A5030533815- Genetics, Bioinformatics, and Biomedical Research
- Computational Drug Discovery Methods
- Inflammatory mediators and NSAID effects
- T-cell and B-cell Immunology
- vaccines and immunoinformatics approaches
- Immune Cell Function and Interaction
- Cancer Immunotherapy and Biomarkers
- Gene expression and cancer classification
- Immunotherapy and Immune Responses
- Monoclonal and Polyclonal Antibodies Research
- Respiratory Support and Mechanisms
- Biomedical and Engineering Education
- Cancer, Hypoxia, and Metabolism
- Genomics and Phylogenetic Studies
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Eicosanoids and Hypertension Pharmacology
- Angiogenesis and VEGF in Cancer
- Pulmonary Hypertension Research and Treatments
- Estrogen and related hormone effects
- Bacteriophages and microbial interactions
- Ethics and Legal Issues in Pediatric Healthcare
- Mast cells and histamine
- Health, Environment, Cognitive Aging
- Polyamine Metabolism and Applications
- Bacillus and Francisella bacterial research
University of Dallas
2019-2024
Pennsylvania State University
2019-2020
William Penn University
2019-2020
Southwestern Medical Center
2016-2019
The University of Texas Southwestern Medical Center
2016-2019
University of Oklahoma Health Sciences Center
2012-2014
OU Health
2014
National Health Council
2011
National Academies of Sciences, Engineering, and Medicine
2011
Civil Aerospace Medical Institute
2011
Abstract Immune repertoire deep sequencing allows comprehensive characterization of antigen receptor–encoding genes in a lymphocyte population. We hypothesized that this method could enable novel approach to diagnose disease by identifying receptor sequence patterns associated with clinical phenotypes. In study, we developed statistical classifiers T-cell (TCR) repertoires distinguish tumor tissue from patient-matched healthy the same organ. The basis both was biophysicochemical motif...
Background: Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive response dynamics various states health and disease. Immune produces large, highly complex data sets, however, which require specialized methods software tools their effective analysis interpretation. Results: VDJServer is a cloud-based portal sequence that provides access to suite complete workflow, including modules pre-processing quality...
Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition populations. This opens door for novel approaches diagnose and prognosticate diseases with a driving immune component by identifying repertoire sequence patterns associated clinical phenotypes. Indeed, recent studies support feasibility this, demonstrating an association between repertoire-level summary statistics (e.g., diversity) patient outcomes several diseases. In...
We hypothesized that hypoxia would activate epidermal growth factor receptor (EGFR) tyrosine kinase, leading to increased arginase expression and resulting in proliferation of human pulmonary microvascular endothelial cell (hPMVEC). To test this hypothesis, hPMVEC were incubated normoxia (20% O(2), 5% CO(2)) or (1% CO(2)). Immunoblotting for EGFR proliferating nuclear antigen was done, protein levels both total greater hypoxic than normoxic hPMVEC. Furthermore, had activity did Hypoxic a...
Acute Respiratory Distress Syndrome (ARDS) is an illness that typically develops in people who are significantly ill or have serious injuries. ARDS characterized by fluid build-up occurs the alveoli. T-cells implicated as playing a role modulation of aberrant response leading to excessive tissue damage and, eventually, ARDS. Complementarity Determining Region 3 (CDR3) sequences derived from key players adaptive immune response. This governed elaborate specificity for distinct molecules and...
Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input downstream analysis. VDJPipe a flexible, high-performance tool that can perform multiple pre-processing tasks with just single pass over the files.Processing provided by include base composition statistics calculation, read filtering, homopolymer length and nucleotide paired-read merging, barcode demultiplexing, 5' 3' PCR primer matching, duplicate reads collapsing....
The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. full set of an individual at single point time is referred to as repertoire. recombination distinguishing feature adaptive immunity enables effective responses against essentially infinite array...
The Bacillus cereus sensu lato group contains ubiquitous facultative anaerobic soil-borne Gram-positive spore-forming bacilli. Molecular phylogeny and comparative genome sequencing have suggested that these organisms should be classified as a single species. While clonal in nature, there do not appear to species-specific lineages, excepting B. anthracis, spite of the wide array phenotypes displayed by organisms.
No-boundary thinking enables the scientific community to reflect in a thoughtful manner and discover new opportunities, create innovative solutions, break through barriers that might have otherwise constrained their progress. This concept encourages without being confined by traditional rules, limitations, or established norms, mindset is not limited previous work, leading fresh perspectives outcomes. So, where do we see field of artificial intelligence (AI) bioinformatics going next 30...
SARS-CoV-2 is a newly discovered virus which causes COVID-19 (coronavirus disease of 2019), initially documented as human pathogen in 2019 the city Wuhan China, has now quickly spread across globe with an urgency to develop effective treatments for and emerging variants. Therefore, identify potential therapeutics, antiviral catalogue compounds from CAS registry, division American Chemical Society was evaluated using pharmacoinformatics approach. A total 49,431 were recovered. After...
SCB34 is a sequence type 131, highly invasive, multidrug-resistant Escherichia coli isolate that produced neonatal bacteremia. Whole-genome sequencing was performed using 250-bp library on the Illumina MiSeq platform; 5,910,264 reads were assembled de novo A5 assembly pipeline. The total contig length 5,227,742 bp; RAST server used for annotation.
The purpose of the meeting described in this review was to decide how best ensure sustainability <a href="https://qubeshub.org/community/groups/niblse">Network for Integrating Bioinformatics into Life Science Education</a> (NIBLSE; pronounced “nibbles”). Biology research today generates large and complex datasets, analysis these datasets is becoming increasingly critical progress field. long-term goal NIBLSE address need achieve full integration bioinformatics undergraduate life...
DATA REPORT article Front. Genet., 09 December 2021Sec. Computational Genomics https://doi.org/10.3389/fgene.2021.750568
Many patients with underlying pulmonary disease travel each year by air. These may be at higher risk for developing complications due to decreased oxygen tension within their lungs, or hypoxia. At high altitudes, the lower air pressure makes it more difficult enter our vascular systems. In addition, aviators who fly above 12,500 feet in an unpressurized aircraft without supplemental susceptible effects of It is unclear what determines individual's response and subsequent compensation We...
Abstract VDJServer is a comprehensive, web-accessible system for analysis of immune repertoire sequencing data. provides complete workflow from pre-processing sequence reads, to V(D)J assignment, characterization and comparison. Recent enhancements in include: --Automatic parallelization tools handle very large data sets running on high-performance supercomputer--Import export subject sample metadata. User-defined groups allows sophisticated group comparison.--Extensive functionality such as...
Background Acute respiratory distress syndrome (ARDS) affects approximately 190,600 patients per year in the United States, with mortality up to 45%.ARDS can occur as primary disease due various factors (e.g.bacterial or viral pneumonia, gastric aspiration, lung contusion, toxic inhalation, and near drowning) secondary sepsis, pancreatitis, severe trauma, massive blood transfusion, burn.We hypothesized that ARDS-affected individuals have patterns of variants their physiological repertoire be...
The use of biological databases has emerged as an exciting part most research laboratories and programs. Until the turn decade, tasks such searching genomes for differences between genes or transcription factors would have seemed daunting perhaps laborious. However nowadays in post‐genomic era, researchers all over world can easily access these various types information. Many suggested that we must find ways to continue inspiring our nation’s young people develop a love appreciation science....
Abstract Despite the widespread use of immune repertoire profiling, there is currently no standardized format for output files from VDJ analysis. Researchers utilize software such as IgBlast and IMGT/High V-Quest to perform analysis infer germline rearrangements. Each these tools produces results in a different file format, can identify same result using labels. These differences make it challenging users additional one next. We have addressed this problem by developing representing results....
Abstract Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input downstream analysis. VDJPipe a flexible, high-performance tool that can perform multiple pre-processing tasks with just single pass the data. These include base composition statistics, read numerous filters, homopolymer filtering, length and nucleotide barcode demultiplexing, 5′ 3′ PCR primer matching, filtering duplicate reads. utilizes “pipeline” approach...
<p>model weights for colorectal cancer model</p>
<p>Supplementary Table 7: Model weights for all 17 breast cancer models</p>