Bakgrunn og aktiviteter

About me

I completed my Masters in Life Sciences and Advanced Post-Graduate Diploma in Bioinformatics from Pondicherry University, Pondicherry, India. I did myPh.D. in Bioinformatics & Biotechnology under the mentorship of Prof. Akhilesh Pandey at Institute of Bioinformatics, Bangalore, India and Johns Hopkins University, Baltimore, USA. The major contributions during my Ph.D. include development of web-based resources such as Human Protein Reference Database, Human Proteinpedia, NetPath and PathBuilder; systematic analysis of mass spectrometry fragmentation methods for detection of PTMs such as phosphorylation; and computational framework for proteogenomic analysis. I joined the laboratory of Prof. Superti-Furga, Center for Molecular Medicine, Vienna, Austria in 2011, where I applied cutting-edge OMICS as well as genome-editing technologies to understand the systems-levels aspects of host-virus interactions, antiviral signaling and inflammation.

My Research Group - The Systems Inflammation Group

Infectious diseases and inflammatory disorders are major contributors to the global burden of disease, thereby having a huge socio-economic impact. Decades of research have unraveled the arsenal of mechanisms by which the host immune system detects an invading microbe and elicit an innate immune response ensuring clearance of the pathogen while exerting a minimal damage to the host. Any failure in this chain could lead to chronic diseases such as Atherosclerosis; as well as devastating conditions like sepsis and sepsis-induced death. It is critical for the host to restore homeostasis and resolve the inflammation upon microbial infections through a collective and meticulous coordination of a number of controlled molecular events such as chromatin remodeling, transcription, translation and post-translational modifications (PTMs). The systems inflammation research group aims to specifically study the role of two major PTMs – phosphorylation and ubiquitination in antiviral signaling and inflammation using state-of-the-art systems-level approaches. We use 1) mass spectrometry-based proteomics to study the dynamics of phosphorylation and ubiquitination; and 2) CRISPR/Cas9-based targeted genetic screens to identify key regulators; upon various inflammatory stimuli. We believe that our basic research-focused systems-level approaches would yield deeper and broader understanding of inflammatory signaling which will have enormous translational potential.

 

The research group currently includes 1 Ph.D. student, 1 post-doc and 1 staff engineers. We work in close collaboration with CEMIR research groups led by Terje Espevik, Trude H. Flo and Geir Bjørkøy; as well as Geir Slupphaug (NTNU Proteomics Core), Giulio Superti-Furga (Center for Molecular Medicine, Vienna) and Akhilesh Pandey (Johns Hopkins University, Baltimore).

 

Education

Jun. 2016 – Present : Associate Professor, Center for Molecular Inflammation Research (CEMIR), Norwegian University of Science and Technology, Trondheim, Norway.

Dec. 2015 – May. 2016: Group Leader, Center for Molecular Inflammation Research (CEMIR), Norwegian University of Science and Technology, Trondheim, Norway.

Dec. 2010 – Nov. 2015 : Post-Doctoral Fellow, CeMM - Center for Molecular Medicine, V

Feb. 2008 : Visiting Scientist, RCAI-RIKEN, Yokohama, Japan.

Mar. 2007 – Dec. 2010 : Joint Ph.D. Student, Johns Hopkins University, Baltimore, USA.

Sep. 2004 – Dec. 2010 : Research Scientist, Institute of Bioinformatics, Bangalore, India.

 

Awards/Honors

2016 Outstanding Academic Fellow, Norwegian University of Science and Technology (NTNU).

2016 Young Research Talent, Research Council of Norway

2016 Onsager fellowship, Norwegian University of Science and Technology (NTNU).

2012 European Molecular Biology Organization Long-Term fellowship (EMBO-ALTF 314-2012).

2003 Received studentship from the Department of Biotechnology, India for pursuing Advanced

Post-Graduate Diploma in Bioinformatics at Pondicherry University.

 

Publications

  • Hansen, M.D., Johnsen, I.B., Stiberg, K.A., Sherstova, T., Wakita, T., Richard, G.M., Kandasamy, R.K., Meurs, E.F. and Anthonsen, M.W. (2017). Hepatitis C virus triggers Golgi fragmentation and autophagy through the immunity-related GTPase M. Proceedings of the National Academy of Sciences of the United States of America. Early edition. DOI:10.1073/pnas.1616683114

 

  • Kandasamy, R. K., Vladimer, G. I., Snijder, B., Müller, A. C., Rebsamen, M., Bigenzahn, J., Moskovskich, A., Sabler, M., Stefanovic, A., Scorzoni, S., Brückner, M., Penz, T., Cleary, C., Kralovics, R., Colinge J., Bennett, K. L. and Superti-Furga, G. (2016). A time-resolved molecular map of the macrophage response to VSV infection. NPJ Systems Biology & Applications. npjsba201627 [Link to article].

 

  • Bhattacharya, A., Hegazy, A. N., Kosack, L., Deigendesch, N., Cupovic, J., Kandasamy, R. K., Hildebrandt, A., Merkler, D., Schliehe, C., Panse, I., Vilagos, B., Khamina, K., Arnold, I., Flatz, L., Xu, H. C., Lang, P. A., Aderem, A., Superti-Furga, G., Colinge, J., Zychlinsky, A., Ludewig, L., Lohning, M. and Bergthaler, A. (2015). Superoxide dismutase 1 protects from interferon-mediated oxidative damage in viral hepatitis. Immunity. 43: 974-986.

 

  • Baumann, C. L., Heinz, L.X., Klein, M., Gawish, R., Shui, G., Sharif, O., Aspalter, I., Müller, A. C., Blüml, S., Kandasamy, R. K., Breitwieser, F. P., Pichlmair, A., Bruckner, M., Karonitsch, T., Fauster, A., Hör, S., Colinge, J., Bennett, K. L., Knapp, S., Wenk, M. R. and Superti-Furga, G. (2015). LiMIT is a negative regulator of TLR induced immune responses. Cell Reports. 11: 1919-1928.

 

  • Rebsamen, M., Pochini, L., Stasyk, T., de Araújo M.E., Galluccio, M., Kandasamy, R.K., Snijder, B., Fauster, A., Rudashevskaya, E.L., Bruckner, M., Scorzoni, S., Filipek, P.A., Huber, K.V., Bigenzahn, J.W., Heinz, L.X., Kraft, C., Bennett, K.L., Indiveri, C., Huber, L.A. and Superti-Furga, G. (2015). SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1. Nature. 519: 477-481

 

  • Schliehe, C., Flynn, E., Richson, U., Vilagos, B., Bosnjak, B., Grießhammer, I., Swaminanthan, S., Kandasamy, R. K., Bauer, L., Kosack, L., Schmitz, F., Sissons, J., Bhattacharya, A., Khamina, K., Merkler, D., Kubicek, S., Knapp, S., Epstein, M. M., Symer, D. E., Aderem, A. and Bergthaler, A. (2015). Setdb2 mediates virus-induced susceptibility to bacterial superinfection. Nature Immunology. 16: 67-74.

 

  • Snijder, B.*, Kandasamy, R. K.* and Superti-Furga, G. (2014). Towards effective sharing of high-dimensional immunology data. Nature Biotechnology. 32: 755-759 * Equal contribution

 

  • Winter, G. E., Radic, B., Mayor-Ruiz, C., Blomen, V. A., Trefzer, C., Kandasamy, R. K., Huber, K., Gridling, M., Chen, D., Klampfl, T., Kralovics, R., Kubicek, S., Fernandez-Capetillo, O., Brummelkamp, T. R. and Superti-Furga, G. (2014). Nature Chemical Biology. 10: 768-773.

 

  • Rebsamen, M.*, Kandasamy, R. K.* and Superti-Furga, G. (2013). Protein interaction networks in innate immunity. Trends in Immunology. S1471-4906(13)00079-3. * Equal contribution

 

  • Pichlmair, A., Kandasamy, K., Alvisi, G., Mulhern, O., Stefanovic, A., Eberle, C., Fauster, A., Goncalves, A., Bürckstümmer, T., Müller, A., Habjan, M., Lindsten, K., Goodbourne, S., Kochs, G., Weber, F., Bartenschlager, R., Bennett, K. L., Bowie, A., Colinge J. and Superti-Furga G. (2012). Viral immune modulators perturb the human molecular network by common and unique strategies. Nature. 487: 486-490.

 

  • Goel, R., Raju, R., Maharudraiah, J., Kumar, G. S. S., Ghosh, K., Kumar, A., Lashmi, P. T., Sharma, J., Sharma, R., Balakrishnan, L., Pan, A., Kandasamy, K., Christopher, R., Krishna, V., Mohan, S. S., Harsha, H. C., Mathur, P. P., Pandey, A. and Prasad, T. S. K. (2012). A signaling network of thyroid-stimulating hormone. Journal of Proteomics and Bioinformatics. 4: 238-241.

 

  • Chaerkady, R., Kelkar, D.S., Muthusamy, B., Kandasamy, K., Dwivedi, S. B., Sahasrabuddhe, N. A., Kim, M. S., Renuse, S., Pinto, S.M., Sharma, R., Pawar, H., Sekhar, N. R., Mohanty, A. K., Getnet, D., Yang, Y., Zhong, J., Dash, A. P., Maccallum, R. M., Delanghe, B., Mlambo, G., Kumar, A., Prasad, K. T., Okulate, M., Kumar, N. and Pandey, A. (2011). A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Research. 21: 1872-1881.

 

  • 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.

 

  • Pawar, H., Kashyap, M. K., Sahasrabuddhe, N. A., Renuse, S., Harsha, H. C., Kumar, P., Sharma, J., Kandasamy, K., Marimuthu, A., Nair, B., Rajagopalan, S., Maharudraiah, J., Premalatha, C. S., Kumar, K. V. V., Vijayakumar, M., Chaerkady, R., Prasad, T. S. K., Kumar, R. V. and Pandey A. (2011). Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biology & Therapy. 12: 510-522.

 

  • Kim, M., Zhong, J., Kandasamy, K., Delanghe, B. and Pandey, A. (2011). Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics. 11: 2568-2572.

 

  • Amanchy, R.*Kandasamy, K.*, Mathivanan, S., Periaswamy, B., Reddy, R., Yoon, W. H., Joore, J., Beer, M. A., Cope, L. and Pandey, A. (2011). Identification of Novel Phosphorylation Motifs through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. Journal of Proteomics & Bioinformatics. 4: 22-35. * Equal contribution

 

  • Zhong, J., Chaerkady, R., Kandasamy, K., Gucek, M., Cole, R. and Pandey, A. (2010). The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. Journal of Proteomics. 74: 294-303.

 

  • 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. Comparative proteomic analysis of Candida albicans and Candida glabrata. Clinical Proteomics. 6: 163-173.

 

  • Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novere, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. and Bader, G. D. (2010). BioPAX - A community standard for pathway data sharing. Nature Biotechnology.  289: 935-942.

 

  • Kashyap, M. K., Harsha, H. C., Renuse, S., Pawar, H., Patankar, N., Kim, M., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T. S. K., Rajagopalan, S., Waddell, K., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A. (2010). SILAC-based quantitative proteomic approach for identification of potential biomarkers from esophageal squamous cell carcinoma secretome. Cancer Biology & Therapy. 10: 796-810.

 

  • Yang, Y., Chaerkady, R., Kandasamy, K., Huang, T. C., Selvan, L. D. N., Dwivedi, S. B., Kent, O. A., Mendell, J. T. and Pandey, A. (2010). Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular BioSystems. 6: 1873-1882. "Top ten most accessed articles in July 2010"

 

  • Kim, M., Kandasamy, K., Chaerkady, R. and Pandey, A. (2010). Optimizing mass resolution for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. Journal of the American Society for Mass Spectrometry. 21: 1606-1611

 

  • Kandasamy, K.*, Mohan, S. 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., Ramachandra, Y. L., 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. Genome Biology11(1):R3. * Equal contribution "Highly accessed" article in Genome Biology and BioMed Central

 

  • Chaerkady, R.*, Kerr, C. L.*, Kandasamy, K., Marimuthu, A., Gearhart, J. D. and Pandey, A. (2010). Comparative proteomics of human embryonic stem cells and embryonic carcinoma cells. Proteomics. 10: 1-15. *Equal contribution

 

  • Keerthikumar, S., Bhadra, S., Kandasamy, K., Raju, R., Ramachandra Y. L., Bhattacharyya, C., 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.

 

  • 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.

 

  • Kandasamy, K., Pandey, A. and Molina, H. (2009). Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Analytical Chemistry. 81: 7170-7180.

 

  • Prasad, T. S. K., Kandasamy, K, and Pandey, A. (2009) "Human Protein Reference Database and Human Proteinpedia as Discovery Tools for Systems Biology” In: Reverse Chemical Genetics, Hisashi Koga (ed.), Methods in Molecular Biology. 577: 67-79

 

  • Harsha, H. C., Kandasamy, K., Ranganathan, P., Rani, S., Ramabadran, S., Gollapudi, S., Balakrishnan, L., Dwivedi, S. B., Telikicherla, D., Selvan, L. D. N., Goel, R., Mathivanan, S., Marimuthu, A., Kashyap, M. K., Vizza, R. F., Mayer, R. J., DeCaprio, J. A., Srivastava, S., Hanash, S. M., Hruban, R. H. and Pandey, A. (2009). A compendium of potential biomarkers of pancreatic cancer. PLoS Medicine. 6: e1000046.

 

  • 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.

 

  • 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.

 

  • 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.

 

  • Molina H, Matthiesen R, Kandasamy, K. and Pandey A. (2008). A Comprehensive Comparison of Collision Induced Dissociation and Electron Induced Dissociation. Analytical Chemistry. 80: 4825-4835.

 

  • 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., Björling, 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 Marzo, A.M., DeSouza, L.V., Deutsch, E.W., Dransfield, E., Drewes, G., Droit, A., Dunn, M.J., Elenitoba-Johnson, K., Ewing, R.M., Van Eyk, J., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagné, 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., Hjernø, 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., Körner, R., Kuster, B., Kwon, M.S., Lee, H.J., Lee, Y.J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M.S., Löbke, 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. (2007). Human Proteinpedia: A portal for sharing and integration of human protein data. Nature Biotechnology. 26: 164-167.

 

  • Mathivanan, S., Periaswamy, B., Gandhi, T. K. B., Kandasamy, K., Suresh, S., Mohmood, R., Ramachandra, Y. L. and Pandey, A. (2006). An Evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics. 7: S19.

 

  • 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.

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