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Oncogenic pathway signatures in human cancers as a guide to targeted therapies
TLDR
It is shown that gene expression signatures can be identified that reflect the activation status of several oncogenic pathways and linked with sensitivity to therapeutics that target components of the pathway provides an opportunity to make use of these oncogens pathway signatures to guide the use of targeted therapeutics. Expand
Gene expression predictors of breast cancer outcomes
TLDR
Multiple aggregate measures of profiles of gene expression define valuable predictive associations with lymph node metastasis and disease recurrence for individual patients, and are capable of predicting outcomes in individual patients with about 90% accuracy. Expand
A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer.
TLDR
The lung metagene model provides a potential mechanism to refine the estimation of a patient's risk of disease recurrence and, in principle, to alter decisions regarding the use of adjuvant chemotherapy in early-stage NSCLC. Expand
An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer.
TLDR
A strategy for treatment of patients with advanced-stage ovarian cancer is defined that uses therapeutic stratification based on predictions of response to chemotherapy, coupled with prediction of oncogenic pathway deregulation, as a method to direct the use of targeted agents. Expand
Genomic signatures to guide the use of chemotherapeutics
TLDR
Using in vitro drug sensitivity data coupled with Affymetrix microarray data, gene expression signatures that predict sensitivity to individual chemotherapeutic drugs are developed that can accurately predict clinical response in individuals treated with these drugs. Expand
Multiplatform single-sample estimates of transcriptional activation
TLDR
The Universal exPression Code (UPC) approach is presented, which corrects for platform-specific background noise using models that account for the genomic base composition and length of target regions and produces standardized UPC values on a zero-to-one scale, thus enabling downstream analysis pipelines to be developed in a platform-agnostic manner. Expand
Gene expression phenotypic models that predict the activity of oncogenic pathways
TLDR
This paper presents a meta-analyses of the determinants of infectious disease in eight operation theatres of the central nervous system using a model derived from the model developed in [Bouchut-Boyaval, M3]. Expand
Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles
TLDR
A formal statistical method to measure the enrichment of each sample in an expression dataset and shows that gene sets built from a model system are indeed enriched in the model system, and employs ASSESS for the use of molecular classification by pathways. Expand
A single-sample microarray normalization method to facilitate personalized-medicine workflows.
TLDR
Single Channel Array Normalization (SCAN), a single-sample technique that models the effects of probe-nucleotide composition on fluorescence intensity and corrects for such effects, dramatically increasing the signal-to-noise ratio within individual samples while decreasing variation across samples is developed. Expand
Cytoplasmic transport of Stat3 by receptor‐mediated endocytosis
TLDR
Results indicate that receptor‐mediated endocytosis may be a general mechanism of transport through the cytoplasm for a subset of cytop lasmic signaling proteins destined for the nucleus for signal transducer and activator of transcription proteins. Expand
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