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CRISPR-array-mediated imaging of non-repetitive and multiplex genomic loci in living cells
Dynamic imaging of genomic loci is key for understanding gene regulation, but methods for imaging genomes, in particular non-repetitive DNAs, are...
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quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data
The volume of public proteomics data is rapidly increasing, causing a computational challenge for large-scale reanalysis. Here, we introduce quantms (
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Systematic comparison of sequencing-based spatial transcriptomic methods
Recent developments of sequencing-based spatial transcriptomics (sST) have catalyzed important advancements by facilitating transcriptome-scale...
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Gapr for large-scale collaborative single-neuron reconstruction
Whole-brain analysis of single-neuron morphology is crucial for unraveling the complex structure of the brain. However, large-scale neuron...
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Special issue: Multiscale simulations of DNA from electrons to nucleosomes
This editorial for Volume 16, Issue 3 of Biophysical Reviews highlights the three-dimensional structural and dynamic information encoded in DNA...
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A high-efficiency transient expression system mediated by Agrobacterium tumefaciens in Spinacia oleracea leaves
BackgroundOptimization of a highly efficient transient expression system is critical for the study of gene function, particularly in those plants in...
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Observing isolated synaptic vesicle association and fusion ex vivo
Here, we present a protocol for isolating functionally intact glutamatergic synaptic vesicles from whole-mouse brain tissue and using them in a...
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An improved bacterial mRNA enrichment strategy in dual RNA sequencing to unveil the dynamics of plant-bacterial interactions
BackgroundDual RNA sequencing is a powerful tool that enables a comprehensive understanding of the molecular dynamics underlying plant-microbe...
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Predicting glycan structure from tandem mass spectrometry via deep learning
Glycans constitute the most complicated post-translational modification, modulating protein activity in health and disease. However, structural...
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Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
Spatial epigenetic map** of tissues enables the study of gene regulation programs and cellular functions with the dependency on their local tissue...
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Pufferfish gasdermin Ea is a significant player in the defense against bacterial pathogens
Gasdermins (GSDMs) are proteins cleaved by caspase (CASP) to trigger pyroptosis. In teleosts, pyroptosis is mediated by gasdermin E (GSDME). The...
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Exploring the biogeography, morphology, and phylogeny of the condylostomatid ciliates (Alveolata, Ciliophora, Heterotrichea), with establishment of four new Condylostoma species and a revision including redescriptions of five species found in China
Species of the ciliate class Heterotrichea Stein, 1859 are a cosmopolitan group of unicellular eukaryotic microorganisms, many of which have been...
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Structure-based prediction of protein-nucleic acid binding using graph neural networks
Protein-nucleic acid (PNA) binding plays critical roles in the transcription, translation, regulation, and three-dimensional organization of the...
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Characterizing the structure of mouse behavior using Motion Sequencing
Spontaneous mouse behavior is composed from repeatedly used modules of movement (e.g., rearing, running or grooming) that are flexibly placed into...
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Matrine-loaded self-adhesive swelling microneedle for inflammation regulation to improve eczema treatment
Eczema is a common chronic dermatological disease. Conventional treatments exhibit limited efficacy due to fast drug release resulting in short-term...
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Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and...
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Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling and cloud-native open-source tools
Contemporary pose estimation methods enable precise measurements of behavior via supervised deep learning with hand-labeled video frames. Although...
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Non-destructive wood identification using X-ray µCT scanning: which resolution do we need?
BackgroundTaxonomic identification of wood specimens provides vital information for a wide variety of academic (e.g. paleoecology, cultural heritage...
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Combining the fractional order derivative and machine learning for leaf water content estimation of spring wheat using hyper-spectral indices
Leaf water content (LWC) is a vital indicator of crop growth and development. While visible and near-infrared (VIS–NIR) spectroscopy makes it...
