Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

Use of Mechanistic Models to Integrate and Analyze Multiple Proteomic Datasets

(2015) Edward C. Stites et al.   BIOPHYSICAL JOURNAL

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

Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis

(2015) Linjie Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Proteomic Landscape of Triple-Negative Breast Cancer

(2015) Robert T. Lawrence et al.   Cell Reports

Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment

(2014) Tujin Shi et al.   ANALYTICAL CHEMISTRY

Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

(2014) Navin Rauniyar et al.   JOURNAL OF PROTEOME RESEARCH

Fine Specificity and Molecular Competition in SLAM Family Receptor Signalling

(2014) Timothy J. Wilson et al.   PLoS One

Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis

(2013) Tujin Shi et al.   ANALYTICAL CHEMISTRY

Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria

(2013) Ronald C. Taylor et al.   Integrative Biology

Quantification of ErbB Network Proteins in Three Cell Types Using Complementary Approaches Identifies Cell-General and Cell-Type-Specific Signaling Proteins

(2013) Christina Kiel et al.   JOURNAL OF PROTEOME RESEARCH

Western BlotsversusSelected Reaction Monitoring Assays: Time to Turn the Tables?

(2013) Ruedi Aebersold et al.   MOLECULAR & CELLULAR PROTEOMICS

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

(2013) Yong Zheng et al.   NATURE

TCPA: a resource for cancer functional proteomics data

(2013) Jun Li et al.   NATURE METHODS

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines

(2013) M. Niepel et al.   Science Signaling

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks

(2012) Daniel C Kirouac et al.   BMC Systems Biology

Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins

(2012) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

Network Analysis of Epidermal Growth Factor Signaling Using Integrated Genomic, Proteomic and Phosphorylation Data

(2012) Katrina M. Waters et al.   PLoS One

Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum

(2012) T. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics

(2012) Tujin Shi et al.   PROTEOMICS

DUSPs, to MAP kinases and beyond

(2012) Ching-Yu Huang et al.   Cell and Bioscience

Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration

(2012) René Meyer et al.   Frontiers in Physiology

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling

(2011) Paweł P. Łabaj et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

(2011) Fang Xie et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

High- and Low-Affinity Epidermal Growth Factor Receptor-Ligand Interactions Activate Distinct Signaling Pathways

(2011) Jordan A. Krall et al.   PLoS One

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Signal Transduction Networks in Cancer: Quantitative Parameters Influence Network Topology

(2010) D. J. Klinke   CANCER RESEARCH

Molecular and clinical analysis ofRAF1in Noonan syndrome and related disorders: dephosphorylation of serine 259 as the essential mechanism for mutant activation

(2010) Tomoko Kobayashi et al.   HUMAN MUTATION

Multiple mechanisms collectively regulate clathrin-mediated endocytosis of the epidermal growth factor receptor

(2010) Lai Kuan Goh et al.   JOURNAL OF CELL BIOLOGY

Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context

(2010) Elizabeth J. Joslin et al.   Molecular BioSystems

Quantifying Western blots: Pitfalls of densitometry

(2009) Max Gassmann et al.   ELECTROPHORESIS

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

(2009) Saw Yen Ow et al.   JOURNAL OF PROTEOME RESEARCH

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

(2009) Nikolay Borisov et al.   Molecular Systems Biology

Linear combinations of docking affinities explain quantitative differences in RTK signaling

(2009) Andrew Gordus et al.   Molecular Systems Biology

PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk

(2009) Chun-Chao Wang et al.   Molecular Systems Biology

Protein promiscuity and its implications for biotechnology

(2009) Irene Nobeli et al.   NATURE BIOTECHNOLOGY

DAnTE: a statistical tool for quantitative analysis of -omics data

(2008) A. D. Polpitiya et al.   BIOINFORMATICS

Multiple Mechanisms Are Responsible for Transactivation of the Epidermal Growth Factor Receptor in Mammary Epithelial Cells

(2008) Karin D. Rodland et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Recurrent design patterns in the feedback regulation of the mammalian signalling network

(2008) Stefan Legewie et al.   Molecular Systems Biology

DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers

(2008) W W Lockwood et al.   ONCOGENE