RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms

RetroPath2.0: A retrosynthesis workflow for metabolic engineers

(2018) Baudoin Delépine et al.   METABOLIC ENGINEERING

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

ClusterCAD: a computational platform for type I modular polyketide synthase design

(2017) Clara H Eng et al.   NUCLEIC ACIDS RESEARCH

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

(2016) Noushin Hadadi et al.   ACS Synthetic Biology

Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

(2015) Noushin Hadadi et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

(2015) James G Jeffryes et al.   Journal of Cheminformatics

Optimal metabolic route search based on atom mappings

(2014) Mario Latendresse et al.   BIOINFORMATICS

Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

(2014) Miguel A. Campodonico et al.   METABOLIC ENGINEERING

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

A Review of Pterostilbene Antioxidant Activity and Disease Modification

(2013) Denise McCormack et al.   Oxidative Medicine and Cellular Longevity

Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms

(2012) Pablo Carbonell et al.   BMC Systems Biology

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

(2011) Pablo Carbonell et al.   BMC Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization

(2008) Torsten Blum et al.   BIOINFORMATICS

LibSBML: an API Library for SBML

(2008) B. J. Bornstein et al.   BIOINFORMATICS

De novo biosynthetic pathways: rational design of microbial chemical factories

(2008) Kristala L Jones Prather et al.   CURRENT OPINION IN BIOTECHNOLOGY

Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels

(2008) Shota Atsumi et al.   NATURE