Nicole L. Washington
A5025956553- Genomics and Rare Diseases
- SARS-CoV-2 and COVID-19 Research
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Genetic Associations and Epidemiology
- Animal Virus Infections Studies
- COVID-19 Clinical Research Studies
- Genomic variations and chromosomal abnormalities
- Scientific Computing and Data Management
- Botanical Studies and Applications
- BRCA gene mutations in cancer
- Invertebrate Taxonomy and Ecology
- Viral gastroenteritis research and epidemiology
- Genetics, Aging, and Longevity in Model Organisms
- Semantic Web and Ontologies
- Patient Safety and Medication Errors
- Hospital Admissions and Outcomes
- SARS-CoV-2 detection and testing
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Healthcare professionals’ stress and burnout
- Innovations in Medical Education
- Research Data Management Practices
- Advanced Proteomics Techniques and Applications
- Evolution and Genetic Dynamics
Helix (United States)
2019-2025
Double Helix (United States)
2024
Children's Hospital of Philadelphia
2018-2023
University of Pennsylvania
2019-2023
San Diego State University
2023
University of Washington
1966-2021
Accreditation Council for Graduate Medical Education
2021
Bayer (United States)
2021
Academic Pediatric Association
2021
Seattle University
2021
From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation still needed characterize how used help produce functional organism (see Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for Caenorhabditis elegans genome, and The modENCODE Consortium 1787 Drosophila melanogaster full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites,...
The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants be genes that have been characterized, model organisms recapitulate human or veterinary filling evolutionary gaps difficult, many resources must queried to find potentially significant genotype–phenotype associations. Non-human proven instrumental revealing...
There are few better examples of the need for data sharing than in rare disease community, where patients, physicians, and researchers must search "the needle a haystack" to uncover rare, novel causes within genome. Impeding pace discovery has been existence many small siloed datasets individual research or clinical laboratory databases and/or disease-specific organizations, hoping serendipitous occasions when two distant investigators happen learn they have phenotype common can "match"...
Abstract As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing infeasible at scale, especially in areas with limited resources, participation, or and/or sequencing capacity, which can also introduce biases 1–3 . RNA concentration wastewater successfully tracks regional infection dynamics provides less biased abundance estimates than 4,5 Tracking virus genomic sequences...
Numerous new disease-gene associations have been identified by whole-exome sequencing studies in the last few years. However, many cases remain unsolved due to sheer number of candidate variants remaining after common filtering strategies such as removing low quality and those deemed unlikely be pathogenic. The observation that each our genomes contains about 100 genuine loss-of-function makes identification causative mutation problematic when using these alone. We propose wealth genotype...
Scientists and clinicians who study genetic alterations disease have traditionally described phenotypes in natural language. The considerable variation these free-text descriptions has posed a hindrance to the important task of identifying candidate genes models for human diseases indicates need computationally tractable method mine data resources mutant phenotypes. In this study, we tested hypothesis that ontological annotation will facilitate discovery new genotype-phenotype relationships...
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...
It is increasingly recognized that SARS-CoV-2 can produce long-term complications after recovery from the acute effects of infection. Here, we report analysis 32 self-reported short and symptoms in a general adult population cohort comprised 357 COVID-19+ cases, 5,497 SARS-CoV-2-negative controls, 19,095 non-tested individuals. The majority our cases are mild, with only 9 having been hospitalized. Our results show 36.1% have lasting longer than 30 days, 14.8% still at least one symptom 90...
Summary As of January 2021, the highly transmissible B.1.1.7 variant SARS-CoV-2, which was first identified in United Kingdom (U.K.), has gained a strong foothold across world. Because sudden and rapid rise B.1.1.7, we investigated prevalence growth dynamics this States (U.S.), tracking it back to its early emergence onward local transmission. We found that RT-qPCR testing anomaly S gene target failure (SGTF), observed U.K., reliable proxy for detection. sequenced 212 SARS-CoV-2 genomes...
Abstract Background Recent data from genome-wide chromosome conformation capture analysis indicate that the human genome is divided into conserved megabase-sized self-interacting regions called topological domains. These domains form regulatory backbone of and are separated by boundary elements or barriers. Copy-number variations can potentially alter domain architecture deleting duplicating barriers thereby allowing enhancers neighboring to ectopically activate genes causing misexpression...
In an effort to comprehensively characterize the functional elements within genomes of important model organisms Drosophila melanogaster and Caenorhabditis elegans, NHGRI organism Encyclopaedia DNA Elements (modENCODE) consortium has generated enormous library genomic data along with detailed, structured information on all aspects experiments. The modMine database (http://intermine.modencode.org) described here been built by modENCODE Data Coordination Center allow broader research community...
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such depends on the discipline science humble bricks mortar that make integration possible; identifiers a core component this infrastructure. Drawing our experience work by other groups, we outline 10 lessons have learned about identifier qualities best practices facilitate large-scale integration. Specifically, propose actions...
The discovery of disease-causing mutations typically requires confirmation the variant or gene in multiple unrelated individuals, and a large number rare genetic diseases remain unsolved due to difficulty identifying second families. To enable secure sharing case records by clinicians disease scientists, we have developed PhenomeCentral portal (https://phenomecentral.org). Each record includes phenotypic description relevant information (exome candidate genes). identifies similar patients...
Medical diagnosis and molecular or biochemical confirmation typically rely on the knowledge of clinician. Although this is very difficult in extremely rare diseases, we hypothesized that recording patient phenotypes Human Phenotype Ontology (HPO) terms computationally ranking putative disease-associated sequence variants improves diagnosis, particularly for patients with atypical clinical profiles.
COVID-19 vaccines are safe and highly effective, but some individuals experience unpleasant reactions to vaccination. As the majority of adults in United States have received a vaccine this year, there is an unprecedented opportunity study genetics vaccination via surveys who already part genetic research studies. Here, we queried 17,440 participants Helix DNA Discovery Project Healthy Nevada about their Our genome-wide association identifies between severe difficulties with daily routine...
FER-1 is required for fusion of specialized vesicles, called membranous organelles, with the sperm plasma membrane during Caenorhabditis elegans spermiogenesis. To investigate its role in organelle fusion, we examined ten fer-1 mutations and found that they all cause same defect fusion. ferlin protein family are proteins four to seven C2 domains. These domains commonly mediate Ca2+ -dependent lipid-processing events. Most fall within these domains, showing have distinct, non-redundant...
<ns4:p>Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers making increased use ontological standards methods to capture the results such with one focus being comparison analysis phenotype information between species.</ns4:p><ns4:p>We have generated a cross-species ontology for human, mouse zebrafish that contains classes from Human Phenotype...