Allows analysis of kinome microarray data. PIIKA permits users to answer complex biological questions about kinome array data. The software covers cluster analysis, statistical analysis, and data visualization. It can assist in the identification of cellular signaling pathways that are upregulated or downregulated in response to a particular treatment. PIIKA can also facilitate the identification of peptides that have inconsistent responses among the technical replicates on a single array or among different biological replicates.
Automates identification of linear B cell epitopes. ArrayPitope allows to analyse peptide microarray data. It identifies the contribution of each amino acid residue of the target protein for recognition of the corresponding antibodies. The tool incorporates binding signals from overlapping peptides into one statistical analysis to map the selectivity of each residue of the target protein involved in the recognition. It can be useful in complete substitution analysis of pre-identified binding peptides from multiple proteins. ArrayPitope is easy to use for non-expert users.
Allows analysis of high-throughput experimental data. MADNet is a data mining and visualization web server that integrates experimental results with the existing biological data in the context of metabolic and signaling pathways, transcription factors and drug targets. The software provides a systems biology approach to complex research problems in a user-friendly interface. It is not only confined to microarray experiments, but can also be used to analyze expression information from different experimental techniques.
Allows automated analysis of high-throughput peptide array data. rapmad is a multi-step approach that combines several computational statistics procedures. Its steps include the preprocessing of the data by removing systematic effects, the exclusion of unreliable measurements and secondary antibody binding peptides and a probabilistic signal call for reactive peptides. It can contribute to establish and broaden the usage of peptide microarrays as a standard tool for a wide-range of peptidomics applications.
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.