State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing

Bench pressing with genomics benchmarkers

(2020) Vivien Marx   NATURE METHODS

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration

(2020) Thomas McGowan et al.   GigaScience

Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield

(2020) Yasunori Ichihashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Harmonization of quality metrics and power calculation in multi-omic studies

(2020) Sonia Tarazona et al.   Nature Communications

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

(2020) Ili Nadhirah Jamil et al.   Frontiers in Plant Science

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

(2019) Amrit Singh et al.   BIOINFORMATICS

Challenges in the Integration of Omics and Non-Omics Data

(2019) Evangelina López de Maturana et al.   Genes

Machine Learning and Integrative Analysis of Biomedical Big Data

(2019) Bilal Mirza et al.   Genes

Systematic benchmarking of omics computational tools

(2019) Serghei Mangul et al.   Nature Communications

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

(2019) Hossein Sharifi-Noghabi et al.   BIOINFORMATICS

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Integration of Metabolomic and Other Omics Data in Population-Based Study Designs: An Epidemiological Perspective

(2019) Su Chu et al.   Metabolites

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

(2019) Farhana R. Pinu et al.   Metabolites

Multiple-kernel learning for genomic data mining and prediction

(2019) Christopher M. Wilson et al.   BMC BIOINFORMATICS

Vertical and horizontal integration of multi-omics data with miodin

(2019) Benjamin Ulfenborg   BMC BIOINFORMATICS

Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries

(2019) Shuai Zeng et al.   BMC GENOMICS

SnapShot: TCGA-Analyzed Tumors

(2018) Amy Blum et al.   CELL

Integrated Omics: Tools, Advances, and Future Approaches

(2018) Biswapriya B Misra et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

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

(2018) Ricard Argelaguet et al.   Molecular Systems Biology

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Integrative omics for health and disease

(2018) Konrad J. Karczewski et al.   NATURE REVIEWS GENETICS

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data

(2018) Rafael Hernández-de-Diego et al.   NUCLEIC ACIDS RESEARCH

shinyGISPA: A web application for characterizing phenotype by gene sets using multiple omics data combinations

(2018) Bhakti Dwivedi et al.   PLoS One

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Multi-omic and multi-view clustering algorithms: review and cancer benchmark

(2018) Nimrod Rappoport et al.   NUCLEIC ACIDS RESEARCH

Discovering and linking public omics data sets using the Omics Discovery Index

(2017) Yasset Perez-Riverol et al.   NATURE BIOTECHNOLOGY

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

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

(2017) Florian Rohart et al.   PLoS Computational Biology

Quantifying Gene Regulatory Relationships with Association Measures: A Comparative Study

(2017) Zhi-Ping Liu   Frontiers in Genetics

R.JIVE for exploration of multi-source molecular data

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

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments

(2016) Ran Bi et al.   BMC BIOINFORMATICS

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

(2016) Chen Meng et al.   BRIEFINGS IN BIOINFORMATICS

Beyond the Central Dogma: Model-Based Learning of How Genes Determine Phenotypes

(2016) Adam Reinagel et al.   CBE-Life Sciences Education

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

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

MODEM: multi-omics data envelopment and mining in maize

(2016) Haijun Liu et al.   Database-The Journal of Biological Databases and Curation

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

From Sample to Multi-Omics Conclusions in under 48 Hours

(2016) Robert A. Quinn et al.   mSystems

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

(2015) Manish Sud et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

A multivariate approach to the integration of multi-omics datasets

(2014) Chen Meng et al.   BMC BIOINFORMATICS

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

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

A promoter-level mammalian expression atlas

(2014)   NATURE

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

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

(2013) Tien-Chueh Kuo et al.   BMC Systems Biology

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

(2013) J. Gao et al.   Science Signaling

Single-Cell Metabolomics: Changes in the Metabolome of Freshly Isolated and Cultured Neurons

(2012) Peter Nemes et al.   ACS Chemical Neuroscience

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Does the central dogma still stand?

(2012) Eugene V Koonin   Biology Direct

MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

(2012) Kenneth Haug et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data

(2011) J. Zhang et al.   Database-The Journal of Biological Databases and Curation

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY