A5025754368- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Immune Cell Function and Interaction
- Computational Drug Discovery Methods
- Immune cells in cancer
- RNA modifications and cancer
- Diabetes Management and Research
- Gene Regulatory Network Analysis
- RNA and protein synthesis mechanisms
- Cytokine Signaling Pathways and Interactions
- Cardiac Arrest and Resuscitation
- HIV/AIDS oral health manifestations
- Oral microbiology and periodontitis research
- Mycobacterium research and diagnosis
- Protein Structure and Dynamics
- Glycogen Storage Diseases and Myoclonus
- HER2/EGFR in Cancer Research
- Platelet Disorders and Treatments
- Advanced Biosensing Techniques and Applications
- Oral Health Pathology and Treatment
- Liver physiology and pathology
- Diabetes Treatment and Management
- Telomeres, Telomerase, and Senescence
- Biomedical Text Mining and Ontologies
University at Buffalo, State University of New York
2025
Sanofi (United States)
2018-2024
Innovation Research Center
2024
Johns Hopkins University
2024
Tainan Municipal Hospital
2018-2019
Genomics Research Center, Academia Sinica
2018
Boston University
2004-2016
Advanced Genomic Technology (United States)
2009-2016
BioZyme (United States)
2004
Robert Bosch Stiftung
2004
The oral microbiome, the complex ecosystem of microbes inhabiting human mouth, harbors several thousands bacterial types. proliferation pathogenic bacteria within mouth gives rise to periodontitis, an inflammatory disease known also constitute a risk factor for cardiovascular disease. While much is about individual species associated with pathogenesis, system-level mechanisms underlying transition from health are still poorly understood. Through sequencing 16S rRNA gene and whole community...
Despite its wide usage in biological databases and applications, the role of gene ontology (GO) network analysis is usually limited to functional annotation genes or sets with auxiliary information on correlations ignored. Here, we report new capabilities VisANT—an integrative software platform for visualization, mining, modeling networks—which extend application GO inference. The VisANT functions can be classified into three categories. (i) Visualization: a tree-based browser allows...
Experimental data exists for only a vanishingly small fraction of sequenced microbial genes. This community page discusses the progress made by COMBREX project to address this important issue using both computational and experimental resources.
With the rapid accumulation of our knowledge on diseases, disease-related genes and drug targets, network-based analysis plays an increasingly important role in systems biology, pharmacology translational science. The new release VisANT aims to provide functions facilitate convenient network therapies, drugs. improved understanding mechanisms complex diseases actions through analysis, novel methods (e.g., repositioning, multi-target combination therapy) can be designed. More specifically,...
The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted (iii) relationships among proteins unknown function and various types experimental data, including molecular structure, associated phenotypes. was created as part the novel (COMputational BRidges EXperiments) effort aimed at accelerating rate gene validation. It currently holds on ∼3.3 million known from over 1000 completely...
COMBREX (http://combrex.bu.edu) is a project to increase the speed of functional annotation new bacterial and archaeal genomes.It consists database predictions produced by computational biologists mechanism for experimental biochemists bid validation those predictions.Small grants are available support successful bids.
The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge the newly expanded version a software tool for analysis biological networks, VisANT 5.0. focus particular on facilitating visual exploration interaction between microbes community, e.g. as predicted by COMETS (Computation Microbial Ecosystems Time Space), dynamic stoichiometric modeling framework. Using VisANT's unique metagraph...
Resveratrol (RSV) has been reported to influence many biological processes, including the stimulation of cellular senescence and inhibition epithelial-mesenchymal transition (EMT). In this research, we explored mechanisms RSV on EMT through expression a DNA damage response (DDR) protein, Rad9, in breast lung cancer cell lines. Upon treating lines with at concentrations 10–50 μM, Rad9 was increased both transcriptional translational levels. The results indicated that RSV-induced expression,...
Abstract This study compares the pharmacokinetics and efficacy of various subcutaneously (SC) dosed insulin analogs, including rapid‐acting, intermediate‐acting, long‐acting, regular human insulin, using mechanistic pharmacokinetic (PK) pharmacodynamic (PD) models. These models were applied to data from euglycemic clamp studies in healthy volunteers, where its effects on glucose utilization monitored. Data published digitized modeled MONOLIX (Version 2024). The PK model described absorption...
Objectives: To compare the efficacy of different types subcutaneous insulin, including rapid-acting, intermediate-acting, long-acting, and human regular using a mechanistic-based pharmacokinetic (PK) pharmacodynamic (PD) model.Methods: An established [1] biophase/indirect response model was used to evaluate effect insulin on glucose utilization during euglycemic clamp studies PK PD parameters between various in healthy volunteers. The data were digitized from all published that could be...
The dramatic reduction in the cost of sequencing has allowed many researchers to join effort and annotating prokaryotic genomes. Annotation methods vary considerably may fail identify some genes. Here we draw attention a large number likely genes missing from annotations using common tools such as Glimmer BLAST. By analyzing 1,474 genome GenBank, 13,602 missed that are homologs non-hypothetical proteins, 11,792 only hypothetical yet have supporting evidence their protein-coding nature...
A shift of the delicate balance between apoptosis and survival-inducing signals determines fate neurons during development central nervous system its homeostasis throughout adulthood. Both pathways, promoting or protecting from apoptosis, trigger a transcriptional program. We conducted whole-genome expression profiling to decipher regulatory elements controlling apoptotic/survival switch in cerebellar granule following induction by serum potassium deprivation their rescue either insulin-like...
ABSTRACT Multiple Sclerosis (MS) is a chronic autoimmune disease affecting the central nervous system (CNS). Despite therapies that reduce relapses, many patients eventually develop secondary progressive MS (SPMS), characterized by ongoing and irreversible neurodegeneration worsening clinical symptoms. Microglia are resident innate immune cells of CNS. While cellular molecular determinants disability progression in remain incompletely understood, they thought to include non-resolving...
During a recent 6-year period we have encountered 10 patients with 'hepatocellular pseudotumour in the cirrhotic liver' (regenerating hyperplastic nodule). The were all male, aged 40-82 years. Seven chronic alcohol consumers. None was positive for HBs-Ag but seven had either anti-HBs or anti-HBc. Serum AFP level ranged from 4 to 28 ng/ml six who did not hepatocellular carcinoma at time of diagnosis pseudotumour. lesions depicted by ultrasonography seven, computed tomography two, and...
While significant advances have been made in understanding renal pathophysiology, less is known about the role of glycosphingolipid (GSL) metabolism driving organ dysfunction. Here, we used a small molecule inhibitor glucosylceramide synthase to modulate GSL levels three mouse models distinct pathologies: Alport syndrome (Col4a3 KO), polycystic kidney disease (Nek8jck), and steroid-resistant nephrotic (Nphs2 cKO). At tissue level, identified core immune-enriched transcriptional signature...
: Isolated traumatic phrenic nerve injury resulting from a stab wound to the neck is very rare. Herein, we report case of patient who was accidentally stabbed with garden shears that pierced her and penetrated spinal canal. She sustained right complicated by diaphragm palsy subsequent respiratory distress. We successfully treated video-assisted thoracoscopic plication.