A5049382437- Viral-associated cancers and disorders
- Genomics and Chromatin Dynamics
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Cytomegalovirus and herpesvirus research
- MicroRNA in disease regulation
- Lymphoma Diagnosis and Treatment
- Immune Cell Function and Interaction
- Molecular Biology Techniques and Applications
- Acute Myeloid Leukemia Research
- Computational Drug Discovery Methods
- Protein Degradation and Inhibitors
- Genomics, phytochemicals, and oxidative stress
- Protein Hydrolysis and Bioactive Peptides
- Phytase and its Applications
- Genomic variations and chromosomal abnormalities
- Genomics and Rare Diseases
Moffitt Cancer Center
2019-2025
Harbin Institute of Technology
2010-2018
Dana-Farber Cancer Institute
2015-2018
Harvard University
1978-2018
City University of Hong Kong
2017
Heilongjiang Institute of Technology
2010-2013
Indiana University – Purdue University Indianapolis
2009-2012
Indiana University School of Medicine
2010-2012
Cardiff University
2012
Pediatrics and Genetics
2011
'miR2Disease', a manually curated database, aims at providing comprehensive resource of microRNA deregulation in various human diseases. The current version miR2Disease documents 1939 relationships between 299 microRNAs and 94 diseases by reviewing more than 600 published papers. Around one-seventh the microRNA–disease represent pathogenic roles deregulated disease. Each entry contains detailed information on relationship, including ID, disease name, brief description an expression pattern...
Until recently, high-throughput gene expression technology, such as RNA-Sequencing (RNA-seq) required hundreds of thousands cells to produce reliable measurements. Recent technical advances permit genome-wide measurement at the single-cell level. Single-cell RNA-Seq (scRNA-seq) is most widely used and numerous publications are based on data produced with this technology. However, RNA-seq scRNA-seq markedly different. In particular, unlike RNA-seq, majority reported levels in zeros, which...
The identification of disease-related microRNAs is vital for understanding the pathogenesis diseases at molecular level, and critical designing specific tools diagnosis, treatment prevention. Experimental poses considerable difficulties. Computational analysis microRNA-disease associations an important complementary means prioritizing further experimental examination. Herein, we devised a computational model to infer potential by entire human microRNAome interest. We tested on 270 known...
In high-throughput studies, hundreds to millions of hypotheses are typically tested. Statistical methods that control the false discovery rate (FDR) have emerged as popular and powerful tools for error control. While classic FDR use only p values input, more modern been shown increase power by incorporating complementary information informative covariates prioritize, weight, group hypotheses. However, there is currently no consensus on how compare one another. We investigate accuracy,...
Obtaining RNA-seq measurements involves a complex data analytical process with large number of competing algorithms as options. There is much debate about which these methods provides the best approach. Unfortunately, it currently difficult to evaluate their performance due in part lack sensitive assessment metrics. We present series statistical summaries and plots terms specificity sensitivity, available R/Bioconductor package ( http://bioconductor.org/packages/rnaseqcomp ). Using two...
Potential epigenetic mechanisms underlying fetal alcohol syndrome (FAS) include alcohol-induced alterations of methyl metabolism, resulting in aberrant patterns DNA methylation and gene expression during development. Having previously demonstrated an essential role for epigenetics neural stem cell (NSC) development that inhibiting prevents NSC differentiation, here we investigated the effect exposure on genome-wide differentiation.Neural cells culture were treated with or without a 6-hour 88...
ABSTRACT Despite high initial efficacy, targeted therapies eventually fail in advanced cancers, as tumors develop resistance and relapse. In contrast to the substantial body of research on molecular mechanisms resistance, understanding how evolves remains limited. Using an experimental model ALK positive NSCLC, we explored evolution different clinical inhibitors. We found that can originate from heterogeneous, weakly resistant subpopulations with variable sensitivity Instead commonly assumed...
Epstein-Barr virus (EBV) infection of human primary resting B lymphocytes (RBLs) leads to the establishment lymphoblastoid cell lines (LCLs) that can grow indefinitely
Abstract Until recently, high-throughput gene expression technology, such as RNA-Sequencing (RNA-seq) required hundreds of thousands cells to produce reliable measurements. Recent technical advances permit genome-wide measurement at the single-cell level. Single-cell RNA-Seq (scRNA-seq) is most widely used and numerous publications are based on data produced with this technology. However, scRNA-seq markedly different. In particular, unlike RNA-Seq, majority reported levels in zeros, which...
Abstract The Epstein–Barr virus (EBV) nuclear antigen leader protein (EBNALP) is essential for the immortalization of naive B lymphocytes (NBLs). However, mechanisms remain elusive. To understand EBNALP’s role in B-cell transformation, we compare NBLs infected with wild-type EBV and an EBNALP-null mutant using multi-omics techniques. EBNALP inactivation alters enhancer–promoter interactions, resulting decreased CCND2 increased CASP1 BCL2L11 expression. Mechanistically, interacts colocalizes...
Somatic mosaicism (SM), the presence of somatic mutations, is classified as clonal hematopoiesis (CH) when it occurs in hematopoietic cells at an age-related rate. CH associated with risk for hematologic malignancies and cardiovascular disease, but most studies are predominately based on individuals European ancestry. Using peripheral blood whole exome sequencing data from 125,748 diverse genetic ancestries, we cataloged 503,703 SM mutations low variant allele frequency distributions 89,361...
Background Constructing and modeling the gene regulatory network is one of central themes systems biology. With growing understanding mechanism microRNA biogenesis its biological function, establishing a microRNA-mediated not only desirable but also achievable. Methodology In this study, we propose bioinformatics strategy to construct using genome-wide binding patterns transcription factor(s) RNA polymerase II (RPol II), derived chromatin immunoprecipitation following next generation...
Abstract Multiple myeloma (MM) incidence, mortality, and survival vary by race ethnicity, but the causes of differences remain unclear. We investigated demographic, clinical, molecular features diverse MM patients to elucidate mechanisms driving clinical disparities. This study included 495 (self-reported Hispanic, n = 45; non-Hispanic Black, 52; White, 398). Hispanic Black individuals had an earlier age onset than White (53 57 vs 63 years, respectively, P < .001). There were no in...
It has been known for several decades that iron inhibits the production of diphtheria toxin by Corynebacterium diphtheriae preventing expression at maximal levels. We examined inhibition kinetics after addition either or rifampin to iron-limited cultures C7 (betatox+). Iron-mediated was found be linear within range 16 nM micron. The following almost identical. [3H]RNA extracted from toxigenic C. hybridize a greater extent corynephage beta DNA than before onset nonlysogenic, nontoxigenic diphtheriae.
Abstract Motivation: Single Molecule Real-Time (SMRT) sequencing has been widely applied in cutting-edge genomic studies. However, it is still an expensive task to align the noisy long SMRT reads reference genome by state-of-the-art aligners, which becoming a bottleneck applications with sequencing. Novel approach on demand for improving efficiency and effectiveness of read alignment. Results: We propose Regional Hashing-based Alignment Tool (rHAT), seed-and-extension-based alignment...
The main application of ChIP-seq technology is the detection genomic regions that bind to a protein interest. A large part functional genomics’ public catalogs based on data. These rely peak calling algorithms infer protein-binding sites by detecting associated with more mapped reads (coverage) than expected chance, as result experimental protocol's lack perfect specificity. We find GC-content bias accounts for substantial variability in observed coverage experiments and this leads...
Epstein-Barr virus (EBV) infects 95% of adults worldwide and causes infectious mononucleosis. EBV is associated with endemic Burkitt lymphoma, Hodgkin posttransplant lymphomas, nasopharyngeal gastric carcinomas. In these cancers in most infected B-cells, maintains a state latency, where nearly 80 lytic cycle antigens are epigenetically suppressed. To gain insights into host epigenetic factors necessary for we recently performed human genome-wide CRISPR screen that identified the chromatin...
Abstract Primary effusion lymphoma (PEL) has a very poor prognosis. To evaluate the contributions of enhancers/promoters interactions to PEL cell growth and survival, here we produce H3K27ac HiChIP datasets in cells. This allows us generate enhancer connectome, which links enhancers promoters genome-wide. We identify more than 8000 genomic each line. By incorporating data with ChIP-seq data, between enhancers/enhancers, enhancers/promoters, promoters/promoters. further super-enhancers...
Abstract Epstein-Barr virus (EBV) immortalization of resting B lymphocytes (RBLs) to lymphoblastoid cell lines (LCLs) models human DNA tumor oncogenesis. RBL and LCL chromatin interaction maps are compared identify the spatial temporal genome architectural changes during EBV transformation. induces global reorganization where contact domains frequently merge or subdivide Repressed compartments in RBLs switch active A LCLs. LCLs gain 40% new domain boundaries. Newly gained boundaries have...
CD40 has major roles in B cell development, activation, and germinal center responses. hypoactivity causes immunodeficiency whereas its overexpression autoimmunity lymphomagenesis. To systematically identify autonomous regulators, we use CRISPR/Cas9 genome-scale screens Daudi cells stimulated by multimeric ligand. These highlight known pathway components reveal multiple additional mechanisms regulating CD40. The nuclear ubiquitin ligase FBXO11 supports expression targeting repressors CTBP1...