Alejandro Barrera

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.

Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow

The paper introduces standardized formats and tools for processing MPRA data to improve reproducibility and integration across studies.

Multi-enhancer regulatory hubs control Th17 cell identity

The paper identifies multi-enhancer regulatory hubs critical for Th17 cell identity by analyzing chromatin accessibility and enhancer function in mouse CD4+ T cell subsets.

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.

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.

Reprogramming of neuronal genome function and phenotype by astrocytes

This paper shows that astrocytes reprogram neuronal gene expression and chromatin accessibility, affecting thousands of genes and regulatory elements, including those linked to schizophrenia and Alzheimer's disease.

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.

SMARCA2 is an essential and potent cofactor for a specific subset of the glucocorticoid response in A549 cells

The paper identifies SMARCA2 as a critical cofactor for a subset of glucocorticoid response genes in A549 cells through a CRISPR screen and functional analysis.

Comprehensive Evaluation of Diverse Massively Parallel Reporter Assays to Functionally Characterize Human Enhancers Genome-wide

This study evaluates multiple MPRA and STARR-seq datasets to identify enhancers, finding inconsistencies due to technical factors and proposing a unified pipeline to improve cross-assay agreement.

Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness

The paper identifies mechanoenhancers that regulate transcription in response to matrix stiffness and shows their potential for reprogramming cellular responses to mechanical cues.

The gene regulatory effects of selective glucocorticoid receptor ligands

The paper evaluates the gene regulatory effects of ten synthetic glucocorticoid receptor ligands using mRNA-seq and STARR-seq, finding their responses correlate with dexamethasone and are not selective to subsets of the molecular GC response.

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.

Activation of the imprinted Prader-Willi Syndrome locus by CRISPR-based epigenome editing

The paper uses CRISPR-based epigenome editing to activate the silenced maternal SNRPN gene in PWS iPSCs, showing that DNA demethylation can lead to stable expression.

Gene regulatory activity associated with PCOS revealed DENND1A-dependent testosterone production

The paper identifies gene regulatory mechanisms in PCOS-associated loci, showing DENND1A-dependent testosterone elevation through experimental and genetic analyses.

Machine learning methods for predicting guide RNA effects in CRISPR epigenome editing experiments

This paper introduces launch-dCas9, a machine learning framework to predict guide RNA effects in CRISPR epigenome editing, showing high accuracy and improved gRNA selection.

Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function

The paper uses CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function, finding BATF3 as a key gene that enhances memory T cell features and improves CAR T cell therapy outcomes.

Multi-center integrated analysis of non-coding CRISPR screens

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

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.

Transgenic mice for in vivo epigenome editing with CRISPR-based systems

This paper describes the generation of two transgenic mouse lines for in vivo epigenome editing using CRISPR-based systems to activate or repress gene expression.

Causal Network Inference from Gene Transcriptional Time Series Response to Glucocorticoids

The paper introduces BETS, a statistical framework for inferring gene regulatory networks from transcriptional time series data, and validates it using glucocorticoid response data and external sources.

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.