|
Patil, K., Yelamanchi, S., Kumar, M., Hinduja, I., Prasad, T. S. K., Gowda, H. and Mukherjee, S. (2019). Quantitative mass spectrometric analysis to unravel glycoproteomic signature of follicular fluid in women with polycystic ovary syndrome. PLoS ONE. In press
Patil, S., Babu, N., Subbannayya, T., Mohan, S. V., Sathe, G., Solanki, H. S., Rajagopalan, P., Patel, K., Advani, J., Bhandi, S., Sidransky, D., Chatterjee, A., Gowda, H.*, Ferrari, M. (2019). Secretome analysis of oral keratinocytes chronically exposed to shisha. Cancer Biomarkers. In Press. (* Corresponding Author)
Rao, A., K., D., M., A., Patel, K., Korivi J., S., Balaiah, M., Sundersingh, S., Velusami, S., Rajkumar, T., Pandey, A., Chatterjee, A., Gowda, H.*, Mani, S. (2019). Identification of lncRNAs associated with early stage breast cancer and their prognostic implications. Molecular Oncology. In Press. (* Corresponding Author)
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)
Patil, S., Patel, K. , Advani, J. , Subbannayya, T., Rajagopalan, P., Babu, N., Solanki, H., Bhandi, S., Sidransky, D., Chatterjee, A., Gowda, H.*, Ferrari, M. (2019). Multiomic analysis of oral keratinocytes chronically exposed to shisha. Journal of Oral Pathology and Medicine. [Epub ahead of print] [PubMed] (* Corresponding Author)
Patil, S. , Subbannayya, T. , Mohan, S. V., Babu, N., Advani, J., Sathe, G., Rajagopalan, P., Patel, K., Solanki, H., Sidransky, D., Gowda, H., Chatterjee, A., Ferrari, M. (2019). Total proteomic analysis of oral keratinocytes chronically treated with shisha. OMICS: A Journal of Integrative Biology. In Press.
Subbannayya, T., Leal-Rojas, P., Zhavoronkov, A., Ozerov, I. V., Korzinkin, M., Babu, N., Radhakrishnan, A., Chavan, S., Raja, R., Pinto, S. M., Patil, A. H., Barbhuiya, M. A., Kumar, P., Guerrero-Preston, R., Navani, S., Tiwari, P. K., Kumar, R. V., Prasad, T. S. K., Roa, J. C., Pandey, A., Sidransky, D., Gowda, H., Izumchenko, E., Chatterjee, A.*, (2018). PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich Akt substrate of 40 kDa (PRAS40). Journal of Cell Communication and Signaling. In Press.
Yelamanchi, S.D., Tyagi, A., Mohanty, V., Dutta, P., Korbonits, M., Chavan, S., Advani, J., Madugundu, A.K., Dey, G., Datta, K.K., Rajyalakshmi, M., Sahasrabuddhe, N.A., Chaturvedi, A., Kumar, A., Das, A.A., Ghosh, D., Jogdand, G.M., Nair, H.H., Saini, K., Panchal, M., Sarvaiya, M.A., Mohanraj, S.S., Sengupta, N., Saxena, P., Subramani, P.A., Kumar, P., Akkali, R., Reshma, S.V., Santhosh, R.S., Rastogi, S., Kumar, S., Ghosh, S.K., Irlapati, V.K., Srinivasan, A., Radotra, B.D., Mathur, P.P., Wong, G.W., Satishchandra, P., Chatterjee, A., Gowda, H., Bhansali, A., Pandey, A., Shankar, S.K., Mahadevan, A., Prasad, T.S.K. (2018). Proteomic Analysis of the Human Anterior Pituitary Gland. OMICS: A Journal of Integrative Biology. 22, 759-769. [PubMed]
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. 20, 617-622. [PubMed]
Bhat, M. Y., Solanki, H. S., Advani, J., Khan, A. A., Prasad, T. S. K., Gowda, H., Thiyagarajan, S. and Chatterjee, A. (2018). Comprehensive network map of interferon gamma signaling. Journal of Cell Communication and Signalingy. 12, 745-751. [PubMed]
Nanjappa, V., Raja, R., Radhakrishnan, A., Jain, A.P., Datta, K.K., Puttamallesh, V. N., Solanki, H, S., Chavan, S., Patil, A., Renuse, S., Jain, A., Mathew, D., Thakur, R., Guerrero-Preston, R., Nair, B., Routray, S., Mohanty, N., Gowda, K.B.L., Jadav, R., Ghosal, S., Kumar, R.V., Ramesha, C., Raghu, V.C., Mathur, P.P., Prasad, T.S.K., Califano, J.A., Sidransky, D., Pal, A., Ganesh, M.S., Ray, J.G., Pandey, A., Gowda, H., and Chatterjee, A. (2018). Testican 1 (SPOCK1) and protein tyrosine phosphatase, receptor type S (PTPRS) show significant increase in saliva of tobacco users with oral cancer. Translational Research in Oral Oncology. [Article]
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. 23, 1-16. [Pubmed]
Bhat, F. A., Advani, J., Khan, A. A., Mohan, S., Pal, A., Gowda, H., Chakrabarti, P., Prasad, T. S. K. and Chatterjee, A. (2018). A network map of thrombopoietin signaling. Journal of Cell Communication and Signaling. [PubMed]
Patil, A. H., Datta, K. K., Behera, S. K., Kasaragod, S., Pinto, S. M., Koyangana, S. G., Mathur, P. P., Gowda, H., Pandey, A. and Prasad T. S. K. (2018). Dissecting Candida pathobiology: Post-translational modifications on the Candida tropicalis proteome. OMICS: A Journal of Integrative Biology. 22, 544-552. [PubMed]
Khan, A. A., Mangalaparthi, K. K., Advani, J., Prasad, T. S. K., Gowda, H., Jain, D. and Chatterjee, A. (2018). Data from quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissues using high-resolution mass spectrometry. Data in Brief. 19, 1631-1637. [PubMed]
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. 23, E1454. [PubMed]
Babu, N., Mohan, S., Nanjappaa, V., Chavan, S., Advani, J., Khan, A. A., Renuse, S., Radhakrishnan, A., Prasad, T. S. K., Kumar, R. V., Ray, J. G., Biswas, M., Thyagarajan, S., Califano, J. A., Sidransky, D., Gowda, H. and Chatterjee, A. (2018). Identification of potential biomarkers of head and neck squamous cell carcinoma using iTRAQ based quantitative proteomic approach. Data in Brief. 19, 1124-1130. [PubMed]
Dhandapani, G., Sikha, T., Pinto, S. M., Kumar, K. M., Patel, K., Kumar, M., Kumar, V., Tennyson, J., Satheeshkumar, P. K., Gowda, H., Prasad, T. S. K. and Madanan, M. G. (2018). Proteomic approach and expression analysis revealed the differential expression of predicted leptospiral proteases capable of ECM degradation. BBA - Proteins and Proteomics. 1866, 712-721. [PubMed]
Danda, R., Ganapathy, K., Sathe, G., Madugundu, A. K., Krishnan, U. M., Khetan, V., Rishi, P., Gowda, H., Pandey, A., Subramanian, K., Prasad, T. S. K. and Elchuri, S. V. (2018). Membrane Proteome of Invasive Retinoblastoma: Differential Proteins and Biomarkers. Protomics – Clinical Applications. 12, e1700101. [PubMed]
Barbhuiya, M. A., Kashyap, M. K., Puttamallesh, V. N., Kumar, R. V., Wu, X., Pandey, A. and Gowda, H.* (2018). Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget. 9, 18422-18434. [PubMed] (* Corresponding Author)
Rajagopalan, P., Jain, A. P., Nanjappa, V., Patel, K., Mangalaparthi, K. K., Babu, N., Cavusoglu, N., Roy, N., Soeur, J., Breton, L., Pandey, A., Gowda, H.*, Chatterjee A. and Misra, N. (2018). Proteome-wide changes in primary skin keratinocytes exposed to diesel particulate extract – a role for antioxidants in skin health. Journal of Dermatological Science. 91, 239-249. [PubMed] (* Corresponding Author)
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. 19, 773-785. [PubMed] (* 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. [PubMed] (* Corresponding Author)
Babu, N., Advani, J., Solanki, H. S., Patel, K., Jain, A. P., Khan, A. A., Radhakrishnan, A., Sahasrabuddhe, N. A., Mathur, P. P., Nair, B., Prasad, T. S. K., Chang, X., Sidransky, D., Gowda, H.* and Chatterjee, A. (2018). miRNA and proteomic dysregulation in non-small cell lung cancer in response to cigarette smoke. MicroRNA. 7, 38-53. [PubMed] (* Corresponding Author)
Solanki, H. S., Raja, R., Zhavoronkov, A., Ozerov. I. V., Artemov, A. V., Advani, J., Radhakrishnan, A., Babu, N., Puttamallesh, V. N., Syed, N., Nanjappa, V., Subbannayya. T., Sahasrabuddhe, N. A., Patil, A. H., Prasad, T. S. K., Daria. G., Chang, X., Sathyendran, R., Mathur, P. P., Rangarajan, A., Sidransky, D., Pandey, A., Evgeny, I., Gowda, H.* and Chatterjee, A. (2018). Targeting Focal Adhesion Kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of Epidermal Growth Factor Receptor. Oncoscience. 5, 21-38. [PubMed] (* Corresponding Author)
Rajagopalan, P., Nanjappa, V., Patel, K., Jain, A. P., Mangalaparthi, K. K., Patil, A. H., Nair, B., Mathur, P. P., Prasad, T. S. K., Califano, J. A., Sidransky, D., Gowda, H.* and Chatterjee A. (2018). Role of protein kinase N2 (PKN2) in cigarette smoke-mediated oncogenic transformation of oral cells. Journal of Cell Communication and Signaling. [PubMed] (* 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.* (2018). Chronic exposure of cigarette smoke and chewing tobacco alters expression of microRNAs in esophageal epithelial cells. MicroRNA. 7, 28-37. [PubMed] (* Corresponding Author)
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., Sidra
nsky, D., Gowda, H. and Chatterjee, A. (2017).
Investigation of curcumin mediated signaling pathways in head and neck squamous cell carcinoma.
Translational Research in Oral Oncology. [Article]
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.* and Chatterjee, A.* (2017).
Cigarette smoke induces mitochondrial metabolic reprogramming in lung cells.
Mitochondrion.. 40, 58-70. [PubMed] (* Corresponding Author)
Solanki, H. S., Advani, J., Kumar, M., Kumar, P., Bhagat, H., Prasad, T. S. K., Sidransky, D., Gowda, H. and Chatterjee, A. (2017).
miRNA profiling of bladder cells chronically exposed to cigarette smoke condensate and its vapor.
Research Reports. [Article]
Arunima, A., Yelamanchi, S. D., Padhi, C., Jaiswal, S., Ryan, D., Gupta, B., Sathe, G.,
Advani, J., Gowda, H.,Prasad, T. S. K., and Suar, M. (2017).
"Omics" of food-borne gastroenteritis: Global proteomic and mutagenic analysis of Salmonella enterica serovar Enteritidis.
OMICS: A Journal of Integrative Biology. 21, 571-583. [PubMed]
Mir, S. A., Renuse, S., Sathe, G. J., Khan, A. A., Patil,
A. H., Nanjappa, V., Bhat, F. A., Prasad, T. S. K., Giri,
A. K., Chatterjee, A. and Gowda, H.* (2017). Altered signaling associated with chronic arsenic exposure in human skin keratinocytes.
Proteomics - Clinical Applications. 11, 11-12.
[PubMed] (* Corresponding Author)
Dammalli, M., Dey, G., Madugundu, A. K., Kumar, M., Rodrigues,
B., Gowda, H., Byachapur, G. S., Mahadevan, A., Shankar S. K. and
Prasad, T. S. K. (2017). Proteomic analysis of the human olfactory bulb. OMICS:
A Journal of Integrative Biology. 21, 440-453.
[PubMed]
Solanki, H. S., Advani, J., Khan, A. A., Radhakrishnan,
A., Sahasrabuddhe, N. A., Pinto, S. M., Chang, X., Prasad,
T. S. K., Mathur, P. P., Sidransky, D., Gowda, H.* and
Chatterjee, A.*. (2017). Chronic cigarette smoke mediated
global changes in lung mucoepidermoid cells: A phosphoproteomic analysis. OMICS: A Journal of Integrative Biology. 21, 474-487.
[PubMed]
(* Corresponding Author)
Puttamallesh, V. N., Patel, K. and Gowda,
H.* (2017). Rapid processing of archival tissue samples for proteomic
analysis using pressure-cycling technology.Journal of Proteins and Proteomics.
[Article] (* Corresponding Author)
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.
21, 413-425. [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. P., Chang, X., Prasad, T. S. K., Sidransky, D., Gowda, H.* and
Chatterjee, A. (2017). Long term cigarette smoke exposure and changes
in miRNA expression
and proteome in non-small cell lung cancer. OMICS: A Journal
of Integrative Biology.
21, 390-403 [PubMed] (* Corresponding Author)
Muthusamy, B., Selvan, L. D. N., Nguyen,
T. T., Manoj, J., Stawiski, E. W., Jaiswal, B. S., Wang, W., Raja,
R., Ramprasad, V. L., Gupta, R., Murugan, S., Kadandale,
J. S., Prasad, T. S. K., Reddy, K.,
Perterson, A., Pandey, A., Seshagiri, S., Girimaji, S. C., and Gowda,
H.* (2017). Next Generation Sequencing Reveals Novel Mutations in X-linked
Intellectual Disability. OMICS: A Journal of Integrative Biology. 21, 295-303.
[PubMed] (* Corresponding Author)
Kumar, S., Kumar, M., Ekka, R., Dvorin,
J. D., Paul, A. S., Madugundu, A. K., Gilberger, T., Gowda, H., Duraisingh,
M. T., Prasad, T. S. K. and Sharma, P. (2017). PfCDPK1 mediated signaling
in erythrocytic stages of Plasmodium falciparum. Nature Communications.
8, 63 [PubMed]
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. 16, 1632-1645.
[PubMed]
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. [PubMed]
Tiwari, R., Sahu, I., Soni, B. L., Sathe,
G. J., Datta, K. K., Thapa, P., Sinha, S., Vadivel, C. K., Dhaka,
B., Sinha, S., Gowda, H. and Vaidya, M. M. (2017). Quantitative phosphoproteomic
analysis
reveals system-wide signaling pathways regulated by site-specific
phosphorylation on Keratin-8 in skin squamous cell carcinoma derived cell-line. Proteomics. 17, 7.
[PubMed]
Dammalli, M., Murthy, K. R., Pinto, S. M., Murthy, K. B.,
Nirujogi, R. S., Madugundu, A. K., Dey, G., Nair, B., Gowda, H. and Prasad,
T. S. K. (2017). Towards post-genomics ophthalmology: A proteomic map
of the human choroid-retinal pigment epithelium tissue. OMICS:
A Journal of Integrative Biology. 21, 114-122.
[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.
[Article] (*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.
27, 133-144. [PubMed]
Mir, S.A., Pinto, S.M., Paul, S., Raja,
R., Nanjappa, V., Syed, N., Advani, J., Renuse, S., Sahasrabuddhe,
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. 17, 6.
[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. 13, 29. [PubMed] (*Corresponding
Author)
Rajagopalan, P., Nanjappa, V., Raja, R., Jain, A. P., Mangalparthi,
K. K., Sathe, G. J., Babu, N., Patel, K., Cavusoglu, N., Soeur, J., Pandey,
A., Roy, N., Breton, L., Chatterjee, A., Misra, N. and Gowda, H *.
(2016). How does chronic cigarette smoke exposure affect human skin? A global
proteomics study in primary human keratinocytes. OMICS: A Journal
of Integrative Biology. 20, 615-626. [PubMed] (*Corresponding author)
Raja, R., Sahasrabuddhe, N. A., Radhakrishnan, A., Syed,
N., Solanki, H. S., Puttamallesh V. N., Balaji S. A., Nanjappa V.,
Datta, K. K., Babu, N., Renuse, S., Patil, A. H., Izumchenko, E., Prasad,
T. S.,
Chang X., Rangarajan A., Sidransky, D., Pandey, A., Gowda, H., 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. 7, 61229-61245. [PubMed]
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]
Murthy, K. R., Dammali, M., Pinto, S. M., Murthy, K. B.,
Nirujogi, R. S., Madugundu, A. K., Dey, G., Subbannayya, Y., Mishra,
U. K., Nair, B., Gowda, H. and 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. 20, 510-519. [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. [PubMed] (*Corresponding author)
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., Patil, A. H., Patel, K., Dey, G., Madugundu, A. K., Renuse, S., Kaviyil, J. E., Nirujogi, R. S., Arunima, A., Daswani, B., Kaur, I., Mohanty, J., Sinha, R., Jaiswal, S., Sivapriya, S., Sonnathi, Y., Chattoo, B. B., Gowda, H., Ravikumar, R. and Prasad, T. S. K. (2016). Proteogenomics of Candida tropicalis - an opportunistic pathogen with importance for global health. OMICS: A Journal of Integrative Biology. 20, 239-247. [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, 219-29. [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. 13, 297-308. [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. 2015, 325721. [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. (2015). A network map of Interleukin-10 signaling pathway. Journal of Cell Communication and Signaling. [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. 4, 374-378. [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. 100, 744-53. [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. 2011, 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 |
