Xuefang Zhao
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View article: Structural and transduction patterns of human-specific polymorphic SVA insertions
Structural and transduction patterns of human-specific polymorphic SVA insertions Open
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: Aberrant recursive splicing in a human disease locus
Aberrant recursive splicing in a human disease locus Open
Recursive splice sites are rare motifs postulated to facilitate splicing across massive introns and shape isoform diversity, especially for long, brain-expressed genes. The necessity of this unique mechanism remains unsubstantiated, as doe…
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: Structure–function insights of natural Ganoderma polysaccharides: advances in biosynthesis and functional food applications
Structure–function insights of natural Ganoderma polysaccharides: advances in biosynthesis and functional food applications Open
View article: A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders 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 (13…
View article: Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders
Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders Open
This study suggests that unsolved oCCDDs are clinically and genetically heterogeneous disorders often overlapping other Mendelian conditions and nominates many candidates for future replication and functional studies.
View article: Mapping recurrent mosaic copy number variation in human neurons
Mapping recurrent mosaic copy number variation in human neurons Open
When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development…
View article: A harmonized public resource of deeply sequenced diverse human genomes
A harmonized public resource of deeply sequenced diverse human genomes Open
Underrepresented populations are often excluded from genomic studies owing in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequen…
View article: Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders
Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders Open
Purpose To identify genetic etiologies and genotype/phenotype associations for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs). Methods We coupled phenotyping with exome or genome sequencing of 467 pedigrees with genet…
View article: Author Correction: GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data
Author Correction: GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data Open
View article: O11: An atlas of 1.2M structural variants across global populations in the Genome Aggregation Database (gnomAD)
O11: An atlas of 1.2M structural variants across global populations in the Genome Aggregation Database (gnomAD) Open
Structural variants (SVs) are an important class of variation that contribute to the diversity of each human genome and a major component of the genetic architecture of human traits and disease. Unfortunately, the field of human genetics h…
View article: A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders
A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders Open
Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modificati…
View article: Structural variants in Lewy body dementia and frontotemporal dementia spectrum
Structural variants in Lewy body dementia and frontotemporal dementia spectrum Open
Background Structural variants range from simple loss or gain of genetic material to complex events that restructure entire chromosomes. This heterogeneity coupled with variant size greater than sequencing read‐length makes structural vari…
View article: Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases
Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases Open
Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that…
View article: A Communication Theory Perspective on Prompting Engineering Methods for Large Language Models
A Communication Theory Perspective on Prompting Engineering Methods for Large Language Models Open
The springing up of Large Language Models (LLMs) has shifted the community from single-task-orientated natural language processing (NLP) research to a holistic end-to-end multi-task learning paradigm. Along this line of research endeavors …
View article: GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data
GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data Open
View article: Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies
Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies Open
View article: Marrying Dialogue Systems with Data Visualization: Interactive Data Visualization Generation from Natural Language Conversations
Marrying Dialogue Systems with Data Visualization: Interactive Data Visualization Generation from Natural Language Conversations Open
Data visualization (DV) has become the prevailing tool in the market due to its effectiveness into illustrating insights in vast amounts of data. To lower the barrier of using DVs, automatic DV tasks, such as natural language question (NLQ…
View article: Rare variants found in clinical gene panels illuminate the genetic and allelic architecture of orofacial clefting
Rare variants found in clinical gene panels illuminate the genetic and allelic architecture of orofacial clefting Open
View article: Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias
Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias Open
View article: Genome‐Wide Analysis of Structural Variants in Parkinson Disease
Genome‐Wide Analysis of Structural Variants in Parkinson Disease Open
Objective Identification of genetic risk factors for Parkinson disease (PD) has to date been primarily limited to the study of single nucleotide variants, which only represent a small fraction of the genetic variation in the human genome. …
View article: A harmonized public resource of deeply sequenced diverse human genomes
A harmonized public resource of deeply sequenced diverse human genomes Open
Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequence…
View article: Evaluation of the resistance to Chinese predominant races of Puccinia triticina and analysis of effective leaf rust resistance genes in wheat accessions from the U.S. National Plant Germplasm System
Evaluation of the resistance to Chinese predominant races of Puccinia triticina and analysis of effective leaf rust resistance genes in wheat accessions from the U.S. National Plant Germplasm System Open
Puccinia triticina , which is the causative agent of wheat leaf rust, is widely spread in China and most other wheat-planting countries around the globe. Cultivating resistant wheat cultivars is the most economical, effective, and environm…
View article: High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios
High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios Open
View article: Rare variants found in clinical gene panels illuminate the genetic and allelic architecture of orofacial clefting
Rare variants found in clinical gene panels illuminate the genetic and allelic architecture of orofacial clefting Open
Purpose Orofacial clefts (OFCs) are common birth defects including cleft lip (CL), cleft lip and palate (CLP), and cleft palate (CP). OFCs have heterogeneous etiologies, complicating clinical diagnostics as it is not always apparent if the…
View article: A neurodevelopmental disorder caused by a novel de novo SVA insertion in exon 13 of the SRCAP gene
A neurodevelopmental disorder caused by a novel de novo SVA insertion in exon 13 of the SRCAP gene Open
View article: Speech-to-SQL: Towards Speech-driven SQL Query Generation From Natural Language Question
Speech-to-SQL: Towards Speech-driven SQL Query Generation From Natural Language Question Open
Speech-based inputs have been gaining significant momentum with the popularity of smartphones and tablets in our daily lives, since voice is the most easiest and efficient way for human-computer interaction. This paper works towards design…
View article: Self-Assembly and Controllable Synthesis of High-Rate Porous Nico2s4 Electrode Materials for Asymmetric Supercapacitors
Self-Assembly and Controllable Synthesis of High-Rate Porous Nico2s4 Electrode Materials for Asymmetric Supercapacitors Open