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, University of Maryland (1997)
  • BA, Computing 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:

  • Ohio Wesleyan University Distinguished Achievement Citation (2023)
  • NIH NCATS ASPIRE Reduction-to-Practice Challenge (2022)
  • 2021 Wiki Science Competition International Winner (2022)
  • 2019 Wiki Science Competition National Finalist (2020)
  • 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 (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)

Research Expertise:

  • Multiscale computational biology; bioinformatics; protein and proteome structure, function, interaction, evolution, and design; translational science; small molecule analysis and engineering

Research Centers:

  • Center for Computational Research (CCR)
  • Clinical and Translational Research Center (CTRC)
  • Witebsky Center for Microbial Pathogenesis and Immunology

UB 2020 Strategic Strengths:

  • Artistic Expression and Performing Arts.
  • Civic Engagement and Public Policy
  • Extreme Events: Mitigation and Response
  • Health and Wellness Across the Lifespan
  • Information and Computing Technology
  • Integrated Nanostructured Systems
  • Molecular Recognition in Biological Systems and Bioinformatics

Grants and Sponsored Research:

  • August 2021–January 2030
    NIH NCATS ASPIRE Reduction-to-Practice Award
    NCATS
    Role: Co-Principal Investigator
    $1,220,000
  • September 2019–January 2030
    NIH NCATS ASPIRE Design Award
    NIH
    Role: Principal Investigator
    $100,000
  • September 2022–August 2027
    Buffalo Research Innovation in Genomic and Healthcare Technology (BRIGHT) Short-Term Training and Education
    NIH
    Role: Principal Investigator
    $672,596
  • July 2017–June 2027
    Buffalo Research Innovation in Genomic and Healthcare Technology (BRIGHT) Training and Education
    NIH/NLM
    Role: Co-Investigator
    $4,546,884
  • December 2019–December 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
    $20,178,410
  • November 2022–October 2023
    High performance computing drug discovery initiative
    NIST
    Role: Principal Investigator
    $1,000,000
  • February 2021–December 2022
    Computational Analysis of Novel Drug Opportunities (CANDO)
    Buffalo Innovation Accelerator Fund
    Role: Principal Investigator
    $80,000
  • April 2020–March 2021
    Retrospective cohort study on opioid-related drug-drug interactions
    UB, prime NIH
    Role: Principal Investigator
    $35,000
  • June 2020–November 2020
    SBIR Phase I: Accelerating understanding of COVID-19 biology and treatment via scaled medical record and biosimulation analytics
    Onai, Inc. Prime: NSF
    Role: Co-Investigator
    $10,000
  • September 2010–April 2017
    Novel Paradigms for Drug Discovery: Computational Multitarget Screening
    National Institute of Health
    Role: Principal Investigator
    $4,200,000

Journal Articles:

See all (115 more)

Presentations:

  • "Prediction of co-prescription induced drug events using the CANDO platform." University at Buffalo Clinical and Translational Sciences Institute Pilot Studies Colloquium. (2022)
  • "How healthcare data will change the world." University at Buffalo Distinctive Dialogues. (2022)
  • "Proteomusic: converting protein structures to complex music patterns." Sigma Xi STEM Art and Film Festival. (2021)
  • "Recent developments in bioinformatics." National Library of Medicine/National Center for Biotechnology Information workshop. (2021)
  • "Broad spectrum coronavirus therapeutic discovery using the CANDO platform." Louisiana Biomedical Research Network Annual Meeting. (2021)
  • "Computational Analysis of Novel Drug Opportunities (CANDO)." International Conference on Protein and RNA Structure Prediction. (2019)
  • "Optimum analgesic discovery by multiscale interactomic profiling." NIH NCATS ASPIRE Design Challenge Winners Conference. (2019)
  • "Computational Analysis of Novel Drug Opportunities (CANDO)." Center for Leading Innovation & Collaboration (CLIC) Un-meeting. (2019)
  • "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)
  • "AI-based shotgun drug discovery to characterise and treat disease." SUNY Germination Space Artificial Intelligence Program. (2018)
  • "Grant application strategies." Research fundamentals workshop. (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: Atomic systems biology translated to drug discovery. From High-throughput Structural Bioinformatics to Integrative Systems Biology." Network Tools and Applications in Biology Conference (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)
See all (11 more)

Service Activities:

  • Drug Screening and Pharmacology Summit. Boston, MA.; organising committee member (2023)
  • Natural Sciences and Engineering Research Council of Canada (NSERC); reviewer (2023)
  • JSMBS Awards Committee; member (2023–present)
  • Faculty and administrator hiring search committees; member (2022)
  • Frontiers in Chemistry; associate editor (2022–present)
  • PhD Program in Biomedical Sciences (PPBS); steering committee member (2022–present)
  • Promotion and tenure committee; dossier reviewer (2020–2023)
  • Biology; editorial board member (2020–present)
  • Clinical Translational Sciences Institute; grant reviewer (2019–2022)
  • Louisiana Biomedical Research Network; External Advisory Committee member (2017–present)
  • PhD Program in Biomedical Sciences (PPBS); admissions committee member (2016–2019)
  • Faculty council; alternate member (2016–present)
  • Bioinformatics, BMC Bioinformatics, BMC Structural Biology, Drug Discovery Today, Frontiers in Chemistry, Frontiers in Pharmacology, Journal of Molecular Biology, Nucleic Acids Research, Proteins: Structure, Function, and Bioinformatics, Protein Science, and several others; reviewer (1995–present)

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Contact Information

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