Scholars@Duke
Warren Alden Kibbe

Warren Alden Kibbe

Professor in Biostatistics & Bioinformatics
Biostatistics & Bioinformatics, Division of Translational Biomedical
warren.kibbe@duke.edu
Duke Box 2721, Durham, NC 27710
2424 Erwin Road, Suite 902, 9025 Hock Plaza, Durham, NC 27705

Selected Publications

Tree-based classification model for Long-COVID infection prediction with age stratification using data from the National COVID Cohort Collaborative.

Journal Article JAMIA Open · December 2024 OBJECTIVES: We propose and validate a domain knowledge-driven classification model for diagnosing post-acute sequelae of SARS-CoV-2 infection (PASC), also known as Long COVID, using Electronic Health Records (EHRs) data. MATERIALS AND METHODS: We developed ... Full text Link to item Cite

Associations of County-Level Social Determinants of Health with COVID-19 Related Hospitalization Among People with HIV: A Retrospective Analysis of the U.S. National COVID Cohort Collaborative (N3C).

Journal Article AIDS Behav · October 2024 Individually, the COVID-19 and HIV pandemics have differentially impacted minoritized groups due to the role of social determinants of health (SDoH) in the U.S. Little is known how the collision of these two pandemics may have exacerbated adverse health ou ... Full text Link to item Cite

The Intersections of COVID-19, HIV, and Race/Ethnicity: Machine Learning Methods to Identify and Model Risk Factors for Severe COVID-19 in a Large U.S. National Dataset.

Journal Article AIDS Behav · October 2024 We investigate risk factors for severe COVID-19 in persons living with HIV (PWH), including among racialized PWH, using the U.S. population-sampled National COVID Cohort Collaborative (N3C) data released from January 1, 2020 to October 10, 2022. We defined ... Full text Link to item Cite

Utility of Skin Tone on Pulse Oximetry in Critically Ill Patients: A Prospective Cohort Study.

Journal Article Crit Care Explor · September 2024 OBJECTIVE: Pulse oximetry, a ubiquitous vital sign in modern medicine, has inequitable accuracy that disproportionately affects minority Black and Hispanic patients, with associated increases in mortality, organ dysfunction, and oxygen therapy. Previous re ... Full text Link to item Cite

Utility of skin tone on pulse oximetry in critically ill patients: a prospective cohort study.

Journal Article medRxiv · February 27, 2024 IMPORTANCE: Pulse oximetry, a ubiquitous vital sign in modern medicine, has inequitable accuracy that disproportionately affects Black and Hispanic patients, with associated increases in mortality, organ dysfunction, and oxygen therapy. Although the root c ... Full text Open Access Link to item Cite

Association of neighborhood-level sociodemographic factors with Direct-to-Consumer (DTC) distribution of COVID-19 rapid antigen tests in 5 US communities.

Journal Article BMC Public Health · September 22, 2023 BACKGROUND: Many interventions for widescale distribution of rapid antigen tests for COVID-19 have utilized online, direct-to-consumer (DTC) ordering systems; however, little is known about the sociodemographic characteristics of home-test users. We aimed ... Full text Link to item Cite

Risk for stillbirth among pregnant individuals with SARS-CoV-2 infection varied by gestational age.

Journal Article Am J Obstet Gynecol · September 2023 BACKGROUND: Despite previous research findings on higher risks of stillbirth among pregnant individuals with SARS-CoV-2 infection, it is unclear whether the gestational timing of viral infection modulates this risk. OBJECTIVE: This study aimed to examine t ... Full text Link to item Cite

Early Empiric Antibiotic Use in Patients Hospitalized With COVID-19: A Retrospective Cohort Study.

Journal Article Crit Care Med · September 1, 2023 OBJECTIVE: To investigate temporal trends and outcomes associated with early antibiotic prescribing in patients hospitalized with COVID-19. DESIGN: Retrospective propensity-matched cohort study using the National COVID Cohort Collaborative (N3C) database. ... Full text Link to item Cite

Cancer Informatics for Cancer Centers: Sharing Ideas on How to Build an Artificial Intelligence-Ready Informatics Ecosystem for Radiation Oncology.

Journal Article JCO Clin Cancer Inform · September 2023 In August 2022, the Cancer Informatics for Cancer Centers brought together cancer informatics leaders for its biannual symposium, Precision Medicine Applications in Radiation Oncology, co-chaired by Quynh-Thu Le, MD (Stanford University), and Walter J. Cur ... Full text Link to item Cite

RADx-UP Testing Core: Access to COVID-19 Diagnostics in Community-Engaged Research with Underserved Populations.

Journal Article J Clin Microbiol · August 23, 2023 Research on the COVID-19 pandemic revealed a disproportionate burden of COVID-19 infection and death among underserved populations and exposed low rates of SARS-CoV-2 testing in these communities. A landmark National Institutes of Health (NIH) funding init ... Full text Open Access Link to item Cite

The Childhood Cancer Data Initiative: Using the Power of Data to Learn From and Improve Outcomes for Every Child and Young Adult With Pediatric Cancer.

Journal Article J Clin Oncol · August 20, 2023 Data-driven basic, translational, and clinical research has resulted in improved outcomes for children, adolescents, and young adults (AYAs) with pediatric cancers. However, challenges in sharing data between institutions, particularly in research, prevent ... Full text Link to item Cite

Informatics tools to implement late cardiovascular risk prediction modeling for population management of high-risk childhood cancer survivors.

Conference Pediatr Blood Cancer · June 7, 2023 BACKGROUND: Clinical informatics tools to integrate data from multiple sources have the potential to catalyze population health management of childhood cancer survivors at high risk for late heart failure through the implementation of previously validated ... Full text Link to item Cite

Risk of severe acute respiratory syndrome coronavirus 2 infection among women with polycystic ovary syndrome.

Journal Article Fertil Steril · May 2023 OBJECTIVE: To determine whether women with polycystic ovary syndrome (PCOS) had a higher incidence of testing positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) than those without PCOS and evaluate whether PCOS diagnosis independentl ... Full text Link to item Cite

Adapting the Evidence Academy model for virtual stakeholder engagement in a national setting during the COVID-19 pandemic.

Journal Article J Clin Transl Sci · 2023 The COVID-19 pandemic raised the importance of adaptive capacity and preparedness when engaging historically marginalized populations in research and practice. The Rapid Acceleration of Diagnostics in Underserved Populations' COVID-19 Equity Evidence Acade ... Full text Link to item Cite

Access to COVID-19 testing by individuals with housing insecurity during the early days of the COVID-19 pandemic in the United States: a scoping review.

Journal Article Front Public Health · 2023 INTRODUCTION: The COVID-19 pandemic focused attention on healthcare disparities and inequities faced by individuals within marginalized and structurally disadvantaged groups in the United States. These individuals bore the heaviest burden across this pande ... Full text Open Access Link to item Cite

Exploring barriers and facilitators of implementing an at-home SARS-CoV-2 antigen self-testing intervention: The Rapid Acceleration of Diagnostics-Underserved Populations (RADx-UP) initiatives.

Journal Article PLoS One · 2023 BACKGROUND: Evaluating community-based programs provides value to researchers, funding entities, and community stakeholders involved in program implementation, and can increase program impact and sustainability. To understand factors related to program imp ... Full text Link to item Cite

Increasing access and uptake of SARS-CoV-2 at-home tests using a community-engaged approach.

Journal Article Prev Med Rep · October 2022 Inequalities around COVID-19 testing and vaccination persist in the U.S. health system. We investigated whether a community-engaged approach could be used to distribute free, at-home, rapid SARS-CoV-2 tests to underserved populations. Between November 18-D ... Full text Open Access Link to item Cite

Standardizing, harmonizing, and protecting data collection to broaden the impact of COVID-19 research: the rapid acceleration of diagnostics-underserved populations (RADx-UP) initiative.

Journal Article J Am Med Inform Assoc · August 16, 2022 OBJECTIVE: The Rapid Acceleration of Diagnostics-Underserved Populations (RADx-UP) program is a consortium of community-engaged research projects with the goal of increasing access to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) tests in un ... Full text Link to item Cite

Use of a Digital Assistant to Report COVID-19 Rapid Antigen Self-test Results to Health Departments in 6 US Communities.

Journal Article JAMA Netw Open · August 1, 2022 IMPORTANCE: Widespread distribution of rapid antigen tests is integral to the US strategy to address COVID-19; however, it is estimated that few rapid antigen test results are reported to local departments of health. OBJECTIVE: To characterize how often in ... Full text Open Access Link to item Cite

Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C).

Journal Article J Am Med Inform Assoc · July 12, 2022 OBJECTIVE: This study sought to evaluate whether synthetic data derived from a national coronavirus disease 2019 (COVID-19) dataset could be used for geospatial and temporal epidemic analyses. MATERIALS AND METHODS: Using an original dataset (n = 1 854 968 ... Full text Link to item Cite

Simulating Colorectal Cancer Trials Using Real-World Data.

Journal Article JCO Clin Cancer Inform · July 2022 PURPOSE: Using real-world data (RWD)-based trial simulation approach, we aim to simulate colorectal cancer (CRC) trials and examine both effectiveness and safety end points in different simulation scenarios. METHODS: We identified five phase III trials com ... Full text Link to item Cite

Association of Mass Distribution of Rapid Antigen Tests and SARS-CoV-2 Prevalence: Results from NIH-CDC funded Say Yes! Covid Test program in Michigan.

Journal Article medRxiv · April 2, 2022 IMPORTANCE: Wide-spread distribution of diagnostics is an integral part of the United States’ COVID-19 strategy; however, few studies have assessed the effectiveness of this intervention at reducing transmission of community COVID-19. OBJECTIVE: To asses ... Full text Link to item Cite

If you build it, will they use it? Use of a Digital Assistant for Self-Reporting of COVID-19 Rapid Antigen Test Results during Large Nationwide Community Testing Initiative.

Journal Article medRxiv · April 1, 2022 IMPORTANCE: Wide-spread distribution of rapid-antigen tests is integral to the United States' strategy to address COVID-19; however, it is estimated that few rapid-antigen test results are reported to local departments of health. OBJECTIVE: To characterize ... Full text Link to item Cite

MITI minimum information guidelines for highly multiplexed tissue images.

Journal Article Nat Methods · March 2022 The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and re ... Full text Link to item Cite

Association of Early Aspirin Use With In-Hospital Mortality in Patients With Moderate COVID-19.

Journal Article JAMA Netw Open · March 1, 2022 IMPORTANCE: Prior observational studies suggest that aspirin use may be associated with reduced mortality in high-risk hospitalized patients with COVID-19, but aspirin's efficacy in patients with moderate COVID-19 is not well studied. OBJECTIVE: To assess ... Full text Link to item Cite

Corrigendum to: The Molecular Analysis for Therapy Choice (NCI-MATCH) Trial: Lessons for Genomic Trial Design

Journal Article JNCI: Journal of the National Cancer Institute · February 7, 2022 Full text Cite

Temporal Events Detector for Pregnancy Care (TED-PC): A rule-based algorithm to infer gestational age and delivery date from electronic health records of pregnant women with and without COVID-19.

Journal Article PLoS One · 2022 OBJECTIVE: Identifying the time of SARS-CoV-2 viral infection relative to specific gestational weeks is critical for delineating the role of viral infection timing in adverse pregnancy outcomes. However, this task is difficult when it comes to Electronic H ... Full text Link to item Cite

At-home testing to mitigate community transmission of SARS-CoV-2: protocol for a public health intervention with a nested prospective cohort study.

Journal Article BMC Public Health · December 4, 2021 BACKGROUND: The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve as a global health crisis. Although highly effective vaccines have been developed, non-pharmaceutical interventions remain crit ... Full text Link to item Cite

Leveraging Clinical Informatics Tools to Extract Cumulative Anthracycline Exposure, Measure Cardiovascular Outcomes, and Assess Guideline Adherence for Children With Cancer.

Journal Article JCO Clin Cancer Inform · October 2021 PURPOSE: Cardiovascular disease is a significant cause of late morbidity and mortality in survivors of childhood cancer. Clinical informatics tools could enhance provider adherence to echocardiogram guidelines for early detection of late-onset cardiomyopat ... Full text Link to item Cite

Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer.

Journal Article JCO Clin Cancer Inform · August 2021 Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world b ... Full text Link to item Cite

Cancer Data Science and Computational Medicine.

Journal Article JCO Clin Cancer Inform · May 2021 Full text Link to item Cite

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

Journal Article J Am Med Inform Assoc · March 1, 2021 OBJECTIVE: Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical data are abundant, these are largely inaccessible to outside researchers. Statistical, machine lear ... Full text Link to item Cite

The Molecular Analysis for Therapy Choice (NCI-MATCH) Trial: Lessons for Genomic Trial Design.

Journal Article J Natl Cancer Inst · October 1, 2020 BACKGROUND: The proportion of tumors of various histologies that may respond to drugs targeted to molecular alterations is unknown. NCI-MATCH, a collaboration between ECOG-ACRIN Cancer Research Group and the National Cancer Institute, was initiated to find ... Full text Link to item Cite

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Journal Article Cell · April 16, 2020 Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial mu ... Full text Open Access Link to item Cite

Investigating sources of inaccuracy in wearable optical heart rate sensors.

Journal Article NPJ Digit Med · February 10, 2020 As wearable technologies are being increasingly used for clinical research and healthcare, it is critical to understand their accuracy and determine how measurement errors may affect research conclusions and impact healthcare decision-making. Accuracy of w ... Full text Link to item Cite

Cancer Informatics for Cancer Centers (CI4CC): Building a Community Focused on Sharing Ideas and Best Practices to Improve Cancer Care and Patient Outcomes.

Journal Article JCO Clin Cancer Inform · February 2020 Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world b ... Full text Link to item Cite

Investigating sources of inaccuracy in wearable optical heart rate sensors.

Journal Article NPJ Digit Med · 2020 As wearable technologies are being increasingly used for clinical research and healthcare, it is critical to understand their accuracy and determine how measurement errors may affect research conclusions and impact healthcare decision-making. Accuracy of w ... Full text Open Access Link to item Cite

Opportunities in technology and connected health for population science.

Conference CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION · 2020 Cite

DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma.

Journal Article Clin Epigenetics · October 21, 2019 BACKGROUND: The two most common repetitive elements (REs) in humans, long interspersed nuclear element-1 (LINE-1) and Alu element (Alu), have been linked to various cancers. Hepatitis C virus (HCV) may cause hepatocellular carcinoma (HCC) by suppressing ho ... Full text Link to item Cite

Data Harmonization for a Molecularly Driven Health System.

Journal Article Cell · August 23, 2018 Data commons have emerged as the best current method for enabling data aggregation across multiple projects and multiple data sources. Good data harmonization techniques are critical to maintain quality of data within a data commons, as well as to allow fu ... Full text Link to item Cite

Complexity of Delivering Precision Medicine: Opportunities and Challenges.

Journal Article Am Soc Clin Oncol Educ Book · May 23, 2018 Precision medicine has emerged as a tool to match patients with the appropriate treatment based on the precise molecular features of an individual patient's tumor. Although examples of targeted therapies exist resulting in dramatic improvements in patient ... Full text Open Access Link to item Cite

Prediction of genome-wide DNA methylation in repetitive elements.

Journal Article Nucleic Acids Res · September 6, 2017 DNA methylation in repetitive elements (RE) suppresses their mobility and maintains genomic stability, and decreases in it are frequently observed in tumor and/or surrogate tissues. Averaging methylation across RE in genome is widely used to quantify globa ... Full text Link to item Cite

Cancer Moonshot Data and Technology Team: Enabling a National Learning Healthcare System for Cancer to Unleash the Power of Data.

Journal Article Clin Pharmacol Ther · May 2017 The Cancer Moonshot emphasizes the need to learn from the experiences of cancer patients to positively impact their outcomes, experiences, and qualities of life. To realize this vision, there has been a concerted effort to identify the fundamental building ... Full text Link to item Cite

A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine.

Journal Article Front Cell Dev Biol · 2017 Advancements in next-generation sequencing and other -omics technologies are accelerating the detailed molecular characterization of individual patient tumors, and driving the evolution of precision medicine. Cancer is no longer considered a single disease ... Full text Open Access Link to item Cite

Corrigendum: A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine.

Journal Article Frontiers in cell and developmental biology · January 2017 [This corrects the article on p. 83 in vol. 5, PMID: 28983483.]. ... Full text Cite

The YPT protein family in yeast

Chapter · January 1, 2017 GTP-binding proteins of the Ypt family are members of the ras superfamily of proteins. The first example of a YPT gene, YPT1, was cloned and sequenced as part of the actin-β-tubulin gene cluster in the yeast Saccharomyces cerevisiae and the homology of the ... Full text Cite

Toward a Shared Vision for Cancer Genomic Data.

Journal Article N Engl J Med · September 22, 2016 Full text Link to item Cite

Abstract 4480: Blood epigenetic age may predict cancer incidence and mortality

Conference Cancer Research · July 15, 2016 AbstractBiological measures of aging are important for understanding age-related cancers as the population ages. Since the epigenome is closely related to aging, epigenetics may help predict these and other ... Full text Cite

Blood Epigenetic Age may Predict Cancer Incidence and Mortality.

Journal Article EBioMedicine · March 2016 Biological measures of aging are important for understanding the health of an aging population, with epigenetics particularly promising. Previous studies found that tumor tissue is epigenetically older than its donors are chronologically. We examined wheth ... Full text Link to item Cite

Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines.

Journal Article Hum Genet · February 2016 Inter-individual variation in cytosine modifications has been linked to complex traits in humans. Cytosine modification variation is partially controlled by single nucleotide polymorphisms (SNPs), known as modified cytosine quantitative trait loci (mQTL). ... Full text Link to item Cite

Cancer Clinical Research: Enhancing Data Liquidity and Data Altruism

Chapter · January 1, 2016 A number of converging factors (including ubiquitous computing, decreased cost of sequencing, imaging, uptake of EHRs driven by the Accountable Care Act and Meaningful Use) have made it possible to generate and aggregate much more detailed molecular, lab, ... Full text Cite

Introduction

Book · July 30, 2015 Cite

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Journal Article Am J Hum Genet · July 2, 2015 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 ... Full text Link to item Cite

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis.

Journal Article Database (Oxford) · 2015 Bio-ontologies provide terminologies for the scientific community to describe biomedical entities in a standardized manner. There are multiple initiatives that are developing biomedical terminologies for the purpose of providing better annotation, data int ... Full text Link to item Cite

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

Journal Article Nucleic Acids Res · January 2015 The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of hum ... Full text Link to item Cite

Defining the role of common variation in the genomic and biological architecture of adult human height.

Journal Article Nat Genet · November 2014 Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that th ... Full text Link to item Cite

Meta-analysis of genome-wide association studies in African Americans provides insights into the genetic architecture of type 2 diabetes.

Journal Article PLoS Genet · August 2014 Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GW ... Full text Link to item Cite

Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing.

Journal Article Cancer Inform · 2014 The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a ... Full text Link to item Cite

The Disease and Gene Annotations (DGA): an annotation resource for human disease.

Journal Article Nucleic Acids Res · January 2013 Disease and Gene Annotations database (DGA, http://dga.nubic.northwestern.edu) is a collaborative effort aiming to provide a comprehensive and integrative annotation of the human genes in disease network context by integrating computable controlled vocabul ... Full text Link to item Cite

Gene Ontology annotations and resources.

Journal Article Nucleic Acids Res · January 2013 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 the past year, the GOC has implemented seve ... Full text Link to item Cite

DictyBase 2013: integrating multiple Dictyostelid species.

Journal Article Nucleic Acids Res · January 2013 dictyBase (http://dictybase.org) is the model organism database for the social amoeba Dictyostelium discoideum. This contribution provides an update on dictyBase that has been previously presented. During the past 3 years, dictyBase has taken significant s ... Full text Link to item Cite

Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro.

Journal Article Environ Toxicol Pharmacol · November 2012 Pesticide exposure has repeatedly been associated with cancers. However, molecular mechanisms are largely undetermined. In this study, we examined whether exposure to diazinon, a common organophosphate that has been associated with cancers, could induce DN ... Full text Link to item Cite

Text data extraction for a prospective, research-focused data mart: implementation and validation.

Journal Article BMC Med Inform Decis Mak · September 13, 2012 BACKGROUND: Translational research typically requires data abstracted from medical records as well as data collected specifically for research. Unfortunately, many data within electronic health records are represented as text that is not amenable to aggreg ... Full text Link to item Cite

DNA methylation alterations in response to pesticide exposure in vitro.

Journal Article Environ Mol Mutagen · August 2012 Although pesticides are subject to extensive carcinogenicity testing before regulatory approval, pesticide exposure has repeatedly been associated with various cancers. This suggests that pesticides may cause cancer via nonmutagenicity mechanisms. The pres ... Full text Link to item Cite

The Gene Ontology: enhancements for 2011.

Journal Article Nucleic Acids Res · January 2012 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. The number of GO annotations of gene products has increased due to cur ... Full text Link to item Cite

Disease Ontology: a backbone for disease semantic integration.

Journal Article Nucleic Acids Res · January 2012 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). The DO web browser has been designed for speed, efficienc ... Full text Link to item Cite

A framework for annotating human genome in disease context.

Journal Article PLoS One · 2012 Identification of gene-disease association is crucial to understanding disease mechanism. A rapid increase in biomedical literatures, led by advances of genome-scale technologies, poses challenge for manually-curated-based annotation databases to character ... Full text Link to item Cite

Using the bioconductor GeneAnswers package to interpret gene lists.

Journal Article Methods Mol Biol · 2012 Use of microarray data to generate expression profiles of genes associated with disease can aid in identification of markers of disease and potential therapeutic targets. Pathway analysis methods further extend expression profiling by creating inferred net ... Full text Link to item Cite

Mining the Gene Wiki for functional genomic knowledge.

Journal Article BMC Genomics · December 13, 2011 BACKGROUND: Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborativ ... Full text Link to item Cite

Direct2Experts: a pilot national network to demonstrate interoperability among research-networking platforms.

Journal Article J Am Med Inform Assoc · December 2011 Research-networking tools use data-mining and social networking to enable expertise discovery, matchmaking and collaboration, which are important facets of team science and translational research. Several commercial and academic platforms have been built, ... Full text Link to item Cite

The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies.

Journal Article BMC Med Genomics · January 26, 2011 INTRODUCTION: The eMERGE (electronic MEdical Records and GEnomics) Network is an NHGRI-supported consortium of five institutions to explore the utility of DNA repositories coupled to Electronic Medical Record (EMR) systems for advancing discovery in genome ... Full text Link to item Cite

dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa.

Journal Article Nucleic Acids Res · January 2011 dictyBase (http://www.dictybase.org), the model organism database for Dictyostelium, aims to provide the broad biomedical research community with well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase house ... Full text Link to item Cite

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis.

Journal Article BMC Bioinformatics · November 30, 2010 BACKGROUND: High-throughput profiling of DNA methylation status of CpG islands is crucial to understand the epigenetic regulation of genes. The microarray-based Infinium methylation assay by Illumina is one platform for low-cost high-throughput methylation ... Full text Link to item Cite

A collection of bioconductor methods to visualize gene-list annotations.

Journal Article BMC Res Notes · January 19, 2010 BACKGROUND: Gene-list annotations are critical for researchers to explore the complex relationships between genes and functionalities. Currently, the annotations of a gene list are usually summarized by a table or a barplot. As such, potentially biological ... Full text Link to item Cite

The Gene Ontology in 2010: extensions and refinements.

Journal Article Nucleic Acids Res · January 2010 The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in cont ... Full text Link to item Cite

Visual presentation as a welcome alternative to textual presentation of gene annotation information.

Journal Article Adv Exp Med Biol · 2010 The functions of a gene are traditionally annotated textually using either free text (Gene Reference Into Function or GeneRIF) or controlled vocabularies (e.g., Gene Ontology or Disease Ontology). Inspired by the latest word cloud tools developed by the In ... Full text Link to item Cite

Annotating the human genome with Disease Ontology.

Journal Article BMC Genomics · July 7, 2009 BACKGROUND: The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases. RESULTS: We used the Unified Medical Language System (UMLS) MetaMap Transfer tool (MMTx) to disco ... Full text Link to item Cite

From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.

Journal Article Bioinformatics · June 15, 2009 Subjective methods have been reported to adapt a general-purpose ontology for a specific application. For example, Gene Ontology (GO) Slim was created from GO to generate a highly aggregated report of the human-genome annotation. We propose statistical met ... Full text Link to item Cite

dictyBase--a Dictyostelium bioinformatics resource update.

Journal Article Nucleic Acids Res · January 2009 dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene mod ... Full text Link to item Cite

Visual annotation of the gene database.

Journal Article Annu Int Conf IEEE Eng Med Biol Soc · 2009 The genes in NCBI databases are currently annotated with itemized text (Gene Reference Into Function, or GeneRIF). A previous work suggests that the visual presentation can be more effective when time and space are under heavy constraints. Here we report a ... Full text Link to item Cite

lumi: a pipeline for processing Illumina microarray.

Journal Article Bioinformatics · July 1, 2008 UNLABELLED: Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies. Unfortunately, most other analyses have not taken ad ... Full text Link to item Cite

Model-based variance-stabilizing transformation for Illumina microarray data.

Journal Article Nucleic Acids Res · February 2008 Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of technical replicates for Affymetrix and cDNA arrays, achi ... Full text Link to item Cite

The Gene Ontology project in 2008.

Journal Article Nucleic Acids Res · January 2008 The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been ext ... Full text Link to item Cite

A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays.

Journal Article Int J Comput Biol Drug Des · 2008 Out-of-memory problem was frequently encountered when processing thousands of CEL files using Bioconductor. We propose a divide-and-conquer strategy combined with randomised resampling to solve this problem. The CAMDA 2007 META-analysis data set which cont ... Full text Link to item Cite

Application of wavelet transform to the MS-based proteomics data preprocessing

Conference Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE · December 1, 2007 Mass Spectrometry (MS) has become one of the major detection technologies for high-throughput proteomics. The preprocessing of mass spectra is crucial for its subsequent analysis like biomarker discovery or protein identification. Wavelet transform is grad ... Full text Cite

OligoCalc: an online oligonucleotide properties calculator.

Journal Article Nucleic Acids Res · July 2007 We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and double-stranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficien ... Full text Link to item Cite

nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays.

Journal Article Biol Direct · May 31, 2007 BACKGROUND: Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completel ... Full text Link to item Cite

Interpreting microarray results with gene ontology and MeSH

Journal Article Methods in Molecular Biology · March 24, 2007 Methods are described to take a list of genes generated from a microarray experiment and interpret these results using various tools and ontologies. A workflow is described that details how to convert gene identifiers with SOURCE and MatchMiner and then us ... Full text Cite

Xanthusbase: adapting wikipedia principles to a model organism database.

Journal Article Nucleic Acids Res · January 2007 xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanisti ... Full text Link to item Cite

Interpreting microarray results with gene ontology and MeSH.

Journal Article Methods Mol Biol · 2007 Methods are described to take a list of genes generated from a microarray experiment and interpret these results using various tools and ontologies. A workflow is described that details how to convert gene identifiers with SOURCE and MatchMiner and then us ... Full text Link to item Cite

Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS).

Journal Article Methods Mol Biol · 2007 Detailed instruction is described for mapping unstructured, free text data into common biomedical concepts (drugs, diseases, anatomy, and so on) found in the Unified Medical Language System using MetaMap Transfer (MMTx). MMTx can be used in applications in ... Full text Link to item Cite

Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.

Journal Article Bioinformatics · September 1, 2006 MOTIVATION: 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 false positive rate is especially problematic in detecting peaks with low amplitudes. Usuall ... Full text Link to item Cite

The NUgene Project: eMR-facilitated biobanking

Conference CELL PRESERVATION TECHNOLOGY · September 1, 2006 Link to item Cite

The NUgene Project: Biospecimen informatics system design

Conference CELL PRESERVATION TECHNOLOGY · September 1, 2006 Link to item Cite

Improved prediction of treatment response using microarrays and existing biological knowledge.

Journal Article Pharmacogenomics · April 2006 A desired application for microarrays in the clinic is to predict treatment response from an often diverse patient population. We present a method for analyzing microarray data that is predicated on biological pathway and function knowledge as opposed to a ... Full text Link to item Cite

Annotating nonspecific SAGE tags with microarray data.

Journal Article Genomics · January 2006 SAGE (serial analysis of gene expression) detects transcripts by extracting short tags from the transcripts. Because of the limited length, many SAGE tags are shared by transcripts from different genes. Relying on sequence information in the general gene e ... Full text Link to item Cite

The Gene Ontology (GO) project in 2006.

Journal Article Nucleic Acids Res · January 1, 2006 The Gene Ontology (GO) project (http://www.geneontology.org) develops and uses a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://song.sourceforge.net/). The GO Consortium contin ... Full text Link to item Cite

dictyBase, the model organism database for Dictyostelium discoideum.

Journal Article Nucleic Acids Res · January 1, 2006 dictyBase (http://dictybase.org) is the model organism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized i ... Full text Link to item Cite

dictyBase, the model organism database for Dictyostelium discoideum.

Journal Article Nucleic acids research · January 1, 2006 dictyBase (http://dictybase.org) is the model organism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized i ... Full text Cite

What is mzXML good for?

Journal Article Expert Rev Proteomics · December 2005 mzXML (extensible markup language) is one of the pioneering data formats for mass spectrometry-based proteomics data collection. It is an open data format that has benefited and evolved as a result of the input of many groups, and it continues to evolve. D ... Full text Link to item Cite

Irrational exuberance in clinical proteomics.

Journal Article Clin Cancer Res · November 15, 2005 Full text Link to item Cite

The case for strategic international alliances to harness nutritional genomics for public and personal health.

Journal Article Br J Nutr · November 2005 Nutrigenomics is the study of how constituents of the diet interact with genes, and their products, to alter phenotype and, conversely, how genes and their products metabolise these constituents into nutrients, antinutrients, and bioactive compounds. Resul ... Full text Link to item Cite

Large-scale mutagenesis of the mouse to understand the genetic bases of nervous system structure and function.

Journal Article Brain Res Mol Brain Res · December 20, 2004 N-ethyl-N-nitrosourea (ENU) mutagenesis is presented as a powerful approach to developing models for human disease. The efforts of three NIH Mutagenesis Centers established for the detection of neuroscience-related phenotypes are described. Each center has ... Full text Link to item Cite

Identification of genes contributing to the obese yellow Avy phenotype: caloric restriction, genotype, diet x genotype interactions.

Journal Article Physiol Genomics · August 11, 2004 The incidence and severity of obesity and type 2 diabetes are increasing in Western societies. The progression of obesity to type 2 diabetes is gradual with overlapping symptoms of insulin resistance, hyperinsulinemia, hyperglycemia, dyslipidemias, ion imb ... Full text Link to item Cite

Mapping and characterization of Noerg-1 mutation in mouse

Conference INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE · April 1, 2004 Link to item Cite

dictyBase: a new Dictyostelium discoideum genome database.

Journal Article Nucleic Acids Res · January 1, 2004 Dictyostelium discoideum is a powerful and genetically tractable model system used for the study of numerous cellular molecular mechanisms including chemotaxis, phagocytosis and signal transduction. The past 2 years have seen a significant expansion in the ... Full text Link to item Cite

The Gene Ontology (GO) database and informatics resource.

Journal Article Nucleic Acids Res · January 1, 2004 The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of gen ... Full text Link to item Cite

dictyBase: A new Dictyostelium discoideum genome database

Journal Article Nucleic Acids Research · January 1, 2004 Dictyostelium discoideum is a powerful and genetically tractable model system used for the study of numerous cellular molecular mechanisms including chemotaxis, phagocytosis and signal transduction. The past 2 years have seen a significant expansion in the ... Cite

The Gene Oncology (GO) database and informatics resource

Journal Article Nucleic Acids Research · January 1, 2004 The Gene Ontology (GO) project (http://www.geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of gene ... Cite

DNA banking study in an ethnically diverse urban university hospital.

Conference AMERICAN JOURNAL OF HUMAN GENETICS · November 1, 2003 Link to item Cite

An assessment of cancer clinical trials vocabulary and IT infrastructure in the U.S.

Conference Proc AMIA Symp · 2001 Twenty-three cancer research centers in the U.S. were assessed to determine data standards, vocabularies, and information infrastructure used in support of clinical trials. Eighteen of the 23 responded. Major findings were related to: 1) clinical trials in ... Link to item Cite

The SV40 core sequence functions as a repressor element in yeast.

Journal Article J Biol Chem · November 15, 1991 Our previous studies showed that the AP-1 recognition element (ARE) present within the SV40 72-base pair (bp) enhancer will activate transcription in yeast when placed upstream of a truncated CYC1 promoter. However, the AP-2/AP-3 recognition element (also ... Link to item Cite

The Saccharomyces and Drosophila heat shock transcription factors are identical in size and DNA binding properties.

Journal Article Cell · February 13, 1987 The heat shock transcription factor (HSTF) has been purified to apparent homogeneity from S. cerevisiae and D. melanogaster by sequence-specific DNA-affinity chromatography. A synthetic oligonucleotide containing an hsp83-like heat shock element (HSE) was ... Full text Link to item Cite