Sr. Bioinformatics Scientist

• Mar 2021 - Present

Assistant Professor

• Dec 2017 - Mar 2021

- Produced and planned audio-visual resources and delivered lectures for 9 bioinformatics theory courses for last three years - Designed laboratory practical, provided instructions and managed performance of 50 students for 6 lab courses amounting to total contact hours of 250 over 6 semesters. - Mentored, supervised and managed 20 undergraduate and postgraduate students in multidisciplinary bioinformatics projects. Teaching: Courses in Bioinformatics - Programming Languages, Computational Genomics, Biological Computation, and Structural Bioinformatics, Programming Languages for Bioinformatics, R Research: - Computational Genomics, Data Mining, Computational Software development Show less

Professional Freelancer (NGS Data Analysis)

• Jan 2017 - Nov 2017

• Setup and maintained Google Cloud-based NGS Data analysis pipelines and tools up to date with various genomic resources for ChIP-seq, RNA-seq, and differential gene expression analysis. • Provided custom solutions for data analysis needs • Setup and maintained Google Cloud-based NGS Data analysis pipelines and tools up to date with various genomic resources for ChIP-seq, RNA-seq, and differential gene expression analysis. • Provided custom solutions for data analysis needs

Postdoctoral Computational Biologist (chromatin epigenetics)

• May 2013 - Oct 2016

- Successfully established and managed computational infrastructure in an experimental lab, including purchasing, installing, and managing 4 workstations, networking, data storage/backup, and software procurement and installations. - Professional awareness and planning as demonstrated by collaborating across 3 projects to develop NGS analysis pipelines and tools for detecting DNA-binding sites, and RNA-seq based differential analysis in human genome. Roles and accomplishments: - Developed/maintained/improved the ChIP-seq data analysis pipeline and use it to process in house and relevant public data. - Developed new computational tools for hypothesis generation that could be used by lab members for experimental testing. - Provided bioinformatics support for studies of chromatin structure and function. - Maintained data storage and backups. - Conducted research and maintained the knowledge-base of relevant computational methodologies and tools, and used them for current research projects. - Providing bioinformatic advice to researchers in the group. Project: Investigating the role of erythroid transcription factors in K562 cells. Project highlights: • ChIP-seq analysis of in-house and publicly available NGS data. • Genome-wide identification of regulatory elements such as enhancers using clustering methods. • Investigating possible role of TF binding motifs arrangement in gene regulation. • RNA-seq data analysis for differential gene expression in knock-out cells. Project: Identifying chromatin boundaries. Project highlights: • Profiling various histones modifications in chromatin. • DNaseDGF and nucleosome data analysis for identification of chromatin boundries. Show less

Postdoctoral Research Scientist

• Sep 2010 - Jan 2013

- Developed EFICAz2.5, a sequence based enzyme function prediction server, and applied to 373 proteomes resulting in a quality publication and commercialization of software. - Collaborated in lab projects to construct molecular models of whole enzyme complement of human proteome, and developed a computational metabolomics approach. Webservers Developed / Contributed 1. EFICAz2.5: A High Precision enzyme function prediction program ( http://pwp.gatech.edu/cssb/eficaz2-5/ ) 2. A Genome-Wide Enzyme Function Annotation Database ( http://cssb.biology.gatech.edu/enzymes ) 3. SUNPRO: A Database of Structure & FUNction Predictions of Proteins from Representative Organisms ( http://cssb.biology.gatech.edu/genome/index.html ) Show less

Research Associate

• Jan 2010 - Aug 2010

- Planned and timely performed modelling of pfCDPK1 in active and inactive conformations in Plasmodium falciparum malarial parasite resulting in a publication. - Team worked and developed the structural visualization module of SBSPKS, a popular webserver for analysis of antibiotic synthesis that resulted in a high quality publication. Contribution to Web-server:SBSPKS: structure based sequence analysis of polyketide synthases (http://www.nii.ac.in/sbspks.html)

Doctoral Thesis

• Jul 2003 - Dec 2009

Thesis title: Modeling protein-peptide complexes using rotamer library approach: application to prediction of substrates for MHC and kinases (Supervisor: Dr. Debasisa Mohanty )Project highlights:• Developed a structure based program for identification of substrates for protein kinases and MHC proteins.• The program models protein-peptide complexes by rotamer library approach and scores substrates using residue based statistical pair-potential/. MM/PBSA approach.• The program has been benchmarked on known substrates of protein kinase and MHC proteins. Show less