Warren A. Kibbe
A5038170232- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- SARS-CoV-2 detection and testing
- Cancer Genomics and Diagnostics
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- COVID-19 Clinical Research Studies
- Epigenetics and DNA Methylation
- Genomics and Rare Diseases
- COVID-19 and healthcare impacts
- SARS-CoV-2 and COVID-19 Research
- Respiratory viral infections research
- Long-Term Effects of COVID-19
- Ethics in Clinical Research
- Health, Environment, Cognitive Aging
- Non-Invasive Vital Sign Monitoring
- RNA modifications and cancer
- Childhood Cancer Survivors' Quality of Life
- Genomics and Chromatin Dynamics
- Nutrition, Genetics, and Disease
- AI in cancer detection
- COVID-19 Impact on Reproduction
- Optical Imaging and Spectroscopy Techniques
- Semantic Web and Ontologies
Duke University
2017-2025
Duke Cancer Institute
2020-2024
Clinical Research Institute
2022-2023
Duke Medical Center
2020-2022
Hispanic Health Council
2022
Puma Biotechnology (United States)
2021
Sanofi (Mexico)
2021
Novartis (Switzerland)
2021
Pfizer (United Kingdom)
2021
Immunomedics (Germany)
2021
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular cellular biology are freely available for community use in the annotation genes, gene products sequences. Many model organism databases genome groups GO contribute their sets to resource. database integrates contributed annotations full access this information formats. Members Consortium continually work collectively,...
Illumina microarray is becoming a popular platform. The BeadArray technology from makes its preprocessing and quality control different other technologies. Unfortunately, most analyses have not taken advantage of the unique properties system, just incorporated methods originally designed for Affymetrix microarrays. lumi Bioconductor package especially to process data. It includes data input, control, variance stabilization, normalization gene annotation portions. In specific,...
High-throughput profiling of DNA methylation status CpG islands is crucial to understand the epigenetic regulation genes. The microarray-based Infinium assay by Illumina one platform for low-cost high-throughput profiling. Both Beta-value and M-value statistics have been used as metrics measure levels. However, there are no detailed studies their relations strengths limitations. We demonstrate that relationship between methods a Logit transformation, show method has severe heteroscedasticity...
The Genomic Data Commons will initially house raw genomic data and diagnostic, histologic, clinical outcome from National Cancer Institute–funded projects. A harmonization process align sequencing to the genome identify mutations alterations.
We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation intra-molecular hairpin loop formation. has familiar 'calculator' look feel, making it readily understandable usable. incorporates three common methods calculating oligonucleotide-melting...
The Disease Ontology (DO) database (http://disease-ontology.org) represents a comprehensive knowledge base of 8043 inherited, developmental and acquired human diseases (DO version 3, revision 2510). DO web browser has been designed for speed, efficiency robustness through the use graph database. Full-text contextual searching functionality using Lucene allows querying name, synonym, definition, DOID cross-reference (xrefs) with complex Boolean search strings. semantically integrates disease...
A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The positive especially problematic detecting peaks with low amplitudes. Usually, various baseline correction and smoothing methods are applied before attempting detection. This approach very sensitive the amount aggressiveness correction, which contribute making results inconsistent between runs, instrumentation analysis methods.Most simply...
The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands utility ontology for examination and comparison genetic variation, phenotype, protein, drug epitope data through lens human disease. DO is a biomedical resource standardized common rare disease concepts with stable identifiers organized by etiology. content has had 192 revisions since 2012, including addition 760 terms. Thirty-two percent all terms now include definitions. expanded...
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over past year, GOC has implemented several processes to increase quantity, quality and specificity GO annotations. First, number manual, literature-based annotations grown at an increasing rate. Second, as result new 'phylogenetic annotation' process, manually reviewed, homology-based...
Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit performance subsequent statistical modeling and inference. Due to often limited number technical replicates for Affymetrix cDNA arrays, achieving variance be difficult. Although Illumina platform provides larger on each array (usually over 30 randomly distributed beads per probe), these have not been leveraged current log2 transformation process. We devised variance-stabilizing (VST) method...
As wearable technologies are being increasingly used for clinical research and healthcare, it is critical to understand their accuracy determine how measurement errors may affect conclusions impact healthcare decision-making. Accuracy of has been a hotly debated topic in both the popular science literature. Currently, technology companies responsible assessing reporting products, but little information about evaluation method made publicly available. Heart rate measurements from wearables...
Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical are abundant, these largely inaccessible to outside researchers. Statistical, machine learning, causal analyses most successful with large-scale beyond what is available in any given organization. Here, we introduce the National COVID Cohort Collaborative (N3C), an open science community focused on analyzing patient-level from many centers.The...
The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally diseases.We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to discover gene-disease relationships from GeneRIF database. We utilized a comprehensive subset of UMLS, which is disease-focused and structured as directed acyclic graph (the Disease Ontology), filter interpret results MMTx. were validated against Homayouni gene collection using...
The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available common disease. Here, we have developed concept-recognition procedure that analyzes frequencies HPO annotations as identified over five million PubMed abstracts by employing an iterative to optimize precision recall terms. We derived...
Abstract Background The proportion of tumors various histologies that may respond to drugs targeted molecular alterations is unknown. NCI-MATCH, a collaboration between ECOG-ACRIN Cancer Research Group and the National Institute, was initiated find efficacy signals by matching patients with refractory malignancies treatment potential tumor drivers regardless cancer histology. Methods Trial development required assumptions about target prevalence, accrual rates, eligibility, enrollment rates...
Biological measures of aging are important for understanding the health an population, with epigenetics particularly promising. Previous studies found that tumor tissue is epigenetically older than its donors chronologically. We examined whether blood Δage (the discrepancy between epigenetic and chronological ages) can predict cancer incidence or mortality, thus assessing potential as a biomarker. In prospective cohort, rate change over time were calculated in 834 leukocyte samples collected...
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. number GO annotations products has increased due to curation efforts among Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. ontologies continue expand improve as result targeted ontology development, introduction computable logical definitions...
DNA methylation in repetitive elements (RE) suppresses their mobility and maintains genomic stability, decreases it are frequently observed tumor and/or surrogate tissues. Averaging across RE genome is widely used to quantify global methylation. However, may vary specific play diverse roles disease development, thus averaging lose significant biological information. The ambiguous mapping of short reads by high cost current bisulfite sequencing platforms make them impractical for quantifying...
Prior observational studies suggest that aspirin use may be associated with reduced mortality in high-risk hospitalized patients COVID-19, but aspirin's efficacy moderate COVID-19 is not well studied.To assess whether early lower odds of in-hospital COVID-19.Observational cohort study 112 269 enrolled from January 1, 2020, through September 10, 2021, at 64 health systems the United States participating National Institute Health's COVID Cohort Collaborative (N3C).Aspirin within first day...
Data-driven basic, translational, and clinical research has resulted in improved outcomes for children, adolescents, young adults (AYAs) with pediatric cancers. However, challenges sharing data between institutions, particularly research, prevent addressing substantial unmet needs children AYA patients diagnosed certain Systematically collecting from every child can enable greater understanding of cancers, improve survivorship, accelerate development new more effective therapies. To...
Abstract Subjective methods have been reported to adapt a general-purpose ontology for specific application. For example, Gene Ontology (GO) Slim was created from GO generate highly aggregated report of the human-genome annotation. We propose statistical general purpose, OBO Foundry Disease (DO) identification gene-disease associations. Thus, we need simplified definition disease categories derived implicated genes. On basis assumption that DO terms having similar associated genes are...