Nan Shen

DNA sequence quantitatively encodes CTCF-binding affinity at genome scale

The paper experimentally measures CTCF-binding affinity across 276,765 human DNA sequences and develops a deep learning model to predict and interpret binding strength based on sequence features.

Phen2Disease: A Phenotype-driven Semantic Similarity-based Integrated Model for Disease and Gene Prioritization

Phen2Disease prioritizes diseases and genes using phenotype similarity scores calculated from HPO terms, outperforming existing methods in cohorts with fewer HPO terms.

CRISPRa screen on a genetic risk locus shared by multiple autoimmune diseases identifies a dysfunctional enhancer that affects IRF8 expression through cooperative lncRNA and DNA methylation machinery

The paper identifies a dysfunctional enhancer linked to IRF8 expression through CRISPRa screening and shows its regulation by a lncRNA and DNA methylation.

Identification of 38 novel loci for systemic lupus erythematosus and genetic heterogeneity that may underly population disparities in this disease

This study identifies 38 novel SLE loci and shows genetic heterogeneity across ancestral groups, highlighting antibody production as a potential mechanism for disease disparities.

SLE non-coding Genetic Risk Variant Determines the Epigenetic Dysfunction of an Immune Cell Specific Enhancer that Controls Disease-critical microRNA Expression

The paper identifies a non-coding genetic variant associated with SLE that regulates miR-146a expression through a cell-type specific enhancer.

Meta-analysis of 208,370 East Asians identifies 113 genomic loci and yields new non-immune cell relevant biological insights for systemic lupus erythematosus

This study identifies 113 genomic loci for SLE in East Asians, including 46 novel loci, and highlights non-immune cell-related biological mechanisms.