• Built the Bioinformatics department from scratch with capabilities to acquire, store, analyze, and report on various kinds of data.• Set up AWS infra structure for data storage, analysis, and deployment of web apps (S3, RDS, EC2, etc.).• Created sophisticated tools to design SiRNAs and CASis.• Set up ELN and Compound Registry database with CDD.• Set up CROs and consultants for large scale data analysis like RNA-SEQ and NGS.• Worked closely with various teams to understand their computational needs and deliver appropriate products.• Part of the senior leadership team to help inform and make policy decisions.

• Created the NGS pipeline and deployed it on AWS – with seamless integration with Benchling, AWS (S3, Aurora), Google Drive.• Created several web app tools for use by strain engineering team and deployed on AWS Fargate• Discovered an enzyme using RNA-SEQ data – patent filed • Set up a Alphafold server on AWS to model protein structures and developed an automated pipeline to dock ligands into the structures.• Created and annotated a reference genome using de novo assembly

Helped build a robust platform for Insilixa’s bioinformatics needs, including building automated systems, databases, etc.

Group Leader: Responsible for all multi-omics and bioinformatics analysis and software development/maintenance.• Designed and built pipelines and webapps to automate the analysis of various types of NGS and other Omics data (DGE for RNA-SEQ and Proteomics, Metabolomics), including associated ETLs and reporting. These automated pipelines resulted in significant time savings (reduced days/weeks of manual work to minutes).    ▸ Built pipelines for Whole Genome NGS analysis (including Variant Calling and Assembly), RNA-SEQ analysis (including DGE), and Proteomics DGE.    ▸ Analyzed NGS data to uncover the effects of mutation at genetic and protein structure/function levels.    ▸ Provided actionable recommendations to project teams based on data analyses.    ▸ Created app to automatically annotate Whole Genome Assembly outputs.    ▸ Developed automated QC systems for genomic NGS, RNA-SEQ and Proteomics data.• Created novel apps to identify unexpected changes in genomes in strain engineering, avoiding months of time waste due to unidentified changes in the genomes.    ▸ Created app to automatically identify the locus of insertion for knock-in constructs in whole genome.    ▸ Created app to automatically identify potential insertion sites of unknown sequences in genome.• Applied machine learning to enzyme engineering data analysis to accelerate the process of enzyme evolution.• Actively worked with NGS team to test and validate new experimental methods including library preparation kitsand protocols.• Extensive experience with Illumina and Pacbio technologies.• Extensive programming experience in Python, Webapps development, bash scripting in Linux/Mac OS platforms, database interactions (raw SQL as well as programmatic), machine learning (enzyme evolution data analysis), app deployments in Docker containers, software versioning with git.

• Built pipeline for NGS data analysis of plasmids (Plasmid Validation) with interactive graphical reporting and filtering of results, thereby saving days of analysis time.• Created apps to analyze, transform, perform calculations, store data in databases, and provide visualization tools through web browser and spotfire for a number of applications including Proteomics, Metabolomics, CGQ, etc.• Designed pathways with heterologous enzymes to produce fine chemicals in bacteria and yeast for over a dozen projects.• Engineered proteins through rational designs and Directed Enzyme Evolution to improve their physico-chemical and catalytic properties.

• Automated the process of docking small molecule ligands into protein structures. • Established crystallographic efforts to crystallize target proteins with ligands and their subsequent structures determination to aid drug design and development.

Developed software systems including data mining for ligands, data management server, automation of refinement of structures, and quality control, resulting in substantial time saving and streamlining of routine operations in research.   • Quality Control Server: This application was widely used by scientists from all over the world.  • Ligand Search Server: This was also widely used from all over the world.  • Refinement Database Server: This was a crystallographic LIMS server that managed and tracked the progress of projects in the lab.

Designed, implemented, and optimized software systems to automate data mining, analysis, and reporting in Crystallography, Assay, and Molecular Biology. These software developments involved working with scientists in Assay, Structural Biology, Molecular Biology and IT departments to plan and design the software architecture with specific deliverables.  • Structural Biology support for Braf project: Provided structural biology support to Braf project, helping design and validation of drug candidates that led to the FDA approval of Vemurafenib for the treatment of melanoma.  • Crystal Screen Maker: This web based tool generates various kinds of crystallization screens. Development of this software saved the company about $30,000 annually and streamlined the process of crystallization.  • Structure Determination and Refinement: This software automates the processes of solving protein structures and refinement. This software cut the time of a typical structural biology project by 40%.  • Set up and managed the computational crystallography department.