About

  • Bioinformatics Engineer with significant experience in various Bioinformatics analyses and high-performance computing environments
  • Skilled in pipeline development methods (Nextflow/Snakemake) and scripting languages (Python/R/Perl) using Agile software principles and containerization for software reproducibility
  • Responsible for project management of customer-facing projects with a strong focus on setting and achieving deadlines
  • Demonstrated ability to respond positively to change and willingness to adapt and face new challenges

Bioinformatics Experience

Senior Staff Engineer, Bioinformatics at Takara Bio USA, San Jose CA

  • Duration: April 2024 to present
  • Led the development and maintenance of Cogent suite of data analysis pipelines for DNA/RNA-Seq data using Nextflow
  • Developed and maintained pipelines and software products to aid design of new products in R&D using Python, Shiny and JavaScript

Staff Scientist, Bioinformatics at Takara Bio USA, San Jose CA

Bioinformatician/Computational Biologist at Michigan Medicine, Ann Arbor MI

  • Duration: September 2016 to January 2021
  • Performed analysis on NGS and array data from ERRBS, ChIP-seq, WGBS, ATAC-Seq (bulk and single cell), EPIC Methylation Array and (h)MeDIP DNA methylation techniques
  • Maintained, developed and documented Epigenomic NGS data analysis pipelines using Snakemake, R, Python, Bash, Perl and other open-source bioinformatics programs (sequence quality control, alignment, differential analysis)
  • Developed analysis plans and budgets for scientists and communicated results to non-expert audiences effectively
  • Analyzed and interpreted bioinformatics, clinical, and physiological data across multiple data types and sources, and across a broad range of analysis approaches and biological and clinical research questions

Bioinformatics Research Assistant at Purdue University

  • Duration: August 2012 to July 2016
  • Developed a novel method for scoring gene models for non-model plants
  • Performed domain co-occurrence analysis for identifying the pairwise probability of kinase protein domains
  • Analyzed RNA-seq data of glyphosate resistant giant ragweed in time course experiments to identify genes responsible for resistance mechanism

Data Science Intern at Monsanto (later acquired by Bayer CropSciences)

  • Duration: May 2015 to August 2015
  • Investigated the effect of metabolites and genes on selected yield-related phenotypes in corn using machine learning algorithms and feature selection methods and generated a list of most predictive features affecting the yield of corn
  • Collaborated with multi-state teams within the company to design and develop web applications in R Shiny
  • Communicated results effectively with non-specialist scientists from other teams

Education

Ph.D. Computational Biology, Purdue University, West Lafayette, IN

  • Completed: July 2016
  • Advisor: Prof. Michael Gribskov
  • Thesis: “Understanding plant response to stress using gene model quality evaluation and transcriptome analysis”

M.S. Bioinformatics, Indiana University, Bloomington, IN

  • Completed: June 2011
  • Advisor: Dr. Sun Kim
  • Thesis: “Comparative expression analysis of two drug-resistant breast cancer cell lines”

B.Tech. Industrial Biotechnology, SASTRA University, Tamil Nadu, India

  • Completed: May 2009

Technical Skills

  • Programming: R, Perl, Python, R Shiny, Bash shell scripting, containerization (singularity/docker) for reproducibility
  • Bioinformatics and Genomics: Various tools used in NGS data analysis ranging from sequence quality measurements to differential expression and methylation analyses, pipeline development tools (Snakemake)
  • Applied Statistics: Machine learning and feature selection (Random forests, Genetic Algorithms, Support Vector Machines, O-PLS), multivariate data analysis, data visualization, probability and statistical inference
  • Web Development: HTML, PHP, REST, Zope, Joomla, Wordpress
  • Miscellaneous: Unix/Mac OS/Windows, vim/nano/MS Office/Latex, version control systems (CVS, git)

Current Résumé

Click here for a PDF copy of my latest résumé

Other Minor Projects

Zebrafish DB

  • Built a database for maintaining zebrafish lines using RShiny for a lab in UCSF
  • Updates status of fish such as birth date, mother, father, generation, etc. to a local SQL database
  • Added function to print label via connected label printer for use with fish tanks in facility

rfeVIP

  • Developed an R package that performs recursive feature elimination based on the variable importance parameter in random forest models using caret
  • Removes negative VIPs and stops when all remaining VIPs are positive

Web Developer

  • Maintained and updated content for the Department of Environmental and Ecological Engineering at Purdue University
  • Overhauled back-end infrastructure to be more robust
  • Updated front-end UI to meet University guidelines
  • Held weekly meetings with the department head and administrative director

Contact