Paul A. Khavari

The paper identifies estrogen-modulated SNVs associated with breast cancer risk and shows their interaction with reproductive factors using polygenic risk scores.

This paper identifies Raf1 within mitochondria where it interacts with GLS to regulate glutamine catabolism and tumorigenesis, independent of MAPK signaling.

The paper identifies ADGRL2's role in epidermal differentiation through Gα13 activation and structural interactions, using CRISPR, Perturb-seq, and cryo-EM.

The paper identifies disease-linked regulatory DNA variants and their impact on epidermal homeostasis by analyzing SNVs, TF binding, and gene dysregulation in polygenic skin diseases.

The paper studies how dietary metabolites interact with genetic variants to influence colon cancer risk through transcriptional regulation.

The paper identifies lncRNAs crucial for cSCC tumor growth using CRISPRi screens and single-cell sequencing.

This study identifies glucose-binding proteins TSC22D4 and IGF2BP2 using thermal proteome profiling, showing their roles in metabolic disease and insulin secretion.

The paper introduces irCLIP-RNP and Re-CLIP methods to identify dynamic RNA-protein assemblies, revealing new patterns of RBP-RNA associations and EGF-induced remodeling.

The paper identifies iron-sensitive RNA regulation by poly C binding proteins through transcriptome analysis under low iron conditions.

This study shows glucose acts as a morphogen that modulates transcription factor dimerization during tissue differentiation.

This paper improves the easyCLIP protocol by addressing its limitations and providing a more reproducible analysis workflow.

This paper introduces a method to combine histology and spatial gene expression data to infer high-resolution transcriptome maps without sequencing or hybridization.

The paper identifies dynamic cis-regulatory elements in epidermal differentiation using multi-omic data and deep learning, revealing combinatorial motif rules linked to gene expression and polygenic skin disease.

The paper uses spatial transcriptomics to analyze copy number variations in benign and malignant tissues, revealing clonal patterns and suggesting early cancer evolution mechanisms.

The paper demonstrates that the XIST RNA-protein complex has a modular architecture that determines RBP binding and m6A modification, beyond sequence motifs.

This study shows Spen binds to endogenous retroviral RNAs and recruits chromatin silencing machinery, linking RNA-mediated retrovirus silencing to X chromosome inactivation.

easyCLIP quantifies RNA-protein interactions and identifies recurrent PCBP1 mutations in cancer by measuring RNA cross-link rates per protein.

Perturb-ATAC combines CRISPR perturbations with single-cell ATAC-seq to identify gene regulatory networks in human cells.

The paper investigates how morphogens and p63 interact to regulate chromatin dynamics during keratinocyte differentiation from hESCs, revealing p63's dependence on morphogenetic signaling for long-range chromatin interactions.

This paper uses HiChIP to map enhancer-promoter interactions in primary human cells, linking disease-associated DNA variants to their target genes.

Omni-ATAC improves ATAC-seq by reducing background noise and enabling analysis of frozen tissues, revealing disease-associated DNA element activities in human brain structures.

HiChIP improves the yield and reduces input requirements of chromatin conformation analysis, revealing multi-scale genome architecture with better signal-to-background.