Subject: New issue: Briefings in Bioinformatics, Volume 26, Issue 5, September 2025

Volume 26, Issue 5, September 2025

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Apply to be a Handling Editor for Briefings in Bioinformatics

Oxford University Press is looking for a new Handling Editor to join the editorial team of Briefings in Bioinformatics. This role is perfect for a researcher with a strong background in AI and Multi-Omics Integration.

As Handling Editor, you will be responsible for managing the peer review process, shaping the journal's content, and serving as an ambassador for the journal. We are particularly interested in candidates with expertise in Artificial Intelligence and Deep Learning in Bioinformatics, Transcriptomic and Single-cell RNA-seq Data Analysis, Multimodal Data Integration, and Computational Proteomics and Metabolomics.

Apply by October 1st, 2025.

Papers

AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes

Hongxu Zhu and others

scSorterDL: a deep neural network-enhanced ensemble LDAs for single cell classifications

Kailun Bai and others

Significantly enhancing human antibody affinity via deep learning and computational biology-guided single-point mutations

Junxin Li and others

MVSGDR: multi-view stacked graph convolutional network for drug repositioning

Guosheng Gu and others

GCNMF-SDA: predicting snoRNA-disease associations based on graph convolution and non-negative matrix factorization

Yaowu Zhang and others

DeepMobilome: predicting mobile genetic elements using sequencing reads of microbiomes

Youna Cho and others

Energy entropy vector: a novel approach for efficient microbial genomic sequence analysis and classification

Hao Wang and others

DeepPhosPPI: a deep learning framework with attention-CNN and transformer for predicting phosphorylation effects on protein'protein interactions

Yinyin Gong and others

A multi-dimensional computational framework of drug-induced hepatotoxicity: integrating molecular structure features with disease pathogenesis

Huayu Zhong and others

Predicting nucleic acid binding sites by attention map-guided graph convolutional network with protein language embeddings and physicochemical information

Xiang Li and others

Graph neural network integrated with pretrained protein language model for predicting human'virus protein'protein interactions

Linyang Jiang and others

Multi-layer matrix factorization for cancer subtyping using full and partial multi-omics dataset

Yingxuan Ren and others

Graph-based deep learning for integrating single-cell and bulk transcriptomic data to identify clinical cancer subtypes

Yixin Liu and others

ISENICS: a model for identifying senescent immune cells and samples and characterization of their roles in tumor microenvironment

Miaomiao Tian and others

CircCode3: integrating deep learning to mine and evaluate translatable circular RNAs from ribosome profiling sequencing and mass spectrometry data

Zonghui Zhu and others

abCAN: a practical and novel attention network for predicting mutant antibody affinity

Chen Gong and others

MIF'DTI: a multimodal information fusion method for drug'target interaction prediction

Jiehong Shan and others

Autoregressive enzyme function prediction with multi-scale multi-modality fusion

Dingyi Rong and others

PEAKQC: periodicity evaluation in single-cell ATAC-seq data for quality assessment

Jan Detleffsen and others

IBI-DT: a novel approach combining individualized Bayesian inference and decision tree for identifying cancer drivers and their interactions

Md Asad Rahman and others

BioWalk-MDA: a novel approach for large-scale predicting metabolite-drug associations based on multi layered biomedical knowledge graphs

Xiaoliang Wu and others

Characterization of the complex TB pharmacogenomic landscape in Africa using bioinformatic tools

Carola Oelofse and others

Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3

Sen Cao and others

scHSC: enhancing single-cell RNA-seq clustering via hard sample contrastive learning

Sheng Fang and others

CKG-TPI: integrating collaborative knowledge graph with sequence interactions for TCR'peptide binding specificity

Yue Liu and others

MVRBind: multi-view learning for RNA-small molecule binding site prediction

Song Chen and others

Clinical and data-driven optimization of Genomiser for rare disease patients: experience from the Hong Kong Genome Project

Anson Man Chun Xi and others

Alignment-free unique molecular identifier clustering suppresses sequencing errors for accurate detection of low-frequency DNA variants

Fei Yu and others

MINERVA'microbiome network research and visualization atlas: a scalable knowledge graph for mapping microbiome-disease associations

Saul Langarica and others

Benchmarking large language models for genomic knowledge with GeneTuring

Xinyi Shang and others

SageTCR: a structure-based model integrating residue- and atom-level representations for enhanced TCR-pMHC binding prediction

Xiangyi Li and others

Growing and linking optimizers: synthesis-driven molecule design

Clarisse Descamps and others

DeCoST: unveiling cell type heterogeneity in spatial transcriptomics based on inter-domain alignment and Gaussian kernel conditional autoregressive

Xinyang Guo and others

scBCN: deep learning-based batch correction network for integration of heterogeneous single-cell data

Lei Wan and others

A multi-omics integration framework using multi-label guided learning and multi-scale fusion

Yuze Li and others

Contrastive hypergraph collaborative filtering for transfer RNA'disease association prediction

Tianxiang Ouyang and others

A simple workflow to identify novel small linear motif (SLiM)-mediated interactions with AlphaFold

Martin Veinstein and others

RMR-ICP: robust Mendelian randomization method accounting for idiosyncratic and correlated pleiotropy with applications to stroke outcomes

Qing Cheng and others

INAB: identify nucleic acid binding domain via cross-modal protein language models and multiscale computation

Jun Zhang and others

DA-HGL: a domain-augmented heterogeneous graph learning framework for protein function prediction

Sai Hu and others

A novel pairwise sequence alignment algorithm for similarity search in massive datasets

Yosef Masoudi-Sobhanzadeh and Yadollah Omidi

AdaSemb: an adaptive knowledge-driven deep learning framework integrating cancer protein assemblies for predicting PI3Kalpha inhibitor response and resistance

Zaiduo Li and others

IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder

Yao Li and others

OligoY pipeline for full Y chromosome painting

Isabela Almeida and others

Benchmarking copy number variation detection with low-coverage whole-genome sequencing

Nan Wang and others

Dual-protein embedding-based graph model with dynamic attention for interaction prediction

Shunpeng Pang and others

Multi-view gene panel characterization for spatially resolved omics

Daniel Kim and others

Predicting disease associations based on the higher order structure of ceRNA networks

Zhaoliang Chai and others

Denoising spatially resolved transcriptomics with consistency of heterogeneous spatial coordinates, transcription, and morphology

Haiyue Wang and others

Network based simultaneous embedding of cells and marker genes from scRNA-seq studies

Namrata Bhattacharya and others

scHDeepInsight: a hierarchical deep learning framework for precise immune cell annotation in single-cell RNA-seq data

Shangru Jia and others

Heterogeneous graph contrastive learning for integration and alignment of spatial transcriptomics data

Yang Gui and others

Disentangled contrastive learning with dynamic intent adaptation for unveiling gene'drug associations

Xiaosong Wang and others

Cell-type-specific cis-eQTLs in pancreatic cell types identify novel risk genes for type 2 diabetes

Xiao-Cao Miao and others

Quantifying antibiotic resistome risks across environmental niches: the L-ARRAP for long-read metagenomic profiling

Yongxin Li and others

Novel methods for temporally varying gene identification in longitudinal studies reveal bleeding and clotting pathway activation caused by blood draws

Wei Chen and others

MODA: a graph convolutional network-based multi-omics integration framework for unraveling hub molecules and disease mechanisms

Jinhui Zhao and others

Data-efficient protein mutational effect prediction with weak supervision by molecular simulation and protein language models

Teppei Deguchi and others

Microllm: a structured information extraction tool using large language models and named entity recognition in microbiology

Jing Lu and others

OmniDoublet: a method for doublet detection in multimodal single-cell sequencing data

Lian Liu and others

BioRAGent: natural language biomedical querying with retrieval-augmented multiagent systems

Manlian Bi and others

Designing high-affinity 3D drug molecules via geometric spatial perception diffusion model

Hao Lu and others

MRDadaptis: self-adaptive parameter configuration enhances minimal residual disease detection in heterogeneous ctDNA samples

Tianci Wang and others

Integrative genetic analysis reveals new relationships between intraocular pressure, glaucoma, and ischemic stroke risk: a study based on combined SNP-to-gene, Mendelian randomization and pathway investigations

Qi Zhang and others

PILOT-GM-VAE: patient-level analysis of single-cell disease atlas with optimal transport of Gaussian mixture variational autoencoders

Mehdi Joodaki and others

Numbat-multiome: inferring copy number variations by combining RNA and chromatin accessibility information from single-cell data

Ruitong Li and others

Enhancing cross-domain protein and peptide interaction with retrained deep learning models

Xin Cao and others

Pepxml: ESM2-based extreme multilabel classification of pathogen-targeted antimicrobial peptides

Yannan Bin and others

PangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis

Zhengfa Xue and others

Read-level DNA methylation deconvolution enhances circulating tumor DNA detection

Ting Qi and others

A transcriptional plasticity-aware framework for RNA-seq differential expression analysis

Cheng Bei and others

Classifier-driven generative adversarial networks for enhanced antimicrobial peptide design

Michaela Areti Zervou and others

BioLLMNet: enhancing RNA-interaction prediction with a specialized cross-LLM transformation network

Abrar Rahman Abir and others

CASTER-DTA: equivariant graph neural networks for predicting drug'target affinity

Rachit Kumar and others

Dual-route embedding-aware graph neural networks for drug repositioning

Yanlong Zhao and others

scDETECT: a novel statistical model accounting for cell type correlation in single-cell RNA-seq differential expression analysis

Yuhan Xu and others

Expression graph network framework for biomarker discovery

Yang Liu and others

Kinship Decouple and Phenotype Selection (KDPS): a tool for phenotype-aware decoupling of related subjects

Wanjun Gu and others

scVGAMF: a novel imputation method for scRNA-seq data by integrating linear and non-linear features

Zhiyuan Zhou and others

A Bayesian framework for genome-wide circadian rhythmicity biomarker detection

Haocheng Ding and others

ChromoPattern: characterizing chromosomal rearrangement patterns of copy number alteration in heterogeneous tumor cell populations at single-cell resolution

Xin Wang and others

BrainGeneBot: a framework for variant prioritization and generative pretrained transformer-informed interpretation across polygenic risk score studies

Gang Qu and others

Prediction of soil probiotics based on foundation model representation enhancement and stacked aggregation classifier

Qiang Kang and others

Hi-C3: a statistical inference-based model for reconstructing higher-order cell'cell communication networks

Yuyan Tong and others

SeekTP: identifying multifunctional therapeutic peptides via graph attention and deep property integration

Guolun Zhong and Lei Deng

Artificial intelligence-driven framework for discovering synthetic binding protein-like scaffolds from the entire protein universe

Zixin Duan and others

Reviews

Beyond rigid docking: deep learning approaches for fully flexible protein'ligand interactions

John Lee and others

CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation

Asif Ali Vadakkethil and others

Case Studies

MCAMEF-BERT: an efficient deep learning method for RNA N7-methylguanosine site prediction via multi-branch feature integration

Junlei Yu and others

The bioinformatics of the finding that the hepatitis delta virus RNA editing mechanism by a conformational switch exists in genotype 7 in addition to genotype 3

Rami Zakh and others

Mapping cancer heterogeneity: a consensus network approach to subtypes and pathways

Geng-Ming Hu and others

AttBiomarker: unveiling preeclampsia biomarkers and molecular pathways through two-stage gene selection techniques and attention-based CNN with gene regulatory network analysis

Sakib Sarker and others

Computational refinement and multivalent engineering of complementarity-determining region-grafted nanobodies on a humanized scaffold for retaining antiviral efficacy

Liyun Huo and others

Predicting response and survival of lung adenocarcinoma under anti-programmed death-1 therapy using biological deep learning

Yuanyuan Wang and others

Neighborhood enrichment for the identification of antigen-specific T-cell receptors

Kseniia R Lupyr and others

Identifying survival subtypes with autoencoder using multiple types of high-dimensional genomic data from studies of glioblastoma multiforme

Imran Parvez and Jie Chen

Advancing ADMET prediction through multiscale fragment-aware pretraining with MSformer-ADMET

Huihui Liu and others

Genetic imputation of transcriptome and proteome illuminates novel therapeutic targets of cutaneous melanoma

Yantao Xu and others

Corrections

Correction to: Alpha_Mesh_Swc: automatic and robust surface mesh generation from the skeleton description of brain cells

Correction to: A comparative evaluation of computational models for RNA modification detection using nanopore sequencing with RNA004 chemistry

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