Chen-Shan Chin

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

This study examines amylase structural haplotypes in humans, finding increased copy numbers in agricultural populations and evidence of recent selection over the last 12,000 years.

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

This study uses long-read sequencing to analyze the genomic architecture of single human cells, revealing high-resolution genetic variation and structural variants.

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

The paper introduces a pangenome research toolkit to analyze complex genomic variations across multiple scales, improving the interpretation of repetitive and clinically relevant genes.

The paper evaluates sequencing and assembly methods to create high-quality diploid human genome assemblies, finding that long reads and haplotype sorting improve accuracy and completeness.

The paper uses a pan-genome graph approach to identify variation within the KIV-2 tandem repeats of the LPA gene across 47 haplotype-resolved assemblies.

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

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.

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

This paper creates a comprehensive benchmark for challenging medically-relevant autosomal genes, improving variant recall from 8% to 100% by addressing reference-specific false duplications.

This study uses rapid diagnostics and metatranscriptomics to analyze SARS-CoV-2 infection, revealing viral evolution, host responses, and drug interactions in NYC samples.

The paper introduces amplification-free long-read sequencing protocols to detect CRISPR-Cas9 off-target binding sites, identifying many previously undetected sites that are not predicted by existing software.

The paper develops a diploid assembly-based benchmark for variants in the MHC region using HG002 data, identifying 21496 small variants with high concordance to clinical HLA types.

This paper introduces a method for chromosome-scale haplotype-resolved genome assembly using long reads and long-range data, achieving high accuracy and contiguity in three human genomes.

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

This paper develops a long-read sequencing protocol to improve variant detection and genome assembly in a human genome, achieving high accuracy and contiguity.

Indexing long reads with sparse hierarchical minimizers removes the all-to-all comparison step, letting Peregrine assemble a 30x human PacBio CCS dataset in roughly 100 wall-clock minutes.

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

The paper uses long-read sequencing to analyze structural variations in the SK-BR-3 breast cancer cell line, revealing complex rearrangements and novel gene fusions.

The paper develops a scaffolding method using Hi-C data to improve long read genome assembly contiguity and demonstrates its accuracy on two organisms.

The paper improves the maize reference genome using single molecule technologies, resulting in longer contigs and better annotation of repetitive elements and genes.

This paper evaluates GRCh38 and de novo haploid assemblies, finding that GRCh38 remains superior for complex genomic regions and coding sequences despite improvements in newer assemblies.

The paper uses PacBio long-read sequencing to generate high-quality, phased genome assemblies for zebra finch and hummingbird, correcting gene structure errors in neuroscience-relevant genes.

The paper introduces Ribbon, a visualization tool for complex genome alignments and structural variation, addressing limitations of one-dimensional genome browsers.

This paper introduces FALCON and FALCON-Unzip algorithms to assemble diploid genomes from SMRT sequencing data, demonstrating improved contiguity and phasing compared to short-read methods.

The paper introduces MHAP, a method using locality-sensitive hashing to improve genome assembly from single-molecule sequencing, achieving high-quality assemblies for multiple organisms.

The paper provides high-coverage SMRT sequencing datasets for five model organisms to support genome assembly and analysis.