Design and implementation of advanced pattern matching algorithms for a novel RNA-based disease diagnostic platform.

Leader of product development for a cloud-based nucleotide design and manufacturing portal that handled the design, ordering, manufacturing and delivery of novel nucleotides. This included requirements gathering and storyboarding with the chemistry team, as well as UX and workflow design, wireframing and the design of test scenarios.

Algorithms were implemented in Python to correlate biomolecule manufacturing outcomes with process parameters, in order to improve the consistency and predictability of the manufacturing process.

We created a dynamic network model of the anti-inflammatory activity of a novel class of oncology drug, with a view to repurposing the drug for use in the clinical treatment of rheumatoid arthritis. The model was created to drive and support the experimental design for the drug's early phase R&D program.

A joint bioinformatics and laboratory-based program for predicting and re-engineering immunogenic regions in biologics that would eventually become a part of the standard workflow for all new biologic development programs throughout a global pharmaceutical company.

Software development of Swarm (swarm.org), a pioneering open-source agent-based modeling toolkit from the Santa Fe Institute, and consulting with scientists using this toolkit to model complex biological systems such as transcription factor networks.

Computer-aided design of interleukin-12 variants for use in novel, targeted oncology immuno-therapeutics. The redesigned molecule is orders of magnitude more stable in patients than the native molecule, and is currently in human clinical trials.

Python for Population Genomics (PyPop) is an open-source framework for large-scale population genomics, implemented to probe genotype data for signatures of natural selection.  It has been used extensively in the population and statistical genetics community in over peer-reviewed 150 publications

A commercial software-as-a-service (Saas) platform built on Amazon Web Services infrastructure, to allow biologists to collaboratively model and simualte cell-signaling networks

Hidden Markov Model algorithms for searching protein sequences for potential prion-like, structured regions of proteins, were implemented in an Open Source software platform available to scientists under the MIT License.

Sophisticated, custom machine control and user interface software for a robotic, medical diagnostic device for characterizing bacterial infections being developed by a team at Harvard Medical School, with a view to commercialization.