Biomarker gene signature discovery integrating network knowledge.

Network and data integration for biomarker signature discovery via network smoothed T-statistics. PLoS One (2013) 0.86

Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. BMC Bioinformatics (2015) 0.76

Comparative network stratification analysis for identifying functional interpretable network biomarkers. BMC Bioinformatics (2017) 0.75

Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net. IEEE/ACM Trans Comput Biol Bioinform (2015) 0.75

Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88

Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A (2001) 71.82

Gene expression profiling predicts clinical outcome of breast cancer. Nature (2002) 71.36

The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37

KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37

Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A (2002) 30.32

Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature (2005) 19.56

Gene selection and classification of microarray data using random forest. BMC Bioinformatics (2006) 12.45

Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18

A global test for groups of genes: testing association with a clinical outcome. Bioinformatics (2004) 10.82

Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res (2010) 9.18

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (2010) 8.44

Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol Cell Proteomics (2007) 7.93

Network-constrained regularization and variable selection for analysis of genomic data. Bioinformatics (2008) 6.01

Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol (2009) 5.41

L1 penalized estimation in the Cox proportional hazards model. Biom J (2010) 4.02

Inferring pathway activity toward precise disease classification. PLoS Comput Biol (2008) 3.48

Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics (2008) 3.00

Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol (2009) 2.47

Classification of microarray data using gene networks. BMC Bioinformatics (2007) 2.44

Gene selection using support vector machines with non-convex penalty. Bioinformatics (2005) 2.16

Towards precise classification of cancers based on robust gene functional expression profiles. BMC Bioinformatics (2005) 2.01

Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer. BMC Cancer (2007) 1.75

GeneRank: using search engine technology for the analysis of microarray experiments. BMC Bioinformatics (2005) 1.71

Incorporating pathway information into boosting estimation of high-dimensional risk prediction models. BMC Bioinformatics (2009) 1.52

Network-based support vector machine for classification of microarray samples. BMC Bioinformatics (2009) 1.49

Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. BMC Bioinformatics (2010) 1.36

Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinformatics (2010) 1.27

Hybrid huberized support vector machines for microarray classification and gene selection. Bioinformatics (2008) 1.24

Improved prognostic classification of breast cancer defined by antagonistic activation patterns of immune response pathway modules. BMC Cancer (2010) 1.22

Identification of coordinately dysregulated subnetworks in complex phenotypes. Pac Symp Biocomput (2010) 1.22

Subnetwork state functions define dysregulated subnetworks in cancer. J Comput Biol (2011) 1.21

Protein networks as logic functions in development and cancer. PLoS Comput Biol (2011) 1.19

Optimally discriminative subnetwork markers predict response to chemotherapy. Bioinformatics (2011) 1.17

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients. Bioinformatics (2010) 1.15

Network analysis of differential expression for the identification of disease-causing genes. PLoS One (2009) 1.14

Identifying cancer biomarkers by network-constrained support vector machines. BMC Syst Biol (2011) 1.14

Inferring cancer subnetwork markers using density-constrained biclustering. Bioinformatics (2010) 1.13

Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data. BMC Bioinformatics (2011) 1.13

Biomolecular network motif counting and discovery by color coding. Bioinformatics (2008) 1.11

Prognostic gene signatures for patient stratification in breast cancer: accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions. BMC Bioinformatics (2012) 1.10

Integrative gene network construction for predicting a set of complementary prostate cancer genes. Bioinformatics (2011) 1.01

Survival models with preclustered gene groups as covariates. BMC Bioinformatics (2011) 0.98

Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer. BMC Bioinformatics (2011) 0.96

Pathway activation patterns in diffuse large B-cell lymphomas. Leukemia (2008) 0.91

Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. Genome Biol (2010) 0.89

Core module biomarker identification with network exploration for breast cancer metastasis. BMC Bioinformatics (2012) 0.84

Statistical aspects of gene signatures and molecular targets. Gastrointest Cancer Res (2009) 0.82

Graph ranking for exploratory gene data analysis. BMC Bioinformatics (2009) 0.81

Integration of gene signatures using biological knowledge. Artif Intell Med (2011) 0.81