| 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 | 293 | 2019 |
| 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 | 259 | 2022 |
| 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 | 182 | 2015 |
| 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 | 165 | 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 | 92 | 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 | 88 | 2018 |
| 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 | 84 | 2019 |
| 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 | 33 | 2019 |
| 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 | 30 | 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 | 26 | 2022 |
| 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 | 25 | 2021 |
| HIPPI: highly accurate protein family classification with ensembles of HMMs N Nguyen, M Nute, S Mirarab, T Warnow BMC genomics 17, 89-100, 2016 | 25 | 2016 |
| Scaling statistical multiple sequence alignment to large datasets M Nute, T Warnow BMC genomics 17, 135-144, 2016 | 19 | 2016 |
| 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 | 12 | 2020 |
| 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 | 10 | 2024 |
| 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 | 10 | 2022 |
| 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 | 6 | 2021 |
| Multiplexed Detection, Partitioning, and Persistence of Wild-Type and Vaccine Strains of Measles, Mumps, and Rubella Viruses in Wastewater J Wu, MX Wang, P Kalvapalle, M Nute, TJ Treangen, K Ensor, L Hopkins, ... Environmental Science & Technology 58 (50), 21930-21941, 2024 | 4 | 2024 |
| Microbial Community Profiling Protocol with Full‐length 16S rRNA Sequences and Emu KD Curry, S Soriano, MG Nute, S Villapol, A Dilthey, TJ Treangen Current Protocols 4 (3), e978, 2024 | 3 | 2024 |
| 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 | 3 | 2017 |
Todd J. TreangenAssociate Professor, Department of Computer Science, Rice UniversityAdresse e-mail validée de rice.edu