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A novel framework for increasing research transparency: Exploring the connection between diversity and innovation.
PLoS One
January 2025
Department of Agricultural Economics, Oklahoma State University, Stillwater, Oklahoma, United States of America.
A split sample/dual method research protocol is demonstrated to increase transparency while reducing the probability of false discovery. We apply the protocol to examine whether diversity in ownership teams increases or decreases the likelihood of a firm reporting a novel innovation using data from the 2018 United States Census Bureau's Annual Business Survey. Transparency is increased in three ways: 1) all specification testing and identifying potentially productive models is done in an exploratory subsample that 2) preserves the validity of hypothesis test statistics from de novo estimation in the holdout confirmatory sample with 3) all findings publicly documented in an earlier registered report and in this journal publication.
View Article and Find Full Text PDFSemblans: Automated assembly and processing of RNA-Seq data.
Bioinformatics
January 2025
Department of Biological Sciences, University of Illinois at Chicago, Illinois 60607, United States.
Motivation: Recent advancements in parallel sequencing methods have precipitated a surge in publicly available short-read sequence data. This has encouraged the development of novel computational tools for the de novo assembly of transcriptomes from RNA-seq data. Despite the availability of these tools, performing an end-to-end transcriptome assembly remains a programmatically involved task necessitating familiarity with best practices.
View Article and Find Full Text PDFWhole-genome automated assembly pipeline for strains from reference, and clinical samples using the integrated CtGAP pipeline.
NAR Genom Bioinform
March 2025
Departments of Medicine and Pediatrics, Division of Infectious Diseases and Global Health, University of California San Francisco School of Medicine, 550 16th Street, 4th Floor Mission Hall, San Francisco, CA, 94158, USA.
Whole genome sequencing (WGS) is pivotal for the molecular characterization of ()-the leading bacterial cause of sexually transmitted infections and infectious blindness worldwide. WGS can inform epidemiologic, public health and outbreak investigations of these human-restricted pathogens. However, challenges persist in generating high-quality genomes for downstream analyses given its obligate intracellular nature and difficulty with propagation.
View Article and Find Full Text PDFNovel Copy Number Deletion Involving Associated With Epilepsy, Tremor, and Intellectual Disability.
Clin Case Rep
January 2025
Copy number variations (CNVs) contribute to various disorders including intellectual disability, developmental disorders, and cancer. This study identifies a de novo 2.62 Mb deletion at 6q22.
View Article and Find Full Text PDFSibling similarity can reveal key insights into genetic architecture.
Elife
January 2025
Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, United States.
The use of siblings to infer the factors influencing complex traits has been a cornerstone of quantitative genetics. Here, we utilise siblings for a novel application: the inference of genetic architecture, specifically that relating to individuals with extreme trait values (e.g.
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