Dr. Naga Bhushana Rao Karampudi, Ph.D.

About Me

I am currently involved in four different projects all involving analysis of transcriptome (RNA-Seq) data.

My past research experience includes structural analysis of proteins including Intrinsically Disordered Proteins (IDPs). Past contributions include a novel algorithm named  "Layers", two web-applications and three prediction models.

Key Skills

Novel Algorithm design and development, automation of workflow pipelines.
Transcriptome (RNA-Seq data) analysis and Reference guided de-novo genome assembly.
Molecular dynamics simulations of biomolecules.
Machine learning and development of Classifier/Prediction models.
Development and deployment Web-applications and Web-servers.     

C, Python, Object Oriented Programming, Algorithm Development, OpenGL, Machine learning (SVM, RF, DL) and prediction models, Molecular dynamics Simulations (Acemd, Gromacs, Namd; +VMD),Web-applications development and deployment (LAMP/LEMP; Django; CSS), CUDA, GUI and Software development. Comfortable working on any major Operating System like Linux, Unix, Windows, Mac.

By virtue of my Undergrad and post-grad studies in Biotechnology and Biochemical Engineering, I am also well versed with wet-lab analytical techniques  which includes: Isolation and purification of DNA/RNA/Proteins, Gel electrophoresis, Chromatography, PCR, RT-PCR, Enzymatic assays, Plant and bacterial cell cultures, Microscopy, Blotting techniques and many more (Please see my CV).

Publications

1. Karampudi, N. B. R., & Bahadur, R. P. (2015). Layers: A molecular surface peeling algorithm and its applications to analyze protein structures. Nature Scientific Reports, 5, 16141. http://doi.org/10.1038/srep16141.
2. Barik, A., Nithin, C., Karampudi, N. B. R., Mukherjee, S., & Bahadur, R. P. (2015). Probing binding hot spots at protein-RNA recognition sites. Nucleic Acids Research. http://doi.org/10.1093/nar/gkv876.
3. Karampudi, N. B. R., & Bahadur, R. P. (2016). Influence of polymorphic conformations of DSS1 on its binding with BRCA2. (Submitted)
4. Karampudi, N.B.R., & Bahadur, R.P. (2016). PeBLes: Prediction of B-cell epitope using molecular layers. arXiv:1611.09648.
5. Three manuscripts under preparation.

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