Munjal, N. S., Dey, G., Parthasarathi, K.T.S., Chauhan, K., Pai, K., Patole M. S., Pawar, H. and Sharma, J. (2024).  A proteogenomic approach for the identification of virulence factors in Leishmania parasites. Methods in Molecular Biology. In Press

Parveen, A. and Kumar, A. (2024). Introduction to integrated proteogenomics pipeline for dealing with pathogenic missense SNPs. Methods in Molecular Biology. In Press.

Kumar, R. and Kumar, A. (2024). Biomarker Discovery via N-Glycoproteomics. Methods in Molecular Biology. In Press.

Kumar, A. (2024).  Proteogenomics for non-model ocean-derived fungus. Methods in Molecular Biology. In Press.

Kumar, A. (2024).  Genome Annotation. Methods in Molecular Biology. In Press.

Kumar, A. and Allmer, K. (2024).  Proteogenomics. Methods in Molecular Biology. In Press.

Deb, B., Venkataramanan, R., Nambiar, A., Limaye, S., Amin, B., M., Pandey, A., Kumar, P. (2024). Phosphorylation of Stathmin 1 (S63) by Protein Kinase A regulates aggressiveness in bladder carcinoma. Molecular and Clinical Oncology. In Press.

Parveen, A., Srivastava, A., Singh, K., Azad, S. K., Nandan, N., Kumari, M., Upadhayay, V., Sarde, S., Kumar, S., Sinha, R. K., Shah, M. P., Kumar, A. & Prasad, K. S. (2024).  Next-generation sequence and biosynthetic genes cluster analysis revealed tetracycline, ampicillin, arsenic resistance as well as nonribosomal peptide presence, in Pseudomonas sp. isolated from municipal sewage water. Biotechnology & Genetic Engineering Reviews. In Press.

Viswanathan, S., Oza, P.S., Bellad, A., Uttarilli, A. (2024). Conotruncal Heart Defects: A narrative review of molecular genetics and genomics research and innovation. OMICS: A Journal of Integrative Biology. 28(7):324-346 [PubMed]

Dakal, T.C., Dhabhai, B., Pant, A., Moar, K., Chaudhary, K., Yadav, V., Ranga, V., Sharma, N.K., Kumar, A., Maurya, P.K., Maciaczyk, J., Schmidt-Wolf I.G.H., Sharma A. (2024). Oncogenes and tumor suppressor genes: functions and roles in cancers. MedComm. 5(6):e582 [PubMed]

Xie, X., Truong, T., Huang, S., Johnston, S.M., Hovanski, S., Robinson, A., Webber, K.G.I., Lin, H.L., Mun, D.G., Pandey, A., Kelly, R.T. (2024). Multicolumn nanoflow liquid chromatography with accelerated offline gradient generation for robust and sensitive single-cell proteome profiling. Analytical Chemistry. Analytical Chemistry. 96(26):10534-10542 [PubMed]

Iyaswamy, A., Wang, X., Zhang, H., Vasudevan, K., Wankhar, D., Lu, K., Krishnamoorthi, S., Guan, X., Su, C.F., Liu, J., Kan, Y., Jaganathan, R., Deng, Z., Li, H.W., Wong, M.S., Li, M. (2024). "Molecular engineering of theranostic molecule that detects Aß plaques, inhibits Iowa and Dutch mutation Aß self-aggregation and promotes lysosomal biogenesis for Alzheimer’s disease". Journal of Materials Chemistry B. [PubMed]

Dakal, T.C., George, N., Xu, C., Suravajhala, P., Kumar, A. (2024). Predictive and prognostic relevance of tumor-infiltrating immune cells: tailoring personalized treatments against different cancer types. Cancers. 16(9):1626 [PubMed]

Vasanthaiah, S., Verma, R., Kumar, A., Bandari, A.K., George, J., Rastogi, M., Manjunath, G.K., Sharma, J., Kumar, A., Subramani, J., Chawla, K., Pandey, A. (2024). Culture-free whole genome sequencing of Mycobacterium tuberculosis using ligand-mediated bead enrichment method. Open Forum Infectious Diseases. 11(7):ofae320 [PubMed]

Sharma, N.K., Dwivedi, P., Bhushan, R., Maurya, P.K., Kumar, A., Dakal, T.C (2024). Engineering circular RNA for molecular and metabolic reprogramming. . Functional & Integrative Genomics. 24(4):117 [PubMed]

Budhraja, R., Radenkovic, S., Jain, A., Muffels, I.J.J., Ismaili, M.H.A., Kozicz, T., Pandey, A., Morava, E. (2024). Liposome-encapsulated mannose-1-phosphate therapy improves global N-glycosylation in different congenital disorders of glycosylation. . Molecular Genetics and Metabolism. 142(2):108487 [PubMed]

Ray, A.K., Shukla, A., Yadav, A., Kaur, U., Singh, A.K., Mago, P., Bhavesh, N.S., Chaturvedi, R., Tandon, R., Shalimar, Kumar, A., Malik, M.Z. (2024). A comprehensive pilot study to elucidate the distinct gut microbial composition and its functional significance in cardio-metabolic disease. Biochemical Genetics. [PubMed]

Raghavendra, B., Dhanushkumar, T., Selvam, P.K., Gopikrishnan, M., Doss, C.G., Vasudevan, K. (2024). Computational design of a multi-epitope-based vaccine targeting the BF. 7 Omicron variant of SARS-CoV-2. Gene Reports.

Parthasarathi, K. T. S., Gaikwad, K.B., Rajesh, S., Rana, S., Pandey, A., Singh, H., Sharma, J.(2024). A machine learning-based strategy to elucidate the identification of antibiotic resistance in bacteria. Frontiers in Antibiotics. [Article]

Radenkovic, S., Budhraja, R., Klein-Gunnewiek, T., King, A.T., Bhatia, T.N., Ligezka, A.N., Driesen, K., Shah, R., Ghesquière, B., Pandey, A., Kasri, N.N., Sloan, S.A., Morava, E., Kozicz, T. (2024). Neural and metabolic dysregulation in PMM2-deficient human in vitro neural models. Cell Reports. 43(3):113883 [PubMed]

Saini, A., Holla, V.V., Kalikavil Puthanveedu, D., Mehta, S., Elavarasi, A., Pillai, K.S., Mohapatra, P., Kumari, R., Bari, S., Singh, I., Cherian, A., Krishnan, S., Radhakrishnan, D.M., Agarwal, A., Garg, D., Garg, K., Singh, M., Garg, A., Muthusamy, B., Lal, V., Kishore, A., Pal, P.K., Srivastava, A., Faruq, M., Rajan, R. (2024). Novel PANK2 Variant in Asian Indians with Atypical Pantothenate Kinase Associated Neurodegeneration. Movement Disorders. [PubMed]

Garapati, K., Jain, A., Madden, B.J., Mun, D.G., Sharma, J., Budhraja, R., Pandey, A. (2024). Defining albumin as a glycoprotein with multiple N-linked glycosylation sites. Journal of Translational Medicine. [PubMed]

Bhat, F.A., Mangalaparthi, K.K., Ding, H., Jain, A., Hsu, J.S., Peterson, J.A., Zenka, R.M., Mun, D.G., Kandasamy, R.K., Pandey, A. (2024). Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies. Molecular & Cellular Proteomics. 23(3):100733 [PubMed]

Kumar, R., Nuñez, N.A., Joshi, N., Joseph, B., Verde, A., Seshadri, A., Cuellar Barboza, A.B., Prokop, L.J., Medeiros, G.C., Singh, B(2024). "Metabolomic biomarkers for (R, S)-ketamine and (S)-ketamine in treatment-resistant depression and healthy controls: A systematic review". Bipolar Disorders. [PubMed]

Budhraja, R., Joshi, N., Radenkovic, S., Kozicz, T., Morava, E., Pandey, A. (2024). Dysregulated proteome and N-glycoproteome in ALG1-deficient fibroblasts. Proteomics. e2400012 [PubMed]

Jain, A.P., Ghose, V., Munshi, S., Bhat, F.A., Dey, G., Nanjappa, V. (2024). Mass spectrometry-based proteomic analysis to characterize cisplatin induced early signaling events in head and neck squamous cell carcinoma. Molecular & Cellular Oncology. 11(1):2328873 [PubMed]

Verma, R., da Silva, K.E., Rockwood, N., Wasmann, R.E., Yende, N., Song, T., Kim, E., Denti, P., Wilkinson, R.J., Andrews, J.R.(2024). A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing. American Journal of Respiratory and Critical Care Medicine. [PubMed]

Jia, J., Ji, W., Saliba, A.N., Csizmar, C.M., Ye, K., Hu, L., Peterson, K.L., Schneider, P.A., Meng, X.W., Venkatachalam, A., Patnaik, M.M., Webster, J.A., Smith, B.D., Ghiaur, G., Wu, X., Zhong, J., Pandey, A., Flatten, K., Deng, Q., Wang, H., Kaufmann, S.H., Dai, H.(2024). AMPK inhibition sensitizes acute leukemia cells to BH3 mimetic-induced cell death. Cell Death and Differentiation. Cell Death & Differentiation. 31(4):405-416 [PubMed]

Jackson, L.E., Jennifer, L., Tomlinson, J.L., Roberto Alva-Ruiz, R., Lindsey, A., Gregory, L.A., Byeon, S.K., Abdelrahman, A.M., Mun, D., Grant, C.W., Fogarty, Z.C., Wang, C., Roberts, L.R., Graham, R.P., Borad, M.J., Ilyas, S.I., Gores, G.J., Pandey, A., Athreya, A.P., Smoot, R. L.(2024). Metabolome-Wide Association Identifies Altered Metabolites and Metabolic Pathways in the Serum of Patients with Cholangiocarcinoma. Journal of Hepatology. 18(6(6)):101068 [PubMed]

Garapati, K., Budhraja, R., Saraswat, M., Kim, J., Joshi, N., Sachdeva, G.S., Jain, A., Ligezka, A.N., Radenkovic, S., Ramarajan, M.G., Udainiya, S., Raymond, K., He, M., Lam, C., Larson, A., Edmondson, A.C., Sarafoglou, K., Larson, N.B., Freeze, H.H., Schultz, M.J., Kozicz, T., Morava, E., Pandey, A.(2024). A complement C4-derived glycopeptide is a biomarker for PMM2-CDG. Journal of Clinical Investigation. 8(9(7)):e172509 [PubMed]

Kang, T., Budhraja, R., Kim, J., Joshi, N., Garapati, K., Pandey, A.(2024). Global O-glycoproteome enrichment and analysis enabled by a robust combinatorial enzymatic workflow. Cell Reports Methods. 22(4(4)):100744 [PubMed]

Bhagchandani,T., Haque, M.M., Sharma S., Malik M.Z., Ray, A.K., Kaur, U. S., Rai, A., Verma, A., Kumar, K., Sawlani K., Chaturvedi, R., Himanshu D., Kumar, A. and Tandon, R.(2024). Plasma virome of HIV-infected subjects on suppressive antiretroviral therapy reveals association of differentially abundant viruses with distinct T cell phenotypes and inflammation. Current Genomics. 8(25(2)):105-119 [PubMed]

Joshi, N., Garapati, K., Ghose, V., Kandasamy, R., K. and Pandey, A. (2024). Recent progress in mass spectrometry-based urinary proteomics. Clinical Proteomic. 21(14). [PubMed]

Verma, R., Ellappan, K., Kempsell K. E., Joseph, N. M. (2024). Triage test to diagnose presumptive pulmonary tuberculosis . The Lancet Global Health. [PubMed]

Singh, S., Parthasarathi, K.T.S, Bhat, M. Y., Gopal, C., Sharma, J. and Pandey, A. (2024).  Profiling Kinase Activities for Precision Oncology in Diffuse Gastric Cancer. OMICS: A Journal of Integrative Biology. [PubMed]

Sambath, J., Noronha, V., Manda, S.S., Mishra, R., Chandrani, P., Patil, V., Menon, N., Chougule, A., Ramachandran, V., Limaye S., Kuriakose M.A., Banavali, S.D., Kumar, P., Prabhash, K. (2024) Whole exome sequencing uncovers HRAS mutations as potential mediators of resistance to metronomic chemotherapy. Gene. 893:147952 [PubMed]

Dubey, N, K., Dash., N, K., Mahapatra, P., Mohanta, S., Sikha, D., Banerjee, A., Sahu, R, P., Kanta, T., Mishra, A., Kumar, S., Rokade, T. P., Kumar, V., Halder, R. R., Singh, R., Taniha., Kumar, S., Goswami. L., Kumar, A., Goswami, C. (2024). Book Chapter: Current understanding of TRP channels and their genomics: Implication in health research. TRP Channels as Therapeutic Targets, 2nd Edition (Editor: Arpad Szallas), Elsevier. (ISBN: 9780443186547). [Article]

Dhar, D., Holla, V. V., Kumari, R., Yadav, R., Kamble, N., Muthusamy, B., and Pal, P. K. (2024). Clinical and genetic profile of patients with dystonia: An experience from a tertiary neurology center from India. Parkinsonism & Related Disorders, 105986. [PubMed]

Bellad, A., Rangiah, K., Sathe, G., Dey, G., Appadorai, P.K., Lokanatha, H., Murthy, P.R., Gowdra, A., Pandey, A. (2024). Identification of a rare[Gγ(Aγδβ)0] thalassemia using tandem mass spectrometry. Proteomics. e2300495 [PubMed]

Joshi, N., Bhat, F. A., Bellad, A., Sathe, G., Jain, A., Chavan, S., Sirdeshmukh, R., and Pandey, A. (2023). Urinary Proteomics for Discovery of Gastric Cancer Biomarkers to Enable Precision Clinical Oncology. 21(14).OMICS: A Journal of Integrative Biology. 27(8):361-371 [PubMed]

Mun, D., Joshi, N., Budhraja, R., Sachdeva, G., Kang, T., Bhat, F., Ding, H., Madden, B., Zhong, J., and Pandey, A. (2023). Automated sample preparation workflow for tandem mass tag-based proteomics. Journal of American Society for Mass Spectrometry. 34(10):2087-2092. [PubMed]

Kamath, S.D., Holla, V.V., Phulpagar, P., Kamble, N., Yadav, R., Muthusamy, B., Pal, P.K. (2023) Clinicogenetic Characterization of Patients with PD and Heterozygous GBA1 Variants in an Indian Cohort. Movement Disorders. [PubMed]

Ganesh, R.A., Venkataraman, K., Sirdeshmukh, R. (2023). GPR56 signaling pathway network and its dynamics in the mesenchymal transition of glioblastoma. Journal of Cell Communication and Signaling. 4:1527-1535. [PubMed]

Dakal, T.C., Kumar, A., Maurya, P.K. (2023). CircRNA-miRNA-mRNA interactome analysis in endometrial cancer. Journal of Biomolecular Structure and Dynamics. 12:1-12. [PubMed]

Garapati, K., Ding, H., Charlesworth, M.C., Kim, Y., Zenka, R., Saraswat, M., Mun, D.G., Chavan, S., Shingade, A., Lucien, F., Zhong, J., Kandasamy, R.K., Pandey, A. (2023). sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides. Clinical Proteomics. 20(1):56. [PubMed]

Patel, K., Rao, D.M., Sundersingh, S., Velusami, S., Rajkumar, T., Nair, B., Pandey, A., Chatterjee, A., Mani, S., Gowda, H. (2023). MicroRNA Expression Profile in Early-Stage Breast Cancers. Microrna. 20(1):56. [PubMed]

Mangalaparthi, K.K., Patel K., Khan, A.A., Nair, B., Kumar, R.V., Prasad, T.S.K., Sidransky, D., Chatterjee, A., Pandey, A., Gowda, H. (2023). Molecular Characterization of Esophageal Squamous Cell Carcinoma Using Quantitative Proteomics. Cancers. [PubMed]

Jain, V., Akhtar, J., Priya, R., Sakhuja, P., Goyal, S., Agarwal, A.K., Ghose, V., Polisetty, R.V., Sirdeshmukh, R., Siraj, F., Gautam, P. (2023). Tissue proteome analysis for profiling proteins associated with lymph node metastasis in gallbladder cancer. BMC Cancer. [PubMed]

Parthasarathi, K.T.S., Mandal, S., George, J.P., Gaikwad, K.B., Sasidharan, S., Gundimeda, S., Jolly, M.K., Pandey, A., Sharma, J. (2023). Aberrations in ion channels interacting with lipid metabolism and epithelial mesenchymal transition in esophageal squamous cell carcinoma. Frontiers in Molecular Biosciences. [PubMed]

Saklani, N., Chauhan, V., Akhtar, J., Upadhyay, S.K., Sirdeshmukh, R., Gautam, P. (2023). In silico analysis to identify novel ceRNA regulatory axes associated with gallbladder cancer. Frontiers in Genetics. [PubMed]

Pujari, G.P., Mangalaparthi, K.K., Madden, B.J., Bhat, F.A., Charlesworth, M.C., French, A.J., Sachdeva, G., Daviso, E., Thomann, U., McCarthy, P., Vasantgadkar, S., Bhattacharyya, D., Pandey, A. (2023). A High-Throughput Workflow for FFPE Tissue Proteomics. Journal of the American Society for Mass Spectrometry. 34, 1225-1229. [PubMed]

Dhar, D., Holla, V.V., Kumari, R., Sriram, N., Saini, J., Yadav, R., Pandey, A., Kamble, N., Muthusamy, B., Pal, P.K. (2023). KMT2B-related dystonia in Indian patients with literature review and emphasis on Asian cohort. Journal of Movement Disorders. [PubMed]

Bellad, A., Holla, V.V., Kumari, R., Kamble, N., Yadav, R., Pandey, A., Pal, P.K., Muthusamy, B. (2023). Loss of function variants in L2HGDH gene causing l‑2‑hydroxyglutaric aciduria. Acta Neurologica Belgica. [PubMed]

Mun, D.G., Bhat, F.A., Ding, H., Madden, B. J., Natesampillai, S., Badley, A.D., Johnson, K. L., Kelly, R.T., Pandey, A. (2023). Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments. Analyst. [PubMed]

YClaverot, E., Sanchez-Maldonado, M. J., Macauda, A., Horst, R. T., Sampaio Marques B., Jurczyszyn, A., Clay-Gilmour, A., Stein, A., Hildebrandt, M. A. T., Weinhold, N., Buda, G. García-Sanz, R., Tomczak, W., Vogel, U., Jerez, A.,Zawirska, D., Wątek, M., Hofmann, J. N., Landi, S., Spinelli, J. J., Butrym, A., Kumar, A., Martínez-López, J., Galimberti, S., Sarasquete, M. E., Subocz, E., Iskierka-Jazdzewska, E., Giles, G. G., Rybicka-Ramos, M., Kruszewski, M., Abildgaard, N., Verdejo, F. G., Rovira, P. S., Filho, M. I. D., Kadar, K., Razny, M., Cozen, W., Pelosini, M., Jurado, M., Bhatti, P., Dudzinski, M., Druzd-Sitek, A., Orciuolo, E., Li, Y., Norman, A. D., Zaucha, J.M., Manuel, R., Reis, V., Markiewicz, M., Sevilla, J. J. R., Andersen, V., Jamroziak, K., Hemminki, K., Berndt, S. I., Rajkumar, V., Mazur, G., Kumar, S. K., Ludovico, P., Nagler, A., Chanock, S. J., Dumontet, C., Machiela, M. J., Varkonyi, J., Camp, N. J., Ziv, E., Vangsted, A. J., Brown, E. E., Campa, D., Vachon C. M., Netea, M. G. Canzian, F., Asta Försti A., & Sainz, J. (2023).  Polymorphisms within autophagy-related genes as susceptibility biomarkers for multiple myeloma: a meta-analysis of three large cohorts and functional characterization. International Journal of Molecular Sciences. 24(10):8500 [PubMed]

Fisher, C. R., Mangalaparthi, K. K., Greenwood-Quaintance, K. E., Abdel, M. P, Pandey, A., Patel, R. (2023).  Mass spectrometry-based proteomic profiling of sonicate fluid differentiates Staphylococcus aureus periprosthetic joint infection from non-infectious failure: A pilot study. TProteomics Clinical Applications, 20;e2200071. [PubMed]

Young, M. F., Faerber, E. C., Mehta, R. V., Ranjan, S., Shetty, S. A., Ramakrishnan, U., Rangiah, K., Bose, B., Devi, S., Dwarkanath, P., Kurpad, A. V., Taneja, S., Martorell, R. , (2023).  Maternal nutritional status and milk volume and composition in India: an observational study. The American Journal of Clinical Nutrition, S0002-9165(23)01597-6. [PubMed]

Niazi, Y., Paramasivam, N., Schlesner, M., Blocka, J., Kumar, A., Stefanie, H., Weinhold, N., Sijmons, R., De Jong, M., Durie, B., Goldschmidt, H., Hemminki, K., and Försti, A., (2023).  Investigation of Rare Non-Coding Variants in Familial Multiple Myeloma . Cells, 12(1), 96.[Article]

Gurram, S., Holla, V.V., Sriram, N., Phulpagar, P., Jha, S., Sharma, P., Mallithavana, S., Kamble, N., Netravathi, M., Yadav, R., Muthusamy, B., and Pal, P.K. (2023). A Rare Case of Ophthalmoplegia with Ataxia in Genetically Proven Abetalipoproteinemia . Movement Disorders Clinical Practice.[Article]

Holla, V.V., Rangarajan, A., Arunachal, G., Muthusamy, B., Kamble, N., Yadav, R., Pal, P.K., and Netravathi, M. (2023). Mirror Movements and Dystonia in SRD5A3-Related Congenital Disorders of Glycosylation: Expanding the Phenotypic and Genotypic Spectrum . Movement Disorders Clinical Practice .[Article]

Vardhan, A., Gowrang, K. M., Pradeep, S., Ravi, N., and Kumar, A. (2022).  In-silico characterization and docking of polyphenols having antihemolytic activity against human P2Y12 receptor. International Journal for Computational Biology. In Press.

Gupta, A., Parveen, A., Kumar, A. and Yadav, P. (2022). Advancement in Deep Learning Methods for Diagnosis and Prognosis of Cervical Cancer. Current Genomics.[Article]

Holla, V. V., Surisetti, B. K., Prasad, S., Neeraja, K., Kamble, N., Muthusamy, B., Pal, P. K. and Yadav, R. (2022). Deep brain stimulation in dopa-responsive parkinsonism – Look out for red flags. Parkinsonism & Related Disorders. [Article]

George, I. A., Chauhan, R., Dhawale,R. E., Iyer, R., Limaye,S., Sankaranarayanan, R., Venkataramanan, R. and Kumar, P. (2022). Insights into therapy resistance in cervical cancer. Advances in Cancer Biology – Metastasis. 6:100074. [Article]

Aarthy, R., Rao, A. K. D. M., Patel, K., Sridevi, V., Rajkumar, T., Gowda, H. and Mani, S. (2022) Alteration of miR-362-5p and miR-454-3p expression elicits diverse responses in breast cancer cell lines. Molecular Biology Reports. 49(1):821-826.[PubMed]

Mol, P., Chatterjee, O., Gopalakrishnan, L., Mangalaparthi, K. K., Bhat, F., Kumar, M., Nair, B., 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. 26(7):382-391. [PubMed]

Balakrishnan, A., Thottian, A. G. F., Govind Babu, K. and Kumar, P. (2022) Drug susceptibility testing of circulating lung cancer cells for personalized treatment. Medical Oncology 40(1):1. [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. 13:854764. [PubMed]

Amit, C., Ghose, V., Narayanan, J., Padmanabhan, P., Sathe, G. and Elchuri, S. (2022) Phosphoprotein network analysis of corneal epithelium of keratoconus patients. Proteomics 22(18): e2100416. [PubMed]

Mol, P., Gopalakrishnan, L., Chatterjee, O., Mangalaparthi, K. K., Kumar, M., Durgad, S. S., Nair, B., Shankar, S. K., Mahadevan, A. and Prasad, T. S. K. (2022) Proteomic Analysis of Adult Human Hippocampal Subfields Demonstrates Regional Heterogeneity in the Protein Expression. Journal Proteome Research. 21(10):2293-231. [PubMed]

Routaray, C. B., Kumar, A., Sundar, S., Sathe, G., Pawar, H. and Pai, K. (2022). An In-depth Proteomic Map of Leishmania donovani Isolate from Post Kala-azar Dermal Leishmaniasis (PKDL) Patient. Acta Parasitologica 67(2):687-696. [PubMed]

Harsha, P. K., Ranganayaki, S., Yale, G., Dey, G., Mangalaparthi, K. K., Yarlagadda, A., Chandrasekhar, Sagar, B. K., Mahadevan, A., Srinivas Bharath, M. M. and Mani, R. S. (2022) Mitochondrial Dysfunction in Rabies Virus-Infected Human and Canine Brains. Neurochemical Research 47(6):1610-1636. [PubMed]

George, I. A., Sathe, G., Ghose, V., Chougule, A., Chandrani, P., Patil, V., Noronha, V., Venkataramanan, R., Limaye, S., Pandey, A., Prabhash, K. and Kumar, P. (2022).  Integrated proteomics and phosphoproteomics revealed druggable kinases in neoadjuvant chemotherapy resistant tongue cancer. Frontiers in Cell and Developmental Biology. [PubMed]

Rai, A., Yelamanchi, S. D., Radotra, B. D., Gupta, S. K., Mukherjee, K. K., Tripathi, M., Chhabra, R., Ahuja, C. K., Kumar, N., Pandey, A., Korbonits, M., Dutta, P. and Gaston-Massuet, C. (2022). Phosphorylation of β-catenin at Serine552 correlates with invasion and recurrence of non-functioning pituitary neuroendocrine tumours. Acta Neuropathologica Communications.10(1):138. [PubMed]

Conboy, C. B., Yonkus, J. A., Buckarma, E. H., Mun, D. G., Werneburg, N. W., Watkins, R. D., Alva-Ruiz, R., Tomlinson, J. L., Guo, Y., Wang, J., O’Brien, D., McCabe, C. E., Jessen, E., Graham, R. P., Buijsman, R. C., Vu, D., de Man, J., Ilyas, S. I., Truty, M. J., Borad, M., Pandey, A., Gores, G. J., Smoot, R. L. (2022). LCK inhibition downregulates YAP activity and is therapeutic in patient-derived models of cholangiocarcinoma. Journal of Hepatology. S0168-8278(22)03121-X. [PubMed]

Saha S., Mohanta, S., Das, R., Ritesh Dalai, R., Divyanshi, Tiwari, N., Tiwari, A., Kumar, A., and Goswami, C. (2022). Ratio of hydrophobic-hydrophilic and positive-negative residues at lipid-water-interface influences surface expression and channel gating of TRPV1. Journal of Membrane Biology. [PubMed]

Badarinath, K., Dam, B., Kataria, S., Zirmire, R. K., Dey, R., Singh, R., Masudi, T. A., Sambath, J., Kumar, P., Gulyani, A., He, Y., Krishna, S. and Jamora, C. (2022).  Snail maintains the stem/progenitor state of skin epithelial cells and carcinomas through the autocrine effect of the matricellular protein Mindin. Cell Reports. [PubMed]

Budhraja, R., Saraswat, M., De Graef, D., Ranatunga, W., Ramarajan, M. G., Mousa, J., Kozicz, T., Pandey, A., Morava, E. (2022). N-glycoproteomics reveals distinct glycosylation alterations in NGLY1-deficient patient-derived dermal fibroblasts. Journal of inherited metabolic disease. [PubMed]

Saraswat, M., Garapati, K., Kim, J., Budhraja, R. and Pandey, A. (2022). Proteomic alterations in extracellular vesicles induced by oncogenic PIK3CA mutations. Proteomics. 11; e2200077. [PubMed]

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Wang, L., Lin, G., Zuo, Z., Li, Y., Byeon, S. K., Pandey, A. and Bellen, H. J. (2022).  Neuronal activity induces glucosylceramide that is secreted via exosomes for lysosomal degradation in glia. Science Advances. 8(28): eabn3326. [PubMed]

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Jain, A., Sambath, J., Sathe, G., George, I. A., Pandey, A., Thompson, E. W. and Kumar, P. (2022). Pan-cancer quantitation of epithelial-mesenchymal transition dynamics using parallel reaction monitoring-based targeted proteomics approach. Journal of Translational Medicine. [PubMed]

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Munjal, N. S., Sapra, D., Parthasarathi, K. T. S., Goyal, A., Pandey, A., Banerjee, M. and Sharma, J. (2022). Deciphering the Interactions of SARS-CoV-2 Proteins with Human Ion Channels Using Machine-Learning-Based Methods. Pathogens 11(2), 259. [PubMed]

Parthasarathi, K. T. S., Mandal, S., Singh, S., Gundimeda, S., Jolly, M. K., Pandey, A. and Sharma, J. (2022). In Silico Analysis of Ion Channels and Their Correlation with Epithelial to Mesenchymal Transition in Breast Cancer. Cancers 14(6), 1444. [PubMed]

Lizhen, Z., Miao, B., Dymerska, D., Kuswik, M., Bueni-Martinez, E., Sanoguera-Miralles, L., Velasco, E., Paramasivam, N., Schlesner, M., Kumar, A., Lubinski., J., Bandapalli, O. R. Hemminki, K. and Försti, A. (2022). Germline variants of CYBA and TRPM4 predispose to familial colorectal cancer. Cancers 14(3), 670. [Article]

Yousef, M., Parveen, A. and Kumar, A. (2022). Computational methods for predicting mature microRNAs. Methods in Molecular Biology. 2022;2257:175-185. [PubMed]

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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 GT1 Strain Virulence and New Protein-Coding Genes with Proteogenomic Analyses. OMICS. 25, 591-604. [PubMed]

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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. 25, 693-710. [PubMed]

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Nakao, Y., Fukushima, M., Mauer, A. S., Liao, C. Y., Ferris, A., Dasgupta, D., Heppelmann, C. J., Vanderboom, P. M., Saraswat, M., Pandey, A., Nair, K. S., Allen, A. M., Nakao, K. and Malhi, H. (2021). A Comparative Proteomic Analysis of Extracellular Vesicles Associated with Lipotoxicity. Frontiers in Cell and Developmental Biology. 9, 735001. [PubMed]

Singh, S., Bhat, M. Y., Sathe, G., Gopal, C., Sharma, J., Madugundu, A. K., Joshi, N. S. and Pandey, A. (2021). Proteomic Signatures of Diffuse and Intestinal Subtypes of Gastric Cancer. Cancers. 13, 5930. [PubMed]

Priya, R., Jain, V., Akhtar, J., Chauhan, G., Sakhuja, P., Goyal, S., Agarwal, A. K., Javed, A., Jain, A. P., Polisetty, R. V., Sirdeshmukh, R., Kar, S. and Gautam, P. (2021). Plasma-derived candidate biomarkers for detection of gallbladder carcinoma. Scientific Reports. 1, 23554. [PubMed]

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Muthusamy, B., Garapati, K. and Girimaji, S. C. (2021). Exome sequencing identifies a novel mutation in THO complex, subunit 2 in non-syndromic X-linked intellectual disability. Research Reports 5: e1-e10. [Article]

Seshadri, P., Deb, B. and Kumar, P. (2021). Multifarious targets beyond microtubules – Role of Eribulin in cancer therapy. Frontiers in Bioscience- Landmark. [PubMed]

Chandran, J., Bellad, A., Ramarajan, M. G. and Rangiah, K. (2021). Applications of quantitative metabolomics to revolutionize early diagnosis of inborn errors of metabolism in India. Analytical Science Advances. [Article]

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Mishra, S., Pai, P., Uttarilli, A. and Girisha, K. M. (2021). Mongolian spots in GM1 gangliosidosis: a pictorial report. Clin Dysmorphol. [PubMed]

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Parthasarathi, K. T. S., Munjal, N. S., Dey, G., Kumar, A., Pandey, A., Balakrishnan, L. and Sharma, J. (2021) A pathway map of signaling events triggered upon SARS-CoV infection. Journal of Cell Communication and Signaling. [PubMed]

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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(2): 269-275. [PubMed]

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Santhoshkumar, R., Preethish-Kumar, V., Mangalaparthi, K. K., Unni, S., Padmanabhan, B., T S, K. P., 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 . MN, 10.1007/s12031-020-01777-4. [PubMed]

Mehta, R., Shetty, S. A., Young, M. F., Ryan, P. B., and Rangiah, K. (2021). Quantification of aflatoxin and ochratoxin contamination in animal milk using UHPLC-MS/SRM method: a small-scale study. Journal of food science and technology. 58(9): 3453-3464 [PubMed]

Bansal, P., Antil, N., Kumar, M., Yamaryo-Botté, Y., Rawat, R. S., Pinto, S., Datta, K. K., Katris, N. J., Botté, C. Y., Prasad, T. S. K., and Sharma, P. (2021). Protein kinase TgCDPK7 regulates vesicular trafficking and phospholipid synthesis in Toxoplasma gondii. PLoS pathogens. 17(2): e1009325. [PubMed]

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Gondkar, K., Sathe, G., Joshi, N., Nair, B., Pandey, A., and Kumar, P. (2021). Integrated Proteomic and Phosphoproteomics Analysis of DKK3 Signaling Reveals Activated Kinase in the Most Aggressive Gallbladder Cancer. Cells. 10(3): 511. [PubMed]

Sivagurunathan, S., Selvan, L., Khan, A. A., Parameswaran, S., Bhattacharjee, H., Gogoi, K., Gowda, H., Keshava 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(3): 647-654. [PubMed]

Kumar, A., Nayakanti, D. S., Mangalaparthi, K. K., Gopinath, V., Reddy, N., Govindan, K., Voolapalli, G., Kumar, P., and Kumar, L. D. (2021). Quantitative proteome profiling stratifies fibroepithelial lesions of the breast. Oncotarget. 12(5): 507-518. [PubMed]

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Jain, A. P., and Sathe, G. (2021). Proteomics Landscape of Alzheimer's Disease. Proteomes. 9(1): 13. [PubMed]

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Sathe, G., Albert, M., Darrow, J., Saito, A., Troncoso, J., Pandey, A., and Moghekar, A. (2021). Quantitative proteomic analysis of the frontal cortex in Alzheimer's disease. Journal of neurochemistry 156(6): 988-1002. [PubMed]

Crook, T., Gaya, A., Page, R., Limaye, S., Ranade, A., Bhatt, A., Patil, S., Kumar, P., Patil, D., and Akolkar, D. (2021). Clinical utility of circulating tumor-associated cells to predict and monitor chemo-response in solid tumors. Cancer chemotherapy and pharmacology. 87(2): 197-205. [PubMed]

Babu, G., Chaudhuri, P., Rajappa, M., Biswas, M., Sansar, B., Rajegowda, C., Radhakrishnan, A., Advani, J., Tewary, B., Radhakrishnan, P., Thiyagarajan, S., Chatterjee, A., Upadhayaya, R. S., and Majumder, P. K. (2021). JAK-STAT inhibitor as a potential therapeutic opportunity in AML patients resistant to cytarabine and epigenetic therapy. Cancer biology & therapy. 22(1): 66-78. [PubMed]

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Tahir, R., Renuse, S., Udainiya, S., Madugundu, A. K., Cutler, J. A., Nirujogi, R. S., Na, C. H., Xu, Y., Wu, X., & Pandey, A. (2021). Mutation-Specific and Common Phosphotyrosine Signatures of KRAS G12D and G13D Alleles. Journal of proteome research. 20(1): 670683. [PubMed]

Mun, D. G., Vanderboom, P. M., Madugundu, A. K., Garapati, K., Chavan, S., Peterson, J. A., Saraswat, M. and Pandey, A. (2021). DIA-based proteome profiling of nasopharyngeal swabs from COVID-19 patients. Journal of Proteome Research. 20, 4165-4175. [PubMed]

Mishra, D., Maurya, R. R., Kumar, K., Munjal, N. S., Bahadur, V., Sharma, S., Singh, P., and Bahadur, I. (2021). Structurally modified compounds of hydroxychloroquine, remdesivir and tetrahydrocannabinol against main protease of SARS-CoV-2, a possible hope for COVID-19: Docking and molecular dynamics simulation studies. Journal of molecular liquids. 335:116185. [PubMed]

Saraswat, M., Garapati, K., Mun, D. G. and Pandey, A. (2021). Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis using size-exclusion chromatography. Molecular Omics [PubMed]

Karon, B. S., Donato, L., Bridgeman, A. R., Blommel, J. H., Kipp, B., Maus, A. D., Renuse, S., Kemp, J., Madugundu, A. K., Vanderboom, P. M., Chavan, S., Dasari, S., Singh, R. J., Grebe, S. K. and Pandey, A. (2021). Analytical sensitivity and specificity of four point of care rapid antigen diagnostic tests for SARS-CoV-2 using real-time quantitative PCR, quantitative droplet digital PCR, and a mass spectrometric antigen assay as comparator methods. Clinical Chemistry. hvab138 [PubMed]

Byeon, S. K., Ramarajan, M. G., Madugundu, A. K., Oglesbee, D., Vernon, H. J., and Pandey A. (2021). High-resolution mass spectrometric analysis of cardiolipin profiles in Barth syndrome. Mitochondrion. 60:27-3.2 [PubMed]

Renuse, S., Madamsetty, V. S., Mun, D. G., Madugundu, A. K., Singh, S., Udainiya, S., Mangalaparthi, K. K., Kim, M. S., Liu, R., Kumar, S. R., Krasnoperov, V., Truty, M., Graham, R. P., Gill, P. S., Mukhopadhyay, D., and Pandey, A. (2021). Tyrosine Phosphoproteomics of Patient-Derived Xenografts Reveals Ephrin Type-B Receptor 4 Tyrosine Kinase as a Therapeutic Target in Pancreatic Cancer. Cancers. 13(14):3404 [PubMed]

Chavan, S., Mangalaparthi, K. K., Singh, S., Renuse, S., Vanderboom, P. M., Madugundu, A. K., Budhraja, R., McAulay, K., Grys, T. E., Rule, A. D., Alexander, M. P., O'Horo, J. C., Badley, A. D. and Pandey, A. (2021). Mass spectrometric analysis of urine from COVID-19 patients for detection of SARS-CoV-2 viral antigen and to study host response. Journal of Proteome Research. 20:3404-3413. [PubMed]

Renuse, S., Vanderboom, P. M., Maus, A. D., Kemp, J. V., Gurtner, K. M., Madugundu, A. K., Chavan, S., Peterson, J. A., Madden, B. J., Mangalaparthi, K. K., Mun, D. G., Singh, S., Kipp, B. R., Dasari, S., Singh, R. J., Grebe, S. K. and Pandey, A. (2021). A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens. EBioMedicine. 69:103465. [PubMed]

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. 20(5):2687-2703. [PubMed]

Patil, S., Bhat, M. Y., Advani, J., Mohan, S. V., Babu, N., Datta, K. K., Subbannayya, T., Rajagopalan, P., Bhat, F. A., Al-Hebshi, N., Sidransky, D., Gowda, H., and Chatterjee, A. (2021). Proteomic and phosphoproteomic profiling of shammah induced signaling in oral keratinocytes.Scientific reports. 11(1):9397. [PubMed]

Skopelitou, D., Miao, B., Srivastava, A., Kumar, A., Kuświk, M., Dymerska, D., Paramasivam, N., Schlesner, M., Lubiński, J., Hemminki, K., Försti, A., and Bandapalli, O. R. (2021). A Novel Low-Risk Germline Variant in the SH2 Domain of the SRC Gene Affects Multiple Pathways in Familial Colorectal Cancer.Journal of personalized medicine. 11(4):262. [PubMed]

Wong, X., Cutler, J. A., Hoskins, V. E., Gordon, M., Madugundu, A. K., Pandey, A., and Reddy, K. L. (2021). Mapping the micro-proteome of the nuclear lamina and lamina-associated domains.Life science alliance. 4(5):e202000774. [PubMed]

Bhat F. A., Mohan S. V., Patil S., Advani J., Bhat M. Y., Patel K., Mangalaparthi K. K., Datta K. K., Routray S., Mohanty N., Nair B., Ganesh M. S., Pal A., Sidransky D., Ray J. G., Gowda H., and Chatterjee A. (2021). Proteomic alterations associated with oral cancer patients with tobacco using habits. OMICS: A Journal of Integrative Biology. 25 (4): 255-268. [PubMed]

Patel K., Bhat F. A., Patil S., Routray S., Mohanty N., Nair B., Sidransky D., Ganesh M. S., Ray J. G., Gowda H., and Chatterjee A. (2021). Whole-exome sequencing analysis of oral squamous cell carcinoma delineated by tobacco usage habits. Frontiers in Oncology. 11:660696. [PubMed]

Kumar, A., Paramasivam, N., Bandapalli, O. R., Schlesner, M., Chen, T., Sijmons, R., Dymerska, D., Golebiewska, K., Kuswik, M. K., Lubinski, J., Hemminki, K. and Försti, A. (2021). A rare large duplication of MLH1 identified in Lynch syndrome. Hereditary Cancer in Clinical Practice. [Article]

Menon, A. M., Ivanti, T., Sharma, A., Purohit, S. D., Saklani, J. S., Kumar, A., Sharma, N. K., Sharma, A. and Dakal, T, C. (2021). Treatment Strategies for COVID 19: New Insights from Comparative Genome Analysis, Pathophysiology, Host-Virus Interaction and Immune Response. International Journal of Computational Biology, 9:24-42. [Article]

Miao, B., Skopelitou., D., Srivastava, A., Kumar, A., Dymerska, D., Paramasivam, N., Lubinski., J., Hemminki, K., Försti, A., and Bandapalli, O. R. (2021). Whole exome sequencing identifies APCDD1 and HDAC5 genes as potentially cancer predisposing in familial colorectal cancer. International Journal of Molecular Sciences, 22(4), 1837. [Article]

Sainz, J., García-Verdejo, F.J., Martínez-Bueno, M., Kumar, A., Sanchez-Maldonado, J.M., Díez-Villanueva, A., Vodickova, L., Vymetálková, V., Sánchez, V. M., Filho, M.I.S. Sampaio-Marques, B., Brezina, S., Butterbach, K., Horst, R., Hoffmeister, M., Ludovico, P., Jurado, M., Li, Y., Sánchez-Rovira, P., Netea, M.G., Gsur, A., Vodička, P., Moreno, V., Hemminki, K., Brenner, H. Chang-Claude, J. and Försti A. (2021). Polymorphisms within autophagy-related genes influence the risk of developing colorectal cancer: a meta-analysis of four large cohorts. Cancers. [Article]

Miao, B., Skopelitou., D., Srivastava, A., Kumar, A., Kuswik, M. K., Dymerska, D., Paramasivam, N.,Schlesner, M., Lubinski., J., Hemminki, K., Försti, A., and Bandapalli, O. R. (2021). A Novel Low-Risk Germline Variant in the SH2 Domain of the SRC Gene Affects Multiple Pathways in Familial Colorectal Cancer. J. Pers. Med., 11(4), 262. [Article]

Kumar, Aw. Kumar, A., and Prasad, T. S. K. (2021). Antibiotic-resistant bacteria in municipal sewage water joining river Ganga, at Prayagraj (India). Gene Reports, 23:101175. [Article]

Uttarilli, A., Amalakanti, S., Kommoju, P., Sharma, S., Goyal, P., Manjunath, G. M., Upadhayay, V., Parveen, A., Tandon, R., Prasad, T. S. K., Dakal, T.C., Shlomo, I.B., Yousef, M., Neerathilingam, M., and Kumar, A. (2021). Super-rapid race for saving lives by developing COVID-19 vaccines. Journal of Integrative Bioinformatics, 18(1): 27–43. [PubMed]

Bellad, A., Girimaji, S.C. and Muthusamy, B. (2021). A novel loss of function mutation in adaptor protein complex 4, subunit mu-1 causing autosomal recessive spastic paraplegia 50. Neurol Sci. Apr 21. [PubMed]

Muthusamy, B., Bellad, A., Girimaji, S.C. and Pandey, A. (2021). Shukla-Vernon Syndrome: A Second Family with a Novel Variant in the BCORL1 Gene. Genes (Basel) Mar 22;12(3):452. [PubMed]

Sathe, G., Deepha, S., Gayathri, N., Nagappa, M., Sankaran, B.P., Taly, A.B., Khanna, T., Pandey, A. and Govindaraj, P. (2021). Ethylmalonic encephalopathy ETHE1 p. D165H mutation alters the mitochondrial function in human skeletal muscle proteome. Mitochondrion. 58: 64-71. [PubMed]

Chakrabarty, S., Govindaraj, P., Sankaran, B.P., Nagappa, M., Kabekkodu, S.P., Jayaram, P.1., Mallya, S., Deepha, S., Jessiena Ponmalar, J.N., Arivinda, H.R., Meena, A.K., Jha, R.K., Sinha, S., Gayathri, N., Taly, A.B., Thangaraj, K. and Satyamoorthy K (2021). Contribution of Nuclear and Mitochondrial Gene Mutations in Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-Like Episodes (MELAS) Syndrome. J Neurol. Jan 23. [PubMed]

Rao, A., K., D., M., Rangan, A., V., Ramasamy, D., Patel, K., Balaiah, M., Ramanathan, P., Sundersingh, S., Velusami, S., Thangarajan, R., Herceg, Z., Gowda, H., Mani, S. (2021). Identification of novel dysregulated circular RNAs in early-stage breast cancer. Journal of Cellular and Molecular Medicine. [PubMed]

Buedenbender, L. Kumar, A., Blümel, M., Kempken, F., Tasdemir, D. (2021). Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B. Marine Drugs. 19, 14. [Article]

Yousef, M., Kumar, A., Bakir-Gungor, B. (2021). Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data. Entropy. 23, 2. [Article]

Renuse, S., Madugundu, A. K., Jung, J. H., Byeon, S. K., Goldschmidt, H. L., Tahir, R., Meyers, D., Kim, D. I., Cutler, J., Kim, K. P., Wu, X., Huganir, R. L., & Pandey, A. (2020). Signature Fragment Ions of Biotinylated Peptides. Journal of the American Society for Mass Spectrometry. 31(2): 394-404. [PubMed]

Nair, R. A., Verma, V. K., Beevi, S. S., Rawoof, A., Alexander, L. E., Prasad, E. R., Kumari, P. K., Kumar, P., and Dinesh Kumar, L. (2020). MicroRNA Signatures in Blood or Bone Marrow Distinguish Subtypes of Pediatric Acute Lymphoblastic Leukemia. Translational oncology. 13(9): 100800. [PubMed]

Sharma, T., Datta, K. K., Kumar, M., Dey, G., Khan, A. A., Mangalaparthi, K. K., Saharan, P., Chinnapparaj, S., Aggarwal, A., Singla, N., Ghosh, S., Rawat, A., Dhandapani, S., Salunke, P., Chhabra, R., Singh, D., Takkar, A., Gupta, S. K., Prasad, T., Gowda, H., and Bhagat, H. (2020). Intracranial Aneurysm Biomarker Candidates Identified by a Proteome-Wide Study. Omics : a journal of integrative biology. 24(8): 483-492. [PubMed]

Khanna, S., Padhan, P., Jaiswal, K. S., Jain, A. P., Ghosh, A., Tripathy, A., Gowda, H., Raghav, S. K., and Gupta, B. (2020). Altered mitochondrial proteome and functional dynamics in patients with rheumatoid arthritis. Mitochondrio. 54: 8-14. [PubMed]

Dey, G., Mohanty, A. K., Sreenivasamurthy, S. K., Kumar, M., Kumar, A., and Prasad, T. (2020). Proteomics dataset of adult Anopheles Stephensi female brain. Data in brief. 32: 106243. [PubMed]

Shetty, S. A., and Rangiah, K. (2020). Simple click chemistry-based derivatization to quantify endogenous formaldehyde in milk using ultra-high-performance liquid chromatography/tandem mass spectrometry in selected reaction monitoring mode. Rapid communications in mass spectrometry : RCM. 34(19): e8865. [PubMed]

Cutler, J. A., Udainiya, S., Madugundu, A. K., Renuse, S., Xu, Y., Jung, J., Kim, K. P., Wu, X., and Pandey, A. (2020). Integrative phosphoproteome and interactome analysis of the role of Ubash3b in BCR-ABL signaling. Leukemia. 34(1): 301-305 [PubMed]

Schubert, A. D., Channah Broner, E., Agrawal, N., London, N., Pearson, A., Gupta, A., Wali, N., Seiwert, T. Y., Wheelan, S., Lingen, M., Macleod, K., Allen, H., Chatterjee, A., Vassiliki, S., Gaykalova, D., Hoque, M. O., Sidransky, D., Suresh, K., and Izumchenko, E. (2020). Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma. Cancer letters. 471: 49-60. [PubMed]

Deb, B., George, I. A., Sharma, J., and Kumar, P. (2020). Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-Targeted Cancer Therapies. Methods in molecular biology (Clifton, N.J.). 2051: 241-264. [PubMed]

Balakrishnan, A., George, I. A., and Kumar, P. (2020). Circulating tumor cells as an emerging tool in cancer therapy. Frontiers in bioscience (Landmark edition). 25: 606-631. [PubMed]

Raja, R., Pandey, A., and Kumar, P. (2020). Epithelial to mesenchymal plasticity: role in cancer progression. Frontiers in bioscience (Landmark edition). 25: 838-873. [PubMed]

Gangadharappa, B. S., Rajashekarappa, S., and Sathe, G. (2020). Proteomic profiling of Serratia marcescens by high-resolution mass spectrometry. BioImpacts : BI. 10(2): 123-135. [PubMed]

Mangalaparthi, K. K., Patel, K., Khan, A. A., Manoharan, M., Karunakaran, C., Murugan, S., Gupta, R., Gupta, R., Khanna-Gupta, A., Chaudhuri, A., Kumar, P., Nair, B., Kumar, R. V., Prasad, T., Chatterjee, A., Pandey, A., and Gowda, H. (2020). Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort. Frontiers in oncology. 10: 1457. [PubMed]

Sharma, J., Balakrishnan, L., Kaushik, S., and Kashyap, M. K. (2020). Editorial: Multi-Omics Approaches to Study Signaling Pathways. Frontiers in bioengineering and biotechnology. 8: 829. [PubMed]

Khan, A. A., Patel, K., Patil, S., Babu, N., Mangalaparthi, K. K., Solanki, H. S., Nanjappa, V., Kumari, A., Manoharan, M., Karunakaran, C., Murugan, S., Nair, B., Kumar, R. V., Biswas, M., Sidransky, D., Gupta, R., Gupta, R., Khanna-Gupta, A., Kumar, P., Chatterjee, A., and Gowda, H. (2020). Multi-Omics Analysis to Characterize Cigarette Smoke Induced Molecular Alterations in Esophageal Cells. Frontiers in oncology. 10: 1666. [PubMed]

Kasaragod, S., Mohanty, V., Tyagi, A., Behera, S. K., Patil, A. H., Pinto, S. M., Prasad, T., 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]

Deb, B., Sengupta, P., Sambath, J., and Kumar, P. (2020). Bioinformatics Analysis of Global Proteomic and Phosphoproteomic Data Sets Revealed Activation of NEK2 and AURKA in Cancers. Biomolecules. 10(2): 237. [PubMed]

Subbannayya, Y., Pinto, S. M., Mohanty, V., Dagamajalu, S., Prasad, T., 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. 24(3): 129-139. [PubMed]

Prasanna, B. K., Balakrishnan, A., and Kumar, P. (2020). Circulating tumor cell clusters and circulating tumor cell-derived explant models as a tool for treatment response. BioTechniques. 69(1): 362-363. [PubMed]

Mohanty, V., Pinto, S. M., Subbannayya, Y., Najar, M. A., Murthy, K. B., Prasad, T., 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. 24(6): 379-389. [PubMed]

Kasarpalkar, N., Deb, B., Kumar, P., and Bhor, V. M. (2020). The Role of Integrin α4β7 Signaling in Human Immunodeficiency Virus-1 Pathogenesis and Viral Entry in Primary CD4+ T Cells As Revealed by Comparative Phosphoproteomic Signatures. Omics : a journal of integrative biology. 24(7): 437-450. [PubMed]

Puttamallesh, V. N., Deb, B., Gondkar, K., Jain, A., Nair, B., Pandey, A., Chatterjee, A., Gowda, H., and Kumar, P. (2020). Quantitative Proteomics of Urinary Bladder Cancer Cell Lines Identify UAP1 as a Potential Therapeutic Target. Genes. 11(7): 763. [PubMed]

Sathe, G., George, I. A., Deb, B., Jain, A. P., Patel, K., Nayak, B., Karmakar, S., Seth, A., Pandey, A., and Kumar, P. (2020). Urinary glycoproteomic profiling of non-muscle invasive and muscle invasive bladder carcinoma patients reveals distinct N-glycosylation pattern of CD44, MGAM, and GINM1. Oncotarget. 11(34):3244-3255. [PubMed]

Thoduvayil, S., Dhandapani, G., Brahma, R., Devasahayam Arokia Balaya, R., Mangalaparthi, K. K., Patel, K., Kumar, M., Tennyson, J., Satheeshkumar, P. K., Kulkarni, M. J., Pinto, S. M., Prasad, T., 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. 20(19-20). [PubMed]

Mun, D. G., Renuse, S., Saraswat, M., Madugundu, A., Udainiya, S., Kim, H., Park, S. R., Zhao, H., Nirujogi, R. S., Na, C. H., Kannan, N., Yates, J. R., 3rd, Lee, S. W., and Pandey, A. (2020). PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies. Analytical chemistry. 92(21): 14466-14475. [PubMed]

Nagarkar, R., Patil, D., Limaye, S., Devhare, P., Ghaisas, A., Srivastava, N., Apurwa, S., Patil, S., John, J., Raazi, Z., Shreenivas, A., Sambath, J., Srinivasan, A., Kumar, P., Akolkar, D., and Datar, R. (2020). Liquid biopsy and multi-analyte testing guided treatment of HER2 positive periampullary adenocarcinoma with durable complete response after trastuzumab based therapy. Oncotarget. 11(45): 4195-4200. [PubMed]

Limaye, S., Kumar, P., Pragya, R., Sambath, J., Patil, D., Srinivasan, A., Apurva, S., Srivastava, N., Patil, S., Patil, R., Datta, V., Akolkar, D., and Datar, R. (2020). A case report of androgen receptor inhibitor therapy in recurrent high-grade serous ovarian cancer. Oncotarget. 11(46): 4358-4363. [PubMed]

Adiga, D., Radhakrishnan, R., Chakrabarty, S., Kumar, P., and Kabekkodu, S. P. (2020). The Role of Calcium Signaling in Regulation of Epithelial-Mesenchymal Transition. Cells tissues organs. 1-23. [PubMed]

Govindaraj, P. and Thangaraj, K. (2020). Targeting mitochondria for health and disease. Research Reports. [Article]

Deepha, S., Govindaraj, P., Sankaran, B. P., Chiplunkar, S., Kashinkunti, C., Nunia, V., Nagappa, M., Sinha, S., Khanna, T., Thangaraj, K., Taly, A. B. and Gayathri, N. (2020). Clinico-pathological and molecular spectrum of mitochondrial polymerase mutations in a cohort from India. J Mol Neurosci. [PubMed]

Ranganayaki, S., Govindaraj, P., Gayathri, N. and Bharath, M. M. (2020). Exposure to the neurotoxin 3-nitropropionic acid in neuronal cells induces unique histone acetylation pattern: Implications for neurodegeneration. Neurochemistry International , 140: 104846. [PubMed]

Thakur, G., Sathe, G., Kundu, I., Gautam, B.B.P., Alkahtani, S.H., Idicula-Thomas, S., Sirdeshmukh, R., Kishore, U., Madan, T. (2020). Membrane interactome of a recombinant fragment of human SP-D reveals GRP78 as a novel binding partner in PC3, a metastatic prostate cancer cell line. Frontiers in Immunology. [PubMed]

Khan, A. A., Patel, K., Patil, S., Babu, N., Mangalaparthi, K. K., Solanki, H. S., Nanjappa, V., Kumari, A., Manoharan, M., Karunakaran, C., Murugan, S., Nair, B., Kumar, R. V., Biswas, M., Sidransky, D., Gupta, Ra., Gupta, Ro., Khanna-Gupta, A., Kumar, P., Chatterjee, A., and Gowda, H. (2020). Multi-omics analysis to characterize cigarette smoke-induced molecular alterations in esophageal cells. Frontiers in Oncology. 10,1666. [PubMed]

Akhtar, J., Priya, R., Jain, V., Sakhuja, P., Agarwal, A.K., Goyal, S., Polisetty, R.V., Sirdeshmukh, R., Kar, S., and Gautam, P. (2020). Immunoproteomics approach revealed elevated autoantibody levels against ANXA1 in early stage gallbladder carcinoma. BMC Cancer. 20,1175. [PubMed]

Ganesh, R.A., Venkataraman, K., and Sirdeshmukh, R. (2020). GPR56: An adhesion GPCR involved in brain development, neurological disorders and cancer. Brain Research. 15,1747-147055. [PubMed]

Sivadasan, P., Gupta, M. K., Sathe, G., Sudheendra, H.V., Sunny, S.P., Renu, D., Hari, P.S., Gowda, H., Suresh, A., Kuriakose, M.A., and Sirdeshmukh, R. (2020). Salivary proteins from dysplastic leukoplakia and oral squamous cell carcinoma and their potential for early detection. Journal of Proteomics. 10,212-103574. [PubMed]

Ali, W. B., Navarro,D., Kumar, A. Drula, E., Turbé-Doan, A., Correia, L. O., Baumberger, S.,Bertrand, E., Faulds, C. B. Henrissat, B., Sciara, G., Mechichi, T., and Record, E. (2020). Characterization of the CAZy Repertoire from the Marine-Derived Fungus Stemphylium lucomagnoense in Relation to Saline Conditions. Marine Drugs. 18, 461. [PubMed]

Sharma, J., Balakrishnan, L., Kaushik, S., and Kashyap, M. K. (2020). Multi-Omics Approaches to Study Signaling Pathways. Frontiers in Bioengineering and Biotechnology. 8, 829. [PubMed]

Srivastava, A., Miao,B., Skopelitou, D., Kumar, V., Kumar, A., Paramasivam, N., Bonora, E.,Hemminki, K., Försti, A., and Bandapalli, O.R. 2020. A Germline Mutation in the POT1 Gene Is a Candidate for Familial Non-Medullary Thyroid Cancer. Cancers (Basel). 12, 1441. [PubMed]

Kant, R., Kumar, A., Sironen, T. (2020) From Microbial Genomics to Metagenomics. International Journal of Genomics. 2020, 9357450. [PubMed]

Mangalaparthi, K. K., Patel, K., Khan A. A., Manoharan, M., Karunakaran, C., Murugan, S., Gupta, Ra., Gupta, Ro., Khanna-Gupta, A., Chaudhuri, A., 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 tobacco users and non-users in the Indian cohort. Frontiers in Oncology. 10, 1457. [PubMed]

Puttamallesh, V. N., Deb, B., Gondkar, K., Jain, A. P., Patel, K., Nair, B., Pandey, A., Chatterjee, A., Kumar, P., Gowda, H. (2020). Quantitative proteomics of urinary bladder cancer cell lines identifies UAP1 as a potential therapeutic target. Genes. 11(7),763. [PubMed]

Kumar, K., Bellad, A., Prasad, P., Girimaji, S.C., and Muthusamy, B. (2020). KIAA1109 gene mutation in surviving patients with Alkuraya-Kučinskas syndrome: a review of literature. BMC Medical Genetics. 21(1):136. [PubMed]

Muthusamy, B., Bellad, A., Prasad, P., Bandari, A. K., Bhuvanalakshmi, G., Kiragasur, R. M., Girimaji, S. C., and Pandey, A. (2020). A Novel LINS1 Truncating Mutation in Autosomal Recessive Nonsyndromic Intellectual Disability. Frontiers in Psychiatry. 11, 354. [PubMed]

Bellad, A., Bandari, A. K., Pandey, A., Girimaji, S. C., and Muthusamy, B. (2020). A Novel Missense Variant in PHF6 Gene Causing Börjeson-Forssman-Lehman Syndrome. Journal of Molecular Neuroscience. [PubMed]

Nagappa, M., Vandana, V.P., Chiplunkar, S., Govindaraj, P., Ponmalar, J. N., Gayathri, N., Sinha, S., Taly, A. B., and Bindu, P. S. (2020). Infantile onset Encephalomyopathy, Heartblock and Sensory Neural Hearing loss: RMND1 Associated Mitochondrial Disease. Journal of Pediatric Neurology. [Article]

Emami, E., Kumar, A., and Kempken, F. (2020). Transcriptomic analysis of poco1, a mitochondrial pentatricopeptide repeat protein mutant in Arabidopsis thaliana. BMC Plant Biology. 20, 209. [Article]

Parveen, A., Kumar, R., Tandon, R., Khurana, S., Goswami, C., and Kumar, A.(2020). Mutational Hotspots of HSP47 and Its Potential Role in Cancer and Bone-Disorders. Genomics. 20, 537-544. [PubMed]

Srivastava, A., Giangiobbe, S., Kumar, A., Paramasivam, N., Dymerska, D., Benisch, W., Witzens-Harig, M., Lubinski, J., Hemminki, K., Försti, A., and Bandapalli, O. R. (2020). Identification of Familial Hodgkin Lymphoma Predisposing Genes Using Whole Genome Sequencing. Frontiers in Bioengineering and Biotechnology. 8, 179. [PubMed]

Chattopadhyay, N. R. Chatterjee, K., Tiwari, N.,Chakrabarti, S., Sahu, S. K., Roy, S. D., Ghosh, A. Reddy, R. R. Das, P., Kanrar, B. B., Das, A. K., Tsering, S., Puii, Z., Zomawia, E., Singh, Y. I., Suryawanshi, A., Kumar, A., Ganguly, D., Goswami, C., and Choudhuri, T. (2020). TLR9 polymorphisms might contribute to the ethnicity bias for EBV-infected Nasopharyngeal Carcinoma. iScience. 23, 100937. [PubMed]

Narayan, V., Jaiswal, J., Sugur, H., Sd, S., Rao, S., Chatterjee, A., Gowda, H., Arivazhagan, A., Somanna, S., Santosh, V. (2020). Proteomic Profiling of Medulloblastoma Reveals Novel Proteins Differentially Expressed Within Each Molecular Subgroup. Clinical Neurology and Neurosurgery. 196, 106028.[PubMed]

Sankaran, B. P., Nagappa, M., Chiplunkar, S., Kothari, S., Govindaraj, P., Sinha, S., Taly, A. B., (2020). Leukodystrophies and Genetic Leukoencephalopathies in Children Specified by Exome Sequencing in an Expanded Gene Panel. Journal of Child Neurology. 35, 433-441. [PubMed]

Deb, B., Sengupta, P., Sambath, J., Kumar, P. (2020). Bioinformatics analysis of global proteomic and phosphoproteomic datasets revealed activations of NEK2 and AURKA in cancers. Biomolecules. [PubMed]

Babu, N., Pinto, S. M., Biswas, M., Subbannayya, T., Rajappa, M., Mohan, S. V., Advani, J., Rajagopalan, P., Sathe, G., Syed, N., Radhakrishna, V. D., Muthusamy, O., Navani, S., Kumar, R. V., Gopisetty, G., Rajkumar, T., Radhakrishnan, P., Thiyagarajan, S., Pandey, A., Gowda, H., Majumder, P., Chatterjee A. (2020). Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer. Gastric Cancer. [PubMed]

Govindaraj, P., Bindu, P. S., Nagappa, M., Arivinda, H. R., Deepha, S., Ponmalar, J. N., Sinha, S., Gayathri, N., and Taly, A. B., (2020). Ethylmalonic encephalopathy. Neurology. 94, e1336-e1339. [PubMed]

Nagappa, M., Sharma, S., Govindaraj, P., Chickabasaviah, Y.T., Siram, R., Shroti, A., Debnath, M., Sinha, S., Bindu, P. S., and Taly, A. B., (2020). PMP22 Gene-Associated Neuropathies: Phenotypic Spectrum in a Cohort from India. Journal of Molecular Neuroscience. Jan 28.[PubMed]

Jain, A. P., Patel, K., Pinto, S., Radhakrishnan, A., Nanjappa, V., Kumar, M., Raja, R., Patil, A. H., Kumari, A., Manoharan, M., Karunakaran, C., Murugan, S., Keshava Prasad, T. S., Chang, X., Mathur, P. P., Kumar, P., Gupta, R., Gupta, R., Khanna-Gupta, A., Sidransky, D.,.. Gowda, H. (2019). MAP2K1 is a potential therapeutic target in erlotinib resistant head and neck squamous cell carcinoma. Scientific reports. 9(1): 18793. [PubMed]

Rajagopalan, P., Jain, A. P., Nanjappa, V., Patel, K., Mangalaparthi, K. K., Babu, N., Cavusoglu, N., Roy, N., Soeur, J., Breton, L., Pandey, A., Gowda, H., Chatterjee, A., & Misra, N. (2019). Proteome-wide changes in primary skin keratinocytes exposed to diesel particulate extract-A role for antioxidants in skin health. Journal of dermatological science. 96(2): 114-124. [PubMed]

De, T., Goyal, S., Balachander, G., Chatterjee, K., Kumar, P., Babu K, G., & Rangarajan, A. (2019). A Novel Ex Vivo System Using 3D Polymer Scaffold to Culture Circulating Tumor Cells from Breast Cancer Patients Exhibits Dynamic E-M Phenotypes. Journal of clinical medicine. 8(9): 1473. [PubMed]

Antil, M., Sharma, J., Brissonnet, Y., Choudhary, M., Gouin, S., & Gupta, V. (2019). Structure-function insights into elusive Mycobacterium tuberculosis protein Rv1916. International journal of biological macromolecules. 141: 927-936. [PubMed]

Dalton, W. B., Helmenstine, E., Walsh, N., Gondek, L. P., Kelkar, D. S., Read, A., Natrajan, R., Christenson, E. S., Roman, B., Das, S., Zhao, L., Leone, R. D., Shinn, D., Groginski, T., Madugundu, A. K., Patil, A., Zabransky, D. J., Medford, A., Lee, J., Cole, A. J., … Park, B. H. (2019). Hotspot SF3B1 mutations induce metabolic reprogramming and vulnerability to serine deprivation. The Journal of clinical investigation. 129(11): 4708-4723. [PubMed]

Dutta, P., Reddy, K. S., Rai, A., Madugundu, A. K., Solanki, H. S., Bhansali, A., Radotra, B. D., Kumar, N., Collier, D., Iacovazzo, D., Gupta, P., Raja, R., Gowda, H., Pandey, A., Devgun, J. S., & Korbonits, M. (2019). Surgery, Octreotide, Temozolomide, Bevacizumab, Radiotherapy, and Pegvisomant Treatment of an AIP Mutation‒Positive Child. The Journal of clinical endocrinology and metabolism. 104(8): 3539-3544. [PubMed]

Shears, M. J., Sekhar Nirujogi, R., Swearingen, K. E., Renuse, S., Mishra, S., Jaipal Reddy, P., Moritz, R. L., Pandey, A., & Sinnis, P. (2019). Proteomic Analysis of Plasmodium Merosomes: The Link between Liver and Blood Stages in Malaria. Journal of proteome research. 18(9): 3404-3418. [PubMed]

Moorchung, N., Puri, B., Bhatti, V., Lahareesh, B. L., Singh, S. P., & Sitaram, W. T. (2019). In the search of a 'fitness gene': an analysis of ACTN gene polymorphisms in serving soldiers. Medical journal: Armed Forces India. 75(3): 246-250. [PubMed]

Mohanty, A. K., Dey, G., Kumar, M., Sreenivasamurthy, S. K., Garg, S., Prasad, T., & Kumar, A. (2019). Proteome data of female Anopheles stephensi antennae. Data in brief. 24: 103911. [PubMed]

Subba, P., Narayana Kotimoole, C., & Prasad, T. (2019). Plant Proteome Databases and Bioinformatic Tools: An Expert Review and Comparative Insights. Omics : a journal of integrative biology.23(4): 190-206. [PubMed]

Gondkar, K., Patel, K., Patil Okaly, G. V., Nair, B., Pandey, A., Gowda, H., & Kumar, P. (2019). Dickkopf Homolog 3 (DKK3) Acts as a Potential Tumor Suppressor in Gallbladder Cancer. Frontiers in oncology. 9: 1121. [PubMed]

Gondkar, K., Patel, K., Krishnappa, S., Patil, A., Nair, B., Sundaram, G. M., Zea, T. T., & Kumar, P. (2019). E74 like ETS transcription factor 3 (ELF3) is a negative regulator of epithelial- mesenchymal transition in bladder carcinoma. Cancer biomarkers : section A of Disease markers 25(2): 223-232. [PubMed]

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., & Prasad, T. (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]

Advani, J., Verma, R., Chatterjee, O., Devasahayam Arokia Balaya, R., Najar, M. A., Ravishankara, N., Suresh, S., Pachori, P. K., Gupta, U. D., Pinto, S. M., Chauhan, D. S., Tripathy, S. P., Gowda, H., & Prasad, T. (2019). Rise of Clinical Microbial Proteogenomics: A Multiomics Approach to Nontuberculous Mycobacterium-The Case of Mycobacterium abscessus UC22. Omics : a journal of integrative biology 23(1): 1-16. [PubMed]

Bindu, P. S., Chiplunkar, S., Vandana, V. P., Nagappa, M., Govindaraj, P., and Taly, A. B., (2019). Huppke-Brendel Syndrome. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2019. [Article]

Govindaraj, P., Rani, B., Sundaravadivel, P., Vanniarajan, A., Indumathi, K. P., Khan, K. A., Dhandapany, P. S., Rani, D. S., Tamang, R., Bahl, A., Narasimhan, C., Rakshak, D., Rathinavel, A., Premkumar, K., Khullar, M., and Thangaraj, K. (2019). Mitochondrial genome variations in idiopathic dilated cardiomyopathy. Mitochondrion. 48: 51-59. [PubMed]

Parveen, A., Mustafa, S. H., Yadav, P., and Kumar, A. (2019). Applications of machine learning in miRNA discovery and target prediction. Current Genomics. 20, 537-544. [Article]

Natarajan, V., Moar, P., Kaur, U. S., Venkatesh, V., Chaturvedi, R., Kumar, A., Himanshu, D., and Tandon, R. (2019). Helicobacter pylori reactivates Human Immunodeficiency Virus-1 in latently infected monocytes with increased expression of IL-1β and CXCL8. Current Genomics. 20, 556-568. [Article]

Jain, A. P., 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. P., Kumar, P., Gupta, R., Gupta, R., Khanna-Gupta, A., Sidransky, D., Chatterjee, A., Gowda, H. (2019). MAP2K1 is a potential therapeutic target in erlotinib-resistant head and neck squamous cell carcinoma. Scientific Reports. 9, 18793. [PubMed]

Gondkar, K., Patel, K., Patil, G., Nair, B., Pandey, A., Gowda, H., Kumar, P. (2019). Dickkopf Homologue 3 (DKK3) acts as a potential tumor suppressor in gallbladder cancer. Frontiers in Oncology. 9, 1121. [PubMed]

Patil, S., Rajagopalan, P., Patel, K., Subbannayya, T., Babu, N., Mohan, S. V., Advani, J., Sathe, G., Bhandi, S., Solanki, H. S., Sidransky, D., Chatterjee, A., Gowda, H., Ferrari, M. (2019). Chronic shisha exposure alters phosphoproteome of oral keratinocytes. Journal of Cell Communication and Signaling. 13, 281-289. [PubMed]

Sivadasan, P., Gupta, M. K., Sathe, G., Sudheendra, H. V., Sunny, S. P., Renu, D., Hari, P. S., Gowda, H., Suresh, A., Kuriakose, M. A., Sirdeshmukh, R. (2019). Salivary proteins from dysplastic leukoplakia and oral squamous cell carcinoma and their potential for early detection. Journal of Proteomics. 212,103574. [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., Coral, K., 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. 8, E949. [PubMed]

Deb, B., Patel, K., Sathe, G., Kumar, P. (2019). N-Glycoproteomic Profiling Reveals Alteration In Extracellular Matrix Organization In Non-Type Bladder Carcinoma. Journal of clinical medicine. 8, E1303. [PubMed]

Srivastava, A., Kumar, A., Giangiobbe, S., Bonora, E., Hemminki, K., Försti, A., and Bandapalli, O. R. (2019). Whole genome sequencing of familial non-medullary thyroid cancer identifies germline alterations in MAPK/ERK and PI3K/AKT signaling pathways. Biomolecules. 9, E605. [Article]

Bandari, A.K, Muthusamy, B., Bhat, S., Govindaraj, P., Rajagopalan, P., Dalvi, A., Shankar, S., Raja, R., Reddy, K.S., Madkaikar, M. and Pandey, A. (2019). A Novel Splice Site Mutation in IFNGR2 in Patients With Primary Immunodeficiency Exhibiting Susceptibility to Mycobacterial Diseases. Frontiers in Immunology. 10, 1964. [PubMed]

Sahoo, S., Majhi, R., Tiwari, A., Acharya, T., Kumar, P.S., Saha, S., Kumar, A., Goswami, C. and Chattopadhyay, S. (2019). Transient Receptor Potential Ankyrin1 channel is endogenously expressed in T cells and is involved in immune functions. Bioscience Reports. 39, BSR20191437. [PubMed]

Gupta, M. K., Polisetty, R. V., Sharma, R., Ganesh, R. A., Gowda, H., Purohit, A. K., Ankathi, P., Prasad, K., Mariswamappa, K., Lakshmikantha, A., Uppin, M. S., Sundaram, C., Gautam, P., Sirdeshmukh, R. (2019). Altered transcriptional regulatory proteins in glioblastoma and YBX1 as a potential regulator of tumor invasion. Scientific Reports. 9, 10986. [PubMed]

Antil, M., Sharma, J., Brissonnet, Y., Choudhary, M., Gouin, S., Gupta, V. (2019). Structure function insights into elusive Mycobacterium tuberculosis protein Rv1916. International Journal of Biological Macromolecules. 141, 927-935. [PubMed]

Gavali, S., Gupta, M. K., Daswani, B., Wani, M. R., Sirdeshmukh, R., Khatkhatay, M. I. (2019). Estrogen enhances human osteoblast survival and function via promotion of autophagy. Biochimica et Biophysica Acta - Molecular Cell Research. 1866, 1498-1507. [PubMed]

Gavali, S., Gupta, M. K., Daswani, B., Wani, M. R., Sirdeshmukh, R., Khatkhatay, M. I. (2019). LYN, a key mediator in estrogen-dependent suppression of osteoclast differentiation, survival, and function. Biochimica et Biophysica Acta - Molecular Basis of Disease. 1865, 547-557. [PubMed]

Balakrishnan, A., Koppaka, D., Anand, A., Deb, B., Grenci, G., Viasnoff, V., Thompson, E., Gowda, H., Bhat, R., Rangarajan, A., Thiery, J. P., Babu, G. and Kumar, P. (2019). Circulating Tumor Cell cluster phenotype allows monitoring response to treatment and predicts survival. Scientific Reports. 9, 7933. [PubMed]

Sharma, J., Deb, B., George, I. A., Kapil, S., Coral, K., Kakkar, N., Pattanaik, S., Mandal, A. K., Mavuduru, R. S., and Kumar, P. (2019). Somatic mutations profile of a young patient with metastatic urothelial carcinoma reveals mutations in genes involved in ion channels. Frontiers in Oncology. 9, 435. [PubMed]

Deb, B., Puttamalesh, N. V., Gondkar, K., Thiery, J. P., Gowda, H. and Kumar, P. (2019). Phosphoproteomic profiling identifies aberrant activation of integrin signaling in aggressive non-type bladder carcinoma. Journal of Clinical Medicine. 8(5), 703. [PubMed]

Gondkar, K., Patel, K., Krishnappa, S., Patil, A., Nair, B., Sundaram, M.K., Tan, T.Z. and Kumar, P. (2019). E74 like ETS transcription factor 3 (ELF3) is a negative regulator of epithelial-mesenchymal transition in bladder carcinoma. Cancer Biomarkers. 25, 223-232. [PubMed]

Bandari, A.K., Bhat, S., Archana, M.V., Yadavalli, S., Patel, K., Rajagopalan, P., Madugundu, A.K., Madkaikar, M., Reddy, K., Muthusamy, B., and Pandey, A. (2019). Family-based next-generation sequencing study identifies an IL2RG variant in an infant with primary immunodeficiency. OMICS: A Journal of Integrative Biology. 23, 285-290. [PubMed]

Na, C.H., Sharma, N., Madugundu, A.K., Chen, R., Atalar Aksit, M., Rosson, G.D., Cutting, G.R., and Pandey, A. (2019). Integrated transcriptomic and proteomic analysis of human eccrine sweat glands identifies missing and novel proteins. Molecular & Cellular Proteomics. 18, 1382-1395. [PubMed]

Madugundu, A.K., Na, C.H., Nirujogi, R.S., Renuse, S., Kim, K.P., Burns, K.H., Wilks, C., Langmead, B., Ellis, S.E., Collado-Torres, L., Halushka, M.K., Kim, M.S., and Pandey, A. (2019). Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial cells. Journal of Proteomics. 19, e1800315. [PubMed]

Vasaikar, S., Huang, C., Wang, X., Petyuk, V.A., Savage, S.R., Wen, B., Dou, Y., Zhang, Y., Shi, Z., Arshad, O.A., Gritsenko, M.A., Zimmerman, L.J., McDermott, J.E., Clauss, T.R., Moore, R.J., Zhao, R., Monroe, M.E., Wang, Y.T., Chambers, M.C., Slebos, R.J.C., Lau, K.S., Mo, Q., Ding, L., Ellis, M., Thiagarajan, M., Kinsinger, C.R., Rodriguez, H., Smith, R.D., Rodland, K.D., Liebler, D.C., Liu, T., Zhang, B., and Clinical Proteomic Tumor Analysis, Consortium. (2019). Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities. Cell. 177, 1035-1049. [PubMed]

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. 18, 1171-1182. [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]

Patil, S., Babu, N., Subbannayya, T., Mohan, S. V., Sathe, G., Solanki, H. S., Rajagopalan, P., Patel, K., Advani, J., Bhandi, S., Sidransky, D., Chatterjee, A., Gowda, H., Ferrari, M. (2019). Secretome analysis of oral keratinocytes chronically exposed to shisha. Cancer Biomarkers.25, 29-41. [PubMed]

Rao, A., K., D., M., Patel, K., Korivi J., S., Balaiah, M., Sundersingh, S., Velusami, S., Rajkumar, T., Pandey, A., Chatterjee, A., Gowda, H., Mani, S. (2019). Identification of lncRNAs associated with early stage breast cancer and their prognostic implications. Molecular Oncology. 13, 1342-1355. [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., Murthy, K.R. (2019). 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]

Barua, P., Lande, N.V., Subba, P., Gayen, D., Pinto, S., Keshava Prasad, T.S., Chakraborty, S., Chakraborty, N. (2019). Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.M) reveals phosphorylation-mediated regulation of stress response. Plant, Cell & Environment. 42, 230-244. [PubMed]

Kumar, M., Mohanty, A.K., Dey, G., Sreenivasamurthy, S.K., Kumar, A., Prasad, K. (2019). Dataset on fat body proteome of Anopheles stephensi Liston. Data in Brief. 22, 1068-1073. [PubMed]

Muthusamy, B., Nguyen, TT., Bandari, AK., Basheer, S., Selvan, LDN., Chandel, D., Manoj, J., Gayen, S., Seshagiri, S., Chandra Girimaji, S., Pandey, A. (2019). Exome sequencing reveals a novel splice site variant in HUWE1 gene in patients with suspected Say-Meyer syndrome. European Journal of Medical Genetics. S1769-7212, 30478-6. [PubMed]

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]

Menon, D., Singh, K., Pinto, S.M., Nandy, A., Jaisinghani, N., Kutum, R., Dash, D., Prasad, T.S.K., Gandotra, S. (2019). Quantitative Lipid Droplet Proteomics Reveals Mycobacterium tuberculosis Induced Alterations in Macrophage Response to Infection. ACS Infectious Diseases. 5, 559-569. [PubMed]

Patil, S., Patel, K. , Advani, J. , Subbannayya, T., Rajagopalan, P., Babu, N., Solanki, H., Bhandi, S., Sidransky, D., Chatterjee, A., Gowda, H., Ferrari, M. (2019). Multiomic analysis of oral keratinocytes chronically exposed to shisha. Journal of Oral Pathology and Medicine. 48, 284-289. [PubMed]

Patil, S. , Subbannayya, T. , Mohan, S. V., Babu, N., Advani, J., Sathe, G., Rajagopalan, P., Patel, K., Solanki, H., Sidransky, D., Gowda, H., Chatterjee, A., Ferrari, M. (2019). Total proteomic analysis of oral keratinocytes chronically treated with shisha. OMICS: A Journal of Integrative Biology. 23. [Article]

Karthikkeyan, G., Subbannayya, Y., Najar, M.A., Mohanty, V., Pinto, S.M., Arunachalam, C., Prasad, T.S.K., Murthy, K.R. (2018). Human Optic Nerve: An Enhanced Proteomic Expression Profile. OMICS: A Journal of Integrative Biology. 22, 642-652. [PubMed]

Dey, G., Mohanty, A.K., Kumar, M., Sreenivasamurthy, S.K., Patil, A.H., Prasad, T.S.K., Kumar, A. (2018). Proteome data of Anopheles stephensi ovary using high-resolution mass spectrometry. Data in Brief. 20, 723-731. [PubMed]

Sreenivasamurthy, S.K., Dey, G., Kumar, M., Mohanty, A.K., Kumar, A., 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]

Yelamanchi, S.D., Tyagi, A., Mohanty, V., Dutta, P., Korbonits, M., Chavan, S., Advani, J., Madugundu, A.K., Dey, G., Datta, K.K., Rajyalakshmi, M., Sahasrabuddhe, N.A., Chaturvedi, A., Kumar, A., Das, A.A., Ghosh, D., Jogdand, G.M., Nair, H.H., Saini, K., Panchal, M., Sarvaiya, M.A., Mohanraj, S.S., Sengupta, N., Saxena, P., Subramani, P.A., Kumar, P., Akkali, R., Reshma, S.V., Santhosh, R.S., Rastogi, S., Kumar, S., Ghosh, S.K., Irlapati, V.K., Srinivasan, A., Radotra, B.D., Mathur, P.P., Wong, G.W., Satishchandra, P., Chatterjee, A., Gowda, H., Bhansali, A., Pandey, A., Shankar, S.K., Mahadevan, A., Prasad, T.S.K. (2018). Proteomic Analysis of the Human Anterior Pituitary Gland. OMICS: A Journal of Integrative Biology. 22, 759-769. [PubMed]

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. (2018). PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich Akt substrate of 40 kDa (PRAS40). Journal of Cell Communication and Signaling. 13, 163-177. [PubMed]

Maldonado, L., Brait, M., Izumchenko, E., Begum., S., Chatterjee., A., Sen, T., Loyo, M., Barbosa, A., Poeta, M. L., Makarev, E., Zhavoronkov, A., Fazio, V. M., Angioli, R., Rabitti, C., Ongenaert, M., Criekinge, W. V., Noordhuis, M. G., Graeff, P., Wisman, B. A., Zee, A. G. J., Hoque, M. O. (2018). Integrated Transcriptomic and Epigenomic Analysis of Ovarian Cancer Reveals Epigenetically Silenced GULP1. Cancer Letters. 433,242-251. [PubMed]

Deb, B. and Kumar, P. (2018). Bladder carcinoma treatment challenges and future directions of immunotherapy. Journal of Proteomics and Bioinformatics. 11. [Article]

Sathe, G., Na, C. H., Renuse, S., Madugundu, A. K., Albert, M., Moghekar, A., Pandey, A. (2018). Quantitative proteomic profiling of cerebrospinal fluid to identify candidate biomarkers for Alzheimer's disease. Proteomics Clin Appl. 13, e1800105. [PubMed]

Advani, J., Sharma, K., Verma, R., Chatterjee, O., Solanki, H. S., Sharma, A., Varma, S., Modi, M., Ray, P., Sharma, M., Dhillion, M. S., Pandey, A., Gowda, H., Prasad, T. S. K. (2018). Data on whole genome sequencing of extrapulmonary tuberculosis clinical isolates from India. Data in Brief. 20, 617-622. [PubMed]

Bhat, M. Y., Solanki, H. S., Advani, J., Khan, A. A., Prasad, T. S. K., Gowda, H., Thiyagarajan, S. and Chatterjee, A. (2018). Comprehensive network map of interferon gamma signaling. Journal of Cell Communication and Signaling. 12, 745-751. [PubMed]

Nanjappa, V., Raja, R., Radhakrishnan, A., Jain, A.P., Datta, K.K., Puttamallesh, V. N., Solanki, H, S., Chavan, S., Patil, A., Renuse, S., Jain, A., Mathew, D., Thakur, R., Guerrero-Preston, R., Nair, B., Routray, S., Mohanty, N., Gowda, K.B.L., Jadav, R., Ghosal, S., Kumar, R.V., Ramesha, C., Raghu, V.C., Mathur, P.P., Prasad, T.S.K., Califano, J.A., Sidransky, D., Pal, A., Ganesh, M.S., Ray, J.G., Pandey, A., Gowda, H., and Chatterjee, A. (2018). Testican 1 (SPOCK1) and protein tyrosine phosphatase, receptor type S (PTPRS) show significant increase in saliva of tobacco users with oral cancer. Translational Research in Oral Oncology. [Article]

Advani, J., Verma, R., Chatterjee, O., Rex, D. A. B., Najar, M. A., Ravishankara, N., Suresh, S., Pachori, P. K., Gupta, U. D., Pinto, S. M., Chauhan, D. S., Tripathy, S. P., Gowda, H. and Prasad, T. S. K. (2018). Rise of clinical microbial proteogenomics: A multi-omics approach to non-tuberculous mycobacterium – the case of Mycobacterium abscessus UC22. OMICS: A Journal of Integrative Biology. 23, 1-16. [Pubmed]

Sharma, J., Deb, B. and Kumar, P. (2018). Developments in the area of bladder cancer genomics and its importance in the treatment selection. Journal of Molecular Oncology Research. 2, 58-62. [Article]

Sathe, G., Na, CH., Renuse, S., Madugundu, A., Albert, M., Moghekar, A., Pandey, A. (2018). Phosphotyrosine profiling of human cerebrospinal fluid. Clinical Proteomics. 15, 29. [PubMed]

Sharma, J., Gondkar, K., Deb, B. and Kumar, P. (2018). Targeting gene fusion events in bladder carcinoma. Journal of Molecular and Genetic Medicine. 12, 361. [Article]

Bhat, S. A., Gurtoo. S., Deolankar, S. C., Fazili, K. M., Advani, J., Shetty, R., Prasad, T. S. K., Andrabi, S., Subbannayya, Y. (2018). A network map of netrin receptor UNC5B-mediated signaling. Journal of Cell Communication and Signaling. 13, 121-127. [PubMed]

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. 12, 731-735. [PubMed]

Bhat, F. A., Advani, J., Khan, A. A., Mohan, S., Pal, A., Gowda, H., Chakrabarti, P., Prasad, T. S. K. and Chatterjee, A. (2018). A network map of thrombopoietin signaling. Journal of Cell Communication and Signaling. 12, 737-743. [PubMed]

Khan, A. A., Mangalaparthi, K. K., Advani, J., Prasad, T. S. K., Gowda, H., Jain, D. and Chatterjee, A. (2018). Data from quantitative proteomic analysis of lung adenocarcinoma and squamous cell carcinoma primary tissues using high-resolution mass spectrometry. Data in Brief. 19, 1631-1637. [PubMed]

Patil, A. H., Datta, K. K., Behera, S. K., Kasaragod, S., Pinto, S. M., Koyangana, S. G., Mathur, P. P., Gowda, H., Pandey, A. and Prasad T. S. K. (2018). Dissecting Candida pathobiology: Post-translational modifications on the Candida tropicalis proteome. OMICS: A Journal of Integrative Biology. 22, 544-552. [PubMed]

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. [Article]

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. [Article]

Madugundu, A. K., Muthusamy, B., Sreenivasamurthy, S. K., Bhavani, C., Sharma, J., Kumar, B., Murthy, K. R., Ravikumar, R. and Pandey, A. (2018). A next generation sequencing-based molecular approach to characterize a tick vector in Lyme disease. OMICS: A Journal of Integrative Biology. 22, 565-574. [PubMed]

Selvan, L. D. N., Danda, R., Madugundu, A. K., Puttamallesh, V. N., Sathe, G. J., Krishnan, U. M., Khetan, V., Rishi, P., Prasad, T. S. K., Pandey, A., Krishnakumar, S., Gowda, H. and Elchuri, A. (2018). Phosphoproteomics of Retinoblastoma: A pilot study identifies aberrant kinases. Molecules. 23, 1454. [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 M. tuberculosis H37Ra redefines virulence attributes. Frontiers in Microbiology. 9, 1314. [PubMed]

Babu, N., Mohan, S., Nanjappaa, V., Chavan, S., Advani, J., Khan, A. A., Renuse, S., Radhakrishnan, A., Prasad, T. S. K., Kumar, R. V., Ray, J. G., Biswas, M., Thyagarajan, S., Califano, J. A., Sidransky, D., Gowda, H. and Chatterjee, A. (2018). Identification of potential biomarkers of head and neck squamous cell carcinoma using iTRAQ based quantitative proteomic approach. Data in Brief. 19, 1124-1130. [PubMed]

Barua, P., Lande N. V, Subba, P., Gayen, D., Pinto, S., Prasad, T. S. K., Chakraborty, S. and Chakraborty, N. (2018). Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response. Plant, Cell & Environment. 42, 230-244. [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]

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]

Deb, B. and Kumar, P. (2018). Biomarkers for Bladder Cancer: Present Challenges and Recent Developments. Journal of Cancer Research and Treatment. 6, 34-38. [PubMed]

Jayaram, S., Balakrishnan, L., Singh, M., Zabihi, A., Ganesh, R. A., Mangalaparthi, K. K., Sonpatki, P., Gupta, M. K., Amaresha, C. B., Prasad, K., Mariswamappa, K., Pillai, S., Lakshmikantha, A., Shah, N. and Sirdeshmukh, R. (2018). Identification of a Novel Splice Variant of Neural Cell Adhesion Molecule (NCAM1) in Glioblastoma through Proteogenomic Analysis. OMICS: A Journal of Integrative Biology. 22, 437-448. [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. 12, e1700101. [PubMed]

Barbhuiya, M. A., Kashyap, M. K., Puttamallesh, V. N., Kumar, R. V., Wu, X., Pandey, A. and Gowda, H. (2018). Identification of spleen tyrosine kinase as a potential therapeutic target for esophageal squamous cell carcinoma using reverse phase protein arrays. Oncotarget. 9, 18422-18434. [PubMed]

Rajagopalan, P., Jain, A. P., Nanjappa, V., Patel, K., Mangalaparthi, K. K., Babu, N., Cavusoglu, N., Roy, N., Soeur, J., Breton, L., Pandey, A., Gowda, H., Chatterjee, A. and Misra, N. (2018). Proteome-wide changes in primary skin keratinocytes exposed to diesel particulate extract – a role for antioxidants in skin health. Journal of Dermatological Science. 18, 30215-9. [PubMed]

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. 3, 1-13. [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. 12, 615-624. [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]

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]

Solanki, H. S., Babu, N., Jain, A. P., Bhat, M. Y., Puttamallesh, V. N., Advani, J., Raja, R., Mangalaparthi, K. K., Kumar, M. M., Prasad, T. S. K., Mathur, P. P., Sidransky, D., Gowda, H. and Chatterjee, A. (2017). Cigarette smoke induces mitochondrial metabolic reprogramming in lung cells. Mitochondrion. 40, 58-70. [PubMed]

Kim, D. I., Cutler, J. A., Na, C. H., Reckel, S., Renuse, S., Madugundu, A. K., Tahir, R., Goldschmidt, H. L., Reddy, K. L., Huganir, R. L., Wu, X., Zachara, N. E., Hantschel, O. and Pandey, A. (2018). BioSITe: A method for direct detection and quantitation of site-specific biotinylation. Journal of Proteome Research. 17, 759-769. [PubMed]

Gowthami, N., Sunitha, B., Kumar, M., Prasad, T. S. K., Gayathri, N., Padmanabhan, B. and Bharath, M. M. S. (2018). 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. 17, 30150-3. [PubMed]

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. 12, e1600187. [PubMed]

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]

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]

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]

Rajagopalan, P., Nanjappa, V., Patel, K., Jain, A. P., Mangalaparthi, K. K., Patil, A. H., Nair, B., Mathur, P. P., Prasad, T. S. K., Califano, J. A., Sidransky, D., Gowda, H. and Chatterjee A. (2018). Role of protein kinase N2 (PKN2) in cigarette smoke-mediated oncogenic transformation of oral cells. Journal of Cell Communication and Signaling. 12, 709-721. [PubMed]

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]

Dammalli, M., Dey, G., Kumar, M., Madugundu, A. K., Gopalakrishnan, L., Byachapur, G. S., Mahadevan, A., Shankar S. K. and Prasad, T. S. K. (2018). Proteomics of the human olfactory tract. OMICS: A Journal of Integrative Biology. 22, 77-87. [PubMed]

Nanjappa, V., Sathe, G. J., Jain, A. P., Rajagopalan, P., Raja, R, Subbannayya, T., Patil, A. H., Kumar, P., Prasad, T. S. K., Mathur, P. P., Sidransky, D., Gowda, H. and Chatterjee, A. (2017). Investigation of curcumin mediated signaling pathways in head and neck squamous cell carcinoma. Translational Research in Oral Oncology. 2, 1-11. [PubMed]

Solanki, H. S., Advani, J., Kumar, M., Kumar, P., Bhagat, H., Prasad, T. S. K., Sidransky, D., Gowda, H. and Chatterjee, A. (2017). miRNA profiling of bladder cells chronically exposed to cigarette smoke condensate and its vapor. Research Reports. 1, e1-e15. [PubMed]

McCall, M. N., Kim. M., Adil, M., Patil, A. H., Lu, Y., Mitchell, C. J., Leal-Rojas, P., Xu, J., Kumar, M., Dawson, V. L., Dawson, T. M., Baras, A. S., Rosenberg, A. Z., Arking, D. E., Burns, K. H., Pandey, A. and Halushka, M. K. (2017). Towards the human cellular microRNAome. Genome Research. 27, 1769-1781. [PubMed]

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]

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]

Mir, S. A., Renuse, S., Sathe, G. J., Khan, A. A., Patil, A. H., Nanjappa, V., Bhat, F. A., Prasad, T. S. K., Giri, A. K., Chatterjee, A. and Gowda, H. (2017). Altered signaling associated with chronic arsenic exposure in human skin keratinocytes. Proteomics - Clinical Applications. 11, 11-12. [PubMed]

Sirdeshmukh, R., Jayaram, S., Gupta, M. K., Sonpatki, P., Singh, M., Ganesh, R. A., Amaresha, C. B. and Shah, N. (2017). Current Proteomic Approaches Applied to Brain Function - Integration of Transcriptomics and Proteomic Data for Disease Insights. NeuroMethods. 325-356. [PubMed]

Dammalli, M., Dey, G., Madugundu, A. K., Kumar, M., Rodrigues, B., Gowda, H., Byachapur, G. S., Mahadevan, A., Shankar S. K. and Prasad, T. S. K. (2017). Proteomic analysis of the human olfactory bulb. OMICS: A Journal of Integrative Biology. 21, 440-453. [PubMed]

Solanki, H. S., Advani, J., Khan, A. A., Radhakrishnan, A., Sahasrabuddhe, N. A., Pinto, S. M., Chang, X., Prasad, T. S. K., Mathur, P. P., Sidransky, D., Gowda, H. and Chatterjee, A. (2017). Chronic cigarette smoke mediated global changes in lung mucoepidermoid cells: A phosphoproteomic analysis. OMICS: A Journal of Integrative Biology. 21, 474-487. [PubMed]

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. 165, 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]

Puttamallesh, V. N., Patel, K. and Gowda, H. (2017). Rapid processing of archival tissue samples for proteomic analysis using pressure-cycling technology. Journal of Proteins and Proteomics. 8, 121-125. [PubMed]

Sharma, K., Verma, R., Advani, J., Chatterjee, O., Solanki, H. S., Sharma, A., Varma, S., Modi, M., Ray, P., Mukherjee, K. K., Sharma, M., Dhillon, M. S., Suar, M., Chatterjee, A., Pandey, A., Prasad, T. S. K. and Gowda, H. (2017). Whole genome sequencing of Mycobacterium tuberculosis isolates from extrapulmonary sites. OMICS: A Journal of Integrative Biology. 21, 413-425. [PubMed]

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]

Advani, J., Subbannayya, Y., Patel, K., Khan, A. A., Patil, A. H., Jain, A. P., Solanki, H. S., Radhakrishnan, A., Pinto, S. M., Sahasrabuddhe, N. A., Thomas, J. K., Mathur, P. P., Nair, B. P., Chang, X., Prasad, T. S. K., Sidransky, D., Gowda, H. and Chatterjee, A. (2017). Long term cigarette smoke exposure and changes in miRNA expression and proteome in non-small cell lung cancer. OMICS: A Journal of Integrative Biology. 21, 390-403. [PubMed]

Muthusamy, B., Selvan, L. D. N., Nguyen, T. T., Manoj, J., Stawiski, E. W., Jaiswal, B. S., Wang, W., Raja, R., Ramprasad, V. L., Gupta, R., Murugan, S., Kadandale, J. S., Prasad, T. S. K., Reddy, K., Perterson, A., Pandey, A., Seshagiri, S., Girimaji, S. C. and Gowda, H. (2017). Next Generation Sequencing Reveals Novel Mutations in X-linked Intellectual Disability. OMICS: A Journal of Integrative Biology. 21, 295-303. [PubMed]

Kumar, S., Kumar, M., Ekka, R., Dvorin, J. D., Paul, A. S., Madugundu, A. K., Gilberger, T., Gowda, H., Duraisingh, M. T., Prasad, T. S. K. and Sharma, P. (2017). PfCDPK1 mediated signaling in erythrocytic stages of Plasmodium falciparum. Nature Communications. 8, 63. [PubMed]

Verma, R., Pinto, S., Patil, A. H., Advani, J., Subba, P., Kumar, M., Sharma, J., Dey, G., Ravikumar, R., Buggi, S., Satishchandra, P., Sharma, K., Suar, M. T., Srikanth, C., Singh, D., Gowda, H., Pandey, A., Gandotra, S. and Prasad, T. S. K. (2017). Quantitative proteomic and phosphoproteomic analysis of H37Ra and H37Rv strains of Mycobacterium tuberculosis. Journal of Proteome Research. 16, 1632-1645. [PubMed]

Cutler, J. A., Tahir, R., Sreenivasamurthy, S. K., Mitchell, C., Renuse, S., Nirujogi, R. S., Patil, A. H., Heydarian, M., Wong, X., Wu, X., Huang, T. C., Kim, M. S., Reddy, K. and Pandey, A. (2017). Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis. Leukemia. 31, 1513-1524. [PubMed]

Yadavalli, S., Jayaram, S., Manda, S. S., Madugundu, A. K., Nayakanti, D. S., Tan, T. Z., Bhat, R., Rangarajan, A., Chatterjee, A., Gowda, H., Thiery, J. P. and Kumar, P. (2017). Data-Driven Discovery of Extravasation Pathway in Circulating Tumor Cells. Scientific Reports. 7, 43710. [PubMed]

Tiwari, R., Sahu, I., Soni, B. L., Sathe, G. J., Datta, K. K., Thapa, P., Sinha, S., Vadivel, C. K., Dhaka, B., Sinha, S., Gowda, H. and Vaidya, M. M. (2017). Quantitative phosphoproteomic analysis reveals system-wide signaling pathways regulated by site-specific phosphorylation on Keratin-8 in skin squamous cell carcinoma derived cell-line. Proteomics. 17, 7. [PubMed]

Dammalli, M., Murthy, K. R., Pinto, S. M., Murthy, K. B., Nirujogi, R. S., Madugundu, A. K., Dey, G., Nair, B., Gowda, H. and Prasad, T. S. K. (2017). Towards post-genomics ophthalmology: A proteomic map of the human choroid-retinal pigment epithelium tissue. OMICS: A Journal of Integrative Biology. 21, 114-122. [PubMed]

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. 7. [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. 27, 133-144. [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]

Patel, K., Singh, M. and Gowda, H. (2017). Bioinformatics Methods to Deduce Biological Interpretation from Proteomics Data. Methods Mol Biol. 1549, 147-161. [PubMed]

Jayaram, S., Gupta, M. K., Raju R., Gautam, P. and Sirdeshmukh, R. (2016). Multi-Omics Data Integration and Mapping of Altered Kinases to Pathways Reveal Gonadotropin Hormone Signaling in Glioblastoma. Omics: A journal of integrative biology. 20, 736-746. [PubMed]

Datta, K. K., Dhaka, B., Patel, K., Puttamallesh, V. N. and Gowda, H. (2016). Phosphoproteomic profiling using biopsy-scale protein amounts. Journal of Proteins and Proteomics. 7, 305-309. [PubMed]

Mir, S. A., Pinto, S. M., Paul, S., Raja, R., Nanjappa, V., Syed, N., Advani, J., Renuse, S., Sahasrabuddhe, N. A., Prasad, T. S. K., Giri, A. K., Gowda, H. and Chatterjee, A. (2016). SILAC-based quantitative proteomic analysis reveals widespread molecular alterations in human skin keratinocytes upon chronic arsenic exposure. Proteomics. 17, 6. [PubMed]

Ugolino, J., Ji J. Y., Conchina, K., Chu, J., Nirujogi, R. S., Pandey, A., Brady, N. R., Hamacher-Brady, A. and Wang. J. (2016). Loss of C9orf72 enhances autophagic activity via deregulated mTOR and TFEB signaling. Plos Genetics. 12, e1006443. [PubMed]

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]

Bhat, A. R., Gupta, M. K., Krithivasan, P., Dhas, K., Nair, J., Reddy, R. B., Sudheendra, H. V., Chavan, S., Vardhan, H., Darsi, S., Balakrishnan, L., Katragadda, S., Kekatpure, V., Suresh, A., Tata, P., Panda, B., Kuriakose, M. A. and Sirdeshmukh, R. (2016). Sample Preparation Method Considerations for Integrated Transcriptomic and Proteomic Analysis of Tumors. Proteomics - Clinical Applications. 11, 3-4. [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]

Sharma, N., LaRusch, J., Sosnay, P., Gottschalk, L. B., Lopez, A., Pellicore, M. J., Evans, T., Davis, E., Atalar, M., Na, C. H., Rosson, G. D., Belchis, D., Milewski, M., Pandey, A. and Cutting, G. R. (2016). A sequence upstream of canonical PDZ binding motif within CFTR C-terminus enhances NHERF1 interaction. American Journal of Physiology-Lung Cellular and Molecular Physiology. 311, 1170-1182. [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. 13, 29. [PubMed]

Rajagopalan, P., Nanjappa, V., Raja, R., Jain, A. P., Mangalparthi, K. K., Sathe, G. J., Babu, N., Patel, K., Cavusoglu, N., Soeur, J., Pandey, A., Roy, N., Breton, L., Chatterjee, A., Misra, N. and Gowda, H. (2016). How does chronic cigarette smoke exposure affect human skin? A global proteomics study in primary human keratinocytes. OMICS: A Journal of Integrative Biology. 20, 615-626. [PubMed]

Raja, R., Sahasrabuddhe, N. A., Radhakrishnan, A., Syed, N., Solanki, H. S., Puttamallesh V. N., Balaji S. A., Nanjappa V., Datta, K. K., Babu, N., Renuse, S., Patil, A. H., Izumchenko, E., Prasad, T. S., Chang X., Rangarajan A., Sidransky, D., Pandey, A., Gowda, H. 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]

Mehta, S., Sreenivasamurthy, S., Banerjee, S., Mukherjee, S., Prasad, 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., Kumar, M., Madugundu, A. K., Gopalakrishnan, L., Dey, G., Chavan, S., Sathe, G., Mathur, P. P., Gowda, H., Mahadevan, A., Shankar, S. K. and Prasad, T. S. K. (2016). Characterization of human pineal gland proteome. Molecular Biosystems. 12, 3622-3632. [PubMed]

Cha, S. J., Kim, M. S., Pandey, A. and Jacobs-Lorena, M. (2016). Identification of GAPDH on the surface of Plasmodium sporozoites as a new candidate for targeting malaria liver invasion. Journal of Experimental Medicine. 213, 2099-2112. [PubMed]

Zhang, H., Liu, T., Zhang, Z., Payne, S. H., Zhang, B., McDermott, J. E., Zhou, J. Y., Petyuk, V. A., Chen, L., Ray, D., Sun, S., Yang, F., Chen, L., Wang, J., Shah, P., Cha, S. W., Aiyetan, P., Woo, S., Tian, Y., Gritsenko, M. A., Clauss, T. R., Choi, C., Monroe, M. E., Thomas, S., Nie, S., Wu, C., Moore, R. J., Yu, K. H., Tabb, D. L., Fenyö, D., Bafna, V., Wang, Y., Rodriguez, H., Boja, E. S., Hiltke, T., Rivers, R. C., Sokoll, L., Zhu, H., Shih, I. M., Cope, L., Pandey, A., Zhang, B., Snyder, M. P., Levine, D. A., Smith, R. D., Chan, D. W., Rodland, K. D. and CPTAC Investigators. (2016). Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. 166, 755-765. [PubMed]

Bhattacharjee, M., Balakrishnan, L., Renuse, S., Advani, J., Goel, R., Sathe, G., Prasad, T. S. K., Nair, B., Jois, R., Shankar, S. and Pandey, A. (2016). Synovial fluid proteome in rheumatoid arthritis. Clinical Proteomics. 13, 12. [PubMed]

Mitchell, C. J., Kim, M. S., Na, C. H. and Pandey, A. (2016). PyQuant: a versatile framework for analysis of quantitative mass spectrometry data. Molecular and Cellular Proteomics. 15, 2829-2838. [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. and Mukherjee, K. K. (2016). Signaling network map of aryl hydrocarbon receptor. Journal of Cell Communication and Signaling. 10, 341-346. [PubMed]

Murthy, K. R., Dammali, M., Pinto, S. M., Murthy, K. B., Nirujogi, R. S., Madugundu, A. K., Dey, G., Subbannayya, Y., Mishra, U. K., Nair, B., Gowda, H. and Prasad, T. S. K. (2016). A comprehensive proteomics analysis of the human iris tissue: Ready to embrace postgenomics precision medicine in ophthalmology? OMICS: A Journal of Integrative Biology. 20, 510-519. [PubMed]

Polisetty, R. V., Gautam, P., Gupta, M. K., Sharma, R., Gowda, H., Renu, D., Shivakumar, B. M., Lakshmikantha, A., Mariswamappa, K., Ankathi, P., Purohit, A. K., Uppin, M. S., Challa, S. and Sirdeshmukh, R. (2016). Microsomal membrane proteome of low grade diffuse astrocytomas: Differentially expressed proteins and candidate surveillance biomarkers. Scientific Reports. 6, 26882. [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, 165-170. [PubMed]

Barua, P., Subba, P., Lande, N. V., Mangalaparthi, K. K., Prasad, T. S. K., Chakraborty, S. and 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., Madugundu, A. K. and Gowda, H. (2016). Proteogenomic methods to improve genome annotation. Methods in Molecular Biology. 1410, 77-89. [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]

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]

Mitchell, C. J., Kim, M. S., Zhong, J., Nirujogi, R. S., Bose, A. K. and Pandey, A. (2016). Unbiased identification of substrates of protein tyrosine phosphatase ptp-3 in C. elegans. Molecular Oncology. 10, 910-920. [PubMed]

Mirsafian, H., Manda, S. S., Mitchell, C. J., Sreenivasamurthy, S., Ripen, A. M., Mohamad, S. B., Merican, A. F. and Pandey, A. (2016). Long non-coding RNA expression in human primary monocytes. Genomics. 108, 37-45. [PubMed]

Marikanty, R. K., Gupta, M. K., Cherukuvada, S. V. B., Kompella, S. S. S., Prayaga, A. K., Konda, S. Polisetty, R. V., Idris, M. M., Rao, P. V., Chandak, G. R. and Dakshinamurty, K. V. (2016). Identification of urinary proteins potentially associated with diabetic kidney disease. Indian Journal of Nephrology. 6, 434-445. [PubMed]

Pawar, H., Manda, S. S., Kashyap, M. K., Sathe, G. J., Chavan, S., Singal, M., Manju, H. C., Kumar, K. V. V., Vijayakumar, M., Sirdeshmukh, R., Pandey, A., Prasad, T. S. K., Gowda, H. and Kumar R. V. (2016). Downregulation of S100 Calcium Binding Protein A9 in Esophageal Squamous Cell Carcinoma. The Scientific World Journal. 2015, 325721. [PubMed]

Subbannayya, Y., Pinto, S. M., Gowda, H. and Prasad, T. S. K. (2015). Proteogenomics for understanding oncology: recent advances and future prospects. Expert Review of Proteomics. 13, 297-308 [PubMed] 

Yelamanchi, S. D., Jayaram, S., Thomas, J. K., Gundimeda, S., Khan, A. A., Singhal, A., Prasad, T. S. K., Pandey, A., Somani, B. L. and Gowda, H. (2015). A pathway map of glutamate metabolism. Journal of Cell Communication and Signaling. 10, 69-75 [PubMed] 

Gupta, M. K., Jayaram, S., Reddy, D. N., Polisetty, R. V. and Sirdeshmukh, R. (2015). Transcriptomic and Proteomic Data Integration and Two-Dimensional Molecular Maps with Regulatory and Functional Linkages: Application to Cell Proliferation and Invasion Networks in Glioblastoma. Journal of Proteome Research. 14, 5017-5027. [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]

Baras, A. S., Mitchell, C. J., Myers, J. R., Gupta, S., Weng, L. C, Ashton, J. M., Cornish, T. C., Pandey, A. and Halushka, M. K. (2015). miRge - A multiplexed method of processing small RNA-Seq data to determine microRNA entropy. PLoS One. 10, e0143066. [PubMed] 

Li, R., Liao, G., Nirujogi, R. S., Pinto, S. M., Shaw, P. G., Huang, T. C., Wan, J., Qian, J., Gowda, H., Wu, X., Lv, D. W., Zhang, K., Manda, S. S., Pandey, A. and Hayward, S. D. (2015). Phosphoproteomic profiling reveals Epstein-Barr Virus protein kinase integration of DNA damage response and mitotic signaling. PLoS Pathogens. 11, e1005346. [PubMed] 

Sharma, A., Varghese, A. M., Vijaylakshmi, K., Sumitha, R., Prasanna, V. K., Shruthi, S., Sagar, C. B. K., Datta, K. K., Gowda, H., Nalini, A., Alladi, P. A., Christopher, R., Sathyaprabha, T. N., Raju, T. R. and Bharath, S. M. M. (2015). Cerebrospinal Fluid from Sporadic Amyotrophic Lateral Sclerosis Patients Induces Mitochondrial and Lysosomal Dysfunction. Neurochemical Research. 41, 965-84. [PubMed]

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

Raju, R., Gadakh, S., Gopal, P., George, B., Advani, J., Soman, S., Prasad, T. S. K. and Reshmi, G. (2015). Differential ligand-signaling network of CCL19/CCL21-CCR7 system. Database. 2015, bav106. [PubMed] 

Beachley, V. Z., Wolf, M. T., Sadtler, K. K., Manda, S. S., Jacobs, H., Blatchley, M. R., Bader, J. S., Pandey, A., Pardoll, D. and Elisseeff, J. H. (2015). Tissue matrix arrays for high-throughput screening and systems analysis of cell function. Nature Methods. 12, 1197-1204. [PubMed]

Wu X., Zahari M. S., Renuse S., Nirujogi R. S., Kim M. S., Manda S. S., Stearns V., Gabrielson E., Sukumar S. and Pandey A. (2015). Phosphoproteomic analysis identifies FAK2 as a potential therapeutic target for tamoxifen resistance in breast cancer. Molecular and Cellular Proteomics. 14, 2887-2900. [PubMed] 

Wu, X., Zahari, M. S., Ma, B., Liu, R., Renuse, S., Sahasrabuddhe N. A., Chen, L., Chaerkady, R., Kim, M. S., Zhong, J., Jelinek, C., Bharbuiya, M. A., Leal-Rojas, P., Yang, Yi., Kashyap, M. K., Marimuthu, A., Ling, M., Fackler, M. J., Merino, V., Zhang, Z., Zahnow, C. A., Gabrielson, E., Stearns, V., Roa, J. C., Sukumar, S., Gill, P. S. and Pandey, A. (2015). Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways. Oncotarget. 6, 29143-29160. [PubMed] 

Zahari, M. S., Wu, X., Blair, B. G., Pinto, S. M., Nirujogi, R. S., Jelinek, C. A., Malhotra, R., Kim, M. S., Park, B. H. and Pandey, A. (2015). Activating mutations in PIK3CA lead to widespread modulation of the tyrosine phosphoproteome. Journal of Proteome Research. 14, 3882-3891. [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]

Zahari, M. S., Wu, X., Pinto, S. M., Nirujogi, R. S., Kim, M. S., Fetics, B., Philip, M., Barnes, S. R., Godfrey, B., Gabrielson, E., Nevo, E. and Pandey, A. (2015). Phosphoproteomic profiling of tumor tissues identifies HSP27 Ser82 phosphorylation as a robust marker of early ischemia. Scientific Reports. 5, 13660. [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] 

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, 1-11. [PubMed]  

Verma, R., Balakrishnan, L., Sharma. K., Khan A. A., Advani, J., Gowda, H., Tripathy, S.P., Suar, M., Pandey, A., Gandotra, S., Prasad, T. S. K. and Subramanian, S. (2015). A network map of Interleukin-10 signaling pathway. Journal of Cell Communication and Signaling. 51, 1-7. [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. and 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] 

Jayaram, S., Gupta M, K., Marigowda, S, B., Ghatge, M., Sharma, A., Vangala, R. K. and Sirdeshmukh, R. (2015). Insights from chromosome-centric mapping of disease associated genes - chromosome 12 perspective. Journal of Proteome Research. 14, 3432-3440. [PubMed] 

Ewing, A. D., Gacita, A., Wood, L. D., Ma, F., Xing, D., Kim, M. S., Manda, S. S., Abril, G., Pereira, G., Makohon-Moore, A., Looijenga, L. H., Gillis, A. J., Hruban, R. H., Anders, R. A., Romans, K. E., Pandey, A., Iacobuzio-Donahue, C. A., Vogelstein, B., Kinzler, K. W., Kazazian, H. H. Jr. and Solyom, S. (2015). Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Research. 25, 1536-1545. [PubMed] 

Sivadasan, P., Gupta, M. K., Sathe, G. J., Balakrishnan, L., Palit, P., Gowda, H., Suresh, A., Kuriakose, M. A. and Sirdeshmukh, R. (2015). Data from Human salivary proteome - a resource of potential biomarkers for oral Cancer. Data in Brief. 4, 374-378. [PubMed] 

Y, Yu., Gaillard, S., Phillip, M. J., Huang, T., Pinto, M. S., Tessarollo, G. N., Zhang, Z., Pandey, A., Wirtz, D., Ayhan, A., Davidson, B., Wang, T. and Shih, I. (2015). Inhibition of Spleen Tyrosine Kinase Potentiates Paclitaxel-Induced Cytotoxicity in Ovarian Cancer Cells by Stabilizing Microtubules. Cancer Cell. 28, 82-96. [PubMed] 

Daswani, B., Gupta, M. K., Gavali, S., Desai, M., Sathe, G. J., Patil, A., Parte, P., Sirdeshmukh, R. and Khatkhatay, M. I. (2015). Monocyte Proteomics Reveals Involvement of Phosphorylated HSP27 in the Pathogenesis of Osteoporosis. Disease Markers. 2015, 196589. [PubMed] 

Sivadasan, P., Gupta, M. K., Sathe, G. J., Balakrishnan, L., Palit, P., Gowda, H., Suresh, A., Kuriakose, M. A. and Sirdeshmukh, R. (2015). Human salivary proteome - a resource of potential biomarkers for oral cancer. Journal of Proteomics. 127, 89-95. [PubMed] 

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

Mir, S. A., Rajagopalan, P., Jain, A. P., Khan, A. A., Datta, K. K., Mohan, S. V., Lateef, S. S., Sahasrabuddhe, N., Somani, B. L., Prasad, T. S. K., Chatterjee, A., Kumar, K. V. V., Kumar, M. V., Kumar, R. V., Gundimeda, S., Pandey, A. and Gowda H. (2015). LC-MS-based serum metabolomic analysis reveals dysregulation of phosphatidylcholines in esophageal squamous cell carcinoma. Journal of Proteomics. S1874-3919. [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. S1874-3919. [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] 

Sirdeshmukh, R. (2015). Indian proteomics efforts and human proteome project. Journal of Proteomics. 127, 147-151. [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] 

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]

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]

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]

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]

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

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

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] 

Zhong, J., Martinez, M., Sengupta, S., Lee, A., Wu, X., Chaerkady, R., Chatterjee, A., O´Meally, R. N., Cole, R. N., Pandey, A. and Zachara, N. E. (2015). Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway. Proteomics. 15, 591-607. [PubMed]

Zhang, X., Belkina, N., Jacob, H. K., Maity, T., Biswas, R., Venugopalan, A., Shaw, P. G., Kim, M. S., Chaerkady, R., Pandey, A. and Guha U. (2015). Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics. Proteomics. 15, 340-355. [PubMed]

Nirujogi, R. S., Wright, J. D., Manda, S. S., Zhong, J., Na, C. H., Meyerhoff, M., Benton, M. B., Jabbour, R., Willis, K., Kim, M. S., Pandey, A. and Sekowski, J. W. (2015). Phosphoproteomic analysis reveals compensatory effects in the piriform cortex of VX nerve agent exposed rats.  Proteomics. 15, 487-499. [PubMed]

Huang, T. C., Renuse, S., Pinto, S., Kumar, P., Yang, Y., Chaerkady, R., Godsey, B., Mendell, J. T., Halushka, M. K., Civin, C. I., Marchionni, L. and Pandey, A. (2015). Identification of miR-145 targets through an integrated omics analysis. Molecular Biosystems. 11, 197-207. [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., Gajbhiye, A., Prasad, T. S. K., Rapole, S., Panda, D. and Srivastava, S. (2015). Comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. Journal of Proteomics. 114, 247-262. [PubMed] 

Kagohara, L. T., Schussel, J., Subbannayya, T., Sahasrabuddhe, N., Lebron, C., Brait, M., Maldonado, L., Valle, V. B., Pirini, F., Jahuira, M., Lopez, J., Letelier, P., Brebi-Mieville, P., Ili, C., Pandey, A., Chatterjee, A., Sidransky, D. and Guerrero-Preston, R. (2015). Global and gene-specific DNA methylation pattern discriminates cholecystitis from gallbladder cancer patients in Chile. Future Oncology. 11, 233-249. [PubMed]

Maras, J. S., Maiwall, R., Harsha, H. C., Das, S., Hussain, S., Kumar, C., Bihari, C., Rastogi, A., Kumar, M., Trehanpati, N., Sharma, S., Pandey, A. and Sarin, S, K. (2015). Dysregulated iron homeostasis is strongly associated with multi-organ failure and early mortality in acute-on-chronic liver failure. Hepatology. 61, 1306-1320.  [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]

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]

Wu, X., Renuse, S., Sahasrabuddhe, N. A., Zahari, M. S., Chaerkady, R., Kim, M. S., Nirujogi, R. S., Mohseni, M., Kumar, P., Raju, R., Zhong, J., Yang, J., Neiswinger, J., Jeong, J. S., Newman, R., Powers, M. A., Somani, B. L., Gabrielson, E., Sukumar, S., Stearns, V., Qian, J., Zhu, H., Vogelstein, B., Park, B. H. and Pandey, A. (2014). Activation of diverse signaling pathways by oncogenic PIK3CA mutations. Nature Communications. 5, 4961.  [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.  

Kim, M. S., Zhong, Y., Yachida, S., Rajeshkumar, N. V., Abel, M., Marimuthu, A., Mudgal, K., Hruban, R. H., Tyner, J. W., Maitra, A., Iacobuzio-Donahue, C. A. and Pandey, A. (2014). Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics.  Molecular and Cellular Proteomics. 13, 2803-11. [PubMed]

Kelkar, D. S., Provost. E., Chaerkady, R., Muthusamy, B., Manda, S. S., Subbannayya, T., Selvan, L. D. N., Wang, C. H., Datta, K. K., Woo, S., Dwivedi, S. B., Renuse, S., Getnet, D., Huang, T. C., Kim, M. S., Pinto, S. M., Mitchell, C. J., Madugundu, A. K., Kumar, P., Sharma, J. Advani, J., Dey, G., Balakrishnan, L., Syed, N., Nanjappa, V., Subbannayya, Y., Goel, R., Prasad, T. S. K., Bafna, V., Sirdeshmukh, R., Gowda, H., Wang, C., Leach, S. D. and Pandey, A. (2014). Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Molecular and Cellular Proteomics. 13, 3184-98. [PubMed]

Renuse, S., Madugundu, A. K., Kumar, P., Nair, B., Gowda, H., Prasad, T. S. K., and Pandey, A. (2014). Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host. Proteomics. 14, 2769-79. [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]

Wu, X., Zahari, M. S., Renuse, S., Sakamuri, S., Singal, M., Gabrielson, E., Sukumar, S. and Pandey, A. (2014). A breast cancer cell microarray (CMA) as a rapid method to characterize candidate biomarkers.  Cancer Biology and Therapy. 15, 1593-9. [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]

Sahasrabuddhe, N. A., Huang, T. C., Ahmad, S., Kim, M. S., Yang, Y., Ghosh, B., Leach, S. D., Gowda, H., Somani, B. L., Chaerkady, R. and Pandey, A. (2014). Regulation of PPAR-alpha pathway by Dicer revealed through Proteomic analysis. Journal of Proteomics. 108, 306-315.  [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]

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]

Jayaram, S., Gupta, M. K., Polisetty, R. V., Cho, W. C. and Sirdeshmukh, R. (2014). Towards developing biomarkers for Glioblastoma Multiforme: a proteomics view. Expert Review of Proteomics. 5, 621-639. [PubMed]

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

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

Manda, S. S., Nirujogi, R. S., Pinto, S., Kim, M. S., Datta, K. 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]

Gupta, M. K., Jayaram, S., Madugundu, A. K., Chavan, S., Advani, J., Pandey, A., Thongboonkerd, V., Sirdeshmukh, R. (2014). Chromosome-Centric Human Proteome Project: Deciphering Proteins Associated with Glioma and Neurodegenerative Disorders on Chromosome 12. Journal of Proteome Research. 13, 3178-3190. [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]

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

Soni, B. L., Marimuthu, A., Pawar, H., Sawant, S. S., Borges, A., Kannan, R., Pandey, A., Ingle, A. D., Harsha, H. C., Vaidya, M. M.(2014). Quantitative proteomic analysis of different stages of rat lingual carcinogenesis. Clinical Communications Oncology. 1, 2. [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, 421-37. [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]

Sahasrabuddhe, N. A., Barbhuiya, M. A., Bhunia, S., Subbannayya, T., Gowda, H., Advani, J., Shrivastav, B. R., Navani, S., Leal, P., Roa, J. C., Chaerkady, R., Gupta, S., Chatterjee, A., Pandey, A. and Tiwari, P. K. (2014). Identification of Prosaposin and Transgelin as potential biomarkers for gallbladder cancer using quantitative proteomics. Biochemical and Biophysical Research Communications. 446, 863-869.  [PubMed]

Subbannayya, Y., Anuja, K., Advani, J., Ojha, U. K., Nanjappa, V., George, B., Sonawane, A., Kumar, R. V., Ramaswamy, G., Pandey, A., Somani, B. L. and Raju, R. (2014). A network map of the Gastrin signaling pathway. Journal of Cell Communication and Signaling. 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]

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]

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]

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

Balakrishnan, L., Bhattacharjee, M., Ahmad, S., Nirujogi, R. S., Renuse, S., Subbannayya, Y., Marimuthu, A., Srikanth, S. M., Raju, R., Dhillon, M., Kaur, N., Jois, R., Vasudev, V., Ramachandra, Y. L., Sahasrabuddhe, N. A., Prasad, T. S. K., Mohan, S., Gowda, H., Shankar, S. and Pandey, A. (2014). Differential proteomic analysis of synovial fluid from rheumatoid arthritis and osteoarthritis patients. Clinical Proteomics. 11, 1. [PubMed]

Ramadasan-Nair, R., Gayathri, N., Mishra, S., Sunitha, B., Mythri, R., Nalini, A., Subbannayya, Y., Harsha, H. C., Kolthur-Seetharam, U. and Bharath, M. M. (2014). Mitochondrial alterations and oxidative stress in an acute transient mouse model of muscle degeneration: Implications for muscular dystrophy and related muscle pathologies. Journal of Biological Chemistry. 289, 485-509. [PubMed]

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

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

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

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

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

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

Hansen, A. M., Chaerkady, R., Sharma, J., Díaz-Mejía, J. J., Tyagi, N., Renuse, S., Jacob, H. K. C., Pinto, S. M., Sahasrabuddhe, N. A., Kim, M. S., Delange, B., Srinivasan, N., Emili, A., Kaper, J. and Pandey, A. (2013). The Escherichia coli phosphotyrosine proteome relates to core pathways and virulence. PLoS Pathogens. 9, e1003403. [PubMed]

Chaerkady, R., Shao, H., Scott, S. G., Pandey, A., Jun A. S. and Chakravarti, S. (2013). The keratoconus corneal proteome: loss of epithelial integrity and stromal degeneration. Journal of Proteomics. 87, 122-131. [PubMed]

Ambekar, S. A., Nirujogi, R. S., Srikanth, S. M., Chavan, S., Kelkar, D. S., Hinduja, I., Zaveri, K., Prasad, T. S. K., Harsha, H. C., Pandey, A. and Mukherjee, S. (2013). Proteomic analysis of human follicular fluid: A new perspective towards understanding folliculogenesis. Journal of Proteomics. 87, 68-77. [PubMed]

Polisetty, R. V., Gautam, P., Gupta, M. K., Sharma, R., Uppin, M. S., Challa, S., Ankathi, P., Purohit, A. K., Renu, D., Harsha, H. C., Pandey, A. and Sirdeshmukh, R. (2013). Heterogeneous nuclear ribonucleoproteins and their interactors are a major class of deregulated proteins in anaplastic astrocytoma – a Grade III malignant glioma. Journal of Proteome Research. 12, 3128-3138. [PubMed]

Marimuthu, A., Chavan, S., Sathe, G. J., Sahasrabuddhe, N. A., Srikanth, S. M., Renuse, S., Ahmad, S., Radhakrishnan, A., Barbhuiya, M. A., Kumar, R. V., Harsha, H. C., Sidransky, D., Califano, J., Pandey, A. and Chatterjee, A. (2013). Identification of head and neck squamous cell carcinoma biomarker candidates through proteomic analysis of cancer cell secretome. BBA - Proteins and Proteomics. 1834, 2308-2316. [PubMed]

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]

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]

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]

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]

Newman, R. H., Hu, J., Rho, H. S., Xie, Z., Woodard, C., Neiswinger, J., Cooper, C., Shirley, M., Clark, H. M., Hu, S., Hwang, W., Jeong, J. S., Wu, G., Lin, J., Gao, X., Ni, Q., Goel, R., Xia, S., Ji, H., Dalby, K. N., Birnbaum, M. J., Cole, P. A., Knapp, S., Ryazanov, A. G, Zack, D. J., Blackshaw, S., Pawson, T., Gingras, A. C., Desiderio, S., Pandey, A., Turk, B. E, Zhang, J., Zhu, H. and Qian, J. (2013). Construction of human activity-based phosphorylation networks. Molecular Systems Biology. 9, 655. [PubMed]

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

Gupta, M. K., Polisetty, R. V., Ramamoorthy, K., Tiwary, S., Kaur, N., Shiras, A. and Sirdeshmukh, R. (2013). Secretome analysis of Glioblastoma cell line - HNGC-2. Molecular BioSystems. 9, 1390-1400. [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]

Mushahary, D., Gautam, P., Sundaram, C. S. and Sirdeshmukh, R. (2013). Expanded protein expression profile of human placenta using two-dimensional gel electrophoresis. Placenta. 34, 193-196. [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]

Huang, T. C., Pinto, S. M. and Pandey, A. (2013). Proteomics for understanding microRNA biology. Proteomics. 13, 558-567. [PubMed]

Soman, S., Raju, R., Sandhya, V. K., Advani, J., Khan, A. A., Harsha, H. C., Prasad, T. S. K., Sudhakaran, P. R., Pandey, A. and Adishesha, P. K. (2013). A multicellular signal transduction network of AGE/RAGE signaling. Journal of Cell Communication and Signaling. 7, 19-23. [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. (2013). Downregulation of cornulin in esophageal squamous cell carcinoma. Acta Histochemica. 115, 89-99. [PubMed]

Marimuthu, A., Subbannayya, Y., Sahasrabuddhe, N. A., Balakrishnan, L., Syed, N., Sekhar, N. R., Katte, T. V., Pinto, S. M., Srikanth, S. M., Kumar, P., Pawar, H., Kashyap, M. K., Maharudraiah, J., Ashktorab, H., Smoot, D. T., Ramaswamy, G., Kumar, R. V., Cheng, Y., Meltzer, S. J., Roa, J. C., Chaerkady, R., Prasad, T. S. K., Harsha, H. C., Chatterjee, A. and Pandey, A. (2012). SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics - Clinical Applications. 7, 355-366. [PubMed]

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]

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]

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]

Gautam, P., Nair, S. C., Gupta, M. K., Sharma, R., Polisetty, R. V., Uppin, M. S., Challa, S., Puligopu, A. K., Ankathi, P., Purohit, A. K., Chandak, G. R., Harsha, H. C. and Sirdeshmukh, R. (2012). Proteins with altered levels in plasma from glioblastoma patients as revealed by iTRAQ-based quantitative proteomic analysis. PLOS ONE. 7, e46153. [PubMed]

Telikicherla, D., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Mohan, S., Roa, J. C., Maharudraiah, J., and Pandey, A. (2012). Overexpression of Ribosome Binding Protein 1 (RRBP1) in breast cancer. Clinical Proteomics. 2012, 9, 7. [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]

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]

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

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]

Telikicherla, D., Maharudraiah, J., Pawar, H., Marimuthu, A., Kashyap, M. K., Ramachandra, Y. L., Roa, J. C. and Pandey, A. (2012). Overexpression of Kinesin Associated Protein 3 (KIFAP3) in Breast Cancer. Journal of Proteomics and Bioinformatics. 5, 122-126. [PubMed]

Martinez-Ferrando, I., Chaerkady, R., Zhong, J., Molina, H., Kishore, H., Herbst-Robinson, K., Dancy, B. M., Katju, V., Bose, R., Zhang, J., Pandey, A. and Cole, P. A. (2012). Identification of targets of c-Src tyrosine kinase by chemical complementation and phosphoproteomics. Molecular and Cellular Proteomics. 11, 355-369. [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]

Venugopal, A. K., Kumar, G. S. S., Mahadevan, A., Selvan, L. D. N., Marimuthu, A., Dikshit, J. B., Tata, P., Ramachandra, Y. L., Chaerkady, R., Sinha, S., Chandramouli, B. A., Arivazhagan, A., Satishchandra, P., Shankar, S. K. and Pandey, A. (2012). Transcriptomic profiling of medial temporal lobe epilepsy. Journal of Proteomics and Bioinformatics. 5, 31-39. [PubMed]

Agyeman, A. S., Chaerkady, R., Shaw, P. G., Davidson, N. E., Visvanathan, K., Pandey, A. and Kensler, T. W. (2012). Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane treated human breast epithelial cells reveals common expression profiles. Breast Cancer Research and Treatment. 132, 175-187. [PubMed]

Zhong, J., Kim, M. S., Chaerkady, R., Wu, X., Huang, T. C., Getnet, D., Mitchell, C. J., Palapetta, S. M., Sharma, J., O'Meally, R. N., Cole, R. N., Yoda, A., Moritz, A., Loriaux, M. M., Rush, J., Weinstock, D. M., Tyner, J. W. and Pandey, A. (2012). TSLP signaling network revealed by SILAC-based phosphoproteomics. Molecular and Cellular Proteomics. 11, M112.017764. [PubMed]

Huang, T. C., Sahasrabuddhe, N. A., Kim, M. S., Getnet, D., Yang, Y., Peterson, J. M., Ghosh, B., Chaerkady, R., Leach, S. D., Marchionni, L., Wong, G. W. and Pandey A. (2012). Regulation of lipid metabolism by Dicer revealed through SILAC Mice. Journal of Proteome Research. 11, 2193-2205. [PubMed]

Polisetty, R. V., Gautam, P., Sharma, R., Harsha, H. C., Nair, S. C., Gupta, M. K., Uppin, M. S., Challa, S., Puligopu, A. K., Ankathi, P., Purohit, A. K., Chandak, G. R., Pandey, A. and Sirdeshmukh, R. (2012). LC-MS/MS analysis of differentially expressed glioblastoma membrane proteome reveals altered calcium signalling and other protein groups of regulatory functions. Molecular and Cellular Proteomics. 11, M111.013565. [PubMed]

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

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

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

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

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]

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

Kinsinger, C. R., Apffel, J., Baker, M., Bian, X., Borchers, C. H., Bradshaw, R. A., Brusniak, M. Y., Chan D. W., Deutsch, E. W., Domon, B., Gorman, J., Grimm, R., Hancock, W., Hermjakob, H., Horn, D., Hunter, C., Kolar, P., Kraus, H. J., Langen, H., Linding, R., Moritz, R. L., Omenn, G. S., Orlando, R., Pandey, A., Ping, P., Rahbar, A., Rivers, R., Seymour, S. L., Simpson, R. L., Slotta, D., Smith, R. D., Stein, S. E., Tabb, D. L., Tagle, D., Yates, J. R. 3rd. and Rodriguez, H. (2011). Recommendations for mass apectrometry data quality metrics for open access data (corollary to the Amsterdam principles). Molecular and Cellular Proteomics. 10, O111.015446. [PubMed]

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. 10, M111.011627. [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., Srikanth, M. S., Sathe, G. J., Ahmad, S., Chavan, S. N., Kumar, G. S. S., Marimuthu, A., Prasad, T. S. K., Harsha, H. C., Rahiman, B. A., Ohara, O., Bader, G. D., Mohan, S. S., Schiemann, W. P. and Pandey, A. (2011). NetSlim: High-confidence curated signaling maps. Database. 2011, bar032. [PubMed]

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

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]

Chaerkady, R., Letzen, B., Renuse, S., Sahasrabuddhe, N. A., Kumar, P., All, A. H., Thakor, N. V., Delanghe, B., Gearhart, J. D., Pandey, A. and Kerr, C. L. (2011). Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells. Proteomics. 11, 4007-4020. [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. 2110, bar021. [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. 12, 510-522. [PubMed]

Shao, H., Chaerkady, R., Chen, S., Pinto, S. M., Sharma, R., Delanghe, B., Birk, D., Pandey, A. and Chakravarti, S. (2011). Proteome profiling of wild type and lumican-deficient mouse corneas. Journal of Proteomics. 74, 1895-1905. [PubMed]

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

Marimuthu, A., O'Meally, R., Chaerkady, R., Subbannayya, Y., Nanjappa, V., Kumar, P., Kelkar, D., Pinto, S., Sharma, R., Renuse, S., Goel, R., Christopher, R., Delanghe, B., Cole, R. N., Harsha, H. C. and Pandey, A. (2011). A comprehensive map of the human urinary proteome. Journal of Proteome Research. 10, 2734-2743. [PubMed]

Shaw, P., Chaerkady, R., Zhang, Z., Davidson, N. and Pandey, A (2011). A monoclonal antibody cocktail as an enrichment tool for acetylome analysis. Analytical Chemistry.83, 3623-3626. [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). Gene expression profiling of tuberculous meningitis. Journal of Proteomics and Bioinformatics. 4, 98-105. [PubMed]

Amanchy, R., Kandasamy, K., Mathivanan, S., Periaswamy, B., Reddy, R., Yoon, W. H., Joore, J., Beer, M. A., Cope, L. and Pandey, A. (2011). Identification of novel phosphorylation motifs through an integrative computational and experimental analysis of the human phosphoproteome. Journal of Proteomics and Bioinformatics. 4, 22-35.[PubMed]

Prasad, T. S. K. and Chaerkady, R. (2011). 'Application of Quantitative Proteomic Approaches to Toxicology' In: Handbook of Systems Toxicology. Daniel A. Casciano and Saura C. Sahu Editors. John Wiley & Sons Limited. pp 217-226 .

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

Wang, Q., Chaerkady, R., Wu, J., Hwang, H., J., Papadopoulos, N., Kopelovich, L., Maitra, A., Matthei, H., Eshleman, J., Hruban, R., Kinzler, K. W., Pandey, A. and Vogelstein, B. (2011). Mutant proteins as cancer-specific biomarkers. Proceedings of the National Academy of Sciences U.S.A. 108, 2444-2449. [PubMed]

Renuse, S., Chaerkady, R. and Pandey, A. (2011). Proteogenomics. Proteomics. 11, 620-630. [PubMed]

Zhong, J., Chaerkady, R., Kandasamy, K., Gucek, M., Cole, R.N. and Pandey, A. (2011). The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. Journal of Proteomics. 74, 294-303. [PubMed]

Harsha, H. C. and Pandey, A. (2010). Phosphoproteomics in Cancer. Molecular Oncology. 4, 482-495. [PubMed]

Chen, H., Pimienta, G., Gu, Y., Sun, X., Hu, J., Kim, M. S., Chaerkady, R., Gucek, M., Cole, R. N., Sukumar, S. and Pandey, A. (2010). Proteomic characterization of Her2/neu-overexpressing breast cancer cells. Proteomics. 10, 3800-3810. [PubMed]

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

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. 48, 87-95. [PubMed]

Zhong, J., Krawczyk, S. A., Chaerkady, R., Huang, H., Goel, R., Bader, J. S., Wong, G. W., Corkey, B. E. and Pandey, A. (2010). Temporal profiling of the secretome during adipogenesis in humans. Journal of Proteome Research. 9, 5228-5238. [PubMed]

Alvarez, H., Montgomery, E. A., Karikari, C., Canto, M. I., Dunbar, K. B., Wang, J. S., Feldmann, G., Hong, S. M., Haffner, M. C., Meeker, A. K., Holland, S. J., Yu , J., Heckrodt, T. J., Zhang, J., Ding, P., Goff, D., Singh, R., Roa, J. C., Marimuthu, A., Riggins, G. J., Eshelman, J. R., Nelkin, B. D., Pandey, A. and Maitra, A. (2010). The Axl receptor tyrosine kinase is an adverse prognostic factor and a therapeutic target in esophageal adenocarcinoma. Cancer Biology and Therapy. 10, 1009-1018. [PubMed]

Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Novere, N. L., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C. and Bader, G. D. (2010). BioPAX - A community standard for pathway data sharing. Nature Biotechnology. 28, 935-942.[PubMed]

Kashyap, M .K., Harsha, H. C., Renuse, S., Pawar, H., Sahasrabuddhe, N. A., Kim, M. S., Marimuthu, A., Keerthikumar, S., Muthusamy, B., Kandasamy, K., Subbannayya, Y., Prasad, T. S. 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]

Yang, Y., Chaerkady, R., Kandasamy, K., Huang, T. C., Selvan, L. D. N., Dwivedi, S. B., Kent, O. A., Mendell, J. T. and Pandey, A. (2010). Identifying targets of miR-143 using a SILAC-based proteomic approach. Molecular Biosystems. 6, 1873-1882 . [PubMed]

Kim, M. S., Kandasamy, K., Chaerkady, R. and Pandey, A. (2010). Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. Journal of The American Society for Mass Spectrometry. 21, 1606-1611. [PubMed]

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

Chaerkady, R., Kerr, C. L., Kandasamy, K., Marimuthu, A., Gearhart, J. D. and Pandey, A. (2010). Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics. 10, 1359-1373. [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]

Zhou, Q., Chaerkady, R., Shaw, P. G., Kensler, T. W., Pandey, A. and Davidson, N. E. (2010). Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells. Proteomics. 10, 1029-1039. [PubMed]

Luo, W., Zhong, J., Chang, R., Hu, H., Pandey, A. and Semenza, G. L. (2010). HSP70 and CHIP selectively mediate ubiquitination and degradation of hypoxia-inducible factor (HIF)-1α but not HIF-2α. Journal of Biological Chemistry. 285, 3651-3663. [PubMed]

Amanchy, R., Zhong, J., Hong, R., Kim, J. H., Gucek, M., Cole, R. N., Molina, H. and Pandey, A. (2009). Identification of c-Src tyrosine kinase substrates in platelet-derived growth factor receptor signaling. Molecular Oncology. 3, 439-450. [PubMed]

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

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

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]

Venugopal, A., Chaerkady, R., Pandey, A. (2009). Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders. Annals of Indian Academy of Neurology. 12, 3-11. [PubMed]

Yang, Y., Chaerkady, R., Beer, M. A., Mendell, J. T. and Pandey, A. (2009). Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. Proteomics. 9, 1374-1384. [PubMed]

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

Ranganathan, P., Harsha, H. C. and Pandey, A. (2009). Molecular alterations in exocrine neoplasms of the pancreas. Archives of Pathology & Laboratory Medicine. 133, 405-412. [PubMed]

Chaerkady, R., Kerr, C. L., Marimuthu, A., Kelkar, D. S., Kashyap, M. K., Gucek, M., Gearhart, J. D. and Pandey, A. (2009). Temporal analysis of neural differentiation using quantitative proteomics. Journal of Proteome Research. 8, 1315-1326. [PubMed]

Molina, H., Yang, Y., Ruch, T., Kim, J. W., Mortensen, P., Otto, T., Nalli, A., Tang, Q. Q., Lane, M. D., Chaerkady, R. and Pandey, A. (2009). Temporal profiling of the adipocyte proteome during differentiation using a 5-plex SILAC based strategy. Journal of Proteome Research. 8, 48-58. [PubMed]

Ghosh, A. K., Devenport, M., Jethwaney, D., Kalume, D. E., Pandey, A., Anderson, V. E., Sultan, A. A., Kumar, N. and Jacobs-Lorena, M. (2009). Malaria parasite invasion of the mosquito salivary gland requires interaction between the Plasmodium TRAP and the Anopheles Saglin proteins. PLoS Pathogens. 5, e1000265. [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]

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]

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

Kristiansen, T. Z., Harsha, H. C., Grønborg, M., Maitra, A. and Pandey, A. (2008). Differential membrane proteomics using ¹⁸O-labeling to identify biomarkers for cholangiocarcinoma. Journal of Proteome Research. 8, 4670-4677. [PubMed]

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

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

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]

Guha, U., Chaerkady, R., Marimuthu, A., Patterson, S., Kashyap, M., Harsha, H. C., Bader, J., Lash, A., Pandey, A. and Varmus, H. E. (2008). Comparisons of tyrosine-phosphorylated proteins in immortalized human bronchial epithelial cells and lung adenocarcinoma cell lines expressing lung cancer-specific alleles of EGFR and KRAS. Proceedings of the National Academy of Sciences U.S.A. 105, 14112-14117. [PubMed]

Song, D., Chaerkady, R., Tan, A., Garcia-Garcia, E., Nalli, A., Gauthier, A., Rios, F., Zhang, X., Solomon, A., Tong, J., Read, M., Fritz, C., Jimeno, A., Pandey, A. and Hidalgo, M. (2008). Antitumor activity and molecular effects of the novel Hsp 90 inhibitor, IPI-504, in pancreatic cancer. Molecular Cancer Therapeutics. 7, 3275-3284. [PubMed].

Mathivanan, S. and Pandey, A. (2008). Human Proteinpedia as a resource for clinical proteomics. Molecular and Cellular Proteomics. 7, 2038-2047. [PubMed]

Sarker, R., Grønborg, M., Cha, B., Mohan, S., Chen, Y., Pandey, A., Litchfield, D., Donowitz, M and Li, X. (2008). CK2 binds to the C-Terminus of NHE3 and stimulates NHE3 basal activity by phosphorylating a separate site in NHE3. Molecular Biology of the Cell. 19, 3859-3870. [PubMed]

Zhong, L., Roybal, J., Chaerkady, R., Zhang, W., Choi, K., Tran, H., Yan, S., Strieter, R. M., Pandey, A. and Kurie, J. M. (2008). Identification of secreted proteins that mediate cell-cell interactions in an in vitro model of the lung cancer microenvironment. Cancer Research. 68, 7237-7245. [PubMed]

Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Grønborg, M., Joore, J., Cope, L. and Pandey, A. (2008). Identification of c-Src tyrosine kinase substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research. 7, 3900-3910. [PubMed]

Luo, W., Slebos, R. J., Hill, S., Li, M., Brabek, J., Amanchy, R., Chaerkady, R., Pandey, A., Ham, A. J. L. and Hanks, S. (2008). Global impact of oncogenic Src on a phosphotyrosine proteome. Journal of Proteome Research. 7, 3447-3460. [PubMed]

Chaerkady, R., Thuluvath, P. J., Nalli, A., Vivekanandan, P., Simmers, J., Torbenson, M. and Pandey, A. (2008). ¹⁸O labeling for a quantitative proteomic analysis of glycoproteins in hepatocellular carcinoma. Clinical Proteomics. 4, 137-155 [PubMed]

Molina, H., Matthiesen, R., Kandasamy, K. and Pandey, A. (2008). Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Analytical Chemistry. 80, 4825-4835. [PubMed]

Chaerkady, R. and Pandey, A. (2008). Applications of proteomics to lab diagnosis. Annual Review of Pathology: Mechanisms of Disease. 3, 485-498. [PubMed]

Basu, B., Desai, R., Balaji, J., Chaerkady, R., Sriram, V., Maiti, S. and Panicker, M. (2008). Serotonin in pre-implantation mouse embryos is localized to the mitochondria and can modulate mitochondrial potential. Reproduction. 135, 657-669. [PubMed]

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

Mathivanan, S., Ahmed, M., 157 coauthors and Pandey, A. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-167. [PubMed]

Chaerkady, R. and Pandey, A. (2007). Quantitative proteomics for identification of cancer biomarkers. Proteomics Clinical Applications. 1, 1080-1089. [PubMed]

Sarker, M., Hanumanthu, G. and Pandey, A. (2007). 'Plasma Proteome Database' in, Proteomics of human body fluids, pages 129-136 Thongboonkerd, V. Editor (Humana Press, Totowa, New Jersey, USA). [PubMed]

Okulate, M., Kalume, D. E., Chaerkady, R., Reddy, R., Kristiansen, K., Bhattacharyya, M., Pandey, A. and Kumar, N. (2007). Identification and molecular characterization of a novel protein Saglin as a target of monoclonal antibodies affecting salivary gland infectivity of Plasmodium sporozoites. Insect Molecular Biology. 16, 711-722. [PubMed]

Lucito, R., Suresh, S., Walter, K., Pandey, A., Lakshmi, B., Krasnitz, A., Sebat, J., Wigler, M., Klein, A. P., Brune, K., Palmisano, E., Maitra, A., Goggins, M. and Hruban, R. H. (2007). Copy-number variants in patients with a strong family history of pancreatic cancer. Cancer Biology & Therapy. 6, 1-8. [PubMed]

Molina, H., Horn, D. M., Tang, N., Mathivanan, S. and Pandey, A. (2007). Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. Proceedings of the National Academy of Sciences, USA. 104, 2199-2204. [PubMed]

Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. (2007). A compendium of curated phosphorylation-based substrate and binding motifs. Nature Biotechnology. 25, 285-286. [PubMed]

Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periyaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. and Pandey, A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293. [PubMed]

Bose, R., Molina, H., Patterson, A. S., Bitok, J. K., Periaswamy, B., Bader, J. S., Pandey, A. and Cole, P. A. (2006). Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proceedings of the National Academy of Sciences, USA . 103, 9773-9778. [PubMed]

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

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]

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

Grønborg, M., Kristiansen, T. Z., Iwahori, A., Chang, R., Reddy, R., Sato, N., Molina, H., Jensen, O. N., Hruban, R. H., Goggins, M. G., Maitra, A. and Pandey, A. (2005). Biomarker discovery from pancreatic cancer secretome using a differential proteomics approach. Molecular and Cellular Proteomics. 5, 157-171. [PubMed]

Rhodes, D. R., Tomlins, S. A., Varambally, S., Mahavisno, V., Barrette, T., Kalyana-Sundaram, S., Ghosh, D., Pandey, A. and Chinnaiyan, A. M. (2005). Probabilistic model of the human protein-protein interaction network. Nature Biotechnology. 23, 951-959. [PubMed]

Haab, B. B., Geierstanger, B. H., Michailidis, G., Vitzthum, F., Forrester, S., Okon, R., Saviranta, P., Brinker, A., Sorette, M., Perlee, L., Suresh, S., Drwal, G., Adkins, J. N. and Omenn, G. S. (2005). Immunoassay and antibody microarray analysis of the HUPO Plasma Proteome Project reference specimens: Systematic variation between sample types and calibration of mass spectrometry data. Proteomics. 5, 3278-3291. [PubMed]

Kalume, D. E., Peri, S., Zhong, J., Okulate, M., Reddy, R., Humar, N. and Pandey, A. (2005). Genome annotation of Anopheles gambiae using mass spectrometry-derived data. BMC Genomics. 6, 128. [PubMed]

Suresh, S., Mohan, S., Mishra, G., Hanumanthu, G., Suresh, M., Reddy, R. and Pandey, A. (2005). Proteomic resources: Integrating biomedical information in humans. Gene. 364, 13-18. [PubMed]

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]

Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K. B., Yang, Z., Menon, R., Kwon, M. S., Cho, S. Y., Drwal, G., Kellmann, M., Peri, S., Suresh, S., Grønborg, M., Molina, H., Chaerkady, R., Rekha, B., Muthusamy, B., Shet, A. S., Gerszten, R. E., Wu, H., Raftery, M., Wasinger, V., Schulz-Knappe, P., Hanash, S. M., Paik, Y. K., Hancock, W. S., States, D. J., Omenn, G. S. and Pandey, A. (2005). A functional annotation of subproteomes in human plasma. Proteomics. 5, 3506-3519. [PubMed]

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

Bala, P., Georgantas, R. W., Sudhir, D., Suresh, M., Shanker, K., Vrushbendra, B. M., Civin, C. I. and Pandey, A. (2005). TAGmapper: A web-based tool for mapping SAGE tags. Gene. 364, 123-129. [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]

Kalume, D. E., Okulate, M., Zhong, J., Reddy, R., Suresh. S., Deshpande, N., Kumar, N. and Pandey, A. (2005). A proteomic analysis of salivary glands of female Anopheles gambiae mosquito. Proteomics. 5, 3765-3777. [PubMed]

Molina, H., Bunkenborg, J., Reddy, G. H., Muthusamy, B., Scheel, P. J. and Pandey, A. (2005). A proteomic analysis of human hemodialysis fluid. Molecular and Cellular Proteomics. 4, 637-650. [PubMed]

Hustinx, S. R., Cao, D., Maitra, A., Sato, N., Martin, S., Sudhir, D., Iacobuzio-Donahue, C., Cameron, J. L., Yeo, C. J., Kern, S. E., Goggins, M., Mollenhauer, J., Pandey, A. and Hruban, R. H. (2004). Differentially expressed genes in pancreatic ductal adenocarcinomas identified through serial analysis of gene expression. Cancer Biology and Therapy, 3. 1254-1261. [PubMed]

Cao, D., Hustinx, S. R., Sui, G., Bala, P., Sato, N., Martin, S., Maitra, A., Murphy, K. M., Cameron, J. L., Yeo, C. J., Kern, S. E., Goggins, M., Pandey, A. and Hruban, R. H. (2004). Identification of novel highly expressed genes in pancreatic ductal adenocarcinomas through a bioinformatics analysis of expressed sequence tags. Cancer Biology and Therapy. 3, 1081-1089. [PubMed]

Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R, Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. (2004). Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proceedings of the National Academy of Sciences, USA. 101, 9309-9314. [PubMed]

Navarro, J. D., Talreja, N., Peri, S., Vrushabendra, B. M., Rashmi, B. P., Padma, N., Surendranath, S., Jonnalagadda, C. K., Kousthub, P. S., Deshpande, N., Shanker, K. and Pandey, A. (2004). BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics. 5, 43. [PubMed]

Ibarrola, N., Chaerkady, R. and Pandey, A. Proteomic analysis of the adipocyte secretome, in, Genomics and Proteomics in Nutrition, Berdanier C. D. and Moustaid-Moussa, N. Eds., Marcel Dekker, Inc. New York. pp 393-411.

Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R, Ghosh, D., Barrette, T., Pandey, A. and Chinnaiyan, A. M. (2004). Oncomine: A cancer microarray database and integrated data-mining platform. Neoplasia. 6, 1-6. [PubMed]

Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S. G. N., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C. and Apweiler, R. (2004). The HUPO PSI Molecular Interaction Format - A community standard for the representation of protein interaction data. Nature Biotechnology. 22, 177-183. [PubMed]

Peri, S., Navarro, J. D., Kristiansen, T. Z., Amanchy, R., Surendranath, V., Muthusamy, B., Gandhi, T. K. B., Chandrika, K. N., Deshpande, N., Suresh, S., Rashmi, B. P., Shanker, K., Padma, N., Niranjan, V., Harsha, H. C., Talreja, N., Vrushabendra, B. M., Ramya, M. A., Yatish, A. J., Joy, M., Shivashankar, H. N., Kavitha, M. P., Menezes, M., Choudhury, D. R., Ghosh, N., Saravana, R., Chandran, S., Mohan, S., Jonnalagadda, C. K., Prasad, C. K., Kumar-Sinha, C., Deshpande, K. S. and Pandey, A. (2004). Human Protein Reference Database as a discovery resource for proteomics. Nucleic Acids Research. 32, 497-501. [PubMed]

Chaerkady, R. and Pandey, A. (2003). Absolute systems biology - measuring dynamics of protein modifications. Trends in Biotechnology. 21, 467-470. [PubMed]

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

Deshpande, K. S., Harsha, H. C. and Pandey, A. (2003). Microarrays and mass spectrometry: The future of proteomics. Current Genomics. 4, 605-613. [PubMed]

Navarro, J. D., Niranjan, V., Peri, S., Jonnalagadda, C. K. and Pandey, A. (2003). From biological databases to platforms for biomedical discovery. Trends in Biotechnology. 21, 263-268. [PubMed]

Pandey, A., Peri, S., Thacker, C., Whipple, C. A., Collins, J. J. and Mann, M. (2003). Computational and experimental analysis reveals a novel Src family kinase in the C. elegans genome. Bioinformatics. 19, 169-172. [PubMed]

Kalume, D. E., Molina, H. and Pandey, A. (2003). Tackling the phosphoproteome: tools and strategies. Current Opinion in Chemical Biology. 7, 64-69. [PubMed]

Pandey, A., Blagoev, B., Kratchmarova, I., Fernandez, M., Nielsen, M., Kristiansen, T., Ohara, O., Podtelejnikov, A., Roche, S., Lodish, H. and Mann, M. (2002). Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases. Oncogene. 21, 8029-8036. [PubMed]

Anand, S. K. and Pandey, A. (2002). Screening large proteins for interaction partners. Trends in Biochemical Sciences. 27, 603. [PubMed]

Muthusamy, B. and Pandey, A. (2002). A roadmap of the mouse genome. Trends in Genetics. 18, 553. [PubMed]

Gandhi, T. K. B. and Pandey, A. (2002). Using bioinformatics to identify cis-regulatory sequences. Trends in Biotechnology. 20, 448. [PubMed]

Blagoev, B., Kratchmarova, I., Nielsen, M. M., Fernandez, M. M., Voldby, J., Andersen, J. S., Kristiansen, K., Pandey, A. and Mann, M. (2002). Inhibition of adipocyte differentiation by Resistin-like molecule alpha. Biochemical characterization of its oligomeric nature. Journal of Biological Chemistry. 277, 42011-42016. [PubMed]

Steen, H., Pandey, A., Andersen, J. S. and Mann, M. (2002). Analysis of tyrosine phosphorylation sites in signaling molecules by a phosphotyrosine-specific immonium ion scanning method. Science STKE 2002(154):PL16. [PubMed]

Grønborg, M., Kristiansen, T. Z., Stensballe, A., Andersen, J. A., Ohara, O., Mann, M., Jensen, O. N. and Pandey, A. (2002). A mass spectrometry-based proteomic approach for identification of serine/threonine-phosphorylated proteins by enrichment with phospho-specific antibodies: Identification of a novel protein, Frigg, as a protein kinase A substrate. Molecular and Cellular Proteomics. 1, 517-527. [PubMed]

Jebanathirajah, J. A., Peri, S. and Pandey, A. (2002). Toll and Interleukin-1 Receptor (TIR) domain-containing proteins in plants: a genomic perspective. Trends in Plant Science. 7, 388-391. [PubMed]

Steen, H. and Pandey, A. (2002). Proteomics goes quantitative: measuring protein abundance. Trends in Biotechnology. 20, 361-364. [PubMed]

Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A. and Mann, M. (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular and Cellular Proteomics. 1, 376-386. [PubMed]

Deshpande, N. and Pandey, A. (2002). Mining gene expression data for functional annotation of genomes. Trends in Biotechnology. 20, 282. [PubMed]

Shankar, S. H. N. and Pandey, A. (2002). A novel mode of activating the JAK-STAT signaling pathway. Trends in Biochemical Sciences. 27, 336. [PubMed]

Kristiansen, T. Z. and Pandey, A. (2002). Resources for full-length cDNAs. Trends in Biochemical Sciences. 27, 266-267. [PubMed]

Schiemann, W. P., Blobe, G. C., Kalume, D. E., Pandey, A. and Lodish, H. F. (2002). Context-specific effects of fibulin-5 (DANCE/ EVEC) on cell proliferation, motility, and invasion: Fibulin-5 is induced by TGF-beta and affects protein kinase cascades. Journal of Biological Chemistry. 277, 27367-27377. [PubMed]

Dan, I., Watanabe, N. M., Kajikawa, E., Ishida, T., Pandey, A. and Kusumi, A. (2002). Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution. Nucleic Acids Research. 30, 2906-2910. [PubMed]

Pandey, A., Dan, I., Kristiansen, T. Z., Watanabe, N. M., Voldby, J., Kajikawa, E., Khosravi-Far, R., Blagoev, B. and Mann, M. (2002). Cloning and characterisation of PAK5, a novel member of mammalian p21-activated kinase-II subfamily that is predominantly expressed in brain. Oncogene. 21, 3939-3948. [PubMed]

Mann, M., Ong, S. E., Grønborg, M., Steen, H., Jensen, O. N. and Pandey, A. (2002). Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. Trends in Biotechnology. 20, 261-268. [PubMed]

Kratchmarova, I., Kalume, D. E., Blagoev, B., Scherer, P. E., Podtelejnikov, A. V., Molina, H., Bickel, P. E., Andersen, J. S., Fernandez, M. M., Bunkenborg, J., Roepstorff, P., Kristiansen, K., Lodish, H. F., Mann, M. and Pandey, A. (2002). A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes. Molecular and Cellular Proteomics. 1, 213-222. [PubMed]

Pandey, A., Ibarrola, N., Kratchmarova, I., Fernandez, M. M., Constantinescu, S. N, Ohara, O., Sawasdikosol, S., Lodish, H. F. and Mann, M. (2002). A novel Src homology 2 domain-containing molecule, Src-like adapter protein-2 (SLAP-2), which negatively regulates T cell receptor signaling. Journal of Biological Chemistry. 277, 19131-19138. [PubMed]

Dan, I., Ong, S. E., Watanabe, N. M., Blagoev, B., Nielsen, M. M., Kajikawa, E., Kristiansen, T. Z., Mann, M. and Pandey, A. (2002). Cloning of MASK, a novel member of the mammalian germinal center kinase-III subfamily, with apoptosis-inducing properties. Journal of Biological Chemistry. 277, 5929-5939. [PubMed]

Blagoev, B., Nielsen, M. M., Angrist, M., Chakravarti, A. and Pandey, A. (2002). Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene. Gene. 284, 161-168. [PubMed]