Dr. Srikanth

Senior Clinical Scientist

Dr. Srikanth has completed his Master’s in biotechnology from Indian Institute of Technology, Bombay, India and thereafter, pursued a Ph.D. in Bioinformatics from Institute of Bioinformatics, Bangalore, India and Johns Hopkins University, Baltimore, USA. He has an extensive experience of more than a decade in analysis and interpretation of data from large-scale cancer genomics, transcriptomics and proteogenomics projects. He has co-authored more than thirty research articles in journals of international reputation in the field of multi- omics, including publications in Nature, Nature Methods, Genome Research, Nature comm., and MCP, among others and is also a reviewer for eight international journals.

Dr Srikanth worked as a Cancer Data scientist in Procan® at Children’s Medical Research Institute, Australia for several years before joining Karkinos Healthcare Pvt Ltd. Working at Procan®, Australia’s and world’s first initiative Dr. Srikanth worked on analysing large-scale proteogenomic datasets from adult and childhood cancers to identify potential biomarkers and therapeutic targets.

As a Research Scientist at Syngene International Pvt. Ltd. he has worked on several metagenomics and transcriptomics projects. Dr. Srikanth also worked with LifeBytes Pvt. Ltd. as a computational biologist to develop WGS, WES, and single cell omics data analysis pipelines for several clients in India and US.

Dr. Srikanth is currently the head of computational biology group at Karkinos and interests in multi-omics data analysis, integration and interpretation of Big Data from genomics, transcriptomics, epigenomics and proteomics.

Publications (Total: 33) H-index=25, Total Citations 4,342

  1. Gonçalves, E., Poulos, R. C., Cai, Z., Barthorpe, S., Manda S. S., Lucas, N., Beck, A., Bucio-Noble, D., Dausmann, M., Hall, C., Hecker, M., Koh, J., Lightfoot, H., Mahboob, S., Mali, I., Morris, J., Richardson, L., Seneviratne, A. J., Shepherd, R., Sykes, E., Thomas, F., Valentini, S., Williams, S. G., Wu, Y., Xavier, D., MacKenzie, K. L., Hains, P. G. , Tully, B., Robinson, P. J., Zhong, Q., Garnett, M. J., Reddel, R. R. (2022). Pan-cancer proteomic map of 949 human cell lines. Cancer Cell, 40, 835-849
  2. Manda, S. S., Noor, Z., Hains, G. P and Zhong, Q (2021). PIONEER: Pipeline for generating High-quality Spectral libraries for DIA-MS Data. Current Protocols in Bioinformatics. e69.
  3. Logan, J., Pearson, M. S., Manda, S. S, Choi, Y.J, Field, M., Eichenberger, R.M., Mulvenna, J., Nagaraj, S.H., Fujiwara, R.T., Gazzinelli-Guimaraes, P., Bueno, L., Mati, V., Bethony, J.M., Mitreva, M., Sotillo, J. and Loukas, A. (2020) Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms. PLoS Negl Trop Dis. 14(5):e0008237.
  4. Poulos, R.C., Hains, P.G., Shah, R., Lucas, N., Xavier, D., Manda, S. S, Anees, A., Koh, J.M.S., Mahboob, S., Wittman, M., Williams, S.G., Sykes, E.K., Hecker, M., Dausmann, M., Wouters, M.A., Ashman, K., Yang, J., Wild, P.J., DeFazio, A., Balleine, R.L., Tully, B., Aebersold, R., Speed, T.P., Liu, Y., Reddel, R.R., Robinson, P.J. and Zhong, Q. Strategies to enable large-scale proteomics for reproducible research. Nat Commun. 2020 Jul 30;11(1):3793.
  5. Manda, S. S., Nirujogi, R. S., Pinto, S. M., Kim, M. S., Datta, K. K., Sirdeshmukh, R., Prasad, T. S., Thongboonkerd, V., Pandey, A., and Gowda, H. (2014) Identification and characterization of proteins encoded by chromosome 12 as part of chromosome-centric human proteome project. Journal of proteome research 13, 3166-3177
  6. Manda, S. S. #, Mirsafian, H. #, Mitchell, C.J., Sreenivasamurthy, S., Ripen, A. M., Mohamad, S. B., Merican, A. F. and Pandey, A. (2016) Long non-coding RNA expression in primary human monocytes. Genomics. S0888-7543(16)30002-7. # (Equal contribution)
  7. Pinto, S. M., Manda, S. S., Kim, M. S., Taylor, K., Selvan, L. D., Balakrishnan, L., Subbannayya, T., Yan, F., Prasad, T. S., Gowda, H., Lee, C., Hancock, W. S., and Pandey, A. (2014) Functional annotation of proteome encoded by human chromosome 22. Journal of proteome research 13, 2749-2760
  8. 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., 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., 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
  9. Yadavalli, S., Jayaram, S., Manda, S. S., Madugundu, A. K., Nayakanti, D. S., Tan, T. Z., Bhat, R., Rangarajan, A., Chatterjee, A., Gowda, H., Thiery, J. P. and Kumar, P. (2017). Data-Driven Discovery of Extravasation Pathway in Circulating Tumor Cells. Scientific Reports. 7:43710
  10. Kelkar, D. S., Provost, E., Chaerkady, R., Muthusamy, B., Manda, S. S., Subbannayya, T., Selvan, L. D., Wang, C. H., Datta, K. K., Woo, S., Dwivedi, S. B., Renuse, S., Getnet, D., Huang, T. C., Kim, M. S., Pinto, S. M., Mitchell, C. J., Madugundu, A. K., Kumar, P., Sharma, J., Advani, J., Dey, G., Balakrishnan, L., Syed, N., Nanjappa, V., Subbannayya, Y., Goel, R., Prasad, T. S., Bafna, V., Sirdeshmukh, R., Gowda, H., Wang, C., Leach, S. D., and Pandey, A. (2014) Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Molecular & cellular proteomics : MCP 13, 3184- 3198
  11. Mitchell, C. J.,# Getnet, D.#, Kim, M. S.#, Manda, S. S., Kumar, P., Huang, T. C., Pinto, S. M., Nirujogi, R. S., Iwasaki, M., Shaw, P. G., Wu, X., Zhong, J., Chaerkady, R., Marimuthu, A., Muthusamy, B., Sahasrabuddhe, N. A., Raju, R., Bowman, C., Danilova, L., Cutler, J., Kelkar, D. S., Drake, C. G., Prasad, T. S., Marchionni, L., Murakami, P. N., Scott, A. F., Shi, L., Thierry-Mieg, J., Thierry-Mieg, D., Irizarry, R., Cope, L., Ishihama, Y., Wang, C., Gowda, H., and Pandey, A. (2015) A multi-omic analysis of human naive CD4+ T cells. BMC systems biology 9, 75
  12. Prasad, T. S., Mohanty, A. K., Kumar, M., Sreenivasamurthy, S. K., Dey, G., Nirujogi, R. S., Pinto, S. M., Madugundu, A. K., Patil A. H., Advani, J., Manda, S. S., Gupta, M. K., Kelkar, D. S., Hall, B., Jiang, X., Peery, A., Rajagopalan, P., Yelamanchi, S. D., Solanki, H. S., Raja, R., Sathe, G. J., Chavan, S., Verma, R., Patel, K. M., Jain, A. P., Syed, N., Datta K. K., Khan, A. A., Dammalli, M., Jayaram, S., Radhakrishnan, A, Mitchell, C. J., Na, C. H., Kumar, N., Sinnis, P., Sharakhov, I. V., Wang. C., Gowda, H., Tu, Z., Kumar, A., Pandey, A. (2017) Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Research. 27(1):133-144
  13. Ewing, A. D., Gacita, A., Wood, L. D., Ma, F., Xing, D., Kim, M. S., Manda, S. S., Abril, G., Pereira, G., Makohon-Moore, A., Looijenga, L. H., Gillis, A. J., Hruban, R. H., Anders, R. A., Romans, K. E., Pandey, A., Iacobuzio-Donahue, C. A., Vogelstein, B., Kinzler, K. W., Kazazian, H. H., Jr., and Solyom, S. (2015) Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Research 25, 1536-1545
  14. Beachley, V. Z., Wolf, M. T., Sadtler, K., Manda, S. S., Jacobs, H., Blatchley, M. R., Bader, J. S., Pandey, A., Pardoll, D., and Elisseeff, J. H. (2015) Tissue matrix arrays for high-throughput screening and systems analysis of cell function. Nature methods 12, 1197- 1204
  15. Pawar, H., Manda, S. S., Kashyap, M. K., Sathe, G. J., Chavan, S., Singal, M., Manju, H. C., Kumar, K. V. V., Vijayakumar, M., Sirdeshmukh, R., Pandey, A., Prasad, T. S. K., Gowda, H., and Kumar, R. V. (2015) Downregulation of S100 Calcium Binding Protein A9 in Esophageal Squamous Cell Carcinoma. The Scientific World Journal
  16. Li, R., Liao, G., Nirujogi, R. S., Pinto, S. M., Shaw, P. G., Huang, T. C., Wan, J., Qian, J., Gowda, H., Wu, X., Lv, D. W., Zhang, K., Manda, S. S., Pandey, A. and Hayward, S. D. (2015). Phosphoproteomic profiling reveals Epstein-Barr Virus protein kinase integration of DNA damage response and mitotic signaling. PLoS Pathogens. 11:e1005346.
  17. Wu, X., Zahari, M. S., Renuse, S., Nirujogi, R. S., Kim, M. S., Manda, S. S., Stearns, V., Gabrielson, E., Sukumar, S., and Pandey, A. (2015) Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer. Molecular & cellular proteomics: MCP 14, 2887-2900
  18. Subbannayya, Y., Syed, N., Barbhuiya, M. A., Raja, R., Marimuthu, A., Sahasrabuddhe, N., Pinto, S. M., Manda, S. S., Renuse, S., Manju, H. C., Zameer, M. A., Sharma, J., Brait, M., Srikumar, K., Roa, J. C., Vijaya Kumar, M., Kumar, K. V., Prasad, T. S., Ramaswamy, G., Kumar, R. V., Pandey, A., Gowda, H., and Chatterjee, A. (2015) Calcium calmodulin dependent kinase kinase 2 - a novel therapeutic target for gastric adenocarcinoma. Cancer biology & therapy 16, 336-345
  19. Sudha, D., Kohansal-Nodehi, M., Kovuri, P., Manda, S. S., Neriyanuri, S., Gopal, L., Bhende, P., Chidambaram, S. and Arunachalam, J. P. (2017) Proteomic profiling of human intraschisis cavity fluid. Clinical Proteomics 14, 13
  20. Subbannayya, Y., Mir, S. A., Renuse, S., Manda, S. S., Pinto, S. M., Puttamallesh, V. N., Solanki, H. S., Manju, H. C., Syed, N., Sharma, R., Christopher, R., Vijayakumar, M., Veerendra Kumar, K. V., Keshava Prasad, T. S., Ramaswamy, G., Kumar, R. V., Chatterjee, A., Pandey, A., and Gowda, H. (2015) Identification of differentially expressed serum proteins in gastric adenocarcinoma. Journal of proteomics 127, 80-88
  21. Pinto, S. M., Nirujogi, R. S., Rojas, P. L., Patil, A. H., Manda, S. S., Subbannayya, Y., Roa, J. C., Chatterjee, A., Prasad, T. S., and Pandey, A. (2015) Quantitative phosphoproteomic analysis of IL-33-mediated signaling. Proteomics 15, 532-544
  22. Nirujogi, R. S., Wright, J. D., Jr., Manda, S. S., Zhong, J., Na, C. H., Meyerhoff, J., Benton, B., Jabbour, R., Willis, K., Kim, M. S., Pandey, A., and Sekowski, J. W. (2015) Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats. Proteomics 15, 487-499
  23. Murthy, K. R., Rajagopalan, P., Pinto, S. M., Advani, J., Murthy, P. R., Goel, R., Subbannayya, Y., Balakrishnan, L., Dash, M., Anil, A. K., Manda, S. S., Nirujogi, R. S., Kelkar, D. S., Sathe, G. J., Dey, G., Chatterjee, A., Gowda, H., Chakravarti, S., Shankar, S., Sahasrabuddhe, N. A., Nair, B., Somani, B. L., Prasad, T. S., and Pandey, A. (2015) Proteomics of human aqueous humor. Omics : a journal of integrative biology 19, 283-293
  24. Nanjappa, V., Thomas, J. K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., Ahmad Khan, A., Balakrishnan, L., Sahasrabuddhe, N. A., Kumar, S., Jhaveri, B. N., Sheth, K. V., Kumar Khatana, R., Shaw, P. G., Srikanth, S. M., Mathur, P. P., Shankar, S., Nagaraja, D., Christopher, R., Mathivanan, S., Raju, R., Sirdeshmukh, R., Chatterjee, A., Simpson, R. J., Harsha, H. C., Pandey, A., and Prasad, T. S. (2014) Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic acids research 42, D959-965
  25. Murthy, K. R., Goel, R., Subbannayya, Y., Jacob, H. K., Murthy, P. R., Manda, S. S., Patil, A. H., Sharma, R., Sahasrabuddhe, N. A., Parashar, A., Nair, B. G., Krishna, V., Prasad Ts, K., Gowda, H., and Pandey, A. (2014) Proteomic analysis of human vitreous humor. Clinical proteomics 11, 29
  26. Balakrishnan, L., Nirujogi, R. S., Ahmad, S., Bhattacharjee, M., Manda, S. S., Renuse, S., Kelkar, D. S., Subbannayya, Y., Raju, R., Goel, R., Thomas, J. K., Kaur, N., Dhillon, M., Tankala, S. G., Jois, R., Vasdev, V., Ramachandra, Y., Sahasrabuddhe, N. A., Prasad Ts, K., Mohan, S., Gowda, H., Shankar, S., and Pandey, A. (2014) Proteomic analysis of human osteoarthritis synovial fluid. Clinical proteomics 11, 6
  27. Balakrishnan, L., Bhattacharjee, M., Ahmad, S., Nirujogi, R. S., Renuse, S., Subbannayya, Y., Marimuthu, A., Srikanth, S. M., Raju, R., Dhillon, M., Kaur, N., Jois, R., Vasudev, V., Ramachandra, Y., Sahasrabuddhe, N. A., Prasad Ts, K., Mohan, S., Gowda, H., Shankar, S., and Pandey, A. (2014) Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients. Clinical proteomics 11, 1
  28. Pawar, H., Maharudraiah, J., Kashyap, M. K., Sharma, J., Srikanth, S. M., Choudhary, R., Chavan, S., Sathe, G., Manju, H. C., Kumar, K. V., Vijayakumar, M., Sirdeshmukh, R., Harsha, H. C., Prasad, T. S., Pandey, A., and Kumar, R. V. (2013) Downregulation of cornulin in esophageal squamous cell carcinoma. Acta histochemica 115, 89-99
  29. Marimuthu, A., Subbannayya, Y., Sahasrabuddhe, N. A., Balakrishnan, L., Syed, N., Sekhar, N. R., Katte, T. V., Pinto, S. M., Srikanth, S. M., Kumar, P., Pawar, H., Kashyap, M. K., Maharudraiah, J., Ashktorab, H., Smoot, D. T., Ramaswamy, G., Kumar, R. V., Cheng, Y., Meltzer, S. J., Roa, J. C., Chaerkady, R., Prasad, T. S., Harsha, H. C., Chatterjee, A., and Pandey, A. (2013) SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics Clinical applications 7, 355-366
  30. Marimuthu, A., Chavan, S., Sathe, G., Sahasrabuddhe, N. A., Srikanth, S. M., Renuse, S., Ahmad, S., Radhakrishnan, A., Barbhuiya, M. A., Kumar, R. V., Harsha, H. C., Sidransky, D., Califano, J., Pandey, A., and Chatterjee, A. (2013) Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome. Biochimica et biophysica acta 1834, 2308-2316
  31. Goel, R., Murthy, K. R., Srikanth, S. M., Pinto, S. M., Bhattacharjee, M., Kelkar, D. S., Madugundu, A. K., Dey, G., Mohan, S. S., Krishna, V., Prasad Ts, K., Chakravarti, S., Harsha, H., and Pandey, A. (2013) Characterizing the normal proteome of human ciliary body. Clinical Proteomics 10, 9
  32. Ambekar, A. S., Nirujogi, R. S., Srikanth, S. M., Chavan, S., Kelkar, D. S., Hinduja, I., Zaveri, K., Prasad, T. S., Harsha, H. C., Pandey, A., and Mukherjee, S. (2013) Proteomic analysis of human follicular fluid: a new perspective towards understanding folliculogenesis. Journal of proteomics 87, 68-77
  33. Raju, R., Nanjappa, V., Balakrishnan, L., Radhakrishnan, A., Thomas, J. K., Sharma, J., Tian, M., Palapetta, S. M., Subbannayya, T., Sekhar, N. R., Muthusamy, B., Goel, R., Subbannayya, Y., Telikicherla, D., Bhattacharjee, M., Pinto, S. M., Syed, N., Srikanth, M. S., Sathe, G. J., Ahmad, S., Chavan, S. N., Kumar, G. S., Marimuthu, A., Prasad, T. S., Harsha, H. C., Rahiman, B. A., Ohara, O., Bader, G. D., Sujatha Mohan, S., Schiemann, W. P., and Pandey, A. (2011) NetSlim: high-confidence curated signaling maps. Database : the journal of biological databases and curation 2011, bar032

Book Chapters:

  • Manda, S. S., Michael, D., Jadhao, S. and Nagaraj, S. H. (2019) Functional enrichment - Encyclopedia of Bioinformatics and Computational Biology. 3: 218-229.
  • Sathyanarayanan, A., Manda, S. S., Poojary, M. and Naragaj, S. H. (2019) Exome Sequencing Data Analysis Encyclopedia of Bioinformatics and Computational Biology. 3: 164-179