Kaili Fan

Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues

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

Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumors

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

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

The paper identifies proteins and regulatory elements associated with vocal learning by analyzing bat neural activity and epigenomic data.

An encyclopedia of enhancer-gene regulatory interactions in the human genome

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

Integrating gene annotation with orthology inference at scale

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

Insights into mammalian TE diversity via the curation of 248 mammalian genome assemblies

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

Evolutionary constraint and innovation across hundreds of placental mammals

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

Title: Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

The paper uses evolutionary constraint scores to identify functional genomic regions and finds they are enriched for variants associated with common diseases.

Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

A catalog of transcription start sites across 115 human tissue and cell types

The paper generates a catalog of experimentally validated transcription start sites (TSSs) across 115 human tissues and cell types, updating TSS annotations for 20% of GENCODE genes and identifying new GWAS candidate genes.

Genetic and Epigenetic Features of Promoters with Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription of Cell-essential Genes

The paper identifies ubiquitously open chromatin regions in human and mouse genomes that support the transcription of cell-essential genes.

Annotation of Chromatin States in 66 Complete Mouse Epigenomes During Development

The paper annotates 18 chromatin states in 66 mouse epigenomes across twelve tissues during development using ChromHMM, identifying bivalent states with evolutionary conservation and gene silencing functions.