Computational Molecular Biology  

The references in this section are on computational molecular biology, in a more general context, and may not end up having any connection to our work in biological computation. I am cataloguing them here for now so I'll know I have them, but eventually they should probably be moved to a separate bibliography.

  

Stahl & Goheen '63

Walter R. Stahl and Harry E. Goheen. "Molecular Algorithms." J. Theoret. Biol. 5:266-287, 1963.

Shows that the operations that cells perform on macromolecules are computable, which is of course instantly obvious to any programmer. Worth a look though, for its historical value in computational molecular biology.

  

Krogh et al. '93

Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjölander and David Haussler. "Hidden Markov Models in Computational Biology: Applications to Protein Modeling." University of California, Santa Cruz technical report UCSC-CRL-93-32.

From Bonnie's class.

  

Board et al. '94

John A. Board Jr., Laxmikant V. Kalé, Klaus Schulten, Robert D. Skeel and Tamar Schlick. "Modeling Biomolecules: Larger Scales, Longer Durations." IEEE Computational Science and Engineering, Winter 1994, pp. 19-30.

I investigated molecular modeling in Fall of '94 as a possible thesis research area.

  

Craven & Shavlik '94

Mark W. Craven and Jude W. Shavlik. "Machine Learning Approaches to Gene Recognition." IEEE Expert, April 1994, pp. 2-10.

  

Karp & Mavrovouniotis '94

Peter D. Karp and Michael L. Mavrovouniotis. "Representing, Analyzing, and Synthesizing Biochemical Pathways." IEEE Expert, April 1994, pp. 11-21.

  

Grate et al. '94

Leslie Grate, Mark Herbster, Richard Hughey, David Haussler, I. Saira Mian and Harry Noller. "RNA Modeling Using Gibbs Sampling and Stochastic Context Free Grammars." ISMB-94. (Conference on Intelligent Systems in Molecular Biology.) Pages 138-146.

  

Sakakibara et al. '94

Yasubumi Sakakibara, Michael Brown, Rebecca C. Underwood, I. Saira Mian and David Haussler. "Stochastic Context-Free Grammars for Modeling RNA." Proceedings of the 27th Annual Hawaii Int'l. Conf. on Systems Sciences, 1994.

From MIT class 18.409, Bonnie Berger, Fall 1994.

  

Berger & Wilson '94

Bonnie Berger and David B. Wilson. "Improved Algorithms for Protein Motif Recognition." Unpublished draft report.

I believe this has been published by now, need to get the reference from Bonnie.