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 …

TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference

A Wang, P Tian, YD Zhang - Bioinformatics, 2024 - academic.oup.com
Motivation Transcriptome-wide association study (TWAS) aims to identify trait-associated
genes regulated by significant variants to explore the underlying biological mechanisms at a …

A Statistical View of Column Subset Selection

A Sood, T Hastie - arxiv preprint arxiv:2307.12892, 2023 - arxiv.org
We consider the problem of selecting a small subset of representative variables from a large
dataset. In the computer science literature, this dimensionality reduction problem is typically …

Second-order group knockoffs with applications to GWAS

BB Chu, J Gu, Z Chen, T Morrison, E Candes… - arxiv preprint arxiv …, 2023 - arxiv.org
Conditional testing via the knockoff framework allows one to identify--among large number
of possible explanatory variables--those that carry unique information about an outcome of …

KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies

Y Yang, Q Wang, C Wang, J Buxbaum… - The American Journal of …, 2024 - cell.com
Both trio and population designs are popular study designs for identifying risk genetic
variants in genome-wide association studies (GWASs). The trio design, as a family-based …

Local genetic correlation via knockoffs reduces confounding due to cross-trait assortative mating

S Ma, F Wang, R Border, J Buxbaum, N Zaitlen… - The American Journal of …, 2024 - cell.com
Local genetic correlation analysis is an important tool for identifying genetic loci with shared
biology across traits. Recently, Border et al. have shown that the results of these analyses …

Second-order group knockoffs with applications to genome-wide association studies

BB Chu, J Gu, Z Chen, T Morrison, E Candès… - …, 2024 - academic.oup.com
Motivation Conditional testing via the knockoff framework allows one to identify—among a
large number of possible explanatory variables—those that carry unique information about …

Pinpointing Important Genetic Variants via A Feature-level Filter and Group Knockoffs

J Gu, Z Chen, Z He - arxiv preprint arxiv:2408.12618, 2024 - arxiv.org
Identifying variants that carry substantial information on the trait of interest remains a core
topic in genetic studies. In analyzing the EADB-UKBB dataset to identify genetic variants …

Knoop: practical enhancement of knockoff with over-parameterization for variable selection

X Zhang, Y Cai, H **ong - Machine Learning, 2025 - Springer
Variable selection plays a crucial role in enhancing modeling effectiveness across diverse
fields, addressing the challenges posed by high-dimensional datasets of correlated …

[HTML][HTML] Controlled Variable Selection from Summary Statistics Only? A Solution via GhostKnockoffs and Penalized Regression

Z Chen, Z He, BB Chu, J Gu, T Morrison, C Sabatti… - Ar**v, 2024 - ncbi.nlm.nih.gov
Identifying which variables do influence a response while controlling false positives
pervades statistics and data science. In this paper, we consider a scenario in which we only …