Computational Methods in Synthetic Biology

1. Using a Design of Experiments Approach to Inform the Design of Hybrid Synthetic Yeast Promoters.- Computational Design of Multiplex Oligonucleotide-Based Assays.- Computational Methods For The Design Of Recombinase Logic Circuits.- Modular Modeling Of Genetic Circuits in SBML Level 3.-- CRISPR-ERA: A Webserver for Guide RNA Design of Gene Editing and Regulation.- iGUIDE Method for CRISPR Off-target Detection.- Web-based Base Editing Toolkits: BE-Designer and BE-Analyzer.- Synthetic Gene Circuit Analysis and Optimization.- Monitoring Single S. cerevisiae Cells with Multi-Frequency Electrical Impedance Spectroscopy in an Electrode-integrated Microfluidic Device.- Construction of Protein Expression Network.- Systems-theoretic Approaches to Design Biological Networks with Desired Functionalities.- A Deterministic Compartmental Modeling Framework for Disease Transmission.- Computer Aided Assembly and Verificationof Synthetic Chromosomes.- Minimal Genome Design Algorithms using Whole-Cell Models.- Tn-Core: Functionally Interpreting Transposon-Sequencing Data with Metabolic Network Analysis.- Genome-scale Metabolic Modeling of Escherichia coli and its Chassis Design for Synthetic Biology Applications.- A Systems Bioinformatics Approach to Interconnect Biological Pathways.