A5062832709- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Fault Detection and Control Systems
- Microbial Metabolic Engineering and Bioproduction
- Advanced Fluorescence Microscopy Techniques
- Eicosanoids and Hypertension Pharmacology
- Gene expression and cancer classification
- Receptor Mechanisms and Signaling
- Mineral Processing and Grinding
- Advanced Control Systems Optimization
- Sphingolipid Metabolism and Signaling
- Inflammatory mediators and NSAID effects
- Protein Kinase Regulation and GTPase Signaling
- Cholesterol and Lipid Metabolism
- Peroxisome Proliferator-Activated Receptors
- RNA Research and Splicing
- Immune cells in cancer
- Risk and Safety Analysis
- Adipokines, Inflammation, and Metabolic Diseases
- Computational Drug Discovery Methods
- Metabolomics and Mass Spectrometry Studies
- Liver Disease Diagnosis and Treatment
- Atherosclerosis and Cardiovascular Diseases
- Cell Image Analysis Techniques
- Liver physiology and pathology
La Jolla Bioengineering Institute
2007-2024
San Diego Supercomputer Center
2013-2024
University of California, San Diego
2015-2024
Universidad Católica Santo Domingo
2024
Xi'an Jiaotong University
2017
University of California, Riverside
2017
Case Western Reserve University
2017
University School
2017
National Yang Ming Chiao Tung University
2017
Purdue University West Lafayette
2003-2010
The spectrum of nonalcoholic fatty liver disease (NAFLD) includes steatosis, steatohepatitis (NASH), and cirrhosis. Recognition timely diagnosis these different stages, particularly NASH, is important for both potential reversibility limitation complications. Liver biopsy remains the clinical standard definitive diagnosis. Diagnostic tools minimizing need invasive procedures or that add information to histologic data are in novel management strategies growing epidemic NAFLD. We describe an...
The optimal expression of endothelial nitric oxide synthase (eNOS), the hallmark homeostasis, is vital to vascular function. Dynamically regulated by various stimuli, eNOS modulated at transcriptional, post-transcriptional, and post-translational levels. However, epigenetic modulations eNOS, particularly through long non-coding RNAs (lncRNAs) chromatin remodeling, remain be explored. Here we identify an enhancer-associated lncRNA that enhances (LEENE). Combining RNA-sequencing conformation...
Significance Endothelial responses to shear stress modulate vascular homeostasis. This study offers a comprehensive temporal mechanistic model of response in cultured human endothelial cells by presenting systematic time-series RNA-sequencing dataset on exposed pulsatile and oscillatory shears, consisting 10 time points across 24 h. The experimental data were used for pathway analysis construction transcription factor-to-gene networks. highlights ( i ) dynamic regulation several key...
Atherosclerosis is a multifaceted inflammatory disease involving cells in the vascular wall (eg, endothelial [ECs]), as well circulating and resident immunogenic monocytes/macrophages). Acting ligand for liver X receptor (LXR), but an inhibitor of SREBP2 (sterol regulatory element-binding protein 2), 25-hydroxycholesterol, its catalyzing enzyme cholesterol-25-hydroxylase (Ch25h) are important regulating cellular status cholesterol biosynthesis both ECs monocytes/macrophages.Bioinformatic...
Understanding the mechanisms that control human cardiomyocyte proliferation might be applicable to regenerative medicine. We screened a whole genome collection of miRNAs, identifying 96 capable increasing (DNA synthesis and cytokinesis) iPSC-derived cardiomyocytes. Chemical screening computational approaches indicated most these miRNAs (67) target different components Hippo pathway their activity depends on nuclear translocation transcriptional effector YAP. 53 67 are present in iPSC...
The two main blood flow patterns, namely, pulsatile shear (PS) prevalent in straight segments of arteries and oscillatory (OS) observed at branch points, are associated with atheroprotective (healthy) atheroprone (unhealthy) vascular phenotypes, respectively. effects flow-induced stress on endothelial cells (ECs) health have generally been studied using human umbilical vein (HUVECs). While there a few studies comparing the differential roles PS OS across different types ECs single time...
The NIH Common Fund Data Ecosystem (CFDE) program was established to facilitate data accessibility and interoperability across multiple (CF) programs promote collaborations new discoveries by combining from different CF programs. CFDE Resource Center (DRC) tasked with developing two web-based portals: an Information Portal serve information about the CFDE, a host harmonized metadata processed contributed participating Coordination Centers (DCCs) other sources. To achieve these goals, DRC...
<h3>Objective</h3> In the setting where two individuals are genetically similar, epigenetic mechanisms could account for discordance in presence or absence of non-alcoholic fatty liver disease (NAFLD). This study investigated if serum microRNAs (miRs) explain NAFLD. <h3>Design</h3> is a cross-sectional analysis prospective cohort 40 (n=80) twin-pairs residing Southern California. All participants underwent standardised research visit, MRI using proton-density fat fraction to quantify content...
Community detection algorithms are fundamental tools to uncover important features in networks. There several studies focused on social networks but only a few deal with biological Directly or indirectly, most of the methods maximize modularity, measure density links within communities as compared between communities. Here we analyze six different community algorithms, namely, Combo, Conclude, Fast Greedy, Leading Eigen, Louvain and Spinglass, two find their evaluate results terms...
In the recent past, graph-based approaches have been proposed by various researchers for safety analysis and fault diagnosis of chemical process systems. Though these shown promise, there are a number important issues that not adequately addressed in literature. The issue systematic development graph representations processes has This is an because digraphs error-prone time-consuming. Further, little attention paid toward understanding conceptual relationship between underlying mathematical...
25-Hydroxycholesterol (25OHC) is an enzymatically derived oxidation product of cholesterol that modulates lipid metabolism and immunity. 25OHC synthesized in response to interferons exerts broad antiviral activity by as yet poorly characterized mechanisms. To gain further insights into the basis for activity, we evaluated time-dependent responses macrophage lipidome transcriptome treatment. In addition altering specific aspects sphingolipid metabolism, found activates integrated stress (ISR)...
Abstract Qualitative process trend representation is an useful approach to model the temporal evolution of sensor data and has been applied in areas such as monitoring, compression, fault diagnosis. However, sheer volume real‐time that needs be processed necessitates automated for extraction. The step recovering important features a difficult procedure automate because absence priori knowledge about characteristics noise varying scales evolution. A novel proposed automatically identify...
The involvement of IL-4 in liver regeneration has not yet been recognized. In this article, we show that IL-4, produced by NKT cells accumulate regenerating livers after partial hepatectomy, contributes to process regulating the activation complement resection mice. mechanism regulation was associated with maintenance an appropriate level IgM mouse blood, because deposited parenchyma most likely initiated during regeneration. By controlling activation, regulated induction IL-6, thereby...
Abstract Background Sphingolipids play important roles in cell structure and function as well the pathophysiology of many diseases. Many intermediates sphingolipid biosynthesis are highly bioactive sometimes have antagonistic activities, for example, ceramide promotes apoptosis whereas sphingosine-1-phosphate can inhibit induce growth; therefore, quantification metabolites modeling network is imperative an understanding biology. Results In this direction, LIPID MAPS Consortium developing...
Studies of macrophage biology have been significantly advanced by the availability cell lines such as RAW264.7 cells. However, it is unclear how these differ from primary macrophages thioglycolate-elicited peritoneal (TGEMs). We used inflammatory stimulus Kdo2-lipid A (KLA) to stimulate and TGEM Temporal changes lipid gene expression levels were concomitantly measured a systems-level analysis was performed on fold-change data. Here we present comprehensive comparison between two types. Upon...
Preeclampsia is a pregnancy-specific syndrome characterized by hypertension and proteinuria after 20 weeks of gestation. However, it not well understood what lipids are involved in the development this condition, even less known how these mediate its formation. To reveal relationship between preeclampsia, we conducted lipidomic profiling maternal sera 44 severe preeclamptic healthy pregnant women from multi-ethnic cohort Hawaii. Correlation network analysis showed that oxidized phospholipids...