Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC)

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

A laser microdissection-based workflow for FFPE tissue microproteomics: Important considerations for small sample processing

(2016) Rémi Longuespée et al.   METHODS

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

A MYC–aurora kinase A protein complex represents an actionable drug target in p53-altered liver cancer

(2016) Daniel Dauch et al.   NATURE MEDICINE

Inflammatory signaling in human tuberculosis granulomas is spatially organized

(2016) Mohlopheni J Marakalala et al.   NATURE MEDICINE

Detection of molecular signatures of oral squamous cell carcinoma and normal epithelium - application of a novel methodology for unsupervised segmentation of imaging mass spectrometry data

(2016) Piotr Widlak et al.   PROTEOMICS

MALDI mass spectrometry imaging: A cutting-edge tool for fundamental and clinical histopathology

(2016) Rémi Longuespée et al.   Proteomics Clinical Applications

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

(2016) Bernd Bodenmiller   Cell Systems

Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research

(2016) Christopher S. Hughes et al.   Scientific Reports

Proteomic developments in the analysis of formalin-fixed tissue

(2015) Ove J.R. Gustafsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

The Use of Mass Spectrometry Imaging to Predict Treatment Response of Patient-Derived Xenograft Models of Triple-Negative Breast Cancer

(2015) Nadine E. Mascini et al.   JOURNAL OF PROTEOME RESEARCH

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs)

(2015) Marie-Therese Mackmull et al.   MOLECULAR & CELLULAR PROTEOMICS

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

(2015) Kornelius Schulze et al.   NATURE GENETICS

The Genomic Landscape of Renal Oncocytoma Identifies a Metabolic Barrier to Tumorigenesis

(2015) Shilpy Joshi et al.   Cell Reports

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

(2014) Graeme C. McAlister et al.   ANALYTICAL CHEMISTRY

p53-Dependent Nestin Regulation Links Tumor Suppression to Cellular Plasticity in Liver Cancer

(2014) Darjus F. Tschaharganeh et al.   CELL

Prosurvival function of the cellular apoptosis susceptibility/importin-α1 transport cycle is repressed by p53 in liver cancer

(2014) Juliane Winkler et al.   HEPATOLOGY

Epidemiology of hepatocellular carcinoma in the United States: Where are we? Where do we go?

(2014) Hashem B. El-Serag et al.   HEPATOLOGY

Plasma minichromosome maintenance complex component 6 is a novel biomarker for hepatocellular carcinoma patients

(2014) Tenghao Zheng et al.   HEPATOLOGY RESEARCH

De novodiscovery of phenotypic intratumour heterogeneity using imaging mass spectrometry

(2014) Benjamin Balluff et al.   JOURNAL OF PATHOLOGY

Ultrasensitive proteome analysis using paramagnetic bead technology

(2014) C. S. Hughes et al.   Molecular Systems Biology

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer

(2014) Ramona Rudalska et al.   NATURE MEDICINE

Tumoral heterogeneity of hepatic cholangiocarcinomas revealed by MALDI imaging mass spectrometry

(2014) Julie Le Faouder et al.   PROTEOMICS

Biomarkers of mitochondrial content in skeletal muscle of healthy young human subjects

(2012) Steen Larsen et al.   JOURNAL OF PHYSIOLOGY-LONDON

Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma

(2012) Cécile Guichard et al.   NATURE GENETICS

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Translational Control in Cancer Etiology

(2012) D. Ruggero   Cold Spring Harbor Perspectives in Biology

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

(2011) Laurent Gatto et al.   BIOINFORMATICS

High Recovery FASP Applied to the Proteomic Analysis of Microdissected Formalin Fixed Paraffin Embedded Cancer Tissues Retrieves Known Colon Cancer Markers

(2011) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

A simple and fast method to determine the parameters for fuzzy c–means cluster analysis

(2010) Veit Schwämmle et al.   BIOINFORMATICS

A Unique Metastasis Gene Signature Enables Prediction of Tumor Relapse in Early-Stage Hepatocellular Carcinoma Patients

(2010) S. Roessler et al.   CANCER RESEARCH

Proteome, Phosphoproteome, and N-Glycoproteome Are Quantitatively Preserved in Formalin-Fixed Paraffin-Embedded Tissue and Analyzable by High-Resolution Mass Spectrometry

(2010) Paweł Ostasiewicz et al.   JOURNAL OF PROTEOME RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Accurate and Sensitive Peptide Identification with Mascot Percolator

(2009) Markus Brosch et al.   JOURNAL OF PROTEOME RESEARCH

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

(2008) K. Strimmer   BIOINFORMATICS

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

STRING 8--a global view on proteins and their functional interactions in 630 organisms

(2008) L. J. Jensen et al.   NUCLEIC ACIDS RESEARCH