A5020020080- SARS-CoV-2 and COVID-19 Research
- Cell Image Analysis Techniques
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- COVID-19 Clinical Research Studies
- Bacterial biofilms and quorum sensing
- Bioinformatics and Genomic Networks
- Microbial Community Ecology and Physiology
- Bacterial Genetics and Biotechnology
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Vaccine Coverage and Hesitancy
- Complex Network Analysis Techniques
- Scientific Computing and Data Management
- Immune responses and vaccinations
- HIV, Drug Use, Sexual Risk
- Immunotherapy and Immune Responses
- Genetics, Bioinformatics, and Biomedical Research
- Cardiac, Anesthesia and Surgical Outcomes
- Amyotrophic Lateral Sclerosis Research
- Evolutionary Algorithms and Applications
- Allergic Rhinitis and Sensitization
- Mobile Health and mHealth Applications
- Machine Learning and Data Classification
- Epigenetics and DNA Methylation
Johns Hopkins University
2017-2025
Johns Hopkins Medicine
2025
Stanford University
2021-2024
University of Pennsylvania
2019-2023
Translational Therapeutics (United States)
2019-2023
Swansea University
2016-2023
University of Massachusetts Chan Medical School
2022-2023
New York Medical College
2022
Duke University
2020-2021
Gordon and Betty Moore Foundation
2021
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation protein function. Results Here, we report on results third CAFA challenge, CAFA3, that featured expanded analysis over previous rounds, both in terms volume data analyzed types performed. In a novel major new development, predictions assessment goals drove some experimental assays, resulting functional annotations for...
The Influenza Research Database (IRD) is a U.S. National Institute of Allergy and Infectious Diseases (NIAID)-sponsored Bioinformatics Resource Center dedicated to providing bioinformatics support for influenza virus research. IRD facilitates the research development vaccines, diagnostics therapeutics against by comprehensive collection influenza-related data integrated from various sources, growing suite analysis visualization tools mining hypothesis generation, personal workbench spaces...
The objective of this study was to characterize the diagnostic timelines and their predictors in people with amyotrophic lateral sclerosis (ALS). Patients were identified through ALS billing codes. Time from presenting symptom first doctor visit, visit suspected diagnosis, confirmed diagnosis (total time) collected. Regression models used analyze delay. Three hundred four patients included analysis. Median total time 11.5 months. Diagnostic longer age > 60 years (p < 0.001), sporadic =...
Significance Pseudomonas aeruginosa , a versatile bacterium that lives in environmental habitats and causes life-threatening opportunistic infections, uses quorum sensing to coordinate gene expression. The lasR gene, which encodes quorum-sensing regulator, is often found have loss-of-function mutations clinical isolates. Interestingly, LasR− strains high activity of the oxygen-sensitive transcription factor Anr microoxic conditions. This report identifies characterizes an Anr-regulated...
Machine learning is a modern approach to problem-solving and task automation. In particular, machine concerned with the development applications of algorithms that can recognize patterns in data use them for predictive modeling. Artificial neural networks are particular class models evolved into what now described as deep learning. Given computational advances made last decade, be applied massive sets innumerable contexts. Therefore, has become its own subfield context biological research,...
The HER2 + subtype of human breast cancer is associated with the malignant transformation luminal ductal cells mammary epithelium. sequence analysis tumor DNA identifies loss function mutations and deletions MAP2 K4 K7 genes that encode direct activators JUN NH 2 -terminal kinase (JNK). We report in vitro studies epithelial CRISPR-induced MAPK MAP2K components JNK pathway caused no change growth 2D culture, but these promoted cell proliferation 3D culture. Analysis gene expression signatures...
A fundamental characteristic of multicellular organisms is the specialization functional cell types through process differentiation. These specialized not only characterize normal functioning different organs and tissues, they can also be used as cellular biomarkers a variety disease states therapeutic/vaccine responses. In order to serve reference for type representation, Cell Ontology has been developed provide standard nomenclature defined comparative analysis biomarker discovery....
Enterovirus D68 (EV-D68) caused a severe respiratory illness outbreak in the United States 2014. Reports of acute flaccid myelitis (AFM)/paralysis (AFP) several independent epidemiological clusters children with detectable EV-D68 have raised concerns that genetic changes could be causing increased disease severity and neurological symptoms. To explore potential link between variations symptom changes, we performed series comparative genomic analyses 2014 isolate sequences using data...
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions people with disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity other coronaviruses that infect humans allowed for rapid insight into mechanisms it uses human hosts, as well ways immune system can respond. Here, we contextualize SARS-CoV-2 among identify what is known be inferred about behavior once inside a host....
Abstract The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation protein function. Here we report on results third CAFA challenge, CAFA3, that featured expanded analysis over previous rounds, both in terms volume data analyzed types performed. In a novel major new development, predictions assessment goals drove some experimental assays, resulting functional annotations for more than 1000...
Background: Neighborhood-level characteristics, including police activity, are associated with HIV and Hepatitis C injection risk-behaviors among people who inject drugs (PWID). However, the pathways through which these neighborhood perceptions shape individual-level risk behaviors unclear. This study helps to explain perceived between activity behavior (i.e., syringe/tool sharing in previous 6 months). Methods: A sample of (n = 366) PWIDs self-reported recent use were recruited using...
Introduction:To evaluate the effect of valveless trocar system (VTS) on intra-operative parameters, peri-operative outcomes, and 30-day postoperative complications in patients undergoing robotic-assisted laparoscopic prostatectomy.Methods:A total 200 consecutive Robot-assisted radical prostatectomy by a single surgeon were prospectively evaluated using either (n = 100) or standard trocars 100). Patient demographics, length stay, presence absence nausea vomiting, analog pain score at 0–6...
Zika virus (ZIKV) is a member of the Flavivirus genus positive-sense single-stranded RNA viruses, which includes Dengue, West Nile, Yellow Fever, and other mosquito-borne arboviruses. Infection by ZIKV can be difficult to distinguish from infection Flaviviruses due high sequence similarity, serum antibody cross-reactivity, co-circulation in endemic areas. Indeed, existing serological methods are not able consistently differentiate Flaviviruses, makes it extremely accurately calculate...
Abstract This study was undertaken to address the increasing need for a strategic approach industry–science data collections in face of reducing resources and growing evidence fisheries management. The aim evaluate progress development plans procedures that can be employed collect, record use fishing industry knowledge base managing fisheries. achieved by reviewing industry‐led initiatives already or ongoing within United Kingdom document how these projects have/are incorporating into...
In the past two decades, scientists in different laboratories have assayed gene expression from millions of samples. These experiments can be combined into compendia and analyzed collectively to extract novel biological patterns. Technical variability, or "batch effects," may result combining samples collected processed at times settings. Such variability distort our ability true underlying As more integrative analysis methods arise data collections get bigger, we must determine how...
After emerging in China late 2019, the novel coronavirus severe acute respiratory syndrome 2 (SARS-CoV-2) spread worldwide, and as of mid-2021, it remains a significant threat globally. Only few coronaviruses are known to infect humans, only two cause infections similar severity SARS-CoV-2:
ABSTRACT Although a large number of immune epitopes have been identified in the influenza A virus (IAV) hemagglutinin (HA) protein using various experimental systems, it is unclear which are involved protective immunity to natural infection humans. We developed data mining approach analyzing H1N1 human isolates identify HA regions that may be targeted by system and can predict evolution IAV. 16 amino acid sites experiencing diversifying selection during prepandemic seasonal strains found 11...
Computer-aided drug discovery and development approaches such as virtual screening, molecular docking, in silico property calculations have been utilized this effort to discover new lead compounds against tuberculosis. The enzyme 7,8-diaminopelargonic acid aminotransferase (BioA) Mycobacterium tuberculosis (Mtb), primarily involved the lipid biosynthesis pathway, was chosen target due fact that humans are not capable of synthesizing biotin endogenously. computational screening 4.5 million...