Chen Sun

An intact primordial interferon antiviral signalling network in amphioxus illuminates the basal chordate origin of vertebrate IFN immunity

This paper identifies an intact primordial interferon signaling network in amphioxus, showing that IFN immunity originated in basal chordates before vertebrates.

Quantitative Full-length transcriptome analysis by nanopore sequencing with Error-Aware UMI mapping

The paper introduces UMImap, a pipeline for accurate UMI identification and error correction in nanopore sequencing, enabling reliable full-length transcriptome analysis and discovery of novel isoforms.

AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

This paper introduces an AI-assisted native proteomics method to identify protein conformations pre- and post-assembly, validated on ribosomal proteins and drug interactions.

Exploring Population Differences in the Human Gut Microbiome: from Microbial Abundance to Single Nucleotide Polymorphisms

This study compares gut microbiome differences between Han Chinese and non-Chinese populations, identifying population-specific genome clusters and SNPs linked to functional traits.

A Full Window Data Independent Acquisition Method for DeeperTop-down Proteomics

This paper introduces a machine learning-assisted Full Window DIA method for top-down proteomics, enhancing signal intensity and sequence coverage in protein analysis.

GCRTcall: a Transformer based basecaller for nanopore RNA sequencing enhanced by gated convolution and relative position embedding via joint loss training

GCRTcall improves RNA basecalling accuracy using a Transformer with gated convolution and relative position embedding, achieving state-of-the-art performance.

BaseNet: A Transformer-Based Toolkit for Nanopore Sequencing Signal Decoding

This paper introduces BaseNet, a transformer-based toolkit for nanopore sequencing signal decoding, showing improved accuracy through autoregressive and non-autoregressive decoding mechanisms.

Novel methods to identify TCM constitution of hyperlipidemic patients and predict atherosclerotic diseases

This study identifies miRNA biomarkers for TCM constitution in hyperlipidemic patients and links constitution types to atherosclerosis risk factors.

Snapshot: clustering and visualizing epigenetic history during cell differentiation

Snapshot generates hierarchical visualizations of epigenetic features along cell differentiation hierarchies using epigenomic data from the VISION project.

Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics

VarGeno improves SNP genotyping speed and accuracy from whole genome sequencing data compared to LAVA.

AllSome Sequence Bloom Trees

The paper introduces an improved Sequence Bloom Tree data structure that enhances query performance for RNA-seq databases.

VarMatch: robust matching of small variant datasets using flexible scoring schemes

VarMatch improves variant matching across datasets by handling complex variant representations and different optimization criteria, outperforming existing methods.