M-GCAT: Multiple Genome Comparison and Alignment Tool. - Todd J. Treangen; Xavier Messeguer (Spanish Bioinformatics Conference, 2004)

Procrastination Leads to Efficient Filtration for Local Multiple Alignment. - Aaron E. Darling; Todd J. Treangen; Louxin Zhang; Carla Kuiken; Xavier Messeguer; Nicole T. Perna (WABI, 2006)

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

Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. - Todd J. Treangen; Aaron E. Darling; Mark A. Ragan; Xavier Messeguer (ISBRA, 2008)

Novel Computational Methods for Large Scale Genome Comparison. - Todd J. Treangen; Xavier Messeguer (IWPACBB, 2008)

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. - Todd J. Treangen; Aaron E. Darling; Guillaume Achaz; Mark A. Ragan; Xavier Messeguer; Eduardo P. C. Rocha (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

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

De novo likelihood-based measures for comparing metagenomic assemblies. - Christopher Michael Hill; Irina Astrovskaya; Howard Huang; Sergey Koren; Atif Memon; Todd J. Treangen; Mihai Pop (BIBM, 2013)

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

Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection. - Amelia Bateman; Todd J. Treangen; Mihai Pop (BCB, 2016)

SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest. - Dreycey Albin; Pravin Muthu; Gene Godbold; Mikael Lindvall; Madeline Diep; Adam A. Porter; Mihai Pop; Krista Ternus; Todd J. Treangen; Dan Nasko; Ryan A. Leo Elworth; Jacob Lu; et al. (BIBM, 2019)

Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster. - Qi Wang 038; Ryan A. Leo Elworth; Tian Rui Liu 003; Todd J. Treangen (WABI, 2019)

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

Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets. - Bryce Kille; Yunxi Liu; Nicolae Sapoval; Michael Nute; Lawrence Rauchwerger; Nancy M. Amato; Todd J. Treangen (IPDPS Workshops, 2021)

Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO). - Gaurav Gupta; Minghao Yan; Benjamin Coleman; Bryce Kille; Ryan A. Leo Elworth; Tharun Medini; Todd J. Treangen; Anshumali Shrivastava (SIGMOD Conference, 2021)

One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence Streams. - Benjamin Coleman; Benito Geordie; Li Chou; Ryan A. Leo Elworth; Todd J. Treangen; Anshumali Shrivastava (ICML, 2022)

SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens. - Advait Balaji; Yunxi Liu; Michael G. Nute; Bingbing Hu; Anthony D. Kappell; Danielle S. Lesassier; Gene D. Godbold; Krista Ternus; Todd J. Treangen (BCB, 2023)

Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence. - Felix Quintana; Todd J. Treangen; Lydia E. Kavraki (BCB, 2023)

Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities. - Qi Wang 038; Michael Nute; Todd J. Treangen (Bioinform., 2023)

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

GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly. - Ali Azizpour; Advait Balaji; Todd J. Treangen; Santiago Segarra (RECOMB, 2024)

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; Rayan Chikhi; Eduardo P. C. Rocha; Todd J. Treangen (Bioinform., 2024)

tMHG-Finder: Tree-Guided Maximal Homologous Group Finder for Bacterial Genomes. - Yongze Yin; Bryce Kille; Huw A. Ogilvie; Todd J. Treangen; Luay Nakhleh (RECOMB-CG, 2025)