Integrated Multi-Omics Analyses in Oncology: A Review of Machine Learning Methods and Tools

Recent Advances of Deep Learning in Bioinformatics and Computational Biology

(2019) Binhua Tang et al.   Frontiers in Genetics

SALMON: Survival Analysis Learning With Multi-Omics Neural Networks on Breast Cancer

(2019) Zhi Huang et al.   Frontiers in Genetics

Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients

(2019) Jonas Béal et al.   Frontiers in Physiology

netDx: interpretable patient classification using integrated patient similarity networks

(2019) Shraddha Pai et al.   Molecular Systems Biology

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

(2019) Nimrod Rappoport et al.   BIOINFORMATICS

Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction

(2019) Lei Huang et al.   BIOINFORMATICS

Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies

(2019) So Yeon Kim et al.   Biology Direct

MOLI: multi-omics late integration with deep neural networks for drug response prediction

(2019) Hossein Sharifi-Noghabi et al.   BIOINFORMATICS

Insights into impact of DNA copy number alteration and methylation on the proteogenomic landscape in human ovarian cancer via a multi-omics integrative analysis

(2019) Xiaoyu Song et al.   MOLECULAR & CELLULAR PROTEOMICS

Multi-omics biomarker pipeline reveals elevated levels of protein-glutamine gamma-glutamyltransferase 4 in seminal plasma of prostate cancer patients

(2019) Andrei P. Drabovich et al.   MOLECULAR & CELLULAR PROTEOMICS

Pan-cancer analysis identifies telomerase-associated signatures and cancer subtypes

(2019) Zhenhua Luo et al.   Molecular Cancer

DriverDBv3: a multi-omics database for cancer driver gene research

(2019) Shu-Hsuan Liu et al.   NUCLEIC ACIDS RESEARCH

Making multi-omics data accessible to researchers

(2019) Ana Conesa et al.   Scientific Data

Network-based integration of multi-omics data for prioritizing cancer genes

(2018) Christos Dimitrakopoulos et al.   BIOINFORMATICS

Multi-omics integration for neuroblastoma clinical endpoint prediction

(2018) Margherita Francescatto et al.   Biology Direct

Detection of multiple perturbations in multi-omics biological networks

(2018) Paula J. Griffin et al.   BIOMETRICS

Affinity network fusion and semi-supervised learning for cancer patient clustering

(2018) Tianle Ma et al.   METHODS

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia

(2018) Su-In Lee et al.   Nature Communications

A multiomics analysis of S100 protein family in breast cancer

(2018) Patrizia Cancemi et al.   Oncotarget

Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response

(2018) Magali Champion et al.   EBioMedicine

Multi-Omics Analysis Reveals a HIF Network and Hub Gene EPAS1 Associated with Lung Adenocarcinoma

(2018) Zhaoxi Wang et al.   EBioMedicine

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2018) Freddie Bray et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Integration of Multi-omics Data for Gene Regulatory Network Inference and Application to Breast Cancer

(2018)   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer

(2018) Raquel L. Costa et al.   Scientific Reports

Multiomics analysis on DNA methylation and the expression of both messenger RNA and microRNA in lung adenocarcinoma

(2018) Zhaoyang Yang et al.   JOURNAL OF CELLULAR PHYSIOLOGY

An Improved Method for Prediction of Cancer Prognosis by Network Learning

(2018) Minseon Kim et al.   Genes

Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma

(2018) Li Zhang et al.   Frontiers in Genetics

Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis

(2018) Rui Benfeitas et al.   EBioMedicine

A novel approach for data integration and disease subtyping

(2017) Tin Nguyen et al.   GENOME RESEARCH

LinkedOmics: analyzing multi-omics data within and across 32 cancer types

(2017) Suhas V Vasaikar et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of genomic and epigenomic regulation of the transcriptome in liver cancer

(2017) Hyun Goo Woo et al.   Nature Communications

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

Reconstruction of pathway modification induced by nicotinamide using multi-omic network analyses in triple negative breast cancer

(2017) Ji Young Kim et al.   Scientific Reports

Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers

(2017) Bin Zhu et al.   Scientific Reports

R.JIVE for exploration of multi-source molecular data

(2016) Michael J. O’Connell et al.   BIOINFORMATICS

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

(2016) Yifeng Li et al.   BRIEFINGS IN BIOINFORMATICS

Detecting the potential cancer association or metastasis by multi-omics data analysis

(2016) L. Hua et al.   GENETICS AND MOLECULAR RESEARCH

An individualized prognostic signature and multi‑omics distinction for early stage hepatocellular carcinoma patients with surgical resection

(2016) Lu Ao et al.   Oncotarget

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

(2016) Hyunghoon Cho et al.   Cell Systems

A Network-Based Data Integration Approach to Support Drug Repurposing and Multi-Target Therapies in Triple Negative Breast Cancer

(2016) Francesca Vitali et al.   PLoS One

Gene network inference by fusing data from diverse distributions

(2015) Marinka Žitnik et al.   BIOINFORMATICS

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

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

Integrative Multi-omics Module Network Inference with Lemon-Tree

(2015) Eric Bonnet et al.   PLoS Computational Biology

ICan: An Integrated Co-Alteration Network to Identify Ovarian Cancer-Related Genes

(2015) Yuanshuai Zhou et al.   PLoS One

Robust Selection Algorithm (RSA) for Multi-Omic Biomarker Discovery; Integration with Functional Network Analysis to Identify miRNA Regulated Pathways in Multiple Cancers

(2015) Vasudha Sehgal et al.   PLoS One

Bayesian joint analysis of heterogeneous genomics data

(2014) Priyadip Ray et al.   BIOINFORMATICS

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

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

Constructing module maps for integrated analysis of heterogeneous biological networks

(2014) David Amar et al.   NUCLEIC ACIDS RESEARCH

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

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

Drug Repositioning: A Machine-Learning Approach through Data Integration

(2013) Francesco Napolitano et al.   Journal of Cheminformatics

PREDICT: a method for inferring novel drug indications with application to personalized medicine

(2011) A. Gottlieb et al.   Molecular Systems Biology

From 'omics' to complex disease: a systems biology approach to gene-environment interactions in cancer

(2010) Sarah S Knox   Cancer Cell International

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

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

(2008) Sara Mostafavi et al.   GENOME BIOLOGY