Computer Science and Statistics

College of Arts and Sciences

Assistant Professor Noah Daniels

Contact Information

Office Tyler 128
Dept. of Computer Science and Statistics
Tyler Hall
9 Greenhouse Road, Suite 2
University of Rhode Island
Kingston, RI, 02881

Telephone (401) 874-2701
Email ndaniels@cs.uri.edu
Personal Webpage cs.uri.edu/~ndaniels

 

Education

2013 Ph.D. Tufts University Computer Science
2006 M.S. Tufts University Computer Science
2001 B.S. cum laude Tufts University Computer Science

Previous Positions

2013 – 2016 Postdoctoral Fellow Massachusetts Institute of Technology
Department of Mathematics and the
Computation and Biology Group in CSAIL
Boston, MA

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).

Teaching

  • CSC 440 – Algorithm Analysis (Fall 2016)

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

 

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