Works in BMC Bioinformatics, 2025, Vol 26, Issue 1
Results: 79
Validating a web application's use of genetic distance to determine helminth species boundaries and aid in identification.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06098-0
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TRain: T-cell receptor automated immunoinformatics.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06074-8
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Robust phylogenetic tree-based microbiome association test using repeatedly measured data for composition bias.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-024-06002-2
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- Article
Transfer learning for accelerated failure time model with microarray data.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06056-w
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FPGA-based accelerator for adaptive banded event alignment in nanopore sequencing data analysis.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-024-06011-1
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- Article
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06096-2
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SNPeBoT: a tool for predicting transcription factor allele specific binding.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06094-4
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Constructing multilayer PPI networks based on homologous proteins and integrating multiple PageRank to identify essential proteins.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06093-5
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GoldPolish-target: targeted long-read genome assembly polishing.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06091-7
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UTAP2: an enhanced user-friendly transcriptome and epigenome analysis pipeline.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06090-8
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- Article
An alignment-free method for phylogeny estimation using maximum likelihood: An alignment-free method for phylogeny estimation...: T. Zahin et al.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06080-w
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Cross-validation for training and testing co-occurrence network inference algorithms: Cross-validation for training and testing co-occurrence network...: D. Agyapong et al.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06083-7
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A distribution-guided Mapper algorithm.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06085-5
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Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06089-1
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ProToDeviseR: an automated protein topology scheme generator.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06088-2
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PyPropel: a Python-based tool for efficiently processing and characterising protein data.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06079-3
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Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06081-9
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- Article
Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model: Microbiome misclassification: M. D. Koslovsky.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06078-4
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Combining single-cell ATAC and RNA sequencing for supervised cell annotation: Multi-omic supervised annotation: J. Gill et al.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06084-6
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A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06051-1
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Conditional similarity triplets enable covariate-informed representations of single-cell data.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06069-5
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CamITree: a streamlined software for phylogenetic analysis of viral and mitochondrial genomes.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06034-2
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Mammalian piRNA target prediction using a hierarchical attention model.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06068-6
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- Article
HGATLink: single-cell gene regulatory network inference via the fusion of heterogeneous graph attention networks and transformer.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06071-x
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SequenceCraft: machine learning-based resource for exploratory analysis of RNA-cleaving deoxyribozymes.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-024-06019-7
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goloco: a web application to create genome scale information from surprisingly small experiments.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06070-y
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scFTAT: a novel cell annotation method integrating FFT and transformer.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06061-z
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Estimation of mosaic loss of Y chromosome cell fraction with genotyping arrays lacking coverage in the pseudoautosomal region.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06076-6
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BHCox: Bayesian heredity-constrained Cox proportional hazards models for detecting gene-environment interactions.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06077-5
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MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06075-7
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A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06055-x
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Harnessing pre-trained models for accurate prediction of protein-ligand binding affinity.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06064-w
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A novel weighted pseudo-labeling framework based on matrix factorization for adverse drug reaction prediction.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06053-z
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Identifying risk factors for Alzheimer's disease from multivariate longitudinal clinical data using temporal pattern mining.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-024-06018-8
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SEGT-GO: a graph transformer method based on PPI serialization and explanatory artificial intelligence for protein function prediction.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06059-7
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Using individual barcodes to increase quantification power of massively parallel reporter assays.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06065-9
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CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06046-y
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HarmonizR: blocking and singular feature data adjustment improve runtime efficiency and data preservation.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06073-9
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TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06058-8
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Correction: HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes.
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- 2025
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- Correction Notice
Omilayers: a Python package for efficient data management to support multi-omic analysis.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06067-7
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Accurate assembly of full-length consensus for viral quasispecies.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06045-z
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- Article
Direct coupling analysis and the attention mechanism: Direct Coupling...: F. Caredda, A. Pagnani.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06062-y
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AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06063-x
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CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06060-0
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BioLake: an RNA expression analysis framework for prostate cancer biomarker powered by data lakehouse.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06050-2
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Instance-level semantic segmentation of nuclei based on multimodal structure encoding: Instance-level semantic segmentation of nuclei based on multimodal...: B. Guan et al.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06066-8
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Hybrid generative adversarial network based on frequency and spatial domain for histopathological image synthesis.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06057-9
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Flexible analysis of spatial transcriptomics data (FAST): a deconvolution approach.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06054-y
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HDN-DDI: a novel framework for predicting drug-drug interactions using hierarchical molecular graphs and enhanced dual-view representation learning.
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- BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06052-0
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