Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data

Targeted proteomics analyses of phosphorylation-dependent signalling networks

(2018) Sara L. Banerjee et al.   Journal of Proteomics

Specter: linear deconvolution for targeted analysis of data-independent acquisition mass spectrometry proteomics

(2018) Ryan Peckner et al.   NATURE METHODS

Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS

(2017) George Rosenberger et al.   NATURE BIOTECHNOLOGY

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

The target landscape of clinical kinase drugs

(2017) Susan Klaeger et al.   SCIENCE

Data-driven reverse engineering of signaling pathways using ensembles of dynamic models

(2017) David Henriques et al.   PLoS Computational Biology

Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling

(2017) Steven M. Hill et al.   Cell Systems

Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes

(2016) Jennifer G. Abelin et al.   MOLECULAR & CELLULAR PROTEOMICS

An atlas of human kinase regulation

(2016) David Ochoa et al.   Molecular Systems Biology

Inferring causal molecular networks: empirical assessment through a community-based effort

(2016) Steven M Hill et al.   NATURE METHODS

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Evolution of protein phosphorylation across 18 fungal species

(2016) R. A. Studer et al.   SCIENCE

Integrating network reconstruction with mechanistic modeling to predict cancer therapies

(2016) M. Halasz et al.   Science Signaling

Integrating network reconstruction with mechanistic modeling to predict cancer therapies

(2016) M. Halasz et al.   Science Signaling

Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks

(2016) Jan Daniel Rudolph et al.   Cell Systems

Recent findings and technological advances in phosphoproteomics for cells and tissues

(2015) Louise von Stechow et al.   Expert Review of Proteomics

SIGNOR: a database of causal relationships between biological entities

(2015) Livia Perfetto et al.   NUCLEIC ACIDS RESEARCH

Empirical inference of circuitry and plasticity in a kinase signaling network

(2015) Edmund H. Wilkes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data

(2015) Camille D. A. Terfve et al.   Nature Communications

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

(2015) Åsmund Flobak et al.   PLoS Computational Biology

Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells

(2015) Anil Korkut et al.   eLife

Causal network inference using biochemical kinetics

(2014) Chris J. Oates et al.   BIOINFORMATICS

Large-Scale Identification of Phosphorylation Sites for Profiling Protein Kinase Selectivity

(2014) Haruna Imamura et al.   JOURNAL OF PROTEOME RESEARCH

Building and exploring an integrated human kinase network: Global organization and medical entry points

(2014) Jacques Colinge et al.   Journal of Proteomics

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast

(2014) S. Vaga et al.   Molecular Systems Biology

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology

(2013) Tapesh Santra et al.   BMC Systems Biology

Network quantification of EGFR signaling unveils potential for targeted combination therapy

(2013) B. Klinger et al.   Molecular Systems Biology

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Kinase-Substrate Enrichment Analysis Provides Insights into the Heterogeneity of Signaling Pathway Activation in Leukemia Cells

(2013) P. Casado et al.   Science Signaling

Network inference and biological dynamics

(2012) Chris. J. Oates et al.   Annals of Applied Statistics

Network inference using steady-state data and Goldbeter–koshland kinetics

(2012) Chris J Oates et al.   BIOINFORMATICS

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line

(2012) Steven M. Hill et al.   BIOINFORMATICS

Systematic Functional Prioritization of Protein Posttranslational Modifications

(2012) Pedro Beltrao et al.   CELL

Targeted Proteomic Quantification on Quadrupole-Orbitrap Mass Spectrometer

(2012) Sebastien Gallien et al.   MOLECULAR & CELLULAR PROTEOMICS

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics

(2012) Amelia C. Peterson et al.   MOLECULAR & CELLULAR PROTEOMICS

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

(2012) Ludovic C. Gillet et al.   MOLECULAR & CELLULAR PROTEOMICS

Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS

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

Signaling Network State Predicts Twist-Mediated Effects on Breast Cell Migration Across Diverse Growth Factor Contexts

(2011) Hyung-Do Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge

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

Large-Scale Discovery of ERK2 Substrates Identifies ERK-Mediated Transcriptional Regulation by ETV3

(2011) S. M. Carlson et al.   Science Signaling

Human SBK1 is dysregulated in multiple cancers and promotes survival of ovary cancer SK-OV-3 cells

(2010) Pingzhang Wang et al.   MOLECULAR BIOLOGY REPORTS

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

(2009) Dominik M Wittmann et al.   BMC Systems Biology

Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography−Tandem Mass Spectrometry

(2009) David L. Tabb et al.   JOURNAL OF PROTEOME RESEARCH

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

Weak functional constraints on phosphoproteomes

(2009) Christian R. Landry et al.   TRENDS IN GENETICS

Network inference using informative priors

(2008) S. Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA