A5017716290- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Genetics, Bioinformatics, and Biomedical Research
- T-cell and B-cell Immunology
- Cell Adhesion Molecules Research
- Cancer, Hypoxia, and Metabolism
- Eicosanoids and Hypertension Pharmacology
- Genomics and Phylogenetic Studies
- HIV/AIDS drug development and treatment
- Neurological diseases and metabolism
- Pregnancy and preeclampsia studies
- Coronary Interventions and Diagnostics
- Erythrocyte Function and Pathophysiology
- Developmental Biology and Gene Regulation
- Extracellular vesicles in disease
- Trace Elements in Health
- Prion Diseases and Protein Misfolding
- Angiogenesis and VEGF in Cancer
- Cancer-related gene regulation
- Cytokine Signaling Pathways and Interactions
- Protein Structure and Dynamics
- Pneumocystis jirovecii pneumonia detection and treatment
- Machine Learning in Bioinformatics
- Single-cell and spatial transcriptomics
University of Sheffield
2020-2024
Insigneo
2024
Weston Park Cancer Centre
2024
Yale University
2017
Duke University
2017
Universidad Nacional Autónoma de México
2017
University of Connecticut
2017
Iowa State University
2017
University of California, Los Angeles
2017
National Museum of Natural History
2017
Zebrafish, a popular organism for studying embryonic development and modeling human diseases, has so far lacked systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium created central repository store process zebrafish developmental genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines total of 1,802 sets unpublished re-analyzed published data, which used improve existing...
Endothelial cell (EC) sensing of disturbed blood flow triggers atherosclerosis, a disease arteries that causes heart attack and stroke, through poorly defined mechanisms. The Notch pathway plays central role in vessel growth homeostasis, but its potential has not been previously studied. Here, we show using porcine murine cultured human coronary artery EC activates the JAG1-NOTCH4 signaling pathway. Light-sheet imaging revealed enrichment JAG1 NOTCH4 atherosclerotic plaques, EC-specific...
Several recent studies have examined different aspects of mammalian higher order chromatin structure – replication timing, lamina association and Hi-C inter-locus interactions — suggested that most these features genome organisation are conserved over evolution. However, the extent evolutionary divergence in has not been rigorously measured across genome, until now little known about characteristics any divergent loci present. Here, we generate a dataset combining multiple measurements many...
Atherosclerotic plaques form unevenly due to disturbed blood flow, causing localized endothelial cell (EC) dysfunction. Obesity exacerbates this process, but the underlying molecular mechanisms are unclear. The transcription factor EPAS1 (HIF2A) has regulatory roles in endothelium, its involvement atherosclerosis remains unexplored. This study investigates potential interplay between EPAS1, obesity, and atherosclerosis.
ABSTRACT Atherosclerosis progresses from fatty streaks to complex plaques, with rupture leading life-threatening complications. Endothelial-to-mesenchymal transition (EndMT) is associated advanced atherosclerotic but its role in plaque progression remains unclear. To investigate this, we analyzed the of TWIST1, a key EndMT-driving transcription factor, development. Using single-cell RNA sequencing plaques hypercholesterolemic mice inducible deletion Twist1 endothelial cells ( ECKO ApoE -/- )...
Gerstmann-Sträussler-Scheinker (GSS) P102L disease is a familial form of transmissible spongiform encephalopathy (TSE) that can present with or without vacuolation neuropil. Inefficient transmission into 101LL transgenic mice was previously observed from GSS vacuolation. However, several aged, healthy had large plaques composed abnormal prion protein (PrP(d)). Here we perform the ultrastructural characterization such and compare them PrP(d) aggregates found in TSE caused by an infectious...
DNA methylation and chromatin states play key roles in development disease. However, the extent of recent evolutionary divergence human epigenome influential factors that have shaped it are poorly understood. To determine links between genome sequence evolution, we examined following segmental duplication events lineage. Chromatin were found to been generally well conserved a event, with evolution largely uncoupled from total number genetic changes surrounding sequence. at tissue-specific,...
BACE1, a membrane-bound aspartyl protease that is implicated in Alzheimer's disease, the first to cut amyloid precursor protein resulting generation of amyloid-β and its aggregation form senile plaques, hallmark feature disease. Few other native BACE1 substrates have been identified despite relatively loose substrate specificity. We report bioinformatics approach identifying several putative substrates. Using our algorithm, we successfully predicted cleavage sites for 70% known further...
Abstract Zebrafish, a popular model for embryonic development and modelling human diseases, has so far lacked systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium created first central repository store process zebrafish developmental genomic data. Our Data Coordination Center ( https://danio-code.zfin.org ) combines total of 1,802 sets unpublished reanalysed published genomics data, which used...
ABSTRACT Endogenous retroviruses (ERVs) are fossils left in our genome from retrovirus infections of the past. Their sequences part every vertebrate and their random integrations thought to have contributed evolution. Although ERVs mainly silenced by host genome, they been found be activated multiple disease states, such as auto-inflammatory disorders neurological diseases. However, numerous copies mammalian genomes lack tools study them make defining role health diseases challenging. In...
Abstract Endothelial cell (EC) sensing of fluid shear stress regulates atherosclerosis, a disease arteries that causes heart attack and stroke. Atherosclerosis preferentially develops at regions exposed to low oscillatory (LOSS), whereas high are protected. We show using inducible EC-specific genetic deletion in hyperlipidaemic mice the Notch ligands JAG1 DLL4 have opposing roles atherosclerosis. While endothelial Jag1 promoted atherosclerosis sites LOSS, Dll4 was atheroprotective. Analysis...
Abstract Endogenous retroviruses (ERVs) are fossils left in our genome from retrovirus infections of the past. Their sequences part every vertebrate and their random integrations thought to have contributed evolution. Although ERVs mainly kept silenced by host genome, they found activated multiple disease states such as auto-inflammatory disorders neurological diseases. What makes defining role health diseases challenging is numerous copies mammalian genomes lack tools study them. In this...
ABSTRACT Background Atherosclerotic plaques form unevenly due to disturbed blood flow, causing localized endothelial cell (EC) dysfunction. Obesity exacerbates this process, but the underlying molecular mechanisms are unclear. The transcription factor EPAS1 (HIF2A) has regulatory roles in endothelium, its involvement atherosclerosis remains unexplored. This study investigates potential interplay between EPAS1, obesity, and atherosclerosis. Methods Responses shear stress were analysed using...
Objective: To quantify the changes in survival for patients with AIDS following antiretroviral therapy (ART). Methods: A retrospective analysis of prospectively collected data on 405 presenting three time periods; 1983–91 (I), 1992–95 (II) and 1996–99 (III). Conclusions: Modern ART has, average, doubled those but toxoplasmosis or Mycobacterium avium intracellulare (MAI) 2-year has increased by 8–10 times.