About
Software for seeing, exploring and publishing biological data¶
Technical product manager for the population-genomics line at Tile.ai (formerly known as TileDB) and a bioinformatics leader with 25+ years bridging genomics R&D and enterprise software. I develop scalable genomics data products from concept through launch, translating genetics research and discovery workflows into enterprise-grade platforms used by pharma and biotech partners, owning product vision, roadmaps, and success metrics while partnering across science, engineering, and business.
I have helped four diagnostic, therapeutic, and SaaS startups define and implement their product strategy, bridging cutting-edge research and practical commercial applications. My expertise spans low-level algorithm development through high-level product strategy and customer engagement.
As a researcher, I have authored over 50 publications with an h-index of 30, contributing to fields including HIV integration site analysis, mitochondrial genetics, reproducible research methodologies, and computational pipeline development. My work has been published in prestigious journals including Cell, Nature, PLoS Computational Biology, and Genome Research.
Research
Selected publications
American Journal of Human Genetics2024
Genome-based newborn screening for severe childhood genetic diseases has high positive predictive value and sensitivity in a NICU pilot trial
Large prospective clinical trials are underway or planned that examine the clinical utility and cost effectiveness of genome-based newborn screening (gNBS).
Paper →
Patterns2021
The role of metadata in reproducible computational research
This paper discusses the critical role of metadata in ensuring reproducible computational research.
Paper →
Briefings in Bioinformatics2017
A review of bioinformatic pipeline frameworks
ISI Top 1% Highly Cited
This paper provides a comprehensive review of bioinformatic pipeline frameworks.
Paper →
Nature2013
De novo mutations in histone-modifying genes in congenital heart disease
This study identifies de novo mutations in histone-modifying genes associated with congenital heart disease.
Paper →
O'Reilly Media2009
Data Mashups in R
This book provides practical guidance for creating data mashups using the R statistical programming language.
Book →
Genome Research2007
HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications
This paper uses massively parallel pyrosequencing to analyze HIV integration site selection and its association with epigenetic modifications.
Paper →Current project
Rhylthyme
A JSON-based markup language and toolchain for describing real-time programs that coordinate parallel tracks of work with resource constraints, timing dependencies, and flexible execution patterns. Includes a CLI runner, web visualizer, and MCP server for AI-assisted schedule generation.
Open source
Software & projects
Web Application
MITOMASTER
Web application that allows clinicians to quickly investigate mitochondrial mutations in sequenced or genotyped samples. Used worldwide for mitochondrial genetics research.
Django/Python
myBiC
Django application that manages user authentication and presentation of bioinformatics deliverables. Streamlines report delivery for core facilities.
Pipeline
InSiPiD
Integration Site Pipeline and Database - comprehensive toolset for managing viral integration site data processing, annotation, and analysis.
Python · 2025
Rhylthyme Case study
A JSON-based markup language and toolchain for describing real-time programs that coordinate parallel tracks of work with resource constraints, timing dependencies, and flexible execution patterns. Includes a CLI runner, web visualizer, and MCP server for AI-assisted schedule generation.
R · 2020
dimoose
R package for dichotomous identification keys. Build a key from a plain spreadsheet with photos, draw it as a box diagram, or turn it into an offline web wizard for the field; also imports FishBase keys and generates keys from photos (CLIP/BioCLIP), sequence alignments and trait matrices. Includes an illustrated key to Montana's native broadleaf trees.
Python · 2017
awesome-reproducible-research
A curated list of reproducible research case studies, projects, tutorials, and media. Community-driven resource with 356+ stars.
Tutorial · 2014
SandwichesWithSnakemake
Beginner's tutorial to Snakemake workflow management system. Popular educational resource with 70+ stars.
CSS/Snakemake · 2014
snakemake-example
RNA-Seq Snakemake example with Jekyll homepage creation. Complete workflow demonstration with 20+ stars.
R · 2011
berrylogo
A better seqLogo implementation for creating sequence logos in R. Enhanced visualization tool with 12+ stars.
HTML/R · 2016
opensnp
Validation of published GWAS studies using OpenSNP volunteered data. Binderized for reproducible analysis.
Node.js · 2013
blast-wrapper
Node.js web-service wrapper for fetching pairwise BLAST alignments against a fixed reference.
R/Bioinformatics
placenta
Comprehensive analysis pipeline and resources for placental genomics research and developmental studies.
Python
clk
Command-line toolkit for bioinformatics workflows and data processing automation.
R/Snakemake · 2016
PAS_Premium
What do people pay to live in the Penn Alexander School catchment? A fully reproducible housing-price analysis of the West Philadelphia catchment, built with Snakemake, R, Conda and Docker.
Interests
What I work on
Reproducible Research & Metadata
Developing frameworks and tools to ensure computational reproducibility in biological research, with focus on metadata standards and pipeline documentation
Genomic Variant Analysis
Creating tools for mitochondrial genetics, exome analysis, and clinical genomics applications with emphasis on rare disease diagnostics
Cloud-Scale Bioinformatics
Building scalable workflows and platforms for population genomics, drug discovery, and precision medicine using AWS and GCP infrastructure
Bioinformatics Product Strategy
Translating research methodologies into commercial bioinformatics products, from startup strategy to enterprise solutions