STAT 3 ‐dependent analysis reveals PDK 4 as independent predictor of recurrence in prostate cancer

Primer3_masker: integrating masking of template sequence with primer design software

(2018) Triinu Kõressaar et al.   BIOINFORMATICS

Stromal Gene Expression is Predictive for Metastatic Primary Prostate Cancer

(2018) Fan Mo et al.   EUROPEAN UROLOGY

Metabolomics and transcriptomics profiles reveal the dysregulation of the tricarboxylic acid cycle and related mechanisms in prostate cancer

(2018) Yaping Shao et al.   INTERNATIONAL JOURNAL OF CANCER

The Role of Pyruvate Dehydrogenase Kinase-4 (PDK4) in Bladder Cancer and Chemoresistance

(2018) Benjamin L Woolbright et al.   MOLECULAR CANCER THERAPEUTICS

Compartmentalized activities of the pyruvate dehydrogenase complex sustain lipogenesis in prostate cancer

(2018) Jingjing Chen et al.   NATURE GENETICS

Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression

(2018) Leena Latonen et al.   Nature Communications

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2018) Freddie Bray et al.   CA-A CANCER JOURNAL FOR CLINICIANS

STAT3 localizes to the ER, acting as a gatekeeper for ER-mitochondrion Ca2+ fluxes and apoptotic responses

(2018) Lidia Avalle et al.   CELL DEATH AND DIFFERENTIATION

Landmarks in prostate cancer

(2018) Niranjan J. Sathianathen et al.   Nature Reviews Urology

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Integrative epigenetic taxonomy of primary prostate cancer

(2018) Suzan Stelloo et al.   Nature Communications

Therapeutic Targeting of the Pyruvate Dehydrogenase Complex/Pyruvate Dehydrogenase Kinase (PDC/PDK) Axis in Cancer

(2017) Peter W Stacpoole   JNCI-Journal of the National Cancer Institute

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Analysis of STAT3-Mediated Transcription during Early Human Th17 Cell Differentiation

(2017) Subhash K. Tripathi et al.   Cell Reports

The emerging role and targetability of the TCA cycle in cancer metabolism

(2017) Nicole M. Anderson et al.   Protein & Cell

Therapeutic Targeting of the Pyruvate Dehydrogenase Complex/Pyruvate Dehydrogenase Kinase (PDC/PDK) Axis in Cancer

(2017) Peter W Stacpoole   JNCI-Journal of the National Cancer Institute

Glucose Metabolism in the Progression of Prostate Cancer

(2017) Francesca Cutruzzolà et al.   Frontiers in Physiology

Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer

(2016) Himisha Beltran et al.   NATURE MEDICINE

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

(2016) Stefka Tyanova et al.   Nature Protocols

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

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A STAT3-mediated metabolic switch is involved in tumour transformation and STAT3 addiction

(2016) Marco Demaria et al.   Aging-US

The Molecular Taxonomy of Primary Prostate Cancer

(2015) Adam Abeshouse et al.   CELL

The Opposing Function of STAT3 as an Oncoprotein and Tumor Suppressor Is Dictated by the Expression Status of STAT3  in Esophageal Squamous Cell Carcinoma

(2015) H.-F. Zhang et al.   CLINICAL CANCER RESEARCH

Cancer metabolism and the Warburg effect: the role of HIF-1 and PI3K

(2015) Rupert Courtnay et al.   MOLECULAR BIOLOGY REPORTS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

Visualization of LC-MS/MS proteomics data in MaxQuant

(2015) Stefka Tyanova et al.   PROTEOMICS

The Placental Gene PEG10 Promotes Progression of Neuroendocrine Prostate Cancer

(2015) Shusuke Akamatsu et al.   Cell Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

STAT3-Mediated Metabolic Reprograming in Cellular Transformation and Implications for Drug Resistance

(2015) Valeria Poli et al.   Frontiers in Oncology

Pyruvate Dehydrogenase Kinases: Therapeutic Targets for Diabetes and Cancers

(2015) Nam Ho Jeoung   Diabetes & Metabolism Journal

Persistent Inflammation Leads to Proliferative Neoplasia and Loss of Smooth Muscle Cells in a Prostate Tumor Model

(2015) Andreas Birbach et al.   NEOPLASIA

PDK4 Protein Promotes Tumorigenesis through Activation of cAMP-response Element-binding Protein (CREB)-Ras Homolog Enriched in Brain (RHEB)-mTORC1 Signaling Cascade

(2014) Zhibo Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

The pivotal role of pyruvate dehydrogenase kinases in metabolic flexibility

(2014) Shuai Zhang et al.   Nutrition & Metabolism

Diisopropylamine Dichloroacetate, a Novel Pyruvate Dehydrogenase Kinase 4 Inhibitor, as a Potential Therapeutic Agent for Metabolic Disorders and Multiorgan Failure in Severe Influenza

(2014) Kazuhiko Yamane et al.   PLoS One

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

STAT3 in Cancer—Friend or Foe?

(2014) Hai-Feng Zhang et al.   Cancers

STAT3 Activities and Energy Metabolism: Dangerous Liaisons

(2014) Annalisa Camporeale et al.   Cancers

STAT3 Target Genes Relevant to Human Cancers

(2014) Richard Carpenter et al.   Cancers

Perfil de expresión génica en el cáncer de próstata: identificación de marcadores candidatos para el diagnóstico no invasivo

(2013) L. Mengual et al.   Actas Urologicas Espanolas

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Regulation of pyruvate metabolism and human disease

(2013) Lawrence R. Gray et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

TCPA: a resource for cancer functional proteomics data

(2013) Jun Li et al.   NATURE METHODS

STAT3 and HIF1α cooperatively activate HIF1 target genes in MDA-MB-231 and RCC4 cells

(2013) M R Pawlus et al.   ONCOGENE

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

(2013) Raul Aguirre-Gamboa et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Ribosome Biogenesis and Control of Cell Proliferation: p53 Is Not Alone

(2012) G. Donati et al.   CANCER RESEARCH

Reciprocal Metabolic Reprogramming through Lactate Shuttle Coordinately Influences Tumor-Stroma Interplay

(2012) T. Fiaschi et al.   CANCER RESEARCH

Hedgehog-EGFR cooperation response genes determine the oncogenic phenotype of basal cell carcinoma and tumour-initiating pancreatic cancer cells

(2012) Markus Eberl et al.   EMBO Molecular Medicine

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

From sequence to molecular pathology, and a mechanism driving the neuroendocrine phenotype in prostate cancer

(2012) Anna V Lapuk et al.   JOURNAL OF PATHOLOGY

Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database

(2012) Christoph Schaab et al.   MOLECULAR & CELLULAR PROTEOMICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Increased expression of NuSAP in recurrent prostate cancer is mediated by E2F1

(2012) Z G Gulzar et al.   ONCOGENE

Hypoxia Induces PDK4 Gene Expression through Induction of the Orphan Nuclear Receptor ERRγ

(2012) Ja Hee Lee et al.   PLoS One

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

The oncogene c-Myc coordinates regulation of metabolic networks to enable rapid cell cycle entry

(2011) Fionnuala Morrish et al.   CELL CYCLE

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

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

Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors

(2011) Jürgen Cox et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Molecular sampling of prostate cancer: a dilemma for predicting disease progression

(2010) Andrea Sboner et al.   BMC Medical Genomics

Integrative Genomic Profiling of Human Prostate Cancer

(2010) Barry S. Taylor et al.   CANCER CELL

Stoichiometry of STAT3 and Mitochondrial Proteins

(2010) Darci Phillips et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

(2009) Gabriela Bindea et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The dark and the bright side of Stat3: proto-oncogene and tumor-suppressor

(2009) Andrea Ecker   Frontiers in Bioscience-Landmark

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Function of Mitochondrial Stat3 in Cellular Respiration

(2009) J. Wegrzyn et al.   SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Signal Transducer and Activator of Transcription 3 Is Required for Hypoxia-Inducible Factor-1  RNA Expression in Both Tumor Cells and Tumor-Associated Myeloid Cells

(2008) G. Niu et al.   MOLECULAR CANCER RESEARCH

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