Subject: New issue: Briefings in Bioinformatics, Volume 26, Issue 3, May 2025

Volume 26, Issue 3, May 2025

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Latest impact metrics for Briefings in Bioinformatics

We are pleased to share the latest impact metrics for Briefings in Bioinformatics. The journal was recently awarded a CiteScoreâ"¢ (Scopus) of 15.8, a new Impact Factor of 7.7 (Journal Citation Reportsâ"¢), and received 3,044,366 total Full-text downloads in 2024.

We invite you to explore the latest breakthroughs published in Briefings in Bioinformatics and consider the journal as the next outlet for your work.

Papers

DeepRNA-Twist: language-model-guided RNA torsion angle prediction with attention-inception network

Abrar Rahman Abir and others

PSTP: accurate residue-level phase separation prediction using protein conformational and language model embeddings

Mofan Feng and others

Chrombus-XMBD: a graph convolution model predicting 3D-genome from chromatin features

Yuanyuan Zeng and others

Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data

Lianchong Gao and others

GKNnet: an relational graph convolutional network-based method with knowledge-augmented activation layer for microbial structural variation detection

Fengyi Guo and others

Advancing promiscuous aggregating inhibitor analysis with intelligent machine learning classification

Luxuan Wang and others

Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE

Lis Arend and others

A novel splicing graph allows a direct comparison between exon-based and splice junction'based approaches to alternative splicing detection

Jelard Aquino and others

SVHunter: long-read-based structural variation detection through the transformer model

Runtian Gao and others

Predicting the structures of cyclic peptides containing unnatural amino acids by HighFold2

Cheng Zhu and others

Decoupled GNNs based on multi-view contrastive learning for scRNA-seq data clustering

Xiaoyan Yu and others

MMsurv: a multimodal multi-instance multi-cancer survival prediction model integrating pathological images, clinical information, and sequencing data

Hailong Yang and others

NNKcat: deep neural network to predict catalytic constants (K_cat) by integrating protein sequence and substrate structure with enhanced data imbalance handling

Jingchen Zhai and others

Accounting for the impact of rare variants on causal inference with RARE: a novel multivariable Mendelian randomization method

Yu Cheng and others

In-silico discovery of type-2 diabetes-causing host key genes that are associated with the complexity of monkeypox and repurposing common drugs

Alvira Ajadee and others

MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data

Ning Wang and others

De-motif sampling: an approach to decompose hierarchical motifs with applications in T cell recognition

Xinyi Tang and Ran Liu

VirNucPro: an identifier for the identification of viral short sequences using six-frame translation and large language models

Jing Li and others

Network analysis of multivariate time series data in biological systems: methods and applications

Hao Mei and others

Influenza virus reassortment patterns exhibit preference and continuity while uncovering cross-species transmission events

Xiao Ding and others

mKmer: an unbiased K-mer embedding of microbiomic single-microbe RNA sequencing data

Fangyu Mo and others

Multi-view clustering for single-cell RNA-seq data based on graph fusion

Jing Wang and others

Mutual information stacking method for prediction of the growth traits in pigs

Ruilin Su and others

GAEDGRN: reconstruction of gene regulatory networks based on gravity-inspired graph autoencoders

Pi-Jing Wei and others

Machine learning'augmented m⁶A-Seq analysis without a reference genome

Jing Yang and others

Large-scale information retrieval and correction of noisy pharmacogenomic datasets through residual thresholded deep matrix factorization

Zhiyue Tom Hu and others

ADCNet: a unified framework for predicting the activity of antibody-drug conjugates

Liye Chen and others

MambaPhase: deep learning for liquid'liquid phase separation protein classification

Jianwei Huang and others

DECEPTICON: a correlation-based strategy for RNA-seq deconvolution inspired by a variation of the Anna Karenina principle

Fulan Deng and others

PhosF3C: a feature fusion architecture with fine-tuned protein language model and conformer for prediction of general phosphorylation site

Yuhuan Liu and others

I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data

Tung Dang and others

PPIxGPN: plasma proteomic profiling of neurodegenerative biomarkers with protein'protein interaction-based eXplainable graph propagational network

Sunghong Park and others

Evaluation of out-of-distribution detection methods for data shifts in single-cell transcriptomics

Lauren Theunissen and others

scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery

Saiyam Jogani and others

PLM-DBPs: enhancing plant DNA-binding protein prediction by integrating sequence-based and structure-aware protein language models

Suresh Pokharel and others

LightCTL: lightweight contrastive TCR-pMHC specificity learning with context-aware prompt

Fei Ye and others

ZSeeker: an optimized algorithm for Z-DNA detection in genomic sequences

Guliang Wang and others

Integrated multimodal hierarchical fusion and meta-learning for enhanced molecular property prediction

Xianjun Han and others

EDS-Kcr: deep supervision based on large language model for identifying protein lysine crotonylation sites across multiple species

Hong-Qi Zhang and others

Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology

Li-Mei Qian and others

RLEAAI: improving antibody'antigen interaction prediction using protein language model and sequence order information

Jun Hu and others

Gated-GPS: enhancing protein'protein interaction site prediction with scalable learning and imbalance-aware optimization

Xin Gao and others

KinaseFusionDB: an integrative knowledge of kinase fusion proteins in multi-scales

Himansu Kumar and others

SCPline: An interactive framework for the single-cell proteomics data preprocessing

Shangwei Guo and others

Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features

Zehua Sun and others

A multivariable cis-Mendelian randomization method robust to weak instrument bias and horizontal pleiotropy bias

Yihe Yang and others

ScInfeR: an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics

Asish Kumar Swain and others

TARGET-SL: precision essential gene prediction using driver prioritisation and synthetic lethality

Rhys Gillman and others

RPSubAlign: a novel sequence-based molecular representation method for retrosynthesis prediction with improved validity and robustness

Yuting Hu and others

Artificial intelligence-driven circRNA vaccine development: multimodal collaborative optimization and a new paradigm for biomedical applications

Yan Zhao and Huaiyu Wang

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

Alex McSweeney-Davis and others

HGCMLDA: predicting lncRNA-disease associations using hypergraph contrastive learning and multi-scale attentional feature fusion

Zequn Zhang and others

Rag2Mol: structure-based drug design based on retrieval augmented generation

Peidong Zhang and others

scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification

Murong Zhou and others

Gene expression inference based on graph neural networks using L1000 data

Tae Hyun Kim and others

KansformerEPI: a deep learning framework integrating KAN and transformer for predicting enhancer'promoter interactions

Tianjiao Zhang and others

scValue: value-based subsampling of large-scale single-cell transcriptomic data for machine and deep learning tasks

Li Huang and others

ProtPhage: a deep learning framework for phage viral protein identification and functional annotation

Yuehua Ou and others

VirulentHunter: deep learning-based virulence factor predictor illuminates pathogenicity in diverse microbial contexts

Chen Chen and others

MultiPep-DLCL: recognition of multifunctional therapeutic peptides through deep learning with label-sequence contrastive learning

Ting Li and others

Enhancing LncRNA-miRNA interaction prediction with multimodal contrastive representation learning

Zhixia Teng and others

2OM-Pred: prediction of 2-O-methylation sites in ribonucleic acid using diverse classifiers

Anas Bilal and others

GTE-PPIS: a protein'protein interaction site predictor based on graph transformer and equivariant graph neural network

Xun Wang and others

Robust signalling entropy estimation for biological process characterisation

Ana Stolnicu and others

Generative prediction of real-world prevalent SARS-CoV-2 mutation with in silico virus evolution

Xudong Liu and others

GC-balanced polar codes correcting insertions, deletions and substitutions for DNA storage

Rui Zhang and Huaming Wu

PrimeNet: rational design of Prime editing pegRNAs by deep learning

Xichen Liao and others

A novel deep learning framework with dynamic tokenization for identifying chromatin interactions along with motif importance investigation

Liangcan Li and others

MORE interpretable multi-omic regulatory networks to characterise phenotypes

Maider Aguerralde-Martin and others

DeepTFtyper: an interpretable morphology-aware graph neural network for translating histopathology images into molecular subtypes in small cell lung cancer

Xin Li and others

Genetic regulation of lncRNA expression in whole human brain and their contribution to CNS disorders

Yijie He and others

Fusion of spatiotemporal and network models to prioritize multiscale effects in single-cell perturbations

Osafu Augustine Egbon and others

IECata: interpretable bilinear attention network and evidential deep learning improve the catalytic efficiency prediction of enzymes

Jingjing Wang and others

Graph-RPI: predicting RNA'protein interactions via graph autoencoder and self-supervised learning strategies

Jiahui Guan and others

Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data

Maren Hackenberg and others

scTsI: an effective two-stage imputation method for single-cell RNA-seq data

Hongyu Zhang and others

DeepExDC interprets genomic compartmentalization changes in single-cell Hi-C data

Hongqiang Lyu and others

cfMethylPre: deep transfer learning enhances cancer detection based on circulating cell-free DNA methylation profiling

Xuchao Zhang and others

An order-preserving batch-effect correction method based on a monotonic deep learning framework

Mingxuan Zhang and Yinglei Lai

Reviews

An overview of computational methods in single-cell transcriptomic cell type annotation

Tianhao Li and others

Advances in multi-trait genomic prediction approaches: classification, comparative analysis, and perspectives

Alain J Mbebi and others

An algorithmic perspective on deciphering cell'cell interactions with spatial omics data

Mike van Santvoort and Federica Eduati

Advances and critical aspects in cancer treatment development using digital twins

Rym Bouriga and others

Robustness and resilience of computational deconvolution methods for bulk RNA sequencing data

Su Xu and others

EvANI benchmarking workflow for evolutionary distance estimation

Sina Majidian and others

Advances and challenges in cell'cell communication inference: a comprehensive review of tools, resources, and future directions

Giulia Cesaro and others

To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era

Sriniketh Vangaru and Debswapna Bhattacharya

Out of distribution learning in bioinformatics: advancements and challenges

Yu Shi and others

Computational modeling of single-cell dynamics data

Wenbo Guo and others

Case Studies

Metabolism-associated protein network constructing and host-directed anti-influenza drug repurposing

Hao Tang and others

High-dimensional mediation analysis for longitudinal mediators and survival outcomes

Lili Liu and others

A novel prognostic framework for HBV-infected hepatocellular carcinoma: insights from ferroptosis and iron metabolism proteomics

Zhiwei Cheng and others

Knowledge-guided multi-level network modeling with experimental characterization identifies PRKCA as a novel biomarker and tumor suppressor triggering ferroptosis in prostate cancer

Yuxin Lin and others

Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms

Feifei Xia and others

StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images

Bingying Luo and others

Decoding herbal combination models through systematic strategies: insights from target information and traditional Chinese medicine clinical theory

Mingjuan Wang and others

Multi-objective computational optimization of human 5² UTR sequences

Keisuke Yamada and others

Multi-omics analysis of Helicobacter pylori'associated gastric cancer identifies hub genes as a novel therapeutic biomarker

Sara H Mohamed and others

Simulation-guided pan-cancer analysis identifies a novel regulator of CpG island hypermethylation heterogeneity

Xianglin Zhang and others

Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids

Kaizhuang Jing and others

Systematic identification of cancer-type-specific drugs based on essential genes and validations in lung adenocarcinoma

Xiang Lian and others

Gene Swin transformer: new deep learning method for colorectal cancer prognosis using transcriptomic data

Yangyang Wang and others

PYF: a multi-functional algorithm for predicting production and optimizing metabolic engineering strategy in Escherichia coli microbial consortia

Chen Yang and others

iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics

Kang-Lin Hsieh and others

TransMA: an explainable multi-modal deep learning model for predicting properties of ionizable lipid nanoparticles in mRNA delivery

Kun Wu and others

Letters to the Editor

Editor's Note on ˜Bioinformatics in Russia: history and present-day landscape'

On "Bioinformatics in Russia: history and present-day landscape" by M.A. Nawaz, I.E. Pamirsky, and K.S. Golokhvast

Mikhail S Gelfand

Response to letter to editor "On ˜Bioinformatics in Russia: history and present-day landscape' by M.A. Nawaz, I.E. Pamirsky, and K.S. Golokhvast" by Mikhail Gelfand

Muhammad Amjad Nawaz and others

Should LLMs be over empowered for high-stake regulatory research?

Partha Pratim Ray

Corrections

Correction to: DOMSCNet: a deep learning model for the classification of stomach cancer using multi-layer omics data

Correction to: ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs

Correction to: Bioinformatics in Russia: history and present-day landscape

Correction to: ScInfeR: an efficient method for annotating cell types and sub-types in single-cell RNA-seq, ATAC-seq, and spatial omics

This email is intended for bionet@evol.mcmaster.ca.