Computational Approaches for Analyzing Information Flow in Biological Networks

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

(2012) Mikhail A. Tsyganov et al.   Molecular BioSystems

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

(2012) Andrea R Tentner et al.   Molecular Systems Biology

A Dynamic Network Model of mTOR Signaling Reveals TSC-Independent mTORC2 Regulation

(2012) P. Dalle Pezze et al.   Science Signaling

cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens

(2011) Xiaohua Douglas Zhang et al.   BIOINFORMATICS

Molecular Predictors of Response to Therapy for Breast Cancer

(2011) Natalie Galanina et al.   CANCER JOURNAL

A Protein Complex Network of Drosophila melanogaster

(2011) K.G. Guruharsha et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Quantitative Phospho-proteomics to Investigate the Polo-like Kinase 1-Dependent Phospho-proteome

(2011) Karin Grosstessner-Hain et al.   MOLECULAR & CELLULAR PROTEOMICS

Rapid Phospho-Turnover by Receptor Tyrosine Kinases Impacts Downstream Signaling and Drug Binding

(2011) Laura B. Kleiman et al.   MOLECULAR CELL

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Few inputs can reprogram biological networks

(2011) Franz-Josef Müller et al.   NATURE

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Mitotic Spindle Proteomics in Chinese Hamster Ovary Cells

(2011) Mary Kate Bonner et al.   PLoS One

A Genome-Wide RNAi Screen Identifies Core Components of the G2-M DNA Damage Checkpoint

(2011) S. Kondo et al.   Science Signaling

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

(2011) R. J. Prill et al.   Science Signaling

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

(2011) B. T. Weinert et al.   Science Signaling

Resistance to MEK Inhibitors: Should We Co-Target Upstream?

(2011) P. I. Poulikakos et al.   Science Signaling

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

(2011) A. Vinayagam et al.   Science Signaling

System-Wide Temporal Characterization of the Proteome and Phosphoproteome of Human Embryonic Stem Cell Differentiation

(2011) K. T. G. Rigbolt et al.   Science Signaling

RNA in pieces

(2011) Alex C. Tuck et al.   TRENDS IN GENETICS

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

(2011) B. Turner et al.   Database-The Journal of Biological Databases and Curation

MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets

(2011) Kristen M. Naegle et al.   PLoS Computational Biology

Switches, Excitable Responses and Oscillations in the Ring1B/Bmi1 Ubiquitination System

(2011) Lan K. Nguyen et al.   PLoS Computational Biology

Logic-Based Models for the Analysis of Cell Signaling Networks

(2010) Melody K. Morris et al.   BIOCHEMISTRY

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

(2010) C. Bender et al.   BIOINFORMATICS

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

(2010) Chen Li et al.   BMC Systems Biology

Functional Roles of Multiple Feedback Loops in Extracellular Signal-Regulated Kinase and Wnt Signaling Pathways That Regulate Epithelial-Mesenchymal Transition

(2010) S.-Y. Shin et al.   CANCER RESEARCH

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

(2010) Takashi Nakakuki et al.   CELL

The Protein Composition of Mitotic Chromosomes Determined Using Multiclassifier Combinatorial Proteomics

(2010) Shinya Ohta et al.   CELL

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Charting the genetic interaction map of a cell

(2010) Michael Costanzo et al.   CURRENT OPINION IN BIOTECHNOLOGY

A Combined Ex Vivo and In Vivo RNAi Screen for Notch Regulators in Drosophila Reveals an Extensive Notch Interaction Network

(2010) Abil Saj et al.   DEVELOPMENTAL CELL

Proteomic and functional analysis of the mitotic Drosophila centrosome

(2010) Hannah Müller et al.   EMBO JOURNAL

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

(2010) K. Malinowsky et al.   JOURNAL OF CELLULAR PHYSIOLOGY

PTMScout, a Web Resource for Analysis of High Throughput Post-translational Proteomics Studies

(2010) Kristen M. Naegle et al.   MOLECULAR & CELLULAR PROTEOMICS

The Plk1-dependent Phosphoproteome of the Early Mitotic Spindle

(2010) Anna Santamaria et al.   MOLECULAR & CELLULAR PROTEOMICS

A human MAP kinase interactome

(2010) Sourav Bandyopadhyay et al.   NATURE METHODS

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

(2010) Michael W Sneddon et al.   NATURE METHODS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

Signalling ballet in space and time

(2010) Boris N. Kholodenko et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

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

Reactome: a database of reactions, pathways and biological processes

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

Revealing strengths and weaknesses of methods for gene network inference

(2010) D. Marbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted large-scale analysis of protein acetylation

(2010) Nikolai Mischerikow et al.   PROTEOMICS

The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier

(2010) O. E. Sturm et al.   Science Signaling

Synthetic Lethal Screen of an EGFR-Centered Network to Improve Targeted Therapies

(2010) I. Astsaturov et al.   Science Signaling

Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

(2010) B. Bodenmiller et al.   Science Signaling

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage

(2010) A. Bensimon et al.   Science Signaling

Inferring Signaling Pathway Topologies from Multiple Perturbation Measurements of Specific Biochemical Species

(2010) T.-R. Xu et al.   Science Signaling

Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows

(2010) Yishai Shimoni et al.   PLoS Computational Biology

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

(2010) Roger L. Chang et al.   PLoS Computational Biology

Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks

(2009) Lars Kaderali et al.   BIOINFORMATICS

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

(2009) E. Antezana et al.   BRIEFINGS IN BIOINFORMATICS

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

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

(2009) S.-Y. Shin et al.   JOURNAL OF CELL SCIENCE

Differential 14-3-3 Affinity Capture Reveals New Downstream Targets of Phosphatidylinositol 3-Kinase Signaling

(2009) Fanny Dubois et al.   MOLECULAR & CELLULAR PROTEOMICS

The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation

(2009) Lea Goentoro et al.   MOLECULAR CELL

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

(2009) Nikolay Borisov et al.   Molecular Systems Biology

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

(2009) Harish Shankaran et al.   Molecular Systems Biology

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

(2009) Julio Saez-Rodriguez et al.   Molecular Systems Biology

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Cell fate decisions are specified by the dynamic ERK interactome

(2009) Alex von Kriegsheim et al.   NATURE CELL BIOLOGY

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

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

(2009) Paola Picotti et al.   NATURE METHODS

A network view of disease and compound screening

(2009) Eric E. Schadt et al.   NATURE REVIEWS DRUG DISCOVERY

Internal coarse-graining of molecular systems

(2009) J. Feret et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scale-Free Networks: A Decade and Beyond

(2009) Albert-László Barabási   SCIENCE

Therapeutically Targeting ErbB3: A Key Node in Ligand-Induced Activation of the ErbB Receptor-PI3K Axis

(2009) B. Schoeberl et al.   Science Signaling

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

(2008) Simon Rogers et al.   BIOINFORMATICS

Functions of Bifans in Context of Multiple Regulatory Motifs in Signaling Networks

(2008) Azi Lipshtat et al.   BIOPHYSICAL JOURNAL

Cytokine-Induced Signaling Networks Prioritize Dynamic Range over Signal Strength

(2008) Kevin A. Janes et al.   CELL

Identification of a Molecular Signaling Network that Regulates a Cellular Necrotic Cell Death Pathway

(2008) Junichi Hitomi et al.   CELL

Network medicine

(2008) Tony Pawson et al.   FEBS LETTERS

Drugs and their molecular targets: an updated overview

(2008) Yves Landry et al.   FUNDAMENTAL & CLINICAL PHARMACOLOGY

Domain-oriented reduction of rule-based network models

(2008) N.M. Borisov et al.   IET Systems Biology

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

(2008) Shai Kaplan et al.   Molecular Systems Biology

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

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

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

(2008) Insuk Lee et al.   NATURE GENETICS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

A Semantic Web Management Model for Integrative Biomedical Informatics

(2008) Helena F. Deus et al.   PLoS One

Dissection of the insulin signaling pathway via quantitative phosphoproteomics

(2008) M. Kruger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Covalent capture of kinase-specific phosphopeptides reveals Cdk1-cyclin B substrates

(2008) J. D. Blethrow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

(2008) H. Yu et al.   SCIENCE

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

(2007) Paul Smolen et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY