Targeted protein-omic methods are bridging the gap between proteomic and hypothesis-driven protein analysis approaches

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

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

(2010) Takashi Nakakuki et al.   CELL

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Comprehensive proteomics

(2010) Martin Beck et al.   CURRENT OPINION IN BIOTECHNOLOGY

Recent advances in DNA sequencing methods – general principles of sample preparation

(2010) Sten Linnarsson   EXPERIMENTAL CELL RESEARCH

Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes

(2010) Leonidas G. Alexopoulos et al.   MOLECULAR & CELLULAR PROTEOMICS

Sequential Multiplex Analyte Capturing for Phosphoprotein Profiling

(2010) Oliver Poetz et al.   MOLECULAR & CELLULAR PROTEOMICS

Identification of Quantitative Trait Loci Underlying Proteome Variation in Human Lymphoblastoid Cells

(2010) Nikhil Garge et al.   MOLECULAR & CELLULAR PROTEOMICS

Cytokine-associated drug toxicity in human hepatocytes is associated with signaling network dysregulation

(2010) Benjamin D. Cosgrove et al.   Molecular BioSystems

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Systems analysis of EGF receptor signaling dynamics with microwestern arrays

(2010) Mark F Ciaccio et al.   NATURE METHODS

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

ErbB receptors and signaling pathways in cancer

(2009) Nancy E Hynes et al.   CURRENT OPINION IN CELL BIOLOGY

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

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

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

Cytokine-Induced Signaling Networks Prioritize Dynamic Range over Signal Strength

(2008) Kevin A. Janes et al.   CELL

Can Proteomics Retire the Western Blot?

(2008) Matthias   Mann   JOURNAL OF PROTEOME RESEARCH

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE

A Genome-Wide Association Study Identifies Protein Quantitative Trait Loci (pQTLs)

(2008) David Melzer et al.   PLoS Genetics