Bioinformatics最新文献

{"title":"MEHunter: Transformer-based mobile element variant detection from long reads","authors":"Tao Jiang, Zuji Zhou, Zhendong Zhang, Shuqi Cao, Yadong Wang, Yadong Liu","doi":"10.1093/bioinformatics/btae557","DOIUrl":"https://doi.org/10.1093/bioinformatics/btae557","url":null,"abstract":"Summary Mobile genetic elements (MEs) are heritable mutagens that significantly contribute to genetic diseases. The advent of long-read sequencing technologies, capable of resolving large DNA fragments, offers promising prospects for the comprehensive detection of ME variants (MEVs). However, achieving high precision while maintaining recall performance remains challenging mainly brought by the variable length and similar content of MEV signatures, which are often obscured by the noise in long reads. Here, we propose MEHunter, a high-performance MEV detection approach utilizing a fine-tuned transformer model adept at identifying potential MEVs with fragmented features. Benchmark experiments on both simulated and real datasets demonstrate that MEHunter consistently achieves higher accuracy and sensitivity than the state-of-the-art tools. Furthermore, it is capable of detecting novel potentially individual-specific MEVs that have been overlooked in published population projects. Availability and Implementation MEHunter is available from https://github.com/120L021101/MEHunter. Supplementary information Supplementary data are available at Bioinformatics online.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"9 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142250870","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}

{"title":"Metabolic syndrome may be more frequent in treatment-naive sarcoidosis patients.","authors":"Arzu Cennet Işık, Murat Kavas, Mehmet Engin Tezcan","doi":"10.1007/s00393-022-01210-8","DOIUrl":"10.1007/s00393-022-01210-8","url":null,"abstract":"<p><strong>Introduction: </strong>Sarcoidosis is a chronic granulomatous multisystem inflammatory disease. An association between sarcoidosis and subclinical atherosclerosis has recently been demonstrated. However, there are limited publications on metabolic syndrome (MetS) and its metabolic changes in sarcoidosis. In this study, we evaluated our hypothesis that the frequency of MetS may also be increased in treatment-naive, newly diagnosed sarcoidosis patients.</p><p><strong>Methods: </strong>We included 133 newly diagnosed sarcoidosis patients, 133 age- and sex-matched controls, and 51 untreated rheumatoid arthritis (RA) patients as diseased controls. We then compared the frequency of MetS and MetS-related items in the three groups. The criteria defined for metabolic syndrome in the National Cholesterol Education Program (NCEP) Adult Treatment Panel III report (ATP III) were used to diagnose MetS.</p><p><strong>Results: </strong>MetS was more common in sarcoidosis than controls (odds ratio, OR: 5.3; 95% confidence interval, CI 95%: 2.4-11.5; p < 0.001) and was similar to RA. In addition, triglyceride and glucose levels, diastolic blood pressure measurements, and waist circumference of female sarcoidosis patients were significantly higher than in controls.</p><p><strong>Conclusion: </strong>We show that MetS is a frequent feature of sarcoidosis even before treatment is started. Therefore, clinicians should be aware of MetS both during treatment and during the course of the disease to reduce the risk of cardiovascular events.</p>","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"10 1","pages":"154-159"},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82812142","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}

{"title":"Coracle—A Machine Learning Framework to Identify Bacteria Associated with Continuous Variables","authors":"Sebastian Staab, Anny Cardénas, Raquel S Peixoto, Falk Schreiber, Christian R Voolstra","doi":"10.1093/bioinformatics/btad749","DOIUrl":"https://doi.org/10.1093/bioinformatics/btad749","url":null,"abstract":"Summary We present Coracle, an Artificial Intelligence (AI) framework that can identify associations between bacterial communities and continuous variables. Coracle uses an ensemble approach of prominent feature selection methods and machine learning (ML) models to identify features, i.e., bacteria, associated with a continuous variable, e.g. host thermal tolerance. The results are aggregated into a score that incorporates the performances of the different ML models and the respective feature importance, while also considering the robustness of feature selection. Additionally, regression coefficients provide first insights into the direction of the association. We show the utility of Coracle by analyzing associations between bacterial composition data (i.e., 16S rRNA Amplicon Sequence Variants, ASVs) and coral thermal tolerance (i.e., standardized short-term heat stress-derived diagnostics). This analysis identified high-scoring bacterial taxa that were previously found associated with coral thermal tolerance. Coracle scales with feature number and performs well with hundreds to thousands of features, corresponding to the typical size of current datasets. Coracle performs best if run at a higher taxonomic level first (e.g., order or family) to identify groups of interest that can subsequently be run at the ASV level. Availability and Implementation Coracle can be accessed via a dedicated web server that allows free and simple access: http://www.micportal.org/coracle/index. The underlying code is open-source and available via GitHub https://github.com/SebastianStaab/coracle.git. Supplementary information Example datasets and a tutorial are available on the web server webpage. Supplementary data are available at Bioinformatics online.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"1 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138823815","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}

{"title":"CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis","authors":"Anisha Haldar, Vishal H Oza, Nathaniel S DeVoss, Amanda D Clark, Brittany N Lasseigne","doi":"10.1093/bioinformatics/btad759","DOIUrl":"https://doi.org/10.1093/bioinformatics/btad759","url":null,"abstract":"Summary High throughput sequencing technologies have enabled cross-species comparative transcriptomic studies; however, there are numerous challenges for these studies due to biological and technical factors. We developed CoSIA (Cross-Species Investigation and Analysis), an Bioconductor R package and Shiny app that provides an alternative framework for cross-species transcriptomic comparison of non-diseased wild-type RNA sequencing gene expression data from Bgee across tissues and species (human, mouse, rat, zebrafish, fly, and nematode) through visualization of variability, diversity, and specificity metrics. Availability and Implementation https://github.com/lasseignelab/CoSIA Supplementary information See Supplementary Material","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"43 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138743822","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}

{"title":"LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism","authors":"Min Zeng, Yifan Wu, Yiming Li, Rui Yin, Chengqian Lu, Junwen Duan, Min Li","doi":"10.1093/bioinformatics/btad752","DOIUrl":"https://doi.org/10.1093/bioinformatics/btad752","url":null,"abstract":"Motivation There is mounting evidence that the subcellular localization of lncRNAs can provide valuable insights into their biological functions. In the real world of transcriptomes, lncRNAs are usually localized in multiple subcellular localizations. Furthermore, lncRNAs have specific localization patterns for different subcellular localizations. Although several computational methods have been developed to predict the subcellular localization of lncRNAs, few of them are designed for lncRNAs that have multiple subcellular localizations, and none of them take motif specificity into consideration. Results In this study, we proposed a novel deep learning model, called LncLocFormer, which uses only lncRNA sequences to predict multi-label lncRNA subcellular localization. LncLocFormer utilizes 8 Transformer blocks to model long-range dependencies within the lncRNA sequence and share information across the lncRNA sequence. To exploit the relationship between different subcellular localizations and find distinct localization patterns for different subcellular localizations, LncLocFormer employs a localization-specific attention mechanism. The results demonstrate that LncLocFormer outperforms existing state-of-the-art predictors on the hold-out test set. Furthermore, we conducted a motif analysis and found LncLocFormer can capture known motifs. Ablation studies confirmed the contribution of the localization-specific attention mechanism in improving the prediction performance. Availability The LncLocFormer web server is available at http://csuligroup.com:9000/LncLocFormer. The source code can be obtained from https://github.com/CSUBioGroup/LncLocFormer. Supplementary information Supplementary data are available at Bioinformatics online.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"20 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2023-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138743953","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}

{"title":"Clumppling: cluster matching and permutation program with integer linear programming","authors":"Xiran Liu, Naama M Kopelman, Noah A Rosenberg","doi":"10.1093/bioinformatics/btad751","DOIUrl":"https://doi.org/10.1093/bioinformatics/btad751","url":null,"abstract":"Motivation In the mixed-membership unsupervised clustering analyses commonly used in population genetics, multiple replicate data analyses can differ in their clustering solutions. Combinatorial algorithms assist in aligning clustering outputs from multiple replicates, so that clustering solutions can be interpreted and combined across replicates. Although several algorithms have been introduced, challenges exist in achieving optimal alignments and performing alignments in reasonable computation time. Results We present Clumppling, a method for aligning replicate solutions in mixed-membership unsupervised clustering. The method uses integer linear programming for finding optimal alignments, embedding the cluster alignment problem in standard combinatorial optimization frameworks. In example analyses, we find that it achieves solutions with preferred values of a desired objective function relative to those achieved by Pong, and that it proceeds with less computation time than Clumpak. It is also the first method to permit alignments across replicates with multiple arbitrary values of the number of clusters K. Availability Clumppling is available at https://github.com/PopGenClustering/Clumppling. Supplementary information Supplementary data are available online.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"25 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138692738","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}

{"title":"Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment","authors":"Marcos Díaz-Gay, Raviteja Vangara, Mark Barnes, Xi Wang, S M Ashiqul Islam, Ian Vermes, Stephen Duke, Nithish Bharadhwaj Narasimman, Ting Yang, Zichen Jiang, Sarah Moody, Sergey Senkin, Paul Brennan, Michael R Stratton, Ludmil B Alexandrov","doi":"10.1093/bioinformatics/btad756","DOIUrl":"https://doi.org/10.1093/bioinformatics/btad756","url":null,"abstract":"Motivation Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. To evaluate the mutational signatures operative in a cancer genome, one first needs to quantify their activities by estimating the number of mutations imprinted by each signature. Results Here we present SigProfilerAssignment, a desktop and an online computational framework for assigning all types of mutational signatures to individual samples. SigProfilerAssignment is the first tool that allows both analysis of copy-number signatures and probabilistic assignment of signatures to individual somatic mutations. As its computational engine, the tool uses a custom implementation of the forward stagewise algorithm for sparse regression and nonnegative least squares for numerical optimization. Analysis of 2,700 synthetic cancer genomes with and without noise demonstrates that SigProfilerAssignment outperforms four commonly used approaches for assigning mutational signatures. Availability SigProfilerAssignment is available under the BSD 2-clause license at https://github.com/AlexandrovLab/SigProfilerAssignment with a web implementation at https://cancer.sanger.ac.uk/signatures/assignment/. Supplementary information Supplementary data are available at Bioinformatics online.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"1 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138693242","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}

{"title":"Benchmarking and improving the performance of variant-calling pipelines with RecallME","authors":"G Vozza, E Bonetti, G Tini, V Favalli, G Frige’, G Bucci, S De Summa, M Zanfardino, F Zapelloni, L Mazzarella","doi":"10.1093/bioinformatics/btad722","DOIUrl":"https://doi.org/10.1093/bioinformatics/btad722","url":null,"abstract":"Motivation The steady increment of Whole Genome/Exome sequencing and the development of novel NGS-based gene panels requires continuous testing and validation of variant calling pipelines and the detection of sequencing-related issues to be maintained up-to-date and feasible for the clinical settings. State of the art tools are reliable when used to compute standard performance metrics. However, the need for an automated software to discriminate between bioinformatic and sequencing issues and to optimize variant calling parameters remains unmet. The aim of the current work is to present RecallME, a bioinformatic suite that tracks down difficult-to-detect variants as insertions and deletions in highly repetitive regions, thus providing the maximum reachable recall for both single nucleotide variants and small insertion and deletions and to precisely guide the user in the pipeline optimization process. Availability Source code is freely available under MIT license at https://github.com/mazzalab-ieo/recallme RecallME web application is available at https://translational-oncology-lab.shinyapps.io/recallme/ To use RecallME, users must obtain a license for ANNOVAR by themselves. Supplementary information Supplementary data are available at Bioinformatics online.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"78 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138684216","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}

{"title":"VSCode-Antimony: A Source Editor for Building, Analyzing, and Translating Antimony Models","authors":"Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H Gennari, Lucian P Smith, Joseph L Hellerstein, Herbert M Sauro","doi":"10.1093/bioinformatics/btad753","DOIUrl":"https://doi.org/10.1093/bioinformatics/btad753","url":null,"abstract":"Motivation Developing biochemical models in systems biology is a complex, knowledge-intensive activity. Some modelers (especially novices) benefit from model development tools with a graphical user interface (GUI). However, as with the development of complex software, text-based representations of models provide many benefits for advanced model development. At present, the tools for text-based model development are limited, typically just a textual editor that provides features such as copy, paste, find, and replace. Since these tools are not ”model aware”, they do not provide features for: (i) model building such as autocompletion of species names; (ii) model analysis such as hover messages that provide information about chemical species; and (iii) model translation to convert between model representations. We refer to these as BAT features. Results We present VSCode-Antimony, a tool for building, analyzing, and translating models written in the Antimony modeling language, a human readable representation of SBML models. VSCode-Antimony is a source editor, a tool with language-aware features. For example, there is autocompletion of variable names to assist with model building, hover messages that aid in model analysis, and translation between XML and Antimony representations of SBML models. These features result from making VSCode-Antimony model-aware by incorporating several sophisticated capabilities: analysis of the Antimony grammar (e.g., to identify model symbols and their types); a query system for accessing knowledge sources for chemical species and reactions; and automatic conversion between different model representations (e.g., between Antimony and SBML). Availability VSCode-Antimony is available as an open source extension in the VSCode Marketplace https://marketplace.visualstudio.com/items?itemName=stevem.vscode-antimony. Source code can be found at https://github.com/sys-bio/vscode-antimony. Supplementary information Documentation and downloads are available at the visual studio marketplace.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"4 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138683693","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}

{"title":"IntelliGenes: A novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles","authors":"William DeGroat, Dinesh Mendhe, Atharva Bhusari, Habiba Abdelhalim, Saman Zeeshan, Zeeshan Ahmed","doi":"10.1093/bioinformatics/btad755","DOIUrl":"https://doi.org/10.1093/bioinformatics/btad755","url":null,"abstract":"In this article, we present IntelliGenes, a novel machine learning (ML) pipeline for the multi-genomics exploration to discover biomarkers significant in disease prediction with high accuracy. IntelliGenes is based on a novel approach, which consists of nexus of conventional statistical techniques and cutting-edge ML algorithms using multi-genomic, clinical, and demographic data. IntelliGenes introduces a new metric i.e., Intelligent Gene (I-Gene) score to measure the importance of individual biomarkers for prediction of complex traits. I-Gene scores can be utilized to generate I-Gene profiles of individuals to comprehend the intricacies of ML used in disease prediction. IntelliGenes is user-friendly, portable, and a cross-platform application, compatible with Microsoft Windows, macOS, and UNIX operating systems. IntelliGenes not only holds the potential for personalized early detection of common and rare diseases in individuals, but also opens avenues for broader research using novel ML methodologies, ultimately leading to personalized interventions and novel treatment targets. Availability The source code of IntelliGenes is available on GitHub (https://github.com/drzeeshanahmed/intelligenes) and Code Ocean (https://codeocean.com/capsule/8638596/tree/v1). Supplementary information Supplementary data are available at Bioinformatics online.","PeriodicalId":8903,"journal":{"name":"Bioinformatics","volume":"6 1","pages":""},"PeriodicalIF":5.8,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138683428","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}