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Volume 25, Issue 6, November 2024
Articles
COFFEE: consensus single cell-type specific inference for gene regulatory networks
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae457, https://doi.org/10.1093/bib/bbae457
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae459, https://doi.org/10.1093/bib/bbae459
3t-seq: automatic gene expression analysis of single-copy genes, transposable elements, and tRNAs from RNA-seq data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae467, https://doi.org/10.1093/bib/bbae467
NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae472, https://doi.org/10.1093/bib/bbae472
Multi-Cover Persistence (MCP)-based machine learning for polymer property prediction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae465, https://doi.org/10.1093/bib/bbae465
Algorithm-agnostic significance testing in supervised learning with multimodal data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae475, https://doi.org/10.1093/bib/bbae475
nsDCC: dual-level contrastive clustering with nonuniform sampling for scRNA-seq data analysis
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae477, https://doi.org/10.1093/bib/bbae477
Protein language models are performant in structure-free virtual screening
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae480, https://doi.org/10.1093/bib/bbae480
CMFHMDA: a prediction framework for human disease-microbe associations based on cross-domain matrix factorization
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae481, https://doi.org/10.1093/bib/bbae481
miniSNV: accurate and fast single nucleotide variant calling from nanopore sequencing data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae473, https://doi.org/10.1093/bib/bbae473
DGCL: dual-graph neural networks contrastive learning for molecular property prediction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae474, https://doi.org/10.1093/bib/bbae474
HIP: a method for high-dimensional multi-view data integration and prediction accounting for subgroup heterogeneity
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae470, https://doi.org/10.1093/bib/bbae470
scEGG: an exogenous gene-guided clustering method for single-cell transcriptomic data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae483, https://doi.org/10.1093/bib/bbae483
DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae484, https://doi.org/10.1093/bib/bbae484
MLSNet: a deep learning model for predicting transcription factor binding sites
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae489, https://doi.org/10.1093/bib/bbae489
DrugReSC: targeting disease-critical cell subpopulations with single-cell transcriptomic data for drug repurposing in cancer
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae490, https://doi.org/10.1093/bib/bbae490
Recover then aggregate: unified cross-modal deep clustering with global structural information for single-cell data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae485, https://doi.org/10.1093/bib/bbae485
Development and experimental validation of computational methods for human antibody affinity enhancement
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae488, https://doi.org/10.1093/bib/bbae488
An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae476, https://doi.org/10.1093/bib/bbae476
scDFN: enhancing single-cell RNA-seq clustering with deep fusion networks
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae486, https://doi.org/10.1093/bib/bbae486
Detecting expressed genes in cell populations at the single-cell level with scGeneXpress
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae494, https://doi.org/10.1093/bib/bbae494
MultiSC: a deep learning pipeline for analyzing multiomics single-cell data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae492, https://doi.org/10.1093/bib/bbae492
PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae497, https://doi.org/10.1093/bib/bbae497
Pioneering bioinformatics with agent-based modelling: an innovative protocol to accurately forecast skin or respiratory allergic reactions to chemical sensitizers
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae506, https://doi.org/10.1093/bib/bbae506
AntigenBoost: enhanced mRNA-based antigen expression through rational amino acid substitution
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae468, https://doi.org/10.1093/bib/bbae468
Digital PCR threshold robustness analysis and optimization using dipcensR
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae507, https://doi.org/10.1093/bib/bbae507
Gene expression prediction from histology images via hypergraph neural networks
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae500, https://doi.org/10.1093/bib/bbae500
MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae504, https://doi.org/10.1093/bib/bbae504
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae511, https://doi.org/10.1093/bib/bbae511
BANDRP: a bilinear attention network for anti-cancer drug response prediction based on fingerprint and multi-omics
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae493, https://doi.org/10.1093/bib/bbae493
Mediation analysis in longitudinal study with high-dimensional methylation mediators
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae496, https://doi.org/10.1093/bib/bbae496
MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae505, https://doi.org/10.1093/bib/bbae505
HMPA: a pioneering framework for the noncanonical peptidome from discovery to functional insights
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae510, https://doi.org/10.1093/bib/bbae510
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae512, https://doi.org/10.1093/bib/bbae512
Reconstructing tumor clonal heterogeneity and evolutionary relationships based on tumor DNA sequencing data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae516, https://doi.org/10.1093/bib/bbae516
Cancerous time estimation for interpreting the evolution of lung adenocarcinoma
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae520, https://doi.org/10.1093/bib/bbae520
SELF-Former: multi-scale gene filtration transformer for single-cell spatial reconstruction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae523, https://doi.org/10.1093/bib/bbae523
scMGATGRN: a multiview graph attention network–based method for inferring gene regulatory networks from single-cell transcriptomic data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae526, https://doi.org/10.1093/bib/bbae526
Diagnostics of viral infections using high-throughput genome sequencing data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae501, https://doi.org/10.1093/bib/bbae501
Building multiscale models with PhysiBoSS, an agent-based modeling tool
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae509, https://doi.org/10.1093/bib/bbae509
Enhancing RNA-seq analysis by addressing all co-existing biases using a self-benchmarking approach with 2D structural insights
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae532, https://doi.org/10.1093/bib/bbae532
Statistical analysis of multiple regions-of-interest in multiplexed spatial proteomics data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae522, https://doi.org/10.1093/bib/bbae522
AptaDiff: de novo design and optimization of aptamers based on diffusion models
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae517, https://doi.org/10.1093/bib/bbae517
MetaDegron: multimodal feature-integrated protein language model for predicting E3 ligase targeted degrons
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae519, https://doi.org/10.1093/bib/bbae519
A two-task predictor for discovering phase separation proteins and their undergoing mechanism
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae528, https://doi.org/10.1093/bib/bbae528
m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae529, https://doi.org/10.1093/bib/bbae529
Therapeutic peptides identification via kernel risk sensitive loss-based k-nearest neighbor model and multi-Laplacian regularization
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae534, https://doi.org/10.1093/bib/bbae534
Predictability of antigen binding based on short motifs in the antibody CDRH3
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae537, https://doi.org/10.1093/bib/bbae537
DeepCheck: multitask learning aids in assessing microbial genome quality
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae539, https://doi.org/10.1093/bib/bbae539
Single-cell mosaic integration and cell state transfer with auto-scaling self-attention mechanism
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae540, https://doi.org/10.1093/bib/bbae540
ACLNDA: an asymmetric graph contrastive learning framework for predicting noncoding RNA–disease associations in heterogeneous graphs
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae533, https://doi.org/10.1093/bib/bbae533
Advancing microbial diagnostics: a universal phylogeny guided computational algorithm to find unique sequences for precise microorganism detection
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae545, https://doi.org/10.1093/bib/bbae545
Cross-population enhancement of PrediXcan predictions with a gnomAD-based east Asian reference framework
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae549, https://doi.org/10.1093/bib/bbae549
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae530, https://doi.org/10.1093/bib/bbae530
Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae535, https://doi.org/10.1093/bib/bbae535
Cell cycle expression heterogeneity predicts degree of differentiation
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae536, https://doi.org/10.1093/bib/bbae536
Structure-preserved integration of scRNA-seq data using heterogeneous graph neural network
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae538, https://doi.org/10.1093/bib/bbae538
Constructing the dynamic transcriptional regulatory networks to identify phenotype-specific transcription regulators
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae542, https://doi.org/10.1093/bib/bbae542
A robust statistical approach for finding informative spatially associated pathways
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae543, https://doi.org/10.1093/bib/bbae543
Optimized patient-specific immune checkpoint inhibitor therapies for cancer treatment based on tumor immune microenvironment modeling
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae547, https://doi.org/10.1093/bib/bbae547
BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae524, https://doi.org/10.1093/bib/bbae524
GexMolGen: cross-modal generation of hit-like molecules via large language model encoding of gene expression signatures
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae525, https://doi.org/10.1093/bib/bbae525
IPFMC: an iterative pathway fusion approach for enhanced multi-omics clustering in cancer research
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae541, https://doi.org/10.1093/bib/bbae541
Multi-view learning framework for predicting unknown types of cancer markers via directed graph neural networks fitting regulatory networks
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae546, https://doi.org/10.1093/bib/bbae546
Deep contrastive learning for predicting cancer prognosis using gene expression values
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae544, https://doi.org/10.1093/bib/bbae544
Multimodal contrastive learning for spatial gene expression prediction using histology images
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae551, https://doi.org/10.1093/bib/bbae551
A consensus-based classification workflow to determine genetically inferred ancestry from comprehensive genomic profiling of patients with solid tumors
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae557, https://doi.org/10.1093/bib/bbae557
Predicting disease-associated microbes based on similarity fusion and deep learning
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae550, https://doi.org/10.1093/bib/bbae550
IMGT/RobustpMHC: robust training for class-I MHC peptide binding prediction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae552, https://doi.org/10.1093/bib/bbae552
STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae553, https://doi.org/10.1093/bib/bbae553
scDTL: enhancing single-cell RNA-seq imputation through deep transfer learning with bulk cell information
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae555, https://doi.org/10.1093/bib/bbae555
Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae558, https://doi.org/10.1093/bib/bbae558
GGN-GO: geometric graph networks for predicting protein function by multi-scale structure features
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae559, https://doi.org/10.1093/bib/bbae559
DEWNA: dynamic entropy weight network analysis and its application to the DNA-binding proteome in A549 cells with cisplatin-induced damage
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae564, https://doi.org/10.1093/bib/bbae564
An unbiased comparison of immunoglobulin sequence aligners
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae556, https://doi.org/10.1093/bib/bbae556
Semi-supervised learning with pseudo-labeling compares favorably with large language models for regulatory sequence prediction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae560, https://doi.org/10.1093/bib/bbae560
Deep learning model for protein multi-label subcellular localization and function prediction based on multi-task collaborative training
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae568, https://doi.org/10.1093/bib/bbae568
Multi-level multi-view network based on structural contrastive learning for scRNA-seq data clustering
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae562, https://doi.org/10.1093/bib/bbae562
Prototype-based contrastive substructure identification for molecular property prediction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae565, https://doi.org/10.1093/bib/bbae565
Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae527, https://doi.org/10.1093/bib/bbae527
siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae563, https://doi.org/10.1093/bib/bbae563
SpaDiT: diffusion transformer for spatial gene expression prediction using scRNA-seq
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae571, https://doi.org/10.1093/bib/bbae571
Graph domain adaptation–based framework for gene expression enhancement and cell type identification in large-scale spatially resolved transcriptomics
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae576, https://doi.org/10.1093/bib/bbae576
A multi-task prediction method based on neighborhood structure embedding and signed graph representation learning to infer the relationship between circRNA, miRNA, and cancer
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae573, https://doi.org/10.1093/bib/bbae573
A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae575, https://doi.org/10.1093/bib/bbae575
scTCA: a hybrid Transformer-CNN architecture for imputation and denoising of scDNA-seq data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae577, https://doi.org/10.1093/bib/bbae577
Unlocking cross-modal interplay of single-cell joint profiling with CellMATE
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae582, https://doi.org/10.1093/bib/bbae582
mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae580, https://doi.org/10.1093/bib/bbae580
ToxGIN: an In silico prediction model for peptide toxicity via graph isomorphism networks integrating peptide sequence and structure information
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae583, https://doi.org/10.1093/bib/bbae583
Deciphering lineage-relevant gene regulatory networks during endoderm formation by InPheRNo-ChIP
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae592, https://doi.org/10.1093/bib/bbae592
Identifying cell types by lasso-constraint regularized Gaussian graphical model based on weighted distance penalty
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae572, https://doi.org/10.1093/bib/bbae572
SpaGIC: graph-informed clustering in spatial transcriptomics via self-supervised contrastive learning
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae578, https://doi.org/10.1093/bib/bbae578
Molecular group and correlation guided structural learning for multi-phenotype prediction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae585, https://doi.org/10.1093/bib/bbae585
Deciphering gene expression patterns using large-scale transcriptomic data and its applications
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae590, https://doi.org/10.1093/bib/bbae590
Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae596, https://doi.org/10.1093/bib/bbae596
AIGen: an artificial intelligence software for complex genetic data analysis
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae566, https://doi.org/10.1093/bib/bbae566
Robust self-supervised learning strategy to tackle the inherent sparsity in single-cell RNA-seq data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae586, https://doi.org/10.1093/bib/bbae586
TIPS: a novel pathway-guided joint model for transcriptome-wide association studies
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae587, https://doi.org/10.1093/bib/bbae587
MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae597, https://doi.org/10.1093/bib/bbae597
MPA-MutPred: a novel strategy for accurately predicting the binding affinity change upon mutation in membrane protein complexes
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae598, https://doi.org/10.1093/bib/bbae598
Nmix: a hybrid deep learning model for precise prediction of 2’-O-methylation sites based on multi-feature fusion and ensemble learning
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae601, https://doi.org/10.1093/bib/bbae601
CMTT-JTracker: a fully test-time adaptive framework serving automated cell lineage construction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae591, https://doi.org/10.1093/bib/bbae591
BFAST: joint dimension reduction and spatial clustering with Bayesian factor analysis for zero-inflated spatial transcriptomics data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae594, https://doi.org/10.1093/bib/bbae594
Digital annealing optimization for natural product structure elucidation
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae600, https://doi.org/10.1093/bib/bbae600
SIngle cell level Genotyping Using scRna Data (SIGURD)
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae604, https://doi.org/10.1093/bib/bbae604
RiceSNP-BST: a deep learning framework for predicting biotic stress–associated SNPs in rice
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae599, https://doi.org/10.1093/bib/bbae599
The mathematical exploration for the mechanism of lung adenocarcinoma formation and progression
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae603, https://doi.org/10.1093/bib/bbae603
A metagene based similarity network fusion approach for multi-omics data integration identified novel subtypes in renal cell carcinoma
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae606, https://doi.org/10.1093/bib/bbae606
Review Article
DrugDoctor: enhancing drug recommendation in cold-start scenario via visit-level representation learning and training
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae464, https://doi.org/10.1093/bib/bbae464
Current computational tools for protein lysine acylation site prediction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae469, https://doi.org/10.1093/bib/bbae469
Knowledge Graphs for drug repurposing: a review of databases and methods
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae461, https://doi.org/10.1093/bib/bbae461
Deep learning in template-free de novo biosynthetic pathway design of natural products
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae495, https://doi.org/10.1093/bib/bbae495
Bioinformatics approaches for studying molecular sex differences in complex diseases
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae499, https://doi.org/10.1093/bib/bbae499
Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae498, https://doi.org/10.1093/bib/bbae498
Thinking points for effective batch correction on biomedical data
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae515, https://doi.org/10.1093/bib/bbae515
Author summary: Batch effects introduce heterogeneity into data and hinder accurate analysis. Despite advancements in biomedical technologies and analysis algorithms, addressing batch effects remains a significant challenge due to their complex nature, which requires diverse considerations. To facilitate better handling of batch effects, we offer a comprehensive set of thinking points designed to help researchers ensure more robust analysis.
Robust variable selection methods with Cox model—a selective practical benchmark study
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae508, https://doi.org/10.1093/bib/bbae508
Bioinformatics in Russia: history and present-day landscape
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae513, https://doi.org/10.1093/bib/bbae513
Progress and opportunities of foundation models in bioinformatics
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae548, https://doi.org/10.1093/bib/bbae548
Making PBPK models more reproducible in practice
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae569, https://doi.org/10.1093/bib/bbae569
A review of feature selection strategies utilizing graph data structures and Knowledge Graphs
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae521, https://doi.org/10.1093/bib/bbae521
Adversarial regularized autoencoder graph neural network for microbe-disease associations prediction
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae584, https://doi.org/10.1093/bib/bbae584
The biological processes and interactions of microorganisms and diseases are studied.
An autoencoding graph neural network predicts associations between microorganisms and diseases.
Generative adversarial networks address the limitations of encoder capture and mitigate sampling sparsity.
A gentle introduction to pangenomics
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae588, https://doi.org/10.1093/bib/bbae588
Graph databases in systems biology: a systematic review
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae561, https://doi.org/10.1093/bib/bbae561
Case Study
Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae458, https://doi.org/10.1093/bib/bbae458
CDHu40: a novel marker gene set of neuroendocrine prostate cancer
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae471, https://doi.org/10.1093/bib/bbae471
AESurv: autoencoder survival analysis for accurate early prediction of coronary heart disease
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae479, https://doi.org/10.1093/bib/bbae479
scPanel: a tool for automatic identification of sparse gene panels for generalizable patient classification using scRNA-seq datasets
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae482, https://doi.org/10.1093/bib/bbae482
Development and validation of an explainable machine learning model for predicting multidimensional frailty in hospitalized patients with cirrhosis
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae491, https://doi.org/10.1093/bib/bbae491
Predicting functional outcome in ischemic stroke patients using genetic, environmental, and clinical factors: a machine learning analysis of population-based prospective cohort study
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae487, https://doi.org/10.1093/bib/bbae487
Long-range alternative splicing contributes to neoantigen specificity in glioblastoma
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae503, https://doi.org/10.1093/bib/bbae503
A multi-omics study of brain tissue transcription and DNA methylation revealing the genetic pathogenesis of ADHD
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae502, https://doi.org/10.1093/bib/bbae502
Mut-Map: Comprehensive Computational Pipeline for Structural Mapping and Analysis of Cancer-Associated Mutations
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae514, https://doi.org/10.1093/bib/bbae514
Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae567, https://doi.org/10.1093/bib/bbae567
Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae581, https://doi.org/10.1093/bib/bbae581
Generating pregnant patient biological profiles by deconvoluting clinical records with electronic health record foundation models
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae574, https://doi.org/10.1093/bib/bbae574
Correction
Correction to: Structure prediction of linear and cyclic peptides using CABS-flex
Briefings in Bioinformatics, Volume 25, Issue 6, November 2024, bbae605, https://doi.org/10.1093/bib/bbae605
