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MSI-DTI: predicting drug-target interaction based on multi-source information and multi-head self-attention.
- Published in:
- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae238
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- Article
Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.
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- 2024
- Publication type:
- Correction Notice
Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae247
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Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae241
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A perspective on genetic and polygenic risk scores—advances and limitations and overview of associated tools.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae240
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CPADS: a web tool for comprehensive pancancer analysis of drug sensitivity.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae237
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- Article
Computational deconvolution of DNA methylation data from mixed DNA samples.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae234
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- Article
Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae233
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- Article
SGCLDGA: unveiling drug–gene associations through simple graph contrastive learning.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae231
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- Article
Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs).
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae230
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- Article
AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae229
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- Article
scMNMF: a novel method for single-cell multi-omics clustering based on matrix factorization.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae228
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Contrastive learning for enhancing feature extraction in anticancer peptides.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae220
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- Article
Correction to: A new paradigm for applying deep learning to protein–ligand interaction prediction.
- Published in:
- 2024
- Publication type:
- Correction Notice
Analysis of Emerging Variants of Turkey Reovirus using Machine Learning.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae224
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- Article
Towards multi-omics synthetic data integration.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae213
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Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae221
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- Article
Optimal fusion of genotype and drug embeddings in predicting cancer drug response.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae227
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- Article
TransPTM: a transformer-based model for non-histone acetylation site prediction.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae219
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- Article
FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae223
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- Article
Removing unwanted variation between samples in Hi-C experiments.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae217
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- Article
Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae216
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- Article
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae215
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- Article
TransAC4C—a novel interpretable architecture for multi-species identification of N4-acetylcytidine sites in RNA with single-base resolution.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae200
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- Article
PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae218
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- Article
DDID: a comprehensive resource for visualization and analysis of diet–drug interactions.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae212
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- Article
Response to Letter to Editor 'Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine'.
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- 2024
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- Publication type:
- Letter to the Editor
Predicting TCR sequences for unseen antigen epitopes using structural and sequence features.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae210
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- Article
Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae214
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- Publication type:
- Article
A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae208
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- Article
AI identifies potent inducers of breast cancer stem cell differentiation based on adversarial learning from gene expression data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae207
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- Article
GSScore: a novel Graphormer-based shell-like scoring method for protein–ligand docking.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae201
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- Article
Single-cell RNA sequencing data imputation using bi-level feature propagation.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae209
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- Article
scCRT: a contrastive-based dimensionality reduction model for scRNA-seq trajectory inference.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae204
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- Article
scEWE: high-order element-wise weighted ensemble clustering for heterogeneity analysis of single-cell RNA-sequencing data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae203
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- Article
Revealing cell–cell communication pathways with their spatially coupled gene programs.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae202
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- Article
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae206
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- Article
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae205
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- Article
Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae199
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- Article
CPPLS-MLP: a method for constructing cell–cell communication networks and identifying related highly variable genes based on single-cell sequencing and spatial transcriptomics data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae198
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- Article
PanDepth, an ultrafast and efficient genomic tool for coverage calculation.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae197
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- Article
DeepSS2GO: protein function prediction from secondary structure.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae196
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- Publication type:
- Article
BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae195
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- Article
DEGAP: Dynamic elongation of a genome assembly path.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae194
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- Article
scBOL: a universal cell type identification framework for single-cell and spatial transcriptomics data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae188
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- Article
SC-Track: a robust cell-tracking algorithm for generating accurate single-cell lineages from diverse cell segmentations.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae192
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- Article
Genotypic–phenotypic landscape computation based on first principle and deep learning.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae191
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- Article
CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae190
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- Publication type:
- Article
SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae189
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- Publication type:
- Article
Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation.
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- Briefings in Bioinformatics, 2024, v. 25, n. 3, p. 1, doi. 10.1093/bib/bbae193
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- Article