Gene expression profiling for targeted cancer treatment

Multiple myeloma: the bone marrow microenvironment and its relation to treatment

(2016) S. W. Andrews et al.   BRITISH JOURNAL OF BIOMEDICAL SCIENCE

Molecular pathways and therapeutic targets in lung cancer

(2015) Emma Shtivelman et al.   Oncotarget

A curated census of autophagy-modulating proteins and small molecules

(2014) Philip L Lorenzi et al.   Autophagy

Novel Aspects of the Liver Microenvironment in Hepatocellular Carcinoma Pathogenesis and Development

(2014) Thomas Tu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The roles of mesenchymal stem cells in tumor inflammatory microenvironment

(2014) Zhao Sun et al.   Journal of Hematology & Oncology

Molecular Tumor Board: The University of California San Diego Moores Cancer Center Experience

(2014) M. Schwaederle et al.   ONCOLOGIST

Clustering Gene Expression Regulators: New Approach to Disease Subtyping

(2014) Mikhail Pyatnitskiy et al.   PLoS One

Potential Therapeutic Targets for Oral Cancer: ADM, TP53, EGFR, LYN, CTLA4, SKIL, CTGF, CD70

(2014) Saurabh Bundela et al.   PLoS One

MicroRNAs in cancer: biomarkers, functions and therapy

(2014) Josie Hayes et al.   TRENDS IN MOLECULAR MEDICINE

Inflammasomes in cancer: a double-edged sword

(2014) Ryan Kolb et al.   Protein & Cell

Chronic Inflammation: Synergistic Interactions of Recruiting Macrophages (TAMs) and Eosinophils (Eos) with Host Mast Cells (MCs) and Tumorigenesis in CALTs. M-CSF, Suitable Biomarker for Cancer Diagnosis!

(2014) Mahin Khatami   Cancers

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis

(2013) Lifang Zhang et al.   BMC BIOINFORMATICS

Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data

(2013) Natalie L Catlett et al.   BMC BIOINFORMATICS

Cancer gene expression signatures – The rise and fall?

(2013) Frederic Chibon   EUROPEAN JOURNAL OF CANCER

Epithelial-mesenchymal plasticity in carcinoma metastasis

(2013) J. H. Tsai et al.   GENES & DEVELOPMENT

Testican-1-mediated epithelial–mesenchymal transition signaling confers acquired resistance to lapatinib in HER2-positive gastric cancer

(2013) H-P Kim et al.   ONCOGENE

A p53 Drug Response Signature Identifies Prognostic Genes in High-Risk Neuroblastoma

(2013) Eveline Barbieri et al.   PLoS One

Cancer-initiating cells derived from human rectal adenocarcinoma tissues carry mesenchymal phenotypes and resist drug therapies

(2013) C-W Fan et al.   Cell Death & Disease

“Role of the B-cell receptor and the microenvironment in chronic lymphocytic leukemia’’

(2013) P Oppezzo et al.   Blood Cancer Journal

Addressing Genetic Tumor Heterogeneity through Computationally Predictive Combination Therapy

(2013) B. Zhao et al.   Cancer Discovery

Tumour-microenvironment interactions: role of tumour stroma and proteins produced by cancer-associated fibroblasts in chemotherapy response

(2013) Matthew David Hale et al.   CELLULAR ONCOLOGY

A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis

(2013) Wanting Liu et al.   PeerJ

MicroRNAs in Cancer: Small Molecules, Big Chances

(2012) Mohammed Abba et al.   Anti-Cancer Agents in Medicinal Chemistry

Causal reasoning on biological networks: interpreting transcriptional changes

(2012) Leonid Chindelevitch et al.   BIOINFORMATICS

Combining multiple approaches for gene microarray classification

(2012) Loris Nanni et al.   BIOINFORMATICS

Gene expression anti-profiles as a basis for accurate universal cancer signatures

(2012) Héctor Corrada Bravo et al.   BMC BIOINFORMATICS

Prognostic gene signatures for patient stratification in breast cancer - accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions

(2012) Yupeng Cun et al.   BMC BIOINFORMATICS

Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma

(2012) Elana J Fertig et al.   BMC GENOMICS

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

(2012) Florian Martin et al.   BMC Systems Biology

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Clinical Applications for microRNAs in Cancer

(2012) S P Nana-Sinkam et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

A combined oncogenic pathway signature ofBRAF,KRASandPI3KCAmutation improves colorectal cancer classification and cetuximab treatment prediction

(2012) Sun Tian et al.   GUT

Tumor Heterogeneity: Mechanisms and Bases for a Reliable Application of Molecular Marker Design

(2012) Salvador J. Diaz-Cano   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The extracellular matrix: A dynamic niche in cancer progression

(2012) Pengfei Lu et al.   JOURNAL OF CELL BIOLOGY

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

A CD44high/EGFRlow Subpopulation within Head and Neck Cancer Cell Lines Shows an Epithelial-Mesenchymal Transition Phenotype and Resistance to Treatment

(2012) Linnea La Fleur et al.   PLoS One

The regulation of cancer cell death and metabolism by extracellular matrix attachment

(2012) Cassandra L. Buchheit et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Significant alterations in the expression pattern of kallikrein-related peptidase genes KLK4, KLK5 and KLK14 after treatment of breast cancer cells with the chemotherapeutic agents epirubicin, docetaxel and methotrexate

(2012) Georgia Papachristopoulou et al.   TUMOR BIOLOGY

Predicting prognosis of breast cancer with gene signatures: are we lost in a sea of data?

(2012) Takayuki Iwamoto et al.   Genome Medicine

Biological signalling activity measurements using mass spectrometry

(2011) Pedro R. Cutillas et al.   BIOCHEMICAL JOURNAL

A microRNA gene expression signature predicts response to erlotinib in epithelial cancer cell lines and targets EMT

(2011) J L Bryant et al.   BRITISH JOURNAL OF CANCER

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

On the dual roles and polarized phenotypes of neutrophils in tumor development and progression

(2011) H. Piccard et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Early transcriptional pattern of angiogenesis induced by EGCG treatment in cervical tumour cells

(2011) Oana Tudoran et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Multidimensionality of microarrays: Statistical challenges and (im)possible solutions

(2011) Stefan Michiels et al.   Molecular Oncology

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

A Two-Gene Signature, SKI and SLAMF1, Predicts Time-to-Treatment in Previously Untreated Patients with Chronic Lymphocytic Leukemia

(2011) Carmen D. Schweighofer et al.   PLoS One

Molecular classification of prostate cancer using curated expression signatures

(2011) E. K. Markert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epithelial–mesenchymal-transition induced by EGFR activation interferes with cell migration and response to irradiation and cetuximab in head and neck cancer cells

(2011) Carmen Holz et al.   RADIOTHERAPY AND ONCOLOGY

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome

(2011) David Venet et al.   PLoS Computational Biology

Variance of Gene Expression Identifies Altered Network Constraints in Neurological Disease

(2011) Jessica C. Mar et al.   PLoS Genetics

A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors

(2010) Andrey Loboda et al.   BMC Medical Genomics

Patterns of human gene expression variance show strong associations with signaling network hierarchy

(2010) Kakajan Komurov et al.   BMC Systems Biology

Stem cell property epithelial-to-mesenchymal transition is a core transcriptional network for predicting cetuximab (Erbitux™) efficacy in KRAS wild-type tumor cells

(2010) Cristina Oliveras-Ferraros et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Phosphoproteomics in cancer

(2010) H.C. Harsha et al.   Molecular Oncology

The unexpected role of lymphotoxin β receptor signaling in carcinogenesis: from lymphoid tissue formation to liver and prostate cancer development

(2010) M J Wolf et al.   ONCOGENE

Epithelial-to-mesenchymal transition and c-myc expression are the determinants of cetuximab-induced enhancement of squamous cell carcinoma radioresponse

(2010) Ira Skvortsova et al.   RADIOTHERAPY AND ONCOLOGY

Comparative study of gene set enrichment methods

(2009) Luca Abatangelo et al.   BMC BIOINFORMATICS

Robustness of transcriptional regulatory program influences gene expression variability

(2009) Zhiming Dai et al.   BMC GENOMICS

Role of transforming growth factor β in cancer microenvironment

(2009) Luis de la Cruz-Merino et al.   Clinical & Translational Oncology

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Copy number variations and cancer

(2009) Adam Shlien et al.   Genome Medicine

Differential variability analysis of gene expression and its application to human diseases

(2008) J. W.K. Ho et al.   BIOINFORMATICS

Validation of PDGFR  and c-Src tyrosine kinases as tumor/vessel targets in patients with multiple myeloma: preclinical efficacy of the novel, orally available inhibitor dasatinib

(2008) A. M. L. Coluccia et al.   BLOOD