A5033330287- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- RNA modifications and cancer
- DNA and Nucleic Acid Chemistry
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Cancer-related molecular mechanisms research
- Advanced Breast Cancer Therapies
- RNA and protein synthesis mechanisms
- Metabolism, Diabetes, and Cancer
- Cancer-related gene regulation
- Caveolin-1 and cellular processes
- Cancer-related Molecular Pathways
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Protein Degradation and Inhibitors
- Acute Myeloid Leukemia Research
- Trace Elements in Health
- Chromosomal and Genetic Variations
- Anomaly Detection Techniques and Applications
- Genomic variations and chromosomal abnormalities
- Advanced Computational Techniques and Applications
- Single-cell and spatial transcriptomics
University of Virginia
2018-2025
Office of Public Health Genomics
2018-2024
University of Alabama at Birmingham
2023
Daqing Oilfield General Hospital
2022
Shandong University
2014-2016
University of Illinois Chicago
2009-2013
University of Illinois Urbana-Champaign
2009-2013
Illinois College
2009
University of Rochester
2006
Air Force Engineering University
2005
Caveolae are plasma membrane invaginations prominent in all endothelial cells lining blood vessels. characteristically bud to form free cytoplasmic vesicles capable of transporting carrier proteins such as albumin through the cell. However, caveolae size distribution and dynamics living ability internalize nanoparticles not well understood. We demonstrate here design a dual-color nanoparticle pair measure noninvasively dynamics. First, we coated with BSA (bovine serum albumin) address...
Abstract Summary Identification of functional transcription factors that regulate a given gene set is an important problem in regulation studies. Conventional approaches for identifying factors, such as DNA sequence motif analysis, are unable to predict binding specific and not sensitive enough detect at distal enhancers. Here, we present analysis (BART), novel computational method software package predicting query or associate with genomic profile, based on more than 6000 existing ChIP-seq...
Abstract Background The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of organization, CCCTC-binding factor (CTCF) has been characterized as DNA-binding protein with important functions maintaining the topological structure chromatin inducing DNA looping. Among prolific binding sites genome, several events altered CTCF occupancy have reported associated effects physiology or disease. However, hitherto...
Abstract Biclustering algorithms, which aim to provide an effective and efficient way analyze gene expression data by finding a group of genes with trend-preserving patterns under certain conditions, have been widely developed since Morgan et al. pioneered work about partitioning matrix into submatrices approximately constant values. However, the identification general biclusters are most meaningful substructures hidden in remains highly challenging problem. We found elementary method...
Abstract Many transcription factors (TFs) have been shown to bind super-enhancers, forming transcriptional condensates activate in various cellular systems. However, the genomic and epigenomic determinants of phase-separated condensate formation remain poorly understood. Questions regarding which TFs tend associate with what influence their association are largely unanswered. Here we systematically analyzed 571 DNA sequence motifs across human genome 6650 TF binding profiles different cell...
Abstract Transcriptional condensates have been shown to play a crucial role in gene regulation and dysregulation cancer. However, genomic approaches investigate the links between transcriptional cancer remain underdeveloped. In this study, we employed an integrative computational framework examine relationships genome-wide binding patterns of factors (TFs) potential at super-enhancers. We found that TFs with motifs exhibiting high clustering tendency are significantly associated also possess...
Transcriptome assembly using RNA-seq data - particularly in non-model organisms has been dramatically improved, but only recently have the pre-assembly procedures, such as sequencing depth and error correction, studied. Increasing read length is viewed a crucial condition to further improve transcriptome assembly, it unknown whether really matters. In addition, though many tools are available now, unclear existing assemblers perform well enough for all with different complexities. this...
Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins human chromosomes in each cell cycle. The are believed to be specified by binding factors like the origin recognition complex (ORC) or CTCF other features G-quadruplexes. We have performed an integrative analysis 113 genome-wide profiles (from five different techniques) and ORC-binding critically evaluate whether most reproducible these features. Out ~7.5 million union...
Abstract CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF site fragility, no study has integrated all fragility-related to understand the mechanism(s) how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) enriched at strong, but not weak, in five human cell types. Energetically favorable alternative secondary structures underlie strong sites. These...
Based on experimentally determined average inter-origin distances of ~100 kb, DNA replication initiates from ~50,000 origins human chromosomes in each cell cycle. The are believed to be specified by binding factors like the origin recognition complex (ORC) or CTCF other features G-quadruplexes. We have performed an integrative analysis 113 genome-wide profiles (from five different techniques) and ORC-binding critically evaluate whether most reproducible these features. Out ~7.5 million union...
Abstract Background Nickel is an occupational and environmental toxicant associated with a number of diseases in humans including pulmonary fibrosis, bronchitis lung nasal cancers. Our earlier studies showed that the nickel-exposure-induced genome-wide transcriptional changes, which persist even after termination exposure may underlie nickel pathogenesis. However, mechanisms drive nickel-induced persistent changes to transcriptome remain elusive. Results To elucidate long-term this study, we...
Replication-dependent canonical histone messenger RNAs (mRNAs) do not terminate with a poly(A) tail at the 3' end. We previously demonstrated that exposure to arsenic, an environmental carcinogen, induces polyadenylation of H3.1 mRNA, causing transformation human cells in vitro. Here we report mRNA increases protein, resulting displacement variant H3.3 active promoters, enhancers, and insulator regions, leading transcriptional deregulation, G2/M cell-cycle arrest, chromosome aneuploidy,...
Abstract Identifying active transcriptional regulators (TRs) associating with cis-regulatory elements in the genome to regulate gene expression is a key task regulation research. TR binding profiles from numerous public ChIP-seq data can be utilized for association analysis query identification, as an alternative DNA sequence motif analysis. However, integration of massive datasets has been major challenge such approaches. Here we present BARTweb, interactive web server identifying TRs whose...
Despite recent advances in single-molecule and structural analysis of condensin activity vitro , mechanisms functional loading loop extrusion that lead to specific chromosomal organization remain unclear. In Saccharomyces cerevisiae the most prominent site is rDNA locus on chromosome XII, but its repetitiveness deters rigorous individual genes. An equally non-rDNA located III (chrIII). It lies promoter a putative non-coding RNA gene called RDT1 which segment recombination enhancer (RE)...
DPY30 facilitates H3K4 methylation by directly binding to ASH2L in the SET1/MLL complexes and plays an important role hematologic malignancies. However, domain on that regulates cancer growth is not evident, potential of pharmacologically targeting this chromatin modulator inhibit has been explored. Here we have developed a peptide-based strategy specifically target activity. We designed cell-penetrating peptides derived from can either bind or show defective enhanced DPY30. The...
Identification of functional transcriptional regulators (TRs) associated with chromatin interactions is an important problem in studies 3-dimensional genome organization and gene regulation. Direct inference TR binding has been limited by the resolution Hi-C data. Here, we present BART3D, a computational method for inferring TRs genome-wide differential comparing maps from two states, leveraging public ChIP-seq data human mouse. We demonstrate that BART3D can detect relevant dynamic profiles...
Based on experimentally determined average inter-origin distances of ∼100 kb, DNA replication initiates from ∼50,000 origins human chromosomes in each cell cycle. The are believed to be specified by binding factors like the Origin Recognition Complex (ORC) or CTCF other features G-quadruplexes. We have performed an integrative analysis 113 genome-wide origin profiles (from five different techniques) and 5 ORC-binding critically evaluate whether most reproducible these features. Out ∼7.5...
Abstract KPNA7 is a member of the Importin- α family nuclear import receptors. forms complex with β and facilitates translocation signal-containing proteins from cytoplasm to nucleus. Exome sequencing siblings severe neurodevelopmental defects clinical features epilepsy identified two amino acid-altering mutations in KPNA7. Here, we show that E344Q substitution reduces binding localization signals, this limits activity. The P339A substitution, by contrast, has little effect on signals. Given...
Abstract Based on experimentally determined average inter-origin distances of ∼100 kb, DNA replication initiates from ∼50,000 origins human chromosomes in each cell cycle. The are believed to be specified by binding factors like the Origin Recognition Complex (ORC) or CTCF other features G-quadruplexes. We have performed an integrative analysis 113 genome-wide origin profiles (from five different techniques) and 5 ORC-binding critically evaluate whether most reproducible these features. Out...
Environmental factors such as the gut microbiome are thought to play an important role in development and treatment of many diseases. But our understanding microbiota compositional dynamics is still unclear incomplete because intestinal microbial community easily-changed ecosystem. It urgently required understand large variations among individuals. These variations, however, will be asset rather than a limitation personalized medicine. For proof-of-concept study on individual-specific...