Longjian Niu

High accuracy methylation identification tools on single molecular level for PacBio HiFi data

The paper introduces hifimeth, a deep learning model that improves 5mC detection accuracy on PacBio HiFi data by using 400 bp context, achieving higher accuracy and F1 score than existing methods.

High-resolution diploid 3D genome reconstruction using Pore-C data

This paper introduces Dip3D, a method to reconstruct high-resolution diploid 3D human genomes from Pore-C data, achieving better performance than existing methods.

Falign: An effective alignment tool for long noisy 3C data

Falign improves alignment of fragmented long noisy 3C data by addressing fragment boundary issues and increasing data utilization.

Systematic Chromatin Architecture Analysis in Xenopus tropicalis Reveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes

This study analyzes chromatin architecture in Xenopus tropicalis, revealing TAD formation dynamics and conserved CTCF-Rad21 orientation patterns across vertebrates.

Resolving a Systematic Error in STARR-seq for QuantitativeEnhancer Activity Mapping

The paper identifies a systematic error in STARR-seq for enhancer activity measurement in Arabidopsis thaliana and proposes a solution using specialized primers to recover self-transcripts, revealing new insights into enhancer function.

Global Quantitative Mapping of Enhancers in Rice Genome by STARR-seq

The paper quantitatively identifies enhancers in the rice genome using STARR-seq and reports their genomic locations and epigenetic features.

Amplification-free Library Preparation Improves Quality of Hi-C Analysis

This paper introduces an amplification-free Hi-C library preparation method that improves chromatin interaction quality and reduces sequencing depth requirements.