Heng Li

HipHap improves haplotype assignment and confidence scoring for diploid genomes by aligning reads to each haplotype separately and introducing a quality score.

Complete genomes from 151 clinical M. tuberculosis isolates show gene conversion between paralogs creating diversity hotspots in PE/PPE/ESX genes and T cell antigens, including PPE18.

This study presents complete subtelomeric sequences from diverse populations, revealing extensive haplotype diversity and gene copy-number variation associated with chromosome arms.

This paper introduces a method for improving long-read somatic structural variant calling by integrating pangenome and de novo personal genome assembly, reducing false positives while maintaining sensitivity.

The paper defines pangenome variants and introduces pantree to identify them, finding 29.6 million variants in the Minigraph-Cactus human pangenome graph.

This paper explores the use of LLM-based coding agents in scientific computing, presenting case studies in the life sciences and discussing their potential and challenges.

This paper presents the first fully phased, diploid, telomere-to-telomere genome of the zebra finch, revealing new genes and structural features.

Savont improves ASV recovery from long-read amplicon sequencing with high accuracy and lower sequencing depth.

The paper introduces rammap, a Rust reimplementation of minimap2 with improved performance and memory safety, demonstrating compatibility and efficiency improvements.

FuFiHLA is a tool for full-field HLA typing from long-read data, achieving high accuracy in allele typing and consensus sequence construction.

Myloasm improves metagenome assembly using long reads, recovering more complete contigs and resolving antibiotic resistance genes.

LongcallD jointly calls and phases small, structural, and mosaic variants from long reads, improving SV discovery and mosaic variant accuracy.

The paper introduces hifiasm (ONT), an algorithm that enables near telomere-to-telomere genome assembly using standard ONT Simplex reads, reducing computational demands and improving chromosome reconstruction.

The paper identifies foldback artifacts in long-read sequencing data and introduces Breakinator, a tool to detect these artifacts and chimeric reads across different sequencing platforms.

The paper analyzes structural variants in three North American jay species using pangenome tools and long-read assemblies, revealing rapid genome evolution and population size effects on SV dynamics.

This study evaluates diploid donor-specific assemblies for improving somatic structural variant detection in cancer genomes, finding they identify more variants and reduce artifacts compared to standard references.

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

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.

The paper introduces longcallR, a tool for SNP calling, haplotype phasing, and allele-specific analysis using long RNA-seq reads, achieving high accuracy and identifying significant allele-specific splicing events in human samples.

The paper evaluates pan-genome analysis methods using M. tuberculosis isolates, finding that annotation discrepancies and assembly quality affect results, and introduces panqc to address these issues.

divider reconstructs haplotypes from long-read sequencing data, achieving higher accuracy than existing methods on synthetic and real datasets.

This paper introduces colorSV, a method for calling long-range somatic structural variants using co-assembly graphs, achieving high precision and sensitivity in translocation detection.

The paper uses long-read sequencing to identify four types of telomere repeat variations in cancer genomes, including neotelomeres and telomere-spanning fusions.

The paper develops a nanopore sequencing method to measure telomere length and finds chromosome-specific and conserved telomere lengths across individuals.

ntsm detects sample swaps in heterogeneous sequencing data without alignment, using k-mer variants and coverage information to improve QC efficiency.

The paper evaluates error correction in HiFi sequencing using hifieval, finding issues in homopolymer and repetitive regions across CHM13 and HG002 datasets.

GALBA is a fully automated gene annotation pipeline combining miniprot and AUGUSTUS, achieving high accuracy in large vertebrate genomes and new species.

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

miniBUSCO improves genome assembly completeness evaluation by being faster and more accurate than BUSCO.

T1K is a computational method for accurately inferring KIR and HLA alleles from next-generation sequencing data, showing enrichment of KIR2DL4 in tumor-specific CD8+ T cells.