A5065917738- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Neural dynamics and brain function
- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Memory and Neural Mechanisms
- Cancer Genomics and Diagnostics
- Neural and Behavioral Psychology Studies
- Epigenetics and DNA Methylation
- Ophthalmology and Visual Impairment Studies
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Corneal surgery and disorders
- EEG and Brain-Computer Interfaces
- Evolution and Genetic Dynamics
- Genetic Associations and Epidemiology
- Retinal Diseases and Treatments
- Cell Image Analysis Techniques
- Molecular Biology Techniques and Applications
- Image Processing and 3D Reconstruction
- Advanced Malware Detection Techniques
- Network Security and Intrusion Detection
- Integrated Circuits and Semiconductor Failure Analysis
- Genomics and Chromatin Dynamics
- Gut microbiota and health
Stanford University
2016-2025
Vanderbilt University
2019-2025
National University of Singapore
2011-2025
St. Jude Children's Research Hospital
2019-2025
Sino Biological (China)
2025
Yale University
2024
Sichuan Normal University
2021-2023
Peking University
2017-2023
Peking University Third Hospital
2020-2023
Imperial College London
2021-2023
The reference human genome sequence set the stage for studies of genetic variation and its association with disease, but epigenomic lack a similar reference. To address this need, NIH Roadmap Epigenomics Consortium generated largest collection so far epigenomes primary cells tissues. Here we describe integrative analysis 111 as part programme, profiled histone modification patterns, DNA accessibility, methylation RNA expression. We establish global maps regulatory elements, define modules...
Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling methods. Here we use accurate linked long reads expand 7 samples include difficult-to-map regions segmental duplications that challenging for short reads. These add more than 300,000 SNVs 50,000 insertions or deletions (indels) 16% exonic variants, many challenging, clinically relevant genes not covered previously, such as PMS2. For HG002, 92% of the autosomal GRCh38...
Abstract The role of intermediate methylation states in DNA is unclear. Here, to comprehensively identify regions and their quantitative relationship with gene activity, we apply integrative comparative epigenomics 25 human primary cell tissue samples. We report 18,452 located near 36% genes enriched at enhancers, exons DNase I hypersensitivity sites. Intermediate average 57% methylation, are predominantly allele-independent conserved across individuals between mouse human, suggesting a...
Abstract There is no effective way to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. Here, we develop a novel third-generation sequencing platform-based (scWGS) method named SMOOTH-seq (single-molecule real-time of long fragments amplified through transposon insertion). We evaluate the for detecting CNVs, SVs, SNVs in human cancer cell lines colorectal sample show that reliably effectively detects SVs ecDNAs individual cells,...
Abstract Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long and linked now enable us construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - Major Histocompatibility Complex (MHC). Here, we develop genome benchmark derived from for openly-consented Genome in Bottle sample HG002. assemble single contig each...
Human gastric cancer is a highly lethal disease, but the underlying multiomic molecular signatures remain largely unclear. Here, we performed multi-regional sampling, parallel single-cell multiomics sequencing and integrated analyses of human cancer. We identified common transcriptomic alterations cells, such as aberrant down-regulation genes associated with normal stomach function up-regulation KRT7, PI3, S100A4, etc. Surprisingly, prevalent expressed in colorectal epithelial cells were...
Long-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored their computational efficiency lower coverage requirements, prominent. Alternative approaches, relying solely on available reads de novo employing assembly-based tools detection via comparison to a reference genome, demand...
Spatial transcriptomics (ST) is advancing our understanding of complex tissues and organisms. However, building a robust clustering algorithm to define spatially coherent regions in single tissue slice aligning or integrating multiple slices originating from diverse sources for essential downstream analyses remains challenging. Numerous clustering, alignment, integration methods have been specifically designed ST data by leveraging its spatial information. The absence comprehensive benchmark...
Single-cell RNA sequencing has enabled to capture the gene activities at single-cell resolution, thus allowing reconstruction of cell-type-specific regulatory networks (GRNs). The available algorithms for reconstructing GRNs are commonly designed bulk RNA-seq data, and few them applicable analyze scRNA-seq data by dealing with dropout events cellular heterogeneity. In this paper, we represent joint expression distribution a pair as an image propose novel supervised deep neural network called...
We propose a simple and novel method for generating 3D human motion from complex natural language sentences, which describe different velocity, direction composition of all kinds actions. Different existing methods that use classical generative architecture, we apply the Denoising Diffusion Probabilistic Model to this task, synthesizing diverse results under guidance texts. The diffusion model converts white noise into structured by Markov process with series denoising steps is efficiently...
Abstract This unit describes the Wash U Epigenome Browser, a next‐generation genomic data visualization system. The Browser currently hosts ENCODE and Roadmap Epigenomics for human model organisms. displays many sequencing‐based sets across all or part of genome, on specific gene pathways, in context their metadata. Investigators can order, filter, aggregate, classify, display interactively based given feature including metadata features, annotated biological user‐defined collections genes...
Summary Genome in a Bottle (GIAB) benchmarks have been widely used to help validate clinical sequencing pipelines and develop new variant calling methods. Here, we use accurate linked reads long expand the prior 7 samples include difficult-to-map regions segmental duplications that are not readily accessible short reads. Our benchmark adds more than 300,000 SNVs, 50,000 indels, 16 % exonic variants, many challenging, clinically relevant genes previously covered (e.g., PMS2 ). For HG002, 92%...
The prefrontal cortex, a cortical area essential for working memory and higher cognitive functions, is modulated by number of neurotransmitter systems, including acetylcholine; however, the impact cholinergic transmission on activity not well understood. We relied systemic administration muscarinic receptor antagonist, scopolamine, to investigate role acetylcholine primate neuronal during execution tasks recorded with chronic electrode arrays single electrodes. Our results indicated...