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Ram                            Samudrala

Ram Samudrala PhD

Department of Biomedical Informatics

Professor and Chief, Division of Bioinformatics

Specialty/Research Focus

Bioinformatics

 
Professional Summary:

My group performs research to understand, through multiscale modelling, how organismal metagenomes specify their behavior and characteristics in conjunction with their environments. We accomplish this by developing novel computational biology and bioinformatics algorithms for predicting protein and proteome structure, function, interaction, design and evolution. We apply these basic science techniques to important practical problems in medicine, genetic and genomic engineering and nanobiotechnology.

I received the 2010 National Institutes of Health (NIH) Director‘s Pioneer Award to develop the Computational Analysis of Novel Drug Opportunities (CANDO) platform (http://protinfo.org/cando/) to repurpose drugs approved for other indications in a shotgun manner. Our integrated informatics platform determines interactions between and among all drugs and all protein structures to create compound-proteome interaction signatures. The compound-proteome interaction signatures are weighted using pharmacological, physiological and chemoinformatics data and compared and analyzed to predict the likelihood of the corresponding compounds being efficacious for all indications simultaneously, in effect inferring homology of drug behavior at a proteomic level.

Using this approach, we have made predictions for all the indications that our library of drugs maps to, with benchmarking accuracies that are two orders of magnitude better than what is observed when using random controls. We have performed prospective in vitro validations of our predictions, demonstrating comparable or better inhibition than existing drugs approved for clinical use in indications such as dengue, dental caries, diabetes, hepatitis B, herpes, lupus, malaria and tuberculosis. Our approach may be generalized to compounds beyond those approved by the FDA, and it can as well consider mutations in protein structures to enable precision medicine. We have also applied our computational techniques to design peptides for vaccines, antibacterial activity and inorganic substrate adhesion and model the structures, functions and interactions of all tractable proteins encoded by several rice genomes.

A consistent theme in our research is the combination of in virtuale simulation and homology inference, followed by in vitro and in vivo verification and application, directed toward holistic multiscale modelling of complex biological systems.

Education and Training:
  • Postdoctoral Fellow, Computational Biology, Stanford University (2000)
  • PhD, Computational Biology, Center for Advanced Research in Biotechnology (1997)
  • BA, Computer Science and Genetics, Ohio Wesleyan University (1993)
Employment:
  • Professor, Biomedical Informatics, University at Buffalo (2014-present)
  • Associate Professor, Microbiology, University of Washington (2006–2014)
  • Assistant Professor, Microbiology, University of Washington (2001–2006)
  • Post Doctoral Fellow, Stanford University, Medicine (1997–2001)
  • Fellow, University of Maryland, Center for Advanced Research in Biotechnology (1993–1997)
Awards and Honors:
  • NIH Director's Pioneer Award (2010)
  • Best Undergraduate Research Mentor Award at the University of Washington (2010)
  • NSF CAREER Award (2005)
  • World's Top Young Innovator Award (TR100) (2003)
  • Searle Scholar (2002)

Grants and Sponsored Research:
  • August 2015–August 2019
    Buffalo Clinical and Translational Research Center Clinical and Translational Science Award(CTSA)
    National Center for Advancing Translational Sciences (NCATS)/National Institutes of Health
    Role: Co-Investigator
    $20,000,000
  • September 2010–April 2017
    Novel Paradigms for Drug Discovery: Computational Multitarget Screening
    National Institute of Health
    Role: Principal Investigator

Journal Articles:
See all (74 more)
Evaluative Studies and Case Reports:

Presentations:
  • "Interactomics: Computational Analysis of Novel Drug Opportunities. International conference on Clinical Sciences and Drug Discovery." (2015)
  • "Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the cando platform." International Conference on Protein Engineering (2015)
  • "Interactome based drug discovery. Intelligent Systems in Molecular Biology." (2015)
  • "Interactomics: Computational Analysis of Novel Drug Opportunities. Significant Advances in Bioengineering." (2015)
  • "Interactomics: Computational Analysis of Novel Drug Opportunities. NIH Common Fund High-Risk High-Reward Symposium." (2014)
  • "Interactomics: Computational Analysis of Novel Drug Opportunities." , Michael Levitt Nobel Memorial Symposium (2014)
  • "Interactomics: Computational Analysis of Novel Drug Opportunities. Systems Biology of Infectious Diseases" (2014)
  • "Interactomics: Computational Analysis of Novel Drug Opportunities. Intelligent Systems in Molecular Biology" (2014)
  • "Interactomics: Atomic systems biology translated to drug discovery. From High-throughput Structural Bioinformatics to Integrative Systems Biology" Network Tools and Applications in Biology Conference

School News:
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Clinical Specialties:
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Contact Information

77 Goodell St
Gateway Building
Buffalo, NY 14203
Phone: 716-888-4858
Email: rams@buffalo.edu


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