The intrinsic substrate specificity of the human tyrosine kinome
Nature » Bioinformatics
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1w ago
The intrinsic substrate specificity of the human tyrosine kinome An atlas of the substrate specificities for the human tyrosine kinome reveals diversity of motif specificities and enables identification of kinase–substrate relationships and kinase regulation in phosphoproteomics experiments ..read more
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Tracking single-cell evolution using clock-like chromatin accessibility loci
Nature » Bioinformatics
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1w ago
Tracking single-cell evolution using clock-like chromatin accessibility loci EpiTrace infers cell mitotic age and evolution from single-cell ATAC-seq data ..read more
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Spatial transcriptomics in health and disease
Nature » Bioinformatics
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1w ago
Spatial transcriptomics in health and disease Spatially resolved transcriptomic technologies enable the mapping of transcripts at single-cell or near single-cell resolution in a multiplex manner. This Review describes current and emerging spatial transcriptomic methods, their applications of relevance to kidney biology and remaining challenges for the field ..read more
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De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore
Nature » Bioinformatics
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1w ago
transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore ..read more
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A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers
Nature » Bioinformatics
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1w ago
A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers ..read more
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Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution
Nature » Bioinformatics
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1w ago
Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution The expansion of the genetic code with synthetic nucleotides has broadened our ability to evolve DNA as a functional material, but we lack analytical tools for the expanded alphabet. Here the authors demonstrate an enzyme-assisted method for the sequencing of six-letter DNA ..read more
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Decoding cell replicational age from single-cell ATAC-seq data
Nature » Bioinformatics
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1w ago
Decoding cell replicational age from single-cell ATAC-seq data The replicational age of single cells provides a temporal reference for tracking cell fate transition trajectories. The computational framework EpiTrace measures cell age using single-cell ATAC-seq data, specifically by considering chromatin accessibility at clock-like genomic loci, enabling the reconstruction of the history of developmental and pathological processes ..read more
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Optimized model architectures for deep learning on genomic data
Nature » Bioinformatics
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3w ago
Optimized model architectures for deep learning on genomic data Introducing GenomeNet-Architect, a neural architecture design framework that automatically optimises the overall layout of the architecture, the hyperparameters, and the training procedure of deep learning models for genome sequence data ..read more
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Identifying autism spectrum disorder from multi-modal data with privacy-preserving
Nature » Bioinformatics
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3w ago
Identifying autism spectrum disorder from multi-modal data with privacy-preserving ..read more
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Annotating cell types in single-cell ATAC data via the guidance of the underlying DNA sequences
Nature » Bioinformatics
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3w ago
Annotating cell types in single-cell ATAC data via the guidance of the underlying DNA sequences SANGO efficiently removed batch effects between the query and reference single-cell ATAC signals through the underlying genome sequences, to enable cell type assignment according to the reference data. The method achieved superior performance on diverse datasets and could detect unknown tumor cells, providing valuable functional biological signals ..read more
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