Research Scientist, Department of Computer Science, Rice University
Mike is a Research Scientist in the Treangen Lab and has been a part of the lab since joining as a Postdoc in 2020 except for a brief stint away to work on a startup. He received his Ph.D. in Statistics in 2019 from the University of Illinois at Urbana-Champaign where he was advised by Dr. Tandy Warnow in the Department of Computer Science and worked on algorithms related to multiple sequence alignment and phylogenetic tree estimation, in particular applying these methods to studying microbial communities. He was co-advised by Dr. Rebecca Stumpf in the Department of Anthropology where he and other lab members developed novel methods to compare the microbiomes of human and non-human primates. From 2012 to 2014 he was also an assistant coach for the Illini Rowing Club.
Improving Parsnp, the lab’s multiple genome alignment software, to extend its alignment beyond the core genome.
Experimenting with new ways to explore microbial community structures using unsupervised deep-learning models.
Comparative genomics of Clostridioides Difficile.
Untangling the potential for the tumor microenvironment in human cancer to host resident microbes that affect patient prognosis, particularly in solid tumors.
…among others.
Previously, Mike was a NLM Biomedical Informatics postdoctoral fellow, funded by NIH grant T15LM007093. Current funding includes NIH NIAID P01 (P01AI152999), NIH NIAID GCID (U19AI144297) and NSF MIM (EF 2126387).
Mike also has a vibrant domestic life as a supportive spouse and father of three. He is the coach of the 2024-2025 Minuteman Sparks Mite Major “Red” hockey team.
References
2024
Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet
Nicolae Sapoval, Yunxi Liu, Kristen Curry, and 8 more authors
@article{sapoval2024lightweight,title={Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet},author={Sapoval, Nicolae and Liu, Yunxi and Curry, Kristen and Kille, Bryce and Huang, Wenyu and Kokroko, Natalie and Nute, Michael G and Tyshaieva, Alona and Dilthey, Alexander T and Molloy, Erin and others},year={2024},journal={bioRxiv},publisher={Cold Spring Harbor Laboratory},pages={2024--06}}
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets
Bryce Kille, Michael G Nute, Victor Huang, and 3 more authors
@article{kille2024parsnp,title={Parsnp 2.0: scalable core-genome alignment for massive microbial datasets},author={Kille, Bryce and Nute, Michael G and Huang, Victor and Kim, Eddie and Phillippy, Adam M and Treangen, Todd J},year={2024},journal={Bioinformatics},publisher={Oxford University Press},volume={40},number={5},pages={btae311}}
2023
Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities
@article{wang2023bakdrive,title={Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities},author={Wang, Qi and Nute, Michael and Treangen, Todd J},year={2023},journal={Bioinformatics},publisher={Oxford University Press},volume={39},number={Supplement\_1},pages={i47--i56}}
SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens
Advait Balaji, Yunxi Liu, Michael G Nute, and 6 more authors
In Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2023
@inproceedings{balaji2023seqscreen,title={SeqScreen-Nano: a computational platform for streaming, in-field characterization of microbial pathogens},author={Balaji, Advait and Liu, Yunxi and Nute, Michael G and Hu, Bingbing and D. Kappell, Anthony and S. Lesassier, Danielle and D. Godbold, Gene and Ternus, Krista and Treangen, Todd},year={2023},booktitle={Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},pages={1--10}}
2022
Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data
Kristen D Curry, Qi Wang, Michael G Nute, and 8 more authors
@article{curry2022emu,title={Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data},author={Curry, Kristen D and Wang, Qi and Nute, Michael G and Tyshaieva, Alona and Reeves, Elizabeth and Soriano, Sirena and Wu, Qinglong and Graeber, Enid and Finzer, Patrick and Mendling, Werner and others},year={2022},journal={Nature methods},publisher={Nature Publishing Group US New York},volume={19},number={7},pages={845--853}}
Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study
Sirena Soriano, Kristen Curry, Saeed S Sadrameli, and 8 more authors
@article{soriano2022alterations,title={Alterations to the gut microbiome after sport-related concussion in a collegiate football players cohort: A pilot study},author={Soriano, Sirena and Curry, Kristen and Sadrameli, Saeed S and Wang, Qi and Nute, Michael and Reeves, Elizabeth and Kabir, Rasadul and Wiese, Jonathan and Criswell, Amber and Schodrof, Sarah and others},year={2022},journal={Brain, Behavior, \& Immunity-Health},publisher={Elsevier},volume={21},pages={100438}}
Multiple genome alignment in the telomere-to-telomere assembly era
Bryce Kille, Advait Balaji, Fritz J Sedlazeck, and 2 more authors
@article{kille2022multiple,title={Multiple genome alignment in the telomere-to-telomere assembly era},author={Kille, Bryce and Balaji, Advait and Sedlazeck, Fritz J and Nute, Michael and Treangen, Todd J},year={2022},journal={Genome Biology},publisher={BioMed Central London},volume={23},number={1},pages={182}}
Current progress and open challenges for applying deep learning across the biosciences
Nicolae Sapoval, Amirali Aghazadeh, Michael G Nute, and 8 more authors
@article{sapoval2022current,title={Current progress and open challenges for applying deep learning across the biosciences},author={Sapoval, Nicolae and Aghazadeh, Amirali and Nute, Michael G and Antunes, Dinler A and Balaji, Advait and Baraniuk, Richard and Barberan, CJ and Dannenfelser, Ruth and Dun, Chen and Edrisi, Mohammadamin and others},year={2022},journal={Nature Communications},publisher={Nature Publishing Group UK London},volume={13},number={1},pages={1728}}
2021
It takes guts to learn: machine learning techniques for disease detection from the gut microbiome
Kristen D Curry, Michael G Nute, and Todd J Treangen
@article{curry2021takes,title={It takes guts to learn: machine learning techniques for disease detection from the gut microbiome},author={Curry, Kristen D and Nute, Michael G and Treangen, Todd J},year={2021},journal={Emerging Topics in Life Sciences},publisher={Portland Press Ltd.},volume={5},number={6},pages={815--827}}
2020
KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities
Advait Balaji, Nicolae Sapoval, Charlie Seto, and 5 more authors
@article{balaji2020komb,title={KOMB: Graph-Based Characterization of Genome Dynamics in Microbial Communities},author={Balaji, Advait and Sapoval, Nicolae and Seto, Charlie and Elworth, RA Leo and Nute, Michael G and Savidge, Tor and Segarra, Santiago and Treangen, Todd J},year={2020},journal={bioRxiv},publisher={Cold Spring Harbor Laboratory},pages={2020--05}}
