Dr. Richard H. Lathrop --- Publications


(UNDER CONSTRUCTION --- eventually more online versions will appear here)


UNREVIEWED BOOK CHAPTERS, EDITED VOLUMES:


"Protein Threading," in Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics, eds. Dunn, M., Jorde, L., Little, P., Subramaniam, S., John Wiley & Sons, West Essex, UK (to appear). Word file (preprint version),


Proceedings, Genome Informatics 2002, eds. Nakai, K., Lathrop, R., Miyano, S., Takagi, T., Universal Academy Press, Tokyo, 2002.


(Guest Editor of Special Issue of Journal). ``Intelligent Systems in Biology II,'' ed. Lathrop, R.H., IEEE Intelligent Systems, 17(2), March/April, 2002.


(Guest Editor of Special Issue of Journal). ``Intelligent Systems in Biology,'' ed. Lathrop, R.H., IEEE Intelligent Systems, 16(6), November/December, 2001.


Proceedings, Sixth Intl. Conf. on Intelligent Systems for Molecular Biology, eds. Glasgow, J., Lathrop, R., Littlejohn, T., Major, F., Peitsch, M., Sankoff, D., Sensen, C., AAAI Press, Menlo Park, 1998.


"Analysis and Algorithms for Protein Sequence-Structure Alignment," Lathrop, R.H., Rogers, R.G. Jr., Bienkowska, J., Bryant, B.K.M., Buturovic, L.J., Gaitatzes, C., Nambudripad, R., White, J.V., and Smith, T.F., Chapter 12, pp. 227--283, in Computational Methods in Molecular Biology, ed. Salzberg, S.L., Searls, D.B., Kasif, S., Elsevier Science, Amsterdam, 1998.
(preprint version. Postscript, PDF)


"Predicting Protein Structure with Probabilistic Models," Stultz, C.M., Nambudripad, R., Lathrop, R.H., and White, J.V., in Protein Structural Biology in Biomedical Research, ed. Allewell, N., Woodward, C., Vol. 22B of Advances in Molecular and Cell Biology, 1997, series ed. Bittar, E.E., JAI Press, Greenwich, CT, USA, 1997.


"The Identification of Protein Functional Patterns," Smith, T.F., Lathrop, R.H. and Cohen, F.E., in Integrative Approaches to Molecular Biology, eds. Collado-Vides, J., Magasanik, B., and Smith, T.F., MIT Press, Cambridge, MA, 1996.


Proceedings, Second Intl. Conf. on Intelligent Systems for Molecular Biology, eds. Altman, R., Brutlag, D., Karp, P., Lathrop, R.H., and Searls, D., AAAI Press, Menlo Park, 1994.


"Massively Parallel Symbolic Induction of Protein Structure / Function Relationships," Lathrop, R.H., Webster, T.A., Smith, T.F., and Winston, P.H., pp. 157-173 in Machine Learning: From Theory to Applications, ed. Hanson, S., Remmele, W., and Rivest, R., Springer-Verlag, Berlin, 1993; also appeared in Proc. 27th Hawaii Intl. Conf. on System Sciences, IEEE Computer Soc. Press, 1991.


"Integrating AI With Sequence Analysis," Lathrop, R.H., Webster, T.A., Smith, R., Winston, P.H., and Smith, T.F., pp. 210-258 in Artificial Intelligence and Molecular Biology, ed. Hunter, L., AAAI Press, Menlo Park, 1993.


"ARIEL: A Massively Parallel Symbolic Learning Assistant for Protein Structure / Function," Lathrop, R.H., Webster, T.A., Smith, T.F., and Winston, P.H., in Artificial Intelligence at MIT: Expanding Frontiers, ed. Winston, P.H., and Shellard, S., MIT Press, Cambridge, MA, 1990.


REFEREED JOURNAL ARTICLES:


"Predicting oligonucleotide-directed mutagenesis failures in protein engineering," Wassman, C.D., Tam, P.Y., Lathrop, R.H., Weiss, G.A., Nucleic Acids Res., (in press).
(PDF Page Proofs)


"Information-Theoretic Dissection of Pairwise Contact Potentials," Cline, M.S., Karplus, K., Lathrop, R.H., Smith, T.F., Rogers, R.G. Jr., Haussler, D., Proteins: Structure, Function, Genetics, 49(1):7-14, 2002.
(PDF)


"Combinatorial Optimization in Rapidly Mutating Drug-Resistant Viruses," Lathrop, R.H., Pazzani, M.J., J. Combinatorial Optimization, 3:301-320, 1999.
(PDF)


"An Anytime Local-To-Global Optimization Algorithm for Protein Threading in O(m2n2) Space," Lathrop, R.H. J. Computational Biology, 6(3/4):405-418, 1999.
(PDF)


"A Bayes-Optimal Probability Theory that Unifies Protein Sequence-Structure Recognition and Alignment." Lathrop, R.H., Rogers, R.G. Jr., Smith, T.F., White, J.V., Bull. Math. Biol., 60:1039-1071, 1998.
(preprint version. Postscript, PDF)


"Current Limitations to Protein Threading Approaches," Smith, T.F., Lo Conte, L., Bienkowska, J., Gaitatzes, C., Rogers, R.G. Jr., and Lathrop, R.H., J. Computational Biol., 4(3):217-225, 1997.


"Solving the Multiple-Instance Problem with Axis-Parallel Rectangles," Dietterich, T.G., Lathrop, R.H., Lozano-Perez, T., Artificial Intelligence, 89:31-71, 1997.
(preprint version; the last three figures are not available online. Postscript, PDF)


"Global Optimum Protein Threading with Gapped Alignment and Empirical Pair Potentials," Lathrop, R.H. and Smith, T.F., J. Mol. Biol. (cover article), 255:641-665, Feb., 1996.
(preprint version; not all figures are available online. Postscript, PDF)


"Compass: A Shape-Based Machine Learning Tool for Drug Design," Jain, A.N., Dietterich, T.G., Lathrop, R.H., Chapman, D.E., Critchlow, R.E., Bauer, B.E., Webster, T.A., Lozano-Perez, T., J. Computer-Aided Molecular Design, 8:635-652, Dec., 1994.


"The Protein Threading Problem With Sequence Amino Acid Interaction Preferences Is NP-Complete," Lathrop, R.H., Protein Engineering, 7(9):1059-1068, Sept., 1994.
PDF


"Acid Helix-Turn Activator Motif," Zhu, Q.-L., Smith, T.F., Lathrop, R.H., and Figge, J., Proteins: Structure, Function, and Genetics, 8:156-163, 1990.


"Potential Structural Motifs for Reverse Transcriptases", Webster, T.A., Patarca, R., Lathrop, R.H., Smith, T.F., Molecular Biology and Evolution, 6(3):317-320, 1989.


"Pattern Descriptors and the Unidentified Reading Frame 6 Human mtDNA Dinucleotide-Binding Site", Webster, T.A., Lathrop, R.H., Smith, T.F., Proteins: Structure, Function, and Genetics, 3:97-101, 1988.


"ARIADNE: Pattern-Directed Inference and Hierarchical Abstraction in Protein Structure Recognition", Lathrop, R.H., Webster, T.A., Smith, T.F., Communications of the ACM, (cover article) 30(11):909-921, Nov., 1987.


"Prediction of a Common Structural Domain in Aminoacyl-tRNA Synthetases through Use of a New Pattern-Directed Inference System", Webster, T.A., Lathrop, R.H., Smith, T.F., Biochemistry, 26(22):6950-6957, Nov., 1987.


"Consensus Topography in the ATP Binding Site of the Simian Virus 40 and Polyomavirus Large Tumor Antigens", Bradley, M.K., Smith, T.F., Lathrop, R.H., Livingston, D.M., Webster, T.A., Proc. National Academy of Science (PNAS), 84:4026-4030, June, 1987.


"Parallelism in Manipulator Dynamics", Lathrop, R.H., Intl. J. of Robotics Research, Summer, 1985, pp. 80-102; also appeared in Proc. IEEE Intl. Conf. on Robotics and Automation, pp. 772-778, St. Louis, MO, March 25-28, 1985.


UNREVIEWED JOURNAL ARTICLES:


"Knowledge-based Avoidance of Drug-Resistant HIV Mutants," Lathrop, R.H., Steffen, N.R., Raphael, M., Deeds-Rubin, S., Pazzani, M.J., Cimoch, P.J., See, D.M., Tilles, J.G., (cover illustration; invited article from IAAI Conference paper of same title, below), AI Magazine, 20(1):13-25, Spring, 1999.
(preprint version. Postscript, PDF)


" `Functional abstraction' anticipates timing glitches," Lathrop, R.H., Hall, R.J., Duffy, G., Alexander, K.M., and Kirk, R.S., IEEE Spectrum, 27(4):41-42, April, 1990.


REFEREED CONFERENCE PROCEEDINGS:


(excludes workshop notes, posters, unrefereed abstracts, etc.)


"The Role of DNA Deformation Energy at Individual Base Steps for the Identification of DNA-Protein Binding Sites," Steffen, N.R., Murphy, S.D., Lathrop, R.H., Opel, M.L., Tolleri, L., Hatfield, G.W., p. 153-162 in Proc. Intl. Conf. on Genome Informatics, Tokyo, Japan, Dec. 16-18, 2002. In Genome Informatics 2002 (Genome Informatics Series No. 13), Universal Academy Press, Inc.
(PDF)


"DNA Sequence and Structure: Direct and Indirect Recognition in Protein-DNA Binding," Steffen, N.R., Murphy, S.D., Tolleri, L., Hatfield, G.W., Lathrop, R.H., p. 22-30 in Proc. Intl. Conf. on Intelligent Systems for Molecular Biology (ISMB'02), Edmonton, Canada, Aug 3--7, 2002. In Bioinformatics, 18 Suppl 1:S22-S30.
(PDF)


"Multi-Queue Branch-and-Bound Algorithm for Anytime Optimal Search with Biological Applications," Lathrop, R.H., Sazhin, A., Sun, Y., Steffen, N., Irani, S., (Best Paper Award), p. 73-82 in Proc. Intl. Conf. on Genome Informatics, Tokyo, Japan, Dec. 17-19, 2001. In Genome Informatics 2001 (Genome Informatics Series No. 12), Universal Academy Press, Inc.
(PDF)


"An Anytime Algorithm for Gapped Block Protein Threading with Pair Interactions," Lathrop, R.H., p. 238-249 in Proc. Intl. Conf. on Computational Molecular Biology (RECOMB'99), Lyon, France, April 11-14, 1999.
(Postscript, PDF)


"Knowledge-based Avoidance of Drug-Resistant HIV Mutants," Lathrop, R.H., Steffen, N.R., Raphael, M., Deeds-Rubin, S., Pazzani, M.J., Cimoch, P.J., See, D.M., Tilles, J.G., (Innovative Application Award winner), pp. 1071-1078 in Proc. Innovative Applications of Artificial Intelligence Conf., Madison, WI, USA, July 27-29, 1998.
(Postscript, PDF)


"Modeling Protein Homopolymeric Repeats: Possible Poly Glutamine Structural Motifs For Huntington's Disease," Lathrop, R.H., Casale, M., Tobias, D.J., Marsh, J.L., Thompson, L.M., pp. 105-114 in Proc. Intl. Conf. on Intelligent Systems and Molecular Biology, Montreal, Quebec, Canada, June 28-July 1, 1998.


"The Threading Approach to the Inverse Protein Folding Problem," Smith, T.F., Lo Conte, L., Bienkowska, J., Rogers, B., Gaitatzes, C., Lathrop, R.H., pp. 287-292 in Proc. Intl. Conf. on Computational Molecular Biology, Santa Fe, NM, Jan. 20-23, 1997.


"On the Learnability of the Uncomputable," Lathrop, R.H., pp. 302-309 in Proc. Intl. Conf. on Machine Learning, Bari, Italy, July 3-6, 1996.
(Postscript, PDF)


"From Electron Density and Sequence to Structure: Integrating Protein Image Analysis and Threading for Structure Determination," Baxter, K., Steeg, E., Lathrop, R.H., Glasgow, J., Fortier, S., pp. 25-33 in Proc. Intl. Conf. on Intelligent Systems and Molecular Biology, St. Louis, MO, USA, June 12-15, 1996.


"A Comparison of Dynamic Reposing and Tangent Distance for Drug Activity Prediction," Dietterich, T.G., Jain, A.N., Lathrop, R.H., Lozano-Perez, T., pp. 216-223 in Advances in Neural Information Processing Systems, 6, ed. Cowan, J.D., Tesauro, G., and Alspector, J., Morgan Kaufmann Press, April, 1994.


"A Branch-and-Bound Algorithm for Optimal Protein Threading with Pairwise (Contact Potential) Amino Acid Interactions," Lathrop, R.H. and Smith, T.F., Proc. 27th Hawaii Intl. Conf. on System Sciences, IEEE Computer Soc. Press, 1994.


"Advances in Functional Abstraction From Structure", Lathrop, R.H., Hall, R.J., Duffy, G., Alexander, K.M., Kirk, R.S., Proc. 25th IEEE/ACM Intl. Design Automation Conf. (DAC'88), Anaheim, CA, Jun 13-15, 1988.


"Automatic Generation of Behavioral Simulation Models Using Functional Abstraction", Alexander, K.M., Kirk, R.S., Lathrop, R.H., Hall, R.J., Duffy, G., Proc. Custom Integrated Circuits Conf. (CICC'88), 1988.


"Functional Abstraction From Structure in VLSI Simulation Models", Lathrop, R.H., Hall, R.J., Kirk, R.S., (Best Paper Award), Proc. 24th ACM / IEEE Intl. Design Automation Conf. (DAC'87), Miami Beach, FL, pp. 822-828, 1987.


"A Multiple Representation Approach to Understanding the Time Behavior of Digital Circuits", Hall, R.J., Lathrop, R.H., and Kirk, R.S., Proc. 6th Natl. Conf. on Artificial Intelligence (AAAI'87), Seattle, WA, 13-17 July, 1987.


"SCORE Cell Development Environment", Kirk, R.S., Lathrop, R.H., Hall, R.J., Proc. 1987 Custom Integrated Circuits Conf. (CICC'87), May, 1987.


"Constrained (Closed-Loop) Robot Simulation by Local Constraint Propagation", Lathrop, R.H., Proc. IEEE Intl. Conf. on Robotics and Automation, pp. 689-694, San Francisco, CA, April 7-10, 1986.


"A System Which Uses Examples to Learn VLSI Structure Manipulations", Lathrop, R.H., Kirk, R.S., Proc. 5th Natl. Conf. on Artificial Intelligence (AAAI'86), pp. 1024-1028, Philadelphia, August 11-15, 1986.


"Precedent-based Manipulation of VLSI Structures", Lathrop, R.H., Kirk, R.S., Proc. 23rd ACM / IEEE Intl. Design Automation Conf. (DAC'86), pp. 667-670, Las Vegas, June 29-July 2, 1986.


"Circuit Improvement Using Precedent-based Reasoning", Kirk, R.S., Lathrop, R.H., Proc. 1986 Custom Integrated Circuits Conf. (CICC'86), Rochester, NY, May 12-15, 1986.


"An Extensible Object-Oriented Mixed-Mode Functional Simulation System", Lathrop, R.H., and Kirk, R.S., Proc. 22nd ACM / IEEE Intl. Design Automation Conf. (DAC'85), paper 39.2, pp. 630-636, Las Vegas, Nev., 23-26 June, 1985.


"An Extensible Datapath Generator", Barrett, W.A., Rogers, R.G., Lathrop, R.H., Kuchinsky, A., Proc. IEEE Intl. Conf. on Computer-Aided Design (ICCAD-83), paper 1.1, Santa Clara, CA, Sept. 12-15, 1983.


UNREVIEWED CONFERENCE PROCEEDINGS:


"DNA Structure, Protein-DNA Interactions, and DNA-Protein Expression," Baldi, P., Lathrop, R.H., Proc. Pacific Symposium on Biocomputing'01, World Scientific Press, 2001.


"Protein Structure Prediction in the Post Genomic Era," Skolnick, J., Lathrop, R.H., Proc. Pacific Symposium on Biocomputing'99, World Scientific Press, 1999.


"Application of a Genotypic Driven Rule-Based Expert Artificial Intelligence Computer System in Treatment Experienced HIV-Infected Patients. Immunologic and Virologic Response," Cimoch, P.J., See, D.M., Pazzani, M.J., Reiter, W.M., Lathrop, R.H., Fasone, W.A., Tilles, J.G., poster abstract for the Twelfth World AIDS Conf., Geneva, Switzerland, 1998.
(Word)


"Protein Structure Prediction," Lathrop, R.H., Proc. Pacific Symposium on Biocomputing'98, World Scientific Press, 1998.


"Understanding and Predicting Protein Structure: Introduction to Session," Fischer, D., Godzik, A., Chung, S., Subbiah, S., Lathrop, R., Proc. Pacific Symposium on Biocomputing'97, World Scientific Press, 1997.


"Discovering, Learning, Analyzing and Predicting Protein Structure: Introduction to Session," Dunker, A.K., Lathrop, R.H., Proc. Pacific Symposium on Biocomputing'96, World Scientific Press, 1996.


"Protein Structure Prediction: Introduction to Session," Lathrop, R.H., Dunker, A.K., Proc. 28th Hawaii Intl. Conf. on System Sciences, IEEE Computer Soc. Press, 1995.


"Protein Structure Prediction: Introduction to Session," Dunker, A.K., Lathrop, R.H., Proc. 27th Hawaii Intl. Conf. on System Sciences, IEEE Computer Soc. Press, 1994.


"Protein Structure Prediction: Introduction to Session," Lathrop, R.H., Proc. 26th Hawaii Intl. Conf. on System Sciences, IEEE Computer Soc. Press, 1993.


"Framework Report", Lathrop, R.H., and Winston, P.H., in Report of the Matrix of Biological Knowledge Workshop, Santa Fe Institute, Santa Fe, NM, eds. Morowitz, H.J., Smith, T.F., Oct., 1987.

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