Todd J. Treangen

According to our database, Todd J. Treangen authored at least 22 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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

GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly.

Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.

Bryce Kille, Erik Garrison, Todd J. Treangen, Adam M. Phillippy

Bioinform., September, 2023

Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.

Qi Wang, Michael Nute, Todd J. Treangen

Bioinform., 2023

Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence.

Felix Quintana, Todd J. Treangen, Lydia E. Kavraki

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

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

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022

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

Proceedings of the International Conference on Machine Learning, 2022

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

Proceedings of the SIGMOD '21: International Conference on Management of Data, 2021

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

Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2021

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

Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster.

Qi Wang, Ryan A. Leo Elworth, Tian-Rui Liu, Todd J. Treangen

Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

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, Advait Balaji, Christian Diaz, Nidhi Shah, Jeremy D. Selengut, Chris Hulme-Lowe

Proceedings of the 2019 IEEE International Conference on Bioinformatics and Biomedicine, 2019

2016

Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection.

Amelia Bateman, Todd J. Treangen, Mihai Pop

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2014

Automated ensemble assembly and validation of microbial genomes.

Sergey Koren, Todd J. Treangen, Christopher Michael Hill, Mihai Pop, Adam M. Phillippy

BMC Bioinform., 2014

2013

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

Proceedings of the 2013 IEEE International Conference on Bioinformatics and Biomedicine, 2013

2011

Bambus 2: scaffolding metagenomes.

Sergey Koren, Todd J. Treangen, Mihai Pop

Bioinform., 2011

2009

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

2008

Novel Computational Methods for Large Scale Genome Comparison.

Todd J. Treangen, Xavier Messeguer

Proceedings of the 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics, 2008

Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats.

Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer

Proceedings of the Bioinformatics Research and Applications, 2008

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

Procrastination Leads to Efficient Filtration for Local Multiple Alignment.

Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

2004

M-GCAT: Multiple Genome Comparison and Alignment Tool.

Todd J. Treangen, Xavier Messeguer

Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004