Director
Publications
Molecular Biology Lab
Proteomics
Infractructure
Phd
funding
Collaborators
visitors gallery
Trainees
 
Ravi Sirdeshmukh, Ph.D.
Distinguished Scientist & Associate Director
 
Institute of Bioinformatics
Discoverer Building, International Tech Park, Whitefield
Bangalore - 560 066
E-mail: ravi at ibioinformatics dot org
Phone: +91-80-28416140 Fax: +91-80-28416132
 
Education
Ph.D. in Biochemistry, Centre for Cellular and Molecular Biology, Hyderabad, India
M.Sc. in Biochemistry, Osmania University, Hyderabad, India
 

Positions Held

Distinguished Scientist & Associate Director, Institute of Bioinformatics, Bangalore, India, 2010-Present
Scientist G, Center for Cellular and Molecular Biology, Hyderabad, India 2007-2009
Scientist F, Center for Cellular and Molecular Biology, Hyderabad, India 2002-2007 
Visiting Scientist, National Cancer Institute, National Institutes of Health, MD, USA 2006 
Scientist E-II, Center for Cellular and Molecular Biology, Hyderabad, India 1996-2002 
Scientist E1, Center for Cellular and Molecular Biology, Hyderabad, India 1992-1996 
Visiting Scientist, National Institute of Neurological Disorders and Stroke, NIH, USA 1996 
Scientist C, Center for Cellular and Molecular Biology, Hyderabad, India 1987-1992 
Post Doctoral Fellow, Washington University Medical School, St Louis, USA 1982-1987 
 

Area of Specialization

Proteomics
Transcriptomics
Oncology
 

Publications

Research papers: 48

Jayaram, S., Gupta, M. K., Raju R., Gautam, P., Sirdeshmukh, R. (2016). Multi-Omics Data Integration and Mapping of Altered Kinases to Pathways Reveal Gonadotropin Hormone Signaling in Glioblastoma. Omics: A journal of integrative biology. 20, 736-746. [PubMed]

Bhat, A. R., Gupta, M. K., Krithivasan, P., Dhas, K., Nair, J., Reddy, R. B., Sudheendra, H. V., Chavan, S., Vardhan, H., Darsi, S., Balakrishnan, L., Katragadda, S., Kekatpure, V., Suresh, A., Tata, P., Panda, B., Kuriakose, M. A., and Sirdeshmukh, R. (2016). Sample Preparation Method Considerations for Integrated Transcriptomic and Proteomic Analysis of Tumors. Proteomics - Clinical Applications. [PubMed]

Gupta, M. K., Jayaram, S., Reddy, D. N., Polisetty, R. V. and Sirdeshmukh, R. (2015). Transcriptomic and Proteomic Data Integration and Two-Dimensional Molecular Maps with Regulatory and Functional Linkages: Application to Cell Proliferation and Invasion Networks in Glioblastoma. Journal of Proteome Research. 14, 5017-5027. [PubMed] 

Jayaram, S., Gupta M, K., Marigowda, S, B., Ghatge, M., Sharma, A., Vangala, R. K. and Sirdeshmukhb, R. (2015). Insights from chromosome-centric mapping of disease associated genes - chromosome 12 perspective. Journal of Proteome Research. [PubMed] 

Sivadasan, P., Gupta, M. K., Sathe, G. J., Balakrishnan, L., Palit, P., Gowda, H., Suresh, A., Kuriakose, M. A. and Sirdeshmukhb, R. (2015). Data from Human salivary proteome - a resource of potential biomarkers for oral Cancer. Data in Brief. [PubMed] 

Daswani, B., Gupta, M. K., Gavali, S., Desai, M., Sathe, G. J., Patil, A., Parte, P., Sirdeshmukh, R. and Khatkhatay, M. I. (2015). Monocyte Proteomics Reveals Involvement of Phosphorylated HSP27 in the Pathogenesis of Osteoporosis. Disease Markers. 2015, 196589. [PubMed] 
Sivadasan, P., Gupta, M. K., Sathe, G. J., Balakrishnan, L., Palit, P., Gowda, H., Suresh, A., Kuriakose, M. A. and Sirdeshmukh, R. (2015). Human salivary proteome - a resource of potential biomarkers for oral cancer. Journal of Proteomics. [PubMed] 
Sirdeshmukh, R. (2015). Indian proteomics efforts and human proteome project. Journal of Proteomics. [PubMed] 
Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., Thomas, J. K., Muthusamy, B., Leal-Rojas, P., Kumar, P., Sahasrabuddhe, N. A., Balakrishnan, L., Advani, J., George, B., Renuse, S., Selvan, L. D. N., Patil, A. H., Nanjappa, V., Radhakrishnan, A., Prasad, S., Subbannayya, T., Raju, R., Kumar, M., Sreenivasamurthy, S. K., Marimuthu, A., Sathe, G. J., Chavan, S., Datta, K. K., Subbannayya, Y., Sahu, A., Yelamanchi, S. D., Jayaram, S., Rajagopalan, P., Sharma, J., Murthy, K. R., Syed, N., Goel, R., Khan, A. A., Ahmad, S., Dey, G., Mudgal, K., Chatterjee, A., Huang, T. C., Zhong, J., Wu, X., Shaw, P. G., Freed, D., Zahari, M. S., Mukherjee, K. K., Shankar, S., Mahadevan, A., Lam, H., Mitchell, C. J., Shankar, S. K., Satishchandra, P., Schroeder, J. T., Sirdeshmukh, R., Maitra, A., Leach, S. D., Drake, C. G., Halushka, M. K., Prasad, T. S. K., Hruban, R. H., Kerr, C. L., Bader, G. D., Iacobuzio-Donahue, C. A., Gowda, H. and Pandey, A. (2014). A draft map of the human proteome. Nature.  509, 575-581. [PubMed]
Gupta, M. K., Jayaram, S., Madugundu, A. K., Chavan, S., Advani, J., Pandey, A., Thongboonkerd, V., Sirdeshmukh, R. (2014). Chromosome-Centric Human Proteome Project: Deciphering Proteins Associated with Glioma and Neurodegenerative Disorders on Chromosome 12. Journal of Proteome Research. [PubMed]
Polisetty, R. V., Gautam, P., Gupta, M. K., Sharma, R., Uppin, M. S., Challa, S., Ankathi, P., Purohit, A. K., Renu, D., Harsha, H. C., Pandey, A. and Sirdeshmukh, R. (2013). Heterogeneous nuclear ribonucleoproteins and their interactors are a major class of deregulated proteins in anaplastic astrocytoma – a Grade III malignant glioma. Journal of Proteome Research. [PubMed]
Gupta, M. K., Polisetty, R. V., Ramamoorthy, K., Tiwary, S., Kaur, N., Shiras, A. and Sirdeshmukh, R. (2013). Secretome analysis of Glioblastoma cell line - HNGC-2. Molecular BioSystems. 9, 1390-1400. [PubMed]
Mushahary, D., Gautam, P., Sundaram, C. S. and Sirdeshmukh, R. (2013). Expanded protein expression profile of human placenta using two-dimensional gel electrophoresis. Placenta. 34, 193-196. [PubMed]
Gautam, P., Nair, S. C., Gupta, M. K., Sharma, R., Polisetty, R. V., Uppin, M. S., Challa, S., Puligopu, A. K., Ankathi, P., Purohit, A. K., Chandak, G. R., Harsha, H. C. and Sirdeshmukh, R. (2012). Proteins with altered levels in plasma from glioblastoma patients as revealed by iTRAQ-based quantitative proteomic analysis. PLOS ONE. 7, e46153. [PubMed]
Pawar, H., Maharudraiah, J., Kashyap, M. K., Sharma, J., Srikanth, M. S., Choudhary, R., Chavan, S., Sathe, G., Manju, H .C., Veerendra Kumar, K. V., Vijayakumar, M., Sirdeshmukh, R., Harsha, H. C., Prasad, T. S. K., Pandey, A. and Kumar, R. V. (2012). Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochemica. 115, 89-99. [PubMed]

Polisetty, R. V., Gautam, P., Sharma, R., Harsha, H. C., Nair, S. C., Gupta, M. K., Uppin, M. S., Challa, S., Puligopu, A. K., Ankathi, P., Purohit, A. K., Chandak, G. R., Pandey, A. and Sirdeshmukh, R. (2012). LC-MS/MS Analysis of Differentially Expressed Glioblastoma Membrane Proteome Reveals Altered Calcium Signalling and other Protein Groups of Regulatory Functions. Molecular and Cellular Proteomics. 11, M111.013565. [PubMed]
Gautam, P., Upadhyay, S. K., Hassan, W., Madan, T., Sirdeshmukh, R., Sundaram, C. S., Gade, W. N., Basir, S. F., Singh, Y. and Sarma, P. U. Transcriptomic and proteomic profile of Aspergillus fumigatus on exposure to artemisinin. Mycopathologia. 2011. 172, 331-346. [PubMed]

Polisetty, R. V., Gupta, M. K., Nair, S. C., Ramamoorthy, K., Tiwary, S., Shiras, A., Chandak, G. R. and Sirdeshmukh, R. Glioblastoma cell secretome: analysis of three glioblastoma cell lines reveal 148 non-redundant proteins. Journal of Proteomics. 2011. 74, 1918-1925. [PubMed]

Peng, L., Kapp, E. A., Fenyo, D., Kwon, M. S., Jiang, P., Wu, S., Jiang, Y., Aguilar, M. I., Ahmed, N., Baker, M. S., Cai, Z., Chen, Y. J., Van, C. h. i., Chung, M. C., He, F., Len, A. C., Liao, P. C., Nakamura, K., Ngai, S. M., Paik, Y. K., Pan, T. L., Poon, T. C., Salekdeh, G. H., Simpson, R. J., Sirdeshmukh, R., Srisomsap, C., Svasti, J., Tyan, Y. C., Dreyer, F. S., McLauchlan, D., Rawson, P. and Jordan, T. W.  The Asia Oceania Human Proteome Organisation Membrane Proteomics Initiative. Preparation and characterisation of the carbonate-washed membrane standard. Proteomics. 2010.  10, 4142-4148. [PubMed]

Govekar, R. B., D'Cruz, A. K., Alok, P., Agarwal, J., Dinshaw, K. A., Chinoy, R. F., Gadewal, N., Kannan, S., Sirdeshmukh, R., Sundaram, C. S., Malgundkar, S. A., Kane, S. V. and Zingde, S. M.  Proteomic profiling of cancer of the gingivo-buccal complex: Identification of new differentially expressed markers. Proteomics - Clinical Applications. 2009.  3, 1451-1462. [PubMed]

Gautam, P., Shankar, J., Madan, T., Sirdeshmukh, R., Sundaram, C. S., Gade, W. N., Basir, S. F. and Sarma, P. U.  Proteomic and transcriptomic analysis of Aspergillus fumigatus on exposure to amphotericin B. Antimicrobial Agents and Chemotherapy. 2008.  52, 4220-4227. [PubMed]

Sirdeshmukh, R.  Proteomics in India: an overview. Molecular & Cellular Proteomics. 2008.  7, 1406-1407. [PubMed]
Mathivanan, S., Ahmed, M., Ahn, N. G., Alexandre, H., Amanchy, R., Andrews, P. C., Bader, J. S., Balgley, B. M., Bantscheff, M., Bennett, K. L., Bjorling, E., Blagoev, B., Bose, R., Brahmachari, S. K., Burlingame, A. S., Bustelo, X. R., Cagney, G., Cantin, G. T., Cardasis, H. L., Celis, J. E., Chaerkady, R., Chu, F., Cole, P. A., Costello, C. E., Cotter, R. J., Crockett, D., DeLany, J. P., De, M., DeSouza, L. V., Deutsch, E. W., Dransfield, E., Drewes, G., Droit, A., Dunn, M. J., Elenitoba-Johnson, K., Ewing, R. M., Van, E. y. k., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagne, P., Gelfi, C., Gevaert, K., Gimble, J. M., Gnad, F., Goel, R., Gromov, P., Hanash, S. M., Hancock, W. S., Harsha, H. C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjerno, K., Hochstrasser, D. F., Hofmann, O., Horn, D. M., Hruban, R. H., Ibarrola, N., James, P., Jensen, O. N., Jensen, P. H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R. F., Korf, U., Korner, R., Kuster, B., Kwon, M. S., Lee, H. J., Lee, Y. J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M. S., Lobke, C., Loo, J. A., Mann, M., Martens, L., Martinez-Heredia, J., McComb, M., McRedmond, J., Mehrle, A., Menon, R., Miller, C. A., Mischak, H., Mohan, S. S., Mohmood, R., Molina, H., Moran, M. F., Morgan, J. D., Moritz, R., Morzel, M., Muddiman, D. C., Nalli, A., Navarro, J. D., Neubert, T. A., Ohara, O., Oliva, R., Omenn, G. S., Oyama, M., Paik, Y. K., Pennington, K., Pepperkok, R., Periaswamy, B., Petricoin, E. F., Poirier, G. G., Prasad, T. S., Purvine, S. O., Rahiman, B. A., Ramachandran, P., Ramachandra, Y. L., Rice, R. H., Rick, J., Ronnholm, R. H., Salonen, J., Sanchez, J. C., Sayd, T., Seshi, B., Shankari, K., Sheng, S. J., Shetty, V., Shivakumar, K., Simpson, R. J., Sirdeshmukh, R., Siu, K. W., Smith, J. C., Smith, R. D., States, D. J., Sugano, S., Sullivan, M., Superti-Furga, G., Takatalo, M., Thongboonkerd, V., Trinidad, J. C., Uhlen, M., Vandekerckhove, J., Vasilescu, J., Veenstra, T. D., Vidal-Taboada, J. M., Vihinen, M., Wait, R., Wang, X., Wiemann, S., Wu, B., Xu, T., Yates, J. R., Zhong, J., Zhou, M., Zhu, Y., Zurbig, P. and Pandey, A.  Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 2008.  26, 164-167. [PubMed]

Shukla, S., Govekar, R. B., Sirdeshmukh, R., Sundaram, C. S., D'Cruz, A. K., Pathak, K. A., Kane, S. V. and Zingde, S. M.  Tumor antigens eliciting autoantibody response in cancer of gingivo-buccal complex. Proteomics - Clinical Applications. 2007.  1, 1592-1604. [PubMed]

Suhasini, A. N. and Sirdeshmukh, R.  Onconase action on tRNA(Lys3), the primer for HIV-1 reverse transcription. Biochemical and Biophysical Research Communications. 2007.  363, 304-309. [PubMed]

Gautam, P., Sundaram, C. S., Madan, T., Gade, W. N., Shah, A., Sirdeshmukh, R. and Sarma, P. U.  Identification of novel allergens of Aspergillus fumigatus using immunoproteomics approach. Clinical and Experimental Allergy : Journal of the British Society for Allergy. 2007.  37, 1239-1249. [PubMed]

Sirdeshmukh, R.  Fostering proteomics in India. Journal of Proteome Research. 2006.  5, 2879. [PubMed]

Sharma, S., Sundaram, C. S., Luthra, P. M., Singh, Y., Sirdeshmukh, R. and Gade, W. N.  Role of proteins in resistance mechanism of Pseudomonas fluorescens against heavy metal induced stress with proteomics approach. Journal of Biotechnology. 2006.  126, 374-382. [PubMed]

Sirdeshmukh, R., Santosh, V., Srikanth, A. (2006) Differential protein expression, protein profiles of human gliomas and clinical implications. Bio Arrays – from Basics to diagnostics, 1st Ed., pp. 145 – 69, Editor- Appasani, K. Humana Press, N.J., USA
Suhasini, A. N. and Sirdeshmukh, R.  Transfer RNA cleavages by onconase reveal unusual cleavage sites. The Journal of Biological Chemistry. 2006.  281, 12201-12209. [PubMed]

Chumbalkar, V. C., Subhashini, C., Dhople, V. M., Sundaram, C. S., Jagannadham, M. V., Kumar, K. N., Srinivas, P. N., Mythili, R., Rao, M. K., Kulkarni, M. J., Hegde, S., Hegde, A. S., Samual, C., Santosh, V., Singh, L. and Sirdeshmukh, R.  Differential protein expression in human gliomas and molecular insights. Proteomics. 2005.  5, 1167-1177. [PubMed]

Chandra, H., Gupta, P. K., Sharma, K., Mattoo, A. R., Garg, S. K., Gade, W. N., Sirdeshmukh, R., Maithal, K. and Singh, Y.  Proteome analysis of mouse macrophages treated with anthrax lethal toxin. Biochimica et Biophysica Acta. 2005.  1747, 151-159. [PubMed]

Saxena, S. K., Sirdeshmukh, R., Ardelt, W., Mikulski, S. M., Shogen, K. and Youle, R. J.  Entry into cells and selective degradation of tRNAs by a cytotoxic member of the RNase A family. The Journal of Biological Chemistry. 2002.  277, 15142-15146. [PubMed]

Murthy, B. S., De, L., Piccoli, R., D'Alessio, G. and Sirdeshmukh, R.  Effects of protein RNase inhibitor and substrate on the quaternary structures of bovine seminal RNase. Biochemistry. 1996.  35, 3880-3885. [PubMed]

Tharun, S. and Sirdeshmukh, R.  Specific endonucleolytic cleavages of mouse albumin mRNA and their modulation during liver development. Nucleic Acids Research. 1995.  23, 641-646. [PubMed]

Rao, K. S., Sirdeshmukh, R. and Gupta, P. D.  Modulation of cytosolic RNase activity by endogenous RNase inhibitor in rat vaginal epithelial cells on estradiol administration. FEBS Letters. 1994.  343, 11-14. [PubMed]

Murthy, B. S. and Sirdeshmukh, R.  Sensitivity of monomeric and dimeric forms of bovine seminal ribonuclease to human placental ribonuclease inhibitor. The Biochemical Journal. 1992.  281 ( Pt 2), 343-348. [PubMed]

Krych, M., Sirdeshmukh, R., Gourse, R. and Schlessinger, D.  Processing of Escherichia coli 16S rRNA with bacteriophage lambda leader sequences. Journal of Bacteriology. 1987.  169, 5523-5529. [PubMed]

King, T. C., Sirdeshmukh, R. and Schlessinger, D. (1986). Nucleolytic processing of ribonucleic acid transcripts in procaryotes. Microbiological Reviews. 428-451. [PubMed]

Schlessinger, D., Thomas, J. R., Krych, M., Sirdeshmukh, R. and Little, R. D.  Ribosomal RNA processing in Escherichia coli and cultured mammalian cells. Biochemical Society Transactions. 1986.  14, 811-813. [PubMed]

Sirdeshmukh, R. and Schlessinger, D.  Why is processing of 23 S ribosomal RNA in Escherichia coli not obligate for its function? Journal of Molecular Biology. 1985.  186, 669-672. [PubMed]

Sirdeshmukh, R. and Schlessinger, D.  Ordered processing of Escherichia coli 23S rRNA in vitro. Nucleic Acids Research. 1985.  13, 5041-5054. [PubMed]

Schlessinger, D., Bolla, R. I., Sirdeshmukh, R. and Thomas, J. R.  Spacers and processing of large ribosomal RNAs in Escherichia coli and mouse cells. BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology. 1985.  3, 14-18. [PubMed]

Sirdeshmukh, R., Krych, M. and Schlessinger, D.  Escherichia coli 23S ribosomal RNA truncated at its 5' terminus. Nucleic Acids Research. 1985.  13, 1185-1192. [PubMed]

Sirdeshmukh, R., Vijayarangam, D. and Bhargava, P. M.  E. coli RNA entrapped in large unilamellar liposomes is partially exposed. Indian Journal of Biochemistry & Biophysics. 1984.  21, 293-298. [PubMed]

King, T. C., Sirdeshmukh, R. and Schlessinger, D.  RNase III cleavage is obligate for maturation but not for function of Escherichia coli pre-23S rRNA. Proceedings of the National Academy of Sciences of the United States of America. 1984.  81, 185-188. [PubMed]

Sirdeshmukh, R. B. and Bhargava, P. M.  Uptake of exogenous RNA by rat-liver parenchymal cells in suspension prepared by the collagenase method. Indian Journal of Biochemistry & Biophysics. 1983.  20, 121-126. [PubMed]

Sirdeshmukh, R. and Bhargava, P. M.  Evidence for the presence of a cell-surface ribonuclease in mechanically prepared rat-liver cells in suspension. Bioscience Reports. 1982.  2, 751-760. [PubMed]

 

Research Support

 

Title of Project

Funding Agency

 

Role
1

Identification of new biomarkers using genomics and proteomics

Council of Scientific and Industrial Research, Government of India

 

PI
2 Proteomics of the effect of alkylating agents on mouse liver   Defence Research and Development Organisation, New Delhi, India

 

PI
3 New insights in cancer biology- Proteomics of glioma   Council of Scientific and Industrial Research, Government of India

 

PI
4 Plasma proteomics for health and disease   Council of Scientific and Industrial Research, Government of India

 

PI
5 Medically important fungus Aspergillus fumigatus   Department of Science & Technology, Government of India

 

Co-PI
6 Identification and functional analysis of genes for yield in rice   Department of Biotechnology, Government of India

 

Co-PI
7 Project on Salivary Proteome of  Oral Cancer patients   Department of Biotechnology, Government of India   Co-PI
8
Program Grant on Head and Neck Oncology Research
  Department of Biotechnology, Government of India   Co-PI
9 Project on Identification of novel peptides in human Glioblastoma   Indian Council of Medical Research, Government of India   PI
 
Member
Expert Group for Non communicable diseases, DBT. Govt.of India
Program Review Committee (BMS-Bioinf.), ICMR,  Govt. of India
Program Advisory and Management Comm. DBT Centre for Mole. Medicine, National Institute of Immunol. New Delhi
SAC, ICPO, ICMR, Govt. of India, Noida
SAC, NIOP, ICMR, Govt. of India,  India
Steering Committee, member scientific advisory committee, DST Advanced Centre for Bioseparation Technology, VIT University, Vellore
Consortium manager of CSIR Proteomics Network for International Collaborations (dedicated to the promotion and growth of Proteomics research in CSIR and other Indian Labs (2007-2009)
Program Advisory Committee, National Facility for Advanced Proteomics and Protein Research, IICB, Kolkatta (2005-07)
Board of Studies in Biotechnology, Osmania University, Hyderabad
Advisory Panel for Protein and Glycoproteins, US Pharmacopeia, USA
Central and Eastern European Proteomics Conference
Council Member, Human Proteome Organization (HUPO Intl.)
Council Member, Asian Oceanean HUPO (AOHUPO)
Founder President, Proteomics Society (India)
Editorial Board Member - Journal of Proteomics and Bioinformatics
Reviewer - Proteomics, Annals of Neurology, Proteomics - Clinical Applications, Journal of Proteome Research, Proteome Science, Molecular Biosystems.