NAR Genomics and Bioinformatics最新文献_第6页

HiCrayon reveals distinct layers of multi-state 3D chromatin organization. HiCrayon揭示了不同层次的多状态三维染色质组织。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-18 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae182

Ben Nolan, Hannah L Harris, Achyuth Kalluchi, Timothy E Reznicek, Christopher T Cummings, M Jordan Rowley

{"title":"HiCrayon reveals distinct layers of multi-state 3D chromatin organization.","authors":"Ben Nolan, Hannah L Harris, Achyuth Kalluchi, Timothy E Reznicek, Christopher T Cummings, M Jordan Rowley","doi":"10.1093/nargab/lqae182","DOIUrl":"10.1093/nargab/lqae182","url":null,"abstract":"Chromatin contact maps are often shown as 2D heatmaps and visually compared to 1D genomic data by simple juxtaposition. While common, this strategy is imprecise, placing the onus on the reader to align features with each other. To remedy this, we developed HiCrayon, an interactive tool that facilitates the integration of 3D chromatin organization maps and 1D datasets. This visualization method integrates data from genomic assays directly into the chromatin contact map by coloring interactions according to 1D signal. HiCrayon is implemented using R shiny and python to create a graphical user interface application, available in both web and containerized format to promote accessibility. We demonstrate the utility of HiCrayon in visualizing the effectiveness of compartment calling and the relationship between ChIP-seq and various features of chromatin organization. We also demonstrate the improved visualization of other 3D genomic phenomena, such as differences between loops associated with CTCF/cohesin versus those associated with H3K27ac. We then demonstrate HiCrayon's visualization of organizational changes that occur during differentiation and use HiCrayon to detect compartment patterns that cannot be assigned to either A or B compartments, revealing a distinct third chromatin compartment.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae182"},"PeriodicalIF":4.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11655295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865633","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

New developments for the Quest for Orthologs benchmark service. Quest for Orthologs基准服务的新开发。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-11 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae167

Adrian Altenhoff, Yannis Nevers, Vinh Tran, Dushyanth Jyothi, Maria Martin, Salvatore Cosentino, Sina Majidian, Marina Marcet-Houben, Diego Fuentes-Palacios, Emma Persson, Thomas Walsh, Odile Lecompte, Toni Gabaldón, Steven Kelly, Yanhui Hu, Wataru Iwasaki, Salvador Capella-Gutierrez, Christophe Dessimoz, Paul D Thomas, Ingo Ebersberger, Erik Sonnhammer

{"title":"New developments for the Quest for Orthologs benchmark service.","authors":"Adrian Altenhoff, Yannis Nevers, Vinh Tran, Dushyanth Jyothi, Maria Martin, Salvatore Cosentino, Sina Majidian, Marina Marcet-Houben, Diego Fuentes-Palacios, Emma Persson, Thomas Walsh, Odile Lecompte, Toni Gabaldón, Steven Kelly, Yanhui Hu, Wataru Iwasaki, Salvador Capella-Gutierrez, Christophe Dessimoz, Paul D Thomas, Ingo Ebersberger, Erik Sonnhammer","doi":"10.1093/nargab/lqae167","DOIUrl":"10.1093/nargab/lqae167","url":null,"abstract":"The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengths and weaknesses of newly developed and existing orthology inference methods. The web server allows different inference methods to be compared in a standardized way using the same proteome data. The benchmark results are useful for developing new methods and can help researchers to guide their choice of orthology method for applications in comparative genomics and phylogenetic analysis. We here present a new release of the Orthology Benchmark Service with a new benchmark based on feature architecture similarity as well as updated reference proteomes. We further provide a meta-analysis of the public predictions from 18 different orthology assignment methods to reveal how they relate in terms of ortholog predictions and benchmark performance. These results can guide users of orthologs to the best suited method for their purpose.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae167"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814425","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

Water-mediated ribonucleotide-amino acid pairs and higher-order structures at the RNA-protein interface: analysis of the crystal structure database and a topological classification. 水介导的核糖核苷酸-氨基酸对和rna -蛋白质界面上的高阶结构：晶体结构数据库分析和拓扑分类。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-11 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae161

Raman Jangra, John F Trant, Purshotam Sharma

{"title":"Water-mediated ribonucleotide-amino acid pairs and higher-order structures at the RNA-protein interface: analysis of the crystal structure database and a topological classification.","authors":"Raman Jangra, John F Trant, Purshotam Sharma","doi":"10.1093/nargab/lqae161","DOIUrl":"10.1093/nargab/lqae161","url":null,"abstract":"Water is essential for the formation, stability and function of RNA-protein complexes. To delineate the structural role of water molecules in shaping the interactions between RNA and proteins, we comprehensively analyzed a dataset of 329 crystal structures of these complexes to identify water-mediated hydrogen-bonded contacts at RNA-protein interface. Our survey identified a total of 4963 water bridges. We then employed a graph theory-based approach to present a robust classification scheme, encompassing triplets, quartets and quintet bridging topologies, each further delineated into sub-topologies. The frequency of water bridges within each topology decreases with the increasing degree of water node, with simple triplet water bridges outnumbering the higher-order topologies. Overall, this analysis demonstrates the variety of water-mediated interactions and highlights the importance of water as not only the medium but also the organizing principle underlying biomolecular interactions. Further, our study emphasizes the functional significance of water-mediated interactions in RNA-protein complexes, and paving the way for exploring how these interactions operate in complex biological environments. Altogether, this understanding not only enhances insights into biomolecular dynamics but also informs the rational design of RNA-protein complexes, providing a framework for potential applications in biotechnology and therapeutics. All the scripts, and data are available at https://github.com/PSCPU/waterbridges.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae161"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632616/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814428","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

In silico and in vivo analyses of a novel variant in MYO6 identified in a family with postlingual non-syndromic hearing loss from Argentina. 在阿根廷舌后非综合征性听力损失家庭中发现的MYO6新变异的计算机和体内分析

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NAR Genomics and Bioinformatics Pub Date : 2024-12-11 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae162

Paula I Buonfiglio, Carlos D Bruque, Lucía Salatino, Vanesa Lotersztein, Mariela Pace, Sofia Grinberg, Ana B Elgoyhen, Paola V Plazas, Viviana Dalamón

{"title":"In silico and in vivo analyses of a novel variant in MYO6 identified in a family with postlingual non-syndromic hearing loss from Argentina.","authors":"Paula I Buonfiglio, Carlos D Bruque, Lucía Salatino, Vanesa Lotersztein, Mariela Pace, Sofia Grinberg, Ana B Elgoyhen, Paola V Plazas, Viviana Dalamón","doi":"10.1093/nargab/lqae162","DOIUrl":"10.1093/nargab/lqae162","url":null,"abstract":"Hereditary hearing loss stands as the most prevalent sensory disorder, with over 124 non-syndromic genes and approximately 400 syndromic forms of deafness identified in humans. The clinical presentation of these conditions spans a spectrum, ranging from mild to profound hearing loss. The aim of this study was to identify the genetic cause of hearing loss in a family and functionally validate a novel variant identified in the MYO6 gene. After Whole Exome Sequencing analysis, the variant c.2775G>C p.Arg925Ser in MYO6 was detected in a family with postlingual non-syndromic hearing loss. By protein modeling a change in the electrostatic charge of the single alpha helix domain surface was revealed. Through a knockdown phenotype rescue assay in zebrafish, the detrimental effects of the identified variant on the auditory system was determined. These findings underscore the significance of a comprehensive approach, integrating both in silico and in vivo strategies, to ascertain the pathogenicity of this candidate variant. Such an approach has demonstrated its effectiveness in achieving an accurate genetic diagnosis and in promoting a more profound comprehension of the mechanisms that underlie the pathophysiology of hearing.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae162"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814386","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

GIN-TONIC: non-hierarchical full-text indexing for graph genomes. 图形基因组的非分层全文索引。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-11 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae159

Ünsal Öztürk, Marco Mattavelli, Paolo Ribeca

{"title":"GIN-TONIC: non-hierarchical full-text indexing for graph genomes.","authors":"Ünsal Öztürk, Marco Mattavelli, Paolo Ribeca","doi":"10.1093/nargab/lqae159","DOIUrl":"10.1093/nargab/lqae159","url":null,"abstract":"This paper presents a new data structure, GIN-TONIC (Graph INdexing Through Optimal Near Interval Compaction), designed to index arbitrary string-labelled directed graphs representing, for instance, pangenomes or transcriptomes. GIN-TONIC provides several capabilities not offered by other graph-indexing methods based on the FM-Index. It is non-hierarchical, handling a graph as a monolithic object; it indexes at nucleotide resolution all possible walks in the graph without the need to explicitly store them; it supports exact substring queries in polynomial time and space for all possible walk roots in the graph, even if there are exponentially many walks corresponding to such roots. Specific ad-hoc optimizations, such as precomputed caches, allow GIN-TONIC to achieve excellent performance for input graphs of various topologies and sizes. Robust scalability capabilities and a querying performance close to that of a linear FM-Index are demonstrated for two real-world applications on the scale of human pangenomes and transcriptomes. Source code and associated benchmarks are available on GitHub.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae159"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814391","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

Human introns contain conserved tissue-specific cryptic poison exons. 人类内含子含有保守的组织特异性隐毒外显子。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-11 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae163

Sergey Margasyuk, Antonina Kuznetsova, Lev Zavileyskiy, Maria Vlasenok, Dmitry Skvortsov, Dmitri D Pervouchine

{"title":"Human introns contain conserved tissue-specific cryptic poison exons.","authors":"Sergey Margasyuk, Antonina Kuznetsova, Lev Zavileyskiy, Maria Vlasenok, Dmitry Skvortsov, Dmitri D Pervouchine","doi":"10.1093/nargab/lqae163","DOIUrl":"10.1093/nargab/lqae163","url":null,"abstract":"Eukaryotic cells express a large number of transcripts from a single gene due to alternative splicing. Despite hundreds of thousands of splice isoforms being annotated in databases, it has been reported that the current exon catalogs remain incomplete. At the same time, introns of human protein-coding (PC) genes contain a large number of evolutionarily conserved elements with unknown function. Here, we explore the possibility that some of them represent cryptic exons that are expressed in rare conditions. We identified a group of cryptic exons that are similar to the annotated exons in terms of evolutionary conservation and RNA-seq read coverage in the Genotype-Tissue Expression dataset. Most of them were poison, i.e. generated an nonsense-mediated decay (NMD) isoform upon inclusion, and many showed signs of tissue-specific and cancer-specific expression and regulation. We performed RNA-seq in A549 cell line treated with cycloheximide to inactivate NMD and confirmed using quantitative polymerase chain reaction that seven of eight exons tested are, indeed, expressed. This study shows that introns of human PC genes contain cryptic poison exons, which reside in conserved intronic regions and remain not fully annotated due to insufficient representation in RNA-seq libraries.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae163"},"PeriodicalIF":4.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814423","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

TGV: suite of tools to visualize transmission graphs. TGV：可视化传输图的工具套件。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-05 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae158

Jody E Phelan, Fatima Niazi, Linfeng Wang, Gabrielle C Ngwana-Joseph, Benjamin Sobkowiak, Ted Cohen, Susana Campino, Taane G Clark

引用次数: 0

IsopretGO-analysing and visualizing the functional consequences of differential splicing. isopretgo -分析和可视化差异剪接的功能后果。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-05 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae165

Guy Karlebach, Peter Hansen, Kristin Köhler, Peter N Robinson

引用次数: 0

AnnoGCD: a generalized category discovery framework for automatic cell type annotation. 用于自动单元格类型注释的通用类别发现框架。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-04 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae166

Francesco Ceccarelli, Pietro Liò, Sean B Holden

{"title":"AnnoGCD: a generalized category discovery framework for automatic cell type annotation.","authors":"Francesco Ceccarelli, Pietro Liò, Sean B Holden","doi":"10.1093/nargab/lqae166","DOIUrl":"10.1093/nargab/lqae166","url":null,"abstract":"The identification of cell types in single-cell RNA sequencing (scRNA-seq) data is a critical task in understanding complex biological systems. Traditional supervised machine learning methods rely on large, well-labeled datasets, which are often impractical to obtain in open-world scenarios due to budget constraints and incomplete information. To address these challenges, we propose a novel computational framework, named AnnoGCD, building on Generalized Category Discovery (GCD) and Anomaly Detection (AD) for automatic cell type annotation. Our semi-supervised method combines labeled and unlabeled data to accurately classify known cell types and to discover novel ones, even in imbalanced datasets. AnnoGCD includes a semi-supervised block to first classify known cell types, followed by an unsupervised block aimed at identifying and clustering novel cell types. We evaluated our approach on five human scRNA-seq datasets and a mouse model atlas, demonstrating superior performance in both known and novel cell type identification compared to existing methods. Our model also exhibited robustness in datasets with significant class imbalance. The results suggest that AnnoGCD is a powerful tool for the automatic annotation of cell types in scRNA-seq data, providing a scalable solution for biological research and clinical applications. Our code and the datasets used for evaluations are publicly available on GitHub: https://github.com/cecca46/AnnoGCD/.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae166"},"PeriodicalIF":4.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11629990/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807220","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

Using paired-end read orientations to assess technical biases in capture Hi-C. 使用对端读取方向来评估捕获Hi-C的技术偏差。

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NAR Genomics and Bioinformatics Pub Date : 2024-12-04 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae156

Peter Hansen, Hannah Blau, Jochen Hecht, Guy Karlebach, Alexander Krannich, Robin Steinhaus, Matthias Truss, Peter N Robinson

{"title":"Using paired-end read orientations to assess technical biases in capture Hi-C.","authors":"Peter Hansen, Hannah Blau, Jochen Hecht, Guy Karlebach, Alexander Krannich, Robin Steinhaus, Matthias Truss, Peter N Robinson","doi":"10.1093/nargab/lqae156","DOIUrl":"10.1093/nargab/lqae156","url":null,"abstract":"Hi-C and capture Hi-C (CHi-C) both leverage paired-end sequencing of chimeric fragments to gauge the strength of interactions based on the total number of paired-end reads mapped to a common pair of restriction fragments. Mapped paired-end reads can have four relative orientations, depending on the genomic positions and strands of the two reads. We assigned one paired-end read orientation to each of the four possible re-ligations that can occur between two given restriction fragments. In a large hematopoietic cell dataset, we determined the read pair counts of interactions separately for each orientation. Interactions with imbalances in the counts occur much more often than expected by chance for both Hi-C and CHi-C. Based on such imbalances, we identified target restriction fragments enriched at only one instead of both ends. By matching them to the baits used for the experiments, we confirmed our assignment of paired-end read orientations and gained insights that can inform bait design. An analysis of unbaited fragments shows that, beyond bait effects, other known types of technical biases are reflected in count imbalances. Taking advantage of distance-dependent contact frequencies, we assessed the impact of such biases. Our results have the potential to improve the design and interpretation of CHi-C experiments.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae156"},"PeriodicalIF":4.0,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11630073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807630","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