Ram Samudrala
Encyclopedia
Ram Samudrala is a professor of computational biology at the University of Washington
in Seattle, USA. He researches protein
and proteome
folding, structure, function, interaction, design, and evolution spanning atomic to organismal levels of description. He has copublished more than 100 manuscripts in a variety of journals including Science
, Nature
, PLoS Biology
, the Proceedings of the National Academy of Sciences
, and the Journal of the American Medical Association
, with a H-index
of 30 and an average journal impact factor of 5.8.
Samudrala is also a musician who has published and recorded work under the pseudonym TWISTED HELICES. In 1994, he published the Free music
Philosophy, 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. His work in this area was reported as early as 1997 by diverse media outlets including Billboard
, Forbes
, Levi's Original Music Magazine, The Free Radical, Wired
and The New York Times
.
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." He was promoted to Associate Professor with tenure
in 2006.
) by MIT Technology Review
in 2003, and was selected to present the University of Washington New Investigator Science in Medicine Lecture in 2004. In 2005, he received a NSF
CAREER Award 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 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). 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 to screen every known drug against every known target structure in a shotgun manner to discover new repurposeable therapeutics, particularly for underserved diseases.
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. He has consistently taken part in, spoken at, and published in the proceedings of these experiments, known as CASP
since its inception in 1994. His performances at CASP2 in 1996 and CASP3 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, function, and interactions known as Protinfo.
Samudrala's group then applied these methods to entire organismal proteomes, creating a framework known as the Bioverse 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. 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; medicine, predicting HIV drug resistance/susceptibility; nanobiotechnology, where small multifunctional peptides that bind to inorganic substrates are designed computationally; and rice interactomics, including the Nutritious Rice for the World
(NRW) project 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 including The New York Times
, BusinessWeek
, NSF
, The Times of India
, and Fortune
.
University of Washington
University of Washington is a public research university, founded in 1861 in Seattle, Washington, United States. The UW is the largest university in the Northwest and the oldest public university on the West Coast. The university has three campuses, with its largest campus in the University...
in Seattle, USA. He researches protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
and proteome
Proteome
The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
folding, structure, function, interaction, design, and evolution spanning atomic to organismal levels of description. He has copublished more than 100 manuscripts in a variety of journals including Science
Science (journal)
Science is the academic journal of the American Association for the Advancement of Science and is one of the world's top scientific journals....
, Nature
Nature (journal)
Nature, first published on 4 November 1869, is ranked the world's most cited interdisciplinary scientific journal by the Science Edition of the 2010 Journal Citation Reports...
, PLoS Biology
PLoS Biology
PLoS Biology is a peer-reviewed scientific journal covering all aspects of biology. Publication began on October 13, 2003.It was the first journal of the Public Library of Science. All content in PLoS Biology is published under the Creative Commons "by-attribution" license...
, the Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
The Proceedings of the National Academy of Sciences of the United States of America, usually referred to as PNAS, is the official journal of the United States National Academy of Sciences...
, and the Journal of the American Medical Association
Journal of the American Medical Association
The Journal of the American Medical Association is a weekly, peer-reviewed, medical journal, published by the American Medical Association. Beginning in July 2011, the editor in chief will be Howard C. Bauchner, vice chairman of pediatrics at Boston University’s School of Medicine, replacing ...
, with a H-index
H-index
The h-index is an index that attempts to measure both the productivity and impact of the published work of a scientist or scholar. The index is based on the set of the scientist's most cited papers and the number of citations that they have received in other publications...
of 30 and an average journal impact factor of 5.8.
Samudrala is also a musician who has published and recorded work under the pseudonym TWISTED HELICES. In 1994, he published the Free music
Free music
Free music is music that, like free software, can freely be copied, distributed and modified for any purpose. Thus free music is either in the public domain or licensed under a free license by the artist or copyright holder themselves, often as a method of promotion. It does not mean that there...
Philosophy, 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. His work in this area was reported as early as 1997 by diverse media outlets including Billboard
Billboard (magazine)
Billboard is a weekly American magazine devoted to the music industry, and is one of the oldest trade magazines in the world. It maintains several internationally recognized music charts that track the most popular songs and albums in various categories on a weekly basis...
, Forbes
Forbes
Forbes is an American publishing and media company. Its flagship publication, the Forbes magazine, is published biweekly. Its primary competitors in the national business magazine category are Fortune, which is also published biweekly, and Business Week...
, Levi's Original Music Magazine, The Free Radical, Wired
Wired (magazine)
Wired is a full-color monthly American magazine and on-line periodical, published since January 1993, that reports on how new and developing technology affects culture, the economy, and politics...
and The New York Times
The New York Times
The New York Times is an American daily newspaper founded and continuously published in New York City since 1851. The New York Times has won 106 Pulitzer Prizes, the most of any news organization...
.
Education and career
Prior to joining the University of Washington faculty, Samudrala was a post-doctoral fellow with Michael LevittMichael Levitt
Professor Michael Levitt FRS is a British biophysicist. He has been Professor of Structural biology, Stanford University, California, since 1987 working in computational biology and bioinformatics....
at Stanford University
Stanford University
The Leland Stanford Junior University, commonly referred to as Stanford University or Stanford, is a private research university on an campus located near Palo Alto, California. It is situated in the northwestern Santa Clara Valley on the San Francisco Peninsula, approximately northwest of San...
from 1997–2000, with a fellowship from the Program in Mathematics and Molecular Biology (funded by the NSF
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
and the Burroughs Wellcome Fund
Burroughs Wellcome Fund
The Burroughs Wellcome Fund is a private, independent biomedical research foundation based in Research Triangle Park, North Carolina. BWF was the corporate foundation of the Burroughs Wellcome Co. until 1994....
). He received his undergraduate degrees in Computing Science and Genetics
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
from Ohio Wesleyan University
Ohio Wesleyan University
Ohio Wesleyan University is a private liberal arts college in Delaware, Ohio, United States. It was founded in 1842 by Methodist leaders and Central Ohio residents as a nonsectarian institution, and is a member of the Ohio Five — a consortium of Ohio liberal arts colleges...
(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
Rockville, Maryland
Rockville is the county seat of Montgomery County, Maryland, United States. It is a major incorporated city in the central part of Montgomery County and forms part of the Baltimore-Washington Metropolitan Area. The 2010 U.S...
(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
Washington State Legislature
The Washington State Legislature is the state legislature of the U.S. state of Washington. It is a bipartisan, bicameral body, composed of the lower Washington House of Representatives, composed of 98 Representatives, and the upper Washington State Senate, with 49 Senators.The State Legislature...
"as a bridge between cutting-edge research and education, and new economic activity." He was promoted to Associate Professor with tenure
Tenure
Tenure commonly refers to life tenure in a job and specifically to a senior academic's contractual right not to have his or her position terminated without just cause.-19th century:...
in 2006.
Awards and honours
Samudrala received a Searle Scholar Award which funds exceptional young scientists in 2002, was named one of the world's top young innovators (TR100TR35
The TR35 is an annual list published by MIT Technology Review magazine, naming the world's top 35 innovators under the age of 35.Some of the most famous winners of the award include Larry Page and Sergey Brin , Linus Torvalds , Jerry Yang , Jonathan Ive , Mark Zuckerberg...
) by MIT Technology Review
Technology Review
Technology Review is a magazine published by the Massachusetts Institute of Technology. It was founded in 1899 as "The Technology Review", and was re-launched without the "The" in its name on April 23, 1998 under then publisher R. Bruce Journey...
in 2003, and was selected to present the University of Washington New Investigator Science in Medicine Lecture in 2004. In 2005, he received a NSF
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
CAREER Award 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
Casma
Casma is a city in the Ancash Region, Peru. It is located in the Casma Valley. Its surface has 1 204,85 km².Its people venerate saint Santa Maria Magdalena and its day is celebrated on July 22....
and Yautan
Yautan District
Yautan District is one of four districts of the province Casma in Peru.-References:...
, Peru
Peru
Peru , officially the Republic of Peru , is a country in western South America. It is bordered on the north by Ecuador and Colombia, on the east by Brazil, on the southeast by Bolivia, on the south by Chile, and on the west by the Pacific Ocean....
, for his work on vaccine discovery. He was a NIH Director's Pioneer Award 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). 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 to screen every known drug against every known target structure in a shotgun manner to discover new repurposeable therapeutics, particularly for underserved diseases.
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. He has consistently taken part in, spoken at, and published in the proceedings of these experiments, known as CASP
CASP
CASP, which stands for Critical Assessment of Techniques for Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994...
since its inception in 1994. His performances at CASP2 in 1996 and CASP3 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
University of Washington
University of Washington is a public research university, founded in 1861 in Seattle, Washington, United States. The UW is the largest university in the Northwest and the oldest public university on the West Coast. The university has three campuses, with its largest campus in the University...
, 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, function, and interactions known as Protinfo.
Samudrala's group then applied these methods to entire organismal proteomes, creating a framework known as the Bioverse 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. 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
Drug discovery
In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are discovered or designed.In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery...
, finding therapeutics that target multiple proteins in multiple diseases simultaneously; medicine, predicting HIV drug resistance/susceptibility; nanobiotechnology, where small multifunctional peptides that bind to inorganic substrates are designed computationally; and rice interactomics, including the Nutritious Rice for the World
Nutritious Rice for the World
Nutritious Rice for the World is a World Community Grid research project in the field of agronomy led by the Samudrala Computational Biology Research Group at the University of Washington. It was launched on May 12, 2008. The objective of this project is to predict the structure of proteins of...
(NRW) project where protein structure prediction methods are applied to all tractable proteins encoded by the rice genome on the IBM
IBM
International Business Machines Corporation or IBM is an American multinational technology and consulting corporation headquartered in Armonk, New York, United States. IBM manufactures and sells computer hardware and software, and it offers infrastructure, hosting and consulting services in areas...
World Community Grid
World Community Grid
World Community Grid is an effort to create the world's largest public computing grid to tackle scientific research projects that benefit humanity...
. 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 including The New York Times
The New York Times
The New York Times is an American daily newspaper founded and continuously published in New York City since 1851. The New York Times has won 106 Pulitzer Prizes, the most of any news organization...
, BusinessWeek
BusinessWeek
Bloomberg Businessweek, commonly and formerly known as BusinessWeek, is a weekly business magazine published by Bloomberg L.P. It is currently headquartered in New York City.- History :...
, NSF
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
, The Times of India
The Times of India
The Times of India is an Indian English-language daily newspaper. TOI has the largest circulation among all English-language newspaper in the world, across all formats . It is owned and managed by Bennett, Coleman & Co. Ltd...
, and Fortune
Fortune (magazine)
Fortune is a global business magazine published by Time Inc. Founded by Henry Luce in 1930, the publishing business, consisting of Time, Life, Fortune, and Sports Illustrated, grew to become Time Warner. In turn, AOL grew as it acquired Time Warner in 2000 when Time Warner was the world's largest...
.