Subject: New issue: Briefings in Bioinformatics, Volume 26, Issue 1, January 2025

Volume 26, Issue 1, January 2025

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Articles

AutoXAI4Omics: an automated explainable AI tool for omics and tabular data

James Strudwick,Laura-Jayne Gardiner and others

tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs

Anna Postovskaya,Koen Vercauteren and others

MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics

Yiwen Yang,Chengming Zhang and others

ONDSA: a testing framework based on Gaussian graphical models for differential and similarity analysis of multiple omics networks

Jiachen Chen,Joanne M Murabito and others

TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data

Xin Ma,Lijing Lin and others

RNADiffFold: generative RNA secondary structure prediction using discrete diffusion models

Zhen Wang,Yizhen Feng and others

VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell'cell communication network

Tianjiao Zhang,Xiang Zhang and others

Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome

Yinhu Li,Guangze Pan and others

PartIES: a disease subtyping framework with Partition-level Integration using diffusion-Enhanced Similarities from multi-omics Data

Yuqi Miao,Huang Xu and others

Repun: an accurate small variant representation unification method for multiple sequencing platforms

Zhenxian Zheng,Yingxuan Ren and others

BioDSNN: a dual-stream neural network with hybrid biological knowledge integration for multi-gene perturbation response prediction

Yuejun Tan,Linhai Xie and others

Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach

Jiaqi Wang,Ronggang Xi and others

CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis

Tianyu Liu,Wenxin Long and others

DiMA: sequence diversity dynamics analyser for viruses

Shan Tharanga,Eyyüb Selim Ünlü and others

LIMO-GCN: a linear model-integrated graph convolutional network for predicting Alzheimer disease genes

Cui-Xiang Lin,Hong-Dong Li and others

miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA

Xiaolong Wu,Lehan Zhang and others

The improved de Bruijn graph for multitask learning: predicting functions, subcellular localization, and interactions of noncoding RNAs

Yuxiao Wei,Qi Zhang and others

FunlncModel: integrating multi-omic features from upstream and downstream regulatory networks into a machine learning framework to identify functional lncRNAs

Yan-Yu Li,Feng-Cui Qian and others

BICEP: Bayesian inference for rare genomic variant causality evaluation in pedigrees

Cathal Ormond,Niamh M Ryan and others

Inferring single-cell resolution spatial gene expression via fusing spot-based spatial transcriptomics, location, and histology using GCN

Shuailin Xue,Fangfang Zhu and others

RIOT'Rapid Immunoglobulin Overview Tool'annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database

Paweł Dudzic,Bartosz Janusz and others

Meta learning for mutant HLA class I epitope immunogenicity prediction to accelerate cancer clinical immunotherapy

Long Xu,Qiang Yang and others

CancerHubs: a systematic data mining and elaboration approach for identifying novel cancer-related protein interaction hubs

Ivan Ferrari,Federica De Grossi and others

UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs

Chi Zhang,Yiran Cheng and others

Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states

Leandro Murgas,Gianluca Pollastri and others

STRsensor: a computationally efficient method for STR allele-typing from massively parallel sequencing data

Xiaolong Zhang,Xianchao Ji and others

Few-shot classification of Cryo-ET subvolumes with deep Brownian distance covariance

Xueshi Yu,Renmin Han and others

TG-CDDPM: text-guided antimicrobial peptides generation based on conditional denoising diffusion probabilistic model

Junhang Cao,Jun Zhang and others

Detection of germline CNVs from gene panel data: benchmarking the state of the art

Elisabet Munté,Carla Roca and others

Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping

Shyamsundar Ravishankar,Vilma Perez and others

Multi-kernel feature extraction with dynamic fusion and downsampled residual feature embedding for predicting rice RNA N⁶-methyladenine sites

Mengya Liu,Zhan-Li Sun and others

Cell-specific priors rescue differential gene expression in spatial spot-based technologies

Ornit Nahman,Timothy J Few-Cooper and others

A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks

Yong Liu,Le Zhong and others

Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data

Willem Stock,Coralie Rousseau and others

THOR: a TMB heterogeneity-adaptive optimization model predicts immunotherapy response using clonal genomic features in group-structured data

Yixuan Wang,Yanfang Guan and others

GSTRPCA: irregular tensor singular value decomposition for single-cell multi-omics data clustering

Lubin Cui,Guiliang Guo and others

scPAS: single-cell phenotype-associated subpopulation identifier

Aimin Xie,Hao Wang and others

NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture

Fatma S Ahmed,Saleh Aly and others

CapHLA: a comprehensive tool to predict peptide presentation and binding to HLA class I and class II

Yunjian Chang,Ligang Wu

Diffusion model assisted designing self-assembling collagen mimetic peptides as biocompatible materials

Xinglong Wang,Kangjie Xu and others

DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering

Junwei Luo,Jiaojiao Wang and others

Heterogeneous graph contrastive learning with gradient balance for drug repositioning

Hai Cui,Meiyu Duan and others

MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification

Yuhan Wang,Zhikang Wang and others

Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison

Dries Heylen,Murih Pusparum and others

scDCA: deciphering the dominant cell communication assembly of downstream functional events from single-cell RNA-seq data

Boya Ji,Xiaoqi Wang and others

CDCM: a correlation-dependent connectivity map approach to rapidly screen drugs during outbreaks of infectious diseases

Junlei Liao,Hongyang Yi and others

Bayesian unsupervised clustering identifies clinically relevant osteosarcoma subtypes

Sergio Llaneza-Lago,William D Fraser and others

GAADE: identification spatially variable genes based on adaptive graph attention network

Tianjiao Zhang,Hao Sun and others

PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data

Qianwen Luo,Shanshan Zhang and others

SatXplor'a comprehensive pipeline for satellite DNA analyses in complex genome assemblies

Marin Volarić,Nevenka Meštrović and others

scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning

Lin Yuan,Shengguo Sun and others

Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep

Konstantina Tzavella,Adrian Diaz and others

Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata

Hao Yuan,Parker Hicks and others

stHGC: a self-supervised graph representation learning for spatial domain recognition with hybrid graph and spatial regularization

Runqing Wang,Qiguo Dai and others

CPARI: a novel approach combining cell partitioning with absolute and relative imputation to address dropout in single-cell RNA-seq data

Yi Zhang,Yin Wang and others

STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution

Bo Wang,Yahui Long and others

Predicting phage'host interactions via feature augmentation and regional graph convolution

Ankang Wei,Zhen Xiao and others

Dual-stage optimizer for systematic overestimation adjustment applied to multi-objective genetic algorithms for biomarker selection

Luca Cattelani,Vittorio Fortino

GADIFF: a transferable graph attention diffusion model for generating molecular conformations

Donghan Wang,Xu Dong and others

Precise identification of somatic and germline variants in the absence of matched normal samples

Hui Li,Lu Meng and others

The iPhylo suite: an interactive platform for building and annotating biological and chemical taxonomic trees

Yueer Li,Chen Peng and others

RNA-ModX: a multilabel prediction and interpretation framework for RNA modifications

Chelsea Chen Yuge,Ee Soon Hang and others

Machine learning'enabled virtual screening indicates the anti-tuberculosis activity of aldoxorubicin and quarfloxin with verification by molecular docking, molecular dynamics simulations, and biological evaluations

Si Zheng,Yaowen Gu and others

microT-CNN: an avant-garde deep convolutional neural network unravels functional miRNA targets beyond canonical sites

Elissavet Zacharopoulou,Maria D Paraskevopoulou and others

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes

Giuseppe Defazio,Marco Antonio Tangaro and others

Online-adjusted evolutionary biclustering algorithm to identify significant modules in gene expression data

Raúl Galindo-Hernández,Katya Rodríguez-Vázquez and others

K_PRR: a novel machine learning approach for effectively capturing nonadditive effects in genomic prediction

Mianyan Li,Thomas Hall and others

GPSD: a hybrid learning framework for the prediction of phosphatase-specific dephosphorylation sites

Cheng Han,Shanshan Fu and others

ProteinF3S: boosting enzyme function prediction by fusing protein sequence, structure, and surface

Mingzhi Yuan,Ao Shen and others

BACT: nonparametric Bayesian cell typing for single-cell spatial transcriptomics data

Yinqiao Yan,Xiangyu Luo

Towards simplified graph neural networks for identifying cancer driver genes in heterophilic networks

Xingyi Li,Jialuo Xu and others

DrugAssist: a large language model for molecule optimization

Geyan Ye,Xibao Cai and others

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

Dominik Lux,Katrin Marcus-Alic and others

The network structural entropy for single-cell RNA sequencing data during skin aging

Zhilong Liu,Hai Lin and others

RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice

Quan Lu,Jiajun Xu and others

STMGraph: spatial-context-aware of transcriptomes via a dual-remasked dynamic graph attention model

Lixian Lin,Haoyu Wang and others

Addressing scalability and managing sparsity and dropout events in single-cell representation identification with ZIGACL

Mingguang Shi,Xuefeng Li

Genome-wide association neural networks identify genes linked to family history of Alzheimer's disease

Upamanyu Ghose,William Sproviero and others

Integrating genetic algorithms and language models for enhanced enzyme design

Yves Gaetan Nana Teukam,Federico Zipoli and others

Deciphering progressive lesion areas in breast cancer spatial transcriptomics via TGR-NMF

Juntao Li,Shan Xiang and others

A novel framework for phage-host prediction via logical probability theory and network sparsification

Ankang Wei,Huanghan Zhan and others

ET-PROTACs: modeling ternary complex interactions using cross-modal learning and ternary attention for accurate PROTAC-induced degradation prediction

Lijun Cai,Guanyu Yue and others

cyclicpeptide: a Python package for cyclic peptide drug design

Liu Yang,Suqi Cao and others

LOGOWheat: deep learning'based prediction of regulatory effects for noncoding variants in wheats

Lingpeng Kong,Hong Cheng and others

PbsNRs: predict the potential binders and scaffolds for nuclear receptors

Genhui Zheng,Dingfeng Wu and others

Supervised analysis of alternative polyadenylation from single-cell and spatial transcriptomics data with spvAPA

Qinglong Zhang,Liping Kang and others

Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks

Lingsheng Cai,Xiuli Ma and others

Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization

Xianliang Liu,Jiawei Luo and others

CellMsg: graph convolutional networks for ligand'receptor-mediated cell-cell communication analysis

Hong Xia,Boya Ji and others

DD-PRiSM: a deep learning framework for decomposition and prediction of synergistic drug combinations

Iljung Jin,Songyeon Lee and others

TRIAGE: an R package for regulatory gene analysis

Qiongyi Zhao,Woo Jun Shim and others

Exploring the potential of compound'protein complex structure-free models in virtual screening using BlendNet

Sangmin Seo,Hwanhee Kim and others

A framework of multi-view machine learning for biological spectral unmixing of fluorophores with overlapping excitation and emission spectra

Ruogu Wang,Yunlong Feng and others

QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics

Zexuan Wang,Qipeng Zhan and others

Identifying cancer prognosis genes through causal learning

Siwei Wu,Chaoyi Yin and others

VirDetect-AI: a residual and convolutional neural network'based metagenomic tool for eukaryotic viral protein identification

Alida Zárate,Lorena Díaz-González and others

Explainable deep neural networks for predicting sample phenotypes from single-cell transcriptomics

Jordi Martorell-Marugán,Raúl López-Domínguez and others

Multi-source biological knowledge-guided hypergraph spatiotemporal subnetwork embedding for protein complex identification

Shilong Wang,Hai Cui and others

A deep learning feature importance test framework for integrating informative high-dimensional biomarkers to improve disease outcome prediction

Baiming Zou,James G Xenakis and others

Towards molecular structure discovery from cryo-ET density volumes via modelling auxiliary semantic prototypes

Ashwin Nair,Xingjian Li and others

A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing

Arnaud Guille,José Adélaïde and others

Multimodal multiobjective optimization with structural network control principles to optimize personalized drug targets for drug discovery of individual patients

Jing Liang,Zhuo Hu and others

AntiBinder: utilizing bidirectional attention and hybrid encoding for precise antibody'antigen interaction prediction

Kaiwen Zhang,Yuhao Tao and others

scHiClassifier: a deep learning framework for cell type prediction by fusing multiple feature sets from single-cell Hi-C data

Xiangfei Zhou,Hao Wu

BIOTIC: a Bayesian framework to integrate single-cell multi-omics for transcription factor activity inference and improve identity characterization of cells

Lan Cao,Wenhao Zhang and others

PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network

Fu Liu,Zhimiao Zhao and others

GOPhage: protein function annotation for bacteriophages by integrating the genomic context

Jiaojiao Guan,Yongxin Ji and others

scGO: interpretable deep neural network for cell status annotation and disease diagnosis

You Wu,Pengfei Xu and others

Therapeutic gene target prediction using novel deep hypergraph representation learning

Kibeom Kim,Juseong Kim and others

Spatially aligned graph transfer learning for characterizing spatial regulatory heterogeneity

Wendong Huang,Yaofeng Hu and others

TargetCLP: clathrin proteins prediction combining transformed and evolutionary scale modeling-based multi-view features via weighted feature integration approach

Matee Ullah,Shahid Akbar and others

Predicting transcriptional changes induced by molecules with MiTCP

Kaiyuan Yang,Jiabei Cheng and others

scMMAE: masked cross-attention network for single-cell multimodal omics fusion to enhance unimodal omics

Dian Meng,Yu Feng and others

Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation

Yongjie Xu,Zelin Zang and others

BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction

Yang Yang,Zixuan Zheng and others

SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline

Sara Potente,Diego Boscarino and others

Inferring the genetic relationships between unsupervised deep learning'derived imaging phenotypes and glioblastoma through multi-omics approaches

Liguo Ye,Cheng Ye and others

Classification-based pathway analysis using GPNet with novel P-value computation

Hao Lu,Mostafa Rezapour and others

A comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions

Xikang Feng,Miaozhe Huo and others

Graph contrastive learning of subcellular-resolution spatial transcriptomics improves cell type annotation and reveals critical molecular pathways

Qiaolin Lu,Jiayuan Ding and others

Novel genetic insight for psoriasis: integrative genome-wide analyses in 863 080 individuals and proteome-wide Mendelian randomization

Shunying Liu,Lingfei Li and others

Attention-aware differential learning for predicting peptide-MHC class I binding and T cell receptor recognition

Rui Niu,Jingwei Wang and others

Cell-type deconvolution for bulk RNA-seq data using single-cell reference: a comparative analysis and recommendation guideline

Xintian Xu,Rui Li and others

Multi-view multi-level contrastive graph convolutional network for cancer subtyping on multi-omics data

Bo Yang,Chenxi Cui and others

Polygenic prediction for underrepresented populations through transfer learning by utilizing genetic similarity shared with European populations

Yiyang Zhu,Wenying Chen and others

TransBic: bucket trend-preserving biclustering for finding local and interpretable expression patterns

Jing Li,Qinglin Mei and others

DeepPFP: a multi-task-aware architecture for protein function prediction

Han Wang,Zilin Ren and others

Benchmarking 13 tools for mutational signature attribution, including a new and improved algorithm

Nanhai Jiang,Yang Wu and others

Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics

Olivier Cinquin

A multi-modal fusion model with enhanced feature representation for chronic kidney disease progression prediction

Yixuan Qiao,Hong Zhou and others

ViTax: adaptive hierarchical viral taxonomy classification with a taxonomy belief tree on a foundation model

YuShuang He,Feng Zhou and others

Deconvolution of spatial transcriptomics data via graph contrastive learning and partial least square regression

Yuanyuan Mo,Juan Liu and others

PTTM: dissecting the profile of tumor tissue microbiome to reveal microbiota features and associations with host transcriptome

Ruiqian Yao,Lu Sun and others

B-Lightning: using bait genes for marker gene hunting in single-cell data with complex heterogeneity

Yiren Shao,Qi Gao and others

Introducing TEC-LncMir for prediction of lncRNA-miRNA interactions through deep learning of RNA sequences

Tingpeng Yang,Yonghong He and others

Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP

Qiqi Lu,Zhixian Liu and others

mmGEBLUP: an advanced genomic prediction scheme for genetic improvement of complex traits in crops through integrative analysis of major genes, polygenes, and genotype'environment interactions

Qi-Xin Zhang,Tianneng Zhu and others

CpGFuse: a holistic approach for accurate identification of methylation states of DNA CpG sites

Sehi Park,Kil To Chong and others

Incremental modelling and analysis of biological systems with fuzzy hybrid Petri nets

George Assaf,Fei Liu and others

Deciphering optimal molecular determinants of non-hemolytic, cell-penetrating antimicrobial peptides through bioinformatics and Random Forest

Ashok Kumar,Sonia Chadha and others

iDOMO: identification of drug combinations via multi-set operations for treating diseases

Xianxiao Zhou,Ling Wu and others

Learning genotype'phenotype associations from gaps in multi-species sequence alignments

Uwaise Ibna Islam,Andre Luiz Campelo dos Santos and others

CSGDN: contrastive signed graph diffusion network for predicting crop gene'phenotype associations

Yiru Pan,Xingyu Ji and others

DECA: harnessing interpretable transformer model for cellular deconvolution of chromatin accessibility profile

Shijie Luo,Ming Zhu and others

FORAlign: accelerating gap-affine DNA pairwise sequence alignment using FOR-blocks based on Four Russians approach with linear space complexity

Yanming Wei,Tong Zhou and others

cfDiffusion: diffusion-based efficient generation of high quality scRNA-seq data with classifier-free guidance

Tianjiao Zhang,Zhongqian Zhao and others

ESM-BBB-Pred: a fine-tuned ESM 2.0 and deep neural networks for the identification of blood'brain barrier peptides

Ansar Naseem,Fahad Alturise and others

Noninvasive fetal genotyping using deep neural networks

Yonathan Schwammenthal,Tom Rabinowitz and others

A large language model framework for literature-based disease'gene association prediction

Peng-Hsuan Li,Yih-Yun Sun and others

scMitoMut for calling mitochondrial lineage-related mutations in single cells

Wenjie Sun,Daphne van Ginneken and others

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