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Briefings in Bioinformatics  
Volume 25 Issue 4
 
July 2024
 
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Editorial
 
 
 
 
Attention mechanism models for precision medicine border= 
 
Liang Cheng
 
 
 
Articles
 
 
 
 
Predicting RNA polymerase II transcriptional elongation pausing and associated histone code border= 
 
Lixin Ren, Wanbiao Ma, Yong Wang
 
 
 
Predicting functional UTR variants by integrating region-specific features border=  
 
Guangyu Li, Jiayu Wu, Xiaoyue Wang
 
 
 
Mutational signatures of colorectal cancers according to distinct computational workflows border= 
 
Paolo Battuello, Giorgio Corti, Alice Bartolini, Annalisa Lorenzato, Alberto Sogari ...
 
 
 
SPIN: sex-specific and pathway-based interpretable neural network for sexual dimorphism analysis border= 
 
Euiseong Ko, Youngsoon Kim, Farhad Shokoohi, Tesfaye B Mersha, Mingon Kang
 
 
 
 
Benchmarking mapping algorithms for cell-type annotating in mouse brain by integrating single-nucleus RNA-seq and Stereo-seq data border= 
 
Quyuan Tao, Yiheng Xu, Youzhe He, Ting Luo, Xiaoming Li ...
 
 
 
RTCpredictor: identification of read-through chimeric RNAs from RNA sequencing data border= 
 
Sandeep Singh, Xinrui Shi, Samuel Haddox, Justin Elfman, Syed Basil Ahmad ...
 
 
 
A comprehensive benchmarking of machine learning algorithms and dimensionality reduction methods for drug sensitivity prediction border= 
 
Lea Eckhart, Kerstin Lenhof, Lisa-Marie Rolli, Hans-Peter Lenhof
 
 
 
Accurate prediction of antibody function and structure using bio-inspired antibody language model border= 
 
Hongtai Jing, Zhengtao Gao, Sheng Xu, Tao Shen, Zhangzhi Peng ...
 
 
 
irGSEA: the integration of single-cell rank-based gene set enrichment analysis border= 
 
Chuiqin Fan, Fuyi Chen, Yuanguo Chen, Liangping Huang, Manna Wang ...
 
 
 
 
A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data border= 
 
Lei Zhang, Shu Liang, Lin Wan
 
 
 
Complementary multi-modality molecular self-supervised learning via non-overlapping masking for property prediction border= 
 
Ao Shen, Mingzhi Yuan, Yingfan Ma, Jie Du, Manning Wang
 
 
 
IDMIR: identification of dysregulated miRNAs associated with disease based on a miRNA'miRNA interaction network constructed through gene expression data border= 
 
Jiashuo Wu, Xilong Zhao, Yalan He, Bingyue Pan, Jiyin Lai ...
 
 
 
SpaNCMG: improving spatial domains identification of spatial transcriptomics using neighborhood-complementary mixed-view graph convolutional network border= 
 
Zhihao Si, Hanshuang Li, Wenjing Shang, Yanan Zhao, Lingjiao Kong ...
 
 
 
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics border= 
 
Lequn Wang, Yaofeng Hu, Kai Xiao, Chuanchao Zhang, Qianqian Shi ...
 
 
 
PIPET: predicting relevant subpopulations in single-cell data using phenotypic information from bulk data border= 
 
Xinjia Ruan, Yu Cheng, Yuqing Ye, Yuhang Wang, Xinyi Chen ...
 
 
 
A hybrid demultiplexing strategy that improves performance and robustness of cell hashing border= 
 
Lei Li, Jiayi Sun, Yanbin Fu, Siriruk Changrob, Joshua J C McGrath ...
 
 
 
Themis: advancing precision oncology through comprehensive molecular subtyping and optimization border= 
 
Yue Xi, Kun Zheng, Fulan Deng, Yujun Liu, Hourong Sun ...
 
 
 
Efficient SARS-CoV-2 variant detection and monitoring with Spike Screen next-generation sequencing border= 
 
Alen Suljič, Tomaž Mark Zorec, Samo Zakotnik, Doroteja Vlaj, Rok Kogoj ...
 
 
 
NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach border= 
 
Zhengfa Xue, Aifen Zhou, Xiaoyan Zhu, Linxuan Li, Huanhuan Zhu ...
 
 
 
Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq border= 
 
Gregory Tong, Nasun Hah, Thomas F Martinez
 
 
 
VISH-Pred: an ensemble of fine-tuned ESM models for protein toxicity prediction border= 
 
Raghvendra Mall, Ankita Singh, Chirag N Patel, Gregory Guirimand, Filippo Castiglione
 
 
 
Integration of protein sequence and protein'protein interaction data by hypergraph learning to identify novel protein complexes border= 
 
Simin Xia, Dianke Li, Xinru Deng, Zhongyang Liu, Huaqing Zhu ...
 
 
 
Approaches to embryonic neurodevelopment: from neural cell to neural tube formation through mathematical models border= 
 
Ali H Rafati, Sâmia Joca, Regina T Vontell, Gregers Wegener, Maryam Ardalan
 
 
 
Deletion variants calling in third-generation sequencing data based on a dual-attention mechanism border= 
 
Han Wang, Chang Li, Xinyu Yu, Jingyang Gao
 
 
 
sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure border= 
 
Leandro A Bugnon, Leandro Di Persia, Matias Gerard, Jonathan Raad, Santiago Prochetto ...
 
 
 
SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition border= 
 
Ran Jia, Ying-Zan Ren, Po-Nian Li, Rui Gao, Yu-Sen Zhang
 
 
 
HiCDiff: single-cell Hi-C data denoising with diffusion models border=  
 
Yanli Wang, Jianlin Cheng
 
 
 
MANOCCA: a robust and computationally efficient test of covariance in high-dimension multivariate omics data border= 
 
Christophe Boetto, Arthur Frouin, Léo Henches, Antoine Auvergne, Yuka Suzuki ...
 
 
 
Improving multi-population genomic prediction accuracy using multi-trait GBLUP models which incorporate global or local genetic correlation information border= 
 
Jun Teng, Tingting Zhai, Xinyi Zhang, Changheng Zhao, Wenwen Wang ...
 
 
 
Spatiotemporal constrained RNA'protein heterogeneous network for protein complex identification border= 
 
Zeqian Li, Shilong Wang, Hai Cui, Xiaoxia Liu, Yijia Zhang
 
 
 
CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data 
 
Junyao Jiang, Jinlian Li, Sunan Huang, Fan Jiang, Yanran Liang ...
 
 
 
Improved prediction of DNA and RNA binding proteins with deep learning models border=  
 
Siwen Wu, Jun-tao Guo
 
 
 
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net border= 
 
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
 
 
 
Revolutionizing GPCR'ligand predictions: DeepGPCR with experimental validation for high-precision drug discovery border= 
 
Haiping Zhang, Hongjie Fan, Jixia Wang, Tao Hou, Konda Mani Saravanan ...
 
 
 
LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing border= 
 
Junbo Duan, Xinrui Zhao, Xiaoming Wu
 
 
 
AITeQ: a machine learning framework for Alzheimer's prediction using a distinctive five-gene signature border= 
 
Ishtiaque Ahammad, Anika Bushra Lamisa, Arittra Bhattacharjee, Tabassum Binte Jamal, Md Shamsul Arefin ...
 
 
 
LogicGep: Boolean networks inference using symbolic regression from time-series transcriptomic profiling data border= 
 
Dezhen Zhang, Shuhua Gao, Zhi-Ping Liu, Rui Gao
 
 
 
dCCA: detecting differential covariation patterns between two types of high-throughput omics data border= 
 
Hwiyoung Lee, Tianzhou Ma, Hongjie Ke, Zhenyao Ye, Shuo Chen
 
 
 
FastBiCmrMLM: a fast and powerful compressed variance component mixed logistic model for big genomic case-control genome-wide association study border= 
 
Jing-Tian Wang, Xiao-Yu Chang, Qiong Zhao, Yuan-Ming Zhang
 
 
 
GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach border= 
 
Cheng Zhu, Chengyun Zhang, Tianfeng Shang, Chenhao Zhang, Silong Zhai ...
 
 
 
Advancing drug-response prediction using multi-modal and -omics machine learning integration (MOMLIN): a case study on breast cancer clinical data border= 
 
Md Mamunur Rashid, Kumar Selvarajoo
 
 
 
Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny border= 
 
Regina Nóra Fiam, Csabai István, Solymosi Norbert
 
 
 
Hierarchical multimodal self-attention-based graph neural network for DTI prediction border= 
 
Jilong Bian, Hao Lu, Guanghui Dong, Guohua Wang
 
 
 
MvMRL: a multi-view molecular representation learning method for molecular property prediction border= 
 
Ru Zhang, Yanmei Lin, Yijia Wu, Lei Deng, Hao Zhang ...
 
 
 
HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses border= 
 
Qiang Yang, Long Xu, Weihe Dong, Xiaokun Li, Kuanquan Wang ...
 
 
 
TP-LMMSG: a peptide prediction graph neural network incorporating flexible amino acid property representation border= 
 
Nanjun Chen, Jixiang Yu, Liu Zhe, Fuzhou Wang, Xiangtao Li ...
 
 
 
Phylogenetic inference of inter-population transmission rates for infectious diseases border= 
 
Skylar A Gay, Gregory Ellison, Jianing Xu, Jialin Yang, Yiliang Wei ...
 
 
 
Optimizing in silico drug discovery: simulation of connected differential expression signatures and applications to benchmarking border= 
 
Catalina Gonzalez Gomez, Manuel Rosa-Calatrava, Julien Fouret
 
 
 
scPLAN: a hierarchical computational framework for single transcriptomics data annotation, integration and cell-type label refinement border= 
 
Qirui Guo, Musu Yuan, Lei Zhang, Minghua Deng
 
 
 
Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair border= 
 
Bijia Chen, Chao Ren, Zhangyi Ouyang, Jingxuan Xu, Kang Xu ...
 
 
 
Inference of gene regulatory networks based on directed graph convolutional networks border= 
 
Pi-Jing Wei, Ziqiang Guo, Zhen Gao, Zheng Ding, Rui-Fen Cao ...
 
 
 
A cloud-based training module for efficient de novo transcriptome assembly using Nextflow and Google cloud border= 
 
Ryan P Seaman, Ross Campbell, Valena Doe, Zelaikha Yosufzai, Joel H Graber
 
 
 
ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers border= 
 
Qingxiong Tan, Jin Xiao, Jiayang Chen, Yixuan Wang, Zeliang Zhang ...
 
 
 
AttABseq: an attention-based deep learning prediction method for antigen'antibody binding affinity changes based on protein sequences border= 
 
Ruofan Jin, Qing Ye, Jike Wang, Zheng Cao, Dejun Jiang ...
 
 
 
Detecting tipping points of complex diseases by network information entropy border=  
 
Chengshang Lyu, Lingxi Chen, Xiaoping Liu
 
 
 
Comprehensive single-cell RNA-seq analysis using deep interpretable generative modeling guided by biological hierarchy knowledge border= 
 
Hegang Chen, Yuyin Lu, Zhiming Dai, Yuedong Yang, Qing Li ...
 
 
 
PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning border= 
 
Renmao Tian, Jizhong Zhou, Behzad Imanian
 
 
 
Design patterns for the construction of computational biological models border=  
 
Mostafa Herajy, Fei Liu, Monika Heiner
 
 
 
CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data border= 
 
Yujin Kim, Minwoo Jeong, In Gyeong Koh, Chanhee Kim, Hyeji Lee ...
 
 
 
Characterizing efficient feature selection for single-cell expression analysis border= 
 
Juok Cho, Bukyung Baik, Hai C T Nguyen, Daeui Park, Dougu Nam
 
 
 
Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet border= 
 
Yuan Gao, Bin Ma, Qianshuai Xu, Yuna Peng, Huimin Gong ...
 
 
 
DrugMetric: quantitative drug-likeness scoring based on chemical space distance border= 
 
Bowen Li, Zhen Wang, Ziqi Liu, Yanxin Tao, Chulin Sha ...
 
 
 
Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster border= 
 
Tao Wang, Han Shu, Jialu Hu, Yongtian Wang, Jing Chen ...
 
 
 
EGPDI: identifying protein'DNA binding sites based on multi-view graph embedding fusion border= 
 
Mengxin Zheng, Guicong Sun, Xueping Li, Yongxian Fan
 
 
 
GLDADec: marker-gene guided LDA modeling for bulk gene expression deconvolution border= 
 
Iori Azuma, Tadahaya Mizuno, Hiroyuki Kusuhara
 
 
 
ctGAN: combined transformation of gene expression and survival data with generative adversarial network border= 
 
Jaeyoon Kim, Junhee Seok
 
 
 
RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies border= 
 
Aleksandr Ianevski, Aleksandr Kushnir, Kristen Nader, Mitro Miihkinen, Henri Xhaard ...
 
 
 
Exploring functional conservation in silico : a new machine learning approach to RNA-editing border= 
 
Michał Zawisza-Álvarez, Jesús Peñuela-Melero, Esteban Vegas, Ferran Reverter, Jordi Garcia-Fernàndez ...
 
 
 
GEMF: a novel geometry-enhanced mid-fusion network for PLA prediction border=  
 
Guoqiang Zhou, Yuke Qin, Qiansen Hong, Haoran Li, Huaming Chen ...
 
 
 
DeepGRNCS: deep learning-based framework for jointly inferring gene regulatory networks across cell subpopulations border= 
 
Yahui Lei, Xiao-Tai Huang, Xingli Guo, Kei Hang Katie Chan, Lin Gao
 
 
 
LDER-GE estimates phenotypic variance component of gene'environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information border= 
 
Zihan Dong, Wei Jiang, Hongyu Li, Andrew T DeWan, Hongyu Zhao
 
 
 
SVDF: enhancing structural variation detect from long-read sequencing via automatic filtering strategies border= 
 
Heng Hu, Runtian Gao, Wentao Gao, Bo Gao, Zhongjun Jiang ...
 
 
 
Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining border= 
 
Wenkai Xiang, Feisheng Zhong, Lin Ni, Mingyue Zheng, Xutong Li ...
 
 
 
Reusable tutorials for using cloud-based computing environments for the analysis of bacterial gene expression data from bulk RNA sequencing border= 
 
Steven Allers, Kyle A O'Connell, Thad Carlson, David Belardo, Benjamin L King
 
 
 
Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder border= 
 
Weibing Wang, Yusen Ye, Lin Gao
 
 
 
Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework border= 
 
Guoqing Zhang, Hui Wang, Zhiguo Zhang, Lu Zhang, Guibing Guo ...
 
 
 
Identifying pleiotropic genes via the composite test amidst the complexity of polygenic traits border= 
 
En-Yu Lai, Yen-Tsung Huang
 
 
 
DeepIDA-GRU: a deep learning pipeline for integrative discriminant analysis of cross-sectional and longitudinal multiview data with applications to inflammatory bowel disease classification border= 
 
Sarthak Jain, Sandra E Safo
 
 
 
GTE: a graph learning framework for prediction of T-cell receptors and epitopes binding specificity border= 
 
Feng Jiang, Yuzhi Guo, Hehuan Ma, Saiyang Na, Wenliang Zhong ...
 
 
 
PTFSpot: deep co-learning on transcription factors and their binding regions attains impeccable universality in plants border= 
 
Sagar Gupta, Veerbhan Kesarwani, Umesh Bhati, Jyoti, Ravi Shankar
 
 
 
MiRAGE: mining relationships for advanced generative evaluation in drug repositioning border= 
 
Aria Hassanali Aragh, Pegah Givehchian, Razieh Moslemi Amirani, Raziyeh Masumshah, Changiz Eslahchi
 
 
 
MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions border= 
 
Elias Farr, Daniel Dimitrov, Christina Schmidt, Denes Turei, Sebastian Lobentanzer ...
 
 
 
CELA-MFP: a contrast-enhanced and label-adaptive framework for multi-functional therapeutic peptides prediction border= 
 
Yitian Fang, Mingshuang Luo, Zhixiang Ren, Leyi Wei, Dong-Qing Wei
 
 
 
Introducing enzymatic cleavage features and transfer learning realizes accurate peptide half-life prediction across species and organs border= 
 
Xiaorong Tan, Qianhui Liu, Yanpeng Fang, Sen Yang, Fei Chen ...
 
 
 
Unveiling promising drug targets for autism spectrum disorder: insights from genetics, transcriptomics, and proteomics border= 
 
Rui Jiang, Wentao Huang, Xinqi Qiu, Jianyi Chen, Ruibang Luo ...
 
 
 
Comparative analyses of gene networks mediating cancer metastatic potentials across lineage types border= 
 
Sheng Wang, Emily K Stroup, Ting-You Wang, Rendong Yang, Zhe Ji
 
 
 
Review
 
 
 
 
Sharing sensitive data in life sciences: an overview of centralized and federated approaches border= 
 
Maria A Rujano, Jan-Willem Boiten, Christian Ohmann, Steve Canham, Sergio Contrino ...
 
 
 
Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides border= 
 
Montserrat Goles, Anamaría Daza, Gabriel Cabas-Mora, Lindybeth Sarmiento-Varón, Julieta Sepúlveda-Yañez ...
 
 
 
Multi-omic analysis tools for microbial metabolites prediction border=  
 
Shengbo Wu, Haonan Zhou, Danlei Chen, Yutong Lu, Yanni Li ...
 
 
 
Morphological profiling for drug discovery in the era of deep learning border=  
 
Qiaosi Tang, Ranjala Ratnayake, Gustavo Seabra, Zhe Jiang, Ruogu Fang ...
 
 
 
A comprehensive review and comparison of existing computational methods for protein function prediction border= 
 
Baohui Lin, Xiaoling Luo, Yumeng Liu, Xiaopeng Jin
 
 
 
Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review border= 
 
Runzhou Yu, Ziyi Huang, Theo Y C Lam, Yanni Sun
 
 
 
Image-based molecular representation learning for drug development: a survey border=  
 
Yue Li, Bingyan Liu, Jinyan Deng, Yi Guo, Hongbo Du
 
 
 
Antibody design using deep learning: from sequence and structure design to affinity maturation border= 
 
Sara Joubbi, Alessio Micheli, Paolo Milazzo, Giuseppe Maccari, Giorgio Ciano ...
 
 
 
Comparative analysis of integrative classification methods for multi-omics data border= 
 
Alexei Novoloaca, Camilo Broc, Laurent Beloeil, Wen-Han Yu, Jérémie Becker
 
 
 
A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation border= 
 
Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li ...
 
 
 
Biclustering data analysis: a comprehensive survey border=  
 
Eduardo N Castanho, Helena Aidos, Sara C Madeira
 
 
 
A survey of experimental and computational identification of small proteins border=  
 
Joshua Beals, Haiyan Hu, Xiaoman Li
 
 
 
A large-scale assessment of sequence database search tools for homology-based protein function prediction border= 
 
Chengxin Zhang, Lydia Freddolino
 
 
 
Case Study
 
 
 
 
Prediction of disease-free survival for precision medicine using cooperative learning on multi-omic data border= 
 
Georg Hahn, Dmitry Prokopenko, Julian Hecker, Sharon M Lutz, Kristina Mullin ...
 
 
 
Mechanistic study of acupuncture on the pterygopalatine ganglion to improve allergic rhinitis: analysis of multi-target effects based on bioinformatics/network topology strategie border= 
 
Meihui Tian, Weifang Sun, Yinhui Mao, Yanan Zhang, Huan Liu ...
 
 
 
Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks border= 
 
Sudipto Baul, Khandakar Tanvir Ahmed, Qibing Jiang, Guangyu Wang, Qian Li ...
 
 
 
CARTAR: a comprehensive web tool for identifying potential targets in chimeric antigen receptor therapies using TCGA and GTEx data border= 
 
Miguel Hernandez-Gamarra, Alba Salgado-Roo, Eduardo Dominguez, Elena María Goiricelaya Seco, Sara Veiga-Rúa ...
 
 
 
A novel deep machine learning algorithm with dimensionality and size reduction approaches for feature elimination: thyroid cancer diagnoses with randomly missing data border= 
 
Onder Tutsoy, Hilmi Erdem Sumbul
 
 
 
Discovering predisposing genes for hereditary breast cancer using deep learning border= 
 
Gal Passi, Sari Lieberman, Fouad Zahdeh, Omer Murik, Paul Renbaum ...
 
 
 
Precision probiotics supplement strategy in aging population based on gut microbiome composition border= 
 
Yi-Fang Chuang, Kang-Chen Fan, Yin-Yuan Su, Ming-Fong Wu, Yen-Ling Chiu ...
 
 
 
Letter to Editor
 
 
 
 
>From machine learning to clinical practice: phenotypic clusters of anti-MDA5 antibody-positive dermatomyositis border= 
 
Jacob J E Koopman, Katherine A Buhler, May Y Choi
 
 
 
Balancing Clinical Applicability and Scientific Depth in ML Models for MDA5-DM Prognosis: Response to From machine learning to clinical practice: phenotypic clusters of anti-MDA5 antibody-positive dermatomyositis'. By Koopman, Jacob; Buhler, Katherine; Choi, May border= 
 
Emily McLeish, Nataliya Slater, Frank L Mastaglia, Merrilee Needham, Jerome D Coudert
 
 
 
Opinion Article
 
 
 
 
A global initiative on addressing bioinformatics' grand challenges border= 
 
Asif M Khan, Esra Büşra Işık, Tin Wee Tan
 
 
 
Correction
 
 
 
 
Correction to: Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model border= 
 
 
 
 
Correction to: Prediction of protein'ligand binding affinity via deep learning models border= 
 
 
 
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