Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

Large scale gene regulatory network inference with a multi-level strategy

(2016) Jun Wu et al.   Molecular BioSystems

Inferring Gene Regulatory Networks Using Conditional Regulation Pattern to Guide Candidate Genes

(2016) Fei Xiao et al.   PLoS One

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

(2016) Ali Khodayari et al.   Nature Communications

One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!

(2016) Thurston Herricks et al.   G3-Genes Genomes Genetics

Model-driven discovery of underground metabolic functions inEscherichia coli

(2015) Gabriela I. Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

(2015) Shuyi Ma et al.   PLoS Computational Biology

Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

(2015) Benjamin D. Heavner et al.   PLoS Computational Biology

Capturing the response of Clostridium acetobutylicumto chemical stressors using a regulated genome-scale metabolic model

(2014) Satyakam Dash et al.   Biotechnology for Biofuels

The growing landscape of lysine acetylation links metabolism and cell signalling

(2014) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Predicting microbial growth

(2014) J. Monk et al.   SCIENCE

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

(2014) Daniel Machado et al.   PLoS Computational Biology

A multi-layer inference approach to reconstruct condition-specific genes and their regulation

(2013) Ming Wu et al.   BIOINFORMATICS

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints

(2013) Anirikh Chakrabarti et al.   Biotechnology Journal

Molecular mechanisms of system responses to novel stimuli are predictable from public data

(2013) Samuel A. Danziger et al.   NUCLEIC ACIDS RESEARCH

A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae

(2013) L. Geistlinger et al.   NUCLEIC ACIDS RESEARCH

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation inSaccharomyces cerevisiae

(2013) Miguel Cacho Teixeira et al.   NUCLEIC ACIDS RESEARCH

Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks

(2013) Natalie J. Stanford et al.   PLoS One

Model-based identification of drug targets that revert disrupted metabolism and its application to ageing

(2013) Keren Yizhak et al.   Nature Communications

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

(2013) Benjamin D. Heavner et al.   Database-The Journal of Biological Databases and Curation

Significance Analysis of Prognostic Signatures

(2013) Andrew H. Beck et al.   PLoS Computational Biology

Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

(2013) Sergio Rossell et al.   PLoS Computational Biology

Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective

(2013) Graham Rockwell et al.   PLoS Computational Biology

Inferring gene regulatory networks by ANOVA

(2012) Robert Küffner et al.   BIOINFORMATICS

Genome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach

(2012) Ali Navid et al.   BMC Systems Biology

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Systems metabolic engineering of microorganisms for natural and non-natural chemicals

(2012) Jeong Wook Lee et al.   Nature Chemical Biology

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

Regulation and control of metabolic fluxes in microbes

(2011) Luca Gerosa et al.   CURRENT OPINION IN BIOTECHNOLOGY

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Functional integration of a metabolic network model and expression data without arbitrary thresholding

(2010) Paul A. Jensen et al.   BIOINFORMATICS

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC Systems Biology

Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

(2010) Sarah-Maria Fendt et al.   Molecular Systems Biology

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface

(2010) D. Abdulrehman et al.   NUCLEIC ACIDS RESEARCH

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

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

(2009) Monica L Mo et al.   BMC Systems Biology

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology