A5051377484- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Bioinformatics and Genomic Networks
- Genetic Syndromes and Imprinting
- Gene expression and cancer classification
- Ferroptosis and cancer prognosis
- Cancer Genomics and Diagnostics
- Environmental DNA in Biodiversity Studies
- Plant Molecular Biology Research
- Genomics and Phylogenetic Studies
- Exercise and Physiological Responses
- Sports injuries and prevention
- CRISPR and Genetic Engineering
- Genetic Mapping and Diversity in Plants and Animals
- Muscle Physiology and Disorders
- Cancer-related gene regulation
- Animal Genetics and Reproduction
- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- Neuroinflammation and Neurodegeneration Mechanisms
- Genetics and Neurodevelopmental Disorders
- Microbial Community Ecology and Physiology
- Immune cells in cancer
- Gene Regulatory Network Analysis
Salk Institute for Biological Studies
2023-2025
Children's Hospital of Philadelphia
2022-2023
East China Normal University
2018-2020
We have developed a mouse DNA methylation array that contains 296,070 probes representing the diversity of biology. present atlas as rich reference resource 1,239 samples encompassing distinct tissues, strains, ages, sexes, and pathologies. describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, patient-derived xenograft assessment, backcross tracing, clocks. dissect processes associated with differentiation, aging, tumorigenesis. Notably, we find...
DNA methylation status is closely associated with diverse diseases, and generally more stable than gene expression, thus abnormal could be important biomarkers for tumor diagnosis, treatment prognosis. However, the signatures regarding changes pan-cancer diagnosis prognosis are less explored. Here we systematically analyzed genome-wide patterns in TCGA cancers machine learning. We identified seven CpG sites that effectively discriminate samples from adjacent normal tissue 12 main of (1216...
Abstract Aberrant DNA methylation plays an important role in cancer progression. However, no resource has been available that comprehensively provides methylation-based diagnostic and prognostic models, expression–methylation quantitative trait loci (emQTL), pathway activity-methylation (pathway-meQTL), differentially variable methylated CpGs, survival analysis, as well functional epigenetic modules for different cancers. These provide valuable information researchers to explore profiles...
Abstract The arrival of the Infinium DNA methylation BeadChips for mice and other nonhuman mammalian species has outpaced development informatics that supports their use epigenetics study in model organisms. Here, we present infrastructure methods to allow easy analysis on multiple species, including domesticated animals inbred laboratory (in SeSAMe version 1.16.0+). First, developed a data-driven pipeline covering inference, genome-specific data preprocessing regression modeling. We...
Abstract Single-cell analyses parse the brain’s billions of neurons into thousands ‘cell-type’ clusters residing in different brain structures 1 . Many cell types mediate their functions through targeted long-distance projections allowing interactions between specific types. Here we used epi-retro-seq 2 to link single-cell epigenomes and for 33,034 dissected from 32 regions projecting 24 targets (225 source-to-target combinations) across whole mouse brain. We highlight uses these data...
Genome-wide association studies (GWAS) have identified loci associated with kidney diseases, but the causal variants, genes, and pathways involved remain elusive. Here, we a disease gene called pancreatic progenitor cell differentiation proliferation factor (PPDPF) through integrating GWAS on function multiomic analysis. PPDPF was predominantly expressed in healthy proximal tubules of human mouse kidneys via single-cell Further investigations revealed that functioned as thiol-disulfide...
Due to differences across species, the mechanisms of cell fate decisions determined in mice cannot be readily extrapolated humans. In this study, we developed a feeder- and xeno-free culture protocol that efficiently induced human pluripotent stem cells (iPSCs) into PLZF+/GPR125+/CD90+ spermatogonium-like (SLCs). These SLCs were enriched with key genes germ development such as MVH, DAZL, GFRα1, NANOS3, DMRT1. addition, small fraction went through meiosis vitro develop haploid cells. We...
PyComplexHeatmap was designed to visualize matrix data and associated metadata through sophisticated, richly annotated heatmap layouts. We have integrated the R grammar-of-graphics semantics with Python-native matplotlib/Pandas-based science ecosystem, allowing users utilize built-in matplotlib colormaps project Pandas DataFrame directly as horizontal or vertical color bars. supports high-level abstraction can display up five dimensions within a single visualization. Advancements in...
Integration analysis of multi-omics data provides a comprehensive landscape for understanding biological systems and mechanisms. The abundance high-quality (genomics, transcriptomics, methylomics phenomics) the model organism Arabidopsis thaliana enables scientists to study genetic mechanism many processes. However, no resource is available provide systematic associations Arabidopsis. Here, we developed an Multi-omics Association Database (AtMAD, http://www.megabionet.org/atmad), public...
Co-occurrence and mutual exclusivity (COME) of DNA methylation refer to two or more genes that tend be positively negatively correlated in among different samples. Although COME gene mutations pan-cancer have been well explored, little is known about the pan-cancer. Here, we systematically explored profile diverse human cancer. A total 5,128,332 events were identified 14 main cancers types The Cancer Genome Atlas (TCGA). We also functional epigenetic modules zinc finger family six cancer by...
SUMMARY We have developed a mouse Infinium DNA methylation array that contains 297,415 probes to capture the diversity of biology. present atlas as rich reference resource 1,239 samples encompassing distinct tissues, strains, age, sex, and pathologies. describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, clocks. dissect processes associated with differentiation, aging tumorigenesis. Notably, we find tissue-specific...
With single-cell DNA methylation studies yielding vast datasets, existing data formats struggle with the unique challenges of storage and efficient operations, highlighting a need for improved solutions.
With single-cell DNA methylation studies yielding vast datasets, existing data formats struggle with the unique challenges of storage and efficient operations, highlighting a need for improved solutions.
Abstract The epigenomic landscape of human immune cells is dynamically shaped by both genetic factors and environmental exposures. However, the relative contributions these elements are still not fully understood. In this study, we employed single-nucleus methylation sequencing ATAC-seq to systematically explore how pathogen chemical exposures, along with variation, influence cell epigenome. We identified distinct exposure-associated differentially methylated regions (eDMRs) corresponding...
Background: DNA methylation status is closely associated with diverse diseases, and could be more stable than gene expression, thus important biomarkers for tumor diagnosis, treatment prognosis. However, the signatures regarding changes pan-cancer diagnosis prognosis are less explored.