Publications

Gene D Godbold, Todd J Treangen, Krista L Ternus (2024). Improved Annotation of Sequences of Concern to Better Understand Biorisk in Engineered Microbes.

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Madeline Wolken, Michael Wang, Julia Schedler, Roberto H Campos, Katherine B Ensor, Loren Hopkins, Todd Treangen, Lauren B Stadler (2024). Prek-12 School and Citywide Wastewater Monitoring of the Enteric Viruses Astrovirus, Rotavirus, and Sapovirus. Rotavirus, and Sapovirus.

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Pilar Gallego-Garcı́a, Dr. Yunxi Liu, Nid́ia Sequeira Trovão, Vincent Pan, Chirag Goel, Mark Briffa, Chanelle Cilia, Christopher Barbara, Rebecca Borg, Laura Grech, others (2024). Evolutionary and Spatiotemporal Analysis Reveal Multiple Introductions and Cryptic Transmission of Sars-Cov-2 VOC/VOI in Malta.

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Qinglong Wu, Shyam Badu, Sik Yu So, Todd J Treangen, Tor C Savidge, others (2024). The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease. The Journal of Clinical Investigation.

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Esther G Lou, Dr. Yilei Fu, Dr. Qi Wang, Todd J Treangen, Lauren B Stadler (2024). Sensitivity and consistency of long-and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater. Journal of Hazardous Materials.

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Dr. Kristen Curry, Feiqiao Brian Yu, Summer E Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo PC Rocha, Todd J Treangen (2024). Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs. bioRxiv.

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Morgan Holcomb, Austin Marshall, Hannah Flinn, Mariana Lozano, Sirena Soriano, Fernando Gomez-Pinilla, Todd Treangen, Sonia Villapol (2024). Probiotic treatment causes sex-specific neuroprotection after traumatic brain injury in mice. bioRxiv.

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Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen (2024). Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets. bioRxiv.

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Dr. Kristen Curry, Sirena Soriano, Michael G Nute, Sonia Villapol, Alexander Dilthey, Todd J Treangen (2024). Microbial Community Profiling Protocol with Full-length 16S rRNA Sequences and Emu. Current Protocols.

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Tu Luan, Victoria Cepeda, Bo Liu, Zac Bowen, Ujjwal Ayyangar, Mathieu Almeida, Christopher M Hill, Sergey Koren, Todd J Treangen, Adam Porter, others (2024). MetaCompass: Reference-guided Assembly of Metagenomes. arXiv preprint arXiv:2403.01578.

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Selvalakshmi Selvaraj Anand, Chin-Ting Wu, Jordan Bremer, Micah Bhatti, Todd J Treangen, Awdhesh Kalia, Samuel A Shelburne, William C Shropshire (2024). Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA. Microbial Genomics.

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Ali Azizpour, Dr. Advait Balaji, Todd J Treangen, Santiago Segarra (2024). GraSSRep: Graph-Based Self-Supervised Learning for Repeat Detection in Metagenomic Assembly. arXiv preprint arXiv:2402.09381.

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Harihara Subrahmaniam Muralidharan, Jacquelyn S Michaelis, Jay Ghurye, Todd Treangen, Sergey Koren, Marcus Fedarko, Mihai Pop (2024). Graph-based variant discovery reveals novel dynamics in the human microbiome. arXiv e-prints.

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Harihara Subrahmaniam Muralidharan, Jacquelyn S Michaelis, Jay Ghurye, Todd Treangen, Sergey Koren, Marcus Fedarko, Mihai Pop (2024). Graph-based variant discovery reveals novel dynamics in the human microbiome. arXiv preprint arXiv:2403.01610.

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Ronan W O'Connell, Kshitij Rai, Trenton C Piepergerdes, Yiduo Wang, Kian D Samra, Jack A Wilson, Shujian Lin, Thomas H Zhang, Eduardo Ramos, Andrew Sun, others (2023). Ultra-high throughput mapping of genetic design space. bioRxiv.

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Todd J Treangen, Moshe Y Vardi (2023). The long game of tenure. Nature Biotechnology.

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Camille McCall, Ryan A Leo Elworth, Kristine M Wylie, Todd N Wylie, Katherine Dyson, Ryan Doughty, Todd Treangen, Loren Hopkins, Katherine B Ensor, Lauren B Stadler (2023). Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance. medRxiv.

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Dr. Advait Balaji, Dr. Yunxi Liu, Michael G Nute, Bingbing Hu, Anthony Kappell, Danielle S LeSassier, Gene D Godbold, Krista L Ternus, Todd J Treangen (2023). SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens. bioRxiv.

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Michael X Wang, Esther G Lou, Dr. Nicolae Sapoval, Eddie Kim, Prashant Kalvapalle, Bryce Kille, Dr. R.A. Leo Elworth, Dr. Yunxi Liu, Dr. Yilei Fu, Lauren B Stadler, others (2023). Olivar: fully automated and variant aware primer design for multiplex tiled amplicon sequencing of pathogen genomes (preprint).

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Bryce Kille, Erik Garrison, Todd J Treangen, Adam M Phillippy (2023). Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. bioRxiv.

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Dr. Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J Treangen, Fritz J Sedlazeck (2023). MethPhaser: methylation-based haplotype phasing of human genomes. bioRxiv.

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Felix Quintana, Todd Treangen, Lydia Kavraki (2023). Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence. Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.

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Dr. Nicolae Sapoval, Marko Tanevski, Todd J Treangen (2023). KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024.

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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 (2023). Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Frontiers in Bioengineering and Biotechnology.

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Nidia S Trovao, Vincent Pan, Chirag Goel, Pilar Gallego-Garcı́a, Dr. Yunxi Liu, Christopher Barbara, Rebecca Borg, Mark Briffa, Chanelle Cilia, Laura Grech, others (2023). Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta. Microbiology Spectrum.

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Dr. Nicolae Sapoval, Dr. Yunxi Liu, Esther G Lou, Loren Hopkins, Katherine B Ensor, Rebecca Schneider, Lauren B Stadler, Todd J Treangen (2023). Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater. Nature Communications.

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Dr. Yunxi Liu, Dr. Nicolae Sapoval, Todd Treangen, Lauren Stadler (2023). Crykey: Comprehensive Identification of SARS-CoV-2 Cryptic Mutations in Wastewater. medRxiv.

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Dr. Qi Wang, Dr. Michael Nute, Todd J Treangen (2023). Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities. Bioinformatics.

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Taryn A Eubank, Anne J Gonzales-Luna, Blake M Hanson, Todd Treangen, Ashlee Earl, Kevin W Garey (2023). 2164. Resistome patterns associated with vancomycin non-susceptibility in clinical Clostridioides difficile isolates. Open Forum Infectious Diseases.

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Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, Fritz J Sedlazeck, Ben Busby, David Molik, Daniela C Soto, Fawaz Dabbaghie, Ahmad Al Khleifat, others (2022). The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

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William C Shropshire, Anna Konovalova, P McDaneld, M Gohel, B Strope, P Sahasrabhojane, Chau N Tran, David Greenberg, Jiwoong Kim, Xiaowei Zhan, others (2022). Systematic Analysis of Mobile Genetic Elements Mediating $β$-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections. Msystems.

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Dr. Advait Balaji, Bryce Kille, Anthony D Kappell, Gene D Godbold, Madeline Diep, Dr. R.A. Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J Nasko, Nidhi Shah, others (2022). SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning. Genome Biology.

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Dr. Yunxi Liu, Joshua Kearney, Medhat Mahmoud, Bryce Kille, Fritz J Sedlazeck, Todd J Treangen (2022). Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data. Nature communications.

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Dr. Nicolae Sapoval, Dr. Yunxi Liu, Esther G Lou, Loren Hopkins, Katherine B Ensor, Rebecca Schneider, Lauren B Stadler, Todd J Treangen (2022). QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater. medRxiv.

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Benjamin Coleman, Benito Geordie, Li Chou, Dr. R.A. Leo Elworth, Todd Treangen, Anshumali Shrivastava (2022). One-pass diversified sampling with application to terabyte-scale genomic sequence streams. International Conference on Machine Learning.

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Amy E Kirby, Rory M Welsh, Zachary A Marsh, T Yu Alexander, Duc J Vugia, Alexandria B Boehm, Marlene K Wolfe, Bradley J White, Shannon R Matzinger, Allison Wheeler, others (2022). Notes from the field: early evidence of the SARS-CoV-2 B. 1.1. 529 (Omicron) variant in community wastewater—United States, November--December 2021. Morbidity and Mortality Weekly Report.

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Bryce Kille, Dr. Advait Balaji, Fritz J Sedlazeck, Dr. Michael Nute, Todd J Treangen (2022). Multiple genome alignment in the telomere-to-telomere assembly era. Genome Biology.

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Pilar Gallego-García, Nair Varela, Nuria Estévez-Gómez, Loretta De Chiara, Iria Fernández-Silva, Diana Valverde, Dr. Nicolae Sapoval, Todd J Treangen, Benito Regueiro, Jorge Julio Cabrera-Alvargonzález, Víctor del Campo, Sonia Pérez, David Posada (2022). Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters. Virus Evolution.

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Pilar Gallego-Garcı́a, Nair Varela, Nuria Estévez-Gómez, Loretta De Chiara, Iria Fernández-Silva, Diana Valverde, Dr. Nicolae Sapoval, Todd J Treangen, Benito Regueiro, Jorge Julio Cabrera-Alvargonzález, others (2022). Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters. Virus Evolution.

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Dr. Advait Balaji, Dr. Nicolae Sapoval, Charlie Seto, Dr. R.A. Leo Elworth, Dr. Yilei Fu, Michael G Nute, Tor Savidge, Santiago Segarra, Todd J Treangen (2022). KOMB: K-core based de novo characterization of copy number variation in microbiomes. Computational and Structural Biotechnology Journal.

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Oluwasanmi O Adenaiye, Jianyu Lai, P Jacob Bueno de Mesquita, Filbert Hong, Somayeh Youssefi, Jennifer German, SH Sheldon Tai, Barbara Albert, Maria Schanz, Stuart Weston, others (2022). Infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in exhaled aerosols and efficacy of masks during early mild infection. Clinical Infectious Diseases.

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Sirena Soriano, Kristen Curry, Dr. Qi Wang, Elsbeth Chow, Todd J Treangen, Sonia Villapol (2022). Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in wild-type controls. International Journal of Molecular Sciences.

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Dr. Nicolae Sapoval, Dr. Yunxi Liu, Esther G Lou, Loren Hopkins, Katherine B Ensor, Rebecca Schneider, Lauren B Stadler, Todd J Treangen (2022). Enabling earlier detection of recently emerged SARS-CoV-2 variants of concern in wastewater. medRxiv.

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Dr. Kristen Curry, Dr. Qi Wang, Michael G Nute, Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, others (2022). Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature methods.

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Esther Lou, Dr. Nicolae Sapoval, Camille McCall, Lauren Bauhs, Russell Carlson-Stadler, Prashant Kalvapalle, Yanlai Lai, Kyle Palmer, Ryker Penn, Whitney Rich, others (2022). Direct Comparison of RT-ddPCR and Targeted Amplicon Sequencing for SARS-CoV-2 Mutation Monitoring in Wastewater (preprint).

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Dr. Yunxi Liu, Dr. R.A. Leo Elworth, Michael D Jochum, Kjersti M Aagaard, Todd J Treangen (2022). De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee. Nature Communications.

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Dr. Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, Dinler A Antunes, Dr. Advait Balaji, Richard Baraniuk, CJ Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, others (2022). Current progress and open challenges for applying deep learning across the biosciences. Nature Communications.

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So Hyun Park, Mingming Cao, Yidan Pan, Timothy H Davis, Lavanya Saxena, Harshavardhan Deshmukh, Dr. Yilei Fu, Todd Treangen, Vivien A Sheehan, Gang Bao (2022). Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing. Science Advances.

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Gene D Godbold, Anthony D Kappell, Danielle S LeSassier, Todd J Treangen, Krista L Ternus (2022). Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis. Infection and Immunity.

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Michael Jochum, Michael D Lee, Kristen Curry, Victoria Zaksas, Elizabeth Vitalis, Todd Treangen, Kjersti Aagaard, Krista L Ternus (2022). Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease. Scientific Reports.

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Sirena Soriano, Kristen Curry, Saeed S Sadrameli, Dr. Qi Wang, Dr. Michael Nute, Elizabeth Reeves, Rasadul Kabir, Jonathan Wiese, Amber Criswell, Sarah Schodrof, others (2022). Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study. Brain, Behavior, & Immunity-Health.

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Dr. Qi Wang (2021). GenomeDepot: Computational Methods for Decoding Biological Information Encoded in Engineered DNA and Microbial Genomes. PhD Thesis, Rice University. Available online.

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Dr. Yilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, Fritz J Sedlazeck, Todd J Treangen (2021). Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. GigaScience.

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J Tyson McDonald, Francisco Javier Enguita, Richard A Bowen, Robert J Griffin, Waldemar Priebe, Mark R Emmett, Marisa McGrath, Mohammad Sajadi, Anthony D Harris, Jean Clement, others (2021). The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection (preprint).

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Dr. Yunxi Liu, Dr. R.A. Leo Elworth, Michael D Jochum, Kjersti M Aagaard, Todd J Treangen (2021). Squeegee: de-novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes. bioRxiv.

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Dr. Advait Balaji, Bryce Kille, Anthony Kappell, Gene D Godbold, Madeline Diep, Dr. R.A. Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J Nasko, Nidhi Shah, others (2021). SeqScreen: Accurate and Sensitive Functional Screening of Pathogenic Sequences via Ensemble Learning. bioRxiv.

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Dr. Nicolae Sapoval, Medhat Mahmoud, Michael D Jochum, Dr. Yunxi Liu, Dr. R.A. Leo Elworth, Dr. Qi Wang, Dreycey Albin, Huw A Ogilvie, Michael D Lee, Sonia Villapol, others (2021). SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome research.

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J Tyson McDonald, Francisco J Enguita, Deanne Taylor, Robert J Griffin, Waldemar Priebe, Mark R Emmett, Mohammad M Sajadi, Anthony D Harris, Jean Clement, Joseph M Dybas, others (2021). Role of miR-2392 in driving SARS-CoV-2 infection. Cell reports.

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Dr. Yunxi Liu, Joshua Kearney, Medhat Mahmoud, Bryce Kille, Fritz J Sedlazeck, Todd J Treangen (2021). Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data. bioRxiv.

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Dr. Nicolae Sapoval, Dr. Yunxi Liu, Esther G Lou, Loren Hopkins, Katherine B Ensor, Rebecca Schneider, Lauren B Stadler, Todd J Treangen (2021). QuaID: Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater. medRxiv.

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Dr. Qi Wang, Bryce Kille, Tian Rui Liu, Dr. R.A. Leo Elworth, Todd J Treangen (2021). PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment. Nature communications.

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Silvia Molino, Andrea Pisarevsky, Fabiana Lopez Mingorance, Patricia Vega, Juan Pablo Stefanolo, Julieta Repetti, Guillermina Ludueña, Pablo Pepa, Juan Ignacio Olmos, Marcelo Rodriguez Fermepin, others (2021). Natural tannin extracts supplementation for COVID-19 patients (TanCOVID): a structured summary of a study protocol for a randomized controlled trial. Trials.

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Pilar Gallego-Garcı́a, Nair Varela, Nuria Estévez-Gómez, Loretta De Chiara, Iria Fernández-Silva, Diana Valverde, Dr. Nicolae Sapoval, Todd Treangen, Benito Regueiro, Jorge Julio Cabrera-Alvargonzález, others (2021). Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters (preprint).

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Dr. Advait Balaji, Dr. Nicolae Sapoval, Charlie Seto, Dr. R.A. Leo Elworth, Michael G Nute, Tor Savidge, Santiago Segarra, Todd J Treangen (2021). KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities. bioRxiv.

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Dr. Kristen Curry, Michael G Nute, Todd J Treangen (2021). It takes guts to learn: machine learning techniques for disease detection from the gut microbiome. Emerging Topics in Life Sciences.

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Dr. Nicolae Sapoval, P Jacob Bueno de Mesquita, Dr. Yunxi Liu, Roger Wang, Tian Rui Liu, Josie Garza, Torrey Williams, Carmelli Cadiz, Gene S Tan, Harm Van Bakel, others (2021). Intrahost-diversity of influenza A virus in upper and lower respiratory tract derived samples from a college community. medRxiv.

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Oluwasanmi Oladapo Adenaiye, Jianyu Lai, P Jacob Bueno de Mesquita, Filbert H Hong, Somayeh Youssefi, Jennifer Rebecca German, S-H Sheldon Tai, Barbara Jean Albert, Maria Schanz, Stuart Weston, others (2021). Infectious SARS-CoV-2 in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection (preprint).

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Irina Maljkovic Berry, Todd Treangen, Christian Fung, Sheldon Tai, Simon Pollett, Filbert Hong, Tao Li, Papa Pireku, Ashley Thomanna, Jennifer German, others (2021). High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings. bioRxiv.

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Ana A Pisarevsky, Fabiana Lopez Mingorance, Patrica Vega, Juan P Stefanolo, Julieta A Repetti, Guillermina Ludueña, Pablo D Pepa, Juan I Olmos, Marcelo Rodrı́guez Fermepin, Silvia Molino, others (2021). Fr578 ORAL TANNINS REDUCE PROINFLAMMATORY CYTOKINES ASSOCIATED WITH DIARRHEA AND PNEUMONIA IN HOSPITALIZED COVID-19 PATIENTS.. Gastroenterology.

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Sirena Soriano, Kristen Curry, Dr. Qi Wang, Elsbeth Chow, Todd Treangen, Sonia Villapol (2021). Fecal microbiota transplantation derived from Alzheimer’s disease mice worsens brain trauma outcomes in young C57BL/6 mice. bioRxiv.

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Gaurav Gupta, Minghao Yan, Benjamin Coleman, Bryce Kille, Dr. R.A. Leo Elworth, Tharun Medini, Todd Treangen, Anshumali Shrivastava (2021). Fast processing and querying of 170tb of genomics data via a repeated and merged bloom filter (rambo). Proceedings of the 2021 International Conference on Management of Data.

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Dr. Nicolae Sapoval, Esther Lou, Loren Hopkins, Katherine B Ensor, Rebecca Schneider, Todd J Treangen, Lauren B Stadler (2021). Enhanced Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater. medRxiv.

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Dr. Kristen Curry, Dr. Qi Wang, Michael G Nute, Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Enid Graeber, Patrick Finzer, Werner Mendling, Qinglong Wu, others (2021). Emu: Species-Level Microbial Community Profiling for Full-Length Nanopore 16S Reads. bioRxiv.

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Gene D Godbold, Anthony D Kappell, Danielle S LeSassier, Todd J Treangen, Krista L Ternus (2021). Categorizing sequences of concern by function to better assess mechanisms of microbial pathogenesis. Infection and immunity.

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Dr. Qi Wang, Dr. Michael Nute, Todd Treangen (2021). Bakdrive: Identifying the Minimum Set of Bacterial Driver Species across Multiple Microbial Communities. bioRxiv.

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Ann M Mc Cartney, Medhat Mahmoud, Michael Jochum, Daniel Paiva Agustinho, Barry Zorman, Ahmad Al Khleifat, Fawaz Dabbaghie, Rupesh K Kesharwani, Moritz Smolka, Moez Dawood, others (2021). An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Research.

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Sirena Soriano, Kristen Curry, Saeed Sadrameli, Dr. Qi Wang, Dr. Michael Nute, Elizabeth Reeves, Rasadul Kabir, Jonathan Wiese, Amber Criswell, Sarah Schodrof, others (2021). Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort. Available at SSRN 3948753.

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Bryce Kille, Dr. Yunxi Liu, Dr. Nicolae Sapoval, Dr. Michael Nute, Lawrence Rauchwerger, Nancy Amato, Todd J Treangen (2021). Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets. 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

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Dr. R.A. Leo Elworth, Dr. Qi Wang, Pavan K Kota, CJ Barberan, Benjamin Coleman, Dr. Advait Balaji, Gaurav Gupta, Richard G Baraniuk, Anshumali Shrivastava, Todd J Treangen (2020). To petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics. Nucleic acids research.

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Dr. R.A. Leo Elworth, Christian Diaz, Jing Yang, Paul de Figueiredo, Krista Ternus, Todd Treangen (2020). Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides. PLoS Pathogens.

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Medhat Mahmoud, Alejandro Rafael Gener, Michael M Khayat, Adam C English, Dr. Advait Balaji, Anbo Zhou, Andreas Hehn, Arkarachai Fungtammasan, Brianna Sierra Chrisman, Chen-Shan Chin, others (2020). Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine. F1000Research.

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Dr. Advait Balaji, Dr. Nicolae Sapoval, Charlie Seto, Dr. R.A. Leo Elworth, Michael G Nute, Tor Savidge, Santiago Segarra, Todd J Treangen (2020). KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities. bioRxiv.

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Dr. Nicolae Sapoval, Medhat Mahmoud, Michael D Jochum, Dr. Yunxi Liu, Dr. R.A. Leo Elworth, Dr. Qi Wang, Dreycey Albin, Huw Ogilvie, Michael D Lee, Sonia Villapol, others (2020). Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission (preprint).

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Willian A da Silveira, Hossein Fazelinia, Sara Brin Rosenthal, Evagelia C Laiakis, Man S Kim, Cem Meydan, Yared Kidane, Komal S Rathi, Scott M Smith, Benjamin Stear, others (2020). Comprehensive multi-omics analysis reveals mitochondrial stress as a central biological hub for spaceflight impact. Cell.

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Jessica Chopyk, Daniel J Nasko, Sarah Allard, Anthony Bui, Todd Treangen, Mihai Pop, Emmanuel F Mongodin, Amy R Sapkota (2020). Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications. Water research.

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Gaurav Gupta, Minghao Yan, Benjamin Coleman, R Elworth, Todd Treangen, Anshumali Shrivastava (2019). Sub-linear sequence search via a Repeated And Merged Bloom Filter (RAMBO): indexing 170 TB data in 14 hours. arXiv preprint arXiv:1910.04358 [cs, q-bio].

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Dreycey Albin, Dan Nasko, Dr. R.A. Leo Elworth, Jacob Lu, Dr. Advait Balaji, Christian Diaz, Nidhi Shah, Jeremy Selengut, Chris Hulme-Lowe, Pravin Muthu, others (2019). SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest. 2019 IEEE international conference on bioinformatics and biomedicine (BIBM).

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Gaurav Gupta, Minghao Yan, Benjamin Coleman, RA Elworth, Tharun Medini, Todd Treangen, Anshumali Shrivastava (2019). RAMBO: Repeated And Merged BloOm filter for ultra-fast Multiple Set Membership Testing (MSMT) on large-scale data. arXiv preprint arXiv:1910.02611.

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Nathan D Olson, Todd J Treangen, Christopher M Hill, Victoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Mihai Pop (2019). Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Briefings in bioinformatics.

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Jay Ghurye, Todd Treangen, Marcus Fedarko, W Judson Hervey, Mihai Pop (2019). MetaCarvel: linking assembly graph motifs to biological variants. Genome biology.

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Dr. Qi Wang, RA Elworth, Tian Rui Liu, Todd J Treangen (2019). Faster pan-genome construction for efficient differentiation of naturally occurring and engineered plasmids with plaster. 19th International Workshop on Algorithms in Bioinformatics (WABI 2019).

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Benito Geordie Benjamin Coleman, Li Chou, Dr. R.A. Leo Elworth, Todd J Treangen, Anshumali Shrivastava (2019). Diversified race sampling on data streams applied to metagenomic sequence analysis. bioRxiv.

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Benjamin Coleman, Benito Geordie, Li Chou, Dr. R.A. Leo Elworth, Todd J Treangen, Anshumali Shrivastava (2019). Diversified RACE sampling on data streams applied to metagenomic sequence analysis. bioRxiv.

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Todd J Treangen, Mihai Pop (2018). You can't always sequence your way out of a tight spot: Next-generation sequencing holds great promise for pathogen detection, but the devil is in the details. EMBO reports.

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Todd J Treangen, Justin Wagner, Mark P Burns, Sonia Villapol (2018). Traumatic brain injury in mice induces acute bacterial dysbiosis within the fecal microbiome. Frontiers in immunology.

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Daniel J Nasko, Sergey Koren, Adam M Phillippy, Todd J Treangen (2018). RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome biology.

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Marcus Fedarko, Jay Ghurye, Todd Treangen, Mihai Pop (2018). Hierarchically visualizing metagenome assembly graphs with metagenomescope.

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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, others (2018). Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018. Microbiome.

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Nathanael D Olson, Chris M Hill, Vistoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Todd J Treangen, Mihai Pop (2017). Metagenomic assembly through the lens of validation: a review of recent advances in assessing and improving the quality of genes and genomes assembled from metagenomes.. Nathanael D. Olson, Chris M. Hill, Vistoria Cepeda-Espinoza, Jay Ghurye~….

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Victoria Cepeda, Bo Liu, Mathieu Almeida, Christopher M Hill, Sergey Koren, Todd J Treangen, Mihai Pop (2017). MetaCompass: reference-guided assembly of metagenomes. BioRxiv.

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Gaurav Gupta, Tharun Medini, Anshumali Shrivastava, Alexander J Smola, M Yan, B Coleman, RA Elworth, T Medini, T Treangen, A Shrivastava, others (2017). Gaurav Gupta.

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Venkateswaran Kasthuri, Checinska Sielaff Aleksandra, Ratnayake Shashikala, Robert K Pope, Thomas E Blank, Victor G Stepanov, George E Fox, P van Tongeren Sandra, Clinton Torres, Jonathan Allen, others (2017). Draft Genome Sequences from a Novel Clade of Bacillus cereusáSensu Lato Strains, Isolated from the International Space Station. Microbiology Resource Announcements.

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K Venkateswaran, A Checinska Sielaff, S Ratnayake, RK Pope, TE Blank, VG Stepanov, GE Fox, SP van Tongeren, C Torres, J Allen, others (2017). Draft genome sequences from a novel clade of Bacillus cereus sensu lato strains, isolated from the International Space Station. Genome Announc 5: e00680-17.

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Robert K Pope, Thomas E Blank, Victor G Stepanov, George E Fox, Sandra P van Tongeren, Clinton Torres, Jonathan Allen, Crystal Jaing, Duane Pierson, Jay Perry, others (2017). Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station.

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Brian D Ondov, Todd J Treangen, Páll Melsted, Adam B Mallonee, Nicholas H Bergman, Sergey Koren, Adam M Phillippy (2016). Mash: fast genome and metagenome distance estimation using MinHash. Genome biology.

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Amelia Bateman, Todd J Treangen, Mihai Pop (2016). Limitations of current approaches for reference-free, graph-based variant detection. Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.

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Todd J Treangen, George Schoeler, Adam M Phillippy, Nicholas H Bergman, Michael J Turell (2016). Identification and genomic analysis of a novel group C Orthobunyavirus isolated from a mosquito captured near Iquitos, Peru. PLoS neglected tropical diseases.

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Michelle Davison, Todd J Treangen, Sergey Koren, Mihai Pop, Devaki Bhaya (2016). Diversity in a polymicrobial community revealed by analysis of viromes, endolysins and CRISPR spacers. PloS one.

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Todd J Treangen, Brian D Ondov, Sergey Koren, Adam M Phillippy (2014). The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome biology.

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Todd J Treangen, Rosslyn A Maybank, Sana Enke, Mary Beth Friss, Lynn F Diviak, David KR Karaolis, Sergey Koren, Brian Ondov, Adam M Phillippy, Nicholas H Bergman, others (2014). Complete genome sequence of the quality control strain Staphylococcus aureus subsp. aureus ATCC 25923. Genome announcements.

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Sergey Koren, Todd J Treangen, Christopher M Hill, Mihai Pop, Adam M Phillippy (2014). Automated ensemble assembly and validation of microbial genomes. BMC bioinformatics.

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Aleksey V Zimin, Adam S Cornish, Mnirnal D Maudhoo, Robert M Gibbs, Xiongfei Zhang, Sanjit Pandey, Daniel T Meehan, Kristin Wipfler, Steven E Bosinger, Zachary P Johnson, others (2014). A new rhesus macaque assembly and annotation for next-generation sequencing analyses. Biology direct.

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Todd J Treangen, Sergey Koren, Daniel D Sommer, Bo Liu, Irina Astrovskaya, Brian Ondov, Aaron E Darling, Adam M Phillippy, Mihai Pop (2013). MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome Biology.

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Robin Harrington, Brian D Ondov, Diana Radune, Mary Beth Friss, Joy Klubnik, Lynn Diviak, Jonathan Hnath, Stephen R Cendrowski, Thomas E Blank, David Karaolis, others (2013). Genome sequence of the attenuated Carbosap vaccine strain of Bacillus anthracis. Genome announcements.

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Christopher M Hill, Irina Astrovskaya, Howard Huang, Sergey Koren, Atif Memon, Todd J Treangen, Mihai Pop (2013). De novo likelihood-based measures for comparing metagenomic assemblies. 2013 IEEE International Conference on Bioinformatics and Biomedicine.

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Human Microbiome Project Consortium, others (2012). Structure, function and diversity of the healthy human microbiome. nature.

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Adam Phillippy, Todd Treangen (2012). Irreconcilable differences: divorcing geographic mutation and recombination rates within a global MRSA clone. Genome Biology.

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Steven L Salzberg, Adam M Phillippy, Aleksey Zimin, Daniela Puiu, Tanja Magoc, Sergey Koren, Todd J Treangen, Michael C Schatz, Arthur L Delcher, Michael Roberts, others (2012). GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome research.

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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, others (2012). Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PloS one.

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Barbara A Methé, Karen E Nelson, Mihai Pop, Heather H Creasy, Michelle G Giglio, Curtis Huttenhower, Dirk Gevers, Joseph F Petrosino, Sahar Abubucker, Jonathan H Badger, others (2012). A framework for human microbiome research. nature.

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(2012). A framework for human microbiome research. nature.

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Sergey Koren, Todd Treangen, Mihai Pop (2011). ScaffViz: visualizing metagenome assemblies. Genome Biology.

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Todd J Treangen, Steven L Salzberg (2011). Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics.

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Todd J Treangen, Dan D Sommer, Florent E Angly, Sergey Koren, Mihai Pop (2011). Next generation sequence assembly with AMOS. Current Protocols in Bioinformatics.

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Todd J Treangen, Eduardo PC Rocha (2011). Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS genetics.

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Jacob Enk, Alison Devault, Regis Debruyne, Christine E King, Todd Treangen, Dennis O'Rourke, Steven L Salzberg, Daniel Fisher, Ross MacPhee, Hendrik Poinar (2011). Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome biology.

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Sergey Koren, Todd J Treangen, Mihai Pop (2011). Bambus 2: scaffolding metagenomes. Bioinformatics.

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Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen, Mihai Pop (2011). Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics.

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Todd J Treangen, Eduardo PC Rocha (2010). Repeatoire: Detecting intragenomic repeat families within the context of intergenomic comparisons. ISBRA 2010.

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Todd Treangen, Xavier Messeguer (2009). Novel computational methods for large scale genome comparison. 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008).

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Todd J Treangen, Anne-Laure Abraham, Marie Touchon, Eduardo PC Rocha (2009). Genesis, effects and fates of repeats in prokaryotic genomes. FEMS microbiology reviews.

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Todd J Treangen, Ole Herman Ambur, Tone Tonjum, Eduardo PC Rocha (2008). The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome biology.

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Aaron E Darling, Todd J Treangen, Xavier Messeguer, Nicole T Perna (2007). Analyzing patterns of microbial evolution using the mauve genome alignment system. Comparative Genomics.

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Aaron E Darling, Todd J Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T Perna (2006). Procrastination leads to efficient filtration for local multiple alignment. International Workshop on Algorithms in Bioinformatics.

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Todd Treangen, Xavier Messeguer (2006). M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC bioinformatics.

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