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An open-source, automated, and cost-effective platform for COVID-19 diagnosis and rapid portable genomic surveillance using nanopore sequencing
The COVID-19 pandemic, caused by SARS-CoV-2, has emphasized the necessity for scalable diagnostic workflows using locally produced reagents and basic...
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An open source knowledge graph ecosystem for the life sciences
Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have...
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Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer
Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis...
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GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas
The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is a prospective cohort study of nearly 155,000 U.S. volunteers aged 55–74...
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MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes
Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets...
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Monkeypox virus genomic accordion strategies
The 2023 monkeypox (mpox) epidemic was caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971....
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Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae
Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements....
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Synthetic reversed sequences reveal default genomic states
Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution,...
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Structural, genomic information and computational analysis of emerging coronavirus (SARS-CoV-2)
BackgroundThe emerging viral pandemic worldwide is associated with a novel coronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2)....
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The landscape of genomic structural variation in Indigenous Australians
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically...
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Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life
In this study, we investigate how an organism’s codon usage bias can serve as a predictor and classifier of various genomic and evolutionary traits...
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Parallel and convergent genomic changes underlie independent subterranean colonization across beetles
Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or...
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Genomic data in the All of Us Research Program
Comprehensively map** the genetic basis of human disease across diverse individuals is a long-standing goal for the field of human genetics
1 –4 . The...
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Uniform genomic data analysis in the NCI Genomic Data Commons
The goal of the National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of...
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Genomic characteristics and comparative genomics analysis of Salmonella enterica subsp. enterica serovar Thompson isolated from an outbreak in South Korea
Salmonella infections represent an important public health problem. In 2018, a multistate outbreak of S. enterica subsp. enterica serovar Thompson...
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Environment and taxonomy shape the genomic signature of prokaryotic extremophiles
This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible...
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A genomic toolkit for winged bean Psophocarpus tetragonolobus
A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from...
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Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm
In this study, genomic and plasmid characteristics of Escherichia coli were determined with the aim of deducing how mcr genes may have spread on a...
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Genomic characterization of cervical lymph node metastases in papillary thyroid carcinoma following the Chornobyl accident
Childhood radioactive iodine exposure from the Chornobyl accident increased papillary thyroid carcinoma (PTC) risk. While cervical lymph node...
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Visualizing genomic characteristics across an RNA-Seq based reference landscape of normal and neoplastic brain
In order to better understand the relationship between normal and neoplastic brain, we combined five publicly available large-scale datasets,...
