Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

(2012) Benjamin D Heavner et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Mathematical optimization applications in metabolic networks

(2012) Ali R. Zomorrodi et al.   METABOLIC ENGINEERING

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS

(2012) Iwona Stelniec-Klotz et al.   Molecular Systems Biology

How cancer metabolism is tuned for proliferation and vulnerable to disruption

(2012) Almut Schulze et al.   NATURE

Boolean modeling in systems biology: an overview of methodology and applications

(2012) Rui-Sheng Wang et al.   PHYSICAL BIOLOGY

Computational Approaches for Analyzing Information Flow in Biological Networks

(2012) B. Kholodenko et al.   Science Signaling

Quantifying the Contribution of the Liver to Glucose Homeostasis: A Detailed Kinetic Model of Human Hepatic Glucose Metabolism

(2012) Matthias König et al.   PLoS Computational Biology

Computational Modeling of the Metabolic States Regulated by the Kinase Akt

(2012) Ettore Mosca et al.   Frontiers in Physiology

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Understanding the transcriptome through RNA structure

(2011) Yue Wan et al.   NATURE REVIEWS GENETICS

The in silico macrophage: toward a better understanding of inflammatory disease

(2011) Peter Ghazal et al.   Genome Medicine

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

Dynamics and Control of the Central Carbon Metabolism in Hepatoma Cells

(2010) Klaus Maier et al.   BMC Systems Biology

Towards a genome-scale kinetic model of cellular metabolism

(2010) Kieran Smallbone et al.   BMC Systems Biology

OptFlux: an open-source software platform for in silico metabolic engineering

(2010) Isabel Rocha et al.   BMC Systems Biology

Ligand-Specific c-Fos Expression Emerges from the Spatiotemporal Control of ErbB Network Dynamics

(2010) Takashi Nakakuki et al.   CELL

Metabolic flux analysis in eukaryotes

(2010) Jens Niklas et al.   CURRENT OPINION IN 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

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

(2009) M. G. Vander Heiden et al.   SCIENCE

Hypergraphs and Cellular Networks

(2009) Steffen Klamt et al.   PLoS Computational Biology

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

(2008) A. Gonzalez et al.   BIOINFORMATICS

Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli

(2008) Markus W. Covert et al.   BIOINFORMATICS

Optimization in computational systems biology

(2008) Julio R Banga   BMC Systems Biology

Regulation of hepatic glucose production and the role of gluconeogenesis in humans: is the rate of gluconeogenesis constant?

(2008) Frank Q. Nuttall et al.   DIABETES-METABOLISM RESEARCH AND REVIEWS

Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics

(2008) I. Emrah Nikerel et al.   METABOLIC ENGINEERING

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

Modelling and analysis of gene regulatory networks

(2008) Guy Karlebach et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic Analysis of Integrated Signaling, Metabolic, and Regulatory Networks

(2008) Jong Min Lee et al.   PLoS Computational Biology