A5066984337- Genomics and Chromatin Dynamics
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Epigenetics and DNA Methylation
- interferon and immune responses
- Genetic Associations and Epidemiology
- Extracellular vesicles in disease
- Diabetes Management and Research
- RNA Research and Splicing
- High Altitude and Hypoxia
- Genetics and Neurodevelopmental Disorders
- Diet and metabolism studies
- Spectroscopy Techniques in Biomedical and Chemical Research
- Genetic Mapping and Diversity in Plants and Animals
- Immune Cell Function and Interaction
- Mental Health Research Topics
- SARS-CoV-2 and COVID-19 Research
- Birth, Development, and Health
- Advanced Image and Video Retrieval Techniques
- Genetic and phenotypic traits in livestock
- Craniofacial Disorders and Treatments
- Endoplasmic Reticulum Stress and Disease
- Immune cells in cancer
Academy of Mathematics and Systems Science
2018-2025
National Center for Mathematics and Interdisciplinary Sciences
2018-2025
Chinese Academy of Sciences
2018-2025
Stanford University
2024-2025
University of Chinese Academy of Sciences
2018-2022
Abstract Continuous glucose monitoring (CGM) technology has grown rapidly to track real-time blood levels and trends with improved sensor accuracy. The ease of use wide availability CGM would facilitate safe effective decision making for diabetes management. Here, we developed an attention-based deep learning model, CGMformer, pretrained on a well-controlled diverse corpus data represent individual's intrinsic metabolic state enable clinical applications. During pretraining, CGMformer...
Abstract High-altitude adaptation of Tibetans represents a remarkable case natural selection during recent human evolution. Previous genome-wide scans found many non-coding variants under selection, suggesting pressing need to understand the functional role regulatory elements (REs). Here, we generate time courses paired ATAC-seq and RNA-seq data on cultured HUVECs hypoxic normoxic conditions. We further develop variant interpretation methodology (vPECA) identify active selected REs (ASREs)...
Abstract Chromatin accessibility, as a powerful marker of active DNA regulatory elements, provides valuable information for understanding mechanisms. The revolution in high-throughput methods has accumulated massive chromatin accessibility profiles public repositories. Nevertheless, utilization these data is hampered by cumbersome collection, time-consuming processing, and manual (openness) annotation genomic regions. To fill this gap, we developed OpenAnnotate...
Abstract Epigenetic information regulates gene expression and development. However, our understanding of the evolution epigenetic regulation on brain development in primates is limited. Here, we compared chromatin accessibility landscapes transcriptomes during fetal prefrontal cortex (PFC) between rhesus macaques humans. A total 304,761 divergent DNase I-hypersensitive sites (DHSs) are identified humans, although many these share conserved DNA sequences. Interestingly, most cis -elements...
Abstract Cranial Neural Crest Cells (CNCC) originate at the cephalic region from forebrain, midbrain and hindbrain, migrate into developing craniofacial region, subsequently differentiate multiple cell types. The entire specification, delamination, migration, differentiation process is highly regulated abnormalities during this development cause birth defects. To better understand molecular networks underlying CNCC, we integrate paired gene expression & chromatin accessibility data...
Single cell RNA-seq data offers us new resource and resolution to study type identity its conversion. However, analyses are challenging in dealing with noise, sparsity poor annotation at single resolution. Detecting cell-type-indicative markers is promising help denoising, clustering annotation.We developed a method, scTIM, reveal markers. scTIM based on multi-objective optimization framework simultaneously maximize gene specificity by considering gene-cell relationship, gene's ability...
ABSTRACT Chromatin accessibility, as a powerful marker of active DNA regulatory elements, provides valuable information for understanding mechanisms. The revolution in high-throughput methods has accumulated massive chromatin accessibility profiles public repositories. Nevertheless, utilization these data is hampered by cumbersome collection, time-consuming processing, and manual (openness) annotation genomic regions. To fill this gap, we developed OpenAnnotate (...
Systems genetics holds the promise to decipher complex traits by interpreting their associated SNPs through gene regulatory networks derived from comprehensive multi-omics data of cell types, tissues, and organs. Here, we propose SpecVar integrate paired chromatin accessibility expression into context-specific network atlas categories, conduct heritability enrichment analysis with genome-wide association studies (GWAS) summary statistics, identify relevant estimate relevance correlation...
Regulatory elements (REs), such as enhancers and promoters, are known regulatory sequences functional in a heterogeneous network to control gene expression by recruiting transcription regulators carrying genetic variants context specific way. Annotating those REs relies on costly labor-intensive next generation sequencing RNA-guided editing technologies many cellular contexts.We propose systematic Gene Ontology Annotation method for Elements (RE-GOA) leveraging the powerful word embedding...
Feature selection is the process of selecting a subset landmark features for model construction when there are many and comparatively few samples. The far-reaching development technologies such as biological sequencing at single cell level make feature more challenging work. difficulty lies in four facts: those measured high dimension with noise; dropouts data much sparse; either redundant or irrelevant; samples not well-labeled experiments. Here, we propose new called ELF (Extract Landmark...
<title>Abstract</title> Capturing glucose dynamics including the rigorous fasting homeostasis and postprandial adaptation is central to diagnosis, subtyping, early warning, lifestyle intervention, treatment for type 2 diabetes (T2D). Recently, continuous monitoring (CGM) technology has revolutionized fields track real-time blood levels trends, facilitated safe effective decision making management. Here, we developed an attention-based deep learning model, CGMformer, pretrained on a...
Antler is the only organ that can fully regenerate annually in mammals. However, regulatory pattern and mechanism of gene expression cell differentiation during this process remain largely unknown. Here, we obtain comprehensive assembly annotation sika deer (
Abstract Systems genetics holds the promise to decipher complex traits by interpreting their associated SNPs through gene regulatory networks derived from comprehensive multi-omics data of cell types, tissues, and organs. Here, we propose SpecVar integrate paired chromatin accessibility expression into context-specific network atlas categories, conduct heritability enrichment analysis with GWAS summary statistics, identify relevant depict shared regulations relevance correlation. Our method...
Human genetic variants can influence the severity of infection with SARS-COV-2. Several genome-wide association studies (GWAS) have been conducted to identify human risk loci that may be involved COVID-19 severity. However, candidate genes were investigated in genomic proximity each locus without considering their functional cellular contexts. Here, we compiled regulatory networks 77 contexts interpret these by revealing relevant and associated transcript factors (TF), elements (REs), target...