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MetaTron: advancing biomedical annotation empowering relation annotation and collaboration
BackgroundThe constant growth of biomedical data is accompanied by the need for new methodologies to effectively and efficiently extract...
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Universal chromatin state annotation of the mouse genome
A large-scale application of the “stacked modeling” approach for chromatin state discovery previously provides a single “universal” chromatin state...
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Re-annotation of the Liriodendron chinense genome identifies novel genes and improves genome annotation quality
Liriodendron chinense is a very popular tree used in landsca** because of its beautiful flowers and unique leaf shape. Although the L. chinense ...
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Manual correction of genome annotation improved alternative splicing identification of Artemisia annua
Gene annotation is essential for genome-based studies. However, algorithm-based genome annotation is difficult to fully and correctly reveal genomic...
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LiLA: lipid lung-based ATLAS built through a comprehensive workflow designed for an accurate lipid annotation
Accurate lipid annotation is crucial for understanding the role of lipids in health and disease and identifying therapeutic targets. However,...
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Structural and Functional Annotation of the Wheat Genome
Wheat genome sequencing has passed through major steps in a decade, starting from the sequencing of large contiguous sequences obtained from...
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Star allele search: a pharmacogenetic annotation database and user-friendly search tool of publicly available 1000 Genomes Project biospecimens
Here we describe a new public pharmacogenetic (PGx) annotation database of a large ( n = 3,202) and diverse biospecimen collection of 1000 Genomes...
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Galba: genome annotation with miniprot and AUGUSTUS
BackgroundThe Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack...
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Automatic annotation of the bHLH gene family in plants
BackgroundThe bHLH transcription factor family is named after the basic helix-loop-helix (bHLH) domain that is a characteristic element of their...
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Improving automatic GO annotation with semantic similarity
BackgroundAutomatic functional annotation of proteins is an open research problem in bioinformatics. The growing number of protein entries in public...
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Improvements in viral gene annotation using large language models and soft alignments
BackgroundThe annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute...
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Assembly, Annotation and Visualization of NGS Data
The next-generation sequencing technologies have revolutionized the field of agriculture with the advent of ever-evolving chemistries and a reduction...
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Cross-phyla protein annotation by structural prediction and alignment
BackgroundProtein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a few model...
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SVAT: Secure outsourcing of variant annotation and genotype aggregation
BackgroundSequencing of thousands of samples provides genetic variants with allele frequencies spanning a very large spectrum and gives invaluable...
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Advances in monolingual and crosslingual automatic disability annotation in Spanish
BackgroundUnlike diseases, automatic recognition of disabilities has not received the same attention in the area of medical NLP. Progress in this...
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Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis
BackgroundSingle-cell RNA-sequencing (scRNA-seq) has become a widely used tool for both basic and translational biomedical research. In scRNA-seq...
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Genome-wide annotation of protein-coding genes in pig
BackgroundThere is a need for functional genome-wide annotation of the protein-coding genes to get a deeper understanding of mammalian biology. Here,...
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Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline
Single-cell RNA-sequencing (scRNA-seq) offers functional insight into complex biology, allowing for the interrogation of cellular populations and...
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Draft assembly and annotation of the Cuban crocodile (Crocodylus rhombifer) genome
ObjectivesThe new data provide an important genomic resource for the Critically Endangered Cuban crocodile ( Crocodylus rhombifer ). Cuban crocodiles...
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De Novo Assembly and Annotation of the Siganus fuscescens (Houttuyn, 1782) Genome: Marking a Pioneering Advance for the Siganidae Family
This study presents the first draft genome of Siganus fuscescens , and thereby establishes the first whole-genome sequence for a species in the...
