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iProL: identifying DNA promoters from sequence information based on Longformer pre-trained model
Promoters are essential elements of DNA sequence, usually located in the immediate region of the gene transcription start sites, and play a critical...
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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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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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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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PxBLAT: an efficient python binding library for BLAT
BackgroundWith the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for...
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Leveraging permutation testing to assess confidence in positive-unlabeled learning applied to high-dimensional biological datasets
BackgroundCompared to traditional supervised machine learning approaches employing fully labeled samples, positive-unlabeled (PU) learning techniques...
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iGenSig-Rx: an integral genomic signature based white-box tool for modeling cancer therapeutic responses using multi-omics data
Multi-omics sequencing is poised to revolutionize clinical care in the coming decade. However, there is a lack of effective and interpretable...
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EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction
BackgroundRecognition of enhancer–promoter Interactions (EPIs) is crucial for human development. EPIs in the genome play a key role in regulating...
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Using GPT-4 to write a scientific review article: a pilot evaluation study
GPT-4, as the most advanced version of OpenAI’s large language models, has attracted widespread attention, rapidly becoming an indispensable AI tool...
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SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions
BackgroundTandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs...
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Minimization of occurrence of retained surgical items using machine learning and deep learning techniques: a review
Retained surgical items (RSIs) pose significant risks to patients and healthcare professionals, prompting extensive efforts to reduce their...
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CPMI: comprehensive neighborhood-based perturbed mutual information for identifying critical states of complex biological processes
BackgroundThere exists a critical transition or tip** point during the complex biological process. Such critical transition is usually accompanied...
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A deep learning framework for predicting disease-gene associations with functional modules and graph augmentation
BackgroundThe exploration of gene-disease associations is crucial for understanding the mechanisms underlying disease onset and progression, with...
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CAraCAl: CAMML with the integration of chromatin accessibility
BackgroundA vital step in analyzing single-cell data is ascertaining which cell types are present in a dataset, and at what abundance. In many...
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Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique
BackgroundAutomated hypothesis generation (HG) focuses on uncovering hidden connections within the extensive information that is publicly available....
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PyMulSim: a method for computing node similarities between multilayer networks via graph isomorphism networks
BackgroundIn bioinformatics, interactions are modelled as networks, based on graph models. Generally, these support a single-layer structure which...
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Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data
BackgroundSingle-cell RNA sequencing (sc-RNASeq) data illuminate transcriptomic heterogeneity but also possess a high level of noise, abundant...
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StatiCAL: an interactive tool for statistical analysis of biomedical data and scientific valorization
BackgroundIn the realm of biomedical research, the growing volume, diversity and quantity of data has escalated the demand for statistical analysis...
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Metric multidimensional scaling for large single-cell datasets using neural networks
Metric multidimensional scaling is one of the classical methods for embedding data into low-dimensional Euclidean space. It creates the...
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Unveiling wearables: exploring the global landscape of biometric applications and vital signs and behavioral impact
The development of neuroscientific techniques enabling the recording of brain and peripheral nervous system activity has fueled research in cognitive...
