- Assistant Professor
- Computer Science
- Email: noah_daniels@uri.edu
- Office Location: Tyler 250
- Website
Research
I am working on algorithms for huge data sets, primarily in computational biology, but also in astronomy and social networks. My research includes “compressive genomics,” which co-opts data compression to accelerate analysis on large genomic data sets. I have also worked extensively in structural bioinformatics, and am also interested in programming languages and functional programming. Most fundamentally, I am interested in how nature makes seemingly intractable problems tractable (such as protein folding).
Education
2013 | Ph.D. | Tufts University | Computer Science |
2006 | M.S. | Tufts University | Computer Science |
2001 | B.S. cum laude | Tufts University | Computer Science |
Selected Publications
- Computational Biology in the 21st Century: Scaling with Compressive Algorithms (with Bonnie Berger and Y. William Yu) Communications of the ACM
- Entropy-scaling search of massive biological data (with Y. William Yu, David Christian Danko, and Bonnie Berger) Cell Systems
- MRFy: Approximate Markov random fields for remote homology detection (with Andrew Gallant, Norman Ramsey, and Lenore Cowen) IEE/ACM TCBB 2015 preprint
- Compressive genomics for protein databases (with Andrew Gallant, Jian Peng, Lenore Cowen, Michael Baym, Bonnie Berger) ISMB 2013 Research project page
- Remote homology detection in proteins using graphical models (my dissertation) ArXiv 2013 / preprint
- Experience Report: Haskell in Computational Biology (with Andrew Gallant and Norman Ramsey) ICFP 2012 / preprint
- Formatt: Correcting Protein Multiple Structural Alignments by Sequence Peeking (with Shilpa Nadimpalli and Lenore Cowen) BMC Bioinformatics 2012 / preprint Software
- SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone (with Raghu Hosur, Bonnie Berger, Lenore Cowen) Bioinformatics 2012 / preprint Webserver
- Touring Protein Space with Matt (with Anoop Kumar, Matt Menke, Lenore Cowen) ACM/TCBB 2012 / preprint Mattbench website
Course Information
- CSC 440 – Algorithm Analysis