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ggcoverage: an R package to visualize and annotate genome coverage for various NGS data
BackgroundVisualizing genome coverage is of vital importance to inspect and interpret various next-generation sequencing (NGS) data. Besides genome...
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Using deep learning to annotate the protein universe
Understanding the relationship between amino acid sequence and protein function is a long-standing challenge with far-reaching scientific and...
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FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
BackgroundGene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include...
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AnnoLnc: A One-Stop Portal to Systematically Annotate Novel Human Long Noncoding RNAs
While more than a hundred thousand long noncoding RNAs (lncRNAs) have been identified in human genome, their biological functions and regulation are...
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DDX3Y is likely the key spermatogenic factor in the AZFa region that contributes to human non-obstructive azoospermia
Non-obstructive azoospermia, the absence of sperm in the ejaculate due to disturbed spermatogenesis, represents the most severe form of male...
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IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics
BackgroundThe advent and continual improvement of high-throughput sequencing technologies has made immunoglobulin repertoire sequencing accessible...
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A Comparative Proteomics Study Revealing the Impact of Growing Region and Cultivar on Protein Expression in the Leaves of Nicotiana tabacum Plants
The physical and chemical properties of tobacco ( Nicotiana tabacum L.) plants are sensitive to changes in genetics and the environment. However, few...
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GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens
Novel methods that combine single cell RNA-seq with CRISPR screens enable high-throughput characterization of transcriptional changes caused by...
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ChromGene: gene-based modeling of epigenomic data
Various computational approaches have been developed to annotate epigenomes on a per-position basis by modeling combinatorial and spatial patterns...
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Identification of functionally important miRNA targeted genes associated with child obesity trait in genome-wide association studies
BackgroundGenome-wide association studies (GWAS) have uncovered thousands of genetic variants that are associated with complex human traits and...
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Differential spatial–temporal dynamics of Alexandrium species revealed using metabarcoding analysis by the 18S rDNA V4 region in Jiaozhou Bay, China
The dinoflagellate genus Alexandrium hosts many toxigenic species with remarkable negative influence on ecosystems and human health by develo**...
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Structural mutations of small single copy (SSC) region in the plastid genomes of five Cistanche species and inter-species identification
BackgroundCistanche is an important genus of Orobanchaceae , with critical medicinal, economic, and desertification control values. However, the...
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A Multi-Label Learning Framework for Predicting Chemical Classes and Biological Activities of Natural Products from Biosynthetic Gene Clusters
Natural products (NP) or secondary metabolites, as a class of small chemical molecules that are naturally synthesized by chromosomally clustered...
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MASI enables fast model-free standardization and integration of single-cell transcriptomics data
Single-cell transcriptomics datasets from the same anatomical sites generated by different research labs are becoming increasingly common. However,...
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topr: an R package for viewing and annotating genetic association results
BackgroundThe successful identification of genetic loci for complex traits in genome-wide association studies (GWAS) has resulted in thousands of...
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Comparative Genome Annotation
Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. A large proportion of such new genomes are...
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Septoglomus species dominate the arbuscular mycorrhiza of five crop plants in an arid region of northern Mexico
Arid zones represent 44% of the world's agricultural land where crops are exposed to stressful conditions, mainly water deficiency and high solar...
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Minimum information guidelines for experiments structurally characterizing intrinsically disordered protein regions
An unambiguous description of an experiment, and the subsequent biological observation, is vital for accurate data interpretation. Minimum...
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Region-specific expression of young small-scale duplications in the human central nervous system
BackgroundThe duplication of genes is one of the main genetic mechanisms that led to the gain in complexity of biological tissue. Although the...
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TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics
Transferring annotations of single-cell-, spatial- and multi-omics data is often challenging owing both to technical limitations, such as low spatial...
