Role of extracellular matrix in cancer



Dr. Shivakumar Keerthikumar obtained his Ph.D. in Bioinformatics from Institute of Bioinformatics, Bangalore, India. As a part of his thesis research work, he worked as Research Associate at Research Center for Allergy and Immunology (RCAI), RIKEN, Japan for the development of Resource for Asian Primary Immunodeficiency Diseases (PID) and has designed algorithm for the prediction of candidate PID genes using support vector machine learning approach. His research interests span from functional genomics to systems biology using computational methods.


He did his postdoctoral research in Intellectual Disability (ID) at Centre for molecular and biomolecular informatics (CMBI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands. His research work was mainly focused on elucidating molecular mechanism involved in ID genes for better diagnosis of the disorders using systems biology approach.


Currently, his research work at Suresh Mathivanan lab is mainly focused on understanding the role of Exosomes in human cancers and neurological disorders using genomics and proteomics data derived from these disorders.

Email: Shivakumar Keerthikumar




Book chapters: 7

1. Keerthikumar, S., Gangoda, L., Gho, Y.S. and Mathivanan, S. (2017). Bioinformatics Tools for Extracellular Vesicles Research. Methods in Molecular Biology. 1545:189-196.


2. Keerthikumar, S. (2017). An Introduction to Proteome Bioinformatics. Methods in Molecular Biology. In press


3. Keerthikumar, S.* and Mathivanan, S. (2017). Proteomic Data Storage and Sharing. Methods in Molecular Biology. In press

* Corresponding author


4. Anand, S., Samuel, M., Ang, CS., Keerthikumar, S. and Mathivanan, S. (2017). Label-Based and Label-Free Strategies for Protein Quantitation. Methods in Molecular Biology. In press


5. Pathan, M., Samuel, M., Keerthikumar, S. and Mathivanan, S. (2017). Unassigned MS/MS Spectra: Who Am I? Methods in Molecular Biology. In press


6. Keerthikumar, S.* and Mathivanan, S. (2017). Proteotypic Peptides and Their Applications. Methods in Molecular Biology. In press

* Corresponding author


7. Chisanga, D., Keerthikumar, S., Mathivanan, S. and Chilamkurti, N. (2017). Network Tools for the Analysis of Proteomic Data. Methods in Molecular Biology. In press



Research papers: 32


32. Dona, SIM., Prendergast, AL., Mathivanan, S., Keerthikumar, S. and Salim, A. (2017) Powerful differential expression analysis incorporating network topology for next-generation sequencing data. Bioinformatics. Jan 5. doi: 10.1093/bioinformatics/btw833.


31. Pathan, M., Keerthikumar, S., Chisanga, D., Alessandro, R., Ang, C.S., Askenase, P., Batagov, A.O., Benito-Martin, A., Camussi, G., Clayton, A., Collino, F., Di Vizio, D., Falcon-Perez, J.M., Fonseca, P., Fonseka, P., Fontana, S., Gho, Y.S., Hendrix, A., Nolte-'t Hoen, E., Iraci, N., Kastaniegaard, K., Kislinger, T., Kowal, J., Kurochkin, I.V., Leonardi, T., Liang, Y., Llorente, A., Lunavat, T.R., Maji, S., Monteleone, F., Overbye, A., Panaretakis, T., Patel, T., Peinado, H., Pluchino, S., Principe, S., Ronquist, G., Royo, F., Sahoo, S., Spinelli, C., Stensballe, A., Thery, C., van Herwijnen, M., Wauben, M., Welton, J., Zhao, J. and Mathivanan, S. (2017) A novel community driven software for functional enrichment analysis of extracellular vesicles data. J Extracellular Vesicles. In press



30. Keerthikumar, S . (2016). A catalogue of human secreted proteins and its implications. AIMS Biophysics. 3(4), 563-570.


29. Worah, K., Mathan, TSM., Vu Manh, TP., Keerthikumar, S., Schreibelt, G., Tel, J., Duiveman-de Boer, T., Skold, AE., van Spriel, AB., de Vries, IJM., Huynen, MA., Wessels, HJ., Gloerich, J., Dalod, M., Lasonder, E., Figdor, CG. and Buschow, SI. (2016). Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function. Cell Reports. 16(11), 2953-2966.


28. Kang, Y., Baker, M.J., Liem, M., Louber, J., McKenzie, M., Atukorala, I., Ang, C.S., Keerthikumar, S., Mathivanan, S. and Stojanovski, D. (2016). Tim29 is a novel subunit of the human TIM22 translocase and is involved in complex assembly and stability. eLife.5:e17463.


27. Cheung, KH., Keerthikumar, S., Roncaglia, P., Subramanian, SL., Roth, ME., Gould, S., Alexander, R., Galas, D., Gerstein, MB., Hill, AF., Kitchen, RR., Lotvall, J., Patel, T., Procaccini, DC., Queensberry, P., Rozowsky, J., Raffai, RL., Shypitsyn, A., Su, AI., Thery, C., Vickers, K., Wauben, M., Mathivanan, S., Milosavljevic, A. and Laurent, L. (2016). Extending Gene Ontology in the Context of Extracellular RNA and Vesicle Communication. Journal of Biomedical Semantics. 7(19).


26. Kochinke, K., Zweier, C., Nijhof, B., Fenckova, M., Cizek, P., Honti, F., Keerthikumar, S., Oortveld, MAW., Kleefstra, T., Kramer, JM., Webber, C., Huynen, MA. and Schenck, A. (2016). Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. The American Journal of Human Genetics. 98(1), 149-64.


25. Chisanga, D., Keerthikumar, S., Pathan, M., Ariyaratne, D., Kalra, H., Boukouris, S., Mathew, N., Al Saffar, H., Gangoda, L., Ang, C.S., Sieber, O., Mariadason, J., Dasgupta, R., Chilamkurti, N. and Mathivanan, S. (2016). Colorectal Cancer Atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissue. Nucleic Acids Research. 44(D1), D969-74.


24. Keerthikumar, S*., Chisanga, D., Ariyaratne, D., Al Saffar, H., Anand, S., Zhao, S., Samuel, M., Pathan, M., Jois, M., Chilamkurti, N., Gangoda, L. and Mathivanan, S*. (2016). ExoCarta: A web-based compendium of exosomal cargo. Journal of Molecular Biology. 428(4), 688-92.

* Corresponding author



23. Pathan, M*., Keerthikumar, S*., Ang, C.S., Gangoda, L., Quek, C.M.J., Williamson, N.J., Mouradov, D., Sieber, O.M., Simpson, R.J., Salim, A., Bacic, A., Hill, A.F., Stroud, D.A., Ryan, M.T., Agbinya, J.A., Mariadason, J.M., Burgess, A.W. and Mathivanan, S. FunRich: a standalone tool for functional enrichment analysis. Proteomics. 15, 2597-2601.

* Authors contributed equally


22. Keerthikumar, S*., Gangoda, L*., Liem, M., Fonseka, P., Atukorala, I., Ozcitti, C., Shambrook, M.C., Scicluna, B.J., Hill, A.F., Mechler, A., Adda, C.G., Ang, C.S. and Mathivanan, S. (2015) Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes. Oncotarget . 6:17, 15375-15396.

* Authors contributed equally


21. Gangoda, L., Keerthikumar, S., Fonseka, P., Edgington, L., Ang, C., Ozcitti, C., Bogyo, M., Parker, B. and Mathivanan, S. (2015). Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin. Oncotarget. 6:13, 11175-11190.



20. Van_de_lagemaat LN, Nijhof B,* Bosch DG*, Kohansal-nodehi M*, Keerthikumar, S*. and Heimel JA. (2014). Age-related decreased inhibitory versus excitatory gene expression in the adult autistic brain. Frontiers in Neuroscience. 8:394. doi:10.3389/fnins.2014.00394

* Authors contributed equally and arranged in alphabetical order



19. Oortveld MAW., Keerthikumar, S., Oti M., Nijhof B., Fernandes AC., Kochinke K., Castells-Nobau A., van Engelen E., Ellenkamp T., Eshuis L., Galy A., van Bokhoven H., Habermann B., Brunner HG., Zweier C., Verstreken P., Huynen MA. and Schenck A. (2013). Human Intellectual Disability Genes Form Conserved Functional Modules in Drosophila. Plos Genetics. Epub 2013 Oct 31.



18. Kashyap, M. K., Pawar, H., Keerthikumar, S., Sharma, J., Goel, R., Mahmood, R., Vijaya Kumar, M., Veerendra Kumar, K. V., Pandey, A., Kumar, R. V., Prasad, T. S. K. and Harsha, H. C. (2012). Evaluation of protein expression pattern of stanniocalcin 2, insulin-like growth factor-binding protein 7, inhibin beta A and four and a half LIM domains 1 in esophageal squamous cell carcinoma. Cancer Biomarkers. 12, 1-9.


17. Pawar, H., Sahasrabuddhe, N. A., Renuse, S., Keerthikumar, S., Sharma, J., Kumar, G. S. S., Venugopal, A., Sekhar, N. R., Kelkar, D. S., Nemade, H. N., Khobragade, S. N., Muthusamy, B., Kandasamy, K., Harsha, H. C., Chaerkady, R., Patole M. S. and Pandey, A. (2012). A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani. Proteomics. 12, 832-844.


16. Prasad, T. S. K., Harsha, H. C., Keerthikumar, S.,  Sekhar, N. R., Selvan, L. D. N.,  Kumar, P., Pinto, S. M., Muthusamy, B., Subbannayya, Y., Renuse, S., Chaerkady, R., Mathur, P. P., Ravikumar, R. and Pandey, A. (2012). Proteogenomic analysis of Candida glabrata using high resolution mass spectrometry. Journal of Proteome Research. 11, 247-260.



15. Barbhuiya, M. A., Sahasrabuddhe, N. A., Pinto, S. M., Muthusamy, B., Singh, T. D., Nanjappa, V., Keerthikumar, S., Delanghe, B., Harsha, H. C., Chaerkady, R., Jalaj, V., Gupta, S., Shrivastav, B. R., Tiwari, P. K. and Pandey, A. (2011). Comprehensive proteomic analysis of human bile. Proteomics. 11, 4443- 4453.


14. Kumar, G. S. S., Venugopal, A. K., Selvan, L. D. N., Marimuthu, A., Keerthikumar, S., Pathare, S., Dikshit, J. B., Tata, P., Hariharan, R., Prasad, T. S. K., Harsha, H. C., Ramachandra, Y. L., Mahadevan, A., Chaerkady, R., Shankar, S. K. and Pandey, A (2011). Gene Expression Profiling of Tuberculous Meningitis. Journal of Proteomics and Bioinformatics. 4, 98-105.


13. Marimuthu, A., Jacob, H. K. C., Jakharia, A., Subbannayya, Y., Keerthikumar, S., Kashyap,  M. K., Goel, R., Balakrishnan, L., Dwivedi, S., Pathare, S., Dikshit, J. B., Maharudraiah, J., Singh, S., Kumar, G. S. S., Vijayakumar, M., Veerendra Kumar, K. V., Premalatha, C. S., Tata, P., Hariharan, R., Roa, J. C., Prasad, T. S. K., Chaerkady, R., Kumar, R. V. and Pandey, A (2011). Gene expression profiling of gastric cancer. Journal of Proteomics and Bioinformatics. 4, 74-82.



12. Prasad, T. S. K., Keerthikumar, S., Chaerkady, R., Kandasamy, K., Renuse, S., Marimuthu, A., Venugopal, A.K., Thomas, J. K., Jacob, H. K. C., Goel, R., Pawar, H., Sahasrabuddhe, N. A., Krishna, V., Nair, B. G., Gucek, M., Cole, R. N., Ravikumar, R., Harsha, H. C., and Pandey, A (2010). Comparative proteomic analysis of Candida albicans and Candida glabrata. Clinical Proteomics. 6, 163-173.


11. Kashyap, M.K., Harsha, H.C., Renuse, S., Pawar, H., Sahasrabuddhe, N.A., Kim, M.S., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T.S.K., Mahmood, R., Chaerkady, R., Meltzer, S.J., Kumar, R.V., Rustgi, A.K. and Pandey, A (2010). SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biology and Therapy. Oct 7; 10(8).


10. Hijikata, A., Raju, R., Keerthikumar, S., Ramabadran, S., Balakrishnan, L., Ramadoss, S. K., Pandey, A., Mohan, S. and Ohara, O. (2010). Mutation@A Glance: an integrative web application for analyzing mutations from human genetic diseases. DNA Research. 17, 197-208.


9. Kandasamy, K*., Mohan, S*., Raju, R., Keerthikumar, S., Kumar, G. S. S., Venugopal, A. K., Telikicherla, D., Navarro, D. J., Mathivanan, S., Pecquet, C., Gollapudi, S. K., Tattikota, S. G., Mohan, S., Padhukasahasram, H., Subbannayya, Y., Goel, R., Jacob1, H. K. C., Zhong, J., Sekhar, R., Nanjappa, V., Balakrishnan, L., Subbaiah, R., Rahiman, B. A., Prasad, T. S. K., Lin, J., Houtman, J. C. D., Desiderio, S., Renauld, J., Constantinescu, S., Ohara, O., Hirano, T., Kubo, M., Singh, S., Khatri, P., Draghici, S., Bader, G. D., Sander, C., Leonard, W. J. and Pandey, A. (2010). NetPath: A Public Resource of Curated Signal Transduction Pathways - Development of an initial set of immune signaling pathways. Genome Biology. 11, R3.

* authors contributed equally



8. Keerthikumar, S., Bhadra, S., Kandasamy, K., Raju, R., Ramachandra, Y. L., Bhattacharyya, C., Imai, K., Ohara, O., Mohan, S. and Pandey, A. (2009). Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. DNA Research. 16, 345-351.


7.Keerthikumar, S., Raju, R., Kandasamy, K., Hijikata, A., Ramabadran, S., Balakrishnan, L., Ahmed, M., Rani, S., Selvan, L. N., Somanathan, D. S., Ray, S., Bhattacharjee, M., Gollapudi, S., Ramachandra, Y. L., Bhadra, S., Bhattacharyya, C., Imai, K., Nonoyama, S., Kanegane, H., Miyawaki, T., Pandey, A., Ohara, O. and Mohan, S. (2009). RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic Acids Research. 37, D863-D867.


6. Kandasamy, K., Keerthikumar, S., Raju, R., Keshava Prasad, T. S., Ramachandra Y. L., Mohan, S. and Pandey, A. (2009). PathBuilder – Open Source Software for Annotating and Developing Pathway Resources. Bioinformatics. 25, 2860-2862.


5. Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Acharya, P. K., Ranganathan, P., Chaerkady, R., Prasad, T. S. K. and Pandey, A. (2009). Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Research. 37, D773-D781.


4. Prasad, T. S. K., Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D. S., Sebastian, A., Rani, S., Ray, S., Kishore, C. J. H., Kanth, S., Ahmed, M., Kashyap, M., Mohmood, R., Ramachandra, Y. L., Krishna, V., Rahiman, A. B., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R. and Pandey, A. (2009). Human Protein Reference Database - 2009 update.Nucleic Acids Research. 37, D767-D772.


3. Kashyap, M.K, Marimuthu, A., Kishore, C. J. H., Peri, S., Keerthikumar, S., Prasad, T. S. K., Mahmood, R., Rao, S., Ranganathan, P., Vijayakumar, M., Veerendra Kumar, K. V., Montgomery, E., Vijay Kumar, R. and Pandey A. (2009). Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biology and Therapy. 8, 16-26.



2. Mathivanan, S., Ahmed, M. et al. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-7.



1. Mishra, G., Suresh, M., Kumaran, K., Kannabiran, N., Suresh, S., Bala, P., Shivakumar, K., Anuradha, N., Reddy, R., Raghavan, T. M., Menon, S., Hanumanthu, G., Gupta, M., Upendran, S., Gupta, S., Mahesh, M., Jacob, B., Matthew, P., Chatterjee, P., Arun, K. S., Sharma, S., Chandrika, K. N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, K., Karathia, H., Rekha, B., Rashmi, N. S., Vishnupriya, G., Kumar, H. G. M., Nagini, M., Kumar, G. S. S., Jose, R., Deepthi, P., Mohan, S. S., Gandhi, T. K. B., Harsha, H. C., Deshpande, K. S., Sarker, M., Prasad, T. S. K. and Pandey, A. (2006). Human Protein Reference Database - 2006 Update.Nucleic Acids Research. 34: D411-D414