Chung-Chau Hon

Federated single-cell QTL meta-analysis reveals novel disease mechanisms

The paper performs a federated cis-eQTL meta-analysis across single-cell datasets to identify cell-type-specific genetic effects and link them to disease mechanisms.

Epigenomic and transcriptomic germ-free ageing atlas reveals sterile inflammation as an intrinsic ageing feature

This study presents a single-cell epigenomic and transcriptomic atlas of aged mice under germ-free conditions, revealing sterile inflammation as an intrinsic ageing feature.

A genome-wide, machine learning-guided exploration of the cis-regulatory code involved in neuronal differentiation

The paper develops a machine learning method to identify cis-regulatory element profiles and their sequence features during neuronal differentiation using single-cell ATAC-seq and RNA-seq data.

Systematic evaluation of single-cell multimodal data integration for comprehensive human reference atlas.

This paper benchmarks multimodal single-cell data integration methods to improve kidney reference atlas quality by identifying adaptive states and rare cell types.

Genomic codes governing enhancer RNA fate

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

Single-cell analysis of human diversity in circulating immune cells

The paper presents AIDA, a diverse single-cell RNA-seq atlas of immune cells, revealing sub-continental diversity impacts on immune cell properties and identifying functional genetic variants.

Integrative Transcriptomics Reveals Layer 1 Astrocytes Altered in Schizophrenia

The paper identifies altered layer 1 astrocytes in schizophrenia using spatial and single-nucleus transcriptomics of the anterior cingulate cortex.

A single-cell atlas of transcribed cis-regulatory elements in the human genome

The paper constructs a single-cell atlas of transcribed cis-regulatory elements in the human genome, revealing gene regulation patterns and trait-gene relationships across cell populations.

CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data

CamoTSS identifies and quantifies alternative transcription start sites from 5' scRNA-seq data, revealing regulatory patterns in human cell types and diseases.

Quantification of escape from X chromosome inactivation with single-cell omics datasets reveals heterogeneity across cell types and tissues

The paper introduces scLinaX, a method to quantify X chromosome inactivation escape using scRNA-seq, revealing heterogeneity across cell types and tissues.

Monopogen: single nucleotide variant calling from single cell sequencing

Monopogen calls single nucleotide variants from single-cell sequencing data, achieving high accuracy in germline variant detection and enabling ancestry inference and variant association analysis.

Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.

Recombination of repeat elements generates somatic complexity in human genomes.

The paper investigates somatic recombination of Alu and L1 repeat elements in human genomes, finding tissue-specific patterns and links to neurodegenerative diseases.

Profiling of transcribed cis-regulatory elements in single cells

This paper introduces sc-end5-seq and SCAFE to profile transcribed cis-regulatory elements in single cells, showing tCREs improve prediction of CRE interactions and disease heritability.

LETR1 is a lymphatic endothelial-specific lncRNA that governs cell proliferation and migration through KLF4 and SEMA3C

Systematic identification of cis-interacting lncRNAs and their targets

The paper identifies cis-interacting lncRNAs and their targets using RNA-chromatin and Hi-C data across 18 human cell types.

Single-cell transcriptomics, scRNA-Seq and C1 CAGE discovered distinct phases of pluripotency during naïve-to-primed conversion in mice

The paper uses single-cell RNA sequencing and C1 CAGE to identify distinct phases of pluripotency during the naive-to-primed transition in mice.

Recounting the FANTOM Cage Associated Transcriptome

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.

Predicting cell-type-specific non-coding RNA transcription from genome sequence

The paper develops MENTR, a machine learning framework to predict cell-type-specific ncRNA transcription from genome sequence, identifying causal variants and ncRNAs associated with complex traits.

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

C1 CAGE detects transcription start sites and enhancer activity in lung cancer cells, revealing subpopulations with distinct responses to TGF-β and enhancer RNA dynamics.

Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis

The paper uses ATAC-seq to analyze chromatin accessibility in knee cartilage from OA patients, identifying enhancer regions linked to OA and potential therapeutic targets.

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

The paper investigates how JQ1 affects BRD2-dependent and independent transcription regulation without altering H4-hyperacetylated chromatin states in NSCLC cells.