Evaluation and comparison of multi-omics data integration methods for cancer subtyping

PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data

(2020) Amina Lemsara et al.   BMC BIOINFORMATICS

DIABLO: an integrative approach for identifying key molecular drivers from multi-omic assays

(2019) Amrit Singh et al.   BIOINFORMATICS

Simultaneous Interrogation of Cancer Omics to Identify Subtypes With Significant Clinical Differences

(2019) Aodan Xu et al.   Frontiers in Genetics

NEMO: cancer subtyping by integration of partial multi-omic data

(2019) Nimrod Rappoport et al.   BIOINFORMATICS

Pathway-based deep clustering for molecular subtyping of cancer

(2019) Tejaswini Mallavarapu et al.   METHODS

Multi-view Subspace Clustering Analysis for Aggregating Multiple Heterogeneous Omics Data

(2019) Qianqian Shi et al.   Frontiers in Genetics

Deep-learning approach to identifying cancer subtypes using high-dimensional genomic data

(2019) Runpu Chen et al.   BIOINFORMATICS

A hierarchical integration deep flexible neural forest framework for cancer subtype classification by integrating multi-omics data

(2019) Jing Xu et al.   BMC BIOINFORMATICS

CEPICS: A Comparison and Evaluation Platform for Integration Methods in Cancer Subtyping

(2019) Ran Duan et al.   Frontiers in Genetics

Classifying tumors by supervised network propagation

(2018) Wei Zhang et al.   BIOINFORMATICS

Oncogenic Signaling Pathways in The Cancer Genome Atlas

(2018) Francisco Sanchez-Vega et al.   CELL

Identification of cancer subtypes by integrating multiple types of transcriptomics data with deep learning in breast cancer

(2018) Yang Guo et al.   NEUROCOMPUTING

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

PINSPlus: A tool for tumor subtype discovery in integrated genomic data

(2018) Hung Nguyen et al.   BIOINFORMATICS

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival

(2018) Daniele Ramazzotti et al.   Nature Communications

A novel approach for data integration and disease subtyping

(2017) Tin Nguyen et al.   GENOME RESEARCH

Clusternomics: Integrative context-dependent clustering for heterogeneous datasets

(2017) Evelina Gabasova et al.   PLoS Computational Biology

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

More Is Better: Recent Progress in Multi-Omics Data Integration Methods

(2017) Sijia Huang et al.   Frontiers in Genetics

Simultaneous discovery of cancer subtypes and subtype features by molecular data integration

(2016) Thanh Le Van et al.   BIOINFORMATICS

Evaluation of O2PLS in Omics data integration

(2016) Said el Bouhaddani et al.   BMC BIOINFORMATICS

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

(2016) Matteo Bersanelli et al.   BMC BIOINFORMATICS

Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns

(2016) Xiaofei Yang et al.   BRIEFINGS IN BIOINFORMATICS

Integrating Omics Data With a Multiplex Network-Based Approach for the Identification of Cancer Subtypes

(2016) Haiying Wang et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Multi-view clustering via spectral partitioning and local refinement

(2016) Nacim Fateh Chikhi   INFORMATION PROCESSING & MANAGEMENT

Integrative and regularized principal component analysis of multiple sources of data

(2016) Binghui Liu et al.   STATISTICS IN MEDICINE

Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery

(2015) Nora K. Speicher et al.   BIOINFORMATICS

Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification

(2015) Dingming Wu et al.   BMC GENOMICS

Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin

(2015) Xiaofei Yang et al.   HUMAN MOLECULAR GENETICS

Subtyping: What It is and Its Role in Precision Medicine

(2015) Suchi Saria et al.   IEEE INTELLIGENT SYSTEMS

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

moCluster: Identifying Joint Patterns Across Multiple Omics Data Sets

(2015) Chen Meng et al.   JOURNAL OF PROTEOME RESEARCH

Methods of integrating data to uncover genotype–phenotype interactions

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

A multivariate approach to the integration of multi-omics datasets

(2014) Chen Meng et al.   BMC BIOINFORMATICS

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation

(2014) Wenyuan Li et al.   PLoS Computational Biology

Global, local and unique decompositions in OnPLS for multiblock data analysis

(2013) Tommy Löfstedt et al.   ANALYTICA CHIMICA ACTA

iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis

(2013) Haoqi Sun et al.   BIOINFORMATICS

Bayesian consensus clustering

(2013) Eric F. Lock et al.   BIOINFORMATICS

Group sparse canonical correlation analysis for genomic data integration

(2013) Dongdong Lin et al.   BMC BIOINFORMATICS

Integrating human omics data to prioritize candidate genes

(2013) Yong Chen et al.   BMC Medical Genomics

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

(2013) Yuanhua Liu et al.   BMC Systems Biology

Pathway-based personalized analysis of cancer

(2013) Y. Drier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Integrating Genomic, Epigenomic, and Transcriptomic Features Reveals Modular Signatures Underlying Poor Prognosis in Ovarian Cancer

(2013) Wei Zhang et al.   Cell Reports

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

Structure-constrained sparse canonical correlation analysis with an application to microbiome data analysis

(2012) J. Chen et al.   BIOSTATISTICS

OnPLS path modelling

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

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

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

(2012) Shihua Zhang et al.   NUCLEIC ACIDS RESEARCH

Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA

(2011) Atanas Kamburov et al.   BIOINFORMATICS

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes

(2011) Yinyin Yuan et al.   PLoS Computational Biology

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Discovering transcriptional modules by Bayesian data integration

(2010) Richard S. Savage et al.   BIOINFORMATICS

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

(2010) Charles J. Vaske et al.   BIOINFORMATICS

A multiway approach to data integration in systems biology based on Tucker3 and N-PLS

(2010) Ana Conesa et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

A Combined Metabonomic and Transcriptomic Approach to Investigate Metabolism during Development in the Chick Chorioallantoic Membrane

(2010) Rachel Cavill et al.   JOURNAL OF PROTEOME RESEARCH

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

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

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Sparse canonical methods for biological data integration: application to a cross-platform study

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

Simultaneous analysis of distinct Omics data sets with integration of biological knowledge: Multiple Factor Analysis approach.

(2009) Marie de Tayrac et al.   BMC GENOMICS

Sparse Canonical Correlation Analysis with Application to Genomic Data Integration

(2009) Elena Parkhomenko et al.   Statistical Applications in Genetics and Molecular Biology

Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data

(2009) Daniela M Witten et al.   Statistical Applications in Genetics and Molecular Biology

A kernel-based integration of genome-wide data for clinical decision support

(2009) Anneleen Daemen et al.   Genome Medicine