Todd J. Treangen

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 14

Top Topics

Protein Structural

Recent Advances

Top Venues

Publications

Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra
GraSSRep: Graph-Based Self-Supervised Learning for Repeat Detection in Metagenomic Assembly. CoRR (2024)
Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra
GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly. RECOMB (2024)
Qi Wang, Michael Nute, Todd J. Treangen
Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities. Bioinform. 39 (Supplement-1) (2023)
Bryce Kille, Erik Garrison, Todd J. Treangen, Adam M. Phillippy
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation. Bioinform. 39 (9) (2023)
Advait Balaji, Yunxi Liu, Michael G. Nute, Bingbing Hu, Anthony D. Kappell, Danielle S. Lesassier, Gene D. Godbold, Krista Ternus, Todd J. Treangen
SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens. BCB (2023)
Felix Quintana, Todd J. Treangen, Lydia E. Kavraki
Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence. BCB (2023)
Benjamin Coleman, Benito Geordie, Li Chou, Ryan A. Leo Elworth, Todd J. Treangen, Anshumali Shrivastava
One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence Streams. ICML (2022)
Bryce Kille, Yunxi Liu, Nicolae Sapoval, Michael Nute, Lawrence Rauchwerger, Nancy M. Amato, Todd J. Treangen
Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets. IPDPS Workshops (2021)
Gaurav Gupta, Minghao Yan, Benjamin Coleman, Bryce Kille, Ryan A. Leo Elworth, Tharun Medini, Todd J. Treangen, Anshumali Shrivastava
Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO). SIGMOD Conference (2021)
Dreycey Albin, Pravin Muthu, Gene Godbold, Mikael Lindvall, Madeline Diep, Adam Porter, Mihai Pop, Krista Ternus, Todd J. Treangen, Dan Nasko, Ryan A. Leo Elworth, Jacob Lu, Advait Balaji, Christian Diaz, Nidhi Shah, Jeremy D. Selengut, Chris Hulme-Lowe
SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest. BIBM (2019)
Gaurav Gupta, Minghao Yan, Benjamin Coleman, Bryce Kille, Ryan A. Leo Elworth, Tharun Medini, Todd J. Treangen, Anshumali Shrivastava
Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO). CoRR (2019)
Nathan D. Olson, Todd J. Treangen, Christopher Michael Hill, Victoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Mihai Pop
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes. Briefings Bioinform. 20 (4) (2019)
Qi Wang, Ryan A. Leo Elworth, Tian-Rui Liu, Todd J. Treangen
Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster. WABI (2019)
Amelia Bateman, Todd J. Treangen, Mihai Pop
Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection. BCB (2016)
Sergey Koren, Todd J. Treangen, Christopher Michael Hill, Mihai Pop, Adam M. Phillippy
Automated ensemble assembly and validation of microbial genomes. BMC Bioinform. 15 (2014)
Christopher Michael Hill, Irina Astrovskaya, Howard Huang, Sergey Koren, Atif Memon, Todd J. Treangen, Mihai Pop
De novo likelihood-based measures for comparing metagenomic assemblies. BIBM (2013)
Sergey Koren, Todd J. Treangen, Mihai Pop
Bambus 2: scaffolding metagenomes. Bioinform. 27 (21) (2011)
Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier Messeguer, Eduardo P. C. Rocha
A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (2) (2009)
Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer
Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. ISBRA (2008)
Todd J. Treangen, Xavier Messeguer
Novel Computational Methods for Large Scale Genome Comparison. IWPACBB (2008)
Todd J. Treangen, Xavier Messeguer
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinform. 7 (2006)
Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna
Procrastination Leads to Efficient Filtration for Local Multiple Alignment. WABI (2006)
Todd J. Treangen, Xavier Messeguer
M-GCAT: Multiple Genome Comparison and Alignment Tool. Spanish Bioinformatics Conference (2004)