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TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences
BackgroundMicroRNAs play a critical role in regulating gene expression by binding to specific target sites within gene transcripts, making the...
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A protein network refinement method based on module discovery and biological information
BackgroundThe identification of essential proteins can help in understanding the minimum requirements for cell survival and development to discover...
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TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing
BackgroundHigh-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce...
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Decoding dynamic miRNA:ceRNA interactions unveils therapeutic insights and targets across predominant cancer landscapes
Competing endogenous RNAs play key roles in cellular molecular mechanisms through cross-talk in post-transcriptional interactions. Studies on ceRNA...
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Biomedical semantic text summarizer
BackgroundText summarization is a challenging problem in Natural Language Processing, which involves condensing the content of textual documents...
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Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed)
BackgroundGenomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying...
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MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
BackgroundWith the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic...
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Evaluation of network-guided random forest for disease gene discovery
BackgroundGene network information is believed to be beneficial for disease module and pathway identification, but has not been explicitly utilized...
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Designing and delivering bioinformatics project-based learning in East Africa
BackgroundThe Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We...
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MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach
Protein toxins are defense mechanisms and adaptations found in various organisms and microorganisms, and their use in scientific research as...
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Biomarker discovery with quantum neural networks: a case-study in CTLA4-activation pathways
BackgroundBiomarker discovery is a challenging task due to the massive search space. Quantum computing and quantum Artificial Intelligence (quantum...
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Control of false discoveries in grouped hypothesis testing for eQTL data
BackgroundExpression quantitative trait locus (eQTL) analysis aims to detect the genetic variants that influence the expression of one or more genes....
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KEGG orthology prediction of bacterial proteins using natural language processing
BackgroundThe advent of high-throughput technologies has led to an exponential increase in uncharacterized bacterial protein sequences, surpassing...
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Pfp-fm: an accelerated FM-index
FM-indexes are crucial data structures in DNA alignment, but searching with them usually takes at least one random access per character in the query...
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Space-efficient computation of k-mer dictionaries for large values of k
Computing k -mer frequencies in a collection of reads is a common procedure in many genomic applications. Several state-of-the-art k -mer counters rely...
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DPI_CDF: druggable protein identifier using cascade deep forest
BackgroundDrug targets in living beings perform pivotal roles in the discovery of potential drugs. Conventional wet-lab characterization of drug...
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Multiple phenotype association tests based on sliced inverse regression
BackgroundJoint analysis of multiple phenotypes in studies of biological systems such as Genome-Wide Association Studies is critical to revealing the...
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CAT-DTI: cross-attention and Transformer network with domain adaptation for drug-target interaction prediction
Accurate and efficient prediction of drug-target interaction (DTI) is critical to advance drug development and reduce the cost of drug discovery....
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Predicting condensate formation of protein and RNA under various environmental conditions
BackgroundLiquid–liquid phase separation (LLPS) by biomolecules plays a central role in various biological phenomena and has garnered significant...
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CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny
BackgroundThe rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These...
