Early Diagnosis of Complex Diseases by Molecular Biomarkers, Network Biomarkers, and Dynamical Network Biomarkers

Assessing the Value of Risk Predictions by Using Risk Stratification Tables

(2013) Holly Janes et al.   ANNALS OF INTERNAL MEDICINE

Detecting tissue-specific early warning signals for complex diseases based on dynamical network biomarkers: study of type 2 diabetes by cross-tissue analysis

(2013) M. Li et al.   BRIEFINGS IN BIOINFORMATICS

A Comparison of the Polytomous Logistic Regression and Joint Cox Proportional Hazards Models for Evaluating Multiple Disease Subtypes in Prospective Cohort Studies

(2013) X. Xue et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

DNA Methylation Alterations Exhibit Intraindividual Stability and Interindividual Heterogeneity in Prostate Cancer Metastases

(2013) M. J. Aryee et al.   Science Translational Medicine

HEPA and PARSE

(2013) Qing-Wen Xu et al.   OncoImmunology

Identifying dysregulated pathways in cancers from pathway interaction networks

(2012) Ke-Qin Liu et al.   BMC BIOINFORMATICS

Consensus embedding: theory, algorithms and application to segmentation and classification of biomedical data

(2012) Satish Viswanath et al.   BMC BIOINFORMATICS

An Integrated Genome-Wide Approach to Discover Tumor-Specific Antigens as Potential Immunologic and Clinical Targets in Cancer

(2012) Q.-W. Xu et al.   CANCER RESEARCH

Leveling the Playing Field: Bringing Development of Biomarkers and Molecular Diagnostics up to the Standards for Drug Development

(2012) G. Poste et al.   CLINICAL CANCER RESEARCH

Network-Induced Classification Kernels for Gene Expression Profile Analysis

(2012) Ofer Lavi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Opportunities and challenges of disease biomarkers: a new section in the journal of translational medicine

(2012) Xiangdong Wang et al.   Journal of Translational Medicine

Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers

(2012) Luonan Chen et al.   Scientific Reports

Identifying critical transitions and their leading biomolecular networks in complex diseases

(2012) Rui Liu et al.   Scientific Reports

DDN: a caBIG® analytical tool for differential network analysis

(2011) Bai Zhang et al.   BIOINFORMATICS

Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach

(2011) Danning He et al.   BMC GENOMICS

A network-based biomarker approach for molecular investigation and diagnosis of lung cancer

(2011) Yu-Chao Wang et al.   BMC Medical Genomics

Statistical methods on detecting differentially expressed genes for RNA-seq data

(2011) Zhongxue Chen et al.   BMC Systems Biology

Decision Tree-Based Modeling of Androgen Pathway Genes and Prostate Cancer Risk

(2011) J. S. Barnholtz-Sloan et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Systems Biology: Confronting the Complexity of Cancer

(2011) A. J. Gentles et al.   CANCER RESEARCH

An integrated genetics approach for identifying protein signal pathways of Alzheimer's disease

(2011) Yue Huang et al.   COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Identifying disease genes and module biomarkers by differential interactions

(2011) Xiaoping Liu et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data

(2010) E. Bonnet et al.   BIOINFORMATICS

Prediction of patient-specific risk and percentile cohort risk of pathological stage outcome using continuous prostate-specific antigen measurement, clinical stage and biopsy Gleason score

(2010) Ying Huang et al.   BJU INTERNATIONAL

Detecting disease associated modules and prioritizing active genes based on high throughput data

(2010) Yu-Qing Qiu et al.   BMC BIOINFORMATICS

Signaling pathway networks mined from human pituitary adenoma proteomics data

(2010) Xianquan Zhan et al.   BMC Medical Genomics

Urine Collection and Processing for Protein Biomarker Discovery and Quantification

(2010) C. E. Thomas et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Development of a mathematical model that predicts the outcome of hormone therapy for prostate cancer

(2010) Yoshito Hirata et al.   JOURNAL OF THEORETICAL BIOLOGY

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

What is a biomarker? Research investments and lack of clinical integration necessitate a review of biomarker terminology and validation schema

(2010) Adam S. Ptolemy et al.   SCANDINAVIAN JOURNAL OF CLINICAL & LABORATORY INVESTIGATION

Genotype Imputation

(2009) Yun Li et al.   Annual Review of Genomics and Human Genetics

Network-based support vector machine for classification of microarray samples

(2009) Yanni Zhu et al.   BMC BIOINFORMATICS

Human Biospecimen Research: Experimental Protocol and Quality Control Tools

(2009) F. Betsou et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Cancer systems biology: a network modeling perspective

(2009) P. K. Kreeger et al.   CARCINOGENESIS

Bioinformatics for protein biomarker panel classification: what is needed to bring biomarker panels intoin vitrodiagnostics?

(2009) Xavier Robin et al.   Expert Review of Proteomics

Cross-platform method for identifying candidate network biomarkers for prostate cancer

(2009) G. Jin et al.   IET Systems Biology

Patterns of monoclonal gammopathy of undetermined significance and multiple myeloma in various ethnic/racial groups: support for genetic factors in pathogenesis

(2009) O Landgren et al.   LEUKEMIA

A New Approach for Quantitative Phosphoproteomic Dissection of Signaling Pathways Applied to T Cell Receptor Activation

(2009) Vinh Nguyen et al.   MOLECULAR & CELLULAR PROTEOMICS

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

Dynamic modularity in protein interaction networks predicts breast cancer outcome

(2009) Ian W Taylor et al.   NATURE BIOTECHNOLOGY

Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases

(2009) Hariklia Eleftherohorinou et al.   PLoS One

Midline and right frontal brain function as a physiologic biomarker of remission in major depression

(2009) Ian A. Cook et al.   PSYCHIATRY RESEARCH-NEUROIMAGING

Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry for metabonomics: Biomarker discovery for diabetes mellitus

(2008) Xiang Li et al.   ANALYTICA CHIMICA ACTA

ATOM: a powerful gene-based association test by combining optimally weighted markers

(2008) Mingyao Li et al.   BIOINFORMATICS

Differential dependency network analysis to identify condition-specific topological changes in biological networks

(2008) Bai Zhang et al.   BIOINFORMATICS

An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer

(2008) Min Xu et al.   BMC GENOMICS

Validation of Biomarker-Based Risk Prediction Models

(2008) J. M.G. Taylor et al.   CLINICAL CANCER RESEARCH

A Personalized Approach to Cancer Treatment: How Biomarkers Can Help

(2008) M. J. Duffy et al.   CLINICAL CHEMISTRY

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

The Knowledge-Integrated Network Biomarkers Discovery for Major Adverse Cardiac Events

(2008) Guangxu Jin et al.   JOURNAL OF PROTEOME RESEARCH

Pivotal Evaluation of the Accuracy of a Biomarker Used for Classification or Prediction: Standards for Study Design

(2008) Margaret S. Pepe et al.   JNCI-Journal of the National Cancer Institute

Long-Term assessment of prostate cancer progression free survival: Evaluation of pathological parameters, nuclear shape and molecular biomarkers of pathogenesis

(2008) Robert W. Veltri et al.   PROSTATE

Inferring Pathway Activity toward Precise Disease Classification

(2008) Eunjung Lee et al.   PLoS Computational Biology