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Todd J. Treangen
Todd J. Treangen
Associate Professor, Department of Computer Science, Rice University
Verifierad e-postadress på rice.edu - Startsida
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Structure, function and diversity of the healthy human microbiome
nature 486 (7402), 207-214, 2012
110532012
Mash: fast genome and metagenome distance estimation using MinHash
BD Ondov, TJ Treangen, P Melsted, AB Mallonee, NH Bergman, S Koren, ...
Genome biology 17, 1-14, 2016
28702016
Repetitive DNA and next-generation sequencing: computational challenges and solutions
TJ Treangen, SL Salzberg
Nature Reviews Genetics, 2011
21152011
A framework for human microbiome research
Nature 486 (7402), 215-221, 2012
17842012
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
TJ Treangen, BD Ondov, S Koren, AM Phillippy
Genome biology 15, 1-15, 2014
16372014
GAGE: A critical evaluation of genome assemblies and assembly algorithms
SL Salzberg, AM Phillippy, A Zimin, D Puiu, T Magoc, S Koren, ...
Genome research 22 (3), 557-567, 2012
9022012
Structure, function and diversity of the healthy human microbiome
HMP Consortium
nature 486 (7402), 207-214, 2012
7002012
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
TJ Treangen, EPC Rocha
PLoS genetics 7 (1), e1001284, 2011
5832011
Deep sequencing of the oral microbiome reveals signatures of periodontal disease
B Liu, LL Faller, N Klitgord, V Mazumdar, M Ghodsi, DD Sommer, ...
PloS one 7 (6), e37919, 2012
4962012
Comprehensive multi-omics analysis reveals mitochondrial stress as a central biological hub for spaceflight impact
WA da Silveira, H Fazelinia, SB Rosenthal, EC Laiakis, MS Kim, ...
Cell 183 (5), 1185-1201. e20, 2020
2882020
Current progress and open challenges for applying deep learning across the biosciences
N Sapoval, A Aghazadeh, MG Nute, DA Antunes, A Balaji, R Baraniuk, ...
Nature Communications 13 (1), 1728, 2022
2732022
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
B Liu, T Gibbons, M Ghodsi, T Treangen, M Pop
BMC Genomics 12 (Suppl 2), S4, 2011
2652011
Next generation sequence assembly with AMOS
TJ Treangen, DD Sommer, FE Angly, S Koren, M Pop
Current Protocols in Bioinformatics 33 (1), 11.8. 1-11.8. 18, 2011
2652011
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
TJ Treangen, S Koren, DD Sommer, B Liu, I Astrovskaya, B Ondov, ...
Genome Biology 14 (1), R2, 2013
2402013
A new rhesus macaque assembly and annotation for next-generation sequencing analyses
AV Zimin, AS Cornish, MD Maudhoo, RM Gibbs, X Zhang, S Pandey, ...
Biology direct 9, 1-15, 2014
1962014
Genesis, effects and fates of repeats in prokaryotic genomes
TJ Treangen, AL Abraham, M Touchon, EPC Rocha
FEMS microbiology reviews 33 (3), 539-571, 2009
1862009
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data
KD Curry, Q Wang, MG Nute, A Tyshaieva, E Reeves, S Soriano, Q Wu, ...
Nature methods 19 (7), 845-853, 2022
1742022
Bambus 2: scaffolding metagenomes
S Koren, TJ Treangen, M Pop
Bioinformatics 27 (21), 2964-2971, 2011
1732011
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
DJ Nasko, S Koren, AM Phillippy, TJ Treangen
Genome biology 19, 1-10, 2018
1722018
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
ND Olson, TJ Treangen, CM Hill, V Cepeda-Espinoza, J Ghurye, S Koren, ...
Briefings in bioinformatics 20 (4), 1140-1150, 2019
1642019
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Artiklar 1–20