Todd J. Treangen

28 papers A* 1B 1C 2Journal 13Unranked 11
YearRankTypeTitle / Venue / Authors
2026 J jnl
AutoCSF: Provably Space-Efficient Indexing of Skewed Key-Value Workloads via Filter-Augmented Compressed Static Functions.
CoRR
David Torres Ramos, Vihan Lakshman, Chen Luo, Todd J. Treangen, Benjamin Coleman
2025 J jnl
A near-tight lower bound on the density of forward sampling schemes.
Bioinform.
Bryce Kille, Ragnar Groot Koerkamp, Drake McAdams, Alan Liu, Todd J. Treangen
2025 — conf
tMHG-Finder: Tree-Guided Maximal Homologous Group Finder for Bacterial Genomes.
RECOMB-CG
Yongze Yin, Bryce Kille, Huw A. Ogilvie, Todd J. Treangen, Luay Nakhleh
2024 J jnl
GraSSRep: Graph-Based Self-Supervised Learning for Repeat Detection in Metagenomic Assembly.
CoRR
Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra
2024 B conf
GraSSRep: Graph-Based Self-supervised Learning for Repeat Detection in Metagenomic Assembly.
RECOMB
Ali Azizpour, Advait Balaji, Todd J. Treangen, Santiago Segarra
2024 J jnl
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets.
Bioinform.
Bryce Kille, Michael G. Nute, Victor Huang, Eddie Kim, Adam M. Phillippy, Todd J. Treangen
2024 J jnl
Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.
Bioinform.
Kristen D. Curry, Feiqiao Brian Yu, Summer E. Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo P. C. Rocha, Todd J. Treangen
2023 J jnl
Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.
Bioinform.
Qi Wang, Michael Nute, Todd J. Treangen
2023 — conf
Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence.
BCB
Felix Quintana, Todd J. Treangen, Lydia E. Kavraki
2023 J jnl
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation.
Bioinform.
Bryce Kille, Erik Garrison, Todd J. Treangen, Adam M. Phillippy
2023 — conf
SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens.
BCB
Advait Balaji, Yunxi Liu, Michael G. Nute, Bingbing Hu, Anthony D. Kappell, Danielle S. Lesassier, Gene D. Godbold, Krista Ternus, Todd J. Treangen
2022 A* conf
One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence Streams.
ICML
Benjamin Coleman, Benito Geordie, Li Chou, Ryan A. Leo Elworth, Todd J. Treangen, Anshumali Shrivastava
2021 — conf
Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets.
IPDPS Workshops
Bryce Kille, Yunxi Liu, Nicolae Sapoval, Michael Nute, Lawrence Rauchwerger, Nancy M. Amato, Todd J. Treangen
2021 — conf
Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO).
SIGMOD Conference
Gaurav Gupta, Minghao Yan, Benjamin Coleman, Bryce Kille, Ryan A. Leo Elworth, Tharun Medini, Todd J. Treangen, Anshumali Shrivastava
2019 J jnl
Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO).
CoRR
Gaurav Gupta, Minghao Yan, Benjamin Coleman, Bryce Kille, Ryan A. Leo Elworth, Tharun Medini, Todd J. Treangen, Anshumali Shrivastava
2019 C conf
Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster.
WABI
Qi Wang, Ryan A. Leo Elworth, Tian Rui Liu, Todd J. Treangen
2019 J jnl
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.
Briefings Bioinform.
Nathan D. Olson, Todd J. Treangen, Christopher Michael Hill, Victoria Cepeda-Espinoza, Jay Ghurye, Sergey Koren, Mihai Pop
2019 — conf
SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest.
BIBM
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
2016 — conf
Limitations of Current Approaches for Reference-Free, Graph-Based Variant Detection.
BCB
Amelia Bateman, Todd J. Treangen, Mihai Pop
2014 J jnl
Automated ensemble assembly and validation of microbial genomes.
BMC Bioinform.
Sergey Koren, Todd J. Treangen, Christopher Michael Hill, Mihai Pop, Adam M. Phillippy
2013 — conf
De novo likelihood-based measures for comparing metagenomic assemblies.
BIBM
Christopher Michael Hill, Irina Astrovskaya, Howard Huang, Sergey Koren, Atif Memon, Todd J. Treangen, Mihai Pop
2011 J jnl
Bambus 2: scaffolding metagenomes.
Bioinform.
Sergey Koren, Todd J. Treangen, Mihai Pop
2009 J jnl
A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats.
IEEE ACM Trans. Comput. Biol. Bioinform.
Todd J. Treangen, Aaron E. Darling, Guillaume Achaz, Mark A. Ragan, Xavier Messeguer, Eduardo P. C. Rocha
2008 — conf
Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats.
ISBRA
Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer
2008 — conf
Novel Computational Methods for Large Scale Genome Comparison.
IWPACBB
Todd J. Treangen, Xavier Messeguer
2006 J jnl
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.
BMC Bioinform.
Todd J. Treangen, Xavier Messeguer
2006 C conf
Procrastination Leads to Efficient Filtration for Local Multiple Alignment.
WABI
Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna
2004 — conf
M-GCAT: Multiple Genome Comparison and Alignment Tool.
Spanish Bioinformatics Conference
Todd J. Treangen, Xavier Messeguer