objective, innovative, applicative
parisodhana.com is about -
"revisiting, rediscovering and redefining Progress, Discipline, Character, Seriousness, Purity, Responsibility and Loyalty which form the core values of Human Beings. The world is facing a serious problem of Illusion. Illusion is dressing/covering the absolute truth. A syndicate of selfish and utterly irresponsible humans in the form of money launderers and power mongers have hijacked the steering wheel of world progress by successfully creating illusion. Parisodhana is about identifying and characterizing illusion. The illusion is the root cause of failing economies or misery. Illusion is affecting countries, society, individuals, intellect, science, technology and progress of the world as a whole. Every Blog/post probes indirectly or directly this problem."
Research is My Life - No Strings attached!
I believe in innovation, which eventually should be applied for the benefit of common man/society. My research areas have always been applicative. Hence the projects/problems I tend to take up are also targeted to reach the pharma market eventually. My research interests are towards developing strategies for better drug designing and increasing biological knowledge base through computational biology. The aim is to finally take them to a stage where they will influence the almost stagnated pharma protocols.
In addition to this, I also like to pursue work towards analysis and algorithm development through studies on gene-expression and proteomics data. I like to develop novel Algorithms, design biologically meaningful & comprehensive databases and web-based tools for studies on the 'omics' data. I have many ideas which are basically extensions of my current activities. All these ideas have commercial angle as well which is even more exciting for me. As said earlier, its my principle to not leave a project half way and look at the problem in entirity to give efficient solutions rather patches and fixes like sympotomatic allopathy or modern medicine.
I am of the opinion that the methodologies Drug discovery need to incorporate more biological knowledge which is currently lacking. Besides the Pharma domain, I also believe we should be adapting to the new technological breakthroughs and use them to our full advantage especially to speed up our research productivity, be it software engineering, wiki based / web technologies or biological knowledge based novel algorithm implementations.
My currrent Project
My current work on microarray data analysis, ~ 1000 samples from GEO, NCBI, has the potential to create a fundamental knowledge base of TF network and associated target gene network specific to tissues. Currently my research is focused on the normalization procedures employed on microarray data. I have been reviewing the relevant articles for some time now. I am hopeful of implementing a better algorithm – a proposal to modify the common used RMA normalization method. Further to this I want to develop my analysis in the lines described as genome‐wide transcriptional modeling (GWTM).
- Test the Wiki I have developed for UCSD-Nature Signaling Gateway Project
- Here is the O2RTE - Object Oriented Rich Text Editor - Check it out!
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Select List of my Publications
- Domain: Biological Software Engineering: Method and Apparatus for Object based Biological Information, Manipulation and Management, June 2004, Prasad V.L.S., Burra. (PAN:US:10/873,923)
- Domain: Protein Engineering, Drug Discovery & Designing: Method of identifying /designing and/or modifying species, June 2004, Prasad V.L.S., Burra. (PAN:US:10/579,171)
Patents: (Filed):
- Domain: Web Technologies, Wikis : Prasad Burra and Shankar Subramaniam, SGWiki: Next generation biomedical authoring and publishing wiki.
- Domain: Biological Software Engineering: Prasad Burra, BOS: An object oriented biological programming environment.
Manuscripts:
- Domain: Protein Structure Twilight, Disordered Protein Analysis: Prasad Burra, Lajos Kalmar, Peter Tompa, “Reduction in structural disorder and functional complexity in the thermal adaptation of prokaryotes” – (Under Review – PLoS Computational Biology)
- Domain: Conformational Speciation, Protein Ensemble: Burra PV, Zhang Y, Godzik A, Stec B. “Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure”, Proc Natl Acad Sci U S A. (2009) Jun 30;106(26):10505-10.
- Domain: Comparative Genomics: D. Ashok Reddy, B.V.L.S. Prasad, Chanchal K. Mitra, “Functional classification of transcription factor binding sites: Information content as a metric”, Journal of Integrative Bioinformatics.(2006)
- Domain: Comparative Genomics: D. Ashok Reddy, B.V.L.S. Prasad, Chanchal K. Mitra, “Comparative analysis of core promoter region: Information content from mono and dinucleotide substitution matrices”, Computational Biology and Chemistry.(2006),30, 58-62.
- Domain: Protein Crystallography, Structural Bioinformatics: B.V.L.S. Prasad and K.Suguna, "Effect of pH on the structure of rhizopuspepsin", Acta Cryst. (2003), D59, 1755 -61.
- Domain: Structural Bioinformatics: B.V.L.S. Prasad and K.Suguna, "Role of water molecules in the structure and function of Aspartic Proteinases", Acta Cryst. (2002), D58, 250 -259.
- Domain: Comparative Genomics, Microsatellite Research: B.V.L.S.Prasad and Mohan C. Vemuri, "Genome Analysis for nucleotide interactions in fully sequenced genomes of selective prokaryotes", J.Biosci. (1998), 23:255 -263.
Publications: