A5112474888- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Advanced Database Systems and Queries
- Gene Regulatory Network Analysis
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Semantic Web and Ontologies
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Algorithms and Data Compression
- Biomedical Text Mining and Ontologies
- Neuroinflammation and Neurodegeneration Mechanisms
- Bone Metabolism and Diseases
- Oral health in cancer treatment
- Data Mining Algorithms and Applications
- Data Management and Algorithms
- Oral Health Pathology and Treatment
- Head and Neck Cancer Studies
- Machine Learning in Bioinformatics
- Bayesian Modeling and Causal Inference
- Advanced Data Storage Technologies
- Traditional Chinese Medicine Studies
- Bone fractures and treatments
University of Connecticut
2015-2024
Scripps (United States)
2023-2024
Scripps Institution of Oceanography
2023-2024
Jaseng Hospital of Korean Medicine
2021-2022
Biocom
2021
Gastrointestinal mucosal injury (mucositis), commonly affecting the oral cavity, is a clinically significant yet incompletely understood complication of cancer chemotherapy. Although antineoplastic cytotoxicity constitutes primary trigger, interaction microbial commensals with tissues could modify response. It not clear, however, whether chemotherapy and its associated treatments affect communities disrupting homeostatic balance between resident microorganisms adjacent mucosa if such...
Fracture healing is a regenerative process that involves coordinated responses of many cell types, but characterization the roles specific populations in this has been limited. We have identified alpha smooth muscle actin (αSMA) as marker population mesenchymal progenitor cells periosteum contributes to osteochondral elements during fracture healing. Using lineage tracing approach, we labeled αSMA-expressing cells, and characterized changes periosteal early stages by histology, flow...
The full repertoire of human microRNAs (miRNAs) that could distinguish common (benign) nevi from cutaneous (malignant) melanomas remains to be established. In an effort gain further insight into the role miRNAs in melanoma, we applied Illumina next-generation sequencing (NGS) platform carry out in-depth analysis miRNA transcriptome biopsies nevi, thick primary (>4.0 mm) and metastatic with matched normal skin parallel melanocytes melanoma cell lines (both metastatic) (n=28). From this data...
There is an increasing need for efficient phenotyping and histopathology of a variety tissues. This evident with the ambitious projects to disrupt every gene in mouse genome. The research community needs rapid inexpensive means phenotype tissues via histology. Histological analyses skeletal are often time consuming semi-quantitative at best, regularly requiring subjective interpretation slides from trained individuals. Here, we present cryohistological paradigm mineralized First, novel...
A genome-wide microarray analysis of gene expression was carried out on human microvascular endothelial cells (HMEC-1) exposed to hyperbaric oxygen treatment (HBOT) under conditions that approximated clinical settings. Highly up-regulated genes included immediate early transcription factors (FOS, FOSB, and JUNB) metallothioneins. Six molecular chaperones were also immediately following HBOT, all these have been implicated in protein damage control. Pathway programs identified the...
Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses mining approach to assess performance merge callsets an ensemble SV-calling algorithms. It includes fusion model built using analysis 27 deep-coverage human genomes the 1000 Genomes Project. identify 843 novel SV calls that were not reported by Project for these samples. Experimental validation subset yields rate 86.7%....
AbstractHistone deacetylase 3 (HDAC3) is over-expressed in approximately half of all colon adenocarcinomas. We took an RNAi approach to determine how HDAC3 influenced chromatin modifications and the expression growth regulatory genes cancer cells. A survey histone revealed that knockdown SW480 cells significantly increased H4-K12 acetylation, a modification present during assembly has been implicated imprinting. This was found be most prominent proliferating intestinal crypt APCMin tumors,...
Broad domain promoters and super enhancers are regulatory elements that govern cell-specific functions harbor disease-associated sequence variants. These characterized by distinct epigenomic profiles, such as expanded deposition of histone marks H3K27ac for H3K4me3 broad domains, however little is known about how they interact with each other the rest genome in three-dimensional chromatin space. Using network theory methods, we studied interactions between domains three ENCODE cell lines...
Background Genetic variation in a region of chromosome 4p12 that includes the GABA A subunit gene GABRA 2 has been reproducibly associated with alcohol dependence ( AD ). However, molecular mechanisms underlying association are unknown. This study examined correlates vitro expression ‐associated rs279858*C‐allele human neural cells using an induced pluripotent stem cell (iPSC) model system. Methods We mRNA genes GABRG 1, 2, 4, and GABRB 1 ) 36 lines differentiated from iPSCs quantitative...
Dynamic and cellular histomorphometry of trabeculae is the most biologically relevant way assessing steady state bone health.Traditional measurement involves manual visual feature identification by a trained qualified professional.Inherent with this methodology time cost expenditure, as well subjectivity that naturally arises under human inspection.In work, we propose rapidly deployable, automated, objective method for dynamic histomorphometry.We demonstrate our highly effective in...
There is an increasing need for efficient phenotyping and histopathology of a variety tissues. This evident with the ambitious projects to disrupt every gene in mouse genome. The research community needs rapid inexpensive means phenotype tissues via histology. Histological analyses skeletal are often time consuming semi-quantitative at best, regularly requiring subjective interpretation slides from trained individuals. Here, we present cryohistological paradigm mineralized First, novel...
GTF2I and GTF2IRD1 encode a family of closely related transcription factors TFII-I BEN critical in embryonic development. Both genes are deleted Williams-Beuren syndrome, complex genetic disorder associated with neurocognitive, craniofacial, dental skeletal abnormalities. Although genome-wide promoter analysis has revealed the existence multiple binding sites stem cells (ESCs), there was no correlation between occupancy gene expression. Surprisingly, recognizes sequences enriched for...
Bayesian network model is widely used for reverse engineering of biological structures. An advantage this its capability to integrate prior knowledge into the learning process, which can lead improving quality reconstruction outcome. Some previous works have explored area with focus on using direct molecular links, except a few recent ones proposing examine effects orderings. In study, we propose that both links and orderings model. Random weights are assigned these two types alleviate bias...
Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET HiC, generate genome-wide maps elements. These interaction datasets are important resources to infer targets non-coding facilitate prioritization critical loci cellular functions. With increasing...
Abstract Excitotoxic events underlying ischaemic and traumatic brain injuries activate degenerative protective pathways, particularly in the hippocampus. To understand opposing pathways that determine brain's response to excitotoxicity, we used hippocampal explants, thereby eliminating systemic variables during a precise protocol of excitatory stimulation. N‐methyl‐ d ‐aspartate (NMDA) was applied for 20 min total RNA isolated one 24 h later neurobiology‐specific microarrays. Distinct groups...
Transcriptome data can provide information on signaling pathways active in cancers, but new computational tools are needed to more accurately quantify pathway activity and identify tissue-specific features. We developed a method called "BioTarget" that incorporates ChIP-seq into cellular analysis. This tool relates the expression of transcription factor TF target genes (based data) with status upstream components for an accurate quantification activity. analysis also reveals targets...