Ram Samudrala PhD

Ram Samudrala

Ram Samudrala
PhD

Professor and Chief, Division of Bioinformatics

Department of Biomedical Informatics

Jacobs School of Medicine & Biomedical Sciences


Specialty/Research Focus

Artificial Intelligence; Bioinformatics; Biomedical Informatics; Biophysical Modeling; Computational Biology; Computational Chemistry; Computational Drug Discovery; Drug Design; Drug Development; Drug Discovery; Genomics and proteomics; Molecular and Cellular Biology; Nanotechnology; Protein Folding; Protein Function and Structure; Proteomics; Structural Biology; Translational Research

Contact Information
77 Goodell St
Gateway Building
Buffalo, New York 14203
Phone: 716-888-4858
rams@buffalo.edu



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/) for multiscale therapeutic drug discovery, repurposing, and design. Our integrated informatics platform determines interactions between and among all drugs/compounds and higher scale entities (proteins, RNA, pathways, cells, tissues, etc.) to generate multiscale interaction signatures. The multiscale signatures are weighted using pharmacological, physiological and chemoinformatics data and compared and analyzed to predict the likelihood of the corresponding compounds being efficacious for any indication, in effect inferring homology of drug/compound behavior at proteomic/interactomic scales.

Using this approach, we made predictions for all the indications that our library of drugs maps to, with benchmarking accuracies that are orders of magnitude better than what is observed when using random controls. We have performed prospective validations of our predictions, demonstrating comparable or better in vitro inhibition than existing drugs approved for clinical use in indications such as COVID-19, dengue, dental caries, diabetes, hepatitis B, herpes, lupus, malaria and tuberculosis. We have implemented drug design capabilities in our platform to generate compounds beyond what is already known for indications such as opioid use disorder and overdose and non-small cell lunger cancer. We have further extended our platform to incorporate genotypic and phenotypic variations to enable precision medicine.

We 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. All this is accomplished in close collaboration with researchers across the world and primarily with Dr. Zackary Falls, also a faculty in the Bioinformatics Division.

Education and Training:

  • Fellowship, 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 Jacobs School of Medicine & Biomedical Sciences (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 NCATS ASPIRE Design Challenge (2019)
  • University at Buffalo Exceptional Scholar (2019)
  • MacArthur Foundation 100&Change Competition Top 50 (2016)
  • NIH Director's Pioneer Award (2010)
  • Best Undergraduate Research Mentor Award at the University of Washington (2010)
  • Alberta Heritage Foundation Medical Research Visiting Scientist Award (2008)
  • Honorary diplomas from the cities of Casma and Yautan, Peru (2008)
  • NSF CAREER Award (2005)
  • University of Washington New Investigator Science in Medicine Lecture (2004)
  • World's Top Young Innovator Award (TR100) (2003)
  • Searle Scholar (2002)
  • NSF Program in Mathematics and Molecular Biology/Burroughs Wellcome Fund Fellowship (1997)
  • Life Technologies Fellowship (1993)
  • Zain-ul-Abedin Memorial Scholarship for Outstanding Graduate Studies in Molecular and Cell Biology (1993)
  • Howard Hughes Internship Award (1992)
  • Wesleyan Scholar (1990)

Grants and Sponsored Research:

  • August 2015–August 2024
    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
  • February 2021–December 2022
    Computational Analysis of Novel Drug Opportunities (CANDO)
    Buffalo Innovation Accelerator Fund
    Role: Principal Investigator
    $80,000
  • September 2010–April 2017
    Novel Paradigms for Drug Discovery: Computational Multitarget Screening
    National Institute of Health
    Role: Principal Investigator
  • August 2021
    NIH NCATS ASPIRE Reduction-to-Practice Award
    NCATS
    Role: Co-Principal Investigator
    $270,000
  • September 2019
    NIH NCATS ASPIRE Design Award
    NIH
    Role: Principal Investigator
    $100,000

Journal Articles:

See all (112 more)

Presentations:

  • "Broad spectrum coronavirus therapeutic discovery using the CANDO platform." Louisiana Biomedical Research Network Annual Meeting. (2021)
  • "The comprehensive solution to characterise and treat disease" Louisiana Biomedical Research Network Annual Meeting. (2019)
  • "AI-based shotgun drug discovery, repurposing, and design." Research Areas Ready for Acceleration and Growth. (2018)
  • "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
See all (2 more)

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Contact Information

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