Integrative omics for health and disease

KJ Karczewski, MP Snyder - Nature Reviews Genetics, 2018 - nature.com
Advances in omics technologies—such as genomics, transcriptomics, proteomics and
metabolomics—have begun to enable personalized medicine at an extraordinarily detailed …

Integrative analysis of multi-omics data for discovery and functional studies of complex human diseases

YV Sun, YJ Hu - Advances in genetics, 2016 - Elsevier
Complex and dynamic networks of molecules are involved in human diseases. High-
throughput technologies enable omics studies interrogating thousands to millions of makers …

Pan-cancer analysis of whole genomes

Nature, 2020 - nature.com
Cancer is driven by genetic change, and the advent of massively parallel sequencing has
enabled systematic documentation of this variation at the whole-genome scale,–. Here we …

[HTML][HTML] Integrative analysis of 111 reference human epigenomes

A Kundaje, W Meuleman, J Ernst, M Bilenky, A Yen… - Nature, 2015 - nature.com
The reference human genome sequence set the stage for studies of genetic variation and its
association with human disease, but epigenomic studies lack a similar reference. To …

Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer

H Guo, M Ahmed, F Zhang, CQ Yao, SD Li, Y Liang… - Nature …, 2016 - nature.com
Long noncoding RNAs (lncRNAs) represent an attractive class of candidates to mediate
cancer risk. Through integrative analysis of the lncRNA transcriptome with genomic data and …

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

RR Catarino, A Stark - Genes & development, 2018 - genesdev.cshlp.org
Enhancers are important genomic regulatory elements directing cell type-specific
transcription. They assume a key role during development and disease, and their …

Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome

YG Tak, PJ Farnham - Epigenetics & chromatin, 2015 - Springer
Considerable progress towards an understanding of complex diseases has been made in
recent years due to the development of high-throughput genotyping technologies. Using …

Current challenges and new opportunities for gene-environment interaction studies of complex diseases

K McAllister, LE Mechanic, C Amos… - American journal of …, 2017 - academic.oup.com
Recently, many new approaches, study designs, and statistical and analytical methods have
emerged for studying gene-environment interactions (G× Es) in large-scale studies of …

PWAS: proteome-wide association study—linking genes and phenotypes by functional variation in proteins

N Brandes, N Linial, M Linial - Genome biology, 2020 - Springer
Abstract We introduce Proteome-Wide Association Study (PWAS), a new method for
detecting gene-phenotype associations mediated by protein function alterations. PWAS …

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

L Yao, H Shen, PW Laird, PJ Farnham, BP Berman - Genome biology, 2015 - Springer
Recent studies indicate that DNA methylation can be used to identify transcriptional
enhancers, but no systematic approach has been developed for genome-wide identification …