Coordination of microbial metabolism

V Chubukov, L Gerosa, K Kochanowski… - Nature Reviews …, 2014 - nature.com
Beyond fuelling cellular activities with building blocks and energy, metabolism also
integrates environmental conditions into intracellular signals. The underlying regulatory …

Progress in Metabolic Engineering of Saccharomyces cerevisiae

E Nevoigt - Microbiology and Molecular Biology Reviews, 2008 - Am Soc Microbiol
The traditional use of the yeast Saccharomyces cerevisiae in alcoholic fermentation has,
over time, resulted in substantial accumulated knowledge concerning genetics, physiology …

Systems-level analysis of mechanisms regulating yeast metabolic flux

SR Hackett, VRT Zanotelli, W Xu, J Goya, JO Park… - Science, 2016 - science.org
INTRODUCTION Metabolism is among the most strongly conserved processes across all
domains of life and is crucial for both bioengineering and disease research, yet we still have …

Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato

Y Zhang, E Butelli, S Alseekh, T Tohge… - Nature …, 2015 - nature.com
Phenylpropanoids comprise an important class of plant secondary metabolites. A number of
transcription factors have been used to upregulate-specific branches of phenylpropanoid …

Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism

D Machado, M Herrgård - PLoS computational biology, 2014 - journals.plos.org
Constraint-based models of metabolism are a widely used framework for predicting flux
distributions in genome-scale biochemical networks. The number of published methods for …

[HTML][HTML] Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds

JG Zalatan, ME Lee, R Almeida, LA Gilbert… - Cell, 2015 - cell.com
Eukaryotic cells execute complex transcriptional programs in which specific loci throughout
the genome are regulated in distinct ways by targeted regulatory assemblies. We have …

[HTML][HTML] A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data

Z Costello, HG Martin - NPJ systems biology and applications, 2018 - nature.com
New synthetic biology capabilities hold the promise of dramatically improving our ability to
engineer biological systems. However, a fundamental hurdle in realizing this potential is our …

[HTML][HTML] Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

P Picotti, B Bodenmiller, LN Mueller, B Domon… - Cell, 2009 - cell.com
The rise of systems biology implied a growing demand for highly sensitive techniques for the
fast and consistent detection and quantification of target sets of proteins across multiple …

Development of a robust and repeatable UPLC− MS method for the long-term metabolomic study of human serum

E Zelena, WB Dunn, D Broadhurst… - Analytical …, 2009 - ACS Publications
A method for performing untargeted metabolomic analysis of human serum has been
developed based on protein precipitation followed by Ultra Performance Liquid …

Network-based prediction of human tissue-specific metabolism

T Shlomi, MN Cabili, MJ Herrgård, BØ Palsson… - Nature …, 2008 - nature.com
Direct in vivo investigation of mammalian metabolism is complicated by the distinct
metabolic functions of different tissues. We present a computational method that successfully …