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De Novo Transcriptomic Analyses to Identify and Compare Allergens in Foods
Food allergens have been traditionally identified using biomolecular and immunological approaches. However, the techniques used in extracting...
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Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea
Chickpea ( Cicer arietinum L.)—an important legume crop cultivated in arid and semiarid regions—has limited genetic diversity. Efforts are being...
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Genome assembly in the telomere-to-telomere era
Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly — the process of reconstructing the genome...
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A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome
Advances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have...
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Genome-resolved metagenomics: a game changer for microbiome medicine
Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome...
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Next-Generation Sequencing
The next-generation sequencing platforms can generate a large amount of high-throughput sequencing data in a short span of time. Reference-based...
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RFGR: Repeat Finder for Complete and Assembled Whole Genomes and NGS Reads
Repetitive DNA sequences cause genomic instability and are important genetic markers. Identification of repeats is a critical step in genome...
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ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs
BackgroundSince the prolonged use of insecticidal proteins has led to toxin resistance, it is important to search for novel insecticidal protein...
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Sequencing-based analysis of microbiomes
Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on...
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Transcriptome Analysis of Persian Oak (Quercus brantii L.) Decline Using RNA-seq Technology
Since the late 1980s, the oak decline has affected the Zagros oak forests in western Iran. Persian oak ( Quercus brantii L.) the most important tree...
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Extraocular Motoneurons and Neurotrophism
Extraocular motoneurons are located in three brainstem nuclei: the abducens, trochlear and oculomotor. They control all types of eye movements by...
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Assembly of Coronaviruses and CoV-Like-Particles
Develo** SARS-CoV-2 virus-like particles assemblyVirus-like particle assembly (VLPs) systems is fundamental to understanding the biophysical...
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Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance
BackgroundIn nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural...
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First Insights into the Guar (Cyamopsis tetragonoloba (L.) Taub.) Genome of the ‘Vavilovskij 130’ Accession, Using Second and Third-Generation Sequencing Technologies
AbstractGuar ( Cyamopsis tetragonoloba (L.) Taub.) is becoming a popular industrial crop in response to industry demand for the guar gum extracted...
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Navigating bottlenecks and trade-offs in genomic data analysis
Genome sequencing and analysis allow researchers to decode the functional information hidden in DNA sequences as well as to study cell to cell...
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A Comprehensive Metagenome Study Identifies Distinct Biological Pathways in Asthma Patients: An In-Silico Approach
Asthma is a multifactorial disease with phenotypes and several clinical and pathophysiological characteristics. Besides innate and adaptive immune...
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Early change of plasma Epstein-Barr virus DNA load and the viral lytic genome level could positively predict clinical outcome in recurrent or metastatic nasopharyngeal carcinoma receiving anti-programmed cell death 1 monotherapy
PurposePatients with recurrent or metastatic nasopharyngeal carcinoma (RM-NPC) have proven benefit from anti-programmed cell death 1 (anti-PD-1)...
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Bioinformatics Algorithms and Software for Predicting Microbiomes
Over the last decade, bioinformatics approaches have been used extensively for analyzing microbiomes from various sources. Microbiomes can vary from...
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RepEnTools: an automated repeat enrichment analysis package for ChIP-seq data reveals hUHRF1 Tandem-Tudor domain enrichment in young repeats
BackgroundRepeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read...
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Evaluating metagenomic assembly approaches for biome-specific gene catalogues
BackgroundFor many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and...
