A5044873580- Epigenetics and DNA Methylation
- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- CRISPR and Genetic Engineering
- Insect Resistance and Genetics
- Chromosomal and Genetic Variations
- Gene Regulatory Network Analysis
- DNA Repair Mechanisms
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Topic Modeling
- Insect symbiosis and bacterial influences
- RNA Interference and Gene Delivery
- Luminescence and Fluorescent Materials
- Plant Reproductive Biology
- Glioma Diagnosis and Treatment
- Insect and Arachnid Ecology and Behavior
- Cancer Genomics and Diagnostics
- Recommender Systems and Techniques
- Genomic variations and chromosomal abnormalities
- Cell Image Analysis Techniques
- Animal Genetics and Reproduction
- Natural Language Processing Techniques
Weill Cornell Medicine
2022-2025
RWTH Aachen University
2025
Cornell University
2022-2025
New York Genome Center
2022-2025
Soochow University
2025
Peking University
2014-2024
Center for Excellence in Molecular Plant Sciences
2021-2024
Anhui Agricultural University
2024
East China Normal University
2022-2024
Nantong University
2024
Recent advances in single-cell transcriptomics have illuminated the diverse neuronal and glial cell types within human brain. However, regulatory programs governing identity function remain unclear. Using a single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq), we explored open landscapes across 1.1 million cells 42 brain regions from three adults. Integrating this data unveiled 107 distinct their specific utilization of 544,735 candidate cis-regulatory DNA...
Resident cardiac fibroblasts (CFs) play crucial roles in sensing injury signals and regulating inflammatory responses post-myocardial infarction (MI). Damaged mitochondria can be transferred extracellularly via various mechanisms, including extracellular vesicles (EVs). In this study, we aimed to investigate whether CFs could transfer damaged mitochondrial components small EVs (sEVs) elucidate their role post-MI. Left anterior descending coronary artery ligation was performed mice....
High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites small-scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base-resolution method for the 5hmC. hmC-CATCH is based on selective 5hmC oxidation, chemical labeling and subsequent C-to-T transition during PCR. Requiring only nanoscale input genomic DNA samples, enabled us to detect hydroxymethylome human embryonic stem cells in cost-effective manner. Further application cell-free (cfDNA)...
The efficient isolation of immune cells with high purity and low cell damage is important for immunotherapy remains highly challenging. We herein report a capture DNA network containing polyvalent multimodules the specific in situ incubation T lymphocytes (T-cells). Two ultralong chains synthesized by an enzymatic amplification process were rationally designed to include functional as anchors adjuvants. Mutually complementary sequences facilitated formation encapsulation T-cells, well...
Abstract Loss of heterochromatin has been implicated as a cause pre-mature aging and age-associated decline in organ functions mammals; however, the specific cell types gene loci affected by this type epigenetic change have remained unclear. To address knowledge gap, we probed chromatin accessibility at single-cell resolution brains, hearts, skeletal muscles, bone marrows from young, middle-aged, old mice, assessed changes 353,126 candidate cis -regulatory elements (cCREs) across 32 major...
We previously reported Paired-Tag, a combinatorial indexing-based method that can simultaneously map histone modifications and gene expression at single-cell resolution scale. However, the lengthy procedure of Paired-Tag has hindered its general adoption in community. To address this bottleneck, we developed droplet-based protocol is faster more accessible than previous method. Using cultured mammalian cells primary brain tissues, demonstrate superior performance identifying candidate...
Abstract The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active‐site residues that contribute to substrate specificity. Swapping such between the leads partially switched demethylation activities. Combined evidence from X‐ray structures enzyme kinetics suggests a role of recognition. Such divergent sequence may aid design selective inhibitors can discriminate...
Significance Oxidative DNA damage can be cytotoxic or mutagenic to cells. NEIL1 (Nei-like 1) is a repair glycosylase guarding the mammalian genome against various oxidized bases; yet how recognizes and catalyzes removal of its substrates remains poorly understood. Here we integrate crystal structures NEIL1/double-stranded complex, computational simulations, biochemical analyses show that promotes tautomerization thymine glycol—a cognate substrate—for efficient substrate recognition excision....
Tn5-mediated transposition of double-strand DNA has been widely utilized in various high-throughput sequencing applications. Here, we report that the Tn5 transposase is also capable direct tagmentation RNA/DNA hybrids vitro. As a proof-of-concept application, this activity to replace traditional library construction procedure RNA sequencing, which contains many laborious and time-consuming processes. Results T ransposase-assisted R NA/DN A C o-tagm E ntation (termed ‘TRACE-seq’) are compared...
Abstract Deoxyribonucleic acid (DNA) hydrogel has been synthesized generally via the molecular interaction of either DNA base‐pairing, covalent bonding, or physical entanglement. To surmount limitations as sole module in materials, new assembly modes are desired to incorporate expand functionalities hydrogel. Herein, a supramacromolecular assembly‐based strategy is reported prepare hybrid interfacial chains and upconversion nanoparticles (UCNPs), remarkably which synthesis process finished...
In 2021, the World Health Organization reclassified glioblastoma, most common form of adult brain cancer, into isocitrate dehydrogenase (IDH)-wild-type glioblastomas and grade IV IDH mutant (G4 IDHm) astrocytomas. For both tumor types, intratumoral heterogeneity is a key contributor to therapeutic failure. To better define this heterogeneity, genome-wide chromatin accessibility transcription profiles clinical samples G4 IDHm astrocytomas were analyzed at single-cell resolution. These...
With the rapid development of online services, recommender systems (RS) have become increasingly indispensable for mitigating information overload. Despite remarkable progress, conventional recommendation models (CRM) still some limitations, e.g., lacking open-world knowledge, and difficulties in comprehending users' underlying preferences motivations. Meanwhile, large language (LLM) shown impressive general intelligence human-like capabilities, which mainly stem from their extensive...
Virtually few accurate and robust prediction models of lower-grade gliomas (LGG) survival exist that may aid physicians in making clinical decisions. We aimed to develop a prognostic model LGG by incorporating demographic, transcriptional biomarkers with either main effects or gene-gene interactions.
Tagging systems play an essential role in various information retrieval applications such as search engines and recommender systems. Recently, Large Language Models (LLMs) have been applied tagging due to their extensive world knowledge, semantic understanding, reasoning capabilities. Despite achieving remarkable performance, existing methods still limitations, including difficulties retrieving relevant candidate tags comprehensively, challenges adapting emerging domain-specific the lack of...
DNA methylation and hydroxymethylation are extensively reprogrammed during mammalian early embryogenesis, studying their regulatory functions requires comprehensive maps at base resolution. Here, we develop single-cell 5-hydroxymethylcytosine (5hmC) chemical-assisted C-to-T conversion-enabled sequencing (schmC-CATCH), a method leveraging selective 5hmC labeling for quantitative, base-resolution, genome-wide landscape of the hydroxymethylome in mouse gametes preimplantation embryos spanning...
Gaseous hormone ethylene regulates numerous stress responses and developmental adaptations in plants by controlling gene expression via transcription factors ETHYLENE INSENSITIVE3 (EIN3) EIN3-Like1 (EIL1). However, our knowledge regarding to the accurate definition of DNA-binding domains (DBDs) within EIN3 also mechanism specific DNA recognition is limited. Here, we identify 82–352 174–306 as optimal core DBDs, respectively. Results from systematic biochemical analyses reveal that both...