Nae-Chyun Chen

A multi-modal cell-free RNA language model for liquid biopsy applications

Exai-1 is a transformer-based model that integrates RNA sequence and expression data to improve cfRNA analysis for disease detection.

Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms

The paper performs genotype inference from aggregated chromatin accessibility data to identify caQTLs and their links to gene expression and complex traits.

Measuring, visualizing and diagnosing reference bias with biastools

The paper introduces biastools to measure and diagnose reference bias in genomic data across different scenarios and finds that inclusive graph genomes and end-to-end alignment reduce bias.

Improved sequence mapping using a complete reference genome and lift-over

The paper introduces levioSAM2, a method for accurate lift-over between genome assemblies, improving variant calling accuracy when mapping to older references.

The complete sequence of a human Y chromosome

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

A refined characterization of large-scale genomic differences in the first complete human genome

The paper identifies and categorizes large-scale genomic differences between the T2T-CHM13 and GRCh38 human genome assemblies, highlighting their implications for disease and evolution.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

LevioSAM: Fast lift-over of alternate reference alignments

LevioSAM lifts SAM/BAM alignments between references using VCF files, achieving faster performance with multi-threading.

Improving variant calling using population data and deep learning

This study improves variant calling by integrating population data into deep learning models, enhancing precision and recall across diverse populations.

Reducing reference bias using multiple population reference genomes

The paper introduces a reference flow alignment method that reduces reference bias using multiple population reference genomes, achieving similar accuracy to graph aligners with lower memory usage and faster speed.

Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite

The paper introduces gAIRR Suite, a toolset for profiling germline adaptive immune receptor repertoire, achieving high accuracy in allele calling and discovering novel alleles across multiple datasets.

FORGe: prioritizing variants for graph genomes

FORGe prioritizes genetic variants for graph genomes to balance alignment accuracy and computational overhead.