IEEE/ACM Transactions on Computational Biology and Bioinformatics最新文献_第3页

Orientation Determination of Cryo-EM Projection Images Using Reliable Common Lines and Spherical Embeddings 利用可靠的共线和球形嵌入确定冷冻电镜投影图像的方向

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-10-09 DOI: 10.1109/TCBB.2024.3476619

Xiangwen Wang;Qiaoying Jin;Li Zou;Xianghong Lin;Yonggang Lu

{"title":"Orientation Determination of Cryo-EM Projection Images Using Reliable Common Lines and Spherical Embeddings","authors":"Xiangwen Wang;Qiaoying Jin;Li Zou;Xianghong Lin;Yonggang Lu","doi":"10.1109/TCBB.2024.3476619","DOIUrl":"10.1109/TCBB.2024.3476619","url":null,"abstract":"Three-dimensional (3D) reconstruction in single-particle cryo-electron microscopy (cryo-EM) is a critical technique for recovering and studying the fine 3D structure of proteins and other biological macromolecules, where the primary issue is to determine the orientations of projection images with high levels of noise. This paper proposes a method to determine the orientations of cryo-EM projection images using reliable common lines and spherical embeddings. First, the reliability of common lines between projection images is evaluated using a weighted voting algorithm based on an iterative improvement technique and binarized weighting. Then, the reliable common lines are used to calculate the normal vectors and local \u0000<inline-formula><tex-math>$X$</tex-math></inline-formula>\u0000-axis vectors of projection images after two spherical embeddings. Finally, the orientations of projection images are determined by aligning the results of the two spherical embeddings using an orthogonal constraint. Experimental results on both synthetic and real cryo-EM projection image datasets demonstrate that the proposed method can achieve higher accuracy in estimating the orientations of projection images and higher resolution in reconstructing preliminary 3D structures than some common line-based methods, indicating that the proposed method is effective in single-particle cryo-EM 3D reconstruction.","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":"21 6","pages":"2496-2509"},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Knowledge Graph-Based Method for Drug-Drug Interaction Prediction With Contrastive Learning 基于知识图谱的药物相互作用预测方法与对比学习。

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-10-09 DOI: 10.1109/TCBB.2024.3477410

Jian Zhong;Haochen Zhao;Qichang Zhao;Jianxin Wang

{"title":"A Knowledge Graph-Based Method for Drug-Drug Interaction Prediction With Contrastive Learning","authors":"Jian Zhong;Haochen Zhao;Qichang Zhao;Jianxin Wang","doi":"10.1109/TCBB.2024.3477410","DOIUrl":"10.1109/TCBB.2024.3477410","url":null,"abstract":"Precisely predicting Drug-Drug Interactions (DDIs) carries the potential to elevate the quality and safety of drug therapies, protecting the well-being of patients, and providing essential guidance and decision support at every stage of the drug development process. In recent years, leveraging large-scale biomedical knowledge graphs has improved DDI prediction performance. However, the feature extraction procedures in these methods are still rough. More refined features may further improve the quality of predictions. To overcome these limitations, we develop a knowledge graph-based method for multi-typed DDI prediction with contrastive learning (KG-CLDDI). In KG-CLDDI, we combine drug knowledge aggregation features from the knowledge graph with drug topological aggregation features from the DDI graph. Additionally, we build a contrastive learning module that uses horizontal reversal and dropout operations to produce high-quality embeddings for drug-drug pairs. The comparison results indicate that KG-CLDDI is superior to state-of-the-art models in both the transductive and inductive settings. Notably, for the inductive setting, KG-CLDDI outperforms the previous best method by 17.49% and 24.97% in terms of AUC and AUPR, respectively. Furthermore, we conduct the ablation analysis and case study to show the effectiveness of KG-CLDDI. These findings illustrate the potential significance of KG-CLDDI in advancing DDI research and its clinical applications.","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":"21 6","pages":"2485-2495"},"PeriodicalIF":3.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Improving Molecule Generation and Drug Discovery with a Knowledge-enhanced Generative Model. 利用知识增强型生成模型改进分子生成和药物发现。

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-10-09 DOI: 10.1109/TCBB.2024.3477313

Aditya Malusare, Vaneet Aggarwal

引用次数: 0

RFLP-Inator: Interactive Web Platform for In Silico Simulation and Complementary Tools of the PCR-RFLP Technique RFLP-inator：用于 PCR-RFLP 技术硅学模拟和补充工具的交互式网络平台。

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-10-08 DOI: 10.1109/TCBB.2024.3476453

Kiefer Andre Bedoya Benites;Wilser Andrés García-Quispes

{"title":"RFLP-Inator: Interactive Web Platform for In Silico Simulation and Complementary Tools of the PCR-RFLP Technique","authors":"Kiefer Andre Bedoya Benites;Wilser Andrés García-Quispes","doi":"10.1109/TCBB.2024.3476453","DOIUrl":"10.1109/TCBB.2024.3476453","url":null,"abstract":"Polymerase chain reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) is an established molecular biology technique leveraging DNA sequence variability for organism identification, genetic disease detection, biodiversity analysis, etc. Traditional PCR-RFLP requires wet-laboratory procedures that can result in technical errors, procedural challenges, and financial costs. With the aim of providing an accessible and efficient PCR-RFLP technique complement, we introduce RFLP-inator. This is a comprehensive web-based platform developed in R using the package Shiny, which simulates the PCR-RFLP technique, integrates analysis capabilities, and offers complementary tools for both pre- and post-evaluation of in vitro results. We developed the RFLP-inator's algorithm independently and our platform offers seven dynamic tools: RFLP simulator, Pattern identifier, Enzyme selector, RFLP analyzer, Multiplex PCR, Restriction map maker, and Gel plotter. Moreover, the software includes a restriction pattern database of more than 250,000 sequences of the bacterial 16S rRNA gene. We successfully validated the core tools against published research findings. This new platform is open access and user-friendly, offering a valuable resource for researchers, educators, and students specializing in molecular genetics. RFLP-inator not only streamlines RFLP technique application but also supports pedagogical efforts in genetics, illustrating its utility and reliability.","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":"21 6","pages":"2510-2517"},"PeriodicalIF":3.6,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10709661","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LINgroups as a Robust Principled Approach to Compare and Integrate Multiple Bacterial Taxonomies 将 LINgroups 作为一种可靠的原则性方法来比较和整合多种细菌分类法。

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-10-07 DOI: 10.1109/TCBB.2024.3475917

Reza Mazloom;N. Tessa Pierce-Ward;Parul Sharma;Leighton Pritchard;C. Titus Brown;Boris A. Vinatzer;Lenwood S. Heath

{"title":"LINgroups as a Robust Principled Approach to Compare and Integrate Multiple Bacterial Taxonomies","authors":"Reza Mazloom;N. Tessa Pierce-Ward;Parul Sharma;Leighton Pritchard;C. Titus Brown;Boris A. Vinatzer;Lenwood S. Heath","doi":"10.1109/TCBB.2024.3475917","DOIUrl":"10.1109/TCBB.2024.3475917","url":null,"abstract":"As a central organizing principle of biology, bacteria and archaea are classified into a hierarchical structure across taxonomic ranks from kingdom to subspecies. Traditionally, this organization was based on observable characteristics of form and chemistry but recently, bacterial taxonomy has been robustly quantified using comparisons of sequenced genomes, as exemplified in the Genome Taxonomy Database (GTDB). Such genome-based taxonomies resolve genomes down to genera and species and are useful in many contexts yet lack the flexibility and resolution of a fine-grained approach. The Life Identification Number (LIN) approach is a common, quantitative framework to tie existing (and future) bacterial taxonomies together, increase the resolution of genome-based discrimination of taxa, and extend taxonomic identification below the species level in a principled way. Utilizing LINgroup as an organizational concept helps resolve some of the confusion and unforeseen negative effects resulting from nomenclature changes of microorganisms that are closely related by overall genomic similarity (often due to genome-based reclassification). Our experimental results demonstrate the value of LINs and LINgroups in mapping between taxonomies, translating between different nomenclatures, and integrating them into a single taxonomic framework. They also reveal the robustness of LIN assignment to hyper-parameter changes when considering within-species taxonomic groups.","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":"21 6","pages":"2304-2314"},"PeriodicalIF":3.6,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LEC-Codec: Learning-Based Genome Data Compression LEC-Codec：基于学习的基因组数据压缩

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-10-03 DOI: 10.1109/TCBB.2024.3473899

Zhenhao Sun;Meng Wang;Shiqi Wang;Sam Kwong

引用次数: 0

MG-TCCA: Tensor Canonical Correlation Analysis across Multiple Groups. MG-TCCA：跨多组的张量典型相关分析。

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-09-30 DOI: 10.1109/TCBB.2024.3471930

Zhuoping Zhou, Boning Tong, Davoud Ataee Tarzanagh, Bojian Hou, Andrew J Saykin, Qi Long, Li Shen

{"title":"MG-TCCA: Tensor Canonical Correlation Analysis across Multiple Groups.","authors":"Zhuoping Zhou, Boning Tong, Davoud Ataee Tarzanagh, Bojian Hou, Andrew J Saykin, Qi Long, Li Shen","doi":"10.1109/TCBB.2024.3471930","DOIUrl":"10.1109/TCBB.2024.3471930","url":null,"abstract":"<p><p>Tensor Canonical Correlation Analysis (TCCA) is a commonly employed statistical method utilized to examine linear associations between two sets of tensor datasets. However, the existing TCCA models fail to adequately address the heterogeneity present in real-world tensor data, such as brain imaging data collected from diverse groups characterized by factors like sex and race. Consequently, these models may yield biased outcomes. In order to surmount this constraint, we propose a novel approach called Multi-Group TCCA (MG-TCCA), which enables the joint analysis of multiple subgroups. By incorporating a dual sparsity structure and a block coordinate ascent algorithm, our MG-TCCA method effectively addresses heterogeneity and leverages information across different groups to identify consistent signals. This novel approach facilitates the quantification of shared and individual structures, reduces data dimensionality, and enables visual exploration. To empirically validate our approach, we conduct a study focused on investigating correlations between two brain positron emission tomography (PET) modalities (AV-45 and FDG) within an Alzheimer's disease (AD) cohort. Our results demonstrate that MG-TCCA surpasses traditional TCCA and Sparse TCCA (STCCA) in identifying sex-specific cross-modality imaging correlations. This heightened performance of MG-TCCA provides valuable insights for the characterization of multimodal imaging biomarkers in AD.</p>","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":"PP ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing Spatial Domain Identification in Spatially Resolved Transcriptomics Using Graph Convolutional Networks With Adaptively Feature-Spatial Balance and Contrastive Learning 利用具有自适应特征空间平衡和对比学习功能的图卷积网络增强空间分辨转录组学中的空间域识别能力

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-09-27 DOI: 10.1109/TCBB.2024.3469164

Xuena Liang;Junliang Shang;Jin-Xing Liu;Chun-Hou Zheng;Juan Wang

{"title":"Enhancing Spatial Domain Identification in Spatially Resolved Transcriptomics Using Graph Convolutional Networks With Adaptively Feature-Spatial Balance and Contrastive Learning","authors":"Xuena Liang;Junliang Shang;Jin-Xing Liu;Chun-Hou Zheng;Juan Wang","doi":"10.1109/TCBB.2024.3469164","DOIUrl":"10.1109/TCBB.2024.3469164","url":null,"abstract":"Recent advancements in spatially transcriptomics (ST) technologies have enabled the comprehensive measurement of gene expression profiles while preserving the spatial information of cells. Combining gene expression profiles and spatial information has been the most commonly used method to identify spatial functional domains and genes. However, most existing spatial domain decipherer methods are more focused on spatially neighboring structures and fail to take into account balancing the self-characteristics and the spatial structure dependency of spots. Therefore, we propose a novel model called SpaGCAC, which recognizes spatial domains with the help of an adaptive feature-spatial balanced graph convolutional network named AFSBGCN. The AFSBGCN can dynamically learn the relationship between spatial local topology structures and the self-characteristics of spots by adaptively increasing or declining the weight on the self-characteristics during message aggregation. Moreover, to better capture the local structures of spots, SpaGCAC exploits a local topology structure contrastive learning strategy. Meanwhile, SpaGCAC utilizes a probability distribution contrastive learning strategy to increase the similarity of probability distributions for points belonging to the same category. We validate the performance of SpaGCAC for spatial domain identification on four spatial transcriptomic datasets. In comparison with seven spatial domain recognition methods, SpaGCAC achieved the highest NMI median of 0.683 and the second highest ARI median of 0.559 on the multi-slice DLPFC dataset. SpaGCAC achieved the best results on all three other single-slice datasets. The above-mentioned results show that SpaGCAC outperforms most existing methods, providing enhanced insights into tissue heterogeneity.","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":"21 6","pages":"2406-2417"},"PeriodicalIF":3.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Protein-Context Enhanced Master Slave Framework for Zero-Shot Drug Target Interaction Prediction 用于零注射药物靶点相互作用预测的蛋白质-上下文增强型主从框架。

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-09-27 DOI: 10.1109/TCBB.2024.3468434

Yuyang Xu;Jingbo Zhou;Haochao Ying;Jintai Chen;Wei Chen;Danny Z. Chen;Jian Wu

{"title":"A Protein-Context Enhanced Master Slave Framework for Zero-Shot Drug Target Interaction Prediction","authors":"Yuyang Xu;Jingbo Zhou;Haochao Ying;Jintai Chen;Wei Chen;Danny Z. Chen;Jian Wu","doi":"10.1109/TCBB.2024.3468434","DOIUrl":"10.1109/TCBB.2024.3468434","url":null,"abstract":"Drug Target Interaction (DTI) prediction plays a crucial role in in-silico drug discovery, especially for deep learning (DL) models. Along this line, existing methods usually first extract features from drugs and target proteins, and use drug-target pairs to train DL models. However, these DL-based methods essentially rely on similar structures and patterns defined by the homologous proteins from a large amount of data. When few drug-target interactions are known for a newly discovered protein and its homologous proteins, prediction performance can suffer notable reduction. In this paper, we propose a novel Protein-Context enhanced Master/Slave Framework (PCMS), for zero-shot DTI prediction. This framework facilitates the efficient discovery of ligands for newly discovered target proteins, addressing the challenge of predicting interactions without prior data. Specifically, the PCMS framework consists of two main components: a Master Learner and a Slave Learner. The Master Learner first learns the target protein context information, and then adaptively generates the corresponding parameters for the Slave Learner. The Slave Learner then perform zero-shot DTI prediction in different protein contexts. Extensive experiments verify the effectiveness of our PCMS compared to state-of-the-art methods in various metrics on two public datasets.","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":"21 6","pages":"2359-2370"},"PeriodicalIF":3.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition 预测稳定群落组成的博弈论通量平衡分析模型

IF 3.6 3区生物学

IEEE/ACM Transactions on Computational Biology and Bioinformatics Pub Date : 2024-09-27 DOI: 10.1109/TCBB.2024.3470592

Garud Iyengar;Mitch Perry

{"title":"Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition","authors":"Garud Iyengar;Mitch Perry","doi":"10.1109/TCBB.2024.3470592","DOIUrl":"10.1109/TCBB.2024.3470592","url":null,"abstract":"Models for microbial interactions attempt to understand and predict the steady state network of inter-species relationships in a community, e.g. competition for shared metabolites, and cooperation through cross-feeding. Flux balance analysis (FBA) is an approach that was introduced to model the interaction of a particular microbial species with its environment. This approach has been extended to analyzing interactions in a community of microbes; however, these approaches have two important drawbacks: first, one has to numerically solve a differential equation to identify the steady state, and second, there are no methods available to analyze the stability of the steady state. We propose a game theory based community FBA model wherein species compete to maximize their individual growth rate, and the state of the community is given by the resulting Nash equilibrium. We develop a computationally efficient method for directly computing the steady state biomasses and fluxes without solving a differential equation. We also develop a method to determine the stability of a steady state to perturbations in the biomasses and to invasion by new species. We report the results of applying our proposed framework to a small community of four \u0000<italic>E. coli</i>\u0000 mutants that compete for externally supplied glucose, as well as cooperate since the mutants are auxotrophic for metabolites exported by other mutants, and a more realistic model for a gut microbiome consisting of nine species.","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":"21 6","pages":"2394-2405"},"PeriodicalIF":3.6,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142345923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0