Methods for biological data integration: perspectives and challenges

Data Fusion by Matrix Factorization

(2015) Marinka Zitnik et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Network Integration of Parallel Metabolic and Transcriptional Data Reveals Metabolic Modules that Regulate Macrophage Polarization

(2015) Abhishek K. Jha et al.   IMMUNITY

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

The foundation of precision medicine: integration of electronic health records with genomics through basic, clinical, and translational research

(2015) Marylyn D. Ritchie et al.   Frontiers in Genetics

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape

(2014) Nicolas Alcaraz et al.   BMC Systems Biology

Data integration in the era of omics: current and future challenges

(2014) David Gomez-Cabrero et al.   BMC Systems Biology

Kernel methods for large-scale genomic data analysis

(2014) X. Wang et al.   BRIEFINGS IN BIOINFORMATICS

The integrated disease network

(2014) Kai Sun et al.   Integrative Biology

Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C

(2013) Daria Grafodatskaya et al.   BMC Medical Genomics

Topology of molecular interaction networks

(2013) Wynand Winterbach et al.   BMC Systems Biology

Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks

(2013) X. Ma et al.   BRIEFINGS IN BIOINFORMATICS

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Predicting Protein–Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization

(2013) Hua Wang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

(2013) Joshua C Denny et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

Drug Target Prediction and Repositioning Using an Integrated Network-Based Approach

(2013) Dorothea Emig et al.   PLoS One

Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

(2013) Yongcui Wang et al.   PLoS One

Drug Repositioning: A Machine-Learning Approach through Data Integration

(2013) Francesco Napolitano et al.   Journal of Cheminformatics

Identifying potential cancer driver genes by genomic data integration

(2013) Yong Chen et al.   Scientific Reports

Discovering disease-disease associations by fusing systems-level molecular data

(2013) Marinka Žitnik et al.   Scientific Reports

Chapter 15: Disease Gene Prioritization

(2013) Yana Bromberg   PLoS Computational Biology

Network biology methods integrating biological data for translational science

(2012) G. Bebek et al.   BRIEFINGS IN BIOINFORMATICS

A gene ontology inferred from molecular networks

(2012) Janusz Dutkowski et al.   NATURE BIOTECHNOLOGY

Co-clustering phenome–genome for phenotype classification and disease gene discovery

(2012) TaeHyun Hwang et al.   NUCLEIC ACIDS RESEARCH

The Comparative Toxicogenomics Database: update 2013

(2012) Allan Peter Davis 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

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Integration of Clinical and Gene Expression Data Has a Synergetic Effect on Predicting Breast Cancer Outcome

(2012) Martin H. van Vliet et al.   PLoS One

Combining many interaction networks to predict gene function and analyze gene lists

(2012) Sara Mostafavi et al.   PROTEOMICS

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

GWASdb: a database for human genetic variants identified by genome-wide association studies

(2011) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Disease Ontology: a backbone for disease semantic integration

(2011) L. M. Schriml et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Graph dual regularization non-negative matrix factorization for co-clustering

(2011) Fanhua Shang et al.   PATTERN RECOGNITION

A Computational Method Based on the Integration of Heterogeneous Networks for Predicting Disease-Gene Associations

(2011) Xingli Guo et al.   PLoS One

Exploring and Exploiting Disease Interactions from Multi-Relational Gene and Phenotype Networks

(2011) Darcy A. Davis et al.   PLoS One

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes

(2011) Yinyin Yuan et al.   PLoS Computational Biology

Protein-protein interactions: Making sense of networks via graph-theoretic modeling

(2010) Nataša Pržulj   BIOESSAYS

Data integration and analysis of biological networks

(2010) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Graph Regularized Nonnegative Matrix Factorization for Data Representation

(2010) Deng Cai et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

A similarity network approach for the analysis and comparison of protein sequence/structure sets

(2010) Ioannis Valavanis et al.   JOURNAL OF BIOMEDICAL INFORMATICS

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

The Path to Personalized Medicine

(2010) Margaret A. Hamburg et al.   NEW ENGLAND JOURNAL OF MEDICINE

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

Matrix Factorization Techniques for Recommender Systems

(2009) Yehuda Koren et al.   COMPUTER

A network view of disease and compound screening

(2009) Eric E. Schadt et al.   NATURE REVIEWS DRUG DISCOVERY

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

On the Complexity of Nonnegative Matrix Factorization

(2009) Stephen A. Vavasis   SIAM JOURNAL ON OPTIMIZATION

Machine learning integration for predicting the effect of single amino acid substitutions on protein stability

(2009) Ayşegül Özen et al.   BMC STRUCTURAL BIOLOGY

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network

(2009) Bolan Linghu et al.   GENOME BIOLOGY

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Systematic Mapping of Genetic Interaction Networks

(2008) Scott J. Dixon et al.   Annual Review of Genetics

Position-dependent motif characterization using non-negative matrix factorization

(2008) Lucie N. Hutchins et al.   BIOINFORMATICS

Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks

(2008) Antonio Reverter et al.   BIOINFORMATICS

Fitting a geometric graph to a protein–protein interaction network

(2008) Desmond J. Higham et al.   BIOINFORMATICS

Gene regulatory network inference: Data integration in dynamic models—A review

(2008) Michael Hecker et al.   BIOSYSTEMS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Convex and Semi-Nonnegative Matrix Factorizations

(2008) C.H.Q. Ding et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Protein-protein interaction networks and biology—what's the connection?

(2008) Luke Hakes et al.   NATURE BIOTECHNOLOGY

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network

(2008) Nicolas Simonis et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Implementation of GenePattern within the Stanford Microarray Database

(2008) J. Hubble et al.   NUCLEIC ACIDS RESEARCH

Human Gene Coexpression Landscape: Confident Network Derived from Tissue Transcriptomic Profiles

(2008) Carlos Prieto et al.   PLoS One

Defining genetic interaction

(2008) R. Mani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Support Vector Machines and Kernels for Computational Biology

(2008) Asa Ben-Hur et al.   PLoS Computational Biology

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

(2008) Karthik Devarajan   PLoS Computational Biology

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY