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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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Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing...
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Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease
Single-cell-based methods such as flow cytometry or single-cell mRNA sequencing (scRNA-seq) allow deep molecular and cellular profiling of...
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Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling
BackgroundPan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic...
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scHolography: a computational method for single-cell spatial neighborhood reconstruction and analysis
Spatial transcriptomics has transformed our ability to study tissue complexity. However, it remains challenging to accurately dissect tissue...
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Reviving resilience: MEcPP-mediated ASK1-IMPα-9-TRP2 stress-responsive module
Chloroplasts are not only critical photosynthesis sites in plants, but they also participate in plastidial retrograde signaling in response to...
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Saliency-driven explainable deep learning in medical imaging: bridging visual explainability and statistical quantitative analysis
Deep learning shows great promise for medical image analysis but often lacks explainability, hindering its adoption in healthcare. Attribution...
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The variability of muscle–blubber interface temperature with activity level in a captive Risso’s dolphin (Grampus griseus)
BackgroundTo reduce heat loss underwater, marine mammals cover their bodies with insulation. Cetaceans in particular rely solely on blubber for...
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Machine learning prediction of prime editing efficiency across diverse chromatin contexts
The success of prime editing depends on the prime editing guide RNA (pegRNA) design and target locus. Here, we developed machine learning models that...
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Development of Cowpea (Vigna unguiculata) Mutant Lines for Dissecting Resilience to Drought Through Physiological and Molecular Crosstalk Analysis
Cowpea ( Vigna unguiculata ) is a legume crop widely grown in tropical and subtropical regions for human consumption and animal feeding. Despite this...
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Network-driven cancer cell avatars for combination discovery and biomarker identification for DNA damage response inhibitors
Combination therapy is well established as a key intervention strategy for cancer treatment, with the potential to overcome monotherapy resistance...
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Deciphering spatial domains from spatial multi-omics with SpatialGlue
Advances in spatial omics technologies now allow multiple types of data to be acquired from the same tissue slice. To realize the full potential of...
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Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs
BackgroundExtracellular vesicle-derived (EV)-miRNAs have potential to serve as biomarkers for the diagnosis of various diseases. miRNA microarrays...
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Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in develo** mouse neurons
BackgroundThe functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay...
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Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
BackgroundCopy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of...
