Andrew S. Allen

Interrogation of noncoding schizophrenia risk variants using CRISPR-based functional genomics

The paper uses CRISPR-based functional genomics to identify noncoding regulatory elements and variants affecting schizophrenia-associated gene expression.

Probabilistic mapping of sub-genic intolerance reveals functional and disease-critical protein regions

PRIME is a Bayesian model that improves estimation of sub-genic intolerance by sharing information across regions, identifying disease-critical protein regions and enhancing variant interpretation.

Region-Level Design and Analysis of CRISPR Perturbation Screens with FRACTEL

FRACTEL improves power and replication in CRISPR screens by analyzing region-level effects and informing experimental design.

Structured Pooling Improves Detection of Rare Regulatory Mutations in Population-Scale Reporter Assays

The paper introduces a structured pooling method for population-scale STARR-seq experiments, improving detection of rare regulatory variants by increasing signal-to-noise ratio and providing Bayesian effect size estimates.

Identifying Inheritance Patterns of Allelic Imbalance, using Integrative Modeling and Bayesian Inference

The paper develops a Bayesian method to infer inheritance patterns of allelic imbalance across trios, improving ASE estimation and linking it to chromatin state and causal variants.

Modeling gene regulatory perturbations via deep learning from high-throughput reporter assays

The paper introduces BlueSTARR, a predictive modeling framework trained on whole-genome STARR-seq data to assess variant effects on regulatory functions, revealing purifying selection against loss-of-function and gain-of-function variants.

Functional Annotation of the Major Histocompatibility Complex Locus

This study identifies hundreds of new cis-regulatory element-gene connections in the MHC locus using CRISPR screens and single-cell transcriptomics, revealing cell type-specific regulatory mechanisms.

Cell modeling and rescue of a novel non-coding genetic cause of Glycogen Storage Disease IX

The paper identifies a non-coding variant causing GSD IX γ2, validates its splicing effects, and demonstrates reversal using antisense oligonucleotides.

Functional Category-Specific Intolerance Reflects Genic Function and Clinical Relevance

This paper introduces CATMINT, a method to estimate gene-level intolerance across variant categories, showing it outperforms existing metrics and reveals category-specific intolerance patterns in disease genes.

Bayesian Estimation of Allele-Specific Expression in the Presence of Phasing Uncertainty

BEASTIE improves allele-specific expression estimation by addressing phasing uncertainty and genotyping errors, enhancing accuracy in detecting rare variants.

Characterization and bioinformatic filtering of ambient gRNAs in single-cell CRISPR screens using CLEANSER

The paper develops CLEANSER, a model to filter ambient gRNAs in single-cell CRISPR screens, improving gRNA-cell assignment accuracy and differential gene expression analysis.

DYNATE: Localizing Rare-Variant Association Regions via Multiple Testing Embedded in an Aggregation Tree

DYNATE identifies rare-variant association regions by dynamically aggregating genomic regions and controlling false discovery rate, finding a new ALS-associated gene.

Ancestry adjustment improves genome-wide estimates of regional intolerance

This study shows that adjusting for ancestry improves genome-wide estimates of regional intolerance by incorporating demographic history, leading to better variant classification.

De Novo Mutation in an Enhancer of EBF3 in simplex autism

Whole-genome sequencing in thousands of families reveals variants relevant to simplex autism in a brain enhancer of the well-established neurodevelopmental disorder gene EBF3.

Genome-wide annotation of gene regulatory elements linked to cell fitness

The paper screens non-coding regulatory elements in human cells to identify those affecting cell fitness and establishes connections between regulatory elements and target genes.

Detecting regulatory elements in high-throughput reporter assays

The paper identifies technical biases in STARR-seq data, develops a statistical model to correct them, and improves detection of regulatory elements with better precision and recall.

Arfgef1 haploinsufficiency in mice alters neuronal endosome composition and decreases membrane surface postsynaptic GABAA receptors

This study shows that Arfgef1 haploinsufficiency in mice reduces dendritic surface GABAAR and alters endosome composition, leading to increased seizure susceptibility.

Regional collapsing of rare variation implicates specific genic regions in ALS

The paper applies two novel collapsing methods to ALS sequencing data to identify risk regions in known ALS genes and candidate genes.

Improved Pathogenic Variant Localization using a Hierarchical Model of Sub-regional Intolerance

The paper improves pathogenic variant localization by using a hierarchical Bayesian model to estimate sub-regional intolerance, showing better performance in identifying ClinVar pathogenic variants and improving classification of de novo missense variants.

Incorporating prior information into signal-detection analyses across biologically informed gene-sets

The paper improves signal detection analyses by incorporating prior information into gene-set analyses, showing increased power in detecting disease associations in ALS.

meaRtools: an R Package for the Analysis of Neuronal Networks Recorded on Microelectrode Arrays

The paper introduces meaRtools, an R package for analyzing neuronal network data from microelectrode arrays, demonstrating its ability to identify epilepsy-like phenotypes in Celf4 knockout mice.

Exploiting expression patterns across multiple gene isoforms to identify radiation response biomarkers in early-stage breast cancer patients.

The paper introduces two statistical methods to identify radiation response biomarkers in early-stage breast cancer by analyzing gene isoform expression patterns.