The REX element is associated with long-range enhancer–promoter interactions.

an AI researcher going back to school for immunology

Screen of minimalistic enhancers in blood progenitor cells demonstrates widespread dual activator-repressor function of transcription factors (TFs) and enables the model-guided design of cell-state-sp...

Understanding how regulatory DNA elements shape gene expression across individual cells is a fundamental challenge in genomics. Joint RNA-seq and epigenomic profiling provides opportunities to build u...

Many of the genetic loci associated with disease are expected to have context-dependent regulatory effects that are underrepresented in the transcriptomes of healthy, steady-state adult tissues. To un...

A small modification to bpnetlite's BPNet to accomodate large validation datasets. - adamyhe/PersonalBPNet

The development of modern genome editing tools has enabled researchers to make such edits with high precision but has left unsolved the problem of designing these edits. As a solution, we propose Ledi...

Biological systems exhibit remarkable heterogeneity, characterized by intricate interplay among diverse cell types. Resolving the regulatory processes of specific cell types is crucial for delineating developmental mechanisms and disease etiologies. While single-cell sequencing methods such as scRNA-seq and scATAC-seq have revolutionized our understanding of individual cellular functions, adapting bulk genome-wide assays to achieve single-cell resolution of other genomic features remains a significant technical challenge. Here, we introduce Deep-learning-based DEconvolution of Tissue profiles with Accurate Interpretation of Locus-specific Signals (DeepDETAILS), a novel quasi-supervised framework to reconstruct cell-type-specific genomic signals with base-pair precision. DeepDETAILS’ core innovation lies in its ability to perform cross-modality deconvolution using scATAC-seq reference libraries for other bulk datasets, benefiting from the affordability and availability of scATAC-seq data. DeepDETAILS enables high-resolution mapping of genomic signals across diverse cell types, with great versatility for various omics datasets, including nascent transcript sequencing (such as PRO-cap and PRO-seq) and ChIP-seq for chromatin modifications. Our results demonstrate that DeepDETAILS significantly outperformed traditional statistical deconvolution methods. Using DeepDETAILS, we developed a comprehensive compendium of high-resolution nascent transcription and histone modification signals across 39 diverse human tissues and 86 distinct cell types. Furthermore, we applied our compendium to fine-map risk variants associated with Primary Sclerosing Cholangitis (PSC), a progressive cholestatic liver disorder, and revealed a potential etiology of the disease. Our tool and compendium provide invaluable insights into cellular complexity, opening new avenues for studying biological processes in various contexts. ### Competing Interest Statement The authors have declared no competing interest.

We present a simple model for analyzing and interpreting data from kinetic experiments that measure engaged RNA polymerase occupancy. The framework represents the densities of nascent transcripts with...

Functional element annotations are critical tools used to provide insight into the molecular processes governing cell development, differentiation, and disease. Run-on and sequencing assays measure th...

Whole genome sequencing has identified over a billion non-coding variants in humans, while GWAS has revealed the non-coding genome as a significant contributor to disease. However, prioritizing causal...

Generative deep learning models can accurately reconstruct genome-wide epigenetic tracks from the reference genome sequence alone. But it is unclear what predictive power they have on sequence divergi...

The success of Large Language Models has inspired the development of Genomic Foundation Models (GFMs) through similar pretraining techniques. However, the relationship between pretraining performance ...

Genome-wide association studies typically identify hundreds to thousands of loci, many of which harbor multiple independent peaks, each parsimoniously assumed to be due to the activity of a single cau...

Despite extensive mapping of cis-regulatory elements (cREs) across cellular contexts with chromatin accessibility assays, the sequence syntax and genetic variants that regulate transcription factor (T...