AIMC Topic: Software

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MuCST: restoring and integrating heterogeneous morphology images and spatial transcriptomics data with contrastive learning.

Genome medicine Mar 13, 2025
Spatially resolved transcriptomics (SRT) simultaneously measure spatial location, histology images, and transcriptional profiles of cells or regions in undissociated tissues. Integrative analysis of multi-modal SRT data holds immense potential for un...
Computational Biology Gene Expression Profiling Transcriptome Image Processing, Computer-Assisted Humans Machine Learning Software
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RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning.

BMC biology Mar 11, 2025
BACKGROUND: RNA-binding proteins (RBPs) play crucial roles in many biological processes, and computationally identifying RNA-RBP interactions provides insights into the biological mechanism of diseases associated with RBPs.
Humans Deep Learning Computational Biology Software Binding Sites RNA-Binding Proteins RNA, Circular RNA
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BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.

NAR genomics and bioinformatics Mar 8, 2025
A terminator is a DNA region that ends the transcription process. Currently, multiple computational tools are available for predicting bacterial terminators. However, these methods are specialized for certain bacteria or terminator type (i.e. intrins...
Software Bacteria Terminator Regions, Genetic Computational Biology Neural Networks, Computer
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FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events.

Nature communications Mar 7, 2025
Non-targeted metabolomics holds great promise for advancing precision medicine and biomarker discovery. However, identifying compounds from tandem mass spectra remains a challenging task due to the incomplete nature of spectral reference libraries. A...
Metabolomics Tandem Mass Spectrometry Software Algorithms Neural Networks, Computer
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PredIDR2: Improving accuracy of protein intrinsic disorder prediction by updating deep convolutional neural network and supplementing DisProt data.

International journal of biological macromolecules Mar 5, 2025
Intrinsically disordered proteins (IDPs) or regions (IDRs) are widespread in proteomes, and involved in several important biological processes and implicated in many diseases. Many computational methods for IDR prediction are being developed to decre...
Intrinsically Disordered Proteins Software Convolutional Neural Networks Computational Biology Databases, Protein ROC Curve Neural Networks, Computer
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SeizyML: An Application for Semi-Automated Seizure Detection Using Interpretable Machine Learning Models.

Neuroinformatics Mar 3, 2025
Despite the vast number of publications reporting seizures and the reliance of the field on accurate seizure detection, there is a lack of open-source software tools in the scientific community for automating seizure detection based on electrographic...
Software Animals Mice Machine Learning Seizures Bayes Theorem Electroencephalography
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Artificial intelligence-driven 3D MRI of lumbosacral nerve root anomalies: accuracy, incidence, and clinical utility.

Neuroradiology Mar 1, 2025
PURPOSE: Lumbosacral nerve root anomalies are relatively rare but can be a risk factor for intraoperative nerve injury. However, it is often difficult to evaluate them with preoperative imaging. We developed a software that automatically generates th...
Humans Artificial Intelligence Lumbosacral Region Magnetic Resonance Imaging Spinal Nerve Roots Middle Aged Adolescent Child Aged Incidence Imaging, Three-Dimensional Adult Male Software Female
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Artificial intelligence-enabled lipid droplets quantification: Comparative analysis of NIS-elements Segment.ai and ZeroCostDL4Mic StarDist networks.

Methods (San Diego, Calif.) Feb 27, 2025
Lipid droplets (LDs) are dynamic organelles that are present in almost all cell types, with a particularly high prevalence in adipocytes. The phenotype of LDs in these cells reflects their maturity, metabolic activity and function. Although LDs quant...
Lipolysis Image Processing, Computer-Assisted Software Lipid Droplets Mice Microscopy, Confocal Adipocytes Neural Networks, Computer Animals 3T3-L1 Cells Deep Learning Artificial Intelligence
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Measuring kidney stone volume - practical considerations and current evidence from the EAU endourology section.

Current opinion in urology Feb 21, 2025
PURPOSE OF REVIEW: This narrative review provides an overview of the use, differences, and clinical impact of current methods for kidney stone volume assessment.
Humans Software Urology Kidney Calculi Reproducibility of Results Tomography, X-Ray Computed Ureteroscopy Predictive Value of Tests
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stDyer enables spatial domain clustering with dynamic graph embedding.

Genome biology Feb 20, 2025
Spatially resolved transcriptomics (SRT) data provide critical insights into gene expression patterns within tissue contexts, necessitating effective methods for identifying spatial domains. We introduce stDyer, an end-to-end deep learning framework ...
Humans Software Algorithms Deep Learning Gene Expression Profiling Cluster Analysis Transcriptome
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