Jen-Chien Chang

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

This paper develops a self-supervised model to predict aging and lifespan from behavioral data in killifish, finding that single-day predictions can match whole-life models for some traits.

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.

The paper identifies ASCL1 as a key regulator of mTEC function and central tolerance by analyzing single-cell RNA sequencing data from thymoma patients and mouse models.

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.

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.

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.

The paper evaluates 23 imputation models for cross-cell type epigenomic data, finding quality assessment challenging due to distributional shifts, data availability, and redundant metrics.

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.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

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.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

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.