Jason Daniel Buenrostro

Bolero predicts cell-state-specific gene regulation from DNA across species by integrating cell-state embeddings and biological variables.

The paper constructs a single-nucleus multi-omic atlas of adult human tissues, identifying regulatory elements and variant effects across 21 tissues.

The paper identifies transcription factor collaborations that shape CD8+ T cell states and demonstrates how engineering these interactions can influence cell fate for therapeutic applications.

The paper creates a mouse model of premalignant oral squamous cell carcinoma and identifies transcriptomic signatures of premalignancy, including immune response enhancement and stem cell dysregulation.

The paper improves sequence-to-activity models by incorporating ATAC-seq profiles, enhancing predictions of chromatin accessibility across immune cell types.

This paper shows that adrenergic signaling coordinates systemic and local stem cell activation after amputation in axolotls, enhancing regeneration.

scooby models scRNA-seq and scATAC-seq data from DNA sequence to capture cell-specific gene regulation and variant effects.

This paper introduces TDAC-seq, a method combining CRISPR perturbations with chromatin accessibility profiling to study cis-regulatory elements at single-nucleotide resolution.

This study identifies engineered histone variants that modulate chromatin structure and function, revealing sequence-to-function patterns and enabling the design of synthetic histones for specific chromatin states.

The paper identifies NRF2-driven myeloid progenitor dysregulation that sustains immunosuppressive macrophages in tumors, showing NRF2 inhibition reduces their survival and enhances antitumor immunity.

OSK factors rejuvenate aged RPE cells by activating a Tet2-independent oxidative resilience pathway through GSTA4, restoring vision and reversing age-related degeneration.

The paper shows that colitis leaves an epigenetic memory in colonic stem cells that promotes tumor growth by enhancing regenerative gene programs and AP-1 activity.

This paper develops a CRISPRi approach using truncated guides to screen multiple transcription factor binding sites, showing they can disrupt enhancer activity and repress transcription factor binding.

The paper introduces ExIGS, a method linking nuclear abnormalities to chromatin repression hotspots in progeria fibroblasts.

The paper develops an antigen-specific assay for T cell exhaustion and identifies IKAROS as a driver of exhaustion, showing that iberdomide prevents exhaustion by blocking chromatin remodeling.

The paper introduces Photoselective Sequencing, a method to measure genomic data with subcellular resolution, and applies it to study chromatin accessibility and nuclear positioning in mouse brain cells.

The paper introduces PRINT, a deep learning method to correct chromatin accessibility data and analyze DNA-protein interactions, revealing structural and functional changes in cis-regulatory elements during hematopoiesis and aging.

This paper develops FigR, a framework to integrate scATAC-seq and scRNA-seq data to infer gene regulatory networks and identify TF regulators in immune responses.

The paper presents a single-cell multiomics atlas of human cortical organoid development, revealing molecular programs of cellular diversification and identifying human-specific gene roles in lineage establishment.

The paper introduces Tangram, a method that aligns single-nucleus RNA-seq data with spatial data to create an anatomically integrated spatial map of the mouse brain.

AtacWorks denoises and identifies accessible chromatin regions from low-quality ATAC-seq data, achieving high-resolution results with minimal input.

The paper introduces SHARE-seq, a method to profile RNA and chromatin in single cells, and identifies DORCs that predict lineage commitment by chromatin accessibility changes.

This study identifies temporally divergent regulatory mechanisms in neuronal development and maturation across mouse and marmoset neocortex.

The paper identifies and quantifies barcode multiplets in 10x Chromium scATAC-seq data, showing their potential to confound single-cell analyses.

The paper benchmarks 10 scATAC-seq analysis methods on synthetic and real datasets, finding SnapATAC, Cusanovich2018, and cisTopic perform best in separating cell populations across varying coverage and noise levels.

STREAM is an interactive pipeline for reconstructing and visualizing complex branching trajectories from single-cell transcriptomic and epigenomic data.

The paper introduces a droplet-based combinatorial indexing method for high-throughput scATAC-seq, enabling large-scale single-cell chromatin accessibility profiling in mouse and human cells.

This study fine-maps genetic variants associated with blood cell traits and identifies cell types and causal mechanisms using single-cell chromatin accessibility data from the UK Biobank.

This study identifies the Gatad2a-Chd4-Mbd3 subcomplex of the NuRD complex as a key inhibitor of naive pluripotency, showing that its disruption enables deterministic reprogramming of somatic cells to iPSCs.

The paper uses gene expression data and GWAS summary statistics to identify disease-relevant tissues and cell types by detecting heritability enrichments in gene-specific expression regions.