Alexias Safi

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

This study quantifies intrinsic dCas9-DNA recognition using TANGO, identifying key factors affecting gRNA performance and revealing new aspects of dCas9 specificity.

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.

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

The paper identifies transcription factors for reprogramming human astrocytes to neurons using CRISPRa screens and scRNA-seq, showing INSM1's broad neurogenic activity and cofactor interactions.

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

The paper constructs an enhancer-driven gene regulatory network from human forebrain organoids with ASD and neurotypical controls, identifying key regulators of excitatory neuron specification in macrocephalic ASD.

The paper introduces TOP, a Bayesian framework that quantifies TF occupancy across many conditions using a single DNase-seq experiment, showing changes in 1500 TF motifs across cell types, hormone exposure, and genetic backgrounds.

The paper identifies enhancer elements that regulate epicardial gene expression during zebrafish heart regeneration by analyzing transcriptomes and chromatin accessibility.

The paper identifies sex-dependent glial-specific chromatin accessibility changes in late-onset Alzheimer's disease brains using ATAC-seq and links them to LOAD-GWAS regions.

The paper identifies genetic regulators of gene expression and chromatin accessibility across multiple tissues using a genetically diverse mouse population and proposes a causal model for gene regulation.

This study connects schizophrenia GWAS findings to specific genes, tissues, and regulatory mechanisms through transcriptome-wide and chromatin activity analyses.

The paper evaluates chromatin accessibility in prefrontal cortex samples from schizophrenia cases and controls, finding high heritability enrichment in open chromatin regions but no differential accessibility between groups.