Principles and methods of integrative genomic analyses in cancer

VN Kristensen, OC Lingjærde, HG Russnes… - Nature Reviews …, 2014 - nature.com
Combined analyses of molecular data, such as DNA copy-number alteration, mRNA and
protein expression, point to biological functions and molecular pathways being deregulated …

A simple new approach to variable selection in regression, with application to genetic fine mapping

G Wang, A Sarkar, P Carbonetto… - Journal of the Royal …, 2020 - academic.oup.com
We introduce a simple new approach to variable selection in linear regression, with a
particular focus on quantifying uncertainty in which variables should be selected. The …

Statistical methods in integrative genomics

S Richardson, GC Tseng, W Sun - Annual review of statistics …, 2016 - annualreviews.org
Statistical methods in integrative genomics aim to answer important biology questions by
jointly analyzing multiple types of genomic data (vertical integration) or aggregating the …

Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus

MR Johnson, J Behmoaras, L Bottolo… - Nature …, 2015 - nature.com
Gene-regulatory network analysis is a powerful approach to elucidate the molecular
processes and pathways underlying complex disease. Here we employ systems genetics …

Deciphering the complex: methodological overview of statistical models to derive OMICS‐based biomarkers

M Chadeau‐Hyam, G Campanella… - Environmental and …, 2013 - Wiley Online Library
Recent technological advances in molecular biology have given rise to numerous large‐
scale datasets whose analysis imposes serious methodological challenges mainly relating …

Joint high-dimensional Bayesian variable and covariance selection with an application to eQTL analysis

A Bhadra, BK Mallick - Biometrics, 2013 - academic.oup.com
We describe a Bayesian technique to (a) perform a sparse joint selection of significant
predictor variables and significant inverse covariance matrix elements of the response …

JAM: a scalable Bayesian framework for joint analysis of marginal SNP effects

PJ Newcombe, DV Conti… - Genetic epidemiology, 2016 - Wiley Online Library
Recently, large scale genome‐wide association study (GWAS) meta‐analyses have boosted
the number of known signals for some traits into the tens and hundreds. Typically, however …

WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling

H Chen, A Moreno-Moral, F Pesce… - Nature …, 2019 - nature.com
Cardiac fibrosis is a final common pathology in inherited and acquired heart diseases that
causes cardiac electrical and pump failure. Here, we use systems genetics to identify a pro …

Dissection of a complex disease susceptibility region using a Bayesian stochastic search approach to fine mapping

C Wallace, AJ Cutler, N Pontikos, ML Pekalski… - PLoS …, 2015 - journals.plos.org
Identification of candidate causal variants in regions associated with risk of common
diseases is complicated by linkage disequilibrium (LD) and multiple association signals …

Simultaneous grouping pursuit and feature selection over an undirected graph

Y Zhu, X Shen, W Pan - Journal of the American Statistical …, 2013 - Taylor & Francis
In high-dimensional regression, grouping pursuit and feature selection have their own merits
while complementing each other in battling the curse of dimensionality. To seek a …