soha hassoun


Computer Science (primary)
Chemical & Biologial Engineering
Electrical & Computer Engineering
Tufts University




Computational Systems

Modeling and Design

Contact Info

161 College Ave
Medford, MA 02155
soha (at)
Follow @sohahassoun

Office Hours

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Hassoun Lab
Computational Systems + Synthetic Biology

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The mission of my research lab is to develop ANALYSIS + DESIGN tools to advance (RE-)DESIGNING BIOLOGY. Our tools provide insight into complex biological systems. They also enable building novel biological components to produce useful chemicals and therapeutics. My lab now focuses on using MACHINE LEARNING to build such tools. My industrial and academic experiences in design automation for electronic systems informs how I approach re-designing biology.
Research Highlights

ProPASS. A workflow that links syntesis pathway construction with the exploration of available enzyme sequences that are predicted soluble in the host. ProSol DB is a database cataloguing the predicted solubility of over 250,000 reviewed enzyme sequences from UNIPROT.
EMMA. This workflow utilizes our tool PROXIMAL to create Extended Metabolic Models (EMMs) that contain not only canonical substrates and products of enzymes already cataloged for an organism, but also metabolites that can form due to substrate promiscuity. EMMA was applied to create an EMM for E. coli and to analyze metabolomics data for CHO and murine cecal microbiota.
gEFM. A method for computing elementary flux modes.
ROXIMAL. A method to derive biotransformation operators from a reaction and to apply them to a target molecule. Operators can be applied to predict xenobiotic products (as suggested in the paper), or applied more generically to identify derivative metabolites for a specific query molecule and a specified enzyme.