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ORCIDTodd J. Treangen
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2020 – today
- 2024
[c14]Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra:
GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly. RECOMB 2024: 372-376- [i2]Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra:
GraSSRep: Graph-Based Self-Supervised Learning for Repeat Detection in Metagenomic Assembly. CoRR abs/2402.09381 (2024) - 2023
- [j7]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) - [j6]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): 47-56 (2023) - [c13]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: 17:1-17:10 - [c12]Felix Quintana, Todd J. Treangen, Lydia E. Kavraki:
Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence. BCB 2023: 103:1-103:6 - 2022
- [c11]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: 4202-4218 - 2021
- [c10]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: 204-208 - [c9]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: 2226-2234
2010 – 2019
- 2019
- [j5]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): 1140-1150 (2019) - [c8]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:
SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest. BIBM 2019: 1729-1736 - [c7]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: 19:1-19:12 - [i1]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 abs/1910.04358 (2019) - 2016
- [c6]Amelia Bateman, Todd J. Treangen, Mihai Pop:
Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection. BCB 2016: 499-500 - 2014
- [j4]Sergey Koren, Todd J. Treangen, Christopher Michael Hill, Mihai Pop, Adam M. Phillippy:
Automated ensemble assembly and validation of microbial genomes. BMC Bioinform. 15: 126 (2014) - 2013
- [c5]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: 94-98 - 2011
- [j3]Sergey Koren, Todd J. Treangen, Mihai Pop:
Bambus 2: scaffolding metagenomes. Bioinform. 27(21): 2964-2971 (2011)
2000 – 2009
- 2009
- [j2]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): 180-189 (2009) - 2008
- [c4]Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer:
Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. ISBRA 2008: 74-86 - [c3]Todd J. Treangen, Xavier Messeguer:
Novel Computational Methods for Large Scale Genome Comparison. IWPACBB 2008: 68-73 - 2006
- [j1]Todd J. Treangen, Xavier Messeguer:
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinform. 7: 433 (2006) - [c2]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: 126-137 - 2004
- [c1]Todd J. Treangen, Xavier Messeguer:
M-GCAT: Multiple Genome Comparison and Alignment Tool. Spanish Bioinformatics Conference 2004: 30-33
Coauthor Index
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