Haoyu Cheng
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View article: Advancing Human Population Genomics with DNA Foundation Models
Advancing Human Population Genomics with DNA Foundation Models Open
DNA foundation models offer a new approach to interpret genetic variation, but their potential in population-scale genomics remains untapped. We introduce a novel analytical framework that integrates a genomic foundation model with human p…
View article: The complete genome of a songbird
The complete genome of a songbird Open
Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch ( Tae…
View article: Author Correction: Complex genetic variation in nearly complete human genomes
Author Correction: Complex genetic variation in nearly complete human genomes Open
View article: Complex genetic variation in nearly complete human genomes
Complex genetic variation in nearly complete human genomes Open
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (med…
View article: Efficient near telomere-to-telomere assembly of Nanopore Simplex reads
Efficient near telomere-to-telomere assembly of Nanopore Simplex reads Open
Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads which are costly and experimentally chal…
View article: Targeted sequencing and iterative assembly of near-complete genomes
Targeted sequencing and iterative assembly of near-complete genomes Open
Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability…
View article: The Complete Genome of a Songbird
The Complete Genome of a Songbird Open
View article: DRCD: A Regional-Contention-Driven Arbitration Policy for CPU-GPU Heterogeneous Systems
DRCD: A Regional-Contention-Driven Arbitration Policy for CPU-GPU Heterogeneous Systems Open
In CPU-GPU heterogeneous systems, there exists intense resource contention between CPUs and GPUs. Traditional resource arbitration policies fail to account for the heterogeneity of cores, leading to inefficient network resource utilization…
View article: Complex genetic variation in nearly complete human genomes
Complex genetic variation in nearly complete human genomes Open
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (13…
View article: Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph Open
View article: Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy Open
View article: De novo reconstruction of satellite repeat units from sequence data
De novo reconstruction of satellite repeat units from sequence data Open
Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats eith…
View article: Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome Open
The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer inde…
View article: Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy Open
Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, a…
View article: HPRC Y1 assemblies (HiFi + UL) evaluated in the hifiasm (UL) paper
HPRC Y1 assemblies (HiFi + UL) evaluated in the hifiasm (UL) paper Open
This repository contains all HPRC Y1 assemblies evaluated in the paper titled: Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.
View article: Plant assemblies evaluated in the hifiasm (UL) paper
Plant assemblies evaluated in the hifiasm (UL) paper Open
This repository contains all plant assemblies evaluated in the paper titled: Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph.
View article: Pangenome graph construction from genome alignments with Minigraph-Cactus
Pangenome graph construction from genome alignments with Minigraph-Cactus Open
View article: A draft human pangenome reference
A draft human pangenome reference Open
View article: Increased mutation and gene conversion within human segmental duplications
Increased mutation and gene conversion within human segmental duplications Open
View article: Recombination between heterologous human acrocentric chromosomes
Recombination between heterologous human acrocentric chromosomes Open
The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications 1,2 . Although the resolution of these regions in the fir…
View article: De novo reconstruction of satellite repeat units from sequence data
De novo reconstruction of satellite repeat units from sequence data Open
Satellite DNA are long tandemly repeating sequences in a genome and may be organized as high-order repeats (HORs). They are enriched in centromeres and are challenging to assemble. Existing algorithms for identifying satellite repeats eith…
View article: Transcriptomics Dissection of Calorie Restriction and Exercise Training in Brown Adipose Tissue and Skeletal Muscle
Transcriptomics Dissection of Calorie Restriction and Exercise Training in Brown Adipose Tissue and Skeletal Muscle Open
Calorie restriction (CR) and exercise training (EX) are two critical lifestyle interventions for the prevention and treatment of metabolic diseases, such as obesity and diabetes. Brown adipose tissue (BAT) and skeletal muscle are two impor…
View article: Co-Linear Chaining on Pangenome Graphs
Co-Linear Chaining on Pangenome Graphs Open
Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topol…
View article: Supplementary Material for: Fourth Report on Chicken Genes and Chromosomes 2022
Supplementary Material for: Fourth Report on Chicken Genes and Chromosomes 2022 Open
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View article: An AOA Optimal Positioning Method Incorporating Station Error and Sensor Deployment
An AOA Optimal Positioning Method Incorporating Station Error and Sensor Deployment Open
In order to improve the computational accuracy of the AOA (angle of arrival) location, an AOA location method based on CTLS (constrained total least squares) and incorporating the effect of station errors is investigated. Its approximate c…
View article: Semi-automated assembly of high-quality diploid human reference genomes
Semi-automated assembly of high-quality diploid human reference genomes Open
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still has many gaps and errors, and does not represent a biological genome a…
View article: A Draft Human Pangenome Reference
A Draft Human Pangenome Reference Open
The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% o…
View article: Metagenome assembly of high-fidelity long reads with hifiasm-meta
Metagenome assembly of high-fidelity long reads with hifiasm-meta Open
View article: Chordin-Like 1 Regulates Epithelial-to-Mesenchymal Transition and Metastasis via the MAPK Signaling Pathway in Oral Squamous Cell Carcinoma
Chordin-Like 1 Regulates Epithelial-to-Mesenchymal Transition and Metastasis via the MAPK Signaling Pathway in Oral Squamous Cell Carcinoma Open
Background Accumulating evidence suggests that dysregulation of Chordin-like 1 (CHRDL1) is associated with malignant biological behaviors in multiple cancers. However, the exact function and molecular mechanism of CHRDL1 in oral squamous c…
View article: The complete sequence of a human genome
The complete sequence of a human genome Open
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomer…