ABOUT ME
I specialize in using statistics and machine learning to derive important conclusions from large amounts of data. I live in New Hampshire with my wife, kids, and cats. I have a pretty eclectic mix of hobbies, including bonsai, weight lifting, hiking, linguistics, and playing the tin whistle. I've been known to make very cheesy dad jokes, but in all fairness, I've been doing that for most of my life. As a computational biologist, I'm excited about bringing scientific insights to software, and as a software engineer, bringing software insights to science across multiple industries.
TECHNICAL SKILLS
Data Visualization
ggplot2, Plotly, R-Shiny, Matplotlib, seaborn
SQL
PostgreSQL, MSSQL, SQLite
Languages
Python, Haskell, R, JavaScript, Matlab, C/C++, Perl
AWS
EC2, EBS, S3, RDS, IAM, CodeCommit, Batch
Data Analysis
NumPyro, JAX, Tidyverse, data.table NumPy, SciPy, Pandas
Platforms
Linux/UNIX, MacOS, Windows, Sun Grid Engine (SGE)
DevOps
Git, Docker, Jenkins, Mercurial, NixOS, Nixpkgs
Office
LibreOffice, LATEX, MS Office, Tibco Spotfire
PROFESSIONAL EXPERIENCE
Pillar Biosciences
Senior Computational Biologist
Natick, MA
November 2021-March 2024
- Optimized hyperparameters for machine learning algorithms to suit different panels, using a random search of the parameter space and custom loss functions.
- Adapted machine learning based CNV caller from proof of concept code to fully operational pipeline component, which reduced false positive calls by ten fold.
- Refactored code bases which had diverged for years of independent development into a coherent whole which met the needs of both. Integrated the git history to reflect the development of both repositories.
- Streamlined the flow of application data between microservices to enforce loose coupling. This helped enable more flexible application execution and faster run times.
- Implemented a BWA based NGS contamination filter to remove known contaminating sequences before they could confound important results.
- Developed an NGS QC application which enabled the production team to spot reagent contamination before it caused costly errors.
- Created a binary parser for raw Illumina outputs to provide data for NGS QC.
Merck Research Laboratories, IT
Senior Specialist, Scientific Solutions Engineering
Boston, MA
April 2020-October 2021
- Drove product discovery for a data visualization tool for gene expression analysis
- Led an international engineering team in implementing an R-Shiny data visualization application from the ground up
- Instituted a Scrum based workflow to maintain feature delivery
- Architected a data model for storing and displaying complex scientific data across several experimental domains: single cell RNA sequencing (scRNA-Seq), CRISPR, bulk RNA-Seq, microarray
- Constructed efficient data queries for a database including tables hundreds of millions of rows in length
- Integrated R-Shiny with a highly specialized scientific Python library (ScanPy) using containerization (Singularity)
- Deployed R-Shiny application to multiple environments automatically using Jenkins
- Designed informative and attractive scientific visualizations and user interfaces used by dozens of biologists to facilitate drug discovery
Merck Research Laboratories
Senior Scientist, Computational Biology
Boston, MA
February 2016-March 2020
- Provisioned and managed AWS resources for computationally intensive bioinformatics applications
- Developed and maintained QC analysis pipeline for next generation sequencing (NGS) datasets on a high performance computing cluster (HPC)
- Ported bioinformatics processing pipelines from on-prem HPC infrastructure to proprietary cloud computational biology platforms Seven Bridges and DNAnexus, as well as to AWS resources using the Cromwell and Nextflow pipeline DSLs
- Productized a single-cell RNA-Seq pipeline using Sun Grid Engine
- Facilitated the transfer and storage of hundreds of TBs of NGS data using Aspera, AWS, Seven Bridges, DNAnexus, and even one time a bunch of hard drives through the mail
Merck Research Laboratories
Genetics Intern
West Point, PA
June 2015-August 2015
- Created visualization workflows and SQL queries to aid drug candidate safety evaluation
- Analyzed and integrated data from next generation sequencing, microarray, nanostring and qPCR experiments
- Developed power analyses to inform genomics experimental design
University of Pennsylvania School of Medicine
Technical Consultant
Philadelphia, PA
June 2015-September 2015
- Instructed PhD level researchers in laser capture microdissection
Merck Research Laboratories
Genetics Intern
West Point, PA
June 2014-August 2014
- Designed workflow to integrate several Matlab data sources into SQL Server database
- Created statistical data visualizations of gene expression data in Tibco Spotfire, and Matlab
- Analyzed and integrated data from next generation sequencing, microarray, and qPCR experiments
Drexel University
Research Technician
Philadelphia, PA
February 2014-June 2014
- Designed flexible command line interfaces for custom tools, accommodating a variety of workflows and standards
- Deployed self-contained Python packages for easy distribution and installation on high-performance computing platforms
- Programmed Python application software to analyze and visualize phylogenetic trees of sequencing data
University of Pennsylvania School of Medicine
Research Specialist
Philadelphia, PA
May 2009-June 2013
- Managed dozens of data sets and thousands of measurements from hundreds of samples
- Coordinated and performed data processing and analysis for high-throughput next-generation sequencing experiments (RNA-Seq)
- Designed a high throughput qPCR experiment which required 3 technicians, handled data from dozens of patients, and used hundreds of samples
- Engineered computational image analysis techniques based on OpenCV for characterization of histology image data, used to automatically quantify hundreds of photomicrographs
- Overhauled gene expression quantitation (qPCR) procedures in laboratory, as well as accompanying data management and statistical analysis strategy
- Programmed custom data acquisition software for a 3rd party sensor with no published interface
- Devised a technique for manual single cell sorting for qPCR experiments with which I was able to collect high quality RNA from as few as 100 cells. I then instructed graduate level researchers in its execution
- Learned flow cytometry, and conducted flow cytometry experiments
- Engineered techniques for extracting high quality RNA from hard to isolate tissue samples
- Performed and instructed PhD researchers in laser capture microdissection
EDUCATION
Drexel University | Philadelphia, PA
December 2015
Master of Science in Biomedical Engineering
Concentration in Bioinformatics, GPA 3.96
University of Pennsylvania | Philadelphia, PA
August 2012
Bachelor of Arts in Biology
Concentration in Neurobiology
Copyright © 2024 Jason Gilliland | Senior Software Engineer - All Rights Reserved.
Powered by GoDaddy Website Builder
This website uses cookies.
We use cookies to analyze website traffic and optimize your website experience. By accepting our use of cookies, your data will be aggregated with all other user data.