(Q37696969)

22 August 2017

1 reference

title

Towards genome-scale signalling network reconstructions (English)

1 reference

22 August 2017

2

Bernhard Ø Palsson

1 reference

22 August 2017

Daniel R Hyduke

1

1 reference

22 August 2017

1 April 2010

1 reference

22 August 2017

Nature Reviews Genetics

1 reference

22 August 2017

11

1 reference

22 August 2017

297-307

1 reference

22 August 2017

4

1 reference

https://scigraph.springernature.com/pub.10.1038/nrg2750

22 August 2017

0 references

cites work

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

1 reference

Prediction of phenotype and gene expression for combinations of mutations

21 January 2018

1 reference

Reconstruction of biochemical networks in microorganisms

21 January 2018

1 reference

Genome-scale gene/reaction essentiality and synthetic lethality analysis

21 January 2018

1 reference

Systems-level interactions between insulin-EGF networks amplify mitogenic signaling.

21 January 2018

1 reference

Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major

21 January 2018

1 reference

21 January 2018

Systems biology of SNPs

1 reference

Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway

21 January 2018

1 reference

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments

21 January 2018

1 reference

Chemical combination effects predict connectivity in biological systems

21 January 2018

1 reference

Engineering key components in a synthetic eukaryotic signal transduction pathway

21 January 2018

1 reference

Small-molecule MDM2 antagonists reveal aberrant p53 signaling in cancer: implications for therapy

21 January 2018

1 reference

Inactivation of the Wip1 phosphatase inhibits mammary tumorigenesis through p38 MAPK-mediated activation of the p16(Ink4a)-p19(Arf) pathway.

31 March 2020

1 reference

DNA repair, damage signaling and carcinogenesis.

31 March 2020

1 reference

The Crohn's disease protein, NOD2, requires RIP2 in order to induce ubiquitinylation of a novel site on NEMO

31 March 2020

1 reference

Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction

31 March 2020

1 reference

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

31 March 2020

1 reference

Redefining the p53 response element

31 March 2020

1 reference

Origins and Mechanisms of miRNAs and siRNAs

31 March 2020

1 reference

Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target

31 March 2020

1 reference

Emergent properties of networks of biological signaling pathways

31 March 2020

1 reference

Identification of potential pathway mediation targets in Toll-like receptor signaling

31 March 2020

1 reference

Global reconstruction of the human metabolic network based on genomic and bibliomic data

31 March 2020

1 reference

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

31 March 2020

1 reference

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

31 March 2020

1 reference

Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data

31 March 2020

1 reference

A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway

31 March 2020

1 reference

Protein modules and signalling networks

31 March 2020

1 reference

A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans.

31 March 2020

1 reference

Understanding complex signaling networks through models and metaphors

31 March 2020

1 reference

Modularity of stress response evolution

31 March 2020

1 reference

The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks.

31 March 2020

1 reference

Circuit diagrams for biological networks

31 March 2020

1 reference

Genetic screening for signal transduction in the era of network biology

31 March 2020

1 reference

Network biology: understanding the cell's functional organization

31 March 2020

1 reference

Variability and robustness in T cell activation from regulated heterogeneity in protein levels

31 March 2020

1 reference

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

31 March 2020

1 reference

Reconstruction of cellular signalling networks and analysis of their properties

31 March 2020

1 reference

Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network

31 March 2020

1 reference

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

31 March 2020

1 reference

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli

31 March 2020

1 reference

Influence of metabolic network structure and function on enzyme evolution

31 March 2020

1 reference

Matrix formalism to describe functional states of transcriptional regulatory systems

31 March 2020

1 reference

A methodology for the structural and functional analysis of signaling and regulatory networks

31 March 2020

1 reference

The transcription unit architecture of the Escherichia coli genome

31 March 2020

1 reference

Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in Escherichia coli

31 March 2020

1 reference

Determination of the Escherichia coli S-nitrosoglutathione response network using integrated biochemical and systems analysis

31 March 2020

1 reference

Network motifs in the transcriptional regulation network of Escherichia coli

31 March 2020

1 reference

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli.

31 March 2020

1 reference

Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae

31 March 2020

1 reference

The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis

31 March 2020

1 reference

A logical model provides insights into T cell receptor signaling

31 March 2020

1 reference

Unravelling the signal-transduction network in B lymphocytes

31 March 2020

1 reference

IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels

31 March 2020

1 reference

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks

31 March 2020

1 reference

A proteomics approach to understanding protein ubiquitination

31 March 2020

1 reference

Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses

31 March 2020

1 reference

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions.

31 March 2020

1 reference

DOMINE: a database of protein domain interactions

31 March 2020

1 reference

The BioGRID Interaction Database: 2008 update

31 March 2020

1 reference

Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk

31 March 2020

1 reference

Rapid evolution of functional complexity in a domain family

31 March 2020

1 reference

Proteome survey reveals modularity of the yeast cell machinery

31 March 2020

1 reference

The protein kinase complement of the human genome

31 March 2020

1 reference

Mechanisms of specificity in protein phosphorylation

31 March 2020

1 reference

A genomic and functional inventory of deubiquitinating enzymes

31 March 2020

1 reference

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

31 March 2020

1 reference

Properties of developmental gene regulatory networks

31 March 2020

1 reference

Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits.

31 March 2020

1 reference

Assembly of Cell Regulatory Systems Through Protein Interaction Domains

31 March 2020

1 reference

Deciphering signaling outcomes from a system of complex networks.

31 March 2020

1 reference

Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets

31 March 2020

1 reference

Rewiring the specificity of two-component signal transduction systems

31 March 2020

1 reference

The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities

31 March 2020

1 reference

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

31 March 2020

1 reference

Genome-scale analysis of Mannheimia succiniciproducens metabolism.

31 March 2020

1 reference

Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel antimicrobial drug targets

31 March 2020

1 reference

Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum

31 March 2020

1 reference

A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189

31 March 2020

1 reference

A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola

31 March 2020

1 reference

Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus

31 March 2020

1 reference

Accelerating the reconstruction of genome-scale metabolic networks

31 March 2020

1 reference

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

31 March 2020

1 reference

Dynamic analysis of integrated signaling, metabolic, and regulatory networks

31 March 2020

1 reference

Dissection of the insulin signaling pathway via quantitative phosphoproteomics

31 March 2020

1 reference

Modular organization of protein interaction networks

31 March 2020

1 reference

Metabolic PathFinding: inferring relevant pathways in biochemical networks

31 March 2020

1 reference

Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology

31 March 2020

1 reference

A computational framework for the topological analysis and targeted disruption of signal transduction networks.

31 March 2020

1 reference

Fault tolerance in protein interaction networks: stable bipartite subgraphs and redundant pathways

31 March 2020

1 reference

Defining genetic interaction

31 March 2020

1 reference

Combinatorial RNAi for quantitative protein network analysis

31 March 2020

1 reference

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

31 March 2020

1 reference

A subsystems-based approach to the identification of drug targets in bacterial pathogens.

31 March 2020

1 reference

Identifying metabolic enzymes with multiple types of association evidence

31 March 2020

1 reference

Systems approach to refining genome annotation

31 March 2020

1 reference

Protein-protein interaction as a predictor of subcellular location

31 March 2020

1 reference

Systematic interpretation of genetic interactions using protein networks

31 March 2020

1 reference

Functional maps of protein complexes from quantitative genetic interaction data

31 March 2020

1 reference

Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions

31 March 2020

1 reference

Global alignment of multiple protein interaction networks with application to functional orthology detection

31 March 2020

1 reference

Conserved pathways within bacteria and yeast as revealed by global protein network alignment

31 March 2020

1 reference

Systematic identification of functional orthologs based on protein network comparison

31 March 2020

1 reference

Conserved patterns of protein interaction in multiple species

31 March 2020

1 reference

Literature-curated protein interaction datasets.

31 March 2020

1 reference

Conserved modular design of an oxygen sensory/signaling network with species-specific output

31 March 2020

1 reference

Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.

31 March 2020

1 reference

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species

31 March 2020

1 reference

Genetic regulatory mechanisms in the synthesis of proteins

31 March 2020

2 references

31 March 2020

12 December 2020

Integrating high-throughput and computational data elucidates bacterial networks

1 reference

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

31 March 2020

1 reference

Integrative model of the response of yeast to osmotic shock

31 March 2020

1 reference

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

31 March 2020

1 reference

Designing new cellular signaling pathways.

31 March 2020

1 reference

A synthetic oscillatory network of transcriptional regulators

31 March 2020

1 reference

Construction of a genetic toggle switch in Escherichia coli

31 March 2020

1 reference

Design of artificial cell-cell communication using gene and metabolic networks

31 March 2020

1 reference

A synthetic gene-metabolic oscillator.

31 March 2020

1 reference

Synthetic ecosystems based on airborne inter- and intrakingdom communication

31 March 2020

1 reference

A fast, robust and tunable synthetic gene oscillator.

31 March 2020

1 reference

Synthetic gene networks that count

31 March 2020

1 reference

Synthetic protein scaffolds provide modular control over metabolic flux.

31 March 2020

1 reference

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks

31 March 2020

1 reference

12 December 2020

Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases

1 reference

12 December 2020

Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks

1 reference

12 December 2020

A comprehensive map of the toll-like receptor signaling network

1 reference

12 December 2020

Identifiers

DOI

10.1038/NRG2750

1 reference

22 August 2017

1 reference

PubMed ID

20177425