Methods for the integration of multi-omics data: mathematical aspects

Correlations between weights and overlap in ensembles of weighted multiplex networks

(2015) Giulia Menichetti et al.   PHYSICAL REVIEW E

netClass: an R-package for network based, integrative biomarker signature discovery

(2014) Y. Cun et al.   BIOINFORMATICS

A multivariate approach to the integration of multi-omics datasets

(2014) Chen Meng et al.   BMC BIOINFORMATICS

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Weighted Multiplex Networks

(2014) Giulia Menichetti et al.   PLoS One

Systems biology and brain activity in neuronal pathways by smart device and advanced signal processing

(2014) Gastone Castellani et al.   Frontiers in Genetics

Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties

(2013) Yuanhua Liu et al.   BMC Systems Biology

Laplacian Dynamics on General Graphs

(2013) Inomzhon Mirzaev et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Network-based analysis of omics with multi-objective optimization

(2013) Ettore Mosca et al.   Molecular BioSystems

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Computational solutions for omics data

(2013) Bonnie Berger et al.   NATURE REVIEWS GENETICS

Identifying In-Trans Process Associated Genes in Breast Cancer by Integrated Analysis of Copy Number and Expression Data

(2013) Miriam Ragle Aure et al.   PLoS One

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations

(2013) Ivan Merelli et al.   PLoS One

Bayesian correlated clustering to integrate multiple datasets

(2012) Paul Kirk et al.   BIOINFORMATICS

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

(2012) W. Li et al.   BIOINFORMATICS

Clustering With Multi-Layer Graphs: A Spectral Perspective

(2012) Xiaowen Dong et al.   IEEE TRANSACTIONS ON SIGNAL PROCESSING

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways

(2012) N. Tuncbag et al.   NUCLEIC ACIDS RESEARCH

CNAmet: an R package for integrating copy number, methylation and expression data

(2011) Riku Louhimo et al.   BIOINFORMATICS

Network-based methods for human disease gene prediction

(2011) X. Wang et al.   Briefings in Functional Genomics

Algorithms for Detecting Significantly Mutated Pathways in Cancer

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

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes

(2011) Yinyin Yuan et al.   PLoS Computational Biology

Discovering transcriptional modules by Bayesian data integration

(2010) Richard S. Savage et al.   BIOINFORMATICS

Genome-wide inferring gene–phenotype relationship by walking on the heterogeneous network

(2010) Yongjin Li et al.   BIOINFORMATICS

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

(2010) Charles J. Vaske et al.   BIOINFORMATICS

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

(2010) Raj Chari et al.   BMC Systems Biology

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Network medicine: a network-based approach to human disease

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

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

(2010) Nynke L. van Berkum et al.   Jove-Journal of Visualized Experiments

Detailing regulatory networks through large scale data integration

(2009) C. Huttenhower et al.   BIOINFORMATICS

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS

integrOmics: an R package to unravel relationships between two omics datasets

(2009) Kim-Anh Lê Cao et al.   BIOINFORMATICS

Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions

(2008) Y. Qi et al.   GENOME RESEARCH

eQED: an efficient method for interpreting eQTL associations using protein networks

(2008) Silpa Suthram et al.   Molecular Systems Biology