Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data

Proteomic Portrait of Human Breast Cancer Progression Identifies Novel Prognostic Markers

(2012) T. Geiger et al.   CANCER RESEARCH

Quantitative Analysis of the Detergent-Insoluble Brain Proteome in Frontotemporal Lobar Degeneration Using SILAC Internal Standards

(2012) Nicholas T. Seyfried et al.   JOURNAL OF PROTEOME RESEARCH

An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies

(2011) Jia Li et al.   Annals of Applied Statistics

Quantitative phosphoproteomics strategies for understanding protein kinase-mediated signal transduction pathways

(2011) Hidetaka Kosako et al.   Expert Review of Proteomics

Large-scale phosphosite quantification in tissues by a spike-in SILAC method

(2011) Mara Monetti et al.   NATURE METHODS

Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map

(2011) Nozomu Yachie et al.   PLoS Computational Biology

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Regulation of cross-talk in yeast MAPK signaling pathways

(2010) Haruo Saito   CURRENT OPINION IN MICROBIOLOGY

Characterization of Substrates That Have a Differential Effect onSaccharomyces cerevisiaeProtein Kinase A Holoenzyme Activation

(2010) Fiorella Galello et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantitative Proteomics Using Stable Isotope Labeling with Amino Acids in Cell Culture Reveals Changes in the Cytoplasmic, Nuclear, and Nucleolar Proteomes in Vero Cells Infected with the Coronavirus Infectious Bronchitis Virus

(2010) Edward Emmott et al.   MOLECULAR & CELLULAR PROTEOMICS

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

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

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

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

(2010) B. Bodenmiller et al.   Science Signaling

Domain Architecture of the Regulators of Calcineurin (RCANs) and Identification of a Divergent RCAN in Yeast

(2009) S. Mehta et al.   MOLECULAR AND CELLULAR BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Global and Site-Specific Quantitative Phosphoproteomics: Principles and Applications

(2008) Boris Macek et al.   Annual Review of Pharmacology and Toxicology

Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress inSaccharomyces cerevisiae

(2008) Katsunori Yoshikawa et al.   FEMS YEAST RESEARCH

Screening for EphB Signaling Effectors Using SILAC with a Linear Ion Trap-Orbitrap Mass Spectrometer

(2008) Guoan Zhang et al.   JOURNAL OF PROTEOME RESEARCH

Analysis of the Yeast Kinome Reveals a Network of Regulated Protein Localization during Filamentous Growth

(2008) Nikë Bharucha et al.   MOLECULAR BIOLOGY OF THE CELL

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates

(2008) Paul J. Boersema et al.   PROTEOMICS

Role of 14-3-3 proteins in the regulation of neutral trehalase in the yeastSaccharomyces cerevisiae

(2007) Simona Panni et al.   FEMS YEAST RESEARCH

Large-Scale Analysis of Yeast Filamentous Growth by Systematic Gene Disruption and Overexpression

(2007) Rui Jin et al.   MOLECULAR BIOLOGY OF THE CELL