Noah Daniels


Previous Positions

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


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).


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