This page lists some of the computational life science projects that the Amber Biology principals have worked on in the course of their careers, to give a better sense of the breadth and depth of their experience and expertise.
Novel RNA-Based Diagnostics Platform
Design and implementation of advanced pattern matching algorithms for a novel RNA-based disease diagnostic platform.
Cloud-Based Nucleotide Design, Manufacturing & Delivery Portal
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.
Data Mining To Optimize A Biological Manufacturing Process
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.
Modeling A Drug's Mechanism of Action
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.
Java-Based Platform For Immuno-Engineering Biotherapeutics
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.
Development Of An Agent-Based Toolkit For Modeling Complex Biological Systems
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.
Design Of Novel Interleukin-12 Variants With Enhanced Pharmacological properties
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
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
Cloud Computing Platform For Simulating Complex Cell-Signaling Networks
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
Algorithm For Scanning Protein Sequences To Identify Potential Prion-Like Regions
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.
Python/C-Based Machine Control/Interface Software For A Blood Diagnostic Robot
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.