A5018628335- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- SARS-CoV-2 and COVID-19 Research
- Histone Deacetylase Inhibitors Research
- Machine Learning in Bioinformatics
- Immunotherapy and Immune Responses
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- Cancer-related gene regulation
- Nuclear reactor physics and engineering
- Nuclear Materials and Properties
- Gene Regulatory Network Analysis
- Cancer Immunotherapy and Biomarkers
- Immune cells in cancer
- CAR-T cell therapy research
- Protist diversity and phylogeny
- Autophagy in Disease and Therapy
- Genomic variations and chromosomal abnormalities
- vaccines and immunoinformatics approaches
Tsinghua University
2018-2025
Yunnan Agricultural University
2025
Center for Life Sciences
2018-2024
Peking University
2020-2024
National Institute of Biological Sciences, Beijing
2024
Xi'an Jiaotong University
2023
Stanford University
2014-2018
Howard Hughes Medical Institute
2015-2018
Donghua University
2015
The Ohio State University
2009-2014
Abstract Motivation: Enhancers are of short regulatory DNA elements. They can be bound with proteins (activators) to activate transcription a gene, and hence play critical role in promoting gene eukaryotes. With the avalanche sequences generated post-genomic age, it is challenging task develop computational methods for timely identifying enhancers from extremely complicated sequences. Although some efforts have been made this regard, they were limited at only whether query element being an...
Playing crucial roles in various cellular processes, such as recognition of specific nucleotide sequences, regulation transcription, and gene expression, DNA-binding proteins are essential ingredients for both eukaryotic prokaryotic proteomes. With the avalanche protein sequences generated postgenomic age, it is a critical challenge to develop automated methods accurate rapidly identifying based on their sequence information alone. Here, novel predictor, called “iDNA-Prot|dis”, was...
Intense infiltration of tumour-associated macrophages (TAMs) facilitates malignant growth glioblastoma (GBM), but the underlying mechanisms remain undefined. Herein, we report that TAMs secrete abundant pleiotrophin (PTN) to stimulate glioma stem cells (GSCs) through its receptor PTPRZ1 thus promoting GBM PTN-PTPRZ1 paracrine signalling. PTN expression correlates with CD11b+/CD163+ and poor prognosis patients. Co-implantation M2-like (MLCs) promoted GSC-driven tumour growth, silencing in...
DNA methylation is an important epigenetic regulator of gene expression. Recent studies have revealed widespread associations between genetic variation and levels. However, the mechanistic links remain unclear. To begin addressing this gap, we collected data at ∼300,000 loci in lymphoblastoid cell lines (LCLs) from 64 HapMap Yoruba individuals, genome-wide bisulfite sequence ten these individuals. We identified (at FDR 10%) 13,915 cis QTLs (meQTLs)—i.e., CpG sites which changes are...
The pandemic of COVID-19, caused by SARS-CoV-2, is a major global health threat. Epidemiological studies suggest that bats (Rhinolophus affinis) are the natural zoonotic reservoir for SARS-CoV-2. However, host range SARS-CoV-2 and intermediate hosts facilitate its transmission to humans remain unknown. interaction coronavirus with receptor key genetic determinant cross-species transmission. uses angiotensin-converting enzyme 2 (ACE2) as enter cells in species-dependent manner. In this study,...
Evolutionary maintenance of gene duplications Understanding genetic redundancy—the multiple copies a after duplication—and its relevance to evolution have long been debated. Lan and Pritchard examined duplicates within human other mammalian genomes. The expression genes appears be controlled by dosage balance tight coregulation tandem duplicates. They found little evidence for evincing significantly different patterns. However, such changes can evolve later, become physically separated the...
Aging is linked to functional deterioration and hematological diseases. The hematopoietic system maintained by stem cells (HSCs), dysfunction within the HSC compartment thought be a key mechanism underlying age-related perturbations. Using single-cell transplantation assays with five blood-lineage analysis, we previously identified myeloid-restricted repopulating progenitors (MyRPs) phenotypic in young mice. Here, determined changes using over 400 assays. Notably, MyRP frequency increased...
Abstract The tumor microenvironment (TME) in gastric cancer (GC) has been shown to be important for control but the specific characteristics GC are not fully appreciated. We generated an atlas of 166,533 cells from 10 patients with matched paratumor tissues and blood. Our results show tumor-associated stromal (TASCs) have upregulated activity Wnt signaling angiogenesis, negatively correlated survival. Tumor-associated macrophages LAMP3 + DCs involved mediating T cell form intercellular...
Protein remote homology detection is one of the most important problems in bioinformatics. Discriminative methods such as support vector machines (SVM) have shown superior performance. However, performance SVM-based depends on representations protein sequences. Prior works demonstrated that sequence-order effects are relevant for discrimination, but little work has explored how to incorporate information along with amino acid physicochemical properties into prediction. In order detection,...
Abstract The pandemic of Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health threat. Epidemiological studies suggest that bats are the natural zoonotic reservoir for SARS-CoV-2. However, host range SARS-CoV-2 and intermediate hosts facilitate its transmission to humans remain unknown. interaction with receptor key genetic determinant cross-species transmission. uses angiotensin-converting enzyme (ACE2) as enter...
Abstract Asparagine synthetase (ASNS) catalyses the ATP-dependent conversion of aspartate to asparagine. However, both regulation and biological functions asparagine in tumour cells remain largely unknown. Here, we report that p53 suppresses synthesis through transcriptional downregulation ASNS expression disrupts asparagine-aspartate homeostasis, leading lymphoma colon growth inhibition vivo vitro. Moreover, removal from culture medium or impairs cell proliferation induces p53/p21-dependent...
Abstract RORγt + group 3 innate lymphoid cells (ILC3s) are essential for intestinal homeostasis. Dysregulation of ILC3s has been found in the gut patients with inflammatory bowel disease and colorectal cancer, yet specific mechanisms still require more investigation. Here we observe increased β-catenin from colon cancer compared healthy donors. In contrast to promoting expression T cells, activation Wnt/β-catenin signaling suppresses expression, inhibits its proliferation function, leads a...
Abstract Extrachromosomal DNA (ecDNA) presents a promising target for cancer therapy; however, its spatial-temporal diversity and influence on tumor evolution the immune microenvironment remain largely unclear. We apply computational methods to analyze ecDNA from whole-genome sequencing data of 595 urothelial carcinoma (UC) patients. demonstrate that drives clonal through structural rearrangements during malignant transformation recurrence UC. This supports model wherein tumors evolve via...
We have analyzed publicly available K562 Hi-C data, which enable genome-wide unbiased capturing of chromatin interactions, using a Mixture Poisson Regression Model and power-law decay background to define highly specific set interacting genomic regions. integrated multiple ENCODE Consortium resources with the DNase-seq data ChIP-seq for 45 transcription factors 9 histone modifications. classified 12 different sets (clusters) loci that can be distinguished by their modifications categorized...
Half of all human transcription factors use C2H2 zinc finger domains to specify site-specific DNA binding and yet very little is known about their role in gene regulation. Based on vitro studies, a code has been developed that predicts motif for particular factor (ZNF). However, few studies have performed genome-wide analyses ZNF patterns, thus, it not clear if the will be useful identifying target genes ZNF. We ChIP-seq ZNF263, contains 9 domains, KRAB repression domain, SCAN domain...
Abstract Glucocorticoids (GCs) have been widely used as coadjuvants in the treatment of solid tumours, but GC may be associated with poor pharmacotherapeutic response or prognosis. The genomic action these tumours is largely unknown. Here we find that dexamethasone (Dex, a synthetic GC)-regulated genes triple-negative breast cancer (TNBC) cells are drug resistance. Importantly, GC-regulated aberrantly expressed TNBC patients and unfavourable clinical outcomes. Interestingly, cells, Compound...
Abstract Variation in human complex traits is connected to variation gene expression, and selection on can be reflected expression. Here, Glassberg Gao et al. analyze polymorphic.... Gene expression a major contributor phenotypic traits. Selection may therefore constraint we explore the effects of stabilizing cis-regulatory genetic humans. We patterns at copy number variants find evidence for against large increases Using allele-specific (ASE) data, further show smaller-effect variants....
Immune checkpoint inhibitor (ICI) therapy is generating remarkable responses in individuals with cancer, but only a small portion of breast cancer respond well. Here we report that tumor-derived Jagged1 key regulator the tumor immune microenvironment. promotes tumorigenesis multiple spontaneous mammary models. Through Jagged1-induced Notch activation, cells increase expression and secretion cytokines to help recruit macrophages into Educated crosstalk tumor-infiltrating T inhibit cell...
Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and data analysis remains challenging. In this study, we generated high depth in MCF-7 cell developed a bi-asymmetric-Laplace model (BALM) perform analysis. We found that efficiency of experiments was achieved by ∼100 million unique mapped tags from combination 500 mM 1000 salt concentration elution cells. Clonal...