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Ram Samudrala

Education | Awards and honours | Major research resources developed | Scientific publications | General publications | Presentations | Professional activities | Contact


Education

  • Associate Professor, University of Washington, Seattle. July 2006-. (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

  • NIH Director's Pioneer Award. 2010.
  • Undergraduate Research Mentor Award. 2010.
  • Honorary diplomas from the cities of Casma and Yautan, Peru; as well as an official Decree of Thanks from the Peruvian Minister of Health for research on vaccine discovery. 2008.
  • Alberta Heritage Foundation for Medical Research Visiting Scientist Award. 2008.
  • NIH Director's Pioneer Award finalist (25/465 applicants selected as finalists). 2006.
  • 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 predict the protein structure of individual molecules and complexes (ABCM, PPC), integrate limited or noisy experimental data with our structure prediction algorithms (PsiCSI, NMR), assign proteins to particular functional categories and predict functionally important residues (MFS, FSSA); predict protein ion binding sites, types, affinities, and specificities from structure (SOAK); and predict HIV-1 drug resistance/susceptibility (PIRSPred). 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 currently consists of more than 50 organismal proteomes and is 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 was developed in collaboration with IBM to predict the structures, functions, and interactions of the rice interactome. More over 200 media outlets have provided coverage on this project.

Scientific publications
97 publications listed, 5 more submitted; * denotes more significant; H-index 30; 78/97 publications in journals with average impact factor of 5.8


General publications
8 publications listed


Presentations
51 conference keynotes, talks, panels, and exhibits (+ 100 invited seminars not displayed here)

  1. Modelling structeomes. Undergraduate Research Program Research Exposed series, University of Washington, Seattle, WA. January 19, 2011. invited.
  2. IGF1R variants associated with isolated single suture craniosynostosis. Ninth Critical Assessment of Structure Prediction (CASP9). Asilomar, CA. December 8, 2010. refereed; presented by Jeremy Horst.
  3. Research authorship. Biomedical Research Integrity Discussion, University of Washington, Seattle, WA. August 3, 2010. two panels.
  4. Understanding life at the atomic level. Paws-on-Science Huskies Weekend at the Pacific Science Center, Seattle, WA. April 10, 2010. exhibit.
  5. 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.
  6. Protein structure refinement. Eighth Critical Assessment of Structure Prediction (CASP8). Asilomar, CA. December 7, 2008. refereed; presented by Jeremy Horst.
  7. Protein folding algorithms. Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008). Melbourne, Australia. October 16, 2008. keynote.
  8. Modelling interactomes. BioC 2008. Fred Hutchinson Cancer Research Center, Seattle, WA. July 28, 2008. invited.
  9. Modelling the Bartonella interactome. Meeting on discovery of a vaccine for Bartonella bacilliformis. National Institutes of Health, Peru. June 26, 2008 invited.
  10. Modelling interactomes. U.S.-India Joint Training Program Workshop on Global Infectious Diseases. Hyderabad, India. January 22, 2008. invited.
  11. Modelling interactomes. The 4th Solanaceae Genome Workshop. Jeju Island, Korea. Sep 10, 2007. invited.
  12. Modelling interactomes. 21st Symposium of the Protein Society. Boston, MA. July 24, 2007. invited.
  13. Modelling interactomes. Asia Pacific Conference on Plant Tissue Culture and Agrobiotechnology. Kuala Lumpur, Malaysia. June 19, 2007. invited.
  14. Computational engineering of bionanostructures. Foundations of Nanoscience: Self-assembled Architectures and Devices Conference. Snowbird, UT. April 21, 2007. invited.
  15. Shotgun structural proteomics. Seventh Critical Assessment of Structure Prediction (CASP7). Asilomar, CA. November 30, 2006. invited.
  16. Modelling proteomes. Molecular Biomimetics and Bionanotechnology conference. Istanbul, Turkey. November 13, 2006. invited.
  17. Designing inorganic binding proteins. First workshop on Molecular Biomimetics. Friday Harbour, WA. September 6, 2006. invited.
  18. Modelling proteomes. Oral Biology Research Symposium. Seattle, WA. October 7, 2005. invited.
  19. Modelling proteomes. BioC. Seattle, WA. August 17, 2005. invited.
  20. Modelling proteomes: Application to understanding HIV disease progression. Center for AIDS Research Symposium. Seattle, WA. May 27, 2005. invited.
  21. Modelling proteomes. Fifth Annual Northwest Gene Expression Conference. Seattle, WA. May 26, 2005. invited.
  22. Computational engineering of bionanostructures. Foundations of Nanoscience: Self-assembled Architectures and Devices Conference. Snowbird, UT. April 25, 2005. invited.
  23. Modelling proteomes. Searle Scholars Meeting. Chicago, IL. April 12, 2005. invited.
  24. An integrated computational framework for systems biology research. LabAutomation Conference. San Jose, CA. February 3, 2005. refereed.
  25. Protinfo/Samudrala: New automated methods for CASP6. Sixth Critical Assessment of Structure Prediction (CASP6). Gaeta, Italy. December 6, 2004. refereed; presented by Ling-Hong Hung.
  26. Structural Bioinformatics. American Crystallographic Association Annual Meeting. Chicago, IL. July 22, 2004. invited.
  27. Modelling proteomes. Fourth Annual Northwest Gene Expression Conference. Seattle, WA. August 28, 2003. invited.
  28. Predicting protein structure from sequence. Biothailand 2003 Post-Congress Workshop. Bangkok, Thailand. July 22, 2003. invited.
  29. Modelling the rice proteome. Conference on Rice Biotechnology 2003. Pattaya, Thailand. July 18, 2003. invited.
  30. Modelling, comparison and analysis of proteomes from different organisms. International Conference on Biodiversity and Bioactive Compounds. Pattaya, Thailand. July 17, 2003. invited.
  31. Violent vs. non-violent approaches to global conflict resolution. Time of Reflection: The War in Iraq symposium. Seattle, WA. April 23,2003. invited.
  32. Modelling proteomes. The International Conference on Bioinformatics 2002. Bangkok, Thailand. February 8, 2002. invited.
  33. Protein Structure Prediction. The International Conference on Bioinformatics 2002. Bangkok, Thailand. February 5, 2002. invited.
  34. Modelling genome structure and function. Statistical Genetics and Computational Molecular Biology Symposium. Seattle, WA. December 2001. invited.
  35. Protein structure prediction: progress and prospects. At the Interface of Biology, Mathematics and Physics Symposium. Tucson, AZ. March 2001. invited.
  36. Protein structure prediction: progress and prospects. Biomedical Computation at Stanford 2000 Symposium. Stanford, CA. October 2000. invited.
  37. Computational biology: from gene to structure to function. Intelligent Systems in Molecular Biology. San Diego, CA. August 2000. invited.
  38. Computational biology: from gene to structure to function. Mathematical and Computational Challenges in Molecular and Cell Biology Symposium. Berkeley, CA. June 2000. invited.
  39. Probing structure-function relationships of proteins using computational approaches. Pacific Symposium on Biocomputing. Honolulu, HI. January 2000. refereed.
  40. Heterogeneous clusters and computational biology. Mellon Institute's Developing and Using Clusters as a Biomedical Research Tool Conference. Pittsburgh, PA. June 1999. invited.
  41. The triumph of technology: the defeat of copyright law. Second Annual MP3 Summit. San Diego, CA. June 1999. invited.
  42. Applying the Cathedral and Bazaar paradigms to the music industry. Alliance for Converging Technologies Lighthouse Conference. Berkeley, CA. March 9, 1999. invited.
  43. 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.
  44. A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pacific Symposium on Biocomputing. Kona, HI. January 1999. refereed.
  45. Bona fide ab initio prediction of protein structures by exhaustive enumeration and successive filtering using knowledge-based scoring functions. Third Critical Assessment of Structure Prediction. Asilomar, CA, December 16, 1998. refereed.
  46. Free Music Philosophy. First Annual MP3 Summit. San Diego, CA. June 1998. invited.
  47. 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.
  48. Creativity and ownership: where is the balance? Third Annual Ethics and Technology Conference. Santa Clara, CA. June 1998. refereed.
  49. 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.
  50. A graph theoretic approach to handle the problem of interconnectedness in the comparative modelling of proteins. Second Critical Assessment of Structure Prediction. Asilomar, CA. December 13, 1996. refereed.
  51. Comparative modelling of the Histidine-containing Phosophocarrier protein, the Cellular Retinoic Acid-binding Protein, and the Eosinophil Derived Neurotoxin. First Critical Assessment of Structure Prediction. Asilomar, CA, December 5, 1994. refereed.

Professional activities

  • Levinson Scholar Review Committee, Undergraduate Research Program, University of Washington, Seattle. 2010.
  • Undergraduate Award Committee, Department of Microbiology, University of Washington, Seattle. 2010-.
  • Consulant for the National Centre for Genetic Engineering and Biotechnology (BIOTEC), Thailand. December 2009-.
  • Chair of the Admissions Committee, Department of Microbiology, University of Washington, Seattle. 2004-2008.
  • Faculty Member, Structural Biology, Faculty of 1000. June 1, 2002-.
  • Adjunct Faculty, Department of Biology, University of Washington, Seattle.
  • Adjunct Faculty, Department of Oral Biology, University of Washington, Seattle.
  • 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, 10/2010.
  • Ad hoc grant application reviewer for Agency for Science, Technology and Research (A*STAR) Singapore, Burroughs Wellcome Fund, Genome Canada, UW Royalty Research Fund, and several others.
  • Associate Editor, BMC Bioinformatics.
  • Editorial Board, Journal of Bioengineering & Biomedical Science.
  • 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 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. February 2001-.
  • Postdoctoral Fellow at Stanford University working on methods to sample main chain conformations in comparative modelling and ab initio scenarios, continued development of all-atom discriminatory functions and side chain prediction methods, comparative modelling and ab initio prediction for the third and fourth Critical Assessment of Structure Prediction (CASP3 and 4) experiments, and computational aspects of structural and functional genomics. With Michael Levitt. September 1997-January 2001.
  • Graduate Research Fellow at the Centre for Advanced Research in Biotechnology 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 Critical Assessment of Structure Prediction (CASP1 and 2) experiments. With John Moult. August 1993-August 1997.
  • Research Intern at East Carolina University, Greenville, NC doing theoretical and experimental work on analysing genetic relationships between the Herpes Simplex Virus and the Pseudo Rabies Virus. With Nels Pederson. Summer 1992.
  • Research Intern at USDA laboratories, Delaware, Ohio performing computational analysis of the performance of various drugs that prevent Dutch Elm disease. With Steve Ishita. Spring 1992.

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).

Contact

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>
W: <compbio.washington.edu>

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