Michael Nute
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Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes
KR Amato, JG Sanders, SJ Song, M Nute, JL Metcalf, LR Thompson, ...
The ISME journal 13 (3), 576-587, 2019
A comparative study of SVDquartets and other coalescent-based species tree estimation methods
J Chou, A Gupta, S Yaduvanshi, R Davidson, M Nute, S Mirarab, ...
BMC genomics 16, 1-11, 2015
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
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
Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows
N Shah, MG Nute, T Warnow, M Pop
Bioinformatics 35 (9), 1613-1614, 2019
Long-branch attraction in species tree estimation: inconsistency of partitioned likelihood and topology-based summary methods
S Roch, M Nute, T Warnow
Systematic biology 68 (2), 281-297, 2019
The Performance of Coalescent-Based Species Tree Estimation Methods under Models of Missing Data
M Nute, J Chou, EK Molloy, T Warnow
BMC Genomics 19 (5), 41-57, 2018
Evaluating statistical multiple sequence alignment in comparison to other alignment methods on protein data sets
M Nute, E Saleh, T Warnow
Systematic biology 68 (3), 396-411, 2019
HIPPI: highly accurate protein family classification with ensembles of HMMs
N Nguyen, M Nute, S Mirarab, T Warnow
BMC genomics 17, 89-100, 2016
Multiple genome alignment in the telomere-to-telomere assembly era
B Kille, A Balaji, FJ Sedlazeck, M Nute, TJ Treangen
Genome Biology 23 (1), 182, 2022
Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study
S Soriano, K Curry, SS Sadrameli, Q Wang, M Nute, E Reeves, R Kabir, ...
Brain, Behavior, & Immunity-Health 21, 100438, 2022
Scaling statistical multiple sequence alignment to large datasets
M Nute, T Warnow
BMC genomics 17, 135-144, 2016
It takes guts to learn: machine learning techniques for disease detection from the gut microbiome
KD Curry, MG Nute, TJ Treangen
Emerging Topics in Life Sciences 5 (6), 815-827, 2021
NJst and ASTRID are not statistically consistent under a random model of missing data
JA Rhodes, MG Nute, T Warnow
arXiv preprint arXiv:2001.07844, 2020
Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets
B Kille, Y Liu, N Sapoval, M Nute, L Rauchwerger, N Amato, TJ Treangen
2021 IEEE International Parallel and Distributed Processing Symposium …, 2021
KOMB: K-core based de novo characterization of copy number variation in microbiomes
A Balaji, N Sapoval, C Seto, RAL Elworth, Y Fu, MG Nute, T Savidge, ...
Computational and Structural Biotechnology Journal 20, 3208-3222, 2022
Statistical consistency of coalescent-based species tree methods under models of missing data
M Nute, J Chou
Comparative Genomics: 15th International Workshop, RECOMB CG 2017, Barcelona …, 2017
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets
B Kille, MG Nute, V Huang, E Kim, AM Phillippy, TJ Treangen
Bioinformatics 40 (5), btae311, 2024
SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens
A Balaji, Y Liu, MG Nute, B Hu, A D. Kappell, D S. Lesassier, ...
Proceedings of the 14th ACM International Conference on Bioinformatics …, 2023
SeqScreen-Nano: a computational platform for rapid, in-field characterization of previously unseen pathogens
A Balaji, Y Liu, MG Nute, B Hu, A Kappell, DS LeSassier, GD Godbold, ...
bioRxiv, 2023.02. 10.528096, 2023
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Articles 1–20