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BMC Systems Biology|April 18, 2015
Discovery of substrate cycles in large scale metabolic networks using hierarchical modularityGautham Vivek Sridharan, Ehsan Ullah, Soha Hassoun, et al.
BMC Systems Biology|December 29, 2012
Metabolic flux-based modularity using shortest retroactive distancesGautham Vivek Sridharan, Michael Yi, Soha Hassoun, et al.
BMC Systems Biology|December 24, 2015
PROXIMAL: a method for Prediction of Xenobiotic MetabolismMona Yousofshahi, Sara Manteiga, Charmian Wu, et al.
Metabolic Engineering Communications|February 23, 2018
Selection Finder (SelFi): A computational metabolic engineering tool to enable directed evolution of enzymesNeda Hassanpour, Ehsan Ullah, Mona Yousofshahi, et al.
Biotechnology and Bioengineering|February 26, 2019
Establishing synthesis pathway-host compatibility via enzyme solubilitySara A Amin, Venkatesh Endalur Gopinarayanan, Nikhil U Nair, et al.
Microbial Cell Factories|June 15, 2019
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics dataSara A Amin, Elizabeth Chavez, Vladimir Porokhin, et al.
Integrative and Comparative Biology|August 27, 2021
Artificial Intelligence for BiologySoha Hassoun, Felicia Jefferson, Xinghua Shi, et al.
Metabolites|April 25, 2020
Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted MetabolomicsNeda Hassanpour, Nicholas Alden, Rani Menon, et al.
ACS Omega|March 16, 2026
Role of Structural, Pharmacokinetic, and Energy Properties in the High-Throughput Prediction of Redox Potentials for Organic Molecules with Experimental CalibrationApurva Kalia, Vladimir Porokhin, Benjamin Blackburn, et al.
NPJ Systems Biology and Applications|May 27, 2024
Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiotaFrancesco Balzerani, Telmo Blasco, Sergio Pérez-Burillo, et al.
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