• Developed protocols/pipelines to streamline bioinformatics analysis of multi-omics data for multiple collaborative large scale public health projects.

  Selected Protocols

  
  

  • In collaboration with sequencing core, standardized quality control and contamination detection workflow - QC’d to detect data quality issues such as library preparation, plate cross contamination and barcode mismatch. Workflow includes assembly, mapping and annotation workflow for an informed QC decision making process.
  • Developed phylo-genomic analysis protocol with SNPKIT to streamline epidemiology, transmission, GWAS and feature extraction machine learning workflows.
  • Established APIs and data mining protocols to download publicly available sequencing data and incorporated into the workflows to provide global context.
  • Developed Nanopore basecalling, hybrid assembly and variant calling analysis workflow for bacterial strains.
  • Developed a workflow called SAMOSA that catalogues genomic signatures for a given species and detects mixed strains from population sequencing data. It has been successfully implemented to track recurrent and mixed C. difficile infections in longitudinal patient data.

• Worked collaboratively in a cross functional environment to provide support and mentorship to graduates and post-docs, bioinformatics data interpretation to collaborators and clinicians.
• Generated hypothesis and led proof of concept pilot studies for grant proposals. (applying novel algorithms to simulated and clinical datasets)
• Designed and set up semester long Genomic Epidemiology course for UM School of Public Health.

• Established computational infrastructure from the ground up to optimally store and retrieve sequence/analysis data for multiple collaborative research projects.
• Developed scalable bioinformatics analysis pipelines for bacterial sequencing projects (large cohort and longitudinal studies)
• Developed strategies to visualize processed genomics and phenotypic metadata, provide variant interpretation and diagnostics using R, Python and IGV.
• Designed, taught and set up Bioinformatics course material for 3-day, hands-on Microbial Genomics workshop.
• Provided Bioinformatics support and mentorship to graduates and post-docs in their research projects.

• Performed a systematic comparison of different typing schemes available for Bordetella pertussis and developed a novel wgMLST scheme using Bionumerics (Applied Maths).

Web application development with C# OOP, MS SQL and ASP.NET stack.