Nute MG - Search Results

1

Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data.

Curry KD, Wang Q, Nute MG, Tyshaieva A, Reeves E, Soriano S, Wu Q, Graeber E, Finzer P, Mendling W, Savidge T, Villapol S, Dilthey A, Treangen TJ. Curry KD, et al. Among authors: nute mg. Nat Methods. 2022 Jul;19(7):845-853. doi: 10.1038/s41592-022-01520-4. Epub 2022 Jun 30. Nat Methods. 2022. PMID: 35773532 Free PMC article.

2

Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets.

Kille B, Liu Y, Sapoval N, Nute M, Rauchwerger L, Amato N, Treangen TJ. Kille B, et al. ArXiv [Preprint]. 2021 May 7:arXiv:2105.03062v1. ArXiv. 2021. PMID: 33972927 Free PMC article. Preprint.

3

It takes guts to learn: machine learning techniques for disease detection from the gut microbiome.

Curry KD, Nute MG, Treangen TJ. Curry KD, et al. Among authors: nute mg. Emerg Top Life Sci. 2021 Dec 21;5(6):815-827. doi: 10.1042/ETLS20210213. Emerg Top Life Sci. 2021. PMID: 34779841 Free PMC article. Review.

4

Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study.

Soriano S, Curry K, Sadrameli SS, Wang Q, Nute M, Reeves E, Kabir R, Wiese J, Criswell A, Schodrof S, Britz GW, Gadhia R, Podell K, Treangen T, Villapol S. Soriano S, et al. Brain Behav Immun Health. 2022 Mar 1;21:100438. doi: 10.1016/j.bbih.2022.100438. eCollection 2022 May. Brain Behav Immun Health. 2022. PMID: 35284846 Free PMC article.

5

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

Sapoval N, Aghazadeh A, Nute MG, Antunes DA, Balaji A, Baraniuk R, Barberan CJ, Dannenfelser R, Dun C, Edrisi M, Elworth RAL, Kille B, Kyrillidis A, Nakhleh L, Wolfe CR, Yan Z, Yao V, Treangen TJ. Sapoval N, et al. Among authors: nute mg. Nat Commun. 2022 Apr 1;13(1):1728. doi: 10.1038/s41467-022-29268-7. Nat Commun. 2022. PMID: 35365602 Free PMC article. Review.

6

KOMB: K-core based de novo characterization of copy number variation in microbiomes.

Balaji A, Sapoval N, Seto C, Leo Elworth RA, Fu Y, Nute MG, Savidge T, Segarra S, Treangen TJ. Balaji A, et al. Among authors: nute mg. Comput Struct Biotechnol J. 2022 Jun 17;20:3208-3222. doi: 10.1016/j.csbj.2022.06.019. eCollection 2022. Comput Struct Biotechnol J. 2022. PMID: 35832621 Free PMC article.

7

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

Kille B, Balaji A, Sedlazeck FJ, Nute M, Treangen TJ. Kille B, et al. Genome Biol. 2022 Aug 29;23(1):182. doi: 10.1186/s13059-022-02735-6. Genome Biol. 2022. PMID: 36038949 Free PMC article. Review.

8

Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.

Wang Q, Nute M, Treangen TJ. Wang Q, et al. Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i47-i56. doi: 10.1093/bioinformatics/btad236. Bioinformatics. 2023. PMID: 37387148 Free PMC article.

9

Parsnp 2.0: scalable core-genome alignment for massive microbial datasets.

Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ. Kille B, et al. Among authors: nute mg. Bioinformatics. 2024 May 2;40(5):btae311. doi: 10.1093/bioinformatics/btae311. Bioinformatics. 2024. PMID: 38724243 Free PMC article.

10

Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet.

Sapoval N, Liu Y, Curry KD, Kille B, Huang W, Kokroko N, Nute MG, Tyshaieva A, Dilthey A, Molloy EK, Treangen TJ. Sapoval N, et al. Among authors: nute mg. bioRxiv [Preprint]. 2024 Aug 25:2024.06.01.596961. doi: 10.1101/2024.06.01.596961. bioRxiv. 2024. PMID: 38895276 Free PMC article. Preprint.

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