Statistical and integrative system-level analysis of DNA methylation data

AE Teschendorff, CL Relton - Nature Reviews Genetics, 2018 - nature.com
Epigenetics plays a key role in cellular development and function. Alterations to the
epigenome are thought to capture and mediate the effects of genetic and environmental risk …

Enter the matrix: factorization uncovers knowledge from omics

GL Stein-O'Brien, R Arora, AC Culhane, AV Favorov… - Trends in Genetics, 2018 - cell.com
Omics data contain signals from the molecular, physical, and kinetic inter-and intracellular
interactions that control biological systems. Matrix factorization (MF) techniques can reveal …

Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front

CM Schürch, SS Bhate, GL Barlow, DJ Phillips, L Noti… - Cell, 2020 - cell.com
Antitumoral immunity requires organized, spatially nuanced interactions between
components of the immune tumor microenvironment (iTME). Understanding this coordinated …

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data

R Argelaguet, D Arnol, D Bredikhin, Y Deloro, B Velten… - Genome biology, 2020 - Springer
Technological advances have enabled the profiling of multiple molecular layers at single-
cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a …

[HTML][HTML] A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

DJ Ahern, Z Ai, M Ainsworth, C Allan, A Allcock… - Cell, 2022 - cell.com
Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete
description of specific immune biomarkers. We present here a comprehensive multi-omic …

Genetic effects on gene expression across human tissues

GTEx Consortium Lead analysts: Aguet François 1 … - Nature, 2017 - nature.com
Abstract Characterization of the molecular function of the human genome and its variation
across individuals is essential for identifying the cellular mechanisms that underlie human …

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

R Argelaguet, B Velten, D Arnol, S Dietrich… - Molecular systems …, 2018 - embopress.org
Multi‐omics studies promise the improved characterization of biological processes across
molecular layers. However, methods for the unsupervised integration of the resulting …

A statistical framework for cross-tissue transcriptome-wide association analysis

Y Hu, M Li, Q Lu, H Weng, J Wang, SM Zekavat, Z Yu… - Nature …, 2019 - nature.com
Transcriptome-wide association analysis is a powerful approach to studying the genetic
architecture of complex traits. A key component of this approach is to build a model to impute …

Unsupervised discovery of demixed, low-dimensional neural dynamics across multiple timescales through tensor component analysis

AH Williams, TH Kim, F Wang, S Vyas, SI Ryu… - Neuron, 2018 - cell.com
Perceptions, thoughts, and actions unfold over millisecond timescales, while learned
behaviors can require many days to mature. While recent experimental advances enable …

Genomic insights into the causes of type 2 diabetes

C Langenberg, LA Lotta - The Lancet, 2018 - thelancet.com
Genome-wide association studies have implicated around 250 genomic regions in
predisposition to type 2 diabetes, with evidence for causal variants and genes emerging for …