A5020882239- Single-cell and spatial transcriptomics
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Circular RNAs in diseases
- Cancer Immunotherapy and Biomarkers
- Immune Cell Function and Interaction
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Immune cells in cancer
- Reproductive Biology and Fertility
- Renal and related cancers
- CAR-T cell therapy research
- Testicular diseases and treatments
- Gene Regulatory Network Analysis
- Monoclonal and Polyclonal Antibodies Research
- Sperm and Testicular Function
- T-cell and B-cell Immunology
- Ubiquitin and proteasome pathways
- Plant and Fungal Interactions Research
- Obstructive Sleep Apnea Research
- Advanced SAR Imaging Techniques
- Prostate Cancer Treatment and Research
Dana-Farber Cancer Institute
2017-2023
University of South Carolina
2021-2023
Zhejiang University
2023
Xi'an Jiaotong University
2023
Central South University
2022
Harvard University
2022
Tongji University
2016-2020
Shanghai Pulmonary Hospital
2017-2020
Nanjing University of Science and Technology
2015
Peking University
2002
Recent clinical successes of cancer immunotherapy necessitate the investigation interaction between malignant cells and host immune system. However, elucidation complex tumor-immune interactions presents major computational experimental challenges. Here, we present Tumor Immune Estimation Resource (TIMER; cistrome.shinyapps.io/timer) to comprehensively investigate molecular characterization interactions. Levels six tumor-infiltrating subsets are precalculated for 10,897 tumors from 32 types....
Abstract We developed Lisa ( http://lisa.cistrome.org/ ) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on input sets, first uses histone mark ChIP-seq and chromatin accessibility profiles construct a model related regulation these genes. Using TR peaks imputed binding sites, probes models using in silico deletion find most relevant TRs. Applied sets derived from targeted TF perturbation experiments, boosted performance cistromes...
Abstract We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow ( http://github.com/liulab-dfci/MAESTRO ) for the integrative analyses single-cell RNA-seq (scRNA-seq) ATAC-seq (scATAC-seq) data from multiple platforms. MAESTRO provides functions pre-processing, alignment, quality control, expression chromatin accessibility quantification, clustering, differential analysis, annotation. By modeling gene regulatory potential...
Abstract Cancer results from a breakdown of normal gene expression control, so the study regulation is critical to cancer research. To gain insight into transcriptional and epigenetic factors regulating abnormal patterns in cancers, we developed Cistrome web resource (http://cistrome.org/CistromeCancer/). We conducted systematic integration modeling over 10,000 tumor molecular profiles The Genome Atlas (TCGA) with 23,000 ChIP-seq chromatin accessibility our collection. include reconstruction...
Abstract Characterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate TF’s biological role. Previously, we developed widely used method, BETA, integrate TF ChIP-seq peaks with differential gene expression (DGE) data infer direct target genes. Here, provide Cistrome-GO, website implementation this method enhanced features conduct ontology analyses regulation TFs in human and mouse. Cistrome-GO has two working modes: solo mode for peak...
Model-based analysis of regulation gene expression (MARGE) is a framework for interpreting the relationship between H3K27ac chromatin environment and differentially expressed sets. The has three main functions: MARGE-potential, MARGE-express, MARGE-cistrome. MARGE-potential defines regulatory potential (RP) each as sum ChIP-seq signals weighted by function genomic distance from transcription start site. MARGE includes compendium RPs derived 365 human 267 mouse data Relative RPs, scaled using...
Abstract Characterization of the genomic distances over which transcription factor (TF) binding influences gene expression is important for inferring target genes from TF chromatin immunoprecipitation followed by sequencing (ChIP-seq) data. Here we systematically examine relationship between thousands and histone modification ChIP-seq data sets with profiles. We develop a model integrating these data, reveals two classes TFs distinct ranges regulatory influence, chromatin-binding...
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...
Abstract Mechanisms by which non-coding RNAs contribute to the progression of hormone-sensitive prostate cancer (PCa) (HSPC) castration-resistant PCa (CRPC) remain largely unknown. We previously showed that microRNA-221/222 is up-regulated in CRPC and plays a critical role modulating androgen receptor function during development. With further investigation, we characterized putative promoter region located 23.3 kb upstream miR-221/222 gene, this differentially activated LNCaP-Abl cells,...
Abstract Long noncoding RNAs (lncRNAs) are involved in various physiological and pathological processes. However, the role of lncRNAs testicular germ cell tumor (TGCT) has been rarely reported. Our purpose is to comprehensively survey expression function TGCT. In this study, we used RNA sequencing construct lncRNA profiles 13 TGCT tissues 4 paraneoplastic explore The bioinformatics analysis showed that many differentially expressed GO KEGG enrichment analyses revealed participated biological...
Recent advances in single-cell RNA sequencing have shown heterogeneous cell types and gene expression states the non-cancerous cells tumors. The integration of multiple scRNA-seq datasets across tumors can indicate common tumor microenvironment (TME). We develop a data driven framework, MetaTiME, to overcome limitations resolution consistency that result from manual labelling using known markers. Using millions TME single cells, MetaTiME learns meta-components encode independent components...
Spermatogonial stem cells (SSCs) are the initial for spermatogenesis. Although much progress has been made on uncovering a number of modulators SSC fate decisions in rodents, genes mediating human SSCs remain largely unclear. Here we report, first time, that TCF3, member basic helix-loop-helix family transcriptional modulator proteins, can stimulate proliferation and suppress apoptosis through targeting podocalyxin-like protein (PODXL). TCF3 was expressed primarily GFRA1-positive...
Perivascular delivery of therapeutic agents against established aetiologies for occlusive vascular remodelling has great potential vein graft failure. However, none the perivascular drug systems tested experimentally have been translated into clinical practice. In this study, we a novel strategy to locally and sustainably deliver cyclin-dependent kinase 8/19 inhibitor Senexin A (SenA), an emerging candidate treat disease, using graphene oxide-hybridised hyaluronic acid-based hydrogels. We...
Spermatogonial stem cells (SSCs) are the origin of male spermatogenesis, which can reconstruct germ cell lineage in mice. However, application SSCs for fertility restoration is hindered due to unclear mechanisms proliferation and self-renewal humans.To investigate role mechanism SPOC domain-containing protein 1 (SPOCD1) human SSC proliferation.We analyzed publicly available testis single-cell RNA sequencing (RNA-seq) data found that SPOCD1 predominantly expressed early developmental stages....
Data breaches are increasingly disruptive and have caused dramatic financial implications for the organizations affected by incidents. Although government has enacted amended relevant legal provisions, number of data is broadly on rise. The laws concerning aim to decrease risk such incidents, but their true efficacy remains be quantitively evaluated. In this study, we use panel in United States from 2005 2019 empirically verify whether can reduce probability breaches. First, attempt confirm...
Abstract To characterize the genomic distances over which transcription factors (TFs) influence gene expression, we examined thousands of TF and histone modification ChIP-seq datasets expression profiles. A model integrating these data revealed two classes TF: one with short-range regulatory influence, other long-range influence. The also had distinct chromatin-binding preferences auto-regulatory properties. range a single bound within different topologically associating domains (TADs)...
Testicular germ cell tumor (TGCT) is the most common malignant in young men and associated with poor prognosis. We assessed RNA expression profiles of 13 TGCT tissues 4 adjacent normal by transcriptome sequencing to identify novel prognostic biomarkers. detected several differentially expressed mRNAs that were functionally annotated GO KEGG enrichment analyses tumorigenesis-related processes such as immunity chemotherapeutic resistance. An mRNA-lncRNA-miRNA regulatory network was constructed...
A significant decrease in LINC00467 expression testicular germ cell tumors (TGCTs) was found our previous study comparison to adjacent tissue. Interestingly, the of correlated with pathological grade tumor TGCT patients. The higher was, worse prognosis patients was. Despite these findings, exact role development TGCTs requires further investigation. downregulated NCCIT and TCam-2 lines via small interfering RNA (siRNA) silencing. levels gene were validated using quantitative real-time...
A new direction of departure (DOD), arrival (DOA) and Doppler frequency estimation algorithm for non-uniform bistatic Multiple-input multiple-output (MIMO) radar is proposed. The snapshots in a coherent processing interval (CPI) also form sequence. Based on tensor decomposition, the factor matrices corresponding to virtual uniform arrays snapshot sequence are obtained parameters estimation. proposed improve method further reduces error noise condition. Simulation results verify effectiveness...
Abstract We developed Lisa ( http://lisa.cistrome.org ) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on input sets, first uses compendia public histone mark ChIP-seq and chromatin accessibility profiles construct a model related regulation these genes. Then using TR peaks imputed binding sites, probes models in silico deletion find most relevant TRs. Applied sets derived from targeted TF perturbation experiments, boosted...