A5039379713- Cancer Immunotherapy and Biomarkers
- Immune Cell Function and Interaction
- RNA Research and Splicing
- Immunotherapy and Immune Responses
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- RNA regulation and disease
- Prostate Cancer Treatment and Research
- Effects of Radiation Exposure
- Monoclonal and Polyclonal Antibodies Research
- Bioinformatics and Genomic Networks
- T-cell and B-cell Immunology
- Immune Response and Inflammation
- Cancer Genomics and Diagnostics
- Bone Tissue Engineering Materials
- MicroRNA in disease regulation
- COVID-19 Clinical Research Studies
- Dental Trauma and Treatments
- Acute Myeloid Leukemia Research
- Nuclear Structure and Function
- interferon and immune responses
Beijing Radiation Center
2016-2024
Academy of Military Medical Sciences
2024
Dana-Farber Cancer Institute
2019-2022
Enhancer elements are noncoding stretches of DNA that play key roles in controlling gene expression programmes. Despite major efforts to develop accurate enhancer prediction methods, identifying sequences continues be a challenge the annotation mammalian genomes. One issues is lack large, sufficiently comprehensive and experimentally validated enhancers for humans or other species. Thus, development computational methods based on limited deciphering transcriptional regulatory code encoded...
Abstract Background Acute myeloid leukemia (AML), caused by the abnormal proliferation of immature cells in blood or bone marrow, is one most common hematologic malignancies. Currently, interactions between malignant and immune microenvironment, especially T B cells, remain poorly characterized. Methods In this study, we systematically analyzed cell receptor (TCR BCR) repertoires from RNA-seq data 145 pediatric 151 adult AML samples as well 73 non-tumor peripheral samples. Results We...
Lnc2Catlas ( http://lnc2catlas.bioinfotech.org/ ) is an atlas of long noncoding RNAs (lncRNAs) associated with cancer risk. LncRNAs are a class functional lengths over 200 nt and play vital role in diverse biological processes. Increasing evidence shows that lncRNA dysfunction many human cancers/diseases. It therefore important to understand the underlying relationship between lncRNAs cancers. To this end, we developed compile quantitative associations cancers using three computational...
Abstract Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) cis-regulatory elements (CREs). The uneven distribution TF binding sites across genome poses challenges in understanding how this evolves to regulate spatio-temporal gene consequent heritable phenotypic variation. In study, chromatin accessibility profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish medaka), chicken. Transcription...
Abstract Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences enhancer regions. Despite extensive efforts devoted to revealing potential functions and underlying mechanisms eRNAs, it remains an open question whether eRNAs mere transcriptional noise or relevant biologically functional species. Here, we identified catalogue in broad range human cell/tissue types extended our understanding by demonstrating their multi-omic signatures....
Abstract Background Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only minority cancer patients respond. Multiple studies have sought to identify general biomarkers ICB response, elucidating the molecular and cellular drivers resistance for individual tumors remains challenging. We determine whether tumor with defined genetic background exhibits stereotypic or heterogeneous response treatment. Results establish unique mouse system that...
RNA editing is a post-transcriptional sequence alteration. Current methods have identified sites and facilitated research but require sufficient genomic annotations prior-knowledge-based filtering steps, resulting in cumbersome, time-consuming identification process. Moreover, these limited generalizability applicability species with insufficient or conditions of prior knowledge. We developed DeepRed, deep learning-based method that identifies from primitive sequences without steps...
A-to-I editing, as a post-transcriptional modification process mediated by ADAR, plays crucial role in many biological processes metazoans. However, how and to what extent editing diversifies shapes population diversity at the RNA level are largely unknown. Here, we used 462 mRNA-sequencing samples from five populations of Geuvadis Project identified 16,518 sites, with false detection rate 1.03%. These sites form landscape editome human genome. By exploring within between populations,...
Advances in studies of long noncoding RNAs (lncRNAs) have provided data regarding the regulatory roles lncRNAs, which perform functional through interactions with other elements. To track underlying relationships among various databases been developed as repositories for lncRNA data. However, ability to comprehensively explore diverse between lncRNAs and elements is limited. this end, we LIVE (LncRNA Interaction Validated Encyclopaedia), an interactive resource integrate lncRNAs. a manually...
Abstract Advances in chromatin mapping have exposed the complex hierarchical organization mammals, including topologically associating domains (TADs) and their substructures, yet functional implications of this hierarchy gene regulation disease progression are not fully elucidated. Our study delves into phenomenon shared TAD boundaries, which pivotal maintaining structure regulating activity. By integrating high-resolution Hi-C data, accessibility, DNA double-strand breaks (DSBs) data from...
Accurately identifying the binding sites of transcription factors (TFs) is crucial to understanding mechanisms transcriptional regulation and human disease. We present incorporating Find Occurrence Regulatory Motifs (iFORM), an easy-to-use efficient tool for scanning DNA sequences with TF motifs described as position weight matrices (PWMs). Both performance assessment a receiver operating characteristic (ROC) curve correlation-based approach demonstrated that iFORM achieves higher accuracy...
Abstract Resin‐based materials (RBMs) are widely applied in dentistry because they withstand the recurrent multi‐dimensional force striking and hydrolysis of teeth. Sub‐nanoscale can enhance mechanical strength bioactivity RBMs, but effects still limited mechanisms to remain unclear. Here, a TiO 2 ‐based sub‐nanocomposite modified with caffeic acid (CA) robustness, structural stability, RBMs is reported. This promote proliferation, adhesion, odontogenic differentiation human dental pulp stem...
<div>Abstract<p>We applied our computational algorithm TRUST4 to assemble immune receptor (T-cell receptor/B-cell receptor) repertoires from approximately 12,000 RNA sequencing samples The Cancer Genome Atlas and seven immunotherapy studies. From over 35 million assembled complete complementary-determining region 3 sequences, we observed that the expression of <i>CCL5</i> <i>MZB1</i> is most positively correlated genes with T-cell clonal expansion B-cell...
<div>Abstract<p>We applied our computational algorithm TRUST4 to assemble immune receptor (T-cell receptor/B-cell receptor) repertoires from approximately 12,000 RNA sequencing samples The Cancer Genome Atlas and seven immunotherapy studies. From over 35 million assembled complete complementary-determining region 3 sequences, we observed that the expression of <i>CCL5</i> <i>MZB1</i> is most positively correlated genes with T-cell clonal expansion B-cell...
Supplementary Data from Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies
Supplementary Data from Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies
Supplementary Figure from Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies
Supplementary Figure from Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies