Volume 40, Issue 10, October 2024

Original Paper

Genome analysis

Second-order group knockoffs with applications to genome-wide association studies

Benjamin B Chu and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae580, https://doi.org/10.1093/bioinformatics/btae580

• Abstract
• View article
• Supplementary data

Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data

Richard Mayne and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae591, https://doi.org/10.1093/bioinformatics/btae591

• Abstract
• View article
• Supplementary data

Sequence analysis

Prediction of antibiotic resistance mechanisms using a protein language model

Kanami Yagimoto and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae550, https://doi.org/10.1093/bioinformatics/btae550

• Abstract
• View article
• Supplementary data

Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network

Baixue Qiao and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae581, https://doi.org/10.1093/bioinformatics/btae581

• Abstract
• View article
• Supplementary data

OligoFormer: an accurate and robust prediction method for siRNA design

Yilan Bai and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae577, https://doi.org/10.1093/bioinformatics/btae577

• Abstract
• View article
• Supplementary data

Anti-symmetric framework for balanced learning of protein–protein interactions

Tao Tang and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae603, https://doi.org/10.1093/bioinformatics/btae603

• Abstract
• View article
• Supplementary data

MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification

Ruipeng Lu and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae601, https://doi.org/10.1093/bioinformatics/btae601

• Abstract
• View article
• Supplementary data

Structural Bioinformatics

Computational prediction of multiple antigen epitopes

Rajalakshmi Viswanathan and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae556, https://doi.org/10.1093/bioinformatics/btae556

• Abstract
• View article
• Supplementary data

Towards the accurate modelling of antibody−antigen complexes from sequence using machine learning and information-driven docking

Marco Giulini and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae583, https://doi.org/10.1093/bioinformatics/btae583

• Abstracts
• View article
• Supplementary data

Pair-EGRET: enhancing the prediction of protein–protein interaction sites through graph attention networks and protein language models

Ramisa Alam and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae588, https://doi.org/10.1093/bioinformatics/btae588

• Abstract
• View article
• Supplementary data

Gene expression

A self-training interpretable cell type annotation framework using specific marker gene

Hegang Chen and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae569, https://doi.org/10.1093/bioinformatics/btae569

• Abstract
• View article
• Supplementary data

LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors

Koichiro Majima and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae520, https://doi.org/10.1093/bioinformatics/btae520

• Abstract
• View article
• Supplementary data

Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics

Yanfang Li and Shihua Zhang

Bioinformatics, Volume 40, Issue 10, October 2024, btae611, https://doi.org/10.1093/bioinformatics/btae611

• Abstract
• View article
• Supplementary data

scDRMAE: integrating masked autoencoder with residual attention networks to leverage omics feature dependencies for accurate cell clustering

Tianjiao Zhang and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae599, https://doi.org/10.1093/bioinformatics/btae599

• Abstract
• View article
• Supplementary data

Biologically weighted LASSO: enhancing functional interpretability in gene expression data analysis

Sofia Mongardi and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae605, https://doi.org/10.1093/bioinformatics/btae605

• Abstract
• View article
• Supplementary data

Genetics and population analysis

The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring

Oliver Pain and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae551, https://doi.org/10.1093/bioinformatics/btae551

• Abstract
• View article
• Supplementary data

BEATRICE: Bayesian fine-mapping from summary data using deep variational inference

Sayan Ghosal and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae590, https://doi.org/10.1093/bioinformatics/btae590

• Abstract
• View article
• Supplementary data

Systems biology

GNN4DM: a graph neural network-based method to identify overlapping functional disease modules

András Gézsi and Péter Antal

Bioinformatics, Volume 40, Issue 10, October 2024, btae573, https://doi.org/10.1093/bioinformatics/btae573

• Abstract
• View article
• Supplementary data

MSDAFL: molecular substructure-based dual attention feature learning framework for predicting drug–drug interactions

Chao Hou and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae596, https://doi.org/10.1093/bioinformatics/btae596

• Abstract
• View article
• Supplementary data

Data and text mining

HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools

Mario Sänger and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae564, https://doi.org/10.1093/bioinformatics/btae564

• Abstract
• View article
• Supplementary data

Chemical reaction enhanced graph learning for molecule representation

Anchen Li and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae558, https://doi.org/10.1093/bioinformatics/btae558

• Abstract
• View article
• Supplementary data

MGRN: toward robust drug recommendation via multi-view gating retrieval network

Fanjun Meng and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae572, https://doi.org/10.1093/bioinformatics/btae572

• Abstract
• View article
• Supplementary data

Structure-inclusive similarity based directed GNN: a method that can control information flow to predict drug–target binding affinity

Jipeng Huang and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae563, https://doi.org/10.1093/bioinformatics/btae563

• Abstract
• View article

Causal enhanced drug–target interaction prediction based on graph generation and multi-source information fusion

Guanyu Qiao and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae570, https://doi.org/10.1093/bioinformatics/btae570

• Abstract
• View article

Learning to explain is a good biomedical few-shot learner

Peng Chen and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae589, https://doi.org/10.1093/bioinformatics/btae589

• Abstracts
• View article
• Supplementary data

Chain-aware graph neural networks for molecular property prediction

Honghao Wang and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae574, https://doi.org/10.1093/bioinformatics/btae574

• Abstract
• View article

PocketDTA: an advanced multimodal architecture for enhanced prediction of drug−target affinity from 3D structural data of target binding pockets

Long Zhao and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae594, https://doi.org/10.1093/bioinformatics/btae594

• Abstract
• View article
• Supplementary data

TarKG: a comprehensive biomedical knowledge graph for target discovery

Cong Zhou and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae598, https://doi.org/10.1093/bioinformatics/btae598

• Abstract
• View article
• Supplementary data

A multi-modality and multi-granularity collaborative learning framework for identifying spatial domains and spatially variable genes

Xiao Liang and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae607, https://doi.org/10.1093/bioinformatics/btae607

• Abstract
• View article
• Supplementary data

Bioimage informatics

TAWFN: a deep learning framework for protein function prediction

Lu Meng and Xiaoran Wang

Bioinformatics, Volume 40, Issue 10, October 2024, btae571, https://doi.org/10.1093/bioinformatics/btae571

• Abstract
• View article
• Supplementary data

Accurate segmentation of intracellular organelle networks using low-level features and topological self-similarity

Jiaxing Huang and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae559, https://doi.org/10.1093/bioinformatics/btae559

• Abstract
• View article
• Supplementary data

Applications Note

Genome analysis

MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants

Weijia Jin and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae578, https://doi.org/10.1093/bioinformatics/btae578

• Abstract
• View article
• Supplementary data

VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation

Yilin Zhu and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae575, https://doi.org/10.1093/bioinformatics/btae575

• Abstract
• View article
• Supplementary data

PCBS: an R package for fast and accurate analysis of bisulfite sequencing data

Kathryn Lande and April E Williams

Bioinformatics, Volume 40, Issue 10, October 2024, btae593, https://doi.org/10.1093/bioinformatics/btae593

• Abstract
• View article
• Supplementary data

BioPred: an R package for biomarkers analysis in precision medicine

Zihuan Liu and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae592, https://doi.org/10.1093/bioinformatics/btae592

• Abstract
• View article
• Supplementary data

Sequence analysis

NeoDesign: a computational tool for optimal selection of polyvalent neoantigen combinations

Wenqian Yu and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae585, https://doi.org/10.1093/bioinformatics/btae585

• Abstract
• View article
• Supplementary data

Phylogenetics

Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique

Hang Yang and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae566, https://doi.org/10.1093/bioinformatics/btae566

• Abstract
• View article
• Supplementary data

Structural bioinformatics

DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules

Claudio Mirabello and Björn Wallner

Bioinformatics, Volume 40, Issue 10, October 2024, btae586, https://doi.org/10.1093/bioinformatics/btae586

• Abstract
• View article

ABodyBuilder3: improved and scalable antibody structure predictions

Henry Kenlay and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae576, https://doi.org/10.1093/bioinformatics/btae576

• Abstract
• View article
• Supplementary data

Analysis of metadynamics simulations by metadynminer.py

Jan Beránek and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae614, https://doi.org/10.1093/bioinformatics/btae614

• Abstracts
• View article
• Supplementary data

Gene expression

vSPACE: exploring virtual spatial representation of articular chondrocytes at the single-cell level

Chenyu Zhang and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae568, https://doi.org/10.1093/bioinformatics/btae568

• Abstract
• View article
• Supplementary data

BatchFLEX: feature-level equalization of X-batch

Joshua T Davis and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae587, https://doi.org/10.1093/bioinformatics/btae587

• Abstract
• View article
• Supplementary data

Systems biology

Combined LC-MS/MS feature grouping, statistical prioritization, and interactive networking in msFeaST

Kevin Mildau and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae584, https://doi.org/10.1093/bioinformatics/btae584

• Abstract
• View article
• Supplementary data

CyCadas: accelerating interactive annotation and analysis of clustered cytometry data

Oliver Hunewald and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae595, https://doi.org/10.1093/bioinformatics/btae595

• Abstract
• View article
• Supplementary data

RTF: an R package for modelling time course data

Eva Brombacher and Clemens Kreutz

Bioinformatics, Volume 40, Issue 10, October 2024, btae597, https://doi.org/10.1093/bioinformatics/btae597

• Abstract
• View article

DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs

Brad T Sherman and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae615, https://doi.org/10.1093/bioinformatics/btae615

• Abstract
• View article
• Supplementary data

Data and text mining

GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console

Anindita Nath and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae500, https://doi.org/10.1093/bioinformatics/btae500

• Abstract
• View article
• Supplementary data

SurvBal: compositional microbiome balances for survival outcomes

Ying Li and others

Bioinformatics, Volume 40, Issue 10, October 2024, btae612, https://doi.org/10.1093/bioinformatics/btae612

• Abstract
• View article
• Supplementary data

Correction

Correction to: AgIn: measuring the landscape of CpG methylation of individual repetitive elements

Bioinformatics, Volume 40, Issue 10, October 2024, btae600, https://doi.org/10.1093/bioinformatics/btae600

• Extract
• View article
• Supplementary data

Correction to: Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students

Bioinformatics, Volume 40, Issue 10, October 2024, btae635, https://doi.org/10.1093/bioinformatics/btae635

• Extract
• View article