NAR Genomics and Bioinformatics最新文献_第4页

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

Predicting the pro-longevity or anti-longevity effect of model organism genes with enhanced Gaussian noise augmentation-based contrastive learning on protein-protein interaction networks. 基于增强高斯噪声增强的蛋白质-蛋白质相互作用网络对比学习预测模式生物基因的促长寿或抗长寿效应。

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NAR Genomics and Bioinformatics Pub Date : 2024-11-28 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae153

Ibrahim Alsaggaf, Alex A Freitas, Cen Wan

引用次数: 0

VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data. VILOCA：测序质量敏感的病毒单倍型重建和突变，需要短读和长读数据。

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NAR Genomics and Bioinformatics Pub Date : 2024-11-28 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae152

Lara Fuhrmann, Benjamin Langer, Ivan Topolsky, Niko Beerenwinkel

{"title":"VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data.","authors":"Lara Fuhrmann, Benjamin Langer, Ivan Topolsky, Niko Beerenwinkel","doi":"10.1093/nargab/lqae152","DOIUrl":"10.1093/nargab/lqae152","url":null,"abstract":"RNA viruses exist as large heterogeneous populations within their host. The structure and diversity of virus populations affects disease progression and treatment outcomes. Next-generation sequencing allows detailed viral population analysis, but inferring diversity from error-prone reads is challenging. Here, we present VILOCA (VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data), a method for mutation calling and reconstruction of local haplotypes from short- and long-read viral sequencing data. Local haplotypes refer to genomic regions that have approximately the length of the input reads. VILOCA recovers local haplotypes by using a Dirichlet process mixture model to cluster reads around their unobserved haplotypes and leveraging quality scores of the sequencing reads. We assessed the performance of VILOCA in terms of mutation calling and haplotype reconstruction accuracy on simulated and experimental Illumina, PacBio and Oxford Nanopore data. On simulated and experimental Illumina data, VILOCA performed better or similar to existing methods. On the simulated long-read data, VILOCA is able to recover on average [Formula: see text] of the ground truth mutations with perfect precision compared to only [Formula: see text] recall and [Formula: see text] precision of the second-best method. In summary, VILOCA provides significantly improved accuracy in mutation and haplotype calling, especially for long-read sequencing data, and therefore facilitates the comprehensive characterization of heterogeneous within-host viral populations.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae152"},"PeriodicalIF":4.0,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781326","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

Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications. 用于反义应用的化学修饰的DNA类似物的重聚合的比较分子动力学计算。

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NAR Genomics and Bioinformatics Pub Date : 2024-11-28 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae155

Rodrigo Galindo-Murillo, Jack S Cohen, Barak Akabayov

{"title":"Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications.","authors":"Rodrigo Galindo-Murillo, Jack S Cohen, Barak Akabayov","doi":"10.1093/nargab/lqae155","DOIUrl":"10.1093/nargab/lqae155","url":null,"abstract":"We have subjected several analogs of DNA that have been widely used as antisense oligonucleotide (ASO) inhibitors of gene expression to comparative molecular dynamics (MD) calculations of their ability to form duplexes with DNA and RNA. The analogs included in this study are the phosphorothioate (PS), peptide nucleic acid (PNA), locked nucleic acid (LNA), morpholino nucleic acid (PMO), the 2'-OMe, 2'-F, 2'-methoxyethyl (2'-MOE) and the constrained cET analogs, as well as the natural phosphodiester (PO) as control, for a total of nine structures, in both XNA-DNA and XNA-RNA duplexes. This is intended as an objective criterion for their relative ability to duplex with an RNA complement and their comparative potential for antisense applications. We have found that the constrained furanose ring analogs show increased stability when considering this study's structural and energetic parameters. The 2'-MOE modification, even though energetically stable, has an elevated dynamic range and breathing properties due to the bulkier moiety in the C2' position of the furanose. The smaller modifications in the C2' position, 2'-F, 2'-OMe and PS also form stable and energetically favored duplexes with both DNA and RNA. The morpholino moiety allows for increased tolerance in accommodating either DNA or RNA and the PNA, with the PNA being the most energetically stable, although with a preference for the B-form DNA. In summary, we can rank the overall preference of hybrid strand formations as PNA > cET/LNA > PS/2'-F/2'-OMe > morpholino > 2'-MOE for the efficacy of duplex formation.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae155"},"PeriodicalIF":4.0,"publicationDate":"2024-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781298","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

CancerPro: deciphering the pan-cancer prognostic landscape through combinatorial enrichment analysis and knowledge network insights. CancerPro：通过组合富集分析和知识网络洞察力解读泛癌症预后景观。

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NAR Genomics and Bioinformatics Pub Date : 2024-11-21 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae157

Zhigang Wang, Yize Yuan, Zhe Wang, Wenjia Zhang, Chong Chen, Zhaojun Duan, Suyuan Peng, Jie Zheng, Yongqun He, Xiaolin Yang

{"title":"CancerPro: deciphering the pan-cancer prognostic landscape through combinatorial enrichment analysis and knowledge network insights.","authors":"Zhigang Wang, Yize Yuan, Zhe Wang, Wenjia Zhang, Chong Chen, Zhaojun Duan, Suyuan Peng, Jie Zheng, Yongqun He, Xiaolin Yang","doi":"10.1093/nargab/lqae157","DOIUrl":"10.1093/nargab/lqae157","url":null,"abstract":"Gene expression levels serve as valuable markers for assessing prognosis in cancer patients. To understand the mechanisms underlying prognosis and explore potential therapeutics across diverse cancers, we developed CancerPro (https:/medcode.link/cancerpro). This knowledge network platform integrates comprehensive biomedical data on genes, drugs, diseases and pathways, along with their interactions. By integrating ontology and knowledge graph technologies, CancerPro offers a user-friendly interface for analyzing pan-cancer prognostic markers and exploring genes or drugs of interest. CancerPro implements three core functions: gene set enrichment analysis based on multiple annotations; in-depth drug analysis; and in-depth gene list analysis. Using CancerPro, we categorized genes and cancers into distinct groups and utilized network analysis to identify key biological pathways associated with unfavorable prognostic genes. The platform further pinpoints potential drug targets and explores potential links between prognostic markers and patient characteristics such as glutathione levels and obesity. For renal and prostate cancer, CancerPro identified risk genes linked to immune deficiency pathways and alternative splicing abnormalities. This research highlights CancerPro's potential as a valuable tool for researchers to explore pan-cancer prognostic markers and uncover novel therapeutic avenues. Its flexible tools support a wide range of biological investigations, making it a versatile asset in cancer research and beyond.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae157"},"PeriodicalIF":4.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781294","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

There will always be variants of uncertain significance. Analysis of VUSs. 总会有意义不确定的变体。VUSs分析。

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NAR Genomics and Bioinformatics Pub Date : 2024-11-21 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae154

Haoyang Zhang, Muhammad Kabir, Saeed Ahmed, Mauno Vihinen

{"title":"There will always be variants of uncertain significance. Analysis of VUSs.","authors":"Haoyang Zhang, Muhammad Kabir, Saeed Ahmed, Mauno Vihinen","doi":"10.1093/nargab/lqae154","DOIUrl":"10.1093/nargab/lqae154","url":null,"abstract":"The ACMG/AMP guidelines include five categories of which variants of uncertain significance (VUSs) have received increasing attention. Recently, Fowler and Rehm claimed that all or most VUSs could be reclassified as pathogenic or benign within few years. To test this claim, we collected validated benign, pathogenic, VUS and conflicting variants from ClinVar and LOVD and investigated differences at gene, protein, structure, and variant levels. The gene and protein features included inheritance patterns, actionability, functional categories for housekeeping, essential, complete knockout, lethality and haploinsufficient proteins, Gene Ontology annotations, and protein network properties. Structural properties included the location at secondary structural elements, intrinsically disordered regions, transmembrane regions, repeats, conservation, and accessibility. Gene features were distributions of nucleotides, their groupings, codons, and location to CpG islands. The distributions of amino acids and their groups were investigated. VUSs did not markedly differ from other variants. The only major differences were the accessibility and conservation of pathogenic variants, and reduced ratio of repeat-locating variants in VUSs. Thus, all VUSs cannot be distinguished from other types of variants. They display one form of natural biological heterogeneity. Instead of concentrating on eradicating VUSs, the community would benefit from investigating and understanding factors that contribute to phenotypic heterogeneity.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae154"},"PeriodicalIF":4.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616676/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781322","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

Bilingual language model for protein sequence and structure. 蛋白质序列和结构的双语语言模型。

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NAR Genomics and Bioinformatics Pub Date : 2024-11-15 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae150

Michael Heinzinger, Konstantin Weissenow, Joaquin Gomez Sanchez, Adrian Henkel, Milot Mirdita, Martin Steinegger, Burkhard Rost

{"title":"Bilingual language model for protein sequence and structure.","authors":"Michael Heinzinger, Konstantin Weissenow, Joaquin Gomez Sanchez, Adrian Henkel, Milot Mirdita, Martin Steinegger, Burkhard Rost","doi":"10.1093/nargab/lqae150","DOIUrl":"10.1093/nargab/lqae150","url":null,"abstract":"Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein structure prediction. Now we can systematically and comprehensively explore the dual nature of proteins that act and exist as three-dimensional (3D) machines and evolve as linear strings of one-dimensional (1D) sequences. Here, we leverage pLMs to simultaneously model both modalities in a single model. We encode protein structures as token sequences using the 3Di-alphabet introduced by the 3D-alignment method Foldseek. For training, we built a non-redundant dataset from AlphaFoldDB and fine-tuned an existing pLM (ProtT5) to translate between 3Di and amino acid sequences. As a proof-of-concept for our novel approach, dubbed Protein 'structure-sequence' T5 (ProstT5), we showed improved performance for subsequent, structure-related prediction tasks, leading to three orders of magnitude speedup for deriving 3Di. This will be crucial for future applications trying to search metagenomic sequence databases at the sensitivity of structure comparisons. Our work showcased the potential of pLMs to tap into the information-rich protein structure revolution fueled by AlphaFold2. ProstT5 paves the way to develop new tools integrating the vast resource of 3D predictions and opens new research avenues in the post-AlphaFold2 era.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae150"},"PeriodicalIF":4.0,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616678/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781229","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

Correction to 'NFixDB (Nitrogen Fixation DataBase)-a comprehensive integrated database for robust 'omics analysis of diazotrophs'. 对“NFixDB（固氮数据库）”的修正-一个全面的集成数据库，用于强大的“重氮营养体组学分析”。

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NAR Genomics and Bioinformatics Pub Date : 2024-11-15 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae164

引用次数: 0

Pymportx: facilitating next-generation transcriptomics analysis in Python. Pymportx：促进Python中的下一代转录组学分析。

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NAR Genomics and Bioinformatics Pub Date : 2024-11-15 eCollection Date: 2024-12-01 DOI: 10.1093/nargab/lqae160

Paula Pena González, Dafne Lozano-Paredes, José Luis Rojo-Álvarez, Luis Bote-Curiel, Víctor Javier Sánchez-Arévalo Lobo

{"title":"Pymportx: facilitating next-generation transcriptomics analysis in Python.","authors":"Paula Pena González, Dafne Lozano-Paredes, José Luis Rojo-Álvarez, Luis Bote-Curiel, Víctor Javier Sánchez-Arévalo Lobo","doi":"10.1093/nargab/lqae160","DOIUrl":"10.1093/nargab/lqae160","url":null,"abstract":"The efficient importation of quantified gene expression data is pivotal in transcriptomics. Historically, the R package Tximport addressed this need by enabling seamless data integration from various quantification tools. However, the Python community lacked a corresponding tool, restricting cross-platform bioinformatics interoperability. We introduce Pymportx, a Python adaptation of Tximport, which replicates and extends the original package's functionalities. Pymportx maintains the integrity and accuracy of gene expression data while improving processing speed and integration within the Python ecosystem. It supports new data formats and includes tools for enhanced data exploration and analysis. Available under the MIT license, Pymportx integrates smoothly with Python's bioinformatics tools, facilitating a unified and efficient workflow across the R and Python ecosystems. This advancement not only broadens access to Python's extensive toolset but also fosters interdisciplinary collaboration and the development of cutting-edge bioinformatics analyses.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 4","pages":"lqae160"},"PeriodicalIF":4.0,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781318","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