Center for Systems Biology and Molecular Medicine

Research papers: 145; Review articles: 5; Book Chapters: 1

 

• Advani, J., Verma, R., Chatterjee, O., Pachouri, P. K., Upadhyay, P., Singh, R., Yadav, J., Naaz, F., Ravikumar, R., Buggi, S., Suar, M., Gupta U. D., Pandey, A., Chauhan, D. S., Tripathy, S. P., Gowda, H^*. and Prasad, T. S. K. (2019). Whole genome sequencing of Mycobacterium tuberculosis clinical isolates from India reveals genetic heterogeneity and region specific variations that might affect drug susceptibility. Frontiers in Microbiology. In Press. (*Corresponding author)
• Advani, J., Sharma, K., Verma, R., Chatterjee, O., Solanki, H. S., Sharma, A., Varma, S., Modi, M., Ray, P. Sharma, M., Dhillion, M. S., Pandey, A., Gowda, H.^*, Prasad, T. S. K. (2018). Data on whole genome sequencing of extrapulmonary tuberculosis clinical isolates from India. Data in Brief. In press. (*Corresponding Author)
• Advani, J., Verma, R., Chatterjee, O., Rex, D. A. B., Najar, M. A., Ravishankara, N., Suresh, S., Pachori, P. K., Gupta, U. D., Pinto, S. M., Chauhan, D. S., Tripathy, S. P., Gowda, H. and Prasad, T. S. K. (2018). Rise of clinical microbial proteogenomics: A multi-omics approach to non-tuberculous mycobacterium – the case of Mycobacterium abscessus UC22. OMICS: A Journal of Integrative Biology. In press.
• Selvan, L. D. N., Danda, R., Madugundu, A. K., Puttamallesh, V. N., Sathe, G. J., Krishnan, U. M., Khetan, V., Rishi, P., Prasad, T. S. K., Pandey, A., Krishnakumar, S., Gowda, H. and Elchuri, A. (2018). Phosphoproteomics of Retinoblastoma: A pilot study identifies aberrant kinases. Molecules. In press.
• Rajagopalan, P., Patel, K., Jain, A. P., Nanjappa, V., Datta, K. K., Subbannayya, T., Mangalaparthi, K. K., Kumari, A., Manoharan, M., Karunakaran, C., Murugan, S., Nair, B., Prasad, T. S. K., Mathur, P. P., Gupta, R., Gupta, R., Khanna-Gupta, A., Califano, J. A., Sidransky, D., Gowda, H.^* and Chatterjee, A. (2018). Molecular alterations associated with chronic exposure to cigarette smoke and chewing tobacco in normal oral keratinocytes. Cancer Biology & Therapy. In press. (*Corresponding author)
• Bhat, M. Y., Advani, J., Rajagopalan, P., Patel, K., Nanjappa, V., Solanki, H. S., Patil, A. H., Bhat, F. A., Mathur, P. P., Nair, B., Prasad, T. S. K., Califano, J. A., Sidransky, D., Gowda, H.^* and Chatterjee A. (2018). Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes. Scientific Reports.In press. (*Corresponding author)
• Khan, A. A., Advani, J., Patel, K., Nanjappa, V., Datta, K. K., Solanki, H. S., Kumar, P., Mathur, P. P., Nair, B. P., Prasad, T. S. K., Chatterjee, A and Gowda, H.^* (2017). Chronic exposure of cigarette smoke and chewing tobacco alters expression of microRNAs in esophageal epithelial cells. MicroRNA. In press. (*Corresponding author)
• Rajagopalan, P., Nanjappa, V., Patel, K., Jain, A. K., Mangalaparthi, K. K., Patil, A. H., Nair, B., Mathur, P. P., Prasad, T. S. K., Califano, J. A., Sidransky, D., Gowda, H^*. Chatterjee, A. (2017). Role of protein kinase N2 (PKN2) in cigarette smoke-mediated oncogenic transformation of oral cells. Journal of Cell Communication and Signaling. In press. (*Corresponding author)
• Advani, J., Subbannayya, Y., Gowda H., Chatterjee, A. (2017). Bioinformatics advances to accelerate omics innovations and applications in the postgenomic era. OMICS: A Journal of Integrative Biology. [PubMed]
• Nanjappa, V., Sathe, G.J., Jain, A. P., Rajagopalan, P., Raja, R, Subbannayya, T., Patil, A. H., Kumar, P., Prasad, T. S. K., Mathur, P. P., Sidransky, D., Gowda, H.^* and Chatterjee, A. Investigation of curcumin mediated signaling pathways in head and neck squamous cell carcinoma. Translational Research in Oral Oncology. In press. (*Corresponding author)
• Solanki, H. S., Babu, N., Jain, A. P., Bhat, M. Y., Puttamallesh, V. N., Advani, J., Raja, R., Mangalaparthi, K. K., Kumar, M. M., Prasad, T. S. K., Mathur, P. P., Sidransky, D., Gowda, H^*. Chatterjee, A. (2017). Cigarette smoke induces mitochondrial metabolic reprogramming in lung cells. Mitochondrion. In press
• Sharma, K., Verma, R., Advani, J., Chatterjee, O., Solanki, H. S., Sharma, A., Varma, S., Modi, M., Ray, P., Mukherjee, K. K., Sharma, M., Dhillon, M. S., Suar, M., Chatterjee, A., Pandey, A., Prasad, T. S. K. and Gowda, H.^* (2017). Whole genome sequencing of Mycobacterium tuberculosis isolates from extrapulmonary sites. OMICS: A Journal of Integrative Biology 7:390-403. [Pubmed](*Corresponding author)
• Advani, J.#, Subbannayya, Y.#, Patel, K., Khan, A. A., Patil, A. H., Jain, A. P., Solanki, H. S., Radhakrishnan, A., Pinto, S. M., Sahasrabuddhe, N. A., Thomas, J. K., Mathur, P. P., Nair, B., Chang, X., Prasad, T. S. K., Sidransky, D., Gowda, H.^* and Chatterjee, A. (2017). Long term cigarette smoke exposure and changes in microRNA expression and proteome in non-small cell lung cancer. OMICS: A Journal of Integrative Biology. [PubMed] (# These authors contributed equally to the manuscript)
• Verma, R., Pinto, S., Patil, A. H., Advani, J., Subba, P., Kumar, M., Sharma, J., Dey, G., Ravikumar, R., Buggi, S., Satishchandra, P., Sharma, K., Suar, M. T., Srikanth, C., Singh, D., Gowda, H., Pandey, A., Gandotra, S. and Prasad, T. S. K. (2017). Quantitative proteomic and phosphoproteomic analysis of H37Ra and H37Rv strains of Mycobacterium tuberculosis. Journal of Proteome Research. [Pubmed]
• Patel K., Singh M. and Gowda, H.^* (2017). Bioinformatics Methods to Deduce Biological Interpretation from Proteomics Data. Methods Mol Biol. 1549, 147-161. [PubMed] (*Corresponding Author)
• Datta, K. K., Dhaka, B., Patel, K., Puttamallesh, V. N. and Gowda, H.^* (2016). Phosphoproteomic profiling using biopsy-scale protein amounts. Journal of Proteins and Proteomics. In press (*Corresponding Author)
• Prasad, T. S. K., 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., Dwivedi, S. B., Kelkar, D. S., Hall, B., Jiang, X., Peery, A., Rajagopalan, P., Yelamanchi, S. D., Solanki, H. S., Raja, R., Sathe, G. J., Chavan, S. N., 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., and Pandey, A. (2016). Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Research. [PubMed]

• Mir, S. A., Pinto, S. M., Paul, S., Raja, R., Nanjappa, V., Syed, N., Advani, J., Renuse, S., ahasrabuddhe, N. A., Prasad, T. S. K., Giri, A. K., Gowda, H^*., and Chatterjee, A. (2016). SILAC-based quantitative proteomic analysis reveals widespread molecular alterations in human skin keratinocytes upon chronic arsenic exposure. Proteomics. [PubMed] (*Corresponding author)
• Radhakrishnan, A., Nanjappa, V., Raja, R., Sathe, G., Puttamallesh, V. N., Jain, A. P., Pinto, S. M., Balaji, S. A., Chavan, S., Sahasrabuddhe, N. A., Mathur, P. P., Kumar, M. M., Prasad, T. S. K., Santosh, V., Sukumar, G., Califano, J. A., Rangarajan, A., Sidransky, D., Pandey, A., Gowda, H^*. and Chatterjee, A. (2016). A dual specificity kinase, DYRK1A, as a potential therapeutic target for head and neck squamous cell carcinoma. Scientific Reports. 6, 36132 [PubMed] (*Corresponding author)

  Danda, R., Ganapathy, K., Sathe, G., Madugundu, A. K., Ramachandran, S., Krishnan, U. M., Khetan, V., Rishi, P., Prasad, T. S. K., Pandey, A., Krishnakumar, S., Gowda, H^*. and Elchuri, S. V. (2016). Proteomic profiling of retinoblastoma by high resolution mass spectrometry. Clinical Proteomics. [PubMed] (*Corresponding author)

• Yelamanchi, S. D., Kumar, M., Madugundu, A., Gopalakrishnan, L., Dey, G., Chavan, S., Sathe, G., Mathur, P. P., Gowda, H^*., Mahadevan, A., Shankar, S. K., Prasad, T. S. K. (2016). Characterization of human pineal gland proteome. Molecular Biosystems. 12, 3622-3632 [PubMed] (*Corresponding author)
• Raja, R., Sahasrabuddhe, N. A., Radhakrishnan, A., Syed, N., Solanki, H., Puttamallesh, V. N., Balaji, S. A., Nanjappa, V., Datta, K. K., Babu, N., Renuse, S. Patil, A. H, Izumchenko, E., Prasad, T. S. K., Chang, X., Rangarajan,A., Sidransky, D., Pandey, A., Gowda, H. and Chatterjee, A. (2016). Chronic exposure to cigarette smoke leads to activation of p21 (RAC1) - activated kinase 6 (PAK6) in non-small cell lung cancer cells. Oncotarget. [PubMed]

• Yelamanchi S. D., Solanki, H. S., Radhakrishnan, A., Balakrishnan, L., Advani, J., Raja, R., Sahasrabuddhe, N. A., Mathur, P. P., Dutta, P., Prasad, T. S. K., Korbonits, M., Chatterjee, A., Gowda, H., Mukherjee, K. K. (2016). Signaling network map of aryl hydrocarbon receptor. Journal of Cell Communication and Signaling. 10, 341-346 [PubMed]
• Murthy, K. R., Dammalli, M., Pinto, S. M., Murthy, K. B., Nirujogi, R. S., Madugundu A. K., Dey, G., Subbannayya, Y., Mishra, U.K., Nair, B., Gowda, H., Prasad, T. S. K. (2016). A comprehensive proteomics analysis of the human iris tissue: Ready to embrace postgenomics precision medicine in ophthalmology?. OMICS: A Journal of Integrative Biology. 9, 510-9 [PubMed]
• Sathe, G. J*., Pinto, S. M*., Syed, N., Nanjappa, V., Solanki, H. S., Renuse, S., Chavan, S., Khan, A. A., Patil, A. H., Nirujogi, R. S., Nair, B., Mathur, P. P., Prasad, T. S. K., Gowda, H and Chatterjee, A. (2016). Phosphotyrosine profiling of curcumin-induced signaling. Clinical Proteomics. 13, 13. [PubMed]
• Subbannayya, T., Variar, P., Advani, J., Nair, B., Shankar, S., Gowda, H., Saussez, S., Chatterjee, A. and Prasad, T. S. K. (2016). An integrated signal transduction network of macrophage migration inhibitory factor. Journal of Cell Communication and Signaling. 10, 165-70. [PubMed]
• Datta, K.K., Madugundu, A.K., Gowda, H. (2016). Proteogenomic Methods to Improve Genome Annotation. Methods in Molecular Biology. 1410, 77-89. [PubMed]

• Radhakrishnan, A., Nanjappa, V., Raja, R., Sathe, G. J., Chavan, S., Nirujogi, R. S., Patil, A., Solanki, H., Renuse, S., Sahasrabuddhe, N. A., Mathur, P. P., Prasad, T. S. K., Kumar, P., Califano, J. A., Sidransky, D., Pandey, A., Gowda, H. and Chatterjee, A. (2016). Dysregulation of splicing proteins in head and neck squamous cell carcinoma. Cancer Biology and Therapy. 17, 219-229. [PubMed] 

• 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. [PubMed] 

• Handu, M., Kaduskar, B., Ravindranathan, R., Soory, A., Giri, R., Elango, V. B., Gowda, H. and Ratnaparkhi, G. S. (2015). SUMO-Enriched Proteome for Drosophila Innate Immune Response. G3. 5, 2137-2154. [PubMed]

• Yelamanchi, S. D., Jayaram, S., Thomas, J. K., Gundimeda, S., Khan, A. A., Singhal, A., Prasad, T. S. K., Pandey, A., Somani, B. L. and Gowda, H. (2015). A pathway map of glutamate metabolism. Journal of Cell Communication and Signaling. [PubMed] 

• Sharma, A., Varghese, A. M., Vijaylakshmi, K., Sumitha, R., Prasanna, V. K., Shruthi, S., Sagar, C. B. K., Datta, K. K., Gowda, H., Nalini, A., Alladi, P. A., Christopher, R., Sathyaprabha, T. N., Raju, T. R and Bharath, S. M. M. (2015). Cerebrospinal Fluid from Sporadic Amyotrophic Lateral Sclerosis Patients Induces Mitochondrial and Lysosomal Dysfunction. Neurochemical Research. [PubMed]

• Subbannayya, Y., Pinto, S. M., Gowda, H. and Prasad, T. S. K. (2015). Proteogenomics for understanding oncology: recent advances and future prospects. Expert Review of Proteomics. [PubMed] 

• 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. [PubMed]

• Subbannayya, T., Leal-Rojas, P., Barbhuiya, M., Raja, R., Renuse, S., Sathe, G., Pinto, S. M., Syed, N., Nanjappa, V., Patil, A. H., Garcia, P., Sahasrabuddhe, N. A., Nair, B., Guerrero-Preston, R., Navani, S., Tiwari, P. K., Santosh, V., Sidransky, D., Prasad, T. S. K., Gowda, H., Roa, J. C., Pandey, A. and Chatterjee, A. (2015). Macrophage migration inhibitory factor - a therapeutic target in gallbladder cancer. BMC Cancer. 15, 843.  [PubMed]

• Mitchell, C. J., Getnet, D., Kim, M. S., Manda, S. S., Kumar, P., Huang, T. C., Pinto, S., Nirujogi, R. S., Iwasaki, M., Shaw, P., 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. K., Marchionni, L., Marukami, P. N., Scott, A. F., Shi, L., Thierry-Mieg, J., Thierry-Mieg, T., 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. [PubMed]

• Pawar, H., Chavan, S., Mahale, K., Khobragade, S., Kulkarni, A., Patil, A., Chaphekar, D., Varriar, P., Sudeep, A., Pai, K., Prasad, T. S. K., Gowda, H. and Patole, M. S. (2015). A Proteomic map of the unsequenced kala-azar vector Phlebotomus papatasi using cell line. Acta Tropica. 152, 80-89. [PubMed]. 

• Verma, R., Balakrishnan, L., Sharma. K., Khan A. A., Advani, J., Gowda, H., Tripathy, S.P., Suar, M., Pandey, A., Gandotra, S., Prasad, T. S. K. and Subramanian, S. (2016). A network map of Interleukin-10 signaling pathway. Journal of Cell Communication and Signaling. 10, 61-67. [PubMed] 

• Selvan, L. D. N., Sreenivasamurthy, S. K., Kumar, S., Yelamanchi, S. D., Madugundu, A. K., Anil, A. K., Renuse, S., Nair, B. G., Gowda, H., Mathur, P. P, Satishchandra, P., Shankar S. K., Mahadevan, A., Prasad, T. S. K. (2015). Characterization of host response to Cryptococcus neoformans through quantitative proteomic analysis of cryptococcal meningitis co-infected with HIV. Molecular BioSystems. 11, 2529-2540. [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] 

• 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. 127, 89-95. [PubMed] 

• Sharma, J., Balakrishnan, L., Datta, K. K., Sahasrabuddhe, N. A., Khan A. A., Sahu, A., Singhal, A., Derese, G., Raju, R., Chatterjee, A., Gowda, H., Prasad, T. S. K., Shankar, S. and Pandey, A. (2015). A knowledgebase resource for Interleukin-17 family mediated signaling. Journal of Cell Communication and Signaling. 9, 291-296. [PubMed] 

• Mir, S. A., Rajagopalan, P., Jain, A. P., Khan, A. A., Datta, K. K., Mohan, S. V., Lateef, S. S., Sahasrabuddhe, N., Somani, B. L., Prasad, T. S. K., Chatterjee, A., Kumar, K. V. V., Kumar, M. V., Kumar, R. V., Gundimeda, S., Pandey, A. and Gowda, H^*. (2015). LC-MS-based serum metabolomic analysis reveals dysregulation of phosphatidylcholines in esophageal squamous cell carcinoma. Journal of Proteomics. 127, 96-102. [PubMed]  (*Corresponding author)

• 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., Prasad, T. S. K., 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. [PubMed]  (*Corresponding author)

• Subbannayya, Y., Syed, N., Barbhuiya, M. A., Raja, R., Marimuthu, A., Sahasrabuddhe, N. A., Pinto, S. M., Manda, S. S., Renuse, S., Manju, H. C., Zameer, M. A. L., Sharma, J., Brait, M., Srikumar, K., Roa, J. C., Vijaya Kumar, M., Veerendra Kumar, K. V., Prasad, T. S. K., Ramaswamy, G., Kumar, R. V., Pandey, A., Gowda, H., Chatterjee, A. (2015). Calcium calmodulin dependent kinase kinase 2 - a novel therapeutic target for gastric adenocarcinoma. Cancer Biology and Therapy. 16, 336-345. [PubMed] 

• 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. M., 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. K. and Pandey, A. (2015). Proteomics of human aqueous humor. OMICS: A Journal of Integrative Biology. 19, 283-293. [PubMed]  

• Sharma, R., Gowda, H., Chavan, S., Advani, J., Kelkar, D., Kumar, S.S., Bhattacharjee, M., Chaerkady, R., Prasad, T.S.K., Pandey, A., Dindagur, N., and Christopher, R. (2015). Proteomic signature of endothelial dysfunction identified in serum of acute ischemic stroke patients by iTRAQ-based LC-MS approach. Journal of Proteome Research. 14, 2466-2479. [PubMed] 

• Jamdhade, M., Pawar, H., Chavan, S., Sathe, G., Mahale, K.N., Kulkarni, A., Dixit, T., Madugundu, A. K., Prasad, T. S. K., Harsha, H. C., Pandey, A. and Patole, M. S. (2015). Comprehensive proteomics analysis of glycosomes from Leishmania donovani. OMICS: A Journal of Integrative Biology. 19, 157-170. [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] (*Corresponding author)

• Maras, J. S., Maiwall, R., Harsha, H. C., Das, S., Hussain, S., Kumar, C., Bihari, C., Rastogi, A., Kumar, M., Trehanpati, N., Sharma, S., Pandey, A. and Sarin, S, K. (2014). Dysregulated iron homeostasis is strongly associated with multi-organ failure and early mortality in acute-on-chronic liver failure. Hepatology.  61, 1306-1320. [PubMed]

• Sahu, A., Kumar, S., Sreenivasamurthy, S. K., Selvan, L. D. N., Madugundu, A. K., Yelamanchi, S. D., Puttamallesh, V. N., Dey, G., Anil, A. K., Srinivasan, A., Mukherjee, K. K., Gowda, H., Satishchandra, P., Mahadevan, A., Pandey, A., Prasad, T. S. K. and Shankar, S. K. (2014). Host response profile of human brain proteome in toxoplasma encephalitis co-infected with HIV. Clinical Proteomics. 11, 39. [PubMed]

• Syed, N., Barbhuiya, M. A., Pinto, S. M., Nirujogi, R. S., Renuse, S., Datta, K. K., Khan, A. A., Srikumar, K., Prasad, T. S. K., Vijaya Kumar, M., Kumar, R. V., Chatterjee, A., Pandey, A. and Gowda, H^*. (2014). Phosphotyrosine profiling identifies ephrin receptor A2 as a potential therapeutic target in esophageal squamous cell carcinoma. Proteomics. 15, 374-382. [PubMed] (*Corresponding author)

• Khan, A. A., Sandhya, V. K., Singh, P., Parthasarathy, D., Kumar, A., Advani, J., Gattu, R., Ranjit, D. V., Vaidyanathan, R., Mathur, P. P., Prasad, T. S. K., Gabhann, F. M., Pandey, A., Raju, R. and Gowda, H*. (2014). Signaling network map of endothelial TEK tyrosine kinase. Journal of Signal Transduction. 2014, 173026. [PubMed] (*Corresponding author)

• Varghese A. M., Sharma A., Mishra P., Vijayalakshmi K., Harsha H. C., Sathyaprabha T. N., Bharath S. M., Nalini A., Alladi P. A., Raju T. R. (2013). Chitotriosidase - a putative biomarker for sporadic amyotrophic lateral sclerosis. Clinical Proteomics. 10, 19. [PubMed]

• Kelkar, D. S., Provost. E., Chaerkady, R., Muthusamy, B., Manda, S. S., Subbannayya, T., Selvan, L. D. N., 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. K., 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 and Cellular Proteomics. 13, 3184-3198. [PubMed]

• Gowda, H., Ivanisevic, J., Johnson, C. H., Kurczy, M. E., Benton, H. P., Rinehart, D., Nguyen, T., Ray, J., Kuehl, J., Arevalo, B., Westenskow, P. D., Wang, J., Arkin, A. P., Deutschbauer, A. M., Patti, G. J. and Siuzdak, G. (2014). Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses. Analytical Chemistry. 86, 6931-6939. [PubMed]

• Soni, B. L., Marimuthu, A., Pawar, H., Sawant, S. S., Borges, A., Kannan, R., Pandey, A., Ingle, A. D., Harsha, H. C. and Vaidya, M. M. (2014). Quantitative proteomic analysis of different stages of rat lingual carcinogenesis. Clinical Communications Oncology. 1, 2. [PubMed]

• Renuse, S., Madugundu, A. K., Kumar, P., Nair, B., Gowda, H., Prasad, T. S. K., and Pandey, A. (2014). Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host. (2014). Proteomics. 14, 2769-2779. [PubMed]

• Syed, N., Chavan, S., Sahasrabuddhe, N. A., Renuse, S., Sathe, G., Nanjappa, V., Radhakrishnan, A., Raja, R., Pinto, S. M., Srinivasan, A., Prasad, T. S. K., Srikumar, K., Gowda, H., Santosh, V., Sidransky, D., Califano, J. A., Pandey, A and Chatterjee, A. (2014). Silencing of high-mobility group box 2 (HMGB2) modulates cisplatin and 5-fluorouracil sensitivity in head and neck squamous cell carcinoma. Proteomics. 15, 383-393. [PubMed]

• Murthy, K. R., Goel, R., Subbannayya, Y., Jacob, H. K. C., Murthy, P. R., Srikanth, S. M., Patil, A. H., Sharma, R., Sahasrabuddhe, N. A., Parashar, A., Nair, B. G., Krishna V., Prasad, T. S. K., Gowda, H. and Pandey, A. (2014). Proteomic analysis of human vitreous humor. Clinical Proteomics. 11, 29. [PubMed]

• Manda, S., Nirujogi, R. S., Pinto, S., Kim, M. S., Datta, K., Sirdeshmukh, R., Prasad, T. S. K., 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. [PubMed]. (*Corresponding author)

• Dwivedi, S. B., Muthusamy, B., Kumar, P., Kim, M. S., Nirujogi, R. S., Getnet, D., Ahiakonu, P., Dey, G., Nair, B., Gowda, H., Prasad, T. S. K., Kumar, N., Pandey, A. and Okulate, M. (2014). Brain proteomics of Anopheles gambiae. OMICS: A Journal of Integrative Biology.   18, 421-437. [PubMed] 

• Marimuthu, A., Huang, T. C., Selvan, L. D. N., Renuse, S., Nirujogi, R. S., Kumar, P., Rajagopalan, S., Pandey, A., Harsha, H. C and Chatterjee, A. (2014). Identification of targets of miR-200b by a SILAC-based quantitative proteomic approach. EuPA Open Proteomics. 4, 10-17 [PubMed]

• Pawar, H., Renuse, S., Khobragade, S. N., Chavan, S., Sathe, G., Kumar, P., Mahale, K. N., Gore, K., Kulkarni, A., Dixit, T., Raju, R., Prasad, T. S. K., Harsha, H. C., Patole, M. S. and Pandey, A. (2014). Neglected tropical diseases and omics science: Proteogenomics analysis of the promastigote stage of Leishmania major parasite. OMICS: A Journal of Integrative Biology. 18, 499-512.[PubMed] 

• Ambekar A. S., Kelkar D. S., Pinto S. M., Sharma R., Hinduja I., Zaveri K., Pandey A., Prasad T. S. K., Gowda H. and Mukherjee S. (2014). Proteomics of Follicular Fluid from Women with Polycystic Ovary Syndrome Suggests Molecular Defects in Follicular Development. Cancer Biology and Therapy. [PubMed] 

• Thomas, J. K., Kim, M. S., Balakrishnan, L., Nanjappa, V., Raju, R., Marimuthu, A., Radhakrishnan, A., Muthusamy, B., Khan, A. A., Sakamuri, S., Tankala, S. G., Singal, M., Nair, B., Sirdeshmukh, R., Chatterjee, A., Prasad, T. S. K., Maitra, A., Gowda, H., Hruban, R. H. and Pandey, A. (2014). Pancreatic Cancer Database: An integrative resource for pancreatic cancer. Cancer Biology and Therapy.  15. [PubMed]

• Sahasrabuddhe, N. A., Huang, T. C., Ahmad, S., Kim, M. S., Yang, Y., Ghosh, B., Leach, S. D., Gowda, H., Somani, B. L., Chaerkady, R. and Pandey, A. (2014). Regulation of PPAR-alpha pathway by Dicer revealed through proteomic analysis. Journal of Proteomics. S1874-3919.  [PubMed]

• Raju, R., Palappetta, S. M., Sandhya, V. K., Sahu, A., Alipoor, A., Balakrishnan, L., Advani, J., George, B., Kini, K. R., Prashanth, G. N., Prakash, H. S., Prasad, T. S. K., Chang, Y., Chen, L., Pandey, A.* and Gowda, H.* (2014).  A network map of FGF-1/FGFR signaling system. Journal of Signal Transduction.  2014, 962962.[PubMed] (*Corresponding author)

• Pinto, S. M., Manda, S. S., Kim, M. S., Taylor, K., Selvan, L. D. N., Balakrishnan, L., Subbannayya, T., Yan, F., Prasad, T. S. K., 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, 2749-60.[PubMed]

• Sahasrabuddhe, N. A., Barbhuiya, M. A., Bhunia, S., Subbannayya, T., Gowda, H., Advani, J., Shrivastav, B. R., Navani, S., Leal, P., Roa, J. C., Chaerkady, R., Gupta, S., Chatterjee, A., Pandey, A. and Tiwari, P. K. (2014).  Identification of Prosaposin and Transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics. Biochemical and Biophysical Research Communications.  446, 863-9.  [PubMed]

• Selvan, L. D. N., Kaviyil, J. E., Nirujogi, R. S., Muthusamy, B., Puttamallesh, V. N., Subbannayya, T., Syed, N., Radhakrishnan, A., Kelkar, D. S., Ahmad, S., Pinto, S. M., Kumar, P., Madugundu, A. K., Nair, B., Chatterjee, A., Pandey, A., Ravikumar, R., Gowda, H. and Prasad, T. S. K. (2014). Proteogenomic analysis of pathogenic yeast Cryptococcus neoformans using high resolution mass spectrometry. Clinical Proteomics. 11, 5.  [PubMed]

• Balakrishnan, L., Nirujogi, R. S., Ahmad, S., Bhattacharjee, M.,  Srikanth, S. M., Renuse, S., Kelkar, D. S., Subbannayya, Y.,  Raju, R.,  Goel, R., Thomas, J. K., Kaur, N., Dhillon, M., Tankala, S. G., Jois, R., Vasudev, V., Ramachandra, Y. L., Sahasrabuddhe, N. A., Prasad, T. S. K., Mohan, S., Gowda, H., Shankar, S. and Pandey, A. (2014). Proteomic analysis of human osteoarthritis synovial fluid. Clinical Proteomics. 11, 6.   [PubMed]

• Selvan, L. D. N., Renuse, S., Jyothi, E. K., Sharma, J., Pinto, S. M., Yelamanchi, S. D., Puttamallesh, V. N., Ravikumar, R., Pandey, A., Prasad, T. S. K.* and Harsha, H. C.* (2014). Phosphoproteome of Cryptococcus neoformans. Journal of Proteomics. 97, 287-95. [PubMed] (*Corresponding author)

• Nirujogi, R. S., Pawar, H., Renuse, S., Kumar, P., Chavan, S., Sathe, G. J., Sharma, J., Khobragade, S., Pande, J., Modak, B., Prasad, T. S. K., Harsha, H. C., Patole, M. S. and Pandey, A. (2014). Moving from unsequenced to sequenced genome: reanalysis of the proteome of Leishmania donovani. Journal of Proteomics. 97, 48-61. [PubMed]

• 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. L., Sahasrabuddhe, N. A., Prasad, T. S. 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. [PubMed]

• Nanjappa, V., Thomas, J. K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., Khan, A. A., Balakrishnan, L., Sahasrabuddhe, N., Kumar, S., Jhaveri, B. N., Sheth, K. V., Khatana, R. K., 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. K. (2013). Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Research. 42, D959-D965. [PubMed]

• Ramadasan-Nair, R., Gayathri, N., Mishra, S., Sunitha, B., Mythri, R., Nalini, A., Subbannayya, Y., Harsha, H. C., Kolthur-Seetharam, U. and Bharath, M. M. (2013). Mitochondrial alterations and oxidative stress in an acute transient mouse model of muscle degeneration: Implications for muscular dystrophy and related muscle pathologies. Journal of Biological Chemistry. 289, 485-509. [PubMed]

• Puttamallesh, V. N., Sreenivasamurthy, S. K., Singh, P. K., Harsha, H. C., Ganjiwale, A., Broor, S., Pandey, A., Narayana, J. and Prasad, T. S. K. (2013). Proteomic profiling of serum samples from chikungunya infected patients provides insights into host response. Clinical Proteomics. 10, 14. [PubMed]

• Bhattacharjee, M., Sharma, R., Goel, R., Balakrishnan, L., Renuse, S., Advani, J.,  Shantal, T. G., Verma, R., Pinto, S. M., Nirujogi, R. S., Nair, B., Prasad, T. S. K., Harsha, H. C., Jois, R., Shankar, S. and Pandey, A. (2013). A Multilectin affinity approach for  comparative glycoprotein profiling of rheumatoid arthritis and spondyloarthropathy. Clinical Proteomics. 10, 11. [PubMed] 

• Goel, R., Murthy, K., Srikanth, S. M., Pinto, S. M., Bhattacharjee, M., Kelkar, D. S., Madugundu, A. K., Dey, G., Mohan, S. S., Krishna, V., Prasad, T. S. K., Chakravarti, S., Harsha, H. C. and Pandey, A. (2013). Characterizing the normal proteome of human ciliary body. Clinical Proteomics. 10, 9. [PubMed]

• Prasad, T. S. K., Verma, R., Kumar, S., Nirujogi, R. S., Sathe, G. J., Madugundu, A. K., Sharma, J., Puttamallesh, V. N., Ganjiwale, A., Myneedu, V. P., Chatterjee, A., Pandey, A., Harsha, H. C. and Narayana, J. (2013). Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis. Clinical Proteomics. 10, 8. [PubMed]

• Sreenivasamurthy, S. K., Dey, G., Ramu, M., Kumar, M., Gupta, M. K., Mohanty, A. K., Harsha, H. C., Sharma, P., Kumar, N., Pandey, A., Kumar, A. and Prasad, T. S. K. (2013). A compendium of molecules involved in vector-pathogen interactions pertaining to malaria. Malaria Journal. 12, 216. [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. 12, 3128-3138. [PubMed]

• Ambekar, S. A., Nirujogi, R. S., Srikanth, S. M., Chavan, S., Kelkar, D. S., Hinduja, I., Zaveri, K., Prasad, T. S. K., 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. [PubMed]

• Marimuthu, A., Chavan, S., Sathe, G. J., 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. BBA - Proteins and Proteomics. 1834, 2308-2316. [PubMed]

• Balakrishnan, L., Soman, S., Patil, Y. B., Advani, J., Thomas, J. K., Venkatesh, D. D., Urmila, K. K., Harsha, H. C., Prasad, T. S. K., Raju, R., Pandey, A., Dimitriadis, E., and Chatterjee, A. (2013). IL-11/IL11RA receptor mediated signaling: a web accessible knowledgebase. Cell Communication and Adhesion. 20, 81-86. [PubMed]

• 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. K., Harsha, H. C., Chatterjee, A. and Pandey, A. (2012). SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics - Clinical Applications. 7, 355-66.[PubMed]

• Harsha, H. C., Pinto, S. M. and Pandey, A. (2013). Proteomic strategies to characterize signaling pathways. Methods in Molecular Biology. 1007, 359-377. [PubMed]

• Venugopal, A. K., Kumar, G. S. S., Selvan, L. D. N., Mahadevan, A., Renuse, S., Kumar, P., Pawar, H., Sahasrabuddhe, N. A., Suja, M. S., Ramachandra, Y. L., Prasad, T. S. K., Madhusudhana, S. N., Harsha, H. C., Chaerkady, R., Satishchandra, P., Pandey, A. and Shankar, S. K. (2013). Quantitative proteomics for identifying biomarkers for Rabies. Clinical Proteomics. 10, 3. [PubMed]

• 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. (2013). 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. [PubMed]

• Kumar, G. S. S., Venugopal, A. K., Mahadevan, A., Renuse, S., Harsha, H. C., Sahasrabuddhe, N. A., Pawar, H., Sharma, R., Kumar, P., Rajagopalan, S., Waddell, K., Ramachandra, Y. L., Satishchandra, P., Chaerkady, R., Prasad, T. S. K., Shankar, S. K. and Pandey, A. (2012). Quantitative proteomics for identifying biomarkers for tuberculous meningitis. Clinical Proteomics. 9, 12-24 [PubMed]

• Soman, S., Raju, R., Sandhya, V. K., Advani, J., Khan, A. A. , Harsha, H. C., Prasad, T. S. K., Sudhakaran, P. R., Pandey, A. and Adishesha, P. K. (2012). A multicellular signal transduction network of AGE/RAGE signaling. Journal of Cell Communication and Signaling. 7, 19-23. [PubMed]

• Kumar, G. S. S., Venugopal, A. K., Kashyap, M. K., Raju, R., Marimuthu, A., Palapetta, S. M., Subbannayya, Y., Goel, R., Chawla, A., Dikshit, J. B., Tata, P., Harsha, H. C., Maharudraiah, J., Ramachandra, Y. L., Satishchandra, P., Prasad, T. S. K., Pandey, A., Mahadevan, A. and Shankar, S. K. (2012). Gene expression profiling of tuberculous meningitis co-infected with HIV. Journal of Proteomics and Bioinformatics.  5, 235-244.  [PubMed]

• Kalra, H., Simpson, R. J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V. C., Borràs, F. E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J. M., Gabrielsson, S., Gho, Y. S., Gupta, D., Harsha, H. C., Hendrix, A., Hill, A. F., Inaal, J. M., Jenster, G., Kiang, L. S., Krämer-Albers, E-M., Llorente, A., Lötvall, J., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E. N. M., Pandey, A., Patel, T., Piper, M. G., Pluchino, S., Prasad, T. S. K., Rajendran, L., Raposo, G., Record, M., Reid, G. E., Sánchez-Madrid, F., Schiffelers, R. M., Siljander, P., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B. W. M., Vázquez, J., Vidal, M., Yáñez-Mó, M., Zoeller, M. and Mathivanan, S. (2012). Vesiclepedia: A compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 10, e1001450. [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]

• Kim, M. S., Kuppireddy, S. V., Sakamuri, S., Singal, M., Getnet, D., Harsha, H. C., Goel, R., Balakrishnan, L., Jacob, H. K. C., Kashyap, M. K., Tankala, S. G., Maitra, A., Iacobuzio-Donahue, C. A., Jaffee, E., Goggins, M. G., Velculescu, V. E., Hruban, R. H. and Pandey, A. (2012). Rapid characterization of candidate biomarkers for pancreatic cancer using cell microarrays (CMAs). Journal of Proteome Research. 11, 5556-5563. [PubMed]

• 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. (2011). A signaling network of thyroid-stimulating hormone. Journal of Proteomics and Bioinformatics. 4, 238-241. [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]

• Nagaraj, S. H., Harsha, H. C., Reverter, A., Colgrave, M. L., Sharma, R., Andronicos, N., Hunt, P., Menzies, M., Lees, M. S., Sekhar, N. R., Pandey, A. and Ingham, A. (2012). Proteomic analysis of the abomasal mucosal response following infection by the nematode, Haemonchus contortus, in genetically resistant and susceptible sheep. Journal of Proteomics. 75, 2141-2152. [PubMed]

• 
  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. [PubMed]

• 
  Goel, R., Harsha, H. C., Pandey, A. and Prasad, T. S. K. (2012). Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Molecular Biosystems. 8, 453-463.[PubMed]

• 
  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., 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. [PubMed]

• 
  Pawar, H., Maharudraiah, J., Kashyap, M. K., Sharma, J., Srikanth, M. S., Choudhary, R., Chavan, S., Sathe, G. J., 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]

• 
  Bhattacharjee, M., Raju, R., Radhakrishnan, A., Nanjappa, V., Muthusamy, B., Singh, K., Kuppusaami, D., Lingala, B. T., Pan, A., Mathur, P. P., Harsha, H. C., Prasad, T. S. K., Atkins, G. J., Pandey, A. and Chatterjee, A. (2012). A bioinformatics resource for TWEAK-Fn14 signaling pathway. Journal of Signal Transduction. Article ID 376470. [PubMed]

• Renuse. S., Harsha, H. C., Kumar, P., Acharya, P. K., Sharma, J., Goel, R., Kumar, G. S. S., Raju, R., Prasad, T. S. K., Slotta, T. and Pandey, A. (2012). Proteomic analysis of an unsequenced plant -Mangifera indica. Journal of Proteomics. 75, 5793-5796. [PubMed]

• Radhakrishnan, A., Raju, R., Tuladhar, N., Subbannayya, T., Thomas, J. K., Goel, R., Telikicherla, D., Palapetta, S. M., Rahiman, B. A., Venkatesh, D. D., Urmila, K. K., Harsha, H. C., Mathur, P. P., Prasad, T. S. K., Pandey, A., Shemanko, C. and Chatterjee, A. (2012). A pathway map of prolactin signaling. Journal of Cell Communication and Signaling. 6, 169-173. [PubMed]
  

• Goel, R., Harsha, H. C., Pandey, A. and Prasad, T. S. K. (2011). Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis. Molecular Biosystems. 8, 453-463. [PubMed]

• Kelkar, D. S., Kumar, D., Kumar, P., Balakrishnan, L., Muthusamy, B., Yadav, A. K., Shrivastava, P., Marimuthu, A., Anand, S., Sundaram, H., Kingsbury, R., Harsha, H. C., Nair, B., Prasad, T. S. K., Chauhan, D. S., Katoch, K., Katoch, V. M., Kumar, P., Chaerkady, R., Ramachandran, S., Dash D. and Pandey, A. (2011). Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Molecular and Cellular Proteomics. 10, M111.011627. [PubMed]

• 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., Veerendra Kumar, K. V., Vijayakumar, M., Chaerkady, R., Prasad, T. S. K., Kumar, R. V. and Pandey, A. Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biology and Therapy. 2011. 12, 510-522.[PubMed]

• 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. Comprehensive proteomic analysis of human bile. Proteomics. 2011. 11, 4443- 4453.[PubMed]

• Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D., Muthusamy, B., Thomas, J. K., Sharma, J., Rahiman, B. A., Harsha, H. C., Shankar, S., Prasad, T. S. K., Mohan, S. S., Bader, G. D., Wani, M. R. and Pandey, A. A comprehensive manually curated reaction map of RANKL/RANK signaling pathway. Database. 2110, bar021. [PubMed]

• 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. Gene expression profiling of tuberculous meningitis. Journal of Proteomics and Bioinformatics. 2011. 4, 98-105. [PubMed]

• 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., Syed, S., Srinivas, S. M., Sathe, G. J., Ahmad, S., Chavan, S. N., Kumar, G. S. S., Marimuthu, A., Prasad, T. S. K., Harsha, H. C., Rahiman, B. A., Ohara, O., Bader, G. D., Mohan, S. S., Schiemann, W. P. and Pandey, A. (2011). NetSlim: High-confidence curated signaling maps. Database. 2011, bar032. [PubMed]
  

• Nanjappa, V., Raju, R., Muthusamy, B., Sharma, J., Thomas, J. K., Nidhina, P. A. H., Harsha, H. C., Pandey, A., Anilkumar G. and Prasad, T. S. K. (2011). A comprehensive curated reaction map of leptin signaling pathway. Journal of Proteomics and Bioinformatics. 4, 184-189. [PubMed]

• Harsha, H. C. and Pandey, A. Phosphoproteomics in cancer. Molecular oncology. 2010. 4, 482-495. [PubMed]

• 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., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A. SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer biology & therapy. 2010. 10. [PubMed]

• 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. 2010. 6, 163-173. [PubMed]

• Harsha, H. C., Kandasamy, K., Ranganathan, P., Rani, S., Ramabadran, S., Gollapudi, S., Balakrishnan, L., Dwivedi, S. B., Telikicherla, D., Selvan, L. D., Goel, R., Mathivanan, S., Marimuthu, A., Kashyap, M., Vizza, R. F., Mayer, R. J., Decaprio, J. A., Srivastava, S., Hanash, S. M., Hruban, R. H. and Pandey, A. A compendium of potential biomarkers of pancreatic cancer. PLoS medicine. 2009. 6, e1000046-0. [PubMed]

• Ranganathan, P., Harsha, H. C. and Pandey, A. Molecular alterations in exocrine neoplasms of the pancreas. Archives of pathology & laboratory medicine. 2009. 133, 405-412.[PubMed]

• Kristiansen, T. Z., Harsha, H. C.*, Gronborg, M., Maitra, A. and Pandey, A. Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma. Journal of proteome research. 2008. 7, 4670-4677. [PubMed] *Shared first author

• Harsha, H. C., Jimeno, A., Molina, H., Mihalas, A. B., Goggins, M. G., Hruban, R. H., Schulick, R. D., Kamath, U., Maitra, A., Hidalgo, M. and Pandey, A.  Activated epidermal growth factor receptor as a novel target in pancreatic cancer therapy. Journal of proteome research. 2008. 7, 4651-4658. [PubMed]

• Guha, U., Chaerkady, R., Marimuthu, A., Patterson, A. S., Kashyap, M. K., Harsha, H. C., Sato, M., Bader, J. S., Lash, A. E., Minna, J. D., Pandey, A. and Varmus, H. E.  Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of the National Academy of Sciences of the United States of America. 2008. 105, 14112-14117. [PubMed]

• Chaerkady, R., Harsha, H. C., Nalli, A., Gucek, M., Vivekanandan, P., Akhtar, J., Cole, R. N., Simmers, J., Schulick, R. D., Singh, S., Torbenson, M., Pandey, A. and Thuluvath, P. J.  A quantitative proteomic approach for identification of potential biomarkers in hepatocellular carcinoma. Journal of proteome research. 2008. 7, 4289-4298. [PubMed]

• Harsha, H. C., Molina, H. and Pandey, A.  Quantitative proteomics using stable isotope labeling with amino acids in cell culture. Nature protocols. 2008. 3, 505-516. [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]

• Mishra, G. R., 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., Mathew, P., Chatterjee, P., Arun, K. S., Sharma, S., Chandrika, K. N., Deshpande, N., Palvankar, K., Raghavnath, R., Krishnakanth, R., Karathia, H., Rekha, B., Nayak, R., Vishnupriya, G., Kumar, H. G., Nagini, M., Kumar, G. S., Jose, R., Deepthi, P., Mohan, S. S., Gandhi, T. K., Harsha, H. C., Deshpande, K. S., Sarker, M., Prasad, T. S. and Pandey, A.  Human Protein Reference Database--2006 update. Nucleic acids research. 2006. 34, D411-3. [PubMed]

• Raghothama, C., Harsha, H. C., Prasad, C. K. and Pandey, A.  Bioinformatics and proteomics approaches for aging research. Biogerontology. 2005. 6, 227-232. [PubMed]

• Muthusamy, B., Hanumanthu, G., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Suresh, M., Kannabiran, N., Niranjan, V., Nalli, A., Prasad, T. S., Arun, K. S., Reddy, R., Chandran, S., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Sudhir, D., Bala, P., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Chaerkady, R., Gandhi, T. K., Harsha, H. C., Mohan, S. S., Deshpande, K. S., Sarker, M. and Pandey, A.  Plasma Proteome Database as a resource for proteomics research. Proteomics. 2005. 5, 3531-3536. [PubMed]

• Harsha, H. C., Suresh, S., Amanchy, R., Deshpande, N., Shanker, K., Yatish, A. J., Muthusamy, B., Vrushabendra, B. M., Rashmi, B. P., Chandrika, K. N., Padma, N., Sharma, S., Badano, J. L., Ramya, M. A., Shivashankar, H. N., Peri, S., Choudhury, D. R., Kavitha, M. P., Saravana, R., Niranjan, V., Gandhi, T. K., Ghosh, N., Chandran, S., Menezes, M., Joy, M., Mohan, S. S., Katsanis, N., Deshpande, K. S., Raghothama, C., Prasad, C. K. and Pandey, A.  A manually curated functional annotation of the human X chromosome. Nature genetics. 2005. 37, 331-332. [PubMed]

• Peri, S., Navarro, J. D., Kristiansen, T. Z., Amanchy, R., Surendranath, V., Muthusamy, B., Gandhi, T. K., Chandrika, K. N., Deshpande, N., Suresh, S., Rashmi, B. P., Shanker, K., Padma, N., Niranjan, V., Harsha, H. C., Talreja, N., Vrushabendra, B. M., Ramya, M. A., Yatish, A. J., Joy, M., Shivashankar, H. N., Kavitha, M. P., Menezes, M., Choudhury, D. R., Ghosh, N., Saravana, R., Chandran, S., Mohan, S., Jonnalagadda, C. K., Prasad, C. K., Kumar-Sinha, C., Deshpande, K. S. and Pandey, A.  Human Protein Reference Database as a discovery resource for proteomics. Nucleic acids research. 2004. 32, D497-4. [PubMed]

• Peri, S., Navarro, J. D., Amanchy, R., Kristiansen, T. Z., Jonnalagadda, C. K., Surendranath, V., Niranjan, V., Muthusamy, B., Gandhi, T. K., Gronborg, M., Ibarrola, N., Deshpande, N., Shanker, K., Shivashankar, H. N., Rashmi, B. P., Ramya, M. A., Zhao, Z., Chandrika, K. N., Padma, N., Harsha, H. C., Yatish, A. J., Kavitha, M. P., Menezes, M., Choudhury, D. R., Suresh, S., Ghosh, N., Saravana, R., Chandran, S., Krishna, S., Joy, M., Anand, S. K., Madavan, V., Joseph, A., Wong, G. W., Schiemann, W. P., Constantinescu, S. N., Huang, L., Khosravi-Far, R., Steen, H., Tewari, M., Ghaffari, S., Blobe, G. C., Dang, C. V., Garcia, J. G., Pevsner, J., Jensen, O. N., Roepstorff, P., Deshpande, K. S., Chinnaiyan, A. M., Hamosh, A., Chakravarti, A. and Pandey, A.  Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome research. 2003. 13, 2363-2371. [PubMed]

• Deshpande, K. S., Harsha, H. C. and Pandey, A. Microarrays and Mass Spectrometry - The Future of Proteomics. Current Genomics. 2003. 4, 605-613