A review on machine learning principles for multi-view biological data integration

Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources

(2017) Yuansheng Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Jumping across biomedical contexts using compressive data fusion

(2016) Marinka Zitnik et al.   BIOINFORMATICS

Sparse group factor analysis for biclustering of multiple data sources

(2016) Kerstin Bunte et al.   BIOINFORMATICS

Integrative clustering of high-dimensional data with joint and individual clusters

(2016) Kristoffer H. Hellton et al.   BIOSTATISTICS

Evaluation of O2PLS in Omics data integration

(2016) Said el Bouhaddani et al.   BMC BIOINFORMATICS

Variable selection in multi-block regression

(2016) Alessandra Biancolillo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Identifying Individual-Cancer-Related Genes by Rebalancing the Training Samples

(2016) Bolin Chen et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Improve Glioblastoma Multiforme Prognosis Prediction by Using Feature Selection and Multiple Kernel Learning

(2016) Ya Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Predicting microRNA-disease associations based on improved microRNA and disease similarities

(2016) Wei Lan et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters

(2016) Yifeng Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

KeyPathwayMinerWeb: online multi-omics network enrichment

(2016) Markus List et al.   NUCLEIC ACIDS RESEARCH

Consistency of random forests

(2015) Erwan Scornet et al.   ANNALS OF STATISTICS

Sparse multi-view matrix factorization: a multivariate approach to multiple tissue comparisons

(2015) Zi Wang et al.   BIOINFORMATICS

Gene network inference by fusing data from diverse distributions

(2015) Marinka Žitnik et al.   BIOINFORMATICS

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

(2015) Zi Yang et al.   BIOINFORMATICS

Prediction of potential disease-associated microRNAs based on random walk

(2015) Ping Xuan et al.   BIOINFORMATICS

The identification of cis-regulatory elements: A review from a machine learning perspective

(2015) Yifeng Li et al.   BIOSYSTEMS

VisRseq: R-based visual framework for analysis of sequencing data

(2015) Hamid Younesy et al.   BMC BIOINFORMATICS

A fast and high performance multiple data integration algorithm for identifying human disease genes

(2015) Bolin Chen et al.   BMC Medical Genomics

Data Fusion by Matrix Factorization

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

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach

(2015) Muxuan Liang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Methods for biological data integration: perspectives and challenges

(2015) Vladimir Gligorijević et al.   Journal of the Royal Society Interface

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

Methods of integrating data to uncover genotype–phenotype interactions

(2015) Marylyn D. Ritchie et al.   NATURE REVIEWS GENETICS

Group Factor Analysis

(2015) Arto Klami et al.   IEEE Transactions on Neural Networks and Learning Systems

Learning Bayesian Networks with thebnlearnRPackage

(2015) Marco Scutari   Journal of Statistical Software

Structure-revealing data fusion

(2014) Evrim Acar et al.   BMC BIOINFORMATICS

Identifying disease genes by integrating multiple data sources

(2014) Bolin Chen et al.   BMC Medical Genomics

A selective review of robust variable selection with applications in bioinformatics

(2014) Cen Wu et al.   BRIEFINGS IN BIOINFORMATICS

Big Data Opportunities and Challenges: Discussions from Data Analytics Perspectives [Discussion Forum]

(2014) Zhi-Hua Zhou et al.   IEEE Computational Intelligence Magazine

Kernelized Bayesian Matrix Factorization

(2014) Mehmet Gonen et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Integrative and Personalized QSAR Analysis in Cancer by Kernelized Bayesian Matrix Factorization

(2014) Muhammad Ammad-ud-din et al.   Journal of Chemical Information and Modeling

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Versatile sparse matrix factorization: Theory and applications

(2014) Yifeng Li et al.   NEUROCOMPUTING

Disease gene identification by using graph kernels and Markov random fields

(2014) BoLin Chen et al.   Science China-Life Sciences

Robust Manifold Nonnegative Matrix Factorization

(2014) Jin Huang et al.   ACM Transactions on Knowledge Discovery from Data

A Fast Algorithm for Nonnegative Matrix Factorization and Its Convergence

(2014) Li-Xin Li et al.   IEEE Transactions on Neural Networks and Learning Systems

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

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

Efficient network-guided multi-locus association mapping with graph cuts

(2013) Chloé-Agathe Azencott et al.   BIOINFORMATICS

OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants

(2013) Vaibhav Srivastava et al.   BMC GENOMICS

Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation

(2013) Yu-Fen Huang et al.   BMC Medical Genomics

Sparse representation approaches for the classification of high-dimensional biological data

(2013) Yifeng Li et al.   BMC Systems Biology

Identifying Protein Complexes Based on Multiple Topological Structures in PPI Networks

(2013) Bolin Chen et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

A survey of multiple classifier systems as hybrid systems

(2013) Michał Woźniak et al.   Information Fusion

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Soft Margin Multiple Kernel Learning

(2013) Xinxing Xu et al.   IEEE Transactions on Neural Networks and Learning Systems

A tutorial on the Lasso approach to sparse modeling

(2012) Morten Arendt Rasmussen et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

OnPLS path modelling

(2012) Tommy Löfstedt et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics

(2012) Warwick B. Dunn et al.   Metabolomics

Drug–target interaction prediction by random walk on the heterogeneous network

(2012) Xing Chen et al.   Molecular BioSystems

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Wisdom of crowds for robust gene network inference

(2012) Daniel Marbach et al.   NATURE METHODS

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

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

SVM-RFE based feature selection for tandem mass spectrum quality assessment

(2011) Jiarui Ding et al.   International Journal of Data Mining and Bioinformatics

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data

(2010) Elana J. Fertig et al.   BIOINFORMATICS

FABIA: factor analysis for bicluster acquisition

(2010) Sepp Hochreiter et al.   BIOINFORMATICS

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

(2010) Yongjin Li et al.   BIOINFORMATICS

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

The group lasso for logistic regression

(2010) Lukas Meier et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Stability selection

(2010) Nicolai Meinshausen et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Transformations in variational Bayesian factor analysis to speed up learning

(2010) Jaakko Luttinen et al.   NEUROCOMPUTING

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

Expression profiling of microRNAs by deep sequencing

(2009) C. J. Creighton et al.   BRIEFINGS IN BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Tensor Decompositions and Applications

(2009) Tamara G. Kolda et al.   SIAM REVIEW

K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space

(2008) Max Bylesjö et al.   BMC BIOINFORMATICS

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Reverse-phase protein lysate microarrays for cell signaling analysis

(2008) Brett Spurrier et al.   Nature Protocols

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE