Ram Samudrala

Box 357242, Department of Microbiology
University of Washington, Seattle, WA 98195-7242
V: 1-206-732-6122
F: 1-206-732-6055
E: <ram@compbio.washington.edu>
U: <compbio.washington.edu>

Education

• Associate Professor, University of Washington, Seattle. July 2006-present (Assistant Professor, February 2001-June 2006).
  • Modelling structure, function, expression, interaction, and evolution of proteins, RNA, DNA, and small molecules.
• Postdoctoral Fellow, Stanford University. September 1997-January 2001.
  • Protein folding, protein structure and function prediction; computational structural and functional genomics.
  • Mentor: Michael Levitt
• Ph.D., Centre for Advanced Research in Biotechnology. August 1993-August 1997.
  • Protein folding and protein structure prediction using computational approaches.
  • Mentor: John Moult.
• B.A., Ohio Wesleyan University. January 1990-May 1993.
  • Majors: Computing Science and Genetics.
  • Minors: Mathematics and Biology.

Awards and honours

• Honorary diplomas from the cities of Caspa and Yautan, Peru; as well as an official Decree of Thanks from the Peruvian Minister of Health (2008).
• Alberta Heritage Foundation for Medical Research Visiting Scientist Award (2008).
• NIH Director's Pioneer Award Finalist in 2006 (25/465 applicants selected as finalists).
• NSF CAREER award (2005-2010).
• UW New Investigator Science in Medicine Lecture (2004).
• Named one of the world's top young innovators (TR100 selection) by MIT Technology Review (2003).
• Searle Scholar (2002-2005).
• NSF Program in Mathematics and Molecular Biology/Burroughs Wellcome Fund Fellow (1997-2001).
• Centre for Advanced Research in Biotechnology Life Technologies Graduate Fellow (1993-1997).
• Zain-ul-Abedin Memorial Scholarship for Outstanding Graduate Studies in Molecular and Cell Biology (1993).
• Howard Hughes Internship Award (1992).
• Dean's List (1990-1993).
• Wesleyan Scholar and Honours Student at Ohio Wesleyan (1990-1993).

Major research resources developed

• Protinfo structure, function, and interaction prediction web server modules <protinfo.compbio.washington.edu>: The web server consists of modules to perform protein structure prediction of individual proteins and protein complexes, integrate limited or noisy experimental data with our structure prediction algorithms, assign proteins to particular functional categories and predict functionally important residues; predict protein ion binding sites, types, affinities, and specificities from structure; and predict HIV-1 drug resistance/susceptibility. Currently structure, function, and interaction predictions for up to 100 molecules/day are performed.
• The Bioverse framework <bioverse.compbio.washington.edu>: The Bioverse provides a framework for exploring the relationships among the molecular, genomic, proteomic, systems, and organismal worlds. Our goal is to perform sophisticated analyses and predictions based on genomic sequence data to annotate and understand the interaction of protein sequence, structure, and function, both at the single molecule as well as at the systems levels. The Bioverse is currently used by several hundred visitors accessing more than 1,000 molecules/day.
• ``Nutritious Rice for the World'' project <protinfo.compbio.washington.edu/rice>: This project is ongoing in collaboration with IBM to predict the structures, functions, and interactions of the rice interactome. Currently over 200 media outlets have provided coverage on this project which has just begun.

Scientific publications
83 publications listed; 20 more submitted; the more significant ones are denoted with *

• Kittichotirat W, Guerquin M, Bumgarner R, Samudrala R. Protinfo PPC: A web server for atomic level prediction of protein complexes. Nucleic Acids Research 2009. in press. *
• Liu T, Horst J, Samudrala R. A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction. Proteins: Structure, Function, and Bioinformatics 2009. in press. *
• Bernard B, Samudrala R. A generalized knowledge-based discriminatory function for biomolecular interactions. Proteins: Structure, Function, and Bioinformatics 2009. in press. *
• Samudrala R, Heffron F, McDermott J. In silico identification of secreted effectors in Salmonella typhimurium. PLoS Pathogens 2009. in press.
• Ngan S-C, Samudrala R. A sequence-space scoring function for de novo protein structure prediction. Protein Engineering, Design and Selection 2009. accepted. *
• McDermott J, Ireton R, Montgomery K, Bumgarner R, Samudrala R (editors). Computational systems biology. Methods in Molecular Biology 541: v-ix. 2009. *
• Frazier Z, McDermott J, Samudrala R. Computational representation of biological systems. Methods in Molecular Biology 541: 535-549, 2009.
• Guerquin M, McDermott J, Samudrala R. The Bioverse API and Web Application. Methods in Molecular Biology 541: 511-534, 2009.
• Rashid I, McDermott J, Samudrala R. Inferring molecular interaction pathways from eQTL data. Methods in Molecular Biology 541: 211-223, 2009.
• Wichadakul D, McDermott J, Samudrala R. Prediction and integration of regulatory and protein-protein interactions. Methods in Molecular Biology 541: 101-143, 2009.
• McDermott J, Wang J, Yu J, Wong GSK, Samudrala R. In Rao GP, Wagner C, Singh RK, Sharma ML, editors. Prediction and annotation of plant protein interaction networks. Plant Genomics and Bioinformatics 2009.
• Wang K, Horst J, Cheng G, Nickle D, Samudrala R. Protein meta-functional signatures from combining sequence, structure, evolution and amino acid property information. PLoS Computational Biology 4: e1000181, 2008. *
• Samudrala R, Oren EE, Cheng C, Horst, J, Bernard B, Gungormus M, Hnilova M, Fong H, Tamerler C, Sarikaya M. Knowledge-based design of inorganic binding peptides. Proceedings of the conference on the Foundations of Nanoscience: Self-Assembled Architectures and Devices, 2008.
• Evans JS, Samudrala R, Walsh TR, Oren EE, Tamerler C. Molecular design of inorganic-binding polypeptides. MRS Bulletin 33: 514-518, 2008. (Accompanying introductory article with biographies, pages 504-512.) *
• Liu T, Guerquin M, Samudrala R. Improving the accuracy of template-based predictions by mixing and matching between initial models. BMC Structural Biology 8: 24, 2008.
• Jenkins C, Samudrala R, Geary S, Djordjevic SP. Structural and functional characterisation of an organic hydroperoxide resistance (Ohr) protein from Mycoplasma gallisepticum. Journal of Bacteriology 190: 2206-2208, 2008.
• Jenwitheesuk E, Horst JA, Rivas K, Van Voorhis WC, Samudrala R. Novel paradigms for drug discovery: Computational multitarget screening. Trends in Pharmacological Sciences 29: 62-71, 2008. *
• Ngan S-C, Hung L-H, Liu T, Samudrala R. Scoring functions for de novo protein structure prediction revisited. Methods in Molecular Biology 413: 243-282, 2007.
• Oren EE, Tamerler C, Sahin D, Hnilova M, Seker UOS, Sarikaya M, Samudrala R. A novel knowledge-based approach for designing inorganic binding peptides. Bioinformatics 23: 2816-2822, 2007. *
• Jenwitheesuk E, Samudrala R. Identification of potential HIV-1 targets of minocycline. Bioinformatics 23: 2797-2799, 2007.
• Chevance FFV, Takahashi N, Karlinsey JE, Gnerer J, Hirano T, Samudrala R, Aizawa S-I, Hughes KT. The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution. Genes and Development 21: 2326-2335, 2007.
• McDermott J, Samudrala R. Bioinformatic characterization of plant networks. Proceedings of the Asia Pacific Conference on Plant Tissue Culture and Agrobiotechnology, 2007.
• Bockhorst J, Lu F, Janes JH, Keebler J, Gamain B, Awadalla P, Su X, Samudrala R, Jojic N, Smith JD. Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. Molecular and Biochemical Parasitology 155: 103-112, 2007.
• Berube PM, Samudrala R, Stahl DA. Transcription of amoC is associated with the recovery of Nitrosomonas europaea from ammonia starvation. Journal of Bacteriology 89: 3935-3944, 2007.
• Hung L-H, Ngan S-C, Samudrala R. De novo protein structure prediction. In Xu Y, Xu D, Liang J, editors. Computational Methods for Protein Structure Prediction and Modeling 2: 43-64, 2007.
• Hung L-H, Samudrala R. An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data. Journal of Biomolecular NMR 36: 189-198, 2006. *
• Wang K, Samudrala R. Incorporating background frequency improves entropy-based residue conservation measures. BMC Bioinformatics 7: 385, 2006.
• Liu T, Samudrala R. The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection. Protein Engineering, Design and Selection 19: 431-437, 2006.
• Korotkova N, Le Trong I, Samudrala R, Korotkov K, Van Loy CP, Bui A-L, Moseley SL, Stenkamp RE. Crystal structure and mutational analysis of the DaaE adhesin of Escherichia coli. Journal of Biological Chemistry 281: 22367-22377, 2006.
• Wang K, Samudrala R. Automated functional classification of experimental and predicted protein structures. BMC Bioinformatics 7: 278, 2006. *
• Howell DPG, Samudrala R, Smith JD. Disguising itself - insights into Plasmodium falciparum binding and immune evasion from the DBL crystal structure. Molecular and Biochemical Parasitology 148: 1-9, 2006.
• Wang K, Mittler J, Samudrala R. Comment on "Evidence for positive epistasis in HIV-1". Science 312:848b, 2006.
• Chang AN, McDermott J, Guerquin M, Frazier Z, Samudrala R. Integrator: Interactive graphical search of large protein interactomes over the Web. BMC Bioinformatics 7: 146, 2006.
• Ngan S-C, Inouye M, Samudrala R. A knowledge-based scoring function based on residue triplets for protein structure prediction. Protein Engineering, Design and Selection 19: 187-193, 2006.
• Jenwitheesuk E, Samudrala R. Heptad-repeat-2 mutations enhance the stability of the enfuvirtide-resistant HIV-1 gp41 hairpin structure. Antiviral Therapy 10: 893-900, 2005. *
• Cheng G, Qian B, Samudrala R, Baker D. Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic Acids Research 33: 5861-5867, 2005.
• Jenwitheesuk E, Samudrala R. Identification of potential multitarget antimalarial drugs. Journal of the American Medical Association 294: 1490-1491, 2005. *
• Wang W, Zheng H, Yang S, Yu H, Li J, Jiang H, Su J, Yang L, Zhang J, McDermott J, Samudrala R, Wang J, Yang H, Yu J, Kristiansen K, Wong GK, Wang J. Origin and evolution of new exons in rodents. Genome Research 15: 1258-1264, 2005.
• Liu T, Jenwitheesuk E, Teller D, Samudrala R. Structural insights into the Cellular Retinaldehyde Binding Protein (CRALBP). Proteins: Structure, Function, and Bioinformatics 61: 412-422, 2005.
• McDermott J, Bumgarner RE, Samudrala R. Functional annotation from predicted protein interaction networks. Bioinformatics 21: 3217-3226, 2005. *
• McDermott J, Guerquin M, Frazier Z, Chang AN, Samudrala R. BIOVERSE: Enhancements to the framework for structural, functional, and contextual annotations of proteins and proteomes. Nucleic Acids Research 33: W324-W325, 2005. *
• Hung L-H, Ngan S-C, Liu T, Samudrala R. PROTINFO: New algorithms for enhanced protein structure prediction. Nucleic Acids Research 33: W77-W80, 2005. *
• Wang K, Samudrala R. FSSA: A novel method for identifying functional signatures from structural alignments. Bioinformatics 21: 2969-2977, 2005. *
• Jenwitheesuk E, Wang K, Mittler J, Samudrala R. PIRSpred: A webserver for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction. Trends in Microbiology 13: 150-151, 2005. *
• Chang AN, McDermott J, Samudrala R. An enhanced java graph applet interface for visualizing interactomes. Bioinformatics 21: 1741-1742, 2005.
• Jenwitheesuk E, Samudrala R. Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics. AIDS 19: 529-533, 2005.
• Jenwitheesuk E, Samudrala R. Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach. Antiviral Therapy 10: 157-166, 2005. *
• Yu J, Wang J, Lin W, Li S, Li H, Zhou J, ..., McDermott J, Samudrala R, Wang J, Wong GK. The genomes of Oryza sativa: A history of duplications. PLoS Biology 3: e38, 2005. *
• Ekwa-Ekok C, Diaza GA, Carlson C, Hasegawad T, Samudrala R, Limf K, Yabug JM, Levya B, Schnapp LM. Genomic organization and sequence variation of the human integrin subunit 8 gene (ITGA8). Matrix Biology 23: 487-496, 2004.
• Wang J, Zhang J, Zheng H, Li J, Liu D, Li H, Samudrala R, Yu J, Wong GK. Mouse transcriptome: Neutral evolution of "non-coding" complementary DNAs. Nature 431, 2004.
• Wang K, Samudrala R, Mittler J. HIV-1 genotypic drug resistance interpretation algorithms need to include hypersusceptibility mutations. Journal of Infectious Diseases 190: 2055-2056, 2004.
• Wang K, Samudrala R, Mittler J. Antivirogram or PhenoSense: a comparison of their reproducibility and an analysis of their correlation. Antiviral Therapy 9: 703-712, 2004.
• Jenwitheesuk E, Wang K, Mittler J, Samudrala R. Improved accuracy of HIV-1 genotypic susceptibility interpretation using a consensus approach. AIDS 18: 1858-1859, 2004.
• Wang K, Fain B, Levitt M, Samudrala R. Improved protein structure selection using decoy-dependent discriminatory functions. BMC Structural Biology 4: 8, 2004. *
• Wang K, Jenwitheesuk E, Samudrala R, Mittler J. Simple linear model provides highly accurate genotypic predictions of HIV-1 drug resistance. Antiviral Therapy 9: 343-352, 2004.
• Wang K, Samudrala R, Mittler J. Weak agreement between predictions of ``reduced susceptibility'' from Antivirogram and PhenoSense assays. Journal of Clinical Microbiology 42: 2353-2354, 2004.
• McDermott J, Samudrala R. Enhanced functional information from protein networks. Trends in Biotechnology 22: 60-62, 2004. *
• Jenwitheesuk E, Samudrala R. Identifying inhibitors of the SARS coronavirus proteinase. Bioorganic & Medicinal Chemistry Letters, 13: 3989-3992, 2003. [Most Cited Paper 2003 - 2006 Award]
• McDermott J, Samudrala R. BIOVERSE: Functional, structural, and contextual annotation of proteins and proteomes. Nucleic Acids Research 31: 3736-3737, 2003. *
• Hung L-H, Samudrala R. PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Research 31: 3296-3299, 2003. *
• Jenwitheesuk E, Samudrala R. Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations. BMC Structural Biology 3: 2, 2003.
• Hung L-H, Samudrala R. Accurate and automated classification of protein secondary structure with PsiCSI. Protein Science 12: 288-295, 2003. *
• Jenkins C, Samudrala R, Anderson I, Hedlund BP, Petroni G, Michailova N, Pinel N, Overbeek R, Rosati G, Staley JT. Genes for the cytoskeletal protein tubulin in the bacteria genus Prosthecobacter. Proceedings of the National Academy of Sciences 99: 17049-17054, 2002.
• McDermott J, Samudrala R. The Bioverse: An object-oriented genomic database and webserver written in Python. In Proceedings of the conference on Objects in Bio- & Chem-Informatics, 2002.
• Samudrala R, Levitt M. A comprehensive analysis of 40 blind protein structure predictions. BMC Structural Biology 2: 3-18, 2002. *
• Van Loy CP, Sokurenko EP, Samudrala R, Moseley S. Identification of a DAF binding domain in the Dr adhesin. Molecular Microbiology 45: 439-452, 2002.
• Samudrala R. Modelling genome structure and function. Pure and Applied Chemistry 6: 907-914, 2002.
• Samudrala R. Lessons from blind protein structure prediction experiments. In Grohima M, Selvaraj S, editors. Recent Research Developments in Protein Folding, Stability, and Design 123-139, 2002.
• Xia Y, Huang ES, Levitt M, Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. Journal of Molecular Biology 300: 171-185, 2000. *
• Samudrala R, Levitt M. Decoys 'R' Us: A database of incorrect protein conformations to improve protein structure prediction. Protein Science 9: 1399-1401, 2000. <http://dd.compbio.washington.edu>
• Huang ES, Samudrala R, Park BH. Scoring functions for ab initio protein structure prediction. Methods in Molecular Biology 143: 223-245, 2000.
• Samudrala R, Huang ES, Koehl P, Levitt M. Constructing side chains on near-native main chains for ab initio protein structure prediction. Protein Engineering 7: 453-457, 2000.
• Samudrala R, Xia Y, Levitt M, Cotton NJ, Huang ES, Davis R. Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches. In Altman R, Dunker K, Hunter L, Klein T, Lauderdale K, editors. Proceedings of the Pacific Symposium on Biocomputing 179-189, 2000.
• Huang ES, Samudrala R, Ponder JW. Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. Journal of Molecular Biology 290:267-281, 1999.
• Samudrala R, Xia Y, Levitt M. Huang ES. Ab initio prediction of protein structure using a combined hierarchical approach. Proteins: Structure, Function, and Genetics S3: 194-198, 1999. *
• Samudrala R, Xia Y, Levitt M, Huang ES. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. In Altman R, Dunker K, Hunter L, Klein T, Lauderdale K, editors. Proceedings of the Pacific Symposium on Biocomputing 505-516, 1999.
• Huang ES, Samudrala R, Ponder JW. Distance geometry generates native-like folds for small helical proteins using the consensus distances of predicted protein structures. Protein Science 7: 1998-2003, 1998.
• Samudrala R, Moult J. Determinants of side chain conformational preferences in protein structures. Protein Engineering 11: 991-997, 1998.
• Samudrala R, Moult J. A graph-theoretic algorithm for comparative modelling of protein structure. Journal of Molecular Biology 279:287-302, 1998. *
• Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. Journal of Molecular Biology 275: 893-914, 1998. *
• Samudrala R, Moult J. Handling context-sensitivity in protein structures using graph theory: bona fide prediction. Proteins: Structure, Function, and Genetics 29S: 43-49, 1997. *
• Samudrala R. A graph-theoretic solution to the context-sensitivity problem in protein structure prediction. Ph.D. thesis, 1997.
• Samudrala R, Pedersen JT, Zhou H, Luo R, Fidelis K, Moult J. Confronting the problem of interconnected structural changes in the comparative modelling of proteins. Proteins: Structure, Function, and Genetics 23: 327-336, 1995.

General publications
8 publications listed

• Samudrala R. Book review: Discovering Genomics, Proteomics, and Bioinformatics by A. Malcolm Campbell and Laurie Heyer. Cell Biology Education 2: 222-223, 2003.
• Samudrala R. Book Review: Structural Bioinformatics by Philip E. Bourne and Helge Weissig. Briefings in Bioinformatics 4: 299-301, 2003.
• Samudrala R. Taking the cost out of firewalls. LinuxWorld Magazine 1: 58-59, 2003.
• Samudrala R. Linux Cluster HOWTO, 2003.
• Samudrala R. Installing and using RAID. In Danesh A, Das G, editors. Special Edition Using Linux System Administration, Que Publishing, 2000.
• Samudrala R. Creativity and ownership: where is the balance?. In Blondeau O, Latrive F, editors. Libres Enfants Du Savoir Numérique, 129-140, éditions de l'éclat, 2000.
• Samudrala R. The future of music. In Blondeau O, Latrive F, editors. Libres Enfants Du Savoir Numérique, 447-462, éditions de l'éclat, 2000.
• Samudrala R. The free music philosophy. In Blondeau O, Latrive F, editors. Libres Enfants Du Savoir Numérique, 463-478, éditions de l'éclat, 2000.

Conference keynotes, talks, and panels

1. In silico design of solid binding peptides as molecular building blocks in technology and medicine. ACS 237th National Meeting. Salt Lake City, UT. March 24, 2009. invited; presented by Ersin Emre Oren.
2. Shotgun structural proteomics. Seventh meeting on the Critical Assessment of protein Structure Prediction (CASP7) methods. Asilomar, CA. December 7, 2008. invited; presented by Jeremy Horst.
3. Protein folding algorithms. Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008). Melbourne, Australia. October 16, 2008. invited.
4. Modelling interactomes. BioC 2008. Fred Hutchinson Cancer Research Center, Seattle, WA. July 28, 2008. invited.
5. Modelling the Bartonella interactome. Meeting on discovery of a vaccine for Bartonella bacilliformis. National Institutes of Health, Peru. June 26, 2008 invited.
6. Modelling interactomes. U.S.-India Joint Training Program Workshop on Global Infectious Diseases. Hyderabad, India. January 22, 2008. invited
7. Modelling interactomes. The 4th Solanaceae Genome Workshop. Jeju Island, Korea. Sep 10, 2007. invited
8. Modelling interactomes. 21st Symposium of the Protein Society. Boston, MA. July 24, 2007. invited
9. Modelling interactomes. Asia Pacific Conference on Plant Tissue Culture and Agrobiotechnology. Kuala Lumpur, Malaysia. June 19, 2007. invited
10. Computational engineering of bionanostructures. Foundations of Nanoscience: Self-assembled Architectures and Devices Conference. Snowbird, UT. April 21, 2007. invited
11. Shotgun structural proteomics. Seventh meeting on the Critical Assessment of protein Structure Prediction methods. Asilomar, CA. November 30, 2006. invited
12. Modelling proteomes. Molecular Biomimetics and Bionanotechnology conference. Istanbul, Turkey. November 13, 2006. invited
13. Designing inorganic binding proteins. First workshop on Molecular Biomimetics. Friday Harbour, WA. September 6, 2006. invited
14. Modelling proteomes. Oral Biology Research Symposium. Seattle, WA. October 7, 2005. invited
15. Modelling proteomes. BioC. Seattle, WA. August 17, 2005. invited
16. Modelling proteomes: Application to understanding HIV disease progression. Center for AIDS Research Symposium. Seattle, WA. May 27, 2005. invited
17. Modelling proteomes. Fifth Annual Northwest Gene Expression Conference. Seattle, WA. May 26, 2005. invited
18. Computational engineering of bionanostructures. Foundations of Nanoscience: Self-assembled Architectures and Devices Conference. Snowbird, UT. April 25, 2005. invited
19. Modelling proteomes. Searle Scholars Meeting. Chicago, IL. April 12, 2005. invited
20. An integrated computational framework for systems biology research. LabAutomation Conference. San Jose, CA. February 3, 2005. refereed
21. Protinfo/Samudrala: New automated methods for CASP6. Sixth meeting on the Critical Assessment of protein Structure Prediction methods. Gaeta, Italy. December 6, 2004. presented by Ling-Hong Hung. refereed
22. Structural Bioinformatics. American Crystallographic Association Annual Meeting. Chicago, IL. July 22, 2004. invited
23. Modelling proteomes. Fourth Annual Northwest Gene Expression Conference. Seattle, WA. August 28, 2003. invited
24. Predicting protein structure from sequence. Biothailand 2003 Post-Congress Workshop. Bangkok, Thailand. July 22, 2003. invited
25. Modelling the rice proteome. Conference on Rice Biotechnology 2003. Pattaya, Thailand. July 18, 2003. invited
26. Modelling, comparison and analysis of proteomes from different organisms. International Conference on Biodiversity and Bioactive Compounds. Pattaya, Thailand. July 17, 2003. invited
27. Violent vs. non-violent approaches to global conflict resolution. Time of Reflection: The War in Iraq symposium. Seattle, WA. April 23,2003. invited
28. Modelling proteomes. The International Conference on Bioinformatics 2002. Bangkok, Thailand. February 8, 2002. invited
29. Protein Structure Prediction. The International Conference on Bioinformatics 2002. Bangkok, Thailand. February 5, 2002. invited
30. Modelling genome structure and function. Statistical Genetics and Computational Molecular Biology Symposium. Seattle, WA. December 2001. invited
31. Protein structure prediction: progress and prospects. At the Interface of Biology, Mathematics and Physics Symposium. Tucson, AZ. March 2001. invited
32. Protein structure prediction: progress and prospects. Biomedical Computation at Stanford 2000 Symposium. Stanford, CA. October 2000. invited
33. Computational biology: from gene to structure to function. Intelligent Systems in Molecular Biology. San Diego, CA. August 2000. invited
34. Computational biology: from gene to structure to function. Mathematical and Computational Challenges in Molecular and Cell Biology Symposium. Berkeley, CA. June 2000. invited
35. Probing structure-function relationships of proteins using computational approaches. Pacific Symposium on Biocomputing. Honolulu, HI. January 2000. refereed
36. Heterogeneous clusters and computational biology. Mellon Institute's Developing and Using Clusters as a Biomedical Research Tool Conference. Pittsburgh, PA. June 1999. invited
37. The triumph of technology: the defeat of copyright law. Second Annual MP3 Summit. San Diego, CA. June 1999. invited
38. Applying the Cathedral and Bazaar paradigms to the music industry. Alliance for Converging Technologies Lighthouse Conference. Berkeley, CA. March 9, 1999. invited
39. Combining an all-atom conditional probability discriminatory function and exhaustive enumeration techniques for protein structure prediction. NSF Program in Mathematics and Molecular Biology meeting VI. Santa Fe, NM. January 1999. invited
40. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pacific Symposium on Biocomputing. Kona, HI. January 1999. refereed
41. Bona fide ab initio prediction of protein structures by exhaustive enumeration and successive filtering using knowledge-based scoring functions. Third meeting on the Critical Assessment of protein Structure Prediction methods. Asilomar, CA, December 16, 1998. refereed
42. Free Music Philosophy. First Annual MP3 Summit. San Diego, CA. June 1998. invited
43. An all-atom conditional probability discriminatory function for protein structure prediction. Burroughs Wellcome Fund's Doing Science at the Interface. Berkeley, CA. June 1998. invited
44. Creativity and ownership: where is the balance? Third Annual Ethics and Technology Conference. Santa Clara, CA. June 1998. refereed
45. Confronting the problem of interconnected structural changes in the comparative modelling of proteins. NSF Program in Mathematics and Molecular Biology meeting V. Santa Fe, NM. January 1997. invited
46. A graph theoretic approach to handle the problem of interconnectedness in the comparative modelling of proteins. Second meeting on the Critical Assessment of protein Structure Prediction methods. Asilomar, CA. December 13, 1996. refereed
47. Comparative modelling of the Histidine-containing Phosophocarrier protein, the Cellular Retinoic Acid-binding Protein, and the Eosinophil Derived Neurotoxin. First meeting on the Critical Assessment of protein Structure Prediction methods. Asilomar, CA, December 5, 1994. refereed

Professional activities

• Chair of the Admissions Committee, Department of Microbiology, University of Washington, Seattle. (2004-2008)
• Adjunct Faculty, Department of Biology, University of Washington, Seattle.
• Adjunct Faculty, Department of Oral Biology, University of Washington, Seattle.
• Faculty Member, Structural Biology, Faculty of 1000. (Since June 1, 2002.)
• Member, Computational Molecular Biology program, University of Washington, Seattle.
• Member, Molecular and Cellular Biology program, University of Washington, Seattle.
• Member, Nanotechnology program, University of Washington, Seattle.
• Member, Center for Ecogenetics and Environmental Health, University of Washington, Seattle.
• Member, Keck Center for Microbial Pathogens, University of Washington, Seattle.
• Member, Biocommons Computing Center Advisory Board, University of Washington, Seattle.
• Member, Bioconductor Advisory Board, Fred Hutchinson Cancer Research Center, Seattle.
• Member, Scientific committee for the International Conference on Bioinformatics 2002, Bangkok, Thailand.
• Member, NIH study sections (BDMA, BCP) and special emphasis panels (6/2003, 3/2004, 6/2004, 12/2004, 10/2007, 11/2007, 2/2009).
• Member, NSF review panels (8/2002, 5/2003, 3/2005, 4/2005, 5/2006, 3/2007).
• Ad-hoc grant application reviewer for Burroughs Wellcome Fund, Genome Canada, UW Royalty Research Fund, and several others.
• Manuscript reviewer for Bioinformatics, BMC Bioinformatics, BMC Structural Biology, Journal of Molecular Biology, Nucleic Acids Research, Proteins: Structure, Function, and Bioinformatics, Protein Science, and several others.

Research experience

• Principal Investigator at the University of Washington (February 2001-present) of a computational genomics research group investigating protein structure and function; bioinformatics/data mining; predicting membrane protein structure; protein design; docking; evolution; and understanding higher level organisation of protein pathways in the cell and simulating their behaviour.
• Postdoctoral Fellow at Stanford University (September 1997-January 2001) working on methods to sample main chain conformations in comparative modelling and ab initio scenarios, continued development of-atom discriminatory functions and side chain prediction methods, comparative modelling and ab initio prediction for the third and fourth meetings on the Critical Assessment of protein Structure Prediction methods (CASP3 and 4), and computational aspects of structural and functional genomics. With Michael Levitt.
• Graduate Research Fellow at the Centre for Advanced Research in Biotechnology (August 1993-August 1997) working on modelling protein structure primarily using graph theoretic methods, development of an all-atom conditional-probability discriminatory function, development of algorithms for side chain prediction, and comparative modelling for the first and second meetings on the Critical Assessment of protein Structure Prediction methods (CASP1 and 2). With John Moult.
• Research Intern at East Carolina University, Greenville, NC (Summer 1992) doing theoretical and experimental work on analysing genetic relationships between the Herpes Simplex Virus and the Pseudo Rabies Virus. With Nels Pederson.
• Research Intern at USDA laboratories, Delaware, Ohio (Spring 1992) performing computational analysis of the performance of various drugs that prevent Dutch Elm disease. With Steve Ishita.

Computing Science experience

• Programming Languages, Operating Systems, Computer Architecture, Structured Computer Organisation, Artificial Intelligence, Algorithms and Data structures, Mathematical Foundations of Computing Science, Compiler Theory and Design, Linear Algebra, Numerical Analysis, and Combinatorics and Graph Theory.
• Programming languages: experience with several procedural languages such as C/C++, FORTRAN, and Perl; functional languages such as Lisp; and formatting languages such as TeX/LaTeX and SGML/HTML.
• Operating systems: experience with several flavours of Unix (mainly Linux, Irix, OSF/1, and AIX), networking protocols, and systems programming.
• Software: I have written several general freeware programs that are used by the Internet community. As part of my research, I have written programs that been used extensively in-house, and are available as a freeware distribution, for prediction of protein structure and function, both at the single molecule as well as the genomic levels.
• Solved several computing problems working as a computing consultant for Information Systems, The Writing Resource Centre, and the Politics and Government Department at Ohio Wesleyan (1990-1993), and at the Centre for Advanced Research in Biotechnology (1993-1997). Designed and implemented high-performance Linux-based computing clusters at Stanford University (1997-2001) and the University of Washington (2001-present).

Molecular Biology experience

• Molecular and Population Genetics, Developmental Biology, Bacterial Physiology, Plant Structure Function and Systematics, Evolution, Developmental Biology, Chemistry of Nucleic Acids, Protein Chemistry and Enzymic Catalysis, Protein Structure and Function, Cell Biology, and Biophysics and Theoretical/Computational Biology.
• Computational techniques: experience with modelling of DNA, RNA, protein, and organismal structure, function, and evolution by simulation.
• Experimental techniques: experience with recombinant DNA technology (cloning, expression, analysis of genetic material).