Subject: New issue: Briefings in Bioinformatics, Volume 27, Issue 2, March 2026

Volume 27, Issue 2, March 2026

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Papers

Master of Metals2: a graph neural network based architecture for the prediction of zinc binding sites in protein structures

Vincenzo Laveglia and others

Integrating feature selection with unsupervised deep embedding for clustering single-cell RNA-seq data

Cheng Zhong and others

ORANGE: a machine learning approach for modeling tissue-specific aging from transcriptomic data

Wasif Jalal and others

Jing Wang and others

MDPD reveals specific microbial signatures in human pulmonary diseases

Paramita Roy and others

Castl: robust identification of spatially variable genes in spatial transcriptomics via an ensemble-based framework

Yiyi Yu and others

Benchmarking large language models for pathogen'disease classification in post-acute infection syndromes

Syed Mohammed Khalid and others

SigRescueR: a pan-system framework for noise correction and mutational signature identification across sequencing platforms

Peter T Nguyen and Maria Zhivagui

De novo functional protein sequence generation: overcoming data scarcity through regeneration and large language models

Chenyu Ren and others

scDIAGRAM: detecting chromatin compartments from individual single-cell Hi-C matrix without imputation or reference features

Yongli Peng and others

BioMNEDR: mechanism-guided network embedding for drug repurposing

Yizhou Zeng and others

Impact of control selection strategies on GWAS results: a study of prostate cancer in the UK Biobank

Jingzhan Lu and others

An integrative association analysis for complex diseases in underrepresented groups by leveraging the trans-ethnic genetic similarity

Shuo Zhang and others

Finding Significant Hits in Networks: a network-based tool for analyzing gene-level P-values to identify significant genes missed by standard methods

Sandeep Acharya and others

MutPPI+: a multimodal framework for predicting mutation effects on protein'protein interactions via mutation-path-based data augmentation

Juntao Deng and others

ML-ExonCNV: a robust XGBoost multi-expert ensemble framework for rare exon CNV detection in whole-exome sequencing data

Shuang-Hao Yang and others

KANPM-DTA: improving drug'target affinity prediction with Kolmogorov'Arnold networks and pretrained models

M D Youshuf Khan Rakib and others

A deep adversarial network model for multi-task analysis of single-cell omics data

Junlin Xu and others

Decoding TCR recognition via geometric deep learning of immunological fingerprints

Chun Shang and others

Differentiation of RNA'protein docking structures through molecular dynamics simulation and machine learning methods

Bui Tien Thanh and others

Sensitive detection of copy number alterations in low-pass liquid biopsy sequencing data

Lotta Eriksson and Eszter Lakatos

Computational identification of lineage-committed precursors in mammalian organogenesis reveals a novel hematopoietic enhancer regulating Bhlhe41 expression

Lihui Jin and others

A progressive fine-tuning framework with dynamic parameter selection for low-resource peptide'GPCR interaction prediction

Mingqing Liu and others

Kun-peng enables scalable and accurate pan-domain metagenomic classification

Qiong Chen and others

Drug screening for alpha -synuclein aggregation inhibitors via multimodal graph neural network

Tingle Gu and others

Enhancing cancer classification accuracy with a self-attention network using panel capture sequencing data

Yi Jia and others

A cancer-type-aware framework for robust multimodal survival prediction under missing modalities

Yiran Song and others

Co-expression network multivariate regression

Hwiyoung Lee and others

Docking of millions: accelerating a million-scale virtual screening using deep learning

Junsu Ha and others

Computational framework for therapeutic target discovery via perturbation simulation: application to cystic fibrosis airway disease

George Sun and Yi-Hui Zhou

Estimating population structure using epigenome-wide methylation data

Ziqing Wang and others

Comparison of variant callers using 60 532 multi-ancestry whole genome sequences

Hufeng Zhou and others

Quantifying transcript complexity via the condition number of gene-specific random matrix

Bo Zhang and others

GWKBR: a novel method integrating machine learning and Bayesian inference framework to improve genomic prediction accuracy

Xue Wang and others

Confidence scoring for deep learning-predicted antibody'antigen complexes: AntiConf as a precision-driven metric

SerbÃ¼lent Ãœnsal and others

Are we ready for causal discovery in biological systems using deep learning?

Hock Chuan Yeo and Kumar Selvarajoo

Interactive visualization of metric distortion in nonlinear data embeddings using the distortions package

Kris Sankaran and others

CrisprPr: a hybrid-driven framework for CRISPR/Cas9 off-target prediction with analysis of prior-information updates

Yingfu Wu and others

Hybrid deep learning with protein language models and dual-path architecture for predicting IDP functions

Jiahui Liang and others

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking

Yu Deng and others

NetCrafter: ontology-derived gene network modeling and functional interpretation

Yeji Lee and others

PLM-effector: unleashing the potential of protein language models for bacterial secreted protein prediction

Dandan Zheng and others

BEASTsim'a benchmarking and analysis platform for spatial transcriptomics simulations

TomÃ¡s Bordoy GarcÃa-Carpintero and others

NetCIS: a network-based common insertion site pipeline for case'control Sleeping Beauty screens

Mathew J Fischbach and others

SpaFun: discovering domain-specific spatial expression patterns and new disease-relevant genes using functional principal component analysis

Xi Jiang and others

Integrated machine learning and molecular dynamics framework for predicting and elucidating ABCB1 allocrite interactions

Jianjia Su and others

Multi-marker testing based on accelerated failure time models under possible left truncation and competing risks

Chenxi Li and others

SpaJoint: a transfer learning method for spatial transcriptomics deconvolution

Zichang Li and others

BCRInsight: an antibody language model to decode biological signals from BCR sequences

Hailong Zhao and others

Analysis of microsatellite instability intensity in single-cell resolution with scMnT reveals tumor heterogeneity in colorectal cancer

Gyumin Park and Jihwan Park

GDSim: accurate simulation for single-cell transcriptomes based on the guided diffusion model

Tao Wang and others

GEiPRS: a fast and powerful machine learning method for polygenic risk score prediction by leveraging genotype'environment interactions

Le Huang and others

scGPD: single-cell informed gene panel design for targeted spatial transcriptomics

Yunshan Guo and others

CRESCENT: a deep learning framework with multi-scale attention for detecting recurrent copy number alterations

Xikang Feng and others

Prediction of minimum inhibitory concentration of antibacterial peptides using geometric graph networks and dynamic loss functions

Yannan Bin and others

MELGene: knowledge-enhanced multimodel ensemble learning for disease'gene association prediction

Haoyu Tian and others

DuaST: an integrated deep learning framework for spatial transcriptomics with cross-branch interaction

Xiao Liang and others

A bio-inspired computational pipeline for antibody screening and repurposing

Junxin Li and others

AICellType: a large language model-based platform for accurate cell type annotation

Chuxing Cheng and others

Spatial-ZEDNet: a unified spatial transcriptomics framework for detecting differential gene activation and expression

Osafu Augustine Egbon and others

SaMCL: a multi-task collaborative learning framework for peptide-protein interaction prediction based on structure-aware protein language models

Siyi He and others

GALA: a unified landmark-free framework for coarse-to-fine spatial alignment across resolutions and modalities in spatial transcriptomics

Tao Ding and Pengcheng Zeng

NyxBind: enhancing deep neural representations for transcription factor binding site prediction via contrastive learning

Xu Yang and others

Evaluating reference-mixture matching in cell-type deconvolution with single-cell RNA-seq references

Yifan Zhao and others

Antibody'antigen neutralization prediction by integrating structural information distillation and physicochemical constraints

Yutian Liu and others

Computational nanobody design using graph neural networks and Metropolis Monte Carlo sampling

Lei Wang and others

Generative design and validation of therapeutic peptides for glioblastoma based on a potential target ATP5A

Hao Qian and others

PDTSyn: a parameter-decomposed transformer for domain-generalized cell line-aware drug synergy prediction

Biyang Zeng and others

Benchmarking cell-type-specific spatially variable gene detection methods

Hui Yao and others

BACON: decoding the dynamic social networks of complex microbial communities at single-cell resolution

Wenxin Qu and others

Building a credibility-based framework for target discovery: Perspectives from tRNA synthetase-linked metabolic diseases

Jaeyoung Choi and others

DeepDrugs: a mechanism-aware tri-linear attention framework for synergistic drug-combination prediction

Gaojia Xin and others

Reconstructing 3D transcriptional organization from spatial transcriptomics reveals consistent oncogenic translocations and developmental dynamics

Yifei Sheng and others

CaHoT-GRN: context-aware high-order topology learning for robust single-cell gene regulatory network inference

Dengju Yao and others

Integrating and mapping single-cell transcriptomics across the entire gene expression space

Shuzhen Ding and others

Integrative multi-omics analysis reveals microbiota alterations and clinical indicators predictive of pulmonary fibrosis progression following SARS-CoV-2 infection

Chang Liu and others

Case Studies

Could statistical potential models achieve comparable or better performance than deep learning models?

Zhihao Wang and others

EpGAT: integrating epigenetics and 3D genome structure to predict alternative splicing and polyadenylation

Sudipto Baul and others

Biochemical-knowledge-driven machine learning pipeline for generating potent antimicrobial peptides

Deliang Yang and others

Spotting a unicorn: spatial transcriptome analysis of the eyelid reveals gene regulatory networks enriched in Moll glands

Tomas Konecny and others

Influ-BERT: a domain-adaptive genomic language model for advancing influenza A virus research

Rongye Ye and others

Causal modeling reveals cell'cell communication dynamics in the tumor microenvironment during anti-PD-1 therapy in breast cancer patients

Aodong Qiu and others

Proteomic analysis across Healthy'NAT'Tumor tissues uncovers clinically relevant biological events in esophageal squamous cell carcinoma

Wei Liu and others

miRBiT: a rules-based single-sample serum miRNA classifier for pan-cancer detection with multi-cohort validation

Pandikannan Krishnamoorthy and others

ZeCardioAI: combining zebrafish, AI, and xAI for an in-depth cardiac phenotyping platform

BayesPI-FLY: a Bayesian neural network approach for inferring feature weighted TF'DNA interaction

Gege Liu and others

A causal glycerophospholipid'IL-18R1'CD9 axis connects lipid metabolism and T-cell activation in atopic dermatitis

Ping-An Zhang and others

Letter to the Editor

Supervisory signals are intriguingly high in even simple features for predicting anticancer effect of antibody drug conjugates

Sunil Nagpal

Letter to the editor: testing the generalizability of DeepPlantAllergy on challenging allergen prediction scenarios

Kazim Okan Dolu

Response to "Addressing biases and limitations in feature attribution for circRNA modification profiling"

Jiayi Li and others

Addressing biases and limitations in feature attribution for circRNA modification profiling

Souichi Oka and others

Benchmark competitiveness and generalization are not equivalent: a critical commentary on HybridSP

Marcio Madrid and others

Discussions on the generalization of HybridSP on more equivalent benchmarks

Zhihao Wang and others

Corrections

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

Correction to: Attention is all you need: utilizing attention in AI-enabled drug discovery

Abstracts

Prognostic biomarker discovery via a connected network-constrained Cox proportional hazards model

Lingyu Li and others

Machine Learning Driven Discovery of Ribosomal Biomarkers in PCOS

Ashitha Washington and Ravindra Kumar

An integrative multi-omics framework for decoding microglial ecosystems in Alzheimer's disease

Chuyun Zhang and Kei Hang Katie Chan

Phylogenetic analysis of TET2 gene variants in Pakistani acute myeloid Leukemia patients

Mawada Elmagboul Abdalla Abakar and others

Publisher's Note

Publisher's Note: Addendum to Volume 26, Issue Supplement 1, December 2025, International Conference on Genome Informatics ISCB-Asia 2025 Abstract Book

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