Center for Systems Biology and Molecular Medicine

An ICMR collaborating centre of excellence (ICMR-CCoE)

Research papers: 263; Review articles: 6; Book chapters: 7

 

2024 (Number of publications - 11)

• Hemavathi, K. N., Middha, S. K., Raju, R., Pilankatta, R., Prasad, T. S. K. and Abhinand, C. S. (2024). Computational screening of phytocompounds from C. amboinicus identifies potential inhibitors of Influenza A (H3N2) virus by targeting hemagglutinin. Journal of Biomolecular Structure & Dynamics.In press.
• Gupta, P., Goswami, S. G., Kumari, G., Saravanakumar, V., Bhargava, N., Rai, A. B., Singh, P., Bhoyar R. C., Arvinden, V. R., Gunda, P., Jain, S., Narayana, V. K., Deolankar, S. C., Prasad, T. S. K., Natarajan, V. T., Scaria, V., Singh, S. and Ramalingam, S. (2024). Development of pathophysiologically relevant models of sickle cell disease and β-thalassemia for therapeutic studies Nature Communications. In press.
• Hemavathi, K. N., Skariyachan, S., Raju, R., Prasad, T. S. K. and Abhinand, C. S. (2024). Computational screening of potential anti-inflammatory leads from Jeevaneeya Rasayana plants targeting COX-2 and 5- LOX by molecular docking and dynamic simulation approaches. Computers in Biology and Medicine. In press.
• Rex, D. A. B., Palollathil, A., Kumar, S. T. A., Chanderasekaran, J., Upadhyay, S. S., Parate, S. S., Sajida, A., Karthikkeyan, G. and Prasad, T. S. K. (2024). Role of Hemigraphis alternata in Wound Healing: Metabolomic Profiling and Molecular Insights into Mechanisms. Scientific Reports. In press.
• Singh, I., Hoti, S. L., Chauhan, N., Joshi, R. K., Prasad, T. S. K., Sarikhani, M., Kaushik, M., Unger, B. S., Jadav, P. and Modi, P. (2024). Immunomodulation of streptozotocin induced Type 1 Diabetes Mellitus in mouse model by Macrophage migration Inhibitory Factor-2 (MIF-2) homologue of human lymphatic filarial parasite, Wuchereria bancrofti. Acta Tropica. In press.
• Shaji, V., Dagamajalu, S., Sanjeev, D., George, M., Kanekar, S., Prasad, G., Prasad, T. S. K., Raju, R. and Rex, D. A. B. (2024). Deciphering the Receptor-Mediated Signaling Pathways of Interleukin-19 and Interleukin-20. Journal of Interferon & Cytokine Research. In press.
• Munjal, A., Rex, D. A. B., Prasad, T. S. K., Mukherjee, S., Pati, S. and Singh, S. (2004). Mass spectrometric identification of the secretome of Plasmodium falciparum merozoites to provide novel candidates for the vaccine development pipeline.TechRxiv.In press.
• Kotimoole, C. N., Ramya, V. K., Kaur, P., Reiling, N., Shandil, R. K., Narayanan, S., Flo, T. H. and Prasad, T. S. K. 2024. Discovery of Species-specific proteotypic peptides to establish a spectral library platform for the identification of non-tuberculosis mycobacteria from mass spectrometry-based proteomics. Journal of Proteome Research. In press.
• Singh, I., Anagha, A., Kotimoole, C. N., Modi, P. K., Prasad, T. S. K. and Hoti, S. L. (2024). Unpacking Immune Modulation as a Site of Therapeutics Innovation for Nematode Parasite Wuchereria bancrofti: A Temporal Quantitative Phosphoproteomics Profiling of Macrophage Migration Inhibitory Factor 2. OMICS: A Journal of Integrative Biology. In press.
• Mahin, A., Sreelakshmi, P. S., Modi, P. K., Raju, R., Prasad, T. S. K. and Abhinand, C. S. (2023). Meta-analysis of the serum/plasma proteome identifies significant associations between COVID-19 with Alzheimer's/ Parkinson's diseases Journal of Neurovirology. In press.
• Suchitha G. P., Jaikanth, C., Saptami, K., George, M., Prasad, T. S. K., Raju, R., Shobha, D. and Rex, D. A. B. (2023). Cisplatin and Procaterol Combination in Gastric Cancer? Targeting Checkpoint Kinase 1 (CHK1) for Cancer Drug Discovery and Repurposing by an Integrated Computational and Experimental Approaches. OMICS: A Journal of Integrative Biology. In press.
 

2023 (Number of publications - 26)

• Sreelakshmi, K., Hemavathi, K. N., Raju, R., Sameer, K., Prasad, T. S. K., Sudhakaran, P. R. and Abhinand, C. S. (2023). Identification and stability analysis of potential ADP-Ribose modification sites on Vascular Endothelial Growth Factor (VEGF) through molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics. In press
• Upadhyay, S. S., Shetty, R. and Prasad, T. S. K. (2023). Prospects for the discovery of actionable molecular targets for Triple Negative Breast Cancer. Book chapter In: "Protein Biomarkers: Discovery and Applications in Clinical Diagnostics". Springer Nature. In press.
• Ramesh, P., Akbar, K. C. J. and Prasad, T. S. K. (2023). Proteins biomarkers for diagnosing gastric cancers: perspectives through mass spectrometry-based discoveries. Book chapter In: "Protein Biomarkers: Discovery and Applications in Clinical Diagnostics". Springer Nature. In press.
• Rex, D. A. B. and Prasad, T. S. K. (2023). Data analysis pipelines, potential pitfalls, and troubleshooting for MS-based biomarker discovery and validation. Book chapter In: "Protein Biomarkers: Discovery and Applications in Clinical Diagnostics". Springer Nature. In press.
• Parate, S. S., Vijayakumar, M. and Prasad, T. S. K. (2023). Ex vivo drug assay as a potential hospital-based testing platform for clinical research and personalized treatment for solid tumors. Book chapter In: "Protein Biomarkers: Discovery and Applications in Clinical Diagnostics". Springer Nature. In press.
• Parate, S. S., Upadhyay, S. S., Amrutha, S., Karthikkeyan, G., Pervaje, R., Abhinand, C. S., Modi, P.K., and Prasad, T. S. K. (2023). Comparative metabolomics and network pharmacology analysis reveals shared neuroprotective mechanisms of Bacopa monnieri (L.) Wettst and Centella asiatica (L.) Urb. Molecular Neurobiology. In press.
• Deepak, K., Babu, S., Mohanan, V. V., Raju, R., Prasad, T. S. K. and Abhinand, C. S. (2023). Epstein-Barr Virus - Human Interactome Reveals New Molecular Insights into Viral Pathogenesis for Potential Therapeutics and Antiviral Drug Discovery. OMICS: A Journal of Integrative Biology. In press.
• Suchitha G. P., Jaikanth, C., Saptami, K., George, M., Prasad, T. S. K., Raju, R., Shobha, D. and Rex, D. A. B. (2023). Cisplatin and Procaterol Combination in Gastric Cancer? Targeting Checkpoint Kinase 1 (CHK1) for Cancer Drug Discovery and Repurposing by an Integrated Computational and Experimental Approaches. OMICS: A Journal of Integrative Biology. In press.
• Rawat, R. S., Gupta, A., Antil, N., Bhatnagar, S., Prasad, T. S. K. and Sharma, P. (2023). Protein kinase PfPK2 mediated signalling is critical for host erythrocyte invasion by malaria parasite. PLoS Pathogens. In press.
• Phukan, H., Sarma, A., Rex, D. A. B., Christie, S., kizhakkemuriyil, S., Hariharan, S., Prasad, T. S. K. and Madanan, M. (2023). Physiological temperature and osmotic changes drive dynamic proteome alterations in Leptospiral outer membrane and enhance protein export systems. Journal of Proteome Research. In press.
• Hegde, A., Upadhyay, S.S., Prasad, T. S. K., Modi, P. K. (2023). Chapter Sixteen - Mass spectrometry-based approaches for the identification of molecular mechanism of action of ayurvedic medicines in Parkinson disease Ayurvedic Herbal Preparations in Neurological Disorders. 425-459
• Kumar, S. T. A., Ammankallu, S., Rex, D. A. B., Soman, P.S., Nisar, M., George, A., Anto, K. C., Sanjeev, D., Kandiyil, K. M., John, L., Raj, S. S., Awasthi, K., Vinod, S. S., Prasad, T. S. K.* and Raju, R.* (2023). VirhostlncR: a comprehensive resource for long-noncoding RNAs and their targets in viral infections. Computers in Biology and Medicine. In press. [PubMed]
• Dcunha, R., Kumari, S., Najar, M. A., Aravind, A., Poojari, K. K., Ananda, H., Mutalik, S. P., Kalthur, S. G., Rajanikant, G. K., Mutalik, S., Siddiqui, S., Alrumman, S., Raghu, S. V., Adiga, S. K., Kannan, N., Prasad, T. S. K. and Kalthur G. (2023). High doses of clethodim-based herbicide GrassOut Max poses reproductive hazard by affecting male reproductive function and early embryogenesis in Swiss albino mice. Chemosphere. [PubMed]
• Devadasan, M. J., Ramesha, K. P., Ramesh, P., Kotimoole, C. N., Jeyakumar, S., Ashwitha, A., Ammankallu, S., Rai, A. B., Kumaresan, A., Vedamurthy, V. G., Raju, R., Das, D. N., Kataktalware, M. A. and Prasad, T. S. K. (2023). Exploring molecular dynamic indicators associated with reproductive performance of Bos indicus cattle in blood plasma samples through data-independent acquisition mass spectrometry. Journal of Proteomics. In press.
• Mangalaparthi, K. K., Patel, K., Khan, A. A., Nair, B., Kumar, R. V., Prasad, T. S. K., Sidransky, D., Chatterjee, A., Pandey, A. and Gowda, H. (2023). Molecular characterization of esophageal squamous cell carcinoma using quantitative proteomics. Cancers. In press.
• Ramesh, P., Behera, S. K., Kotimoole, C. N., Mohanty, V., Raju, R., Prasad, T. S. K. and Codi, J. A. K. (2023). Mining proteomics data to extract post-translational modifications associated with gastric cancer. Amino Acids. In press.
• Kumar, S., Rex, D. A. B., Saptami, K., Raju, R., Prasad, T. S. K. and Kandasamy, R. K. (2023). Computational tools for exploring peptide-membrane interactions in Gram-positive bacteria. Computational and Structural Biotechnology Journal. 21, 1995-2008. [PubMed]
• Suchitha, G. P., Rex, D. A. B., Raju, R., Prasad, T. S. K. and Dagamajalu, S. (2023). A network map of Cytoskeleton-associated protein 4 (CKAP4)-mediated signaling pathway in cancer. Journal of Cell Communication and Signaling. [DOI]
• Upadhyay, S. S., Rex, D. A. B., Parate, S. S., Dagamajalu, S., Prasad, T. S. K., Shetty, R. and Raju, R. (2023). An assembly of TROP2-mediated signaling events. Journal of Cell Communication and Signaling. [PubMed]
• Kotimoole, C. N., Antil, N., Kasaragod, S., Behera, S. K., Aravind, A., Reiling, N., Flo, T. H. and Prasad, T. S. K. (2023). Development of a spectral library for the discovery of altered genomic events in Mycobacterium avium associated with virulence using mass spectrometry-based proteogenomic analysis. Molecular and Cellular Proteomics. [PubMed]
• Sanjeev, D., Dagamajalu, S., Shaji, V., George, M., Subbannayya, Y., Prasad, T. S. K., Raju, R. and Rex, D. A. B. (2023). A network map of Macrophage-stimulating protein (MSP) signaling. Journal of Cell Communication and Signaling. [PubMed]
• Rex, D. A .B., Jaikanth, C., Saptami, K., Modi, P., Shobha, D., Raju, R., and Prasad, T. S. K. (2023). Computational design of novel Calcium/Calmodulin-Dependent protein kinase kinase 2 (CAMKK2) inhibitors. Journal of Biomolecular Structure and Dynamics. In press.
• Abhinand, C. S., Galipon, J., Mori, M., Ramesh, P., Prasad, T. S. K., Raju, R., Sudhakaran, P.R. and Tomita, M. (2023). Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis. Journal of Cell Communication and Signaling. 1-13.[PubMed]
• Mol, P., Rex, D. A. B., Dagamajalu, S., Babu, S., Chandrasekaran, P., Raghavan, R., Suresh, S., Ravishankara, N., Raju, A. H., Nair, B., Modi, P. K., Mahadevan, A., Prasad, T. S. K. and Raju, R. (2023). A network map of GDNF/RET signaling pathway in physiological and pathological conditions. Journal of Cell Communication and Signaling. [PubMed]
• Husain, A. A., Pinto, S. M., Agarwal, N., Behera, S. K., Khulkhule, P. R., Bhartiya, N. M., Subbannayya, Y., Prasad, T. S. K., Singh, L. R., Daginawala, H. F. and Kashyap, R. S. (2023). Comprehensive Proteomic Analysis of Brucella melitensis ATCC23457 Strain Reveals Metabolic Adaptations in Response to Nutrient Stress. Current Microbiology. [DOI]
• Ramesh, P., Babu, S., Ammankallu, S., Codi, J. A. K., Prasad, T. S. K., and Raju, R. (2023). Helicobacter pylori regulated microRNA map of human gastric cells. Helicobacter. [PubMed]
 

2022 (Number of publications - 51)

• Ashwitha, A., Ramesha, K. P., Ramesh, P., Kootimole, C. N., Devadasan, M. J., Ammankallu, S., Jeyakumar, S., Kumaresan, A., Veerappa, V. G., Das, D. N. and Prasad, T. S. K. (2022). Quantitative proteomics profiling of spermatozoa and seminal plasma reveals proteins associated with semen quality in Bos indicus bulls. Journal of Proteomics. [DOI]
• Abhinand, C. S., Athira, P., Krishnamurthy, A., Raju, R., Prasad, T. S. K., Nair, A. S., Rajasekharan, K. N., Oommen, O. V. and Sudhakaran, P. R. (2022). SARS-CoV-2 variants infectivity prediction and therapeutic peptide design using computational approaches. Journal of Biomolecular Structure & Dynamics. In Press.
• Husain, A. A., Pinto, S. M., Agarwal, N., Behera, S. K., Khulkhule, P. R., Bhartiya, N. M., Subbannayya, Y., Prasad, T. S. K., Singh, L. R., Daginawala, H. F. and Kashyap, R. S. (2021). Comprehensive Proteomic Analysis of Brucella melitensis ATCC23457 Strain Reveals Metabolic Adaptations in Response to Nutrient Stress. Current Microbiology. [DOI]
• Abhinand, C. S., Ibrahim, J. M., Prasad, T. S. K., Raju, R., Oommen, O. V. and Nair, A. S. (2022). Molecular docking and dynamics studies for the identification of Nipah virus glycoprotein inhibitors from Indian medicinal plants. Journal of Biomolecular Structure & Dynamics. [PubMed]
• Ramesh, P., Babu, S., Ammankallu, A., Codi, J.A.K., Prasad, T. S. K., and Raju, R. (2023). "Helicobacter pylori regulated MicroRNA map of human gastric cells". Helicobacter. [PubMed]
• Dagamajalu, S., Rex, D. A. B.,Suchitha, G. P., Rai, A. B., Kumar, S., Joshi, S., Raju, R. and Prasad, T. S. K. (2022). A network map of Discoidin Domain Receptor 1(DDR1)-mediated signaling in pathological conditions. Journal of Cell Communication and Signaling. [DOI]
• Arefian, M. and Prasad, T. S. K. (2022). Susceptibility of rice crop to salt threat: Proteomic, metabolomic, and physiological inspections. Journal of Proteome Research. [DOI]
• Deolankar, S. C., Najar, M. A., Ramesh, P., Kanichery, A., Kudva, A. K., Raghu, S. V. and Prasad, T. S. K. (2022). Discovery of molecular networks of neuroprotection conferred by Brahmi extract in Aβ42- induced toxicity model of Drosophila melanogaster using a quantitative proteomic approach. Molecular Neurobiology. [PubMed]
• Ramesh, P., Bajire, S.K., Kanichery, A., Najar, M.A., Shastry, R. P., and Prasad, T. S. K.(2022). 6-methylcoumarin rescues bacterial quorum sensing induced ribosome inactivating stress in Caenorhabditis elegans. Microbial Pathogenesis. [PubMed]
• Yarlagadda, A. K., Mol, P., Dey, G., Bhat, F. A., Chatterjee, O., Deolankar, S. C., Phillip, M.,Prasad, T. S. K., Bharath, M. M. S., and Mahadevan, A*. (2022). Regional heterogeneity in mitochondrial function underlies region-specific vulnerability in human brain aging: Implications for neurodegeneration. Free Radical Biology and Medicine [PubMed]
• Najar, M. A., Arefian, M., Sidransky, D., Gowda, H., Prasad, T. S. K., Modi, P. K. and Chatterjee, A. (2022). Tyrosine Phosphorylation Profiling Revealed the Signaling Network Characteristics of CAMKK2 in Gastric Adenocarcinoma. Frontiers in Genetics. [PubMed]
• Nizamuddin, A., Ramesha, K. P., Rana, E., Kasargod, S., Behera, S. K., Ashokan, M., Patil, A. H., Jeyakumar, S., Kumaresan, A., Kataktalware, M. A., Das, A. N., Srinisvasan, N. K. G. and Prasad, T. S. K. (2022). Transcriptomic analysis of PBMCs reveals COX3, BCL2, ATP2B4, B4GALT1, LACTB, FASN and CSN family genes regulating milk performance in lactating Bos indicus cows of Southern India. Research Square. Preprint
• Chatterjee, O., Gopalakrishnan, L., Pullimamidi, D., Raj, C., Yelamanchi, S., Gangadharappa, B. S., Nair, B., Mahadevan, A., Raju, R. and Prasad, T.S.K. (2022). A molecular network map of orexin-orexin receptor signaling system. Journal of Cell Communication and Signaling. [DOI]
• Gopalakrishnan, L., Chatterjee, O., Ravishankar, N., Suresh, S., Raju, R., Mahadevan, A. and Prasad, T. S. K. (2022). Opioid receptors signaling network. Journal of Cell Communication and Signaling. [PubMed]
• Kumari, G., Rex, D. A. B., Goswami, S., Mukherjee, S., Biswas, S., Maurya, P., Jain, R., Garg, S., Prasad, T. S. K., Pati, S., Ramalingam, S., Mohandas, N. and Singh, S. (2022). Dynamic palmitoylation of Red cell membrane proteins governs susceptibility to invasion by malarial parasite. ACS Infectious Diseases. [PubMed]
• Husain, A. A., Pinto, S.M., Subbannayya, Y., Kapoor, S., Khulkhule, P., Bhartiya, N., Prasad, T. S. K., Daginawala, H. F., Singh, L. R. and Kashyap, R. S. (2022). Development of Multiple Reaction Monitoring (MRM) assays to identify Brucella abortus proteins in the serum of humans and livestock’s. Proteomics Clinical Applications. [PubMed]
• Mol, P., Gopalakrishnan, L., Chatterjee, O., Mangalaparthi, K., Kumar, M., Durgad, S., Nair, B., Shankar, S., Mahadevan, A. and Prasad, T. S. K. (2022). Proteomic analysis of adult human hippocampal subfields demonstrates regional heterogeneity in the protein expression Journal of Proteome Research. [PubMed]
• Anam, E. Z*., Kumari, G*., Mukherjee, S*., Rex, D.A.B*., Sah, R. K., Chaurasiya, A., Singhal, J., Singh, N., Kaushik, S., Prasad, T. S. K., Pati, S., Ranganathan, A. and Singh, S. (2022). Complementary crosstalk between palmitoylation and phosphorylation events in MTIP regulate its role during Plasmodium falciparum invasion. Frontiers in Cellular and Infection Microbiology.[PubMed]
*Shared first author
• Rex, D. A. B., Dagamajalu, S., Gouda, M., Suchitha G. P., Chanderasekaran, J., Raju, R., Prasad, T. S. K., and Bhandary, Y. P (2022). A comprehensive network map of IL-17A signaling pathway. Journal of Cell Communication and Signaling. [PubMed]
• Rex, D. A. B., Prasad, T. S. K., Kandasamy, R. K. (2022). Revisiting Regulated Cell Death Responses in Viral Infection. [PubMed]
• Deolankar, S. C., Najar, M. A., Ramesh, P., Kanichery, A., Kudva, A. K., Raghu, S. V. and Prasad, T. S. K. (2022). Discovery of molecular networks of neuroprotection conferred by Brahmi extract in Aβ42-induced toxicity model of Drosophila melanogaster using a quantitative proteomic approach. Research Square. [PubMed]
• Subba, P. and Prasad, T. S. K. (2022). Scope of Proteogenomic Analysis for Indian Sandalwood (Santalum album). "The Sandalwood Genome". ISBN 978-3-030-93393-7, Chittaranjan Kole, Malali Gowda, H.B. Mahesh (Eds.): Springer. 89-97
• Kasaragod, S., Kotimoole, C. N., Gurtoo, S., Prasad, T. S. K., Gowda, H. and Modi, P. K. (2022). A computational workflow for predicting cancer neo-antigens. Bioinformation. 18, 214-218.
• Shah, S. R., Mohanty, V., Chaudhury, D., Prasad, T. S. K. and Shenoy, M. M. (2022). Evaluation of serum proteome from Indian psoriasis patients. Bioinformation. 18, 141-146.
• Mol, P., Chatterjee, O., Gopalakrishnan, L., Mangalaparthi, K., Bhat, F., Kumar, M., Nair, P., Shankar, S. K., Mahadevan, A. and Prasad, T. S. K. (2022). Age-associated molecular changes in human hippocampus subfields as determined by quantitative proteomics. OMICS: A Journal of Integrative Biology. [PubMed]
• Yelamanchi, S. D., Mishra, A., Behra, S. K., Karthikkeyan, G., Prasad, T. S. K. and Surolia, A. (2022). Rifampicin-mediated metabolic changes in Mycobacterium tuberculosis. Metabolites. [PubMed]
• Deolankar, S. C., Koyangana, S. G., Patil, A. H., Subbannayya, Y., Modi, P. K. and Prasad, T. S. K. (2022). Data on multiple post-translational modifications in Alzheimer’s disease. Neuroscience Research Notes. In press.
• Arefian, M., Antil, N., Najar, M. A., Subba, P. and Prasad, T. S. K. (2022). Phosphoproteome profiling of rice tissues provides new insights into responsive mechanisms and kinase activity upon salt stress Environmental and Experimental Botany. In press.
• Phukan, S., Sarma, A., Rex, D. A. B., Rai, B. A., Prasad, T. S. K., Madanan, M. G. (2022). Unique post-translational modification sites for acetylation, glutarylation, and phosphorylation are found specific to the proteins partitioned in the Triton X-114 fractions of Leptospira. ACS-Omega. [PubMed]
• Thimmappa, P. Y., Nair, A. S., Najar, M. A., Mohanty, V., Shastry, S., Prasad, T. S. K. and Joshi, M. B. (2022). Quantitative Phosphoproteomics Reveals Diverse Stimuli Activate Distinct Signaling Pathways During Neutrophil Activation. Cell and Tissue Research. [PubMed]
• Antil, N., Arefian, M., Kandiyil, M. K., Awasthi, K., Prasad, T. S. K. and Raju, R. (2022). The Core Human MicroRNAs regulated by Toxoplasma gondii. MicroRNA. [PubMed]
• Rex, D. A. B., Vaid, N., K. Deepak, K., Dagamajalu, S., Prasad, T. S. K. (2022). A comprehensive review on current understanding of Bradykinin in COVID-19 and inflammatory diseases. Molecular Biology Reports. [PubMed]
• Rex, D. A. B., Chanderasekaran, J., Rai, B. A., Phukan, S., Sarma, A., Prasad, T. S. K. and Madanan, M. G. (2022). Leptospira and Leptospirosis: New systems science insights on proteome, posttranslational modifications and pathogen-host interaction. OMICS: A Journal of Integrative Biology. [PubMed]
• Venugopal, G., Gangaraj, K. P., Muralikrishna, K. S., Prasad, T. S. K.* and Rajesh, M. K.* (2022). Transcriptome assembly of coconut endosperm callus (Laccadive Micro Tall cv.) and its functional annotation. Journal of Plantation Crops. 49, 225-230. (* Corresponding author)
• Karthikkeyan, G., Behera, S. K., Upadhyay, S. S., Pervaje, R., Prasad, T. S. K. * and Modi, P. K. * (2022). Metabolomics analysis highlights Yashtimadhu (Glycyrrhiza glabra L.) mediated neuroprotection in a rotenone-induced cellular model of Parkinson’s disease by restoring the mTORC1-AMPK1 axis in autophagic regulation. Phytotherapy Research. [PubMed]
• Subba, P., Saha, P., Karthikkeyan, G., Biswas, M., Prasad, T. S. K.* and Roy-Barman, S.* (2022). Metabolite profiling reveals overexpression of the global regulator, MoLAEA leads to increased synthesis of metabolites in Magnaporthe oryzae. Journal of Applied Microbiology. [PubMed]
• Nekrakalaya, B., Arefian, M., Kotimoole, C. N., Krishna, R. M., Palliyath, G. K., Najar, M. A., Behera, S. K., Kasaragod, S., Santhappan, P., Hegde, V. and Prasad, T. S. K. (2022). Toward Phytopathogen Diagnostics? Coconut Bud Rot Pathogen Phytophthora palmivora Mycelial Proteome Analysis Informs Genome Annotation. OMICS A Journal of Integrative Biology. [PubMed]
• Rex, D. A. B., Patil, A. H., Modi, P. K., Kandiyil, M. K., Tanneru, N., Pinto, S. M., Tanneru, N., Kasaragod, S., Sijwali, P. S. and Prasad, T. S. K. (2022). Dissecting Plasmodium yoelii pathobiology: proteomics approaches for decoding novel translational and post-translational modifications. ACS Omega. [PubMed]
• Rex, D. A. B., Suchitha G. P., Palollathil, A., Kanichery, A., Prasad, T. S. K. and Dagamajalu, S. (2022). The network map of Urotensin-II mediated signaling pathway in physiological and pathological conditions. Journal of Cell Communication and Signaling. Feb 16. [PubMed]
• Yelamanchi, S. D., Kumar, S. T. A., Mishra, A., Prasad, T. S. K. and Surolia, A. (2022). Metabolite dysregulation by Pranlukast in Mycobacterium tuberculosis. Molecules. 27, 1520. [PubMed]
• Dagamajalu, S., Rex, D. A. B., Suchitha G. P., Rai, B. A., Rainey, J. K., and Prasad, T. S. K. (2022). The network map of Elabela signaling pathway in physiological and pathological conditions. Journal of cell communication and signaling. 16, 145-154. [PubMed]
• Revikumar, A., Kashyap, V., Palollathil, A., Aravind , A., Raguraman , R., Kumar, K. M. K., Vijayakumar , M., Prasad, T. S. K. and Raju, R. (2022). Multiple G-quadruplex binding ligand induced transcriptomic map of cancer cell lines. Journal of Cell Communication and Signaling. 16, 129-135.
• Dagamajalu, S., Rex, D. A. B., Philem, P. D., Rainey, J. K., and Prasad, T. S. K. (2022). A network map of apelin-mediated signaling. Journal of cell communication and signaling. 16, 137-143. [PubMed]
• Maurya, R., Tripathi, A., Kumar, M., Antil, N., Yamaryo-Botté, Y., Kumar, P., Bansal, P., Doerig, C., Botte, C., Prasad, T. S. K. and Sharma, P. (2022). PI4-kinase and PfCDPK7 signaling regulate phospholipid biosynthesis in P. falciparum. EMBO Reports. 23, e54022 [PubMed]
• Gupta, M. D., Kumaresan, A., Saraf, K., Paul, N., Kumar, S., Karthikkeyan, G., Prasad, T. S. K., Modi, P. K., Ramesha, K. P., Manimaran, A. and Jeyakumar, S. (2022). Deciphering metabolomic alterations in seminal plasma of crossbred (Bos taurus X Bos indicus) bulls through comparative deep metabolomic analysis. Andrologia. 54, e14253. [PubMed]
• Awasthi, K., Kootimole, C. N., Aravind, A. and Prasad, T. S. K. (2022). Data Independent Acquisition Approach to Proteome: A Case Study and a Spectral Library for Mass Spectrometry-Based Investigation of Mycobacterium tuberculosis. OMICS: A Journal of Integrative Biology. Jan 28 [PubMed]
• Arefian, M., Antil, N., Najar, N. A., Behera, S. K., Subba, P. and Prasad, T. S. K. (2022). Identifying novel genes and proteins involved in salt stress perception and signaling of rice seedlings. OMICS: A Journal of Integrative Biology. Jan 24. [PubMed]
• Deolankar S. C., Najar A, Raghu S.V, and Prasad, T. S. K. (2022). Aβ42 expressing Drosophila melanogaster model for Alzheimer’s disease: Quantitative proteomics identifies altered protein dynamics of relevance to neurodegeneration. OMICS: A Journal of Integrative Biology. 26, 51-63. [PubMed]
• Rex, D. A. B., Subbannayya, Y., Modi, P. K., Palollathil, A., Gopalakrishnan, L., Bhandary, Y. P., Prasad, T. S. K.* and Pinto, S. M.* (2022). Temporal quantitative phosphoproteomics profiling of Interleukin-33 signaling network reveals unique modulators of monocyte activation. Cells. 11, 138 (* Corresponding authors) [PubMed]
• Rex, D. A. B., K. Deepak, K., Vaid, N., Dagamajalu, S., Kandasamy, R. K., Flo, T. H. and Prasad, T. S. K. (2022). A modular map of Bradykinin-mediated inflammatory signaling network. Journal of Cell Communication and Signaling. 16, 301-310. [PubMed]
• Aravind, A., Palollathil, A., D. A. B. Rex, Kumar, K. M. K., Vijayakumar, M., Shetty, R., Codi, J. A. K., Prasad, T. S. K. and Raju, R. (2022). A multi-cellular molecular signaling and functional network map of C-C Motif Chemokine Ligand 18 (CCL18): A chemokine with immunosuppressive and pro-tumor functions. Journal of Cell Communication and Signaling. 16, 293-300. [PubMed]

2021 (Number of publications - 40)

• Kalal, B. S., Modi, P. K., Najar, M. A., Behera, S. K., Upadhya, D., Prasad, T. S. K. and Pai, V. R. (2021). Hyperphosphorylation of HDAC2 promotes drug resistance in a novel dual drug resistant mouse melanoma cell line model: an in vitro study. American Journal of Cancer Research. 11, 5881–5901. [PubMed]
• Dasgupta, M., Kumaresan, A., Saraf, K. K., Nag, P., Sinha, M. K., Aslam, M. K. M., Karthikkeyan, G., Prasad, T. S. K., Modi, P. K., Datta, T. K., Ramesha, K. P., Manimaran, A. and Jeyakumar, S. (2021). Deep metabolomic profiling reveals alterations in fatty acid synthesis and ketone body degradations in spermatozoa and seminal plasma of astheno-oligozoospermic bulls. Frontiers in Veterinary Science. 10.3389/fvets.2021.755560. [PubMed]
• Subba, P. and Prasad, T. S. K.(2021). Plant Phosphoproteomics: Known Knowns, Known Unknowns and Unknown Unknowns of an Emerging Systems Science Frontier. OMICS: A Journal of Integrative Biology. 25, 750-769. [PubMed]
• Behera, S. K., Modi, P. K., Karthikkeyan, G., Pervaje, S. K., Pervaje, R., Raju, R., Prasad, T. S. K. and Subbannayya, Y. (2021). From LC-MS/MS metabolomics profiling of Kanchanara Guggulu to molecular docking and dynamics simulation of quercetin pentaacetate with aldose reductase. Bioinformation 17, 911-915.
• Gayathree, K., Prabhu, A., Pervaje, R., Pervaje S. K., Modi, P.K.* and Prasad, T. S. K.* (2021). Data on dose-dependent cytotoxicity of rotenone and neuroprotection conferred by Yashtimadhu (Glycyrrhiza glabra L.) in an in vitro Parkinson’s disease model. Data in Brief. 39, 107535. (* Corresponding authors) [PubMed]
• Gopalakrishnan, L., Chatterjee, O., Ravishankar, N., Suresh, S., Raju, R.*, Mahadevan, A. and Prasad, T. S. K.* (2021). Opioid receptors signaling network. Journal of Cell Communication and Signaling. (* Corresponding authors) [PubMed]
• Rajesh, M. K., Gangurde, S. S., Pandey, M. K., Niral, V., Sudha, R., Jerard, B. A., Kadke, G. N., Sabana, A. A., Muralikrishna, K. S., Samsudeen, K., Karun, A. and Prasad, T. S. K. (2021). Insights on genetic diversity, population structure and linkage disequilibrium in globally diverse coconut accessions using genotyping-by-sequencing. OMICS: A Journal of Integrative Biology. 25, 796-809.
• Chatterjee, O., Gopalakrishnan, L., Mol, P., Advani, J., Nair, B., Shankar, S. K., Mahadevan, A. and Prasad, T. S. K. (2021). The Normal Human Adult Hypothalamus Proteomic Landscape: Rise of Neuroproteomics in Biological Psychiatry and Systems Biology. OMICS: A Journal of Integrative Biology. 25, 693-710.
• Subba, P. and Prasad, T. S. K. (2021).Protein Crotonylation Expert Review: A New Lens to Take Post-Translational Modifications and Cell Biology to New Heights OMICS: A Journal of Integrative Biology. 25, 617-625. [PubMed]
• Gupta, M. D., Kumaresan, A., Saraf, K., Paul, N., Kumar, S., Karthikkeyan, G., Prasad, T. S. K., Modi, P. K., Ramesha, K. P., Manimaran, A. and Jeyakumar, S. (2021). Deciphering metabolomic alterations in seminal plasma of crossbred (Bos taurus X Bos indicus) bulls through comparative deep metabolomic analysis. Andrologia. In press.
• Najar, M. A., Aravind, A., Dagamajalu, S., Sidransky, D., Ashktorab, H., Smoot, D. T., Gowda, H., Prasad, T. S. K., Modi, P. K. and Chatterjee, A. (2021). Hyperactivation of MEK/ERK pathway by Ca 2+ /calmodulin-dependent protein kinase kinase 2 promotes cellular proliferation by activating cyclin-dependent kinases and minichromosome maintenance protein in gastric cancer cells. Molecular Carcinogenesis. [PubMed]
• Kalal, B. S., Modi, P. K., Upadhya, D., Saha, P., Prasad, T. S. K. and Pai, V. R. (2021). Inhibition of Bone morphogenetic proteins signaling suppresses metastasis melanoma: A proteomics approach. American Journal of Translational Research. 13, 11081-11093. [PubMed]
• Antil, N., Kumar, M., Behera, S. K., Arefian, M., Kotimoole, C. N., Rex, D. A. B. and Prasad, T. S. K. (2021). Unraveling Toxoplasma gondii GT strain virulence and new protein-coding genes with proteogenomic analyses. OMICS: A Journal of Integrative Biology. 25, 591-604.
• Jain, A. P., Radhakrishnan, A., Pinto, S., Patel, K., Kumar, M., Nanjappa, V., Raja, R., Prasad, T. S. K., Mathur, P. P., Sidransky, D., Chatterjee, A. and Gowda, H. (2021). How to Achieve Therapeutic Response in Erlotinib Resistant Head and Neck Squamous Cell Carcinoma? New Insights from SILAC-based Quantitative Tyrosine Phosphoproteomics. OMICS: A Journal of Integrative Biology. In press.
• Sarma, A., Dhandapani, G., Rex, D. A. B., Thoduvayil, S., Phukan, H., Kumar, M., Pinto, S. M., Prasad, T. S. K. and Madanan, M. G. (2021). Extracellular proteome analysis shows the abundance of Histidine kinase sensor protein (LIC_11528), DNA helicase (LIC_11624), Putative lipoprotein (LIC_10713) and Peptidase C39 domain protein (LIC_10511) in Leptospira interrogans grown in EMJH medium. Pathogens 10, 852. [PubMed]
• Rex, D. A. B., Dagamajalu, S., Raju, R., Kandasamy, R. K. and Prasad, T. S. K. (2021). SARS-CoV-2 signaling pathway map: A functional landscape of molecular mechanism in COVID-19. Journal of Cell Communication and Signaling. 15, 601-608.
• Deolankar S. C., Patil, A. H., Rex, D. A. B., Subba, P., Mahadevan, A. and Prasad, T. S. K. (2021). Mapping Post-Translational Modifications in Brain Regions in Alzheimer’s Disease Using Proteomics Data Mining. OMICS: A Journal of Integrative Biology. 25, 525-536.
• Rex, D. A. B., Kumar, S. T. A., Modi, P. K. and Prasad, T. S. K. (2021). Broadening COVID-19 Interventions to Drug Innovation: Neprilysin Pathway as a Friend, Foe or Promising Molecular Target? OMICS: A Journal of Integrative Biology. 25, 408-416.
• Rex, D. A. B., Kumar, S. T. A., Rai, B. A., Kotimoole, C. N., Modi, P. K. and Prasad, T. S. K. (2021). Novel Post-translational Modifications and Molecular Substrates in Glioma Identified by Bioinformatics. OMICS: A Journal of Integrative Biology. 25, 463-473
• Gopalakrishnan, L., Chatterjee, O., Raj, C., Pullimamidi, D., Advani, J., Mahadevan, A. and Prasad, T. S. K. (2021). An assembly of galanin–galanin receptor signaling network. Journal of Cell Communication and Signaling. 15, 269–275 [PubMed]
• Najar, M. A., Rex, D. A. B., Modi, P. K., Agarwal, N., Dagamajalu, S., Karthikkeyan, G., Vijayakumar, M., Chatterjee, A., Sankar, A. and Prasad, T. S. K. (2021). A complete map of the Calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) signaling pathway. Journal of Cell Communication and Signaling. 15, 283–290. [PubMed]
• Dagamajalu, S., Rex, D. A. B., Gopalakrishnan, L., Karthikkeyan, G., Gurtoo. S., Modi, P. K., Mohanty, V., Rahiman, M., Soman, S., Raju, R., Tiwari, V. and Prasad, T. S. K. (2021). A network map of endothelin mediated signaling pathway. Journal of Cell Communication and Signaling. 15, 277-282. [PubMed]
• Dagamajalu, S., Rex, D. A. B., Palollathil, A., Shetty, R., Bhat, G., Cheung, L.W.T. and Prasad, T. S. K. (2021). A pathway map of AXL receptor-mediated signaling network. Journal of Cell Communication and Signaling. 15, 143-148 [PubMed]
• Patavardhan, S. S., Awasthi, K., Suresh, S., Subba, P., Najar, M. A., D'Souza, L., Nivas, S. K. and Prasad, T. S. K. (2021). Proteome dataset of chili pepper plant (Capsicum frutescens) infested by broad mite (Polyphagotarsonemus latus). Data in Brief.36, 107095. [PubMed]
• Palollathil, A., Aravind, A., Vijayakumar, M., Kotimoole, C. N., Mohanty, V., Behera, S. K., Kashyap, V., Mallikarjunaiah, K. K. K., Shetty, R., Codi, J. A. K., Raju, R. and Prasad, T. S. K. (2021). OMICs data mining for MultiPTMs in oral cancer: cellular proteome and secretome of chronic tobacco treated oral keratinocytes. OMICS: A Journal of Integrative Biology.25, 450-462. [PubMed]
• Arefian, M., Bhagya, N. and Prasad, T. S. K. (2021). Phosphorylation‐mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops. Biological Reviews. 96, 2164-2191.
• Behera, S. K., Kasaragod, S., Karthikkeyan, G., Kotimoole, C. N., Raju, R., Prasad, T. S. K., and Subbannayya, Y. (2021). MS2Compound: A user friendly compound identification tool for LC-MS/MS based metabolomics data. OMICS: A Journal of Integrative Biology. In press.
• Mohanty, V., Subbannayya, Y., Patil, S., Abdulla, R., Ganesh, M. S., Pal, A., Ray, J. G., Sidransky, D., Gowda, H., Prasad, T. S. K.* and Chatterjee, A.* (2021). Molecular alterations in oral cancer between tobacco chewers and smokers using serum proteomics. Cancer Biomarkers. In press. (* Corresponding author)
• Shaikh, S. B., Najar. M. A., Prasad, T. S. K. and Bhandary, Y. P. (2021). Comparative Protein Profiling Reveals inhibitory role of curcumin on IL-17A mediated Minichromosome Maintenance (MCM) Proteins as novel putative markers for acute lung injury in vivo. Biomedicine & Pharmacotherapy. In press.
• Najar. M. A., Modi. P. K., Ramesh. P., Sidransky. D., Gowda. H., Prasad, T. S. K., and Chatterjee, A. (2021). Molecular profiling associated with Calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) mediated carcinogenesis in gastric cancer. Journal of Proteome Research. 7, 2687-2703. [PubMed]
• Shaikh, S., Najar, M. A., Prabhu, A., Rex, D. A. B., Chanderasekaran, J., Behera, S., Modi, P., Prasad, T. S. K. and Bhandary, Y. (2021). The unique molecular targets associated anti-oxidant and anti-fibrotic activity of curcumin in in vitro model of acute lung injury: A proteomic approach. BioFactors. In press.
• Karthikkeyan, G., Pervaje, R., Pervaje, S. K., Prasad, T. S. K. , and Modi, P.K. (2021). Prevention of MEK-ERK-1/2 hyper-activation underlines the neuroprotective effect of Glycyrrhiza glabra L. (Yashtimadhu) against rotenone-induced cellular and molecular aberrations. Journal of Ethnopharmacology. In Press
• Sivagurunathan, S., Selvan, L. D. N., Khan, A. A., Parameswaran, S., Bhattacharjee, H., Gogoi, K., Gowda, H., Prasad, T. S. K. , Pandey, A., Kumar, S. A., Rishi, P., Rishi, E., Ratra, D., Bhende, M., Janakiraman, N., Biswas, J., and Krishnakumar, S. (2021). Proteomics-based approach for differentiation of age-related macular degeneration sub-types. Indian Journal of Ophthalmology. 69, 647-654. [PubMed]
• Santhoshkumar, R., Preethish-Kumar, V., Mangalaparthi, K. K., Unni, S., Padmanabhan, B., Prasad, T. S. K. , Nongthomba, U., Atchayaram, N. and Narayanappa, G. (2021). A Dominant C150Y Mutation in FHL1 Induces Structural Alterations in LIM2 Domain Causing Protein Aggregation In Human and Drosophila Indirect Flight Muscles. Journal of Molecular Neuroscience. 10.1007/s12031-020-01777-4. [PubMed]
• DasGupta, M., Kumaresan, A., Saraf, K. K., Karthikkeyan, G., Prasad, T. S. K. , Modi, P. K., Ramesha, K., Jeyakumar, S. and Manimaran, A. (2021). Preliminary comparative deep-metabolomic analysis of spermatozoa from zebu and crossbred cattle suggests associations between metabolites, sperm quality and fertility. Reproduction, Fertility and Development. In Press

• Mohanty, V., Subbannayya, Y., Patil, S. S., Puttamallesh, V. N., Najar, M. A., Datta, K. K., Pinto S. M., Begum, S., Mohanty, N., Routray, S., Abdulla, R., Ray, J. G., Sidransky, D., Gowda, H., Prasad, T. S. K. and Chatterjee, A. (2021). Molecular alterations in oral cancer using high-throughput proteomic analysis of formalin-fixed paraffin-embedded tissue. Journal of Cell Communication and Signaling. In Press.
• Ashokan, M., Ramesha, K. P., Hallur, S., Karthikkeyan, G., Rana, E., Azharuddin, N., Raj, S. R., Jeyakumar, S., Kumaresan, A., Mukund, A., Kataktalware, M. A., Das, D. N. and Prasad, T. S. K. (2021). Differences in milk metabolites in Malad Gidda (Bos indicus) cows reared under pasture-based feeding system. Scientific Reports. 11, 2831 [PubMed]
• Bansal, P., Antil, N., Kumar, M., Botte, Y. Y., Rawat, R. S., Pinto, S., Datta, K., Katris, N., Botte, C., Prasad, T. S. K. and Sharma, P., (2021). Protein kinase TgCDPK7 regulates vesicular trafficking and phospholipid synthesis in Toxoplasma gondii. PLOS Pathogens. In press
• Jain, A., Kotimoole, C. N., Ghoshal, S., Bakshi, J., Chatterjee, A., Prasad, T. S. K. and Pal, A. (2021). Identification of a potential salivary biomarker panel for Oral Squamous Cell Carcinoma. Scientific Reports. 11, 3365 [PubMed]
• Subbannayya, Y., Haug, M., Pinto, S. M., Mohanty, V., Meas, H. Z., Flo, T. H., Prasad, T. S. K. and Kandasamy, R. K. (2021). The proteomic landscape of resting and activated CD4+ T cells reveal insights into cell differentiation and function. International Journal of Molecular Sciences. 22, 275 [PubMed]

 

2020 (Number of publications - 23)

• Subbannayya, Y., Haug, M., Pinto, S. M., Mohanty, V., Meas, H. Z., Prasad, T. S. K., Flo, T. H. and Kandasamy, R. K. (2020). The proteomic landscape of resting and activated CD4+ T cells reveal insights into cell differentiation and function. 10.1101/2020.11.17.385096. [bioRxiv]
• Shaikh, S., Bhandary, Y. P., Najar, M. A., Prabhu, A., Prasad, T. S. K., Gouda, M. M., Irfan, K., Modi, P, K. (2020). In depth mass spectrometry based proteomic approach to explore the effect of curcumin in IL17A mediated alveolar barrier injury. European Respiratory Society. 10.1183/13993003.congress-2020.3383. [PubMed]
• Patavardhan, S. S., Subba, P., Najar, A., Awasthi, K., D'Souza, L., Prasad, T. S. K. and Nivas, S. K., Plant–Pathogen Interactions: Broad Mite (Polyphagotarsonemus latus)-Induced Proteomic Changes in Chili Pepper Plant (Capsicum frutescens). OMICS: A Journal of Integrative Biology. 10.1089/omi.2020.0080. [PubMed]
• Jain, A., Kotimoole, C. N., Ghoshal, S., Bakshi, J., Chatterjee, A., Prasad, T. S. K. and Pal, A. (2020). Development of a potential salivary biomarker panel for Oral Squamous Cell Carcinoma. 10.1101/2020.02.27.968016. [medRxiv]
• Rajesh, M. K., Gangaraj, K. P., Prabhudas, S. K., Prasad, T. S. K.^* (2020). The complete chloroplast genome data of Areca catechu (Arecaceae). Data in Brief. 10.1016/j.dib.2020.106444. [PubMed] (*Corresponding author)
• Dagamajalu, S., Vijayakumar, M., Shetty, R., Rex, D. A. B., Narayana Kotimoole, C., Prasad, T. S. K.^* (2020). Proteogenomic examination of esophageal squamous cell carcinoma (ESCC): new lines of inquiry. Expert Review of Proteomics. 10.1080/14789450.2020.1845146. [PubMed] (* Corresponding author)
• Rajesh, M. K., Chowdappa, P., Behera S. K., Kasaragod, S., Gangaraj, K. P., Kotimoole, C. N., Nekrakalaya, B., Mohanty, V., Sampgod, R. B., Banerjee, G. B., Das, A. J. Niral, V., Karun, A., Gaikwad, K., Singh, N. K. and Prasad, T. S. K.^*, (2020). Assembly and annotation of the nuclear and organellar genomes of a dwarf coconut (Chowghat Green Dwarf) possessing enhanced disease resistance. OMICS: A Journal of Integrative Biology. 10.1089/omi.2020.0147. [PubMed] (* Corresponding author)
• Karthikkeyan, G., Pervaje, R., Subbannayya, Y., Patil, A. H., Modi, P. K. and Prasad, T. S. K.^* (2020). Plant Omics: Metabolomics and Network Pharmacology of Liquorice, Indian Ayurvedic medicine Yashtimadhu. OMICS: A Journal of Integrative Biology. In Press. (* Corresponding author)
• Karthikkeyan, G., Najar, M. A.,Pervaje, R., Pervaje, S. K., Modi, P. K. and Prasad, T. S. K.^* (2020). Identification of Molecular Network Associated with Neuro protective Effects of Yashtimadhu (Glycyrrhiza glabra L.) by Quantitative Proteomics of Rotenone-Induced Parkinson’s Disease Model. ACS Omega. 10.1021/acsomega.0c03420. [PubMed] (* Corresponding author)
• Yadav, R., Parihar, R. D., Dhiman, U., Dhamija, P., Upadhyay, S.K., Imran, M., Behera, S. K., Prasad, T. S. K. (2020). Docking of FDA Approved Drugs Targeting NSP-16, N-Protein and Main Protease of SARS-CoV-2 as Dual Inhibitors. Biointerface Research in Applied Chemistry. 11, 9848 -9861. [PubMed]
• Thoduvayil, S., Dhandapani, G., Brahma, R., Rex, D. A. B., Mangalaparthi, K. K., Patel, K., Kumar, M., Tennyson, J., Satheeshkumar, P. K., Kulkarni, A., Pinto, S. M., Prasad, T. S. K.^*and Madanan, M. G. (2020). Triton X-114 fractionated subcellular proteome of Leptospira interrogans shows selective enrichment of pathogenic and outer membrane proteins in the detergent fraction. Proteomics. 19-20:e2000170. [PubMed] (* Corresponding author)
• Mangalaparthi, K. K., Patel, K., Khan, A., Manoharan, M., Karunakaran, C., Murugan, S., Gupta, R., Gupta, R., Gupta, A. K., Chaudhuri, A., Kumar, P., Nair, B., Kumar, R. V., Prasad, T. S. K., Chatterjee, A., Pandey, A. and Gowda, H. (2020). Mutational landscape of esophageal squamous cell carcinoma in an Indian cohort. Frontiers in Oncology. 10.3389/fonc.2020.01457. [PubMed]
• Kasaragod, S., Mohanty, V., Tyagi, A., Behera, S. K., Patil, A. H., Pinto, S. M., Prasad, T. S. K., Modi, P. K. and Gowda, H. (2020). CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets. F1000Research. 9, 344. [PubMed]
• Singla, N., Ghosh, S., Rawat, A., Dhandapani, S., Salunke, P., Chhabra, Rajesh., Singh, D., Takkar, A., Gupta, S. K., Prasad, T. S. K., Gowda H., Mukherjee, K. K., Pandey, A. and Bhagat, H. (2020). Intracranial Aneurysm Biomarker Candidates Identified by a Proteome-Wide Study. OMICS: A Journal of Integrative Biology. 8, 483-492. [PubMed]
• Saraf, K. K., Kumaresan, A., Gupta, M. D., Karthikkeyan, G., Prasad, T. S. K., Modi, P. K., Ramesha, K., Jeyakumar, S. and Manimaran, A. (2020). Metabolomics Fingerprinting of Bull Spermatozoa for Identification of Fertility Signature Metabolites. Molecular Reproduction and Development. 6, 692-703. [PubMed]
• Deolankar, S. C., Modi, P. K., Subbannayya, Y., Pervaje, R. and Prasad, T. S. K.^* (2020). Molecular targets from traditional medicine for neuroprotection in human neurodegenerative diseases.OMICS: A Journal of Integrative Biology. 7, 394-403. [PubMed] (* Corresponding author)
• Mohanty, V., Pinto, S. M., Subbannayya, Y., Najar, M. A., Murthy, K. B., Prasad, T. S. K.^*, and Murthy, K. R. (2020). Digging deeper for the eye proteome in vitreous substructures: A high-resolution proteome map of the normal human vitreous base. OMICS: A Journal of Integrative Biology. 6, 379-389. [PubMed] (* Corresponding author)
• Rajesha, M. K., Muralikrishnaa, K. S., Nair, S. S., Kumar, B. K., Subrahmanya, T. M., Sonu, K. P., Subaharan, K., Sweta, H., Prasad, T. S. K., Neeli, C., Karunasagar, I., Hebbara, K. B., Karun, Anitha. (2020). Facile coconut inflorescence sap mediated synthesis of silver nanoparticles and its diverse antimicrobial and cytotoxic properties. Materials Science and Engineering: C. 111:110834. [PubMed]
• Pati, S., Yadav, P., Kumari, G., Rex, D.A.B., Goswami, S., Garg, S., Prasad, T. S. K. and Ramalingam, S. (2020). Role of RBC membrane protein palmitoylation in regulation of molecular topology and susceptibility to Plasmodium falciparum invasion. bioRxiv.
• Gowda, M., Narendran, P., Begum, N., Bhatt, A., Kukkupuni, S. K., Venkatasubramanian, P., Prasad, T. S. K., Najar, M. A., & Arunkumar, K. P. (2020). Integrated omics approach to understand Pistacia-aphid gall development. (2020). Preprint.
• Sunitha, B., Kumar, M., Gowthami, N., Unni, S., Gayathri, N., Prasad, T. S. K., Nalini, A., Polavarapu, K., Vengalil, S., Preethish-Kumar, V. and Padmanabhan, B. (2020). Human muscle pathology is associated with altered phosphoprotein profile of mitochondrial proteins in the skeletal muscle. Journal of proteomics. 16;211:103556. [PubMed]
• Subbannayya, Y., Pinto, S. M., Mohanty, V., Dagamajalu, S., Prasad, T. S. K.^*, and Murthy, K. R. (2020). What makes cornea immunologically unique and privileged? Mechanistic clues from a high-resolution proteomic landscape of the human cornea. OMICS: A Journal of Integrative Biology. 3, 129-139. [PubMed] (* Corresponding author)
• Rex, D. A. B., Agarwal, N., Prasad, T. S. K., Kandasamy, R. K., Subbannayya, Y. and Pinto, S. M. (2019). A comprehensive pathway map of IL-18-mediated signalling. Journal of Cell Communication and Signaling. 1, 121-127. [PubMed]

2019 (Number of publications - 19)

• Jain, A., Patel, K., Pinto, S. M., Radhakrishnan, A., Nanjappa, V., Kumar, M., Raja, R., Patil, A. H., Kumari, A., Manoharan, M., Karunakaran, C., Murugan, S., Prasad, T. S. K., Chang, X., Mathur, P., Kumar, P., Gupta, R., Gupta, R., Khanna-Gupta, A., Sidransky, D., Chatterjee, A. and Gowda, H. (2019). MAP2K1 is a potential therapeutic target in erlotinib-resistant head and neck squamous cell carcinoma. Scientific Reports. [PubMed]
• Datta, K.K., Patil, S., Patel, K., Babu, N., Raja, R., Nanjappa, V., Mangalaparthi, K. K., Dhaka, B., Rajagopalan, P., Deolankar, S. C., Kannan, R., Kumar, P., Prasad, T. S. K., Mathur, P. P., Kumari, A., Manoharan, M., Karunakaran, C., Murugan, S., Sidransky, D., Gupta, R., Gupta, R., Khanna-Gupta, A., Chatterjee, A., Gowda, H. (2019). Chronic exposure to chewing tobacco induces metabolic reprogramming and cancer stem cell-like properties in esophageal epithelial cells. Cells. 9, E949. [PubMed]
• Deolankar, S. C., Patil, A. H., Koyangana, S. G., Subbannayya, Y., Prasad, T. S. K.^* and Modi, P. K. (2019). Dissecting Alzheimer’s disease molecular substrates by proteomics and discovery of novel post-translational modifications (PTMs). OMICS: A Journal of Integrative Biology. 23, 350-361. [PubMed]
• Subbannayya, Y., Pinto, S. M., Bösl, K., Prasad, T. S. K. and Kandasamy, R. K. (2019). Dynamics of dual specificity phosphatases and their interplay with protein kinases in immune signaling. International Journal of Molecular Sciences. 27, 20. [PubMed]
• Agrawal, A., Ravikumar, R., Varun, C. N., Kumar, M., Chatterjee, O., Advani, J., Gopalakrishnan, L., Nagaraj, S, Mohanty, V., Patil, A. H., Sreeramulu, B., Malik, A., Pinto, S. M. and Prasad, T. S. K.^* (2019). Global proteome profiling reveals drug-resistant traits in Elizabethkingia meningoseptica: an opportunistic nosocomial pathogen. OMICS: A Journal of Integrative Biology. 23, 318-326. [PubMed] (* Corresponding author)
• Mohanty, A. K., Dey, G., Kumar, M., Sreenivasamurthy, S. K., Garg, S., Prasad, T. S. K.^* and Kumar, A.* (2019). Proteome data of female Anopheles stephensi antennae. Data in Brief. 8, 24. [PubMed] (*Corresponding author)
• 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. 14, e0214742. [PubMed]
• Sinha, S., Ray, A., Abhilash, L., Kumar, M., Sreenivasamurthy, S. K., Prasad, T. S. K. and Inamdar, M. S. (2019). Proteomics of Asrij perturbation in Drosophila lymph glands for identification of new regulators of hematopoiesis. Molecular & Cellular Proteomics. 8, 1171-1182. [PubMed]
• Subba, P., Kemmai, C. N. and Prasad, T. S. K.^* (2019). Plant proteome databases and bioinformatic tools: An expert review and comparative insights. OMICS A Journal of Integrative Biology. 23, 190-206. [PubMed] (*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. 10, 309. [PubMed] (*Corresponding author)
• Menon, D., Singh, K., Pinto, S. M., Nandy, A., Jaisinghani, N., Kutum, R., Dash, D., Prasad, T. S. K. and Gandotra, S. (2019). Quantitative lipid droplet proteomics reveals Mycobacterium tuberculosis induced alterations in macrophage response to infection. ACS Infectious Diseases. 5, 559-569. [PubMed]
• Pinto, S. M., Subbannayya, Y. and Prasad, T. S. K. (2019). “Functional Proteomic Analysis to Characterize Signaling Crosstalk” In: Functional Proteomics: Methods and Protocols. X. Wang and M. Kuruc Editors. New York, NY, Springer New York: 197-224. [PubMed]
• 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. and Chatterjee, A. (2019). PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich Akt substrate of 40 kDa (PRAS40). 13, 163-177. Journal of Cell Communication and Signaling. [PubMed]
• 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.^* (2019). 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] (* Corresponding author)
• Kumar, M., Mohanty, A. K., Dey, G., Sreenivasamurthy, S. K., Kumar, A. and Prasad, T. S. K. (2019). Dataset on fat body proteome of Anopheles stepensi Liston. Data in Brief. 22,1068-1073. [PubMed]
• Barua, P., Lande N. V, Subba, P., Gayen, D., Pinto, S., Prasad, T. S. K., Chakraborty, S., Chakraborty, N. (2019). Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response. Plant, Cell & Environment. 42, 230-244. [PubMed]
• Gowthami, N. B., Sunitha, B., Kumar, M., Prasad, T. S. K., Gayathri, N., Padmanabhan, B. and Bharath, M. M. S. (2019) Mapping the protein phosphorylation sites in human mitochondrial complex I (NADH: ubiquinone oxidoreductase): A bioinformatics study with implications for brain aging and neurodegeneration. Journal of Chemical Neuroanatomy. 95, 13-28. [PubMed]
• Mohanty, V., Subbannayya, Y., Najar, M. A., Pinto, S. M., Kasaragod, S., Karuppiah, H., Sreeramulu, B., Singh, K. K., Dalal, S., Manikkoth, S., Arunachalam, C., Prasad, T. S. K.^* and Murthy, K. R. (2018). Proteomics and visual health research: Proteome of the human sclera using high-resolution mass spectrometry. OMICS: A Journal of Integrative Biology. 23, 98-110. [PubMed] (*Corresponding Author)
• Bhat, S. A., Gurtoo. S., Deolankar, S. C., Fazili, K. M., Advani, J., Shetty, R., Prasad, T. S. K., Andrabi, S., Subbannayya, Y. (2019). A network map of netrin receptor UNC5B-mediated signaling. Journal of Cell Communication and Signaling. 13, 121-127. [PubMed]

 

2018 (Number of publications - 31)

• 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. [PubMed]
• 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., Anita 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] (*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. and Prasad, T. S. K.^* (2018). Data on whole genome sequencing of extrapulmonary tuberculosis clinical isolates from India. Data in Brief. 20, 617-622. [PubMed] (*Corresponding Author)
• Sreenivasamurthy, S. K., Dey, G., Kumar, M., Mohanty, A. K., Kumar, A.*, and Prasad, T. S. K.^* (2018). Quantitative proteome of midgut, Malpighian tubules, ovaries and fat body from sugar-fed adult An. stephensi mosquitoes. Data in Brief. 20, 1861-1866. [PubMed] (*Corresponding Author)
• Dey, G., Mohanty, A. K., Kumar, M., Sreenivasamurthy, S. K., Patil, A. H., Prasad, T. S. K.^* and Kumar, A.* (2018). Proteome data of Anopheles stephensi ovary using high-resolution mass spectrometry. Data in Brief. 20, 723-731. [PubMed]. (*Corresponding Author)
• Karthikkeyan, G., Subbannayya, Y., Najar, M. A., Mohanty, V., Pinto, S. M., Arunachalam, C., Prasad, T. S. K.^* and Murthy, K. R. (2018). Human optic nerve - an enhanced proteomic expression profile. OMICS: A Journal of Integrative Biology. 22, 642-652. [PubMed] (*Corresponding author)
• Sahu, A., Gopalakrishnan, L., Gaur, N., Chatterjee, O., Mol, P., Modi, P. K., Dagamajalu, S., Advani, J., Jain, S. and Prasad, T. S. K.^* (2018). The 5-Hydroxytryptamine signaling map: an overview of the serotonin-serotonin receptor-mediated signaling network. Journal of Cell Communication and Signaling. [PubMed] (*Corresponding author)
• 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] (*Corresponding author)
• 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. [PubMed] (*Corresponding author)
• Subbannayya, Y., Karthikkeyan, G., Pinto, S. M., Kapoor, S., Tyagi, A., Pervaje, S. K., Pervaje, R. and Prasad, T. S. K.^* (2018). Global metabolite profiling and network pharmacology of Triphala identifies neuromodulatory receptor proteins as potential targets. Journal of Proteins and Proteomics. [PubMed] (*Corresponding author)
• Subba, P.*, Pinto, S. M., Kasaragod, S., Chatterjee, O., Najar, A. M. and Prasad, T. S. K.^* (2018). Nuclear proteome of an orphan legume - Cajanus cajan L. Journal of Proteins and Proteomics. [PubMed] (*Corresponding author)
• 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. [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. [PubMed]
• Pinto, S. M., Verma, R, Advani, J., Chatterjee, O., Patil, A. H., Kapoor, S., Subbannayya, Y., Raja, R., Gandotra, S. and Prasad, T. S. K.^* (2018). Integrated multi-omic analysis of Mycobacterium tuberculosis H37Ra redefines virulence attributes. Frontiers in Microbiology. [PubMed] (*Corresponding author)
• 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. [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. Proteomics - Clinical Applications. [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. [PubMed]

• Dey, G., Mohanty, A. K., Kumar, M., Sreenivasamurthy S. K., Kumar, A. and Prasad, T. S. K.^* (2018). Proteome data of Anopheles stephensi hemolymph using high resolution mass spectrometry. Data in Brief. 18, 1441-1447. [PubMed] (*Corresponding author)

• 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]

• Pinto, S. M., Subbannayya, Y., Rex, D. A. B., Raju, R., Chatterjee, O., Advani, J., Radhakrishnan, A., Prasad, T. S. K., Wani, M. R. and Pandey, A. (2018). A network map of IL-33 signaling pathway. Journal of Cell Communication and Signaling. [PubMed]
• 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. 8, 7040. [PubMed]
• Mohanty, A. K., Dey, G., Kumar, M., Sreenivasamurthy S. K., Garg, S., Prasad, T. S. K.^* and Kumar, A. (2018). Mapping Anopheles stephensi midgut proteome using high-resolution mass spectrometry. Data in Brief. 17, 1295-1303. [PubMed] (*Corresponding author)
• Bannerjee, D., Kumar, M., Prasad, T. S. K., Natarajan, A., Christopher, R., Bindu, P. S., Gayathri, N., Nalini, A., and Bharath, M. M. S. (2018). Mitochondrial dysfunction in human skeletal muscle biopsies of lipid storage disorder. Journal of Neurochemistry. 145, 323-341. [PubMed]
• Kumar, M., Varun, C. N., Dey, G., Ravikumar, R., Mahadevan, A., Shankar, S. K. and Prasad, T. S. K.^* (2018). Identification of host-response in cerebral malaria patients using quantitative proteomic analysis. Proteomics - Clinical Applications. [PubMed] (*Corresponding author)
• Mahesh, H. B., Subba, P., Advani, J., Shirke, M. D., Loganathan, R. M., Chandana, S., Shilpa, S., Chatterjee, O., Pinto, S. M., Prasad, T. S. K.^* and Gowda, M. (2018). Multi-omics driven assembly and annotation of the sandalwood (Santalum album) genome. Plant Physiology. 176, 2772-2788. [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]
• Dammalli, M., Dey, G., Kumar, M., Madugundu, A. K., Gopalakrishnan, L., Byachapur, G. S., Mahadevan, A., Shankar S. K., Prasad, T. S. K.^* (2018). Proteomics of the human olfactory tract. OMICS: A Journal of Integrative Biology. 22, 77-78. [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]
• Mol, P., Kannegundla, U., Dey, G., Gopalakrishnan, L., Dammalli, M., Kumar, M., Patil, A., Basavaraju, M., Rao, A., Ramesha, K. P. and Prasad, T. S. K.^* (2018). Bovine Milk Comparative Proteome Analysis from Early, Mid and Late Lactation in the Cattle Breed, Malnad Gidda (​​Bos indicus​). OMICS: A Journal of Integrative Biology​. 22, 223-235. ​[PubMed] (*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. 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]
• 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]

2017 (Number of publications - 20)

• 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. OMICS: A Journal of Integrative Biology. 11, 11-12. [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., Chatterjee, A. Investigation of curcumin mediated signaling pathways in head and neck squamous cell carcinoma. Translational Research in Oral Oncology. [PubMed]
• 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. S1567-7249, 30221-0. [PubMed]
• Solanki, H. S., Advani, J., Kumar, M., Kumar, P., Bhagat, H., Prasad, T. S. K., Sidransky, D., Gowda, H., Chatterjee, A. (2017). miRNA profiling of bladder cells chronically exposed to cigarette smoke condensate and its vapor. Research Reports. [PubMed]
• Kumar, M., Mohanty, A. K., Sreenivasamurthy, S. K., Dey, G., Advani, J., Pinto, S. M., Kumar, A.* and Prasad, T. S. K.^* (2017). Response to blood meal in the fat body of Anopheles stephensi using quantitative proteomics: Towards new vector control strategies against malaria. OMICS: A Journal of Integrative Biology. 21, 520-530. [PubMed] (*Corresponding author)
• Dammalli, M., Dey, G., Madugundu, A. K., Kumar, M., Rodrigues, B., Gowda, H., Byachapur, G. S., Mahadevan, A., Shankar S. K., Prasad, T. S. K.^* (2017). Proteomic analysis of the human olfactory bulb. OMICS: A Journal of Integrative Biology. 21, 440-453. [PubMed] (*Corresponding author)
• 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]
• Lande, N. V., Subba, P., Barua, P., Gayen, D., Prasad, T. S. K., Chakraborty, S. and Chakraborty, N. (2017). Dissecting the chloroplast proteome of chickpea (Cicer arietinum L.) provides new insights into classical and non-classical functions. Journal of Proteomics. 8, 11-20. [PubMed]
• Sreenivasamurthy, S. K., Madugundu, A. K., Patil, A. H., Dey, G., Mohanty, A. K., Kumar, M., Patel, K., Wang, C., Kumar, A., Pandey, A. and Prasad, T. S. K.^* (2017). Mosquito-borne diseases and Omics: Tissue-restricted expression and alternative splicing revealed by transcriptome profiling of Anopheles stephensi. OMICS: A Journal of Integrative Biology. 21, 488-497. [PubMed] (*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. 7, 413-425. [PubMed] (*Corresponding author)
• Dhawan, R., Mohanty, A. K., Kumar, M., Dey, G., Advani, J., Prasad, T. S. K.^* and Kumar, A*. (2017). Data from salivary gland proteome analysis of female Aedes aegypti Linn. Data in Brief. 13, 274–277. [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., 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. 7, 390-403. [PubMed] (# These authors contributed equally to the manuscript)
• 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. 3, 63. [PubMed]
• 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., Peterson, 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]
• 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*. (2017). Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes. Genome Research. 1, 133-144. [PubMed] (*Corresponding author)
• 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] (*Corresponding author)
• 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] (*Corresponding author)
• Nirujogi, R. S., Muthusamy, B., Kim, M. S., Sathe, G. J., Lakshmi, P. T. V., Kovbasnjuk, O. N., Prasad, T. S. K., Wade, M. and Jabbour, R. E. (2017). Secretome analysis of diarrhea-inducing strains of Eschreichia coli. Proteomics. [PubMed]
• Dhawan, R., Kumar, M., Mohanty, A. K., Dey, G., Advani, J., Prasad, T. S. K.^* and Kumar, A^*. (2017). Mosquito-borne diseases and Omics: salivary gland proteome of the female Aedes aegypti mosquito. OMICS: A Journal of Integrative Biology. 21, 45-54. [PubMed](*Corresponding author)

2016 (Number of publications - 20)

• 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]
• 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]
• 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. 26, 13-29. [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] (*Corresponding author)
• Chatterjee, O., Patil, K., Sahu, A., Gopalakrishnan, L., Mol, P., Advani, J., Mukherjee, S., Christopher, R. and Prasad, T. S. K.^* (2016). An overview of the Oxytocin-Oxytocin receptor signaling network. Journal of Cell Communication and Signalling. 10, 355-360. [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. 7, 61229-61245. [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., 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. 9, 510-9. [PubMed] (*Corresponding author)
• Bhattacharjee, M., Balakrishnan, L., Renuse, S., Advani, J., Goel, R., Sathe, G., Prasad, T. S. K., Nair, B., Jois, R., Shankar, S., Pandey, A. (2016). Synovial fluid proteome in rheumatoid arthritis. Clinical Proteomics. 13, 12. [PubMed]
• Mehta, S., Sreenivasamurthy, S., Banerjee, S., Mukherjee, S., Prasad, T. S. K., and Chowdhary, A. (2016). Pathway Analysis of Proteomics Profiles in Rabies Infection: Towards Future Biomarkers? OMICS: A Journal of Integrative Biology. 20, 97-109. [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]
• 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]
• Anand, A., Sharma, K., Sharma, S. K., Singh, R., Sharma, N. K. and Prasad, T. S. K. (2016). AMD genetics in India: The missing links. Frontiers in Aging Neuroscience. 8, 115. [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] (*Corresponding author)
• Barua, P., Subba, P., Lande, N.V., Mangalaparthi, K.K., Prasad, T. S. K., Chakraborty, S., Chakraborty, N. (2016). Gel based and gel-free search for plasma membrane proteins in chickpea (Cicer arietinum L.) augments the comprehensive data sets of membrane protein repertoire. Journal of Proteomics.143, 199-208. [PubMed]
• Sunitha, B., Gayathri, N., Kumar, M., Prasad, T. S. K., Nalini, A., Padmanabhan, B., and Bharath, M. M. S. (2016). Muscle biopsies from human neuromuscular diseases with myopathic pathology reveal common alterations in mitochondrial function. Journal of Neurochemistry. 138, 174-191. [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] (*Corresponding author)
• Subbannayya, Y., Pinto, S. M., Gowda, H. and Prasad, T. S. K.^* (2016). Proteogenomics for understanding oncology: recent advances and future prospects. Expert Review of Proteomics. 13, 297-308. [PubMed] (*Corresponding author)

• 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]

• 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. (2016). A pathway map of glutamate metabolism. Journal of Cell Communication and Signaling. 10, 69-75. [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] (*Corresponding author) 

2015 (Number of publications - 23)

• 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]

• Raju, R., Gadakh, S., Gopal, P., George, B., Advani, J., Soman, S., Prasad, T. S. K., Reshmi, G. (2015). Differential ligand-signaling network of CCL19/CCL21-CCR7 system. Database. [PubMed] 

• Nanjappa, V., Renuse, S., Sathe, G. J., Raja, R., Syed, N., Radhakrishnan, A., Subbannayya, T., Patil, A., Marimuthu, A., Sahasrabuddhe, N. A., Guerrero-Preston, R., Somani, B. L., Nair, B., Kundu, G. C., Prasad, T. S. K., Califano, J. A., Gowda, H., Sidransky, D., Pandey, A. and Chatterjee, A. (2015). Chronic exposure to chewing tobacco selects for overexpression of stearoyl-CoA desaturase in normal oral keratinocytes. Cancer Biology and Therapy. 16, 1593-1603. [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] 

• 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] (*Corresponding author) 

• 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] 

• 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]  

• Reddy, P. J., Sinha, S., Ray, S., Sathe, G. J., Chatterjee, A., Prasad, T. S. K., Dhali, S., Rapole, S., Panda, D. and Srivastava, S. (2015). Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment. PLOS ONE. 10, e0120620. [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]  

• Reddy, P. J., Atak, A., Ghantasala, S., Kumar, S., Gupta, S., Prasad, T. S. K., Zingde, S. M. and Srivastava, S. (2015). An Update on Proteomic Research in India. Journal of Proteomics. 127, 7-17. [PubMed] 

• Reddy, P. J., Ray, S., Sathe, G. J., Gajbhiye, A., Prasad, T. S. K., Rapole, S., Panda, D. and Srivastava, S. (2015). A comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. Journal of Proteomics. 114, 247-262. [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] 

• Pinto, S. M., Nirujogi, R. S., Leal-Rojas, P., Patil, A. H., Manda, S. S., Subbannayya, Y., Roa, J. C., Chatterjee, A., Prasad, T. S. K. and Pandey, A. (2015). Quantitative phosphoproteomic analysis of IL-33 mediated signaling. Proteomics. 15, 532-544. [PubMed]

• 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. and Chatterjee, A. (2015). Calcium calmodulin dependent kinase kinase 2 - a novel therapeutic target for gastric adenocarcinoma. Cancer Biology and Therapy. 16, 336-345. [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. (2015). 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]

• 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] 

• 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. (2015). Phosphotyrosine profiling identifies ephrin receptor A2 as a potential therapeutic target in esophageal squamous cell carcinoma. Proteomics. 15, 374-382. [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. (2015). Proteomics of Follicular Fluid from Women with Polycystic Ovary Syndrome Suggests Molecular Defects in Follicular Development. Journal of Clinical Endocrinology & Metabolism. 100, 744-753. [PubMed]

• Harish, G., Mahadevan, A., Pruthi, N., Sreenivasamurthy, S. K., Puttamallesh, N. V., Prasad, T. S. K., Shankar S. K. and Bharath M. M. S (2015). Characterization of traumatic brain injury in human brains reveals distinct cellular and molecular changes in contusion and pericontusion. Journal of Neurochemistry. 134, 156-172. [PubMed] 

• Reddy, P. J., Ray, S., Sathe, G. J., Prasad, T. S. K., Rapole, S., Panda, D. and Srivastava, S. (2015). Proteomics analyses of Bacillus subtilis after treatment with Plumbagin, a plant-derived naphthoquinone. OMICS: A Journal of Integrative Biology. 19, 12-23. [PubMed]

  2014 (Number of publications - 20)

• 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]

• 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] (*Corresponding author)

• 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]

• Mohanty, A. K., Prasad, T. S. K., Garg, S. and Kumar, A. (2014). "Proteogenomics of Vector Mosquitoes: Progress and Prospects" In: Major Tropical Diseases: Public Health Perspective. Ashwani Kumar, Savio Rodrigues and Amit Dias Editors. Broadway Publication House. pp 38-50.

• 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. Proteomics. 14, 2769-79. [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] 

• 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] (*Corresponding author)

• 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, 287-295. [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]

• 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]

• 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] 

• 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, 2749-2760. [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]

• 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] 

• 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. 8, 165-170. [PubMed]

• Zhong, J., Sharma, J., Raju, R., Palapetta, S. M., Prasad, T. S. K., Huang, T. C., Yoda, A.,  Tyner, J. W., van Bodegom, D., Weinstock, D. M., Ziegler, S. F. and Pandey, A. (2014). TSLP signaling pathway map: A platform for analysis of TSLP mediated signaling. Database. bau007. [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] 

• 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] 

• 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, 8. [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.^* (2014). Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Research. 42, D959-D965. [PubMed] (*Corresponding author)

  2013 (Number of publications - 13)

• 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] (*Corresponding author)

• 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] (*Corresponding author)

• 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] (*Corresponding author)

• 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]

• Sandhya, V. K., Raju, R., Verma, R., Advani, J., Sharma, R., Radhakrishnan, A., Nanjappa, V., Narayana, J., Somani, B. L., Mukherjee, K. K., Pandey, A., Christopher, R. and Prasad, T. S. K.^* (2013). A network map of BDNF/TRKB and BDNF/p75NTR signaling system. Journal of Cell Communication and Signaling. 4, 301-307. [PubMed] (*Corresponding author)

• 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]

• Subbannayya, T., Balakrishnan, L., Sudarshan, G., Advani, J., Kumar, S., Mahmood, R.,  Nair, B., Sirdeshmukh, R., Mukherjee, K. K., Umathe, S. N., Raju, R. and Prasad, T. S. K.^* (2013). An integrated map of corticotropin-releasing hormone signaling pathway. Journal of Cell Communication and Signaling. 4, 295-300. [PubMed] (*Corresponding author)

• 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]

• Muthusamy, B., Thomas, J. K., Prasad, T. S. K. and Pandey, A. (2013). Access guide to Human Proteinpedia. Current Protocols in Bioinformatics. 41, 1.21.1-1.21.15. [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] (*Corresponding author)

• 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. (2013). A multicellular signal transduction network of AGE/RAGE signaling. Journal of Cell Communication and Signaling. 7, 19-23. [PubMed]

  2012 (Number of publications -11)

• Dey, G., Radhakrishnan, A., Syed, N., Thomas, J. K., Nadig, A., Srikumar, K., Mathur, P. P., Pandey, A., Lin, S. K., Raju, R. and Prasad, T. S. K.^* (2012). Signaling network of Oncostatin M pathway. Journal of Cell Communication and Signaling. 7, 103-108. [PubMed] (*Corresponding author)

• 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. [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]

• 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]

• 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]

• 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]

• 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]
  

• 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]

• 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]

• 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] (*Corresponding author)

• 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, 453-63. [PubMed] (*Corresponding author)

2011 (Number of publications -11)

• 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] (*Corresponding author)

• Telikicherla, D., Ambekar, A., Palapetta, S. M., Dwivedi, S. B., Raju, R., Sharma, J., Prasad, T. S. K., Ramachandra, Y. L., Mohan, S. S., Maharudraiah, J., Mukherjee, S. and Pandey, A. (2011). A comprehensive curated resource for follicle stimulating hormone signaling. BMC Research Notes. 4, 408. [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<. 12, M111.011627. [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]. (*Corresponding author)

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

• 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. (2011) Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biology and Therapy. 6, 510-22. [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. (2011) A comprehensive manually curated reaction map of RANKL/RANK signaling pathway. Database. 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. (2011)

  2010 (Number of publications - 5)

• Prasad, T. S. K., Keerthikumar, S., Chaerkady, R., Kandasamy, K., Renuse, S., Marimuthu, A., Venugopal, A. K., Thomas, J. K., Jacob, H. K. C., Goel, R., Pawar, H., Sahasrabuddhe, N. A., Krishna, V., Nair, B. G., Gucek, M., Cole, R. N., Ravikumar, R., Harsha, H. C. and Pandey, A. (2010) Comparative proteomic analysis of Candida albicans and Candida glabrata. Clinical Proteomics 6, 163-173. [PubMed]
• Goel, R., Muthusamy, B., Pandey, A. and Prasad, T. S. K.* (2010) Human Protein Reference Database and Human Proteinpedia as discovery resources for molecular biotechnology. Molecular Biotechnology Oct 7. [PubMed] (*Corresponding author)
• Kashyap, M .K., Harsha, H. C., Renuse, S., Pawar, H., Sahasrabuddhe, N. A., Kim, M. S., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T. S. K., Mahmood, R., Chaerkady, R., Meltzer, S. J., Kumar, R. V., Rustgi, A. K. and Pandey, A. (2010) SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biology and Therapy 10, 796-810. [PubMed]
• Kandasamy, K., Mohan, S. S., Raju, R., Keerthikumar, S., Kumar, G. S. S., Venugopal, A. K., Telikicherla, D., Navarro, J. D., Mathivanan, S., Pecquet, C., Gollapudi, S. K., Tattikota, S. G., Mohan, S., Padhukasahasram, H., Subbannayya, Y., Goel, R., Jacob, H. K. C., Zhong, J., Sekhar, R., Nanjappa, V., Balakrishnan, L., Subbaiah, R., Ramachandra, Y. L., Rahiman, B. A., Prasad, T. S. K., Lin, J., Houtman, J. C. D., Desiderio, S., Renauld, J., Constantinescu, S. N., Ohara, O., Hirano, T., Kubo, M., Singh, S., Khatri, P., Draghici, S., Bader, G. D., Sander, C., Leonard, W. J. and Pandey, A. (2010) NetPath: A public resource of curated signal transduction pathways. Genome Biology 11, R3. [PubMed]
• Kashyap, M. K., Marimuthu, A., Peri, S., Kumar, G. S. S., Jacob, H. C. K., Prasad, T. S. K., Mahmood, R., Veerendra Kumar, K. V., Vijayakumar, M., Meltzer, S. J., Montgomery, E. A., Kumar, R. V. and Pandey, A. (2010) Overexpression of periostin and lumican in esophageal squamous cell carcinoma. Cancers 2, 133-142. [PubMed]

2009 (Number of publications -11)

• Kandasamy, K., Keerthikumar, S., Raju, R., Prasad, T. S. K., Ramachandra, Y. L., Mohan, S. and Pandey, A. (2009) PathBuilder - open source software for annotating and developing pathway resources. Bioinformatics 25, 2860-2862. [PubMed]
• Prasad, T. S. K., Kandasamy, K. and Pandey, A. (2009) “Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology.” In: Reverse Chemical Genetics: Methods and Protocols. Hisashi Koga, Editor. (Humana Press, Totowa, New Jersey, USA) Methods in Molecular Biology 577, 67-79. [PubMed]
• Prasad, T. S. K.^*, Goel, R., Kandasamy, K., Keerthikumar, S., Kumar, S., Mathivanan, S., Telikicherla, D., Raju, R., Shafreen, B., Venugopal, A., Balakrishnan, L., Marimuthu, A., Banerjee, S., Somanathan, D. S., Sebastian, A., Rani, S., Ray, S., Kishore, C. J. H., Kanth, S., Ahmed, M., Kashyap, M., Mohmood, R., Ramachandra, Y. L., Krishna, V., Rahiman, A. B., Mohan, S., Ranganathan, P., Ramabadran, S., Chaerkady, R. and Pandey, A. (2009) Human Protein Reference Database - 2009 update. Nucleic Acids Research 37, D767-D772. [PubMed] (*Corresponding author)
• Kashyap, M., Marimuthu, A., Kishore, C. J. H., Peri, S., Keerthikumar, S., Prasad, T. S. K., Mahmood, R., Rao, S., Ranganathan, P., Vijayakumar, M., Veerendra Kumar, K. V., Montgomery, E., Kumar, R.V. and Pandey, A. (2009) Genomewide mRNA profiling of esophageal squamous cell carcinoma for identification of cancer biomarkers. Cancer Biology and Therapy 8, 16-26. [PubMed]
• Kandasamy, K., Keerthikumar, S., Goel, R., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Acharya, P. K., Ranganathan, P., Chaerkady, R., Prasad, T. S. K. and Pandey, A. (2009) Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Research 37, D773-D781. [PubMed]

2008 (Number of publications - 2)

• Dixon, S., Fedyshyn, Y., Koh, J., Prasad, T. S. K., Chahwan, C., Chua, G., Toufighi, K., Baryshnikova, A., Hayles, J., Hoe, K., Kim, D., Park, H., Myers, C., Pandey, A., Durocher, D., Andrews, B. and Boone, C. (2008) Significant conservation of synthetic lethal genetic interaction networks between distantly-related eukaryotes. Proceedings of the National Academy of Sciences U.S.A. 105, 16653-16658. [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., Björling, E., Blagoev, B., Bose, R., Brahmachari, S. K., Burlingame, A. S., Bustelo, X. R., Cagney, G., Cantin, G. T., Cardasis, H. L., Celis, J. E., Chaerkady, R., Chu, F., Cole, P. A., Costello, C. E., Cotter, R. J., Crockett, D., DeLany, J. P., De Marzo, A. M., DeSouza, L. V., Deutsch, E. W., Dransfield, E., Drewes, G., Droit, A., Dunn, M. J., Elenitoba-Johnson, K., Ewing, R. M., Van Eyk, J., Faca, V., Falkner, J., Fang, X., Fenselau, C., Figeys, D., Gagné, P., Gelfi, C., Gevaert, K., Gimble, J. M., Gnad, F., Goel, R., Gromov, P., Hanash, S. M., Hancock, W. S., Harsha, H. C., Hart, G., Hays, F., He, F., Hebbar, P., Helsens, K., Hermeking, H., Hide, W., Hjernø, K., Hochstrasser, D. F., Hofmann, O., Horn, D. M., Hruban, R. H., Ibarrola, N., James, P., Jensen, O. N., Jensen, P. H., Jung, P., Kandasamy, K., Kheterpal, I., Kikuno, R. F., Korf, U., Körner, R., Kuster, B., Kwon, M. S., Lee, H. J., Lee, Y. J., Lefevre, M., Lehvaslaiho, M., Lescuyer, P., Levander, F., Lim, M. S., Löbke, C., Loo, J. A., Mann, M., Martens, L., Martinez-Heredia, J., McComb, M., McRedmond, J., Mehrle, A., Menon, R., Miller, C. A.., Mischak, H., Mohan, S. S., Mohmood, R., Molina, H., Moran, M. F., Morgan, J. D., Moritz, R., Morzel, M., Muddiman, D. C., Nalli, A., Navarro, J. D., Neubert, T. A., Ohara, O., Oliva, R., Omenn, G. S., Oyama, M., Paik, Y. K., Pennington, K., Pepperkok. R., Periaswamy, B., Petricoin, E. F., Poirier, G. G., Prasad, T. S. K., 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. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology 26, 164-167. [PubMed]

2007 (Number of publications - 1)

• Prasad, T. S. K. and Bhat, D. J. (2007) “Fungi and Development of Mycoinsecticides.” In: Fungi: Multifaceted Microbes. B. N. Ganguli and S. K. Deshmukh (Eds.). Anamaya Publishers, New Delhi. pp. 248-271.

2006 (Number of publications - 1)

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

2005 (Number of publications - 2)

• Muthusamy, B., Hanumanthu, G., Reshmi, R., Sriranjini, S., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Rashmi, B. P., Kadekar, S., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Suresh, M., Kannabiran, N., Niranjan, V., Nalli, A., Prasad, T. S. K., Arun, K. S., Reddy, R., Chandran, S., Jadhav, T., Julie, D., Mahesh, M., John, S. L., Palvankar, K., Sudhir, D., Bala, P., Jithesh, M. K., Rashmi, N. S., Vishnupriya, G., Dhar, K., Reshma, S., Chaerkady, R., Prasad, C. K., Gandhi, T. K. B., Harsha, H. C., Mohan, S. S., Deshpande, K. S., Sarker, M. and Pandey, A. (2005) Plasma Proteome Database as a resource for proteomics research. Proteomics 5, 3531-3536. [PubMed]
• Gandhi, T. K. B., Chandran, S., Peri, S., Saravana, R., Amanchy, R., Prasad, T. S. K. and Pandey, A. (2005) A bioinformatics analysis of protein tyrosine phosphatases in humans. DNA Research 12, 79-89. [PubMed]

2004 (Number of publications - 1)

• Prasad, T. S. K., Kumar, A. and Bhat, D. J. (2004) New records of Aschersonia species from the forests of Western Ghats, India. Journal of Mycology and Plant Pathology 34, 7-14.

2003 (Number of publications - 3)

• Prasad, T. S. K., Asha, L. G. and Bhat, D. J. (2003) A new species of Memnoniella from India. Mycotaxon 85, 341-344. [PubMed]
• Prasad, T. S. K., D'Souza, M. A. and Bhat, D. J. (2003) “Vermiculariopsiella Bender: Present Status of Species Diversity.” In: Frontiers of Fungal Diversity in India (Prof. Kamal Festschrift). G.P. Rao, C. Manoharachari, D. J. Bhat, R. C. Rajak and T. N. Lakhanpal (Eds.). International Book Distributing Co. Lucknow, India. pp: 503-511.
• Prasad, T. S. K., Kumar, A. and Bhat, D. J. (2003) “Mosquito larvicidal and pathogenic fungi from Goa.” In: Prospects and Problems of Environment: Across the Millennium. M. N. Madhyastha, K. R. Shridhar and A. Lakshmi (Eds). Daya Publishing House, Delhi, India. pp, 142-149. [PubMed]

2002 (Number of publications - 3)

• Prasad, T. S. K. and Bhat, D. J. (2002) Speiropsis rogergoosensis sp. nov. from India. Mycotaxon. 82,127-132. [PubMed]

• Prasad, T. S. K. and Bhat, D. J. (2002) A new species of Phalangispora from India. Mycotaxon. 83, 403-407. [PubMed]

• Prasad, T. S. K. and Bhat, D. J. (2002) Stellomyces kendrickii, a new hyphomycete from India. Mycotaxon. 84, 61-63. [PubMed]