Todd J Treangen (Todd Treangen, T J Treangen)

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 65

Top Topics

Machine Learning

Dna Methylation

Mild Traumatic Brain Injury

Top Venues

Nature communications

bioRxiv : the preprint server for biology

Bioinformatics (Oxford, England)

This page only lists publications with an associated author ORCID identifier.

Publications

Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J Treangen, Fritz J Sedlazeck
MethPhaser: methylation-based long-read haplotype phasing of human genomes. Nature communications 15 (1) (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. Bioinformatics (Oxford, England) 40 (5) (2024)
Kristen D Curry, Feiqiao Brian Yu, Summer E Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo P C Rocha, Todd J Treangen
Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs. bioRxiv : the preprint server for biology (2024)
Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J Treangen, Fritz J Sedlazeck
MethPhaser: methylation-based long-read haplotype phasing of human genomes. Nature communications 15 (1) (2024)
Nicolae Sapoval, Yunxi Liu, Kristen D Curry, Bryce Kille, Wenyu Huang, Natalie Kokroko, Michael G Nute, Alona Tyshaieva, Alexander T Dilthey, Erin K Molloy, Todd J Treangen
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet. bioRxiv : the preprint server for biology (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. Bioinformatics (Oxford, England) 40 (5) (2024)
Daniel Paiva Agustinho, Yilei Fu, Vipin K Menon, Ginger A Metcalf, Todd J Treangen, Fritz J Sedlazeck
Unveiling microbial diversity: harnessing long-read sequencing technology. Nature methods 21 (6) (2024)
Nicolae Sapoval, Yunxi Liu, Kristen D Curry, Bryce Kille, Wenyu Huang, Natalie Kokroko, Michael G Nute, Alona Tyshaieva, Alexander T Dilthey, Erin K Molloy, Todd J Treangen
Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet. bioRxiv : the preprint server for biology (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets. bioRxiv : the preprint server for biology (2024)
Nicolae Sapoval, Yunxi Liu, Kristen D Curry, Bryce Kille, Wenyu Huang, Natalie Kokroko, Michael G Nute, Alona Tyshaieva, Alexander T Dilthey, Erin K Molloy, Todd J Treangen
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet. bioRxiv : the preprint server for biology (2024)
Ali Azizpour, Advait Balaji, Todd J Treangen, Santiago Segarra
Graph-based self-supervised learning for repeat detection in metagenomic assembly. Genome research (2024)
Michael Xiangjiang Wang, Esther G Lou, Nicolae Sapoval, Eddie Kim, Prashant Bharadwaj Kalvapalle, Bryce Kille, R A Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, Todd J Treangen
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens. Nature communications 15 (1) (2024)
Yunxi Liu, Nicolae Sapoval, Pilar Gallego-García, Laura Tomás, David Posada, Todd J Treangen, Lauren B Stadler
Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater. Nature communications 15 (1) (2024)
Michael Xiangjiang Wang, Esther G Lou, Nicolae Sapoval, Eddie Kim, Prashant Bharadwaj Kalvapalle, Bryce Kille, R A Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, Todd J Treangen
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens. Nature communications 15 (1) (2024)
Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J Treangen, Fritz J Sedlazeck
MethPhaser: methylation-based long-read haplotype phasing of human genomes. Nature communications 15 (1) (2024)
Nicolae Sapoval, Yunxi Liu, Kristen D Curry, Bryce Kille, Wenyu Huang, Natalie Kokroko, Michael G Nute, Alona Tyshaieva, Alexander T Dilthey, Erin K Molloy, Todd J Treangen
Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet. bioRxiv : the preprint server for biology (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets. bioRxiv : the preprint server for biology (2024)
Michael Xiangjiang Wang, Esther G Lou, Nicolae Sapoval, Eddie Kim, Prashant Bharadwaj Kalvapalle, Bryce Kille, R A Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, Todd J Treangen
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens. Nature communications 15 (1) (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. Bioinformatics (Oxford, England) 40 (5) (2024)
Kristen D Curry, Feiqiao Brian Yu, Summer E Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo P C Rocha, Todd J Treangen
Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs. bioRxiv : the preprint server for biology (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets. bioRxiv : the preprint server for biology (2024)
Michael Xiangjiang Wang, Esther G Lou, Nicolae Sapoval, Eddie Kim, Prashant Bharadwaj Kalvapalle, Bryce Kille, R A Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, Todd J Treangen
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens. Nature communications 15 (1) (2024)
Nicolae Sapoval, Yunxi Liu, Kristen D Curry, Bryce Kille, Wenyu Huang, Natalie Kokroko, Michael G Nute, Alona Tyshaieva, Alexander T Dilthey, Erin K Molloy, Todd J Treangen
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet. bioRxiv : the preprint server for biology (2024)
Bryce Kille, Michael G Nute, Victor Huang, Eddie Kim, Adam M Phillippy, Todd J Treangen
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. Bioinformatics (Oxford, England) 40 (5) (2024)
Nicolae Sapoval, Yunxi Liu, Kristen D Curry, Bryce Kille, Wenyu Huang, Natalie Kokroko, Michael G Nute, Alona Tyshaieva, Alexander T Dilthey, Erin K Molloy, Todd J Treangen
Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet. bioRxiv : the preprint server for biology (2024)
Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J Treangen, Fritz J Sedlazeck
MethPhaser: methylation-based long-read haplotype phasing of human genomes. Nature communications 15 (1) (2024)
Yunxi Liu, Nicolae Sapoval, Pilar Gallego-García, Laura Tomás, David Posada, Todd J Treangen, Lauren B Stadler
Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater. Nature communications 15 (1) (2024)
Yunxi Liu, Nicolae Sapoval, Pilar Gallego-García, Laura Tomás, David Posada, Todd J Treangen, Lauren B Stadler
Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater. Nature communications 15 (1) (2024)
Daniel Paiva Agustinho, Yilei Fu, Vipin K Menon, Ginger A Metcalf, Todd J Treangen, Fritz J Sedlazeck
Unveiling microbial diversity: harnessing long-read sequencing technology. Nature methods 21 (6) (2024)
Chin-Ting Wu, William C Shropshire, Micah M Bhatti, Sherry Cantu, Israel K Glover, Selvalakshmi Selvaraj Anand, Xiaojun Liu, Awdhesh Kalia, Todd J Treangen, Roy F Chemaly, Amy Spallone, Samuel Shelburne
Rapid Whole Genome Characterization of High-Risk Pathogens Using Long-Read Sequencing to Identify Potential Healthcare Transmission. medRxiv : the preprint server for health sciences (2024)
Nicolae Sapoval, Yunxi Liu, Kristen D Curry, Bryce Kille, Wenyu Huang, Natalie Kokroko, Michael G Nute, Alona Tyshaieva, Alexander T Dilthey, Erin K Molloy, Todd J Treangen
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet. bioRxiv : the preprint server for biology (2024)
Kristen D Curry, Feiqiao Brian Yu, Summer E Vance, Santiago Segarra, Devaki Bhaya, Rayan Chikhi, Eduardo P C Rocha, Todd J Treangen
Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs. bioRxiv : the preprint server for biology (2024)
Daniel Paiva Agustinho, Yilei Fu, Vipin K Menon, Ginger A Metcalf, Todd J Treangen, Fritz J Sedlazeck
Unveiling microbial diversity: harnessing long-read sequencing technology. Nature methods (2024)
Yunxi Liu, Nicolae Sapoval, Pilar Gallego-García, Laura Tomás, David Posada, Todd J Treangen, Lauren B Stadler
Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater. Nature communications 15 (1) (2024)
Todd J Treangen, Moshe Y Vardi
The long game of tenure. Nature biotechnology (2023)
Michael Xiangjiang Wang, Esther G Lou, Nicolae Sapoval, Eddie Kim, Prashant Bharadwaj Kalvapalle, Bryce Kille, R A Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, Todd J Treangen
Olivar: fully automated and variant aware primer design for multiplex tiled amplicon sequencing of pathogen genomes. bioRxiv : the preprint server for biology (2023)
Yunxi Liu, Nicolae Sapoval, Pilar Gallego-García, Laura Tomás, David Posada, Todd J Treangen, Lauren B Stadler
Crykey: Rapid Identification of SARS-CoV-2 Cryptic Mutations in Wastewater. medRxiv : the preprint server for health sciences (2023)
Nídia Sequeira Trovão, Vincent Pan, Chirag Goel, Pilar Gallego-García, Yunxi Liu, Christopher Barbara, Rebecca Borg, Mark Briffa, Chanelle Cilia, Laura Grech, Mario Vassallo, Todd J Treangen, David Posada, Afshin Beheshti, Joseph Borg, Graziella Zahra
Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta. Microbiology spectrum (2023)
Nicolae Sapoval, Yunxi Liu, Esther G Lou, Loren P Hopkins, Katherine B Ensor, Rebecca Schneider, Lauren B Stadler, Todd J Treangen
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater. Nature communications 14 (1) (2023)
Nicolae Sapoval, Yunxi Liu, Esther G Lou, Loren P Hopkins, Katherine B Ensor, Rebecca Schneider, Lauren B Stadler, Todd J Treangen
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater. Nature communications 14 (1) (2023)
Nicolae Sapoval, Yunxi Liu, Esther G Lou, Loren P Hopkins, Katherine B Ensor, Rebecca Schneider, Lauren B Stadler, Todd J Treangen
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater. Nature communications 14 (1) (2023)
Michael Xiangjiang Wang, Esther G Lou, Nicolae Sapoval, Eddie Kim, Prashant Bharadwaj Kalvapalle, Bryce Kille, R A Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, Todd J Treangen
Olivar: fully automated and variant aware primer design for multiplex tiled amplicon sequencing of pathogen genomes. bioRxiv : the preprint server for biology (2023)
Qi Wang, Michael Nute, Todd J Treangen
Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities. Bioinformatics (Oxford, England) 39 (39 Suppl 1) (2023)
Michael Xiangjiang Wang, Esther G Lou, Nicolae Sapoval, Eddie Kim, Prashant Bharadwaj Kalvapalle, Bryce Kille, R A Leo Elworth, Yunxi Liu, Yilei Fu, Lauren B Stadler, Todd J Treangen
Olivar: fully automated and variant aware primer design for multiplex tiled amplicon sequencing of pathogen genomes. bioRxiv : the preprint server for biology (2023)
Ronan W O'Connell, Kshitij Rai, Trenton C Piepergerdes, Kian D Samra, Jack A Wilson, Shujian Lin, Thomas H Zhang, Eduardo M Ramos, Andrew Sun, Bryce Kille, Kristen D Curry, Jason W Rocks, Todd J Treangen, Pankaj Mehta, Caleb J Bashor
Ultra-high throughput mapping of genetic design space. bioRxiv : the preprint server for biology (2023)
Advait Balaji, Bryce Kille, Anthony D Kappell, Gene D Godbold, Madeline Diep, R A Leo Elworth, Zhiqin Qian, Dreycey Albin, Daniel J Nasko, Nidhi Shah, Mihai Pop, Santiago Segarra, Krista L Ternus, Todd J Treangen
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning. Genome biology 23 (1) (2022)
Pilar Gallego-García, Nair Varela, Nuria Estévez-Gómez, Loretta De Chiara, Iria Fernández-Silva, Diana Valverde, Nicolae Sapoval, Todd J Treangen, Benito Regueiro, Jorge Julio Cabrera-Alvargonzález, Víctor Del Campo, Sonia Pérez-Castro, David Posada
Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters. Virus evolution 8 (1) (2022)
Kristen D Curry, Qi Wang, Michael G Nute, Alona Tyshaieva, Elizabeth Reeves, Sirena Soriano, Qinglong Wu, Enid Graeber, Patrick Finzer, Werner Mendling, Tor C Savidge, Sonia Villapol, Alexander T Dilthey, Todd J Treangen
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nature methods 19 (7) (2022)
Sirena Soriano, Kristen D Curry, Qi Wang, Elsbeth Chow, Todd J Treangen, Sonia Villapol
Fecal Microbiota Transplantation Derived from Alzheimer's Disease Mice Worsens Brain Trauma Outcomes in Wild-Type Controls. International journal of molecular sciences 23 (9) (2022)
Yunxi Liu, Joshua Kearney, Medhat Mahmoud, Bryce Kille, Fritz J Sedlazeck, Todd J Treangen
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data. Nature communications 13 (1) (2022)
So Hyun Park, Mingming Cao, Yidan Pan, Timothy H Davis, Lavanya Saxena, Harshavardhan Deshmukh, Yilei Fu, Todd J Treangen, Vivien A Sheehan, Gang Bao
Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing. Science advances 8 (42) (2022)
Nicolae Sapoval, Yunxi Liu, Esther G Lou, Loren Hopkins, Katherine B Ensor, Rebecca Schneider, Lauren B Stadler, Todd J Treangen
Enabling Earlier Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater. medRxiv : the preprint server for health sciences (2022)
Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, Dinler Amaral Antunes, Advait Balaji, Richard Baraniuk, C J Barberan, Ruth Dannenfelser, Chen Dun, Mohammadamin Edrisi, R A Leo Elworth, Bryce Kille, Anastasios Kyrillidis, Luay K Nakhleh, Cameron R Wolfe, Zhi Yan, Victoria Yao, Todd J Treangen
Current progress and open challenges for applying deep learning across the biosciences. Nature communications 13 (1) (2022)
Michael D Jochum, Michael D Lee, Kristen D Curry, Viktorija Zaksas, Elizabeth Vitalis, Todd J Treangen, Kjersti M Aagaard, Krista L Ternus
Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease. Scientific reports 12 (1) (2022)
Yilei Fu, Medhat Mahmoud, Viginesh Vaibhav Muraliraman, Fritz J Sedlazeck, Todd J Treangen
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. GigaScience 10 (9) (2022)
Yunxi Liu, R A Leo Elworth, Michael D Jochum, Kjersti M Aagaard, Todd J Treangen
De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee. Nature communications 13 (1) (2022)
William C Shropshire, Anna Konovalova, P McDaneld, M Gohel, B Strope, P Sahasrabhojane, C N Tran, David E Greenberg, J Kim, X Zhan, Samuel L Aitken, Micah M Bhatti, T C Savidge, Todd J Treangen, Blake M Hanson, César A Arias, Samuel A Shelburne Iii
Systematic Analysis of Mobile Genetic Elements Mediating β-Lactamase Gene Amplification in Noncarbapenemase-Producing Carbapenem-Resistant Enterobacterales Bloodstream Infections. mSystems 7 (5) (2022)
Bryce Kille, Advait Balaji, Fritz J Sedlazeck, Michael Nute, Todd J Treangen
Multiple genome alignment in the telomere-to-telomere assembly era. Genome biology 23 (1) (2022)
J Tyson McDonald, Francisco Javier Enguita, Deanne Taylor, Robert J Griffin, Waldemar Priebe, Mark R Emmett, Marisa McGrath, Mohammad M Sajadi, Anthony D Harris, Jean Clement, Joseph M Dybas, Nukhet Aykin-Burns, Joseph W Guarnieri, Larry N Singh, Peter Grabham, Stephen B Baylin, Aliza Yousey, Andrea N Pearson, Peter M Corry, Amanda Saravia-Butler, Thomas R Aunins, Prashant Nagpal, Cem Meydan, Jonathan Foox, Christopher Mozsary, Bianca Cerqueira, Viktorija Zaksas, Urminder Singh, Eve Syrkin Wurtele, Sylvain V Costes, Diego Galeano, Alberto Paccanaro, Suzanne L Meinig, Robert S Hagan, Natalie M Bowman, null null, Matthew C Wolfgang, Selin Altinok, Nicolae Sapoval, Todd J Treangen, Matthew Frieman, Charles R Vanderburg, Douglas C Wallace, Jonathan C Schisler, Christopher E Mason, Anushree Chatterjee, Robert Meller, Afshin Behesti
The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection. bioRxiv : the preprint server for biology (2021)
Nicolae Sapoval, Medhat Mahmoud, Michael D Jochum, Yunxi Liu, R A Leo Elworth, Qi Wang, Dreycey Albin, Huw A Ogilvie, Michael D Lee, Sonia Villapol, Kyle M Hernandez, Irina Maljkovic Berry, Jonathan Foox, Afshin Behesti, Krista L Ternus, Kjersti M Aagaard, David Posada, Christopher E Mason, Fritz J Sedlazeck, Todd J Treangen
SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission. Genome research 31 (4) (2021)
Kristen D Curry, Michael G Nute, Todd J Treangen
It takes guts to learn: machine learning techniques for disease detection from the gut microbiome. Emerging topics in life sciences (2021)
Qi Wang, Bryce Kille, Tian Rui Liu, R A Leo Elworth, Todd J Treangen
PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment. Nature communications 12 (1) (2021)
Yunxi Liu, Joshua Kearney, Medhat Mahmoud, Bryce Kille, Fritz J Sedlazeck, Todd J Treangen
Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data. bioRxiv : the preprint server for biology (2021)
R A Leo Elworth, Christian Diaz, Jing Yang, Paul de Figueiredo, Krista L Ternus, Todd J Treangen
Synthetic DNA and biosecurity: Nuances of predicting pathogenicity and the impetus for novel computational approaches for screening oligonucleotides. PLoS pathogens 16 (8) (2020)
Daniel J Nasko, Sergey Koren, Adam M Phillippy, Todd J Treangen
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification. Genome biology 19 (1) (2018)