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Reference EntriesFull Text
Treangen, Todd J
Journal title:American Men & Women of Science : A Biographical Directory of Today’s Leaders in Physical, Biological and Related Sciences: TRA-WID, 2022, p.11517-11517
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Reference EntriesFull Text
Treangen, Todd J
Journal title:American Men & Women of Science : A Biographical Directory of Today’s Leaders in Physical, Biological and Related Sciences: SOR-TRN, 2021, p.11487-11487
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ArticlesPeer ReviewedFull Text
Repetitive DNA and next-generation sequencing: computational challenges and solutions
Author / Creator:Treangen, Todd J. ; Salzberg, Steven L.
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Genetics, 2012-01, Vol.13 (1), p.36-46
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ArticlesPeer ReviewedFull Text
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Author / Creator:Treangen, Todd J ; Ondov, Brian D ; Koren, Sergey ; Phillippy, Adam M
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2014-11, Vol.15 (11), p.524-524, Article 524
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ArticlesPeer ReviewedFull Text
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Author / Creator:Nasko, Daniel J. ; Koren, Sergey ; Phillippy, Adam M. ; Treangen, Todd J.
Publisher:England: BioMed Central
Journal title:Genome Biology, 2018-10, Vol.19 (1), p.165-165, Article 165
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ArticlesPeer ReviewedFull Text
Current progress and open challenges for applying deep learning across the biosciences
Author / Creator:Sapoval, Nicolae ; Aghazadeh, Amirali ; Nute, Michael G. ; Antunes, Dinler A. ; Balaji, Advait ; Baraniuk, Richard ; Barberan, C. J. ; Dannenfelser, Ruth ; Dun, Chen ; Edrisi, Mohammadamin ; Elworth, R. A. Leo ; Kille, Bryce ; Kyrillidis, Anastasios ; Nakhleh, Luay ; Wolfe, Cameron R. ; Yan, Zhi ; Yao, Vicky ; Treangen, Todd J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-04, Vol.13 (1), p.1728-1728, Article 1728
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ArticlesPeer ReviewedFull Text
Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
Author / Creator:Liu, Bo ; Faller, Lina L. ; Klitgord, Niels ; Mazumdar, Varun ; Ghodsi, Mohammad ; Sommer, Daniel D. ; Gibbons, Theodore R. ; Treangen, Todd J. ; Chang, Yi-Chien ; Li, Shan ; Stine, O. Colin ; Hasturk, Hatice ; Kasif, Simon ; Segrè, Daniel ; Pop, Mihai ; Amar, Salomon
Publisher:United States: Public Library of Science
Journal title:PloS one, 2012-06, Vol.7 (6), p.e37919
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ArticlesPeer ReviewedFull Text
Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes
Author / Creator:Treangen, Todd J. ; Rocha, Eduardo P. C.
Publisher:United States: Public Library of Science
Journal title:PLoS genetics, 2011-01, Vol.7 (1), p.e1001284
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ArticlesPeer ReviewedFull Text
Multiple genome alignment in the telomere-to-telomere assembly era
Author / Creator:Kille, Bryce ; Balaji, Advait ; Sedlazeck, Fritz J. ; Nute, Michael ; Treangen, Todd J.
Publisher:London: BioMed Central Ltd
Journal title:Genome Biology, 2022-08, Vol.23 (1), p.182-182, Article 182
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ArticlesPeer ReviewedFull Text
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
Author / Creator:Olson, Nathan D ; Treangen, Todd J ; Hill, Christopher M ; Cepeda-Espinoza, Victoria ; Ghurye, Jay ; Koren, Sergey ; Pop, Mihai
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1140-1150
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ArticlesPeer ReviewedFull Text
MethPhaser: methylation-based long-read haplotype phasing of human genomes
Author / Creator:Fu, Yilei ; Aganezov, Sergey ; Mahmoud, Medhat ; Beaulaurier, John ; Juul, Sissel ; Treangen, Todd J. ; Sedlazeck, Fritz J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-06, Vol.15 (1), p.5327-12, Article 5327
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ArticlesPeer ReviewedFull Text
Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data
Author / Creator:Liu, Yunxi ; Kearney, Joshua ; Mahmoud, Medhat ; Kille, Bryce ; Sedlazeck, Fritz J. ; Treangen, Todd J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-03, Vol.13 (1), p.1321-1321, Article 1321
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ArticlesPeer ReviewedFull Text
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
Author / Creator:Sapoval, Nicolae ; Liu, Yunxi ; Lou, Esther G. ; Hopkins, Loren ; Ensor, Katherine B. ; Schneider, Rebecca ; Stadler, Lauren B. ; Treangen, Todd J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-05, Vol.14 (1), p.2834-2834, Article 2834
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ArticlesPeer ReviewedFull Text
PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment
Author / Creator:Wang, Qi ; Kille, Bryce ; Liu, Tian Rui ; Elworth, R. A. Leo ; Treangen, Todd J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-02, Vol.12 (1), p.1167-1167, Article 1167
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ArticlesPeer ReviewedFull Text
De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee
Author / Creator:Liu, Yunxi ; Elworth, R. A. Leo ; Jochum, Michael D. ; Aagaard, Kjersti M. ; Treangen, Todd J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2022-11, Vol.13 (1), p.6799-6799, Article 6799
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ArticlesPeer ReviewedFull Text
Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater
Author / Creator:Liu, Yunxi ; Sapoval, Nicolae ; Gallego-García, Pilar ; Tomás, Laura ; Posada, David ; Treangen, Todd J. ; Stadler, Lauren B.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-05, Vol.15 (1), p.4545-4545, Article 4545
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ArticlesPeer ReviewedFull Text
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning
Author / Creator:Balaji, Advait ; Kille, Bryce ; Kappell, Anthony D. ; Godbold, Gene D. ; Diep, Madeline ; Elworth, R. A. Leo ; Qian, Zhiqin ; Albin, Dreycey ; Nasko, Daniel J. ; Shah, Nidhi ; Pop, Mihai ; Segarra, Santiago ; Ternus, Krista L. ; Treangen, Todd J.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2022-06, Vol.23 (1), p.133-133, Article 133
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ArticlesPeer ReviewedFull Text
Probiotic treatment induces sex-dependent neuroprotection and gut microbiome shifts after traumatic brain injury
Author / Creator:Holcomb, Morgan ; Marshall, Austin G. ; Flinn, Hannah ; Lozano-Cavazos, Mariana ; Soriano, Sirena ; Gomez-Pinilla, Fernando ; Treangen, Todd J. ; Villapol, Sonia
Publisher:England: BioMed Central Ltd
Journal title:Journal of neuroinflammation, 2025-04, Vol.22 (1), p.114-24, Article 114
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ArticlesPeer ReviewedFull Text
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
Author / Creator:Wang, Michael X. ; Lou, Esther G. ; Sapoval, Nicolae ; Kim, Eddie ; Kalvapalle, Prashant ; Kille, Bryce ; Elworth, R. A. Leo ; Liu, Yunxi ; Fu, Yilei ; Stadler, Lauren B. ; Treangen, Todd J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-07, Vol.15 (1), p.6306-12, Article 6306
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ArticlesPeer ReviewedFull Text
Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers
Author / Creator:Davison, Michelle ; Treangen, Todd J. ; Koren, Sergey ; Pop, Mihai ; Bhaya, Devaki
Publisher:United States: Public Library of Science
Journal title:PloS one, 2016-09, Vol.11 (9), p.e0160574-e0160574
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Showing 1 to 20 of 67 results

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Treangen, Todd J

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Treangen, Todd J

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Repetitive DNA and next-generation sequencing: computational challenges and solutions

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The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

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RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

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Current progress and open challenges for applying deep learning across the biosciences

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Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

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Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

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Multiple genome alignment in the telomere-to-telomere assembly era

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Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes

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MethPhaser: methylation-based long-read haplotype phasing of human genomes

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Rescuing low frequency variants within intra-host viral populations directly from Oxford Nanopore sequencing data

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Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

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PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment

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De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee

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Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater

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SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning

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Probiotic treatment induces sex-dependent neuroprotection and gut microbiome shifts after traumatic brain injury

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Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens

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Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers

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