Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. by Todd J Treangen, Eduardo P C Rocha

Get full text

Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome by Todd J. Treangen, Justin Wagner, Mark P. Burns, Sonia Villapol

Get full text

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

Get full text

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

Get full text

Multiple genome alignment in the telomere-to-telomere assembly era by Bryce Kille, Advait Balaji, Fritz J. Sedlazeck, Michael Nute, Todd J. Treangen

Get full text

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

Get full text

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

Get full text

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

Get full text

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

Get full text

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

Get full text

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

Get full text

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

Get full text

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

Get full text

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

Get full text

Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens by Michael X. Wang, Esther G. Lou, Nicolae Sapoval, Eddie Kim, Prashant Kalvapalle, Bryce Kille, R. A. Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B. Stadler, Todd J. Treangen

Get full text

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

Get full text

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

Get full text

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

Get full text

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

Get full text

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

Get full text