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Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein–protein interfaces
BackgroundProtein–protein interactions (PPIs) are conveyed through binding interfaces or surface patches on proteins that become buried upon binding....
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The effect of data transformation on low-dimensional integration of single-cell RNA-seq
BackgroundRecent developments in single-cell RNA sequencing have opened up a multitude of possibilities to study tissues at the level of cellular...
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Assessing the reliability of point mutation as data augmentation for deep learning with genomic data
BackgroundDeep neural networks (DNNs) have the potential to revolutionize our understanding and treatment of genetic diseases. An inherent limitation...
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Cauchy hyper-graph Laplacian nonnegative matrix factorization for single-cell RNA-sequencing data analysis
Many important biological facts have been found as single-cell RNA sequencing (scRNA-seq) technology has advanced. With the use of this technology,...
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NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model
Copy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the...
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Revisiting the complexity of and algorithms for the graph traversal edit distance and its variants
The graph traversal edit distance (GTED), introduced by Ebrahimpour Boroojeny et al. (2018), is an elegant distance measure defined as the minimum...
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Fast, parallel, and cache-friendly suffix array construction
PurposeString indexes such as the suffix array ( sa ) and the closely related longest common prefix ( lcp ) array are fundamental objects in...
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Optimizing spatio-temporal correlation structures for modeling food security in Africa: a simulation-based investigation
This study investigates the impact of spatio- temporal correlation using four spatio-temporal models: Spatio-Temporal Poisson Linear Trend Model...
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Exploring combinations of dimensionality reduction, transfer learning, and regularization methods for predicting binary phenotypes with transcriptomic data
BackgroundNumerous transcriptomic-based models have been developed to predict or understand the fundamental mechanisms driving biological phenotypes....
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Orthogonal multimodality integration and clustering in single-cell data
Multimodal integration combines information from different sources or modalities to gain a more comprehensive understanding of a phenomenon. The...
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Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
BackgroundThe Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology....
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OrthoRefine: automated enhancement of prior ortholog identification via synteny
BackgroundIdentifying orthologs continues to be an early and imperative step in genome analysis but remains a challenging problem. While synteny...
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Improvements in viral gene annotation using large language models and soft alignments
BackgroundThe annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute...
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OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies
BackgroundThe results of high-throughput biology (‘omic’) experiments provide insight into biological mechanisms but can be challenging to explore,...
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Mora: abundance aware metagenomic read re-assignment for disentangling similar strains
BackgroundTaxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but...
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Machine-learning-based models to predict cardiovascular risk using oculomics and clinic variables in KNHANES
BackgroundRecent researches have found a strong correlation between the triglyceride-glucose (TyG) index or the atherogenic index of plasma (AIP) and...
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SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses
BackgroundThe reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a...
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Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning
BackgroundAccurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning,...
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Noisecut: a python package for noise-tolerant classification of binary data using prior knowledge integration and max-cut solutions
BackgroundClassification of binary data arises naturally in many clinical applications, such as patient risk stratification through ICD codes. One of...
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MMGAT: a graph attention network framework for ATAC-seq motifs finding
BackgroundMotif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of...
