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Annotation of cell types (ACT): a convenient web server for cell type annotation
BackgroundThe advancement of single-cell sequencing has progressed our ability to solve biological questions. Cell type annotation is of vital...
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Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics
BackgroundMicrobiota are closely associated with human health and disease. Metaproteomics can provide a direct means to identify microbial proteins...
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Phytoplankton Image Segmentation and Annotation Method Based on Microscopic Fluorescence
Microscopic phytoplankton segmentation is an important part of water quality assessment. The segmentation of microscopic phytoplankton still faces...
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Examination of a novel expression-based gene-SNP annotation strategy to identify tissue-specific contributions to heritability in multiple traits
Complex traits show clear patterns of tissue-specific expression influenced by single nucleotide polymorphisms (SNPs), yet current strategies...
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CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that...
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Classification of the Epileptic Seizure Onset Zone Based on Partial Annotation
Epilepsy is a chronic disorder caused by excessive electrical discharges. Currently, clinical experts identify the seizure onset zone (SOZ) channel...
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Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells
Mutations in the BRCA2 gene are associated with sporadic and familial cancer, cause genomic instability and sensitize cancer cells to inhibition by...
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Human Cerebrospinal Fluid Sample Preparation and Annotation for Integrated Lipidomics and Metabolomics Profiling Studies
Cerebrospinal fluid (CSF) is a metabolically diverse biofluid and a key specimen for exploring biochemical changes in neurodegenerative diseases....
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Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation
High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale...
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Temporo-basal sulcal connections: a manual annotation protocol and an investigation of sexual dimorphism and heritability
The temporo-basal region of the human brain is composed of the collateral, the occipito-temporal, and the rhinal sulci. We manually rated (using a...
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MmisAT and MmisP: an efficient and accurate suite of variant analysis toolkit for primary mitochondrial diseases
Recent advances in next-generation sequencing (NGS) technology have greatly accelerated the need for efficient annotation to accurately interpret...
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De novo assembly and annotation of the mangrove cricket genome
ObjectivesThe mangrove cricket, Apteronemobius asahinai , shows endogenous activity rhythms that synchronize with the tidal cycle (i.e., a...
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Using optimal transport theory to optimize a deep convolutional neural network microscopic cell counting method
AbstractMedical image processing has become increasingly important in recent years, particularly in the field of microscopic cell imaging. However,...
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Prevalence of Pathogenic and Potentially Pathogenic Inborn Error of Immunity Associated Variants in Children with Severe Sepsis
PurposeOur understanding of inborn errors of immunity is increasing; however, their contribution to pediatric sepsis is unknown.
Methods ...
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Annotation of immune genes in the extinct thylacine (Thylacinus cynocephalus)
Advances in genome sequencing technology have enabled genomes of extinct species to be sequenced. However, given the fragmented nature of these...
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Unraveling metagenomics through long-read sequencing: a comprehensive review
The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of...
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Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries
We develop a method, SBayesRC, that integrates genome-wide association study (GWAS) summary statistics with functional genomic annotations to improve...
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VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
BackgroundViruses are central to microbial community structure in all environments. The ability to generate large metagenomic assemblies of mixed...
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Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A
The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough...
