Integrated omics: tools, advances and future approaches

WGCNA: an R package for weighted correlation network analysis

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Regularization and Variable Selection Via the Elastic Net

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The FAIR Guiding Principles for scientific data management and stewardship

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Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

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An Analysis of Transformations

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Universal sample preparation method for proteome analysis

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Causal analysis approaches in Ingenuity Pathway Analysis

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Proposed minimum reporting standards for chemical analysis: Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)

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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

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NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

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Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

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

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Regression Shrinkage and Selection via The Lasso: A Retrospective

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Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

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mapman : a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes

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ProteomeXchange provides globally coordinated proteomics data submission and dissemination

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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

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Mass-spectrometric exploration of proteome structure and function

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Machine learning applications in genetics and genomics

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The single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: twenty-something years on

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The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

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Transcriptome and genome sequencing uncovers functional variation in humans

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Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

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Deep learning in bioinformatics

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KNIME - the Konstanz information miner

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The minimum information about a genome sequence (MIGS) specification

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Methods of integrating data to uncover genotype-phenotype interactions

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DNA sequencing at 40: past, present and future

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Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools

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The PeptideAtlas project

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WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

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Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

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

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Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

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

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The minimum information about a proteomics experiment (MIAPE)

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OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

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

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RNA-Seq differential expression analysis: An extended review and a software tool

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Visualization of omics data for systems biology

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

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Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data

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The Metabolomics Standards Initiative (MSI)

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[19] Gene Expression Omnibus: Microarray Data Storage, Submission, Retrieval, and Analysis

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An integrated approach to uncover drivers of cancer

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

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

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

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Library preparation methods for next-generation sequencing: Tone down the bias

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

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Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950–Metabolites in Frozen Human Plasma

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

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Dimension reduction techniques for the integrative analysis of multi-omics data

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Sample preparation for plant metabolomics

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Multiscale Embedded Gene Co-expression Network Analysis

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Sparse Canonical Correlation Analysis with Application to Genomic Data Integration

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Investigation of Human Blood Plasma Sample Preparation for Performing Metabolomics Using Ultrahigh Performance Liquid Chromatography/Mass Spectrometry

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A multivariate approach to the integration of multi-omics datasets

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‘Spin’ in published biomedical literature: A methodological systematic review

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Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

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How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

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Sequencing thousands of single-cell genomes with combinatorial indexing

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Systems proteomics of liver mitochondria function

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Making sense of big data in health research: towards an EU action plan

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Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

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Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic’ Layers

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OMICtools: an informative directory for multi-omic data analysis

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MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

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Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

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Bayesian correlated clustering to integrate multiple datasets

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Network inference using informative priors

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Weighted Multiplex Networks

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3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data

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Scalable whole-genome single-cell library preparation without preamplification

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MetaboLights: An Open‐Access Database Repository for Metabolomics Data

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Significance estimation for large scale metabolomics annotations by spectral matching

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Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

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Genomic, Proteomic, and Metabolomic Data Integration Strategies

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Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology

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Multi -omics and metabolic modelling pipelines: Challenges and tools for systems microbiology

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Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data

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An Integrative -omics Approach to Identify Functional Sub-Networks in Human Colorectal Cancer

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Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles

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Integration of Multi-omics Data from Mouse Diversity Panel Highlights Mitochondrial Dysfunction in Non-Alcoholic Fatty Liver Disease

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Updates in metabolomics tools and resources: 2014–2015

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Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

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Multi-omics enrichment analysis using the GeneTrail2 web service

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Performance of PLS regression coefficients in selecting variables for each response of a multivariate PLS for omics-type data

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Error correction of high-throughput sequencing datasets with non-uniform coverage

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A universal protocol for the combined isolation of metabolites, DNA , long RNA s, small RNA s, and proteins from plants and microorganisms

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Unscrambling butterfly oogenesis

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Label-Based and Label-Free Strategies for Protein Quantitation

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Proteomics Standards Initiative: Fifteen Years of Progress and Future Work

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Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism

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MS1-Based Label-Free Proteomics Using a Quadrupole Orbitrap Mass Spectrometer

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Recent Progress in the Development of Metabolome Databases for Plant Systems Biology

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Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

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Sample preparation optimization in fecal metabolic profiling

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

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Compliance with minimum information guidelines in public metabolomics repositories

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

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Omics Pipe: a community-based framework for reproducible multi-omics data analysis

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Ariadne's ChemEffect and Pathway Studio knowledge base

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

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Exploring the molecular basis of age-related disease comorbidities using a multi-omics graphical model

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From Sample to Multi-Omics Conclusions in under 48 Hours

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A practical data processing workflow for multi-OMICS projects

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nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data

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

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Integrative Analysis of Longitudinal Metabolomics Data from a Personal Multi-Omics Profile

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Multi-omics Analysis of Serum Samples Demonstrates Reprogramming of Organ Functions Via Systemic Calcium Mobilization and Platelet Activation in Metastatic Melanoma

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A Biologist's Field Guide to Multiplexed Quantitative Proteomics

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Integrated analysis of multidimensional omics data on cutaneous melanoma prognosis

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Review of emerging metabolomic tools and resources: 2015–2016

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An Integrated Systems Genetics and Omics Toolkit to Probe Gene Function

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Pathway and Network Approaches for Identification of Cancer Signature Markers from Omics Data

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MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data

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Introduction to the 2015 Brainhack Proceedings

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Applications of Fuzzy Logic in Bioinformatics

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Omics and Integrated Omics for the Promotion of Food and Nutrition Science

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An integrative imputation method based on multi-omics datasets

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The KUPKB: a novel Web application to access multiomics data on kidney disease

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MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis

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Untitled work

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Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection

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sciReptor: analysis of single-cell level immunoglobulin repertoires

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Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics*

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CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases

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Integrated Multiple “-omics” Data Reveal Subtypes of Hepatocellular Carcinoma

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

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Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity

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Metabolizing Data in the Cloud

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Metabolism and microenvironment in cancer plasticity

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Integrating ‘-omics’ and natural product discovery platforms to investigate metabolic exchange in microbiomes

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Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation

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Proteomics in non-human primates: utilizing RNA-Seq data to improve protein identification by mass spectrometry in vervet monkeys

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Multi-Omics Model Applied to Cancer Genetics

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From multi-omics approaches to personalized medicine in myocardial infarction

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Metabolic GWAS of elite athletes reveals novel genetically-influenced metabolites associated with athletic performance

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Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective

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Analysis of Nanotoxicity with Integrated Omics and Mechanobiology

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Community Detection in Protein-Protein Interaction Networks and Applications

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Towards a Multi-Omics of Male Infertility

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Integrative Multi-Omics and Artificial Intelligence: A New Paradigm for Systems Biology

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