Prof. Subha Srinivasan

Research Focus Key Words

Metagenome, Nutrition, Prostate Cancer, Rhyzosphere, Grain maranth,  non-coding RNA, Malaria, An. stephensi, TIGS, ADBS

Background

Structural bioinformatics, computational biology, protein engineering, bioinformatics,

Education

1. Postdoc at Roswell Park Memorial Institute, Buffalo, NY (1984-1987)
2. Ph. D., Physics, Madras University, Chennai, India

Professional experience

1. Institute of Bioinformatics and Applied Biotechnology (IBAB)
   Faculty Scientist: April 2015-Present
2. Faculty Scientist/DBT Fellow, Institute of Bioinformatics and Applied Biotechnology (IBAB) (DBT, GoI): July 2010-March 2015
3. Founder and Chief Scientific Officer,  Jivan Biologics, Larkspur, CA (2001-2010)
4. Head, Bioinformatics Berlex Biosciences, Richmond, CA (1998-2001)
5. Head, Bioinformatics , Immunex Corporation, Seattle, WA (1994-1997)
6. Head, Computational Chemistry, Immunex Corporation, Seattle, WA (1989-1994)
7. Visiting Scientist , IDEC Pharmaceutical, San Diego, CA (1987-1989)

Research Interest Profile

Dr. Subha Srinivasan and team members use genomics and bioinformatics techniques to diverse application areas of biology including cancer biomarker discovery, plant genomics, root metagenomics, nutritional genomics and noninvasive diagnostics. Dr. Srinivasan is also involved in teaching both basic and advanced bioinformatics courses to Masters level students, which includes concepts/algorithms behind every major bioinformatics tools.  She also provides training in big data analysis through interns programs. Her lectures are recorded and can be made available.

Collaborators

An. stephensi genomics, Tata Institute of Genomics and Society; India-specific SNPs from exomes, ADBS; Basil genomics and bioinformatics, University of Padova; metagenomics, King Abdullah University, Saudi Arabia; Amaranth translational worh , ISSER/University of Hyderabad; Amoeba genomics, CHG

Group members

Research Publications

1. Bawa Pushpinder, Ravi Samathmika, Paul Swagatika, Chaudhary Bibha, Srinivasan Subhashini., (2018)
   “ A novel molecular mechanism for a long non-coding RNA PCAT92 implicated in prostate cancer, Oncotarget
2. Sunil Meeta., Hariharan Niedita, Dixit Shubham, Choudhary Bibha., Srinivasan Subhashini (2017)
   “ Differential genomic arrangements in Caryophyllales through deep transcriptome sequencing of A. hypochondriacus”, PLoS One.
3. Karthikeyan S., Bawa Pushpinder., Srinivasan, S (2017)
   “hg19K: addressing a significant lacuna in hg19-based variant calling”, Molecular Genetics and Genomic Medicine
4. Meghnath Geeta, SEn Titash, Rakesh Kumar, Pushpinder Bawa, Subha Srinivasan, Usha Vijayraghavan. (2017)
   “Functions for fission yeast splicinf factors SpSlu7 and SpPrp18 in alternative splice site choice and stress-specific regulated splicing”, PLoS One. 2017 Dec 13;12(12):e0188159
5. Hariharan N., Ravi S., Pradeep BE., Subramanyam N., Choudhary B., Srinivasan S., Khanchandani P., (2018),
   “A novel loss-of-function mutation in HACE1 is linked to a genetic disorder in a patient from India” Human Genome Variations 5, 17061
6. Bawa P., Zacharia S., Srivatsan R., and Srinivasan S. (2015)
   “Up-regulation is the norm for lincRNAs specific to prostate cancer”, PLoS One, 01 May 2015.
7. Sunil M., Nayak S., Hariharan A., Gupta RP., Panda B., Choudhury B., Srinivasan S.  (2014)
   “The draft genome and transcriptome of Amaranthus hypochondriacus: A C4 dicot producing high-lysine edible pseudo- cereal”, DNA Research, Dec;21(6):585-602.
8. Srinivasan S., Patil AH, Verma M., Bingham JL., Srivatsan R. (2012)
   “Genome-wide profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays.” J. Clinical Bioinformatics, 2:21 (HIGHLY ACCESSED status by BioMed Central)
9. Patil, AH M., Deshmukh, M. Singh, NK., Srivastava, R., Verma, M., Gupta, S., Veeresh, S., Srivatsan, R., Srinivasan, S. (2012),
   “From data repositories to biomarker discovery: Application to prostate cancer.” Current Science, April 2012, 102 (08)
10. Johnson ED, Sudarsanam S, Bingham J, Srinivasan, S. (2012)
    “Translational biology approach to identify causative factors for rare toxicities in humans and animals.”Curr Drug DiscovTechnol,9(1):77-80.
11. Srinivasan, S. (2011)
    “Alternative Splicing in Eukaryotes: The Norm, Not an Anomaly”. Current Science,  March 2011, 100 (06)
12. Carrigan PE, Bingham JL, Srinvasan S, Brentnall TA, Miller LJ. (2011)
    “Characterization of alternative spliceoforms and the RNA splicing machinery in pancreatic cancer.” Pancreas, 40(2):281-8
13. Srinivasan, S., Bingham, J., Johnson, D. (2009)
    “The ABC’s of Alternative Splicing: A Review of ATP-Binding Cassette Transporter Splicing”. CODD, 12, 149-158
14. Bingham, J.L, Carrigan, P.E., Miller, L.J., Srinivasan, S. (2008)
    “Extent and diversity of human alternative splicing established by complementary database annotation and microarray analysis”.Omics, 12, 1-6
15. Bingham, J., Sudarsanam, S., Srinivasan, S. (2006)
    “Profiling human phosphodiesterase genes and splice isoforms”. Biochemical and Biophysical Research Communications, Vol. 350, 25-32
16. Seto, M., Whitlow, M., McCarrick, MA., Srinivasan, S., Zhu, Y., Paglia, R., Mintzer, R., Light, D., Johns, A., Meurer-Ogden, JA., (2004)
    “A Model of Acid Sphingomyelnase Phosphoesterase Domain Based on its Remote Structural Homolog Purple Acid Phosphatase”. Protein Science, 13, 3172-3186
17. Srinivasan. S. (1998)
    “Homology Folding of Proteins: Application to Cytokine Engineering”. Springer-Verlog, Berlin
18. Black, R. A., Rauch, C. T., Kozlosky, C. J., Peschon, J. J., Slack, J. L., Wolfson, M. F., Castner, B. J., Stocking. K. L., Reddy, P., Srinivasan, S., Nelson, N., Boiani, N., Schooley, K. A., Gerhart, M., Davis, R., Fitzner, J. N., Johnson, R. S., Paxton, R. J., March, C. J., and Cerretti, D. P. (1997)
    “A Metalloproteinase Disintegrin that Releases Tumor Necrosis Factor- from Cells”. Nature 385, 729-733
19. Graddis, T. J., Brasel, K., Friend, D., Srinivasan, S., Wee, S., Lyman, S. D., March, C. J. and McGrew, J. T. (1998)
    “Struncture-function analysis of flt3 ligand-flt3 receptor interactions using a rapid functional screen”. J. Biol. Chemistry, Vol. 273 (28), 17626-17633.
20. Pettit, D. K., Bonnert, T. P., Eisenman, J., Srinivasan, S., Paxton, R., Beers, C., Lynch, D., Miller, B., Yost, J., Grabstein, K. H., Gombotz, W. R. (1997)
    “Structure-function studies of interleukin15 using site-specific mutagenesis, polyethylene glycol conjugation, and homology modeling”. J. Biol. Chem. 272, 2312-2318.
21. Sudarsanam, S. and Srinivasan S.  (1997)
    “Sequence dependent conformational sampling using a database of i+1, i angles for predicting polypeptide backbone conformations”.  Protein Engineering  Vol. 10, 1155-1162.
22. Srinivasan, S. and Sudarsanam, S.  (1996)
    “Homology Guided Protein Folding: Application to Protein Therapeutic Design, Biomolecules: From 3D Structures to application”. Proceedings of the Thirty-Fourth Hanford Symposium on health and the Environment, Edited by Rick L. Ornstein, 67-81.
23. Sudarsanam,  S., DuBose, R.,  March, C. J., and Srinivasan S. (1995)
    “Modeling Protein Loops Using a i+1, i  dimer database”. Protein Science 4, 1412-1420.
24. Sudarsanam, S.,  March, C. J., and Srinivasan, S. (1994)
    “Homology Modeling of Divergent Proteins”. J. Mol. Biol. 241, 143-149.
25. Sudarsanam, S.. and Srinivasan, S. (1995)
    “Searching for Protein Loop Conformations  in Parallel”.  CABIOS 11, 591-593.
26. Baum, P.,  Gayle, R. B.,  Ramsdell, F., Srinivasan, S.,  Sorensen, R.,  Watson, M.,  Seldin. M.,  Baker, E.,  Sutherland, G., Clifford, K.,  Anderson, M.,  Goodwin, R., and Fanslow, W. (1994)
    “Molecular Characterization of Murine and Human OX40/OX40 ligand systems: Identification of Human OX40 Ligand as the HTLV-1 Regulated Protein gp34”.  EMBO J, 13, 3992.
27. Peter Baum,  Gayle, R. B.,  Ramsdell, F., Srinivasan, S.,  Sorensen, R.,  Watson, M.,  Seldin. M.,  Baker, E.,  Sutherland, G., Clifford, K.,  Anderson, M., Goodwin, R., and Fanslow, W. (1994)
    “Identification of OX40 ligand and preliminary characterization of its activities on OX40 receptor”.  Circ. Shock 44, 30.
28. Fanslow, W. C., Srinivasan, S.,  Paxton,  R.,  Gibson, M.,  Spriggs, M. K., and Armitage, R. J. (1994) “Structural Characteristics of CD40 ligand that Determine Biological Function”.  Seminars in Immunology  6,  267-278.
29. Beckmann, P. M.,  Gayle, R. B.,  Crrretti, D. P.,  March, C. J.,  Srinivasan, S., and Sleath P. R. (1993)
    “Structural and Functional Charaterization of the Interleukin-8 Receptors”. The Chemokines,Edited by I. J. D. Lindley et al., Plenum Press New York, 155-169.
30. Kozlosky, C. J., Maraskovsky, E., McGrew, J. T., Vandenbos, T., Teepe, M., Lynman, S. D., Srinivasan, S.,  Fletcher, F. A., Gayle, R. B., Cerretti, D. P., and Beckmann, P. (1995)
    “Ligands for the Receptor Tyrosine Kinases Hek and Elk: Isolation and cDNAs Encoding a Family of Proteins”. Oncogene,  10,  299.
31. Srinivasan, S., March, C.J. and Sudarsanam, S. (1993)
    “Sequence into Structure: A Holistic Approach To Protein Modeling”. Bio/Technology magazine, December, 1579-1580.
32. Grabstein, K.H., Shanebeck, K., Rauch, C., Srinivasan, S., Fung, V., Beer. C., Richardson, J., Schoenborn, M., King, J., Johnson, L., Anderson, M., Watson, James., Anderson, D.M. and Eisenman J. (1994)
    “Cloning of the T-cell growth factor that interacts with the b Chain of the Interleukin-2 Receptor”. Science 264, 965-968.
33. Gayle, R. B., Sleath, P. R., Srinivasan, S., Birk, C. W., Weerawarna, K. S., Cerretti, D. P., Kozlosky, C. J., Nelson, N., VandenBos, T. and Beckmann, M. P. (1993)
    “Importance of the amino terminus of the interleikin-8 receptor in ligand interactions”.  J. Biol. Chem., 268, 7283.
34. Srinivasan, S., Deeley, M. M., Park, C. J., Sassenfeld, H. and Sudarsanam, S. (1993)
    “A Model od IL-7 and the Extra-cellular Domains of its Receptor Complex using Distance Geometry and Structure-Function Data”. Protein Engineering, 6 Supp., 107.
35. Gayle, R. B., Cosman, D., Dower, S., Hopp, T., Jerzy, R., Kronheim, S., March, C. J., Poindexter, K. and Srinivasan S. (1993)
    “Identification of Regions in Interleukin-1 Important  for Activity”. J.  Biol. Chem. 268, 22105-22111.
36. Srinivasan, S., March, C. J. and Sudarsanam, S. (1993)
    “An Automated Method for Modeling Proteins on known Templates using Distance Geometry”. Protein Sciences, 2,  277-289.
37. Sudarsanam, S., Virca, G. D., March, C. J. and Srinivasan, S. (1992)
    “An Approach to Computer-Aided Inhibitor Design: Application to Cathepsin-L”. J. Computer Aided Molecular Design, 6,  223-233.
38. Curtis, B., Presnell, S. R., Srinivasan, S., Sassenfeld, H., Klinke, R., Jeffery, E., Cosman, D., March, C. J. and Cohen, F. (1991)
    “Experimental and Theoretical Studies of the Three-Dimensional Structure of Human Interleukin-4”. Proteins: Structure, Function and Genetics 11, 111-119.
39. Subhashini Srinivasan, Mihir Rayshowdhury, Masayuki Shibata, Robert Rein (1987),
    “Multistep modeling of protein structure: Application towards refinement of tyr-tRNAsynthetase”, International Journal of Quantum Chemistry”, International Journal of Quantum Chemistry, volume 32, Issue Supplement 14, pages 281–288
40. Srinivasan, S.,Raghunathan, G.; Shibata, M.; Rein, R.,(1986)
    “Multistep modeling (MSM) of biomolecular structure application to the A-G mispair in the B-DNA environment”,  International journal of quantum chemistry (QBS), Volume 12; 217-27
41. Srinivasan S., Masayuki Shibata,Robert Rein (1986),
    “Multistep modeling of protein structure: Application to bungarotoxi”, International Journal of Quantum Chemistry”, volume 30, Issue Supplement S13, pages 167–174
42. S. Srinivasan and K. Sundaram, (1983)
    “Molecular structure by the constrained damped least-squares (CDLS) method”, Biopolymers, Volume 22, Issue 5, pages 1373–1381

Patents