Chunlin Xiao

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

This study benchmarks five scCNV inference methods across multiple scRNA-seq platforms and mixed samples, finding variations in performance based on data characteristics and batch effects.

The paper creates a variant benchmark for X and Y chromosomes using a complete assembly of HG002, highlighting challenges in variant detection in complex regions.

The paper provides comprehensive reference materials with genomic, epigenomic, transcriptomic, scRNA-seq, and proteomic characterizations of two cell lines for benchmarking and validation.

This study evaluates the impact of sequencing technologies and bioinformatic protocols on SARS-CoV-2 variant calling and introduces standardized parameters to improve pipeline consistency.

The paper presents a high coverage whole genome sequencing resource of 3,202 samples, including 602 trios, generated from the expanded 1000 Genomes Project.

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.

The paper presents whole-genome and whole-exome sequencing datasets from a multi-center, cross-platform study to benchmark NGS technologies and bioinformatics pipelines in cancer genomics.

The paper establishes reference samples with high-coverage whole-genome sequencing to create truth sets for somatic mutation and germline variant detection using NGS technologies.

This study evaluates reproducibility and accuracy of cancer mutation detection using whole-genome and whole-exome sequencing across multiple sequencing centers and bioinformatics pipelines.

This study compares somatic mutation detection accuracy using personalized genome assembly versus standard reference in cancer samples, showing improved results with personalized assemblies.

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.

The paper introduces SVCurator, a crowdsourcing app for evaluating structural variants in the human genome, finding high concordance among curators and with existing benchmarks.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

The paper presents high-coverage long-read sequencing data from a Han Chinese trio for developing and evaluating long-read bioinformatics methods.

The paper develops a reproducible pipeline to integrate sequencing datasets for high-confidence SNP, indel, and reference calls in five human genomes, showing improved variant detection compared to prior methods.

The paper presents extensive sequencing data from seven human genomes to serve as benchmark reference materials for improving sequencing technologies and variant calling.