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Volume 25, Issue 3, May 2024
IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae179, https://doi.org/10.1093/bib/bbae179
Editorial
Integrated modeling of protein and RNA
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae139, https://doi.org/10.1093/bib/bbae139
Computational model for drug research
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae158, https://doi.org/10.1093/bib/bbae158
Articles
Meta-DHGNN: method for CRS-related cytokines analysis in CAR-T therapy based on meta-learning directed heterogeneous graph neural network
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae104, https://doi.org/10.1093/bib/bbae104
Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae109, https://doi.org/10.1093/bib/bbae109
Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae115, https://doi.org/10.1093/bib/bbae115
Generalized reporter score-based enrichment analysis for omics data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae116, https://doi.org/10.1093/bib/bbae116
scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae112, https://doi.org/10.1093/bib/bbae112
A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae119, https://doi.org/10.1093/bib/bbae119
Benchmarking digital PCR partition classification methods with empirical and simulated duplex data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae120, https://doi.org/10.1093/bib/bbae120
FAIR Header Reference genome: a TRUSTworthy standard
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae122, https://doi.org/10.1093/bib/bbae122
Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae123, https://doi.org/10.1093/bib/bbae123
DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae125, https://doi.org/10.1093/bib/bbae125
MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae127, https://doi.org/10.1093/bib/bbae127
IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae128, https://doi.org/10.1093/bib/bbae128
SpatialcoGCN: deconvolution and spatial information–aware simulation of spatial transcriptomics data via deep graph co-embedding
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae130, https://doi.org/10.1093/bib/bbae130
Graphormer supervised de novo protein design method and function validation
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae135, https://doi.org/10.1093/bib/bbae135
PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae136, https://doi.org/10.1093/bib/bbae136
Multilevel superposition for deciphering the conformational variability of protein ensembles
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae137, https://doi.org/10.1093/bib/bbae137
ConvNeXt-MHC: improving MHC–peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae133, https://doi.org/10.1093/bib/bbae133
PUTransGCN: identification of piRNA–disease associations based on attention encoding graph convolutional network and positive unlabelled learning
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae144, https://doi.org/10.1093/bib/bbae144
A new paradigm for applying deep learning to protein–ligand interaction prediction
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae145, https://doi.org/10.1093/bib/bbae145
Biologically meaningful regulatory logic enhances the convergence rate in Boolean networks and bushiness of their state transition graph
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae150, https://doi.org/10.1093/bib/bbae150
HyGAnno: hybrid graph neural network–based cell type annotation for single-cell ATAC sequencing data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae152, https://doi.org/10.1093/bib/bbae152
SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae146, https://doi.org/10.1093/bib/bbae146
sOCP: a framework predicting smORF coding potential based on TIS and in-frame features and effectively applied in the human genome
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae147, https://doi.org/10.1093/bib/bbae147
scINRB: single-cell gene expression imputation with network regularization and bulk RNA-seq data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae148, https://doi.org/10.1093/bib/bbae148
Improving drug response prediction via integrating gene relationships with deep learning
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae153, https://doi.org/10.1093/bib/bbae153
TripHLApan: predicting HLA molecules binding peptides based on triple coding matrix and transfer learning
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae154, https://doi.org/10.1093/bib/bbae154
DSNetax: a deep learning species annotation method based on a deep-shallow parallel framework
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae157, https://doi.org/10.1093/bib/bbae157
KDGene: knowledge graph completion for disease gene prediction using interactional tensor decomposition
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae161, https://doi.org/10.1093/bib/bbae161
Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae163, https://doi.org/10.1093/bib/bbae163
BEERS2: RNA-Seq simulation through high fidelity in silico modeling
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae164, https://doi.org/10.1093/bib/bbae164
MUSCLE: multi-view and multi-scale attentional feature fusion for microRNA–disease associations prediction
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae167, https://doi.org/10.1093/bib/bbae167
Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae118, https://doi.org/10.1093/bib/bbae118
Bayesian functional analysis for untargeted metabolomics data with matching uncertainty and small sample sizes
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae141, https://doi.org/10.1093/bib/bbae141
GLDM: hit molecule generation with constrained graph latent diffusion model
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae142, https://doi.org/10.1093/bib/bbae142
DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae143, https://doi.org/10.1093/bib/bbae143
MGCNSS: miRNA–disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae168, https://doi.org/10.1093/bib/bbae168
Fuzzy kernel evidence Random Forest for identifying pseudouridine sites
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae169, https://doi.org/10.1093/bib/bbae169
Understanding YTHDF2-mediated mRNA degradation by m6A-BERT-Deg
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae170, https://doi.org/10.1093/bib/bbae170
Community cohesion looseness in gene networks reveals individualized drug targets and resistance
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae175, https://doi.org/10.1093/bib/bbae175
stDiff: a diffusion model for imputing spatial transcriptomics through single-cell transcriptomics
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae171, https://doi.org/10.1093/bib/bbae171
TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae159, https://doi.org/10.1093/bib/bbae159
Topological and geometric analysis of cell states in single-cell transcriptomic data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae176, https://doi.org/10.1093/bib/bbae176
A comparative benchmarking and evaluation framework for heterogeneous network-based drug repositioning methods
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae172, https://doi.org/10.1093/bib/bbae172
Guided diffusion for molecular generation with interaction prompt
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae174, https://doi.org/10.1093/bib/bbae174
Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae180, https://doi.org/10.1093/bib/bbae180
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae182, https://doi.org/10.1093/bib/bbae182
CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae183, https://doi.org/10.1093/bib/bbae183
Prior knowledge-guided multilevel graph neural network for tumor risk prediction and interpretation via multi-omics data integration
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae184, https://doi.org/10.1093/bib/bbae184
CoT: a transformer-based method for inferring tumor clonal copy number substructure from scDNA-seq data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae187, https://doi.org/10.1093/bib/bbae187
DEGAP: Dynamic elongation of a genome assembly path
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae194, https://doi.org/10.1093/bib/bbae194
DeepKEGG: a multi-omics data integration framework with biological insights for cancer recurrence prediction and biomarker discovery
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae185, https://doi.org/10.1093/bib/bbae185
scBOL: a universal cell type identification framework for single-cell and spatial transcriptomics data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae188, https://doi.org/10.1093/bib/bbae188
CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae190, https://doi.org/10.1093/bib/bbae190
SC-Track: a robust cell-tracking algorithm for generating accurate single-cell lineages from diverse cell segmentations
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae192, https://doi.org/10.1093/bib/bbae192
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
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae198, https://doi.org/10.1093/bib/bbae198
RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae166, https://doi.org/10.1093/bib/bbae166
Scoring alignments by embedding vector similarity
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae178, https://doi.org/10.1093/bib/bbae178
SpatialCells: automated profiling of tumor microenvironments with spatially resolved multiplexed single-cell data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae189, https://doi.org/10.1093/bib/bbae189
Genotypic–phenotypic landscape computation based on first principle and deep learning
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae191, https://doi.org/10.1093/bib/bbae191
Recognition of cyanobacteria promoters via Siamese network-based contrastive learning under novel non-promoter generation
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae193, https://doi.org/10.1093/bib/bbae193
BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae195, https://doi.org/10.1093/bib/bbae195
DeepSS2GO: protein function prediction from secondary structure
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae196, https://doi.org/10.1093/bib/bbae196
PanDepth, an ultrafast and efficient genomic tool for coverage calculation
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae197, https://doi.org/10.1093/bib/bbae197
TransAC4C—a novel interpretable architecture for multi-species identification of N4-acetylcytidine sites in RNA with single-base resolution
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae200, https://doi.org/10.1093/bib/bbae200
scEWE: high-order element-wise weighted ensemble clustering for heterogeneity analysis of single-cell RNA-sequencing data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae203, https://doi.org/10.1093/bib/bbae203
scCRT: a contrastive-based dimensionality reduction model for scRNA-seq trajectory inference
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae204, https://doi.org/10.1093/bib/bbae204
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae205, https://doi.org/10.1093/bib/bbae205
AI identifies potent inducers of breast cancer stem cell differentiation based on adversarial learning from gene expression data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae207, https://doi.org/10.1093/bib/bbae207
Mix-Key: graph mixup with key structures for molecular property prediction
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae165, https://doi.org/10.1093/bib/bbae165
Evaluating large language models for annotating proteins
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae177, https://doi.org/10.1093/bib/bbae177
GSScore: a novel Graphormer-based shell-like scoring method for protein–ligand docking
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae201, https://doi.org/10.1093/bib/bbae201
Revealing cell–cell communication pathways with their spatially coupled gene programs
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae202, https://doi.org/10.1093/bib/bbae202
Single-cell RNA sequencing data imputation using bi-level feature propagation
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae209, https://doi.org/10.1093/bib/bbae209
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae206, https://doi.org/10.1093/bib/bbae206
A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae208, https://doi.org/10.1093/bib/bbae208
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae215, https://doi.org/10.1093/bib/bbae215
Predicting TCR sequences for unseen antigen epitopes using structural and sequence features
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae210, https://doi.org/10.1093/bib/bbae210
DDID: a comprehensive resource for visualization and analysis of diet–drug interactions
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae212, https://doi.org/10.1093/bib/bbae212
Towards multi-omics synthetic data integration
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae213, https://doi.org/10.1093/bib/bbae213
Removing unwanted variation between samples in Hi-C experiments
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae217, https://doi.org/10.1093/bib/bbae217
Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae216, https://doi.org/10.1093/bib/bbae216
Contrastive learning for enhancing feature extraction in anticancer peptides
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae220, https://doi.org/10.1093/bib/bbae220
Single-cell RNA-seq data analysis reveals functionally relevant biomarkers of early brain development and their regulatory footprints in human embryonic stem cells (hESCs)
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae230, https://doi.org/10.1093/bib/bbae230
PRIEST: predicting viral mutations with immune escape capability of SARS-CoV-2 using temporal evolutionary information
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae218, https://doi.org/10.1093/bib/bbae218
FERREG: ferroptosis-based regulation of disease occurrence, progression and therapeutic response
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae223, https://doi.org/10.1093/bib/bbae223
AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae229, https://doi.org/10.1093/bib/bbae229
Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae221, https://doi.org/10.1093/bib/bbae221
Analysis of Emerging Variants of Turkey Reovirus using Machine Learning
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae224, https://doi.org/10.1093/bib/bbae224
scMNMF: a novel method for single-cell multi-omics clustering based on matrix factorization
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae228, https://doi.org/10.1093/bib/bbae228
SGCLDGA: unveiling drug–gene associations through simple graph contrastive learning
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae231, https://doi.org/10.1093/bib/bbae231
MSI-DTI: predicting drug-target interaction based on multi-source information and multi-head self-attention
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae238, https://doi.org/10.1093/bib/bbae238
CPADS: a web tool for comprehensive pancancer analysis of drug sensitivity
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae237, https://doi.org/10.1093/bib/bbae237
Normalization of RNA-Seq data using adaptive trimmed mean with multi-reference
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae241, https://doi.org/10.1093/bib/bbae241
Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae247, https://doi.org/10.1093/bib/bbae247
Review
Advances in phage–host interaction prediction: in silico method enhances the development of phage therapies
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae117, https://doi.org/10.1093/bib/bbae117
Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae132, https://doi.org/10.1093/bib/bbae132
From tradition to innovation: conventional and deep learning frameworks in genome annotation
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae138, https://doi.org/10.1093/bib/bbae138
Deep learning in structural bioinformatics: current applications and future perspectives
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae042, https://doi.org/10.1093/bib/bbae042
Interpretation of 10 years of Alzheimer’s disease genetic findings in the perspective of statistical heterogeneity
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae140, https://doi.org/10.1093/bib/bbae140
A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae162, https://doi.org/10.1093/bib/bbae162
Optimal fusion of genotype and drug embeddings in predicting cancer drug response
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae227, https://doi.org/10.1093/bib/bbae227
Computational deconvolution of DNA methylation data from mixed DNA samples
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae234, https://doi.org/10.1093/bib/bbae234
A perspective on genetic and polygenic risk scores—advances and limitations and overview of associated tools
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae240, https://doi.org/10.1093/bib/bbae240
Case Study
D3EGFR: a webserver for deep learning-guided drug sensitivity prediction and drug response information retrieval for EGFR mutation-driven lung cancer
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae121, https://doi.org/10.1093/bib/bbae121
PANoptosis, an indicator of COVID-19 severity and outcomes
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae124, https://doi.org/10.1093/bib/bbae124
IBPGNET: lung adenocarcinoma recurrence prediction based on neural network interpretability
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae080, https://doi.org/10.1093/bib/bbae080
SEAOP: a statistical ensemble approach for outlier detection in quantitative proteomics data
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae129, https://doi.org/10.1093/bib/bbae129
The HLA-I landscape confers prognosis and antitumor immunity in breast cancer
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae151, https://doi.org/10.1093/bib/bbae151
SEGCECO: Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae160, https://doi.org/10.1093/bib/bbae160
Attention-guided variational graph autoencoders reveal heterogeneity in spatial transcriptomics
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae173, https://doi.org/10.1093/bib/bbae173
Eravacycline, an antibacterial drug, repurposed for pancreatic cancer therapy: insights from a molecular-based deep learning model
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae108, https://doi.org/10.1093/bib/bbae108
Data-balanced transformer for accelerated ionizable lipid nanoparticles screening in mRNA delivery
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae186, https://doi.org/10.1093/bib/bbae186
Metabolic models predict fotemustine and the combination of eflornithine/rifamycin and adapalene/cannabidiol for the treatment of gliomas
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae199, https://doi.org/10.1093/bib/bbae199
TransPTM: a transformer-based model for non-histone acetylation site prediction
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae219, https://doi.org/10.1093/bib/bbae219
Error modelled gene expression analysis (EMOGEA) provides a superior overview of time course RNA-seq measurements and low count gene expression
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae233, https://doi.org/10.1093/bib/bbae233
Letter to Editor
Response to Letter to Editor ‘Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine’
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae211, https://doi.org/10.1093/bib/bbae211
Timely need for navigating the potential and downsides of LLMs in healthcare and biomedicine
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae214, https://doi.org/10.1093/bib/bbae214
Opinion Article
Leveraging multi-omics data to empower quantitative systems pharmacology in immuno-oncology
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae131, https://doi.org/10.1093/bib/bbae131
Corrections
Correction to: Introducing π-HelixNovo for practical large-scale de novo peptide sequencing
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae134, https://doi.org/10.1093/bib/bbae134
Correction to: Adjustment of scRNA-seq data to improve cell-type decomposition of spatial transcriptomics
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae155, https://doi.org/10.1093/bib/bbae155
Correction to: Inflated false discovery rate due to volcano plots: problem and solutions
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae149, https://doi.org/10.1093/bib/bbae149
Correction to: DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae181, https://doi.org/10.1093/bib/bbae181
Correction to: A new paradigm for applying deep learning to protein–ligand interaction prediction
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae226, https://doi.org/10.1093/bib/bbae226
Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
Briefings in Bioinformatics, Volume 25, Issue 3, May 2024, bbae253, https://doi.org/10.1093/bib/bbae253
