A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data

A Computational Approach to Identifying Gene-microRNA Modules in Cancer

(2015) Daeyong Jin et al.   PLoS Computational Biology

Joint and individual variation explained (JIVE) for integrated analysis of multiple data types

(2013) Eric F. Lock et al.   Annals of Applied Statistics

Systematic tracking of dysregulated modules identifies novel genes in cancer

(2013) Sriganesh Srihari et al.   BIOINFORMATICS

Bayesian consensus clustering

(2013) Eric F. Lock et al.   BIOINFORMATICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Structural and functional discovery in dynamic networks with non-negative matrix factorization

(2013) Shawn Mankad et al.   PHYSICAL REVIEW E

Pattern discovery and cancer gene identification in integrated cancer genomic data

(2013) Qianxing Mo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

(2013) Sushmita Roy et al.   PLoS Computational Biology

Methods and approaches in the topology-based analysis of biological pathways

(2013) Cristina Mitrea et al.   Frontiers in Physiology

Identifying multi-layer gene regulatory modules from multi-dimensional genomic data

(2012) W. Li et al.   BIOINFORMATICS

Transcriptional and metabolic data integration and modeling for identification of active pathways

(2012) A. Jauhiainen et al.   BIOSTATISTICS

Integrated Proteomic, Transcriptomic, and Biological Network Analysis of Breast Carcinoma Reveals Molecular Features of Tumorigenesis and Clinical Relapse

(2012) Marcin Imielinski et al.   MOLECULAR & CELLULAR PROTEOMICS

Discovery of multi-dimensional modules by integrative analysis of cancer genomic data

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

Integrated Analyses of microRNAs Demonstrate Their Widespread Influence on Gene Expression in High-Grade Serous Ovarian Carcinoma

(2012) Chad J. Creighton et al.   PLoS One

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Incorporating biological information into linear models: A Bayesian approach to the selection of pathways and genes

(2011) Francesco C. Stingo et al.   Annals of Applied Statistics

A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules

(2011) Shihua Zhang et al.   BIOINFORMATICS

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Inferring Dynamic Genetic Networks with Low Order Independencies

(2009) Sophie Lèbre   Statistical Applications in Genetics and Molecular Biology

PTEN and the PI3-Kinase Pathway in Cancer

(2008) Nader Chalhoub et al.   Annual Review of Pathology-Mechanisms of Disease

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

(2008) C. Li et al.   BIOINFORMATICS

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

(2008) Karthik Devarajan   PLoS Computational Biology