Ravi Sachidanandam, PhD
- ASSISTANT PROFESSOR | Oncological Sciences
Research Topics:Bioinformatics, Gene Discovery, Gene Expressions, Genetics, Genomics, RNA Transport & Localization
Personalizing medicine requires systemic understanding of biology. The nuclear genome is relatively static and not predictive for complex dynamic behavior. We are exploring several dynamic sub-systems in biology, collaborating with variety of groups with wide-ranging interests to explore; 1. The genetics of mitochondria and the stability of its genome. This will provide a better understanding of the role of mitochondria in neurological disorders as well as tumor-resistance to therapeutic agents. 2. The diversity of the TCR-repertoire and its plasticity and elasticity that allows it to respond to invasions and remember them. We want to characterize this diversity and understand its interactions with the genome in various disorders such as auto-immunity. 3. The defense of the germline against attacks from transposons. We are working towards understanding the role of the piRNA pathway in this defense. Technology development is a big part of our work; we can only understand the results if we understand and control our tools. The research depends on wet-bench work and computational analyses, primarily concerning sequencing of RNA and DNA. Results from computational analyses guide wet-bench practices and vice-versa. This two-way flow of information has enabled the development of innovative and powerful approaches, including new techniques and technologies in the laboratory and advances in computational algorithms and tools.
Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001 Feb; 409(6822).
Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 2007 Mar; 128(6).
Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R. Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC bioinformatics 2008; 9.
Roca X, Olson AJ, Rao AR, Enerly E, Kristensen VN, Børresen-Dale AL, Andresen BS, Krainer AR, Sachidanandam R. Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomics. Genome research 2008 Jan; 18(1).
Sheth N, Roca X, Hastings ML, Roeder T, Krainer AR, Sachidanandam R. Comprehensive splice-site analysis using comparative genomics. Nucleic acids research 2006; 34(14).