Active and machine learning-based approaches to rapidly enhance microbial chemical production

Biosystems Design by Machine Learning

(2020) Michael Jeffrey Volk et al.   ACS Synthetic Biology

A machine learning Automated Recommendation Tool for synthetic biology

(2020) Tijana Radivojević et al.   Nature Communications

Functional genomics for the oleaginous yeast Yarrowia lipolytica

(2018) Kurt Patterson et al.   METABOLIC ENGINEERING

Chemical genomic guided engineering of gamma-valerolactone tolerant yeast

(2018) Scott Bottoms et al.   Microbial Cell Factories

iSCHRUNK – I n S ilico Approach to Ch aracterization and R eduction of Un certainty in the K inetic Models of Genome-scale Metabolic Networks

(2016) Stefano Andreozzi et al.   METABOLIC ENGINEERING

A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

(2016) Ali Khodayari et al.   Nature Communications

Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems

(2016) Nicholas Roehner et al.   ACS Synthetic Biology

Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering

(2016) Peng Xu et al.   ACS Synthetic Biology

Quantifying Biomass Composition by Gas Chromatography/Mass Spectrometry

(2014) Christopher P. Long et al.   ANALYTICAL CHEMISTRY

Multivariate modular metabolic engineering for pathway and strain optimization

(2014) Bradley Walters Biggs et al.   CURRENT OPINION IN BIOTECHNOLOGY

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

(2014) I. Farasat et al.   Molecular Systems Biology

Production of medium chain length fatty alcohols from glucose in Escherichia coli

(2013) J. Tyler Youngquist et al.   METABOLIC ENGINEERING

Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates

(2013) J. M. Skerker et al.   Molecular Systems Biology

Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay

(2013) Michael E. Lee et al.   NUCLEIC ACIDS RESEARCH

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites

(2013) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IsoCor: correcting MS data in isotope labeling experiments

(2012) P. Millard et al.   BIOINFORMATICS

Strategy for directing combinatorial genome engineering in Escherichia coli

(2012) N. R. Sandoval et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli

(2011) Sabine Bastian et al.   METABOLIC ENGINEERING

Fed-batch culture of Escherichia coli for L-valine production based on in silico flux response analysis

(2010) Jin Hwan Park et al.   BIOTECHNOLOGY AND BIOENGINEERING

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

Production of biofuels and biochemicals: in need of an ORACLE

(2010) Ljubisa Miskovic et al.   TRENDS IN BIOTECHNOLOGY

The elucidation of metabolic pathways and their improvements using stable optimization of large-scale kinetic models of cellular systems

(2009) Evgeni V. Nikolaev   METABOLIC ENGINEERING

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Ensemble Modeling for Aromatic Production in Escherichia coli

(2009) Matthew L. Rizk et al.   PLoS One