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Advancing drug–target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05593-6
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BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05601-9
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PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05606-4
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GPDRP: a multimodal framework for drug response prediction with graph transformer.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05618-0
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PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05589-2
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IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05624-2
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ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05599-0
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PWSC: a novel clustering method based on polynomial weight-adjusted sparse clustering for sparse biomedical data and its application in cancer subtyping.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05595-4
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Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05598-1
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PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05613-5
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TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05615-3
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scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05579-4
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Cellstitch: 3D cellular anisotropic image segmentation via optimal transport.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05608-2
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A novel and innovative cancer classification framework through a consecutive utilization of hybrid feature selection.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05605-5
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Machine learning-based donor permission extraction from informed consent documents.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05568-7
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- Article
A compressed large language model embedding dataset of ICD 10 CM descriptions.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05597-2
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- Article
Subtyping irritable bowel syndrome using cluster analysis: a systematic review.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05567-8
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ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05602-8
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- Article
DL-PPI: a method on prediction of sequenced protein–protein interaction based on deep learning.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05594-5
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PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science, and its application on natural product (NP) occurrence database processing.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05588-3
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Twnbiome: a public database of the healthy Taiwanese gut microbiome.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05585-6
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Predicting potential microbe-disease associations based on auto-encoder and graph convolution network.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05611-7
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Performance analysis of conventional and AI-based variant callers using short and long reads.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05596-3
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Rendering protein mutation movies with MutAmore.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05610-8
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primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05609-1
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A score-based method of immune status evaluation for healthy individuals with complete blood cell counts.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05603-7
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- Article
An oscillating reaction network with an exact closed form solution in the time domain.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05600-w
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- Article
Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05604-6
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- Article
Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05529-0
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- Article
CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05477-9
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- Article
Detection of continuous hierarchical heterogeneity by single-cell surface antigen analysis in the prognosis evaluation of acute myeloid leukaemia.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05561-0
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- Article
AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05577-6
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- Article
Transformer-based tool recommendation system in Galaxy.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05573-w
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pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05578-5
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- Article
scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05563-y
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- Article
Predicting anticancer synergistic drug combinations based on multi-task learning.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05524-5
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- Article
Protein–protein interaction site prediction by model ensembling with hybrid feature and self-attention.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05592-7
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- Article
HostNet: improved sequence representation in deep neural networks for virus-host prediction.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05582-9
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- Article
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05583-8
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- Article
Completing a genomic characterisation of microscopic tumour samples with copy number.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05576-7
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- Article
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05566-9
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- Article
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05574-9
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- Article
Machine learning-based approaches for ubiquitination site prediction in human proteins.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05581-w
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- Article
CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05571-y
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- Article
A cell abundance analysis based on efficient PAM clustering for a better understanding of the dynamics of endometrial remodelling.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05569-6
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- Article
Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05553-0
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- Article
Relating mutational signature exposures to clinical data in cancers via signeR 2.0.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05550-3
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- Article
Similarity-assisted variational autoencoder for nonlinear dimension reduction with application to single-cell RNA sequencing data.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05552-1
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- Article
Optimizing diabetes classification with a machine learning-based framework.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05467-x
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- Article
Image-centric compression of protein structures improves space savings.
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- BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05570-z
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