Ram Samudrala
| Ram Samudrala | |
|---|---|
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| Born | March 23, 1972 |
| Fields | Computational biology |
| Institutions | University of Washington |
| Alma mater | Ohio Wesleyan University, Center for Advanced Research in Biotechnology, Stanford University |
| Doctoral advisor | John Moult |
| Doctoral students | Ekachai Jenwitheesuk Kai Wang Tianyun Liu Gong Cheng Stewart Moughon Brady Bernard Aaron Goldman Jeremy Horst |
| Known for | All atom knowledge based simulations, free music philosophy |
| Influences | Douglas Hofstadter |
| Notable awards | Searle Scholar (2002),[1] TR100 (2003),[2] NSF CAREER Award (2005), NIH Director's Pioneer Award (2010) |
Ram Samudrala is a professor of computational biology at the University of Washington in Seattle, USA.[3] He researches protein and proteome folding, structure, function, interaction, design, and evolution spanning atomic to organismal levels of description.[4] He has copublished more than 100 manuscripts[5] in a variety of journals including Science,[6] Nature,[7] PLoS Biology,[8] the Proceedings of the National Academy of Sciences,[9] and the Journal of the American Medical Association,[10] with a H-index of 30[11] and an average journal impact factor of 5.8.[12]
Samudrala is also a musician who has published and recorded work under the pseudonym TWISTED HELICES.[13] In 1994, he published the Free music Philosophy,[14] which accurately predicted how the ease of copying and transmitting digital information by the Internet would lead to unprecedented violations of copyright laws and new models of distribution for music and other digital media.[15][16][17] His work in this area was reported as early as 1997 by diverse media outlets including Billboard,[18] Forbes,[19] Levi's Original Music Magazine,[20] The Free Radical,[21] Wired[22][23] and The New York Times.[24]
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[edit] Education and career
Prior to joining the University of Washington faculty, Samudrala was a post-doctoral fellow with Michael Levitt at Stanford University from 1997–2000, with a fellowship from the Program in Mathematics and Molecular Biology (funded by the NSF and the Burroughs Wellcome Fund). He received his undergraduate degrees in Computing Science and Genetics from Ohio Wesleyan University (1990–1993) and completed his Ph.D. in Computational Structural Biology with John Moult at the Center for Advanced Research in Biotechnology in Rockville, MD (1993–1997). In 2001, Samudrala became the first faculty member to be recruited, as an Assistant Professor, under the Advanced Technology Initiative in Infectious Diseases created by the Washington State Legislature "as a bridge between cutting-edge research and education, and new economic activity."[25] He was promoted to Associate Professor with tenure in 2006.[5]
[edit] Awards and honours
Samudrala received a Searle Scholar Award which funds exceptional young scientists in 2002,[1] was named one of the world's top young innovators (TR100) by MIT Technology Review in 2003,[2][26][27] and was selected to present the University of Washington New Investigator Science in Medicine Lecture in 2004.[28] In 2005, he received a NSF CAREER Award[29] which recognizes "outstanding scientists and engineers who show exceptional potential for leadership at the frontiers of knowledge". In 2008, he received the Alberta Heritage Foundation for Medical Research Visiting Scientist Award. That same year, he was awarded honorary diplomas from the cities of Casma and Yautan, Peru, for his work on vaccine discovery. He was a NIH Director's Pioneer Award[30] finalist in 2006 (25/465 applicants were selected as finalists) for a novel idea to determine the structures of all proteins in a solution that he then presented at the seventh community wide assessment of protein structure prediction methods (CASP7).[31] In 2010, he again became a finalist and went on to receive the Pioneer Award for his Computational Analysis of Novel Drug Opportunities (CANDO) drug discovery pipeline[32] to screen every known drug against every known target structure in a shotgun manner to discover new repurposeable therapeutics, particularly for underserved diseases.
[edit] Research
Samudrala's research has focussed on understanding how the genome of an organism specifies its behaviour and characteristics, and how that information may be used to improve quality of life. His vision is to produce a computer model of life focussed on atomic level detail, organisation, and arrangements of all the components involved, which he calls the "structeome". The structeome, which is the actual structural organization of components at the atomic level, by its very nature includes single molecules such as DNA, RNA, proteins, and metabolites, as well larger groupings such genomes, proteome, interactomes, connectomes, and so on. Since the vision is of a large collection of atoms with subgroupings of atoms that work together in a complex dynamic manner, a protein would be a collection of atoms, many of which are covalently bonded, that interact together to perform a specific biological function. Samudrala's work has thus focussed on proteins, which is the fundamental unit of biological function within the structeome. Atoms in a structeome interact with the environment which may include other structeomes (or components thereof) thereby causing a strange loop or a tangled hierarchy of interactions. Thus a structeome would include not only all atoms and their interactions within that structeome, but also all interactions to other structeomes.
Specifically, on a more grounded level, he was the first to develop and apply an all heavy atom knowledge-based conditional probability discriminatory function for protein structure prediction in blind protein structure prediction experiments.[33] He has consistently taken part in, spoken at, and published in the proceedings of these experiments, known as CASP since its inception in 1994.[34] His performances at CASP2 in 1996[35] and CASP3[36] in 1998 highlight some of the first improvements of blinded protein structure prediction in both the comparative and template free modelling categories.
After he joined the faculty of the University of Washington, Samudrala expanded his research interests to encompass all areas that deal with the information contained within the genome of an organism, and how that information specifies an organism's behaviour and characteristics. Samudrala's Computational Biology Research Group developed a series of algorithms and web server modules to predict protein structure,[37] function,[38] and interactions[39] known as Protinfo.[40][41]
Samudrala's group then applied these methods to entire organismal proteomes, creating a framework known as the Bioverse[42][43] for exploring the relationships among the atomic, molecular, genomic, proteomic, systems, and organismal worlds. The Bioverse framework performs 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. A set of first pass predictions is available for more than 50 organismal proteomes and the framework was used to annotate the finished rice genome sequence published in 2005.[8] He is currently working on integrating a vast amount of protein interaction data (to other proteins, DNA, RNA, and smaller ligands) and modelling them at the atomic level. The end goal of the Bioverse project is to understand and simulate life at an atomic level.
Some applications of Samudrala's group are in the areas of drug discovery, finding therapeutics that target multiple proteins in multiple diseases simultaneously;[44] medicine, predicting HIV drug resistance/susceptibility;[45] nanobiotechnology, where small multifunctional peptides that bind to inorganic substrates are designed computationally;[46] and rice interactomics, including the Nutritious Rice for the World (NRW) project[47] where protein structure prediction methods are applied to all tractable proteins encoded by the rice genome on the IBM World Community Grid. The NRW project harnessed the power of individual PCs via the Grid to perform its computations to help design better rice strains with higher yield and range of bioavailable nutrients, and was covered by more than 200 media outlets worldwide[48] including The New York Times,[49] BusinessWeek,[50] NSF,[51] The Times of India,[52] and Fortune.[53]
[edit] References
- ^ a b Searle Scholar Award profile for Ram Samudrala
- ^ a b MIT Technology Review Profile naming Ram Samudrala one of the world's top young innovators
- ^ Ram Samudrala's personal web site
- ^ Samudrala Computational Biology Group
- ^ a b Ram Samudrala's curriculum vitae
- ^ Wang K, Mittler J, Samudrala R. Comment on "Evidence for positive epistasis in HIV-1". Science 312: 848b, 2006.
- ^ 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.
- ^ a b 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.
- ^ 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.
- ^ Jenwitheesuk E, Samudrala R. Identification of potential multitarget antimalarial drugs. Journal of the American Medical Association 294: 1490-1491, 2005.
- ^ H-index based on Google Scholar calculated on March 1, 2010.
- ^ Average SCI journal impact factor based on publications summary retrieved on June 29, 2011.
- ^ TWISTED HELICES
- ^ Free Music Philosophy
- ^ Samudrala R. The future of music, 1997
- ^ Story of a Revolution: Napster & the Music Industry. MusicDish, 2000
- ^ Schulman BM. The song heard 'round the world: The copyright implications of MP3s and the future of digital music. Harvard Journal of Law and Technology 12: 3, 1999.
- ^ Reece D. Industry grapples with MP3 dilemma. Billboard, July 18 1998.
- ^ Penenberg A. Habias copyrightus. Forbes, July 11 1997.
- ^ Durbach D. Short fall to freedom: The free music insurgency. Levi's Original Music Magazine, November 19, 2008.
- ^ Ballin M. Unfair Use. The Free Radical 47, 2001.
- ^ Oakes C. Recording industry goes to war against web sites. Wired, June 10 1997.
- ^ Stutz M. They (used to) write the songs. Wired, June 12 1998.
- ^ Napoli L. Fans of MP3 forced the issue. The New York Times, December 16 1998.
- ^ Roseth B. Funding forward vision. University Week, March 1 2001.
- ^ Kurian V. 10 Indian innovators in MIT list. The Hindu Business Line, October 4 2003.
- ^ 10 of Indian Origin in MIT's Technology Review. Hindustan Times, March 1 2007.
- ^ Dietz C. How genomes make proteomes. University Week 22: 17, 2005.
- ^ CAREER Award
- ^ NIH Director's Pioneer Award
- ^ Shotgun structural proteomics. NIH Director's Pioneer Award finalist interview for Ram Samudrala, Bethesda, MD. August 9, 2006.
- ^ Computational analysis of novel drug opportunities (CANDO)
- ^ 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, 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.
- ^ 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, 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.
- ^ 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 77: 220-234, 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.
- ^ Kittichotirat W, Guerquin M, Bumgarner R, Samudrala R. Protinfo PPC: A web server for atomic level prediction of protein complexes. Nucleic Acids Research 37: W519-W525, 2009.
- ^ Hung L-H, Samudrala R. PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Research 31: 3296-3299, 2003.
- ^ 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.
- ^ McDermott J, Samudrala R. BIOVERSE: Functional, structural, and contextual annotation of proteins and proteomes. Nucleic Acids Research 31: 3736-3737, 2003.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ 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.
- ^ Nutritious Rice for the World web site
- ^ Nutritious Rice for the World press coverage
- ^ Lohr S. Join the Hunt for Super-Rice. The New York Times, May 14 2008.
- ^ Hamm S. IBM's Answer to the Food Crisis. Business Week, May 14 2008.
- ^ Ram Samudrala and Michal Guerguin discuss the World Community Grid to study rice protein structures, NSF, Oct 16 2008.
- ^ Rajghatta C. Help the poor, lend some computing time. The Times of India, May 19 2008.
- ^ Gunther M. IBM: From supercomputers to superrice. Fortune, May 16 2008.
