim, Shashikala Ratnayake, Stephanie M. Rogers, M. J. Rosovitz, Eric G. Sakowski, Nils Oliver Schliebs, Daniel D. Sommer, Krista L. Ternus, Gherman Uritskiy, Sean X. Zhang, Mihai Pop, Todd J. Treangen
Published 2018-11-01