(Q38003247)

26 August 2017

title

Computational approaches for analyzing information flow in biological networks (English)

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26 August 2017

1

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26 August 2017

3

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26 August 2017

Michael B Yaffe

2

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26 August 2017

publication date

17 April 2012

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26 August 2017

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26 August 2017

volume

5

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26 August 2017

issue

220

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26 August 2017

page(s)

re1

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Interactome networks and human disease

26 August 2017

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ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage

21 January 2018

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ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage

21 January 2018

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System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

21 January 2018

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Targeted large-scale analysis of protein acetylation

21 January 2018

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Proteome-Wide Mapping of the Drosophila Acetylome Demonstrates a High Degree of Conservation of Lysine Acetylation

21 January 2018

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Decoding signalling networks by mass spectrometry-based proteomics

21 January 2018

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Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data

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Deciphering signaling pathways in clinical tissues for personalized medicine using protein microarrays.

21 January 2018

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Role of the kinase MST2 in suppression of apoptosis by the proto-oncogene product Raf-1.

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RASSF1A elicits apoptosis through an MST2 pathway directing proapoptotic transcription by the p73 tumor suppressor protein

21 January 2018

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Data-driven modelling of signal-transduction networks

21 January 2018

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Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules

21 January 2018

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Dissection of the insulin signaling pathway via quantitative phosphoproteomics

21 January 2018

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Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization

21 January 2018

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Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate.

21 January 2018

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14-3-3sigma controls mitotic translation to facilitate cytokinesis

21 January 2018

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21 January 2018

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21 January 2018

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Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast

21 January 2018

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21 January 2018

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21 January 2018

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Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data

21 January 2018

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Cytokine-induced signaling networks prioritize dynamic range over signal strength

21 January 2018

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Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress

21 January 2018

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21 January 2018

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Causal protein-signaling networks derived from multiparameter single-cell data

21 January 2018

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Bayesian network approach to cell signaling pathway modeling

21 January 2018

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Metabolic stability and epigenesis in randomly constructed genetic nets

21 January 2018

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Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

21 January 2018

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Functional roles of multiple feedback loops in extracellular signal-regulated kinase and Wnt signaling pathways that regulate epithelial-mesenchymal transition

21 January 2018

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Modeling of signal-response cascades using decision tree analysis.

21 January 2018

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Logic-based models for the analysis of cell signaling networks

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Stochastic simulation of chemical kinetics

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Analysis of a generic model of eukaryotic cell-cycle regulation

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors

21 January 2018

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Intrinsic noise in gene regulatory networks

21 January 2018

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Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics

21 January 2018

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Molecular Control Analysis: Control within Proteins and Molecular Processes

21 January 2018

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Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses

21 January 2018

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Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity

21 January 2018

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Predicting temporal fluctuations in an intracellular signalling pathway

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Rules for modeling signal-transduction systems

21 January 2018

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Internal coarse-graining of molecular systems

21 January 2018

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BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

21 January 2018

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Automatic generation of cellular reaction networks with Moleculizer 1.0.

21 January 2018

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Domain-oriented reduction of rule-based network models.

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

21 January 2018

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Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains.

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Reconstruction of cellular signalling networks and analysis of their properties

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Revealing strengths and weaknesses of methods for gene network inference

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Untangling the wires: a strategy to trace functional interactions in signaling and gene networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Quantification of information transfer via cellular signal transduction pathways.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

From the top down: towards a predictive biology of signalling networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Unravelling gene networks from noisy under-determined experimental perturbation data

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Plato's cave algorithm: inferring functional signaling networks from early gene expression shadows

21 January 2018

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From reaction networks to information flow--using modular response analysis to track information in signaling networks.

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Network motifs: simple building blocks of complex networks

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Reading protein modifications with interaction domains

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Functions of bifans in context of multiple regulatory motifs in signaling networks

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Structure and function of the feed-forward loop network motif

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

The incoherent feed-forward loop can generate non-monotonic input functions for genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

The incoherent feedforward loop can provide fold-change detection in gene regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Defining network topologies that can achieve biochemical adaptation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Cell signaling by receptor tyrosine kinases

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Beta4 integrin activates a Shp2-Src signaling pathway that sustains HGF-induced anchorage-independent growth

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

An amplified sensitivity arising from covalent modification in biological systems

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Bistable MAP kinase activity: a plausible mechanism contributing to maintenance of late long-term potentiation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Quantitative analysis of signaling networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Raf family kinases: old dogs have learned new tricks

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Positive- and negative-feedback regulations coordinate the dynamic behavior of the Ras-Raf-MEK-ERK signal transduction pathway

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Signalling ballet in space and time

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Crowdsourcing network inference: the DREAM predictive signaling network challenge

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

A dynamic network model of mTOR signaling reveals TSC-independent mTORC2 regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

High-quality binary protein interaction map of the yeast interactome network

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Systematic Discovery of In Vivo Phosphorylation Networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Charting the genetic interaction map of a cell

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Evolution and functions of long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

A Semantic Web management model for integrative biomedical informatics

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Biological knowledge management: the emerging role of the Semantic Web technologies

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Controllability of complex networks.

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Few inputs can reprogram biological networks.

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Cycloheximide treatment to identify components of the transitional transcriptome in PACAP-induced PC12 cell differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Drugs and their molecular targets: an updated overview

21 January 2018

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https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Biochemical pathway modeling tools for drug target detection in cancer and other complex diseases.

21 January 2018

1 reference

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A network view of disease and compound screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Predicting selective drug targets in cancer through metabolic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Synthetic lethal screen of an EGFR-centered network to improve targeted therapies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Resistance to MEK inhibitors: should we co-target upstream?

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Molecular predictors of response to therapy for breast cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Network medicine: a network-based approach to human disease

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

The human disease network

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Dynamic modularity in protein interaction networks predicts breast cancer outcome

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

The topology design principles that determine the spatiotemporal dynamics of G-protein cascades

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

Quantitative proteomic assessment of very early cellular signaling events

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCISIGNAL.2002961

10.1126/SCISIGNAL.2002961

21 January 2018

Identifiers

DOI

1 reference

26 August 2017

1 reference