Fine-map** from summary data with the “Sum of Single Effects” model

Y Zou, P Carbonetto, G Wang, M Stephens - PLoS genetics, 2022 - journals.plos.org
In recent work, Wang et al introduced the “Sum of Single Effects”(SuSiE) model, and showed
that it provides a simple and efficient approach to fine-map** genetic variants from …

A more accurate method for colocalisation analysis allowing for multiple causal variants

C Wallace - PLoS genetics, 2021 - journals.plos.org
In genome-wide association studies (GWAS) it is now common to search for, and find,
multiple causal variants located in close proximity. It has also become standard to ask …

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

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 …

A spectrum of explainable and interpretable machine learning approaches for genomic studies

AM Conard, A DenAdel… - Wiley Interdisciplinary …, 2023 - Wiley Online Library
The advancement of high‐throughput genomic assays has led to enormous growth in the
availability of large‐scale biological datasets. Over the last two decades, these increasingly …

Functionally informed fine-map** and polygenic localization of complex trait heritability

O Weissbrod, F Hormozdiari, C Benner, R Cui… - Nature …, 2020 - nature.com
Fine-map** aims to identify causal variants impacting complex traits. We propose
PolyFun, a computationally scalable framework to improve fine-map** accuracy by …

False discovery rate control in genome-wide association studies with population structure

M Sesia, S Bates, E Candès, J Marchini… - Proceedings of the …, 2021 - pnas.org
We present a comprehensive statistical framework to analyze data from genome-wide
association studies of polygenic traits, producing interpretable findings while controlling the …

Transcriptome data are insufficient to control false discoveries in regulatory network inference

E Kernfeld, R Keener, P Cahan, A Battle - Cell systems, 2024 - cell.com
Inference of causal transcriptional regulatory networks (TRNs) from transcriptomic data
suffers notoriously from false positives. Approaches to control the false discovery rate (FDR) …

Improving fine-map** by modeling infinitesimal effects

R Cui, RA Elzur, M Kanai, JC Ulirsch, O Weissbrod… - Nature …, 2024 - nature.com
Fine-map** aims to identify causal genetic variants for phenotypes. Bayesian fine-
map** algorithms (for example, SuSiE, FINEMAP, ABF and COJO-ABF) are widely used …

False discovery rate control via data splitting

C Dai, B Lin, X **ng, JS Liu - Journal of the American Statistical …, 2023 - Taylor & Francis
Selecting relevant features associated with a given response variable is an important
problem in many scientific fields. Quantifying quality and uncertainty of a selection result via …

Fast and powerful conditional randomization testing via distillation

M Liu, E Katsevich, L Janson, A Ramdas - Biometrika, 2022 - academic.oup.com
We consider the problem of conditional independence testing: given a response and
covariates, we test the null hypothesis that. The conditional randomization test was recently …