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Article
Open AccessIntercellular cross-talk through lineage-specific gap junction of cancer-associated fibroblasts related to stromal fibrosis and prognosis
Stromal fibrosis in cancer is usually associated with poor prognosis and chemotherapy resistance. It is thought to be caused by fibroblasts; however, the exact mechanism is not yet well understood. The study a...
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Article
Open AccessS-Pred: protein structural property prediction using MSA transformer
Predicting the local structural features of a protein from its amino acid sequence helps its function prediction to be revealed and assists in three-dimensional structural modeling. As the sequence-structure g...
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Open AccessAuthor Correction: Deep learning method for comet segmentation and comet assay image analysis
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Open AccessA-Prot: protein structure modeling using MSA transformer
The accuracy of protein 3D structure prediction has been dramatically improved with the help of advances in deep learning. In the recent CASP14, Deepmind demonstrated that their new version of AlphaFold (AF) p...
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Article
Open AccessRetrosynthetic reaction pathway prediction through neural machine translation of atomic environments
Designing efficient synthetic routes for a target molecule remains a major challenge in organic synthesis. Atom environments are ideal, stand-alone, chemically meaningful building blocks providing a high-resol...
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Article
Open AccessSubstructure-based neural machine translation for retrosynthetic prediction
With the rapid improvement of machine translation approaches, neural machine translation has started to play an important role in retrosynthesis planning, which finds reasonable synthetic pathways for a target...
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Article
Open AccessDeep learning method for comet segmentation and comet assay image analysis
Comet assay is a widely used method, especially in the field of genotoxicity, to quantify and measure DNA damage visually at the level of individual cells with high sensitivity and efficiency. Generally, compu...
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Article
TaF: a web platform for taxonomic profile-based fungal gene prediction
The accurate prediction and annotation of gene structures from the genome sequence of an organism enable genome-wide functional analyses to obtain insight into the biological properties of an organism.
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Article
Open AccessComparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes
Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial ti...
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Open AccessThe first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures
The cinereous vulture, Aegypius monachus, is the largest bird of prey and plays a key role in the ecosystem by removing carcasses, thus preventing the spread of diseases. Its feeding habits force it to cope with ...
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Open AccessWhole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan
Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This r...
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Open AccessGenome-wide analysis of DNA methylation patterns in horse
DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and ...
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Article
Open AccessMinke whale genome and aquatic adaptation in cetaceans
Jung-Hyun Lee, Jong Bhak and their colleagues report the whole-genome sequencing and de novo assembly of a male minke whale genome, as well as the genome sequences of three additional minke whales, a fin whale, a...
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Open AccessThe tiger genome and comparative analysis with lion and snow leopard genomes
Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white ...
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Open AccessWhole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq
Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is av...
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Open AccessGalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions
Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is challenging to obtain structures more accurate th...
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Article
Open AccessA protein domain interaction interface database: InterPare
Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Ratio...
