Manoj Hariharan

Genomic Analysis Laboratory

Manoj Hariharan
Salk Institute for Biological Studies - Manoj Hariharan

Manoj Hariharan

Staff Scientist
Genomic Analysis Laboratory and Center of Excellence for Stem Cell Genomics

Gene expression is an intricately coordinated event. The spatio-temporal regulation of gene expression is controlled at several levels. I focus on four facets - the genomic, epigenetic, transcriptional and post-transcriptional layers of gene regulation. As a computational biologist, I analyze genomics data generated by high-throughput technologies in an effort to uncover these molecular connections, with special focus on human health and disease.

I conceived and am leading a project to accurately assess mitochondrial heteroplasmy. Mitochondrial DNA (mtDNA) tend to accumulate somatic variations. The balance of wild-type versus mutant mtDNA within cells is a major factor underlying neurological and other disorders, cancers, differentiation and aging. We envision that these studies will open new horizons in the prevention, diagnosis and treatment of the numerous mitochondria-related disorders. This work is part of Salk AHA-Allen Institute Center for Aging and Alzheimer’s Disease (more info here).

I am also the lead Investigator in the Defense Advanced Research Projects Agency (DARPA) project Epigenetic CHaracterization and Observation (ECHO) where our work is focused on single cell DNA methylation profiling of various blood cell types from samples exposed to various biological and non-biological agents. I also lead another DARPA-funded project called Measuring Biological Aptitude (MBA) program which is focused on methylation profiles of cell-free DNA and single cell analysis of DNA methylation in blood from military and non-military personnel. In an earlier project we used base-resolution, high-throughput bisulfite sequencing to discover tissue specific methylation signatures that are correlated to gene expression.

I also play a lead role in the activities of the recently established Center of Excellence for Stem Cell Genomics (CESCG). This center, funded by the California Institute of Regenerative Medicine (CIRM), aims to foster collaborations with stem-cell biologists in the state of California and the two nodal CESCGs (at Salk Institute and Stanford University). We have initiated several interesting projects, which "apply genomics and bioinformatics approaches to stem cell research to accelerate fundamental understanding of human biology and disease mechanisms, enhance cell and tissue production and advance personalized cellular therapeutics."

For more information on my research activities (including past research) and background, please visit my website by clicking here»


Postdoctoral associate, Stanford University, CA
Postdoctoral fellow, Yale University, CT
PhD in Biotechnology, University of Pune, Pune, India (Bioinformatics work done at the CSIR Institute for Genomics and Integrative Biology, Delhi)
MSc in Bioinformatics, Bharathiar University, Coimbatore, India.
BSc in Biotechnology, Dr. GRD College of Science, Coimbatore, India.

Awards & Honors

  • Patent granted: Human microRNA targets in HIV (PCT/IB2006/002802 & US/7825230)
  • Patent filed: Targets for human microRNAs in Avian Influenza virus genome (US/200845472)
  • Senior Research Fellowship from Council for Scientific & Industrial Research Ministry of Science & Technology India (Apr 2007 - Feb 2009)
  • Selected as AAAS (American Association for the Advancement of Science) member through Program for Excellence in Science; member since May 2012.
  • Short-listed for the Merck Millipore India Innovation Award 2012.

Selected Publications

  1. Schultz, M. D., He, Y., Whitaker, J. W., Hariharan, M., Mukamel, E. A., Leung, D., ... & Lin, S. (2015). Human body epigenome maps reveal noncanonical DNA methylation variation. Nature, 523(7559), 212.
  2. Gerstein, M. B., Kundaje, A., Hariharan, M., Landt, S. G., Yan, K. K., Cheng, C., ... & Min, R. (2012). Architecture of the human regulatory network derived from ENCODE data. Nature, 489(7414), 91.
  3. Kasowski, M., Grubert, F., Heffelfinger, C., Hariharan, M., Asabere, A., Waszak, S. M., ... & Hong, M. Y. (2010). Variation in transcription factor binding among humans. science, 328(5975), 232-235.
  4. Hariharan, M., Scaria, V., & Brahmachari, S. K. (2009). dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation. BMC bioinformatics, 10(1), 108.
  5. Hariharan, M., Scaria, V., Pillai, B., & Brahmachari, S. K. (2005). Targets for human encoded microRNAs in HIV genes. Biochemical and biophysical research communications, 337(4), 1214-1218.

For full (and current) list of publications, please click here.