Leveraging external knowledge on molecular interactions in classification methods for risk prediction of patients

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients

(2010) Marc Johannes et al.   BIOINFORMATICS

Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context

(2010) Gad Abraham et al.   BMC BIOINFORMATICS

Integrating gene expression and GO classification for PCA by preclustering

(2010) Jorn R De Haan et al.   BMC BIOINFORMATICS

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways

(2010) Michael C Wu et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

An integrative pathway-based clinical–genomic model for cancer survival prediction

(2010) Xi Chen et al.   STATISTICS & PROBABILITY LETTERS

Pathway analysis using random forests with bivariate node-split for survival outcomes

(2009) Herbert Pang et al.   BIOINFORMATICS

Incorporating Predictor Network in Penalized Regression with Application to Microarray Data

(2009) Wei Pan et al.   BIOMETRICS

Improved Detection of Differentially Expressed Genes Through Incorporation of Gene Locations

(2009) Guanghua Xiao et al.   BIOMETRICS

Network-based support vector machine for classification of microarray samples

(2009) Yanni Zhu et al.   BMC BIOINFORMATICS

Incorporating pathway information into boosting estimation of high-dimensional risk prediction models

(2009) Harald Binder et al.   BMC BIOINFORMATICS

Knowledge-based data analysis comes of age

(2009) M. F. Ochs   BRIEFINGS IN BIOINFORMATICS

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

MINT, the molecular interaction database: 2009 update

(2009) Arnaud Ceol et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2010

(2009) B. Aranda et al.   NUCLEIC ACIDS RESEARCH

Predicting pathway membership via domain signatures

(2008) Holger Fröhlich et al.   BIOINFORMATICS

Network-constrained regularization and variable selection for analysis of genomic data

(2008) C. Li et al.   BIOINFORMATICS

Semantically linking and browsing PubMed abstracts with gene ontology

(2008) Bhanu C Vanteru et al.   BMC GENOMICS

Literature mining in support of drug discovery

(2008) P. Agarwal et al.   BRIEFINGS IN BIOINFORMATICS

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

ConsensusPathDB—a database for integrating human functional interaction networks

(2008) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Variable breakpoints target PAX5 in patients with dicentric chromosomes: A model for the basis of unbalanced translocations in cancer

(2008) Q. An et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA