Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification

Laboratory diagnosis of Ebola virus disease

(2015) Philippe Martin et al.   INTENSIVE CARE MEDICINE

Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens

(2014) Torsten Nielsen et al.   BMC CANCER

LocFuse: Human protein–protein interaction prediction via classifier fusion using protein localization information

(2014) Javad Zahiri et al.   GENOMICS

Advancing research diagnostic criteria for Alzheimer's disease: the IWG-2 criteria

(2014) Bruno Dubois et al.   LANCET NEUROLOGY

Integrating Pathways of Parkinson's Disease in a Molecular Interaction Map

(2013) Kazuhiro A. Fujita et al.   MOLECULAR NEUROBIOLOGY

Using random walks to identify cancer-associated modules in expression data

(2013) Deanna Petrochilos et al.   BioData Mining

Causal reasoning on biological networks: interpreting transcriptional changes

(2012) Leonid Chindelevitch et al.   BIOINFORMATICS

EnrichNet: network-based gene set enrichment analysis

(2012) Enrico Glaab et al.   BIOINFORMATICS

Pathway-based classification of cancer subtypes

(2012) Shinuk Kim et al.   Biology Direct

Cluster-based assessment of protein-protein interaction confidence

(2012) Atanas Kamburov et al.   BMC BIOINFORMATICS

graphite - a Bioconductor package to convert pathway topology to gene network

(2012) Gabriele Sales et al.   BMC BIOINFORMATICS

AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease

(2012) Satoshi Mizuno et al.   BMC Systems Biology

Mammostrat As an Immunohistochemical Multigene Assay for Prediction of Early Relapse Risk in the Tamoxifen Versus Exemestane Adjuvant Multicenter Trial Pathology Study

(2012) John M.S. Bartlett et al.   JOURNAL OF CLINICAL ONCOLOGY

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

PrePPI: a structure-informed database of protein–protein interactions

(2012) Qiangfeng Cliff Zhang et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Using Rule-Based Machine Learning for Candidate Disease Gene Prioritization and Sample Classification of Cancer Gene Expression Data

(2012) Enrico Glaab et al.   PLoS One

Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks

(2012) Oded Magger et al.   PLoS Computational Biology

PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data

(2011) Enrico Glaab et al.   BIOINFORMATICS

Extending pathways and processes using molecular interaction networks to analyse cancer genome data

(2011) Enrico Glaab et al.   BMC BIOINFORMATICS

Development of a blood-based gene expression algorithm for assessment of obstructive coronary artery disease in non-diabetic patients

(2011) Michael R Elashoff et al.   BMC Medical Genomics

Diagnostic markers for Parkinsonʼs disease

(2011) Lama M. Chahine et al.   CURRENT OPINION IN NEUROLOGY

The Human Protein Atlas as a proteomic resource for biomarker discovery

(2011) F. Pontén et al.   JOURNAL OF INTERNAL MEDICINE

Validation and Reproducibility of a Microarray-Based Gene Expression Test for Tumor Identification in Formalin-Fixed, Paraffin-Embedded Specimens

(2011) Raji Pillai et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Selective Neuronal Vulnerability in Neurodegenerative Diseases: from Stressor Thresholds to Degeneration

(2011) Smita Saxena et al.   NEURON

Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data

(2010) Antonio Reverter et al.   BIOINFORMATICS

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

Biomarkers for Colorectal Cancer

(2010) Takuji Tanaka et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Prediction of Risk of Distant Recurrence Using the 21-Gene Recurrence Score in Node-Negative and Node-Positive Postmenopausal Patients With Breast Cancer Treated With Anastrozole or Tamoxifen: A TransATAC Study

(2010) Mitch Dowsett et al.   JOURNAL OF CLINICAL ONCOLOGY

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

Assessing the Performance of Prediction Models

(2009) Ewout W. Steyerberg et al.   EPIDEMIOLOGY

Heterogeneity and Power in Clinical Biomarker Studies

(2009) Melania Pintilie et al.   JOURNAL OF CLINICAL ONCOLOGY

Tissue specificity and the human protein interaction network

(2009) Alice Bossi et al.   Molecular Systems Biology

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Fault Tolerance in Protein Interaction Networks: Stable Bipartite Subgraphs and Redundant Pathways

(2009) Arthur Brady et al.   PLoS One

Accurate and Reliable Cancer Classification Based on Probabilistic Inference of Pathway Activity

(2009) Junjie Su et al.   PLoS One

A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation

(2009) Nicholas J. Hudson et al.   PLoS Computational Biology

Comment on ‘network-constrained regularization and variable selection for analysis of genomic data’

(2008) Harald Binder et al.   BIOINFORMATICS

Gene set enrichment analysis using linear models and diagnostics

(2008) Assaf P. Oron et al.   BIOINFORMATICS

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

(2008) C. Li et al.   BIOINFORMATICS

The Performance of Risk Prediction Models

(2008) Thomas A. Gerds et al.   BIOMETRICAL JOURNAL

Presenting and exploring biological pathways with PathVisio

(2008) Martijn P van Iersel et al.   BMC BIOINFORMATICS

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

PRINCESS, a Protein Interaction Confidence Evaluation System with Multiple Data Sources

(2008) Dong Li et al.   MOLECULAR & CELLULAR PROTEOMICS

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Mapping Genetically Compensatory Pathways from Synthetic Lethal Interactions in Yeast

(2008) Xiaotu Ma et al.   PLoS One

WikiPathways: Pathway Editing for the People

(2008) Alexander R Pico et al.   PLOS BIOLOGY

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology