Todd J. Treangen

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Sergey KorenAssociate Investigator, NHGRI/NIHVerified email at nih.gov
Adam M. PhillippyDirector, Center for Genomics and Data Science Research, NHGRI, NIHVerified email at nih.gov
Mihai PopProfessor of Computer Science, University of Maryland, College ParkVerified email at umd.edu
Ryan Leo ElworthPostdoctoral Scientist, Rice UniversityVerified email at rice.edu
Nicolae SapovalPostdoctoral Researcher, Department of Computer Science, Rice UniversityVerified email at rice.edu
Brian OndovYale School of MedicineVerified email at yale.edu
Nicholas BergmanDirector, National Biodefense Analysis and Countermeasures CenterVerified email at st.dhs.gov
Michael NuteRice UniversityVerified email at rice.edu
Steven SalzbergBloomberg Distinguished Professor, Johns Hopkins UniversityVerified email at jhu.edu
Sonia VillapolHouston Methodist Research InstituteVerified email at houstonmethodist.org
Bryce KilleRice UniversityVerified email at rice.edu
Advait BalajiRice UniversityVerified email at rice.edu
Kristen D. CurryPhD student in Computer Science, Rice UniversityVerified email at rice.edu
Eduardo RochaCNRS, Institut PasteurVerified email at pasteur.fr
Daniel D SommerNational Biodefense Analysis and Countermeasures CenterVerified email at nbacc.dhs.gov
Yunxi LiuDepartment of Computer Science, Rice UniversityVerified email at rice.edu
Lauren B. StadlerRice UniversityVerified email at rice.edu
Aaron DarlingIllumina Australia; Professor @ University of Technology SydneyVerified email at illumina.com
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030Verified email at bcm.edu
Krista (Fritz) TernusSignature Science, LLCVerified email at signaturescience.com

Todd J. Treangen

Associate Professor, Department of Computer Science, Rice University

Verified email at rice.edu - Homepage

Bioinformatics Computational Genomics Metagenomics


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Structure, function and diversity of the healthy human microbiome nature 486 (7402), 207-214, 2012	10709	2012
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	2704	2016
A framework for human microbiome research nature 486 (7402), 215-221, 2012	2478	2012
Repetitive DNA and next-generation sequencing: computational challenges and solutions TJ Treangen, SL Salzberg Nature Reviews Genetics, 2011	2088	2011
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	1593	2014
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	898	2012
Structure, function and diversity of the healthy human microbiome HMP Consortium nature 486 (7402), 207-214, 2012	655	2012
Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes TJ Treangen, EPC Rocha PLoS genetics 7 (1), e1001284, 2011	587	2011
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	486	2012
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	270	2020
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	262	2011
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	261	2011
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	245	2022
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	240	2013
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	189	2014
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	182	2009
Bambus 2: scaffolding metagenomes S Koren, TJ Treangen, M Pop Bioinformatics 27 (21), 2964-2971, 2011	174	2011
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	161	2018
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	157	2019
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	147	2022

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