A5011470209- COVID-19 and healthcare impacts
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- COVID-19 Clinical Research Studies
- Amyloidosis: Diagnosis, Treatment, Outcomes
- Biomedical Text Mining and Ontologies
- Pancreatic function and diabetes
- Cardiovascular Function and Risk Factors
- Semantic Web and Ontologies
- Diabetes and associated disorders
- Immune Cell Function and Interaction
- Economic and Financial Impacts of Cancer
- Cancer Genomics and Diagnostics
- Global Cancer Incidence and Screening
- Peptidase Inhibition and Analysis
- Artificial Intelligence in Healthcare
- Data Management and Algorithms
- Heart Rate Variability and Autonomic Control
- Diabetes Management and Research
- Cytomegalovirus and herpesvirus research
- Acute Myeloid Leukemia Research
- Machine Learning in Bioinformatics
- Single-cell and spatial transcriptomics
- Healthcare Systems and Public Health
- Infection Control and Ventilation
Ollscoil na Gaillimhe – University of Galway
2015-2024
Stanford University
2019-2024
Yale University
2024
Palo Alto University
2020-2024
MemorialCare Health System
2024
Weill Cornell Medicine
2022-2024
Center for Neuro-Oncology
2022-2024
Cornell University
2022-2024
Christian Medical College & Hospital
2023
Cardiovascular Institute of the South
2020-2022
The eye is highly susceptible to inflammation-mediated tissue damage evoked during bacterial infection. However, mechanisms regulating inflammation protect the remain elusive. Here, we used integrated metabolomics and transcriptomics show that immunomodulatory metabolite itaconate immune-responsive gene 1 (Irg1) are induced in (Staphylococcus aureus)-infected mouse eyes, bone-marrow-derived macrophages (BMDMs), Müller glia. Itaconate levels also elevated vitreous of patients with...
<h3>Importance</h3> Androgen deprivation therapy (ADT) has been theorized to decrease the severity of SARS-CoV-2 infection in patients with prostate cancer owing a potential tissue-based expression coreceptor transmembrane protease, serine 2 (TMPRSS2). <h3>Objective</h3> To examine whether ADT is associated decreased rate 30-day mortality from among cancer. <h3>Design, Setting, and Participants</h3> This cohort study analyzed patient data recorded COVID-19 Cancer Consortium registry between...
Abstract The coding variant (p.Arg192His) in the transcription factor PAX4 is associated with an altered risk for type 2 diabetes (T2D) East Asian populations. In mice, Pax4 essential beta cell formation but its role on human development and/or function unknown. Participants carrying p.His192 allele exhibited decreased pancreatic compared to homozygotes p.192Arg a cross-sectional study which we carried out intravenous glucose tolerance test and oral test. pedigree of patient young onset...
Data retrieval systems are facing a paradigm shift due to the proliferation of specialized data storage engines (SQL, NoSQL, Column Stores, MapReduce, Stream, and Graph) supported by varied models (CSV, JSON, RDB, RDF, XML).One immediate consequence this results into bottleneck over web; which means, web applications unable retrieve with intensity at being generated from different facilities.Especially in genomics healthcare verticals, growing petascale exascale, biomedical stakeholders...
The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from inference impacts somatic variants to pathway analysis biomarker development subtype discovery. ICGC-TCGA DREAM Somatic Mutation Calling (SMC-RNA) challenge was a crowd-sourced effort benchmark methods isoform quantification fusion detection bulk sequencing (RNA-seq) data. It concluded 2018 with comparison 77 entries 65 on 51 synthetic tumors 32 cell lines...
Abstract Physiological variability in pancreatic cell type gene regulation and the impact on diabetes risk is poorly understood. In this study we mapped types using single multiomic (joint RNA-seq ATAC-seq) profiling 28 non-diabetic donors combination with data from 35 Human Pancreas Analysis Program. We identified widespread associations age, sex, BMI, HbA1c, where regulatory responses were highly type- phenotype-specific. beta cells, donor age associated hypoxia, apoptosis, unfolded...
Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing massive amount of sequencing datasets. Often, these datasets published from isolated different facilities. Consequently, process sharing aggregating multisite thwarted by issues such as need to discover relevant data sources, built scalable repositories, automation linkage, volume data, efficient querying mechanism, information rich...
A mishap in anti-cancer drug distribution is critical breast cancer patients due to poor prediction model identify the treatment regime ER+ve and ER-ve (Estrogen Receptor (ER)) patients. The traditional method for depends on change expression across normal-disease pair. However, it certainly misses multidimensional aspect underlying cause of relapse, such as various mutations, dosage side effects, methylation, etc. In this paper, we have developed a multi-layer neural network classify...
Abstract Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment how cancers initiate, progress and respond selective pressures. We launched the ICGC–TCGA (International Cancer Genome Consortium–The Atlas) DREAM Somatic Mutation Calling Tumor Heterogeneity Evolution Challenge benchmark existing subclonal algorithms. This 7-year community effort used cloud computing 31 on 51 simulated tumors. Algorithms were scored...
Type 2 diabetes (T2D) and prediabetes are classically defined by the level of fasting glucose or surrogates such as hemoglobin HbA1c. This classification does not take into account heterogeneity in pathophysiology dysregulation, identification which could inform targeted approaches to treatment prevention and/or predict clinical outcomes. We performed gold-standard metabolic tests a cohort individuals with early dysregulation quantified four distinct subphenotypes known contribute T2D:...
Abstract Background Clonal hematopoiesis of indeterminate potential (CHIP) has been shown to increase all-cause mortality and risk cardiomyopathy in patients with solid malignancies. CHIP also T cell activation heart failure patients. It is unclear whether can affect the immune checkpoint inhibitor (ICI) myocarditis cancer treated immunotherapy. Methods We enrolled tumors a prospective study, determined status at time enrollment through blood whole exome sequencing, assessed incidence ICI...
Identifying the transcripts which mediate genetic association signals for type 2 diabetes (T2D) is critical to understand disease mechanisms. Studies in pancreatic islets support transcription factor ZMIZ1 as a transcript underlying T2D GWAS signal, but how it influences risk unknown. β-Cell-specific Zmiz1 knockout (Zmiz1βKO) mice were generated and phenotypically characterised. Glucose homeostasis was assessed Zmiz1βKO their control littermates on chow diet (CD) high fat (HFD). Islet...
Abstract CMV infection is a significant complication after solid organ transplantation. We used single cell TCR αβ sequencing to determine how memory inflation impacts clonality and diversity of the CMV-responsive CD8 CD4 T repertoire in first year transplantation human subjects. observed but no changes clonal diversity, indicating homeostatic stability clones. In contrast, was diverse stable over time, with evidence expansion. identified shared CDR3 motifs among patients public CMV-specific...
The database, semantic web, and linked data communities have proposed solutions that federate queries over multiple sources using a single model. Nowadays, the retrieval requirements originating from versatile broad domains like healthcare life sciences (HCLS) are changing this conventional trend - of federating query model primarily due to simultaneous use different models (CSV, JSON, RDB, RDF, XML, etc.) in real-life scenario. It's now impractical assume variety (graph, key-value, stream,...
Abstract The targeting of metabolic pathways is emerging as an exciting new approach for modulating immune cell function and polarization states. In this study, carbon tracing systems biology approaches integrating metabolomic transcriptomic profiling data were used to identify adaptations in human T metabolism important fueling pro-inflammatory function. Results study demonstrate that receptor (TCR) stimulation leads a significant increase glucose amino acid trigger downstream biosynthetic...
Abstract Introduction COVID-19 particularly impacted patients with co-morbid conditions, including cancer. Patients melanoma have not been specifically studied in large numbers. Here, we sought to identify factors that associated severity among melanoma, assessing outcomes of on active targeted or immune therapy. Methods Using the and Cancer Consortium (CCC19) registry, identified 307 diagnosed COVID-19. We used multivariable models assess demographic, cancer-related, treatment-related a...
Background Hospitalizations account for almost one-third of the US $4.1 trillion health care cost in United States. A substantial portion these hospitalizations are attributed to readmissions, which led establishment Hospital Readmissions Reduction Program (HRRP) 2012. The HRRP reduces payments hospitals with excess readmissions. In 2018, >US $700 million was withheld; this is expected exceed $1 billion by 2022. More importantly, there nothing more physically and emotionally taxing...
Abstract Prediction of metastatic sites from the primary site origin is a impugn task in breast cancer (BRCA). Multi-dimensionality such - bone, lung, kidney, and brain, using large-scale multi-dimensional Poly-Omics (Transcriptomics, Proteomics Metabolomics) data various type, for example, CNV (Copy number variation), GE (Gene expression), DNA methylation, path-ways, drugs with clinical associations makes classification metastasis multi-faceted challenge. In this paper, we have approached...