About

Shankar Subramaniam is a distinguished Professor of Bioengineering, Computer Science & Engineering, Cellular & Molecular Medicine, and Nanoengineering at the University of California San Diego. He holds the Joan and Irwin Jacobs Endowed Chair in Bioengineering and Systems Biology and was the founding Director of the Bioinformatics and Systems Biology Interdisciplinary Program. His research spans several areas including bioinformatics, systems biology, and medicine. In bioinformatics, he develops novel strategies for identifying protein interaction networks, intracellular localization of proteins, and functional networks in cells. In systems biology, he works on deciphering mammalian cellular networks from high throughput and phenotypic data, as well as developing strategies for modeling cellular signaling networks. His work in systems medicine involves collaboration with biomedical scientists to understand diseases associated with insulin resistance and inflammation. His laboratory focuses on mapping cellular circuitry to mechanisms and phenotypes in physiology and pathology, and developing quantitative models of cellular pathways. Subramaniam has contributed significantly to developing state-of-the-art infrastructure for bioinformatics, including the Molecule Pages Database, recognized as an innovative resource for signaling proteins, and the LipidMaps database, the first integrated resource for mammalian lipids with gene and protein data. He has also developed a widely used microarray server that combines sophisticated statistical analysis with biochemical annotations to provide insights into transcriptional changes in mammalian cells. His work integrates complex computer science strategies with expert-driven curation to advance understanding in cellular signaling and function. Recognized for his contributions, he was named a distinguished scientist at the San Diego Supercomputer Center in 2010 and is a Fellow of the American Institute for Medical and Biological Engineering and the American Association for the Advancement of Science. He has received numerous awards including the UCSD Chancellor’s Award for Research Excellence, Genome All Star, Smithsonian Foundation, and Laboratory Automation awards. Subramaniam earned his Ph.D. from the Indian Institute of Technology.

Research topics

• Biology
• Virology
• Artificial Intelligence
• Natural Language Processing
• Immunology
• Computer Science
• Information Retrieval
• Chemistry
• Computational biology
• Mathematics
• Arithmetic
• Zoology

Selected publications

• Adjuvanting a subunit COVID-19 vaccine to induce protective immunity

  Nature · 2021 · 351 citations

  • Virology
  • Chemistry
  • Immunology
  DOI

• T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers

  Nature Medicine · 2020 · 168 citations

  • Virology
  • Immunology
  • Biology

  T cells. We propose that cellular immune responses reduce the threshold of nAbs required to confer superior and durable protection.

  DOI

• Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures

  Journal of Lipid Research · 2020 · 843 citations

  • Natural Language Processing
  • Computer Science
  • Artificial Intelligence

  A comprehensive and standardized system to report lipid structures analyzed by MS is essential for the communication and storage of lipidomics data. Herein, an update on both the LIPID MAPS classification system and shorthand notation of lipid structures is presented for lipid categories Fatty Acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Sphingolipids (SP), and Sterols (ST). With its major changes, i.e., annotation of ring double bond equivalents and number of oxygens, the updated shorthand notation facilitates reporting of newly delineated oxygenated lipid species as well. For standardized reporting in lipidomics, the hierarchical architecture of shorthand notation reflects the diverse structural resolution powers provided by mass spectrometric assays. Moreover, shorthand notation is expanded beyond mammalian phyla to lipids from plant and yeast phyla. Finally, annotation of atoms is included for the use of stable isotope-labeled compounds in metabolic labeling experiments or as internal standards. This update on lipid classification, nomenclature, and shorthand annotation for lipid mass spectra is considered a standard for lipid data presentation.

  DOI

Recent grants

• NIH Grant U54GM062114

  NIH · $65.3M · 2008

• MicroRNA Control of Dilated Cardiomyopathy

  NIH · $4.6M · 2023–2027

• Graduate Training Program in Bioinformatics

  NIH · $5.8M · 2001–2022

• NIH Grant U54GM069338

  NIH · $139.8M · 2014

• NIH Grant R33HL08737502

  NIH · $365k · 2010

Frequent coauthors

• Mano R. Maurya

  University of California, San Diego

  177 shared

• Shakti Gupta

  University of California, San Diego

  120 shared

• Eoin Fahy

  La Jolla Bioengineering Institute

  86 shared

• Kavitha Mukund

  Dr. Hari Singh Gour University

  71 shared

• John Y.‐J. Shyy

  University of California, San Diego

  53 shared

• Eric Jakobsson

  40 shared

• Marcy Martin

  University of Zurich

  40 shared

• Jian Kang

  National University of Malaysia

  38 shared

Awards & honors

• Fellow of the American Institute for Medical and Biological…
• Fellow of the American Association for the Advancement of Sc…
• UCSD Chancellor’s Award for Research Excellence
• Genome All Star, Smithsonian Foundation
• Laboratory Automation awards

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