Bioinformatics advances最新文献_第6页

Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction. 评估优点：对肿瘤亚克隆重建中模拟技术有效性的看法。

IF 2.4

Bioinformatics advances Pub Date : 2024-06-26 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae094

Jiaying Lai, Yi Yang, Yunzhou Liu, Robert B Scharpf, Rachel Karchin

引用次数: 0

Perspectives on computational modeling of biological systems and the significance of the SysMod community. 关于生物系统计算建模的观点以及 SysMod 社区的意义。

IF 2.4

Bioinformatics advances Pub Date : 2024-06-26 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae090

Bhanwar Lal Puniya, Meghna Verma, Chiara Damiani, Shaimaa Bakr, Andreas Dräger

{"title":"Perspectives on computational modeling of biological systems and the significance of the SysMod community.","authors":"Bhanwar Lal Puniya, Meghna Verma, Chiara Damiani, Shaimaa Bakr, Andreas Dräger","doi":"10.1093/bioadv/vbae090","DOIUrl":"10.1093/bioadv/vbae090","url":null,"abstract":"Motivation: In recent years, applying computational modeling to systems biology has caused a substantial surge in both discovery and practical applications and a significant shift in our understanding of the complexity inherent in biological systems.Results: In this perspective article, we briefly overview computational modeling in biology, highlighting recent advancements such as multi-scale modeling due to the omics revolution, single-cell technology, and integration of artificial intelligence and machine learning approaches. We also discuss the primary challenges faced: integration, standardization, model complexity, scalability, and interdisciplinary collaboration. Lastly, we highlight the contribution made by the Computational Modeling of Biological Systems (SysMod) Community of Special Interest (COSI) associated with the International Society of Computational Biology (ISCB) in driving progress within this rapidly evolving field through community engagement (via both in person and virtual meetings, social media interactions), webinars, and conferences.Availability and implementation: Additional information about SysMod is available at https://sysmod.info.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11213628/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141474678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

racoon_clip-a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data. racoon_clip - 用于 iCLIP 和 eCLIP 数据单核苷酸分析的完整管道。

IF 2.4

Bioinformatics advances Pub Date : 2024-06-26 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae084

Melina Klostermann, Kathi Zarnack

{"title":"racoon_clip-a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data.","authors":"Melina Klostermann, Kathi Zarnack","doi":"10.1093/bioadv/vbae084","DOIUrl":"10.1093/bioadv/vbae084","url":null,"abstract":"Motivation: A vast variety of biological questions connected to RNA-binding proteins can be tackled with UV crosslinking and immunoprecipitation (CLIP) experiments. However, the processing and analysis of CLIP data are rather complex. Moreover, different types of CLIP experiments like iCLIP or eCLIP are often processed in different ways, reducing comparability between multiple experiments. Therefore, we aimed to build an easy-to-use computational tool for the processing of CLIP data that can be used for both iCLIP and eCLIP data, as well as data from other truncation-based CLIP methods.Results: Here, we introduce racoon_clip, a sustainable and fully automated pipeline for the complete processing of iCLIP and eCLIP data to extract RNA binding signal at single-nucleotide resolution. racoon_clip is easy to install and execute, with multiple pre-settings and fully customizable parameters, and outputs a conclusive summary report with visualizations and statistics for all analysis steps.Availability and implementation: racoon_clip is implemented as a Snakemake-powered command line tool (Snakemake version ≥7.22, Python version ≥3.9). The latest release can be downloaded from GitHub (https://github.com/ZarnackGroup/racoon_clip/tree/main) and installed via pip. A detailed documentation, including installation, usage, and customization, can be found at https://racoon-clip.readthedocs.io/en/latest/. The example datasets can be downloaded from the Short Read Archive (SRA; iCLIP: SRR5646576, SRR5646577, SRR5646578) or the ENCODE Project (eCLIP: ENCSR202BFN).","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11213630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Optimal linear ensemble of binary classifiers. 二元分类器的最优线性组合。

IF 2.4

Bioinformatics advances Pub Date : 2024-06-25 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae093

Mehmet Eren Ahsen, Robert Vogel, Gustavo Stolovitzky

{"title":"Optimal linear ensemble of binary classifiers.","authors":"Mehmet Eren Ahsen, Robert Vogel, Gustavo Stolovitzky","doi":"10.1093/bioadv/vbae093","DOIUrl":"10.1093/bioadv/vbae093","url":null,"abstract":"Motivation: The integration of vast, complex biological data with computational models offers profound insights and predictive accuracy. Yet, such models face challenges: poor generalization and limited labeled data.Results: To overcome these difficulties in binary classification tasks, we developed the Method for Optimal Classification by Aggregation (MOCA) algorithm, which addresses the problem of generalization by virtue of being an ensemble learning method and can be used in problems with limited or no labeled data. We developed both an unsupervised (uMOCA) and a supervised (sMOCA) variant of MOCA. For uMOCA, we show how to infer the MOCA weights in an unsupervised way, which are optimal under the assumption of class-conditioned independent classifier predictions. When it is possible to use labels, sMOCA uses empirically computed MOCA weights. We demonstrate the performance of uMOCA and sMOCA using simulated data as well as actual data previously used in Dialogue on Reverse Engineering and Methods (DREAM) challenges. We also propose an application of sMOCA for transfer learning where we use pre-trained computational models from a domain where labeled data are abundant and apply them to a different domain with less abundant labeled data.Availability and implementation: GitHub repository, https://github.com/robert-vogel/moca.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11249386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621894","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SlowMoMan: a web app for discovery of important features along user-drawn trajectories in 2D embeddings. SlowMoMan：一款在二维嵌入中沿着用户绘制的轨迹发现重要特征的网络应用程序。

IF 2.4

Bioinformatics advances Pub Date : 2024-06-21 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae095

Kiran Deol, Griffin M Weber, Yun William Yu

{"title":"SlowMoMan: a web app for discovery of important features along user-drawn trajectories in 2D embeddings.","authors":"Kiran Deol, Griffin M Weber, Yun William Yu","doi":"10.1093/bioadv/vbae095","DOIUrl":"10.1093/bioadv/vbae095","url":null,"abstract":"Motivation: Nonlinear low-dimensional embeddings allow humans to visualize high-dimensional data, as is often seen in bioinformatics, where datasets may have tens of thousands of dimensions. However, relating the axes of a nonlinear embedding to the original dimensions is a nontrivial problem. In particular, humans may identify patterns or interesting subsections in the embedding, but cannot easily identify what those patterns correspond to in the original data.Results: Thus, we present SlowMoMan (SLOW Motions on MANifolds), a web application which allows the user to draw a one-dimensional path onto a 2D embedding. Then, by back-projecting the manifold to the original, high-dimensional space, we sort the original features such that those most discriminative along the manifold are ranked highly. We show a number of pertinent use cases for our tool, including trajectory inference, spatial transcriptomics, and automatic cell classification.Availability and implementation: Software: https://yunwilliamyu.github.io/SlowMoMan/; Code: https://github.com/yunwilliamyu/SlowMoMan.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11220466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Making proteomics accessible: RokaiXplorer for interactive analysis of phospho-proteomic data. 让蛋白质组学变得触手可及：用于交互式分析磷酸蛋白组数据的 RokaiXplorer。

IF 2.4

Bioinformatics advances Pub Date : 2024-06-20 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae077

Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Marzieh Ayati, Mark R Chance, Mehmet Koyutürk

{"title":"Making proteomics accessible: RokaiXplorer for interactive analysis of phospho-proteomic data.","authors":"Serhan Yılmaz, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Marzieh Ayati, Mark R Chance, Mehmet Koyutürk","doi":"10.1093/bioadv/vbae077","DOIUrl":"10.1093/bioadv/vbae077","url":null,"abstract":"Summary: We present RokaiXplorer, an intuitive web tool designed to address the scarcity of user-friendly solutions for proteomics and phospho-proteomics data analysis and visualization. RokaiXplorer streamlines data processing, analysis, and visualization through an interactive online interface, making it accessible to researchers without specialized training in proteomics or data science. With its comprehensive suite of modules, RokaiXplorer facilitates phospho-proteomic analysis at the level of phosphosites, proteins, kinases, biological processes, and pathways. The tool offers functionalities such as data normalization, statistical testing, activity inference, pathway enrichment, subgroup analysis, automated report generation, and multiple visualizations, including volcano plots, bar plots, heat maps, and network views. As a unique feature, RokaiXplorer allows researchers to effortlessly deploy their own data browsers, enabling interactive sharing of research data and findings. Overall, RokaiXplorer fills an important gap in phospho-proteomic data analysis by providing the ability to comprehensively analyze data at multiple levels within a single application.Availability and implementation: Access RokaiXplorer at: http://explorer.rokai.io.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11415779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Differentiable phylogenetics via hyperbolic embeddings with Dodonaphy. 通过双曲嵌入与 Dodonaphy 的可微分系统学

IF 2.4

Bioinformatics advances Pub Date : 2024-06-19 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae082

Matthew Macaulay, Mathieu Fourment

{"title":"Differentiable phylogenetics via hyperbolic embeddings with Dodonaphy.","authors":"Matthew Macaulay, Mathieu Fourment","doi":"10.1093/bioadv/vbae082","DOIUrl":"10.1093/bioadv/vbae082","url":null,"abstract":"Motivation: Navigating the high dimensional space of discrete trees for phylogenetics presents a challenging problem for tree optimization. To address this, hyperbolic embeddings of trees offer a promising approach to encoding trees efficiently in continuous spaces. However, they require a differentiable tree decoder to optimize the phylogenetic likelihood. We present soft-NJ, a differentiable version of neighbour joining that enables gradient-based optimization over the space of trees.Results: We illustrate the potential for differentiable optimization over tree space for maximum likelihood inference. We then perform variational Bayesian phylogenetics by optimizing embedding distributions in hyperbolic space. We compare the performance of this approximation technique on eight benchmark datasets to state-of-the-art methods. Results indicate that, while this technique is not immune from local optima, it opens a plethora of powerful and parametrically efficient approach to phylogenetics via tree embeddings.Availability and implementation: Dodonaphy is freely available on the web at https://www.github.com/mattapow/dodonaphy. It includes an implementation of soft-NJ.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evergene: an interactive webtool for large-scale gene-centric analysis of primary tumours. Evergene：以基因为中心对原发性肿瘤进行大规模分析的交互式网络工具。

IF 2.4

Bioinformatics advances Pub Date : 2024-06-18 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae092

Anna Kennedy, Ella Richardson, Jonathan Higham, Panagiotis Kotsantis, Richard Mort, Barbara Bo-Ju Shih

{"title":"Evergene: an interactive webtool for large-scale gene-centric analysis of primary tumours.","authors":"Anna Kennedy, Ella Richardson, Jonathan Higham, Panagiotis Kotsantis, Richard Mort, Barbara Bo-Ju Shih","doi":"10.1093/bioadv/vbae092","DOIUrl":"10.1093/bioadv/vbae092","url":null,"abstract":"Motivation: The data sharing of large comprehensive cancer research projects, such as The Cancer Genome Atlas (TCGA), has improved the availability of high-quality data to research labs around the world. However, due to the volume and inherent complexity of high-throughput omics data, analysis of this is limited by the capacity for performing data processing through programming languages such as R or Python. Existing webtools lack functionality that supports large-scale analysis; typically, users can only input one gene, or a gene list condensed into a gene set, instead of individual gene-level analysis. Furthermore, analysis results are usually displayed without other sample-level molecular or clinical annotations. To address these gaps in the existing webtools, we have developed Evergene using R and Shiny.Results: Evergene is a user-friendly webtool that utilizes RNA-sequencing data, alongside other sample and clinical annotation, for large-scale gene-centric analysis, including principal component analysis (PCA), survival analysis (SA), and correlation analysis (CA). Moreover, Evergene achieves in-depth analysis of cancer transcriptomic data which can be explored through dimensional reduction methods, relating gene expression with clinical events or other sample information, such as ethnicity, histological classification, and molecular indices. Lastly, users can upload custom data to Evergene for analysis.Availability and implementation: Evergene webtool is available at https://bshihlab.shinyapps.io/evergene/. The source code and example user input dataset are available at https://github.com/bshihlab/evergene.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11213629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Discovering genomic islands in unannotated bacterial genomes using sequence embedding. 利用序列嵌入发现未注释细菌基因组中的基因组岛

IF 2.4

Bioinformatics advances Pub Date : 2024-06-17 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae089

Priyanka Banerjee, Oliver Eulenstein, Iddo Friedberg

{"title":"Discovering genomic islands in unannotated bacterial genomes using sequence embedding.","authors":"Priyanka Banerjee, Oliver Eulenstein, Iddo Friedberg","doi":"10.1093/bioadv/vbae089","DOIUrl":"10.1093/bioadv/vbae089","url":null,"abstract":"Motivation: Genomic islands (GEIs) are clusters of genes in bacterial genomes that are typically acquired by horizontal gene transfer. GEIs play a crucial role in the evolution of bacteria by rapidly introducing genetic diversity and thus helping them adapt to changing environments. Specifically of interest to human health, many GEIs contain pathogenicity and antimicrobial resistance genes. Detecting GEIs is, therefore, an important problem in biomedical and environmental research. There have been many previous studies for computationally identifying GEIs. Still, most of these studies rely on detecting anomalies in the unannotated nucleotide sequences or on a fixed set of known features on annotated nucleotide sequences.Results: Here, we present TreasureIsland, which uses a new unsupervised representation of DNA sequences to predict GEIs. We developed a high-precision boundary detection method featuring an incremental fine-tuning of GEI borders, and we evaluated the accuracy of this framework using a new comprehensive reference dataset, Benbow. We show that TreasureIsland's accuracy rivals other GEI predictors, enabling efficient and faster identification of GEIs in unannotated bacterial genomes.Availability and implementation: TreasureIsland is available under an MIT license at: https://github.com/FriedbergLab/GenomicIslandPrediction.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11193100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sensitive and error-tolerant annotation of protein-coding DNA with BATH. 利用 BATH 对蛋白质编码 DNA 进行灵敏且容错的注释。

IF 2.4

Bioinformatics advances Pub Date : 2024-06-14 eCollection Date: 2024-01-01 DOI: 10.1093/bioadv/vbae088

Genevieve R Krause, Walt Shands, Travis J Wheeler

{"title":"Sensitive and error-tolerant annotation of protein-coding DNA with BATH.","authors":"Genevieve R Krause, Walt Shands, Travis J Wheeler","doi":"10.1093/bioadv/vbae088","DOIUrl":"10.1093/bioadv/vbae088","url":null,"abstract":"Summary: We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes.Availability and implementation: The software is available at https://github.com/TravisWheelerLab/BATH.","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11223822/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141536125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0