NAR Genomics and Bioinformatics最新文献_第5页

The divergent intron-containing actin in sponge morphogenetic processes. 海绵形态发生过程中发散的含内含子的肌动蛋白。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2025-06-04 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf071

Yulia V Lyupina, Kim I Adameyko, Vasiliy M Zubarev, Alexander V Cherkasov, Alina V Ryabova, Kirill V Mikhailov, Sergey A Golyshev, Anton V Burakov, Alexander D Finoshin, Pavel A Erokhov, Marat S Sabirov, Anna I Zhurakovskaya, Rustam H Ziganshin, Nikolai G Gornostaev, Vasilina M Ignatyuk, Aleksei M Kulikov, Victor S Mikhailov, Guzel R Gazizova, Elena I Shagimardanova, Oleg A Gusev, Ekaterina E Khrameeva, Oksana I Kravchuk

{"title":"The divergent intron-containing actin in sponge morphogenetic processes.","authors":"Yulia V Lyupina, Kim I Adameyko, Vasiliy M Zubarev, Alexander V Cherkasov, Alina V Ryabova, Kirill V Mikhailov, Sergey A Golyshev, Anton V Burakov, Alexander D Finoshin, Pavel A Erokhov, Marat S Sabirov, Anna I Zhurakovskaya, Rustam H Ziganshin, Nikolai G Gornostaev, Vasilina M Ignatyuk, Aleksei M Kulikov, Victor S Mikhailov, Guzel R Gazizova, Elena I Shagimardanova, Oleg A Gusev, Ekaterina E Khrameeva, Oksana I Kravchuk","doi":"10.1093/nargab/lqaf071","DOIUrl":"10.1093/nargab/lqaf071","url":null,"abstract":"The ability of eukaryotic cells to orchestrate mechanical interactions from the subcellular to the organismal levels is mediated by their cytoskeleton. One of the key components of the eukaryotic cytoskeleton is actin, a highly conserved building block of the actin filaments, which interact with many other proteins and underlie diverse cell structures, necessary for organizing intracellular transport, phagocytosis and cell movement. Many organisms have evolved multiple actin variants, which share similar amino acid sequences but differ more dramatically at the gene level, including the presence and number of introns. In the current study, we show that the intron-containing and intronless actin genes are present in the poriferan Halisarca dujardini and that the encoded actins can perform different functions. These actins differ in the gene expression profiles, post-translational modifications, cellular, and subcellular localizations. The intronless actin genes of H. dujardini, HdA1/2/3, are products of recent duplications, exhibit low divergence between paralogs, and serve as the primary cytoskeletal actins. The divergent intron-containing actin gene, HdA6, is differentially expressed in a specific cell lineage and its expression is dependent on the state of cell aggregation, which indicates its unique functions in the morphogenetic processes of the sponge.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 2","pages":"lqaf071"},"PeriodicalIF":4.0,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259053","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

KILDA: identifying KIV-2 repeats from kmers. KILDA：从kmers中鉴定KIV-2重复序列。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2025-05-30 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf070

Corentin Molitor, Timothy Labidi, Antoine Rimbert, Bertrand Cariou, Mathilde Di Filippo, Claire Bardel

{"title":"KILDA: identifying KIV-2 repeats from kmers.","authors":"Corentin Molitor, Timothy Labidi, Antoine Rimbert, Bertrand Cariou, Mathilde Di Filippo, Claire Bardel","doi":"10.1093/nargab/lqaf070","DOIUrl":"10.1093/nargab/lqaf070","url":null,"abstract":"High concentration of lipoprotein(a) [Lp(a)], a lipoprotein with proatherogenic properties, is an important risk factor for cardiovascular disease. This concentration is mostly genetically determined by a complex interplay between the number of kringle IV type 2 repeats and Lp(a)-affecting variants. Besides Lp(a) plasma concentration, there is an unmet need to identify individuals most at risk based on their LPA genotype. We developed KILDA (KIv2 Length Determined from a kmer Analysis), a Nextflow pipeline, to identify the number of kringle IV type 2 repeats and Lp(a)-affecting variants directly from kmers generated from FASTQ files. The pipeline was tested on the 1000 Genomes Project (n = 2459) and results were equivalent to DRAGEN-LPA (R 2= 0.92). In silico datasets proved the robustness of KILDA's predictions under different scenarios of sequencing coverage and quality. In brief, KILDA is a robust, open-source, and free-to-use pipeline that can identify the number of kringle IV type 2 repeats and Lp(a)-associated variants even when inputting low-coverage libraries.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 2","pages":"lqaf070"},"PeriodicalIF":4.0,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12123407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144200253","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 'Current state and future prospects of Horizontal Gene Transfer detection'. 修正“水平基因转移检测的现状和未来展望”。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2025-05-30 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf078

引用次数: 0

Integrating gene expression, genomic, and phosphoproteomic data to infer transcription factor activity in lung cancer. 整合基因表达、基因组和磷蛋白组学数据推断肺癌中转录因子的活性。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2025-05-30 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf068

Chiara Carrino, Gerardo Pepe, Luca Parca, Manuela Helmer-Citterich, Pier Federico Gherardini

引用次数: 0

VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction. VariantFoldRNA：一个灵活的，容器化的，可扩展的全基因组riboSNitch预测管道。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2025-05-29 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf066

Kobie J Kirven, Philip C Bevilacqua, Sarah M Assmann

{"title":"VariantFoldRNA: a flexible, containerized, and scalable pipeline for genome-wide riboSNitch prediction.","authors":"Kobie J Kirven, Philip C Bevilacqua, Sarah M Assmann","doi":"10.1093/nargab/lqaf066","DOIUrl":"10.1093/nargab/lqaf066","url":null,"abstract":"Single nucleotide polymorphisms (SNPs) can alter RNA structure by changing the proportions of existing conformations or leading to new conformations in the structural ensemble. Such structure-changing SNPs, or riboSNitches, have been associated with diseases in humans and climate adaptation in plants. While several computational tools are available for predicting whether an SNP is a riboSNitch, these tools were generally developed to analyze individual RNAs and are not optimized for genome-wide analyses. To fill this gap, we developed VariantFoldRNA, a flexible, containerized, and automated pipeline for genome-wide prediction of riboSNitches. Our pipeline automatically installs all dependencies, can be run locally or on high-performance clusters, and is modular, enabling the user to customize the analysis for the research question of interest. VariantFoldRNA can predict riboSNitches genome-wide at user-specified temperatures and splicing conditions, opening the door to novel analyses. The pipeline is an open-source command-line tool that is freely available at https://github.com/The-Bevilacqua-Lab/variantfoldrna.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 2","pages":"lqaf066"},"PeriodicalIF":4.0,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12121482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182273","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

IEIVariantFilter: a bioinformatics tool to speed up genetic diagnosis of inborn errors of immunity patients. IEIVariantFilter：一种生物信息学工具，可加快免疫患者先天性错误的遗传诊断。

IF 2.8

NAR Genomics and Bioinformatics Pub Date : 2025-05-28 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf069

Juan Pereda, Rafael Espinosa, Blanca García-Solís, Teresa Guerra-Galán, Ana Van-Den-Rym, Meltem Ece Kars, Rocío Mena, Victor Galán, Ana de Andrés-Martín, Carlos Rodríguez-Gallego, Alberto López-Lera, Fernando Corvillo, Antonio Pérez-Martínez, Eduardo López-Collazo, Silvia Sánchez-Ramón, Rubén Martínez-Barricarte, Lluis Quintana-Murci, José Miguel Lorenzo-Salazar, Yuval Itan, Carlos Flores, Rebeca Pérez-de-Diego

{"title":"IEIVariantFilter: a bioinformatics tool to speed up genetic diagnosis of inborn errors of immunity patients.","authors":"Juan Pereda, Rafael Espinosa, Blanca García-Solís, Teresa Guerra-Galán, Ana Van-Den-Rym, Meltem Ece Kars, Rocío Mena, Victor Galán, Ana de Andrés-Martín, Carlos Rodríguez-Gallego, Alberto López-Lera, Fernando Corvillo, Antonio Pérez-Martínez, Eduardo López-Collazo, Silvia Sánchez-Ramón, Rubén Martínez-Barricarte, Lluis Quintana-Murci, José Miguel Lorenzo-Salazar, Yuval Itan, Carlos Flores, Rebeca Pérez-de-Diego","doi":"10.1093/nargab/lqaf069","DOIUrl":"10.1093/nargab/lqaf069","url":null,"abstract":"Severe infectious diseases remain the leading cause of death in children and young adults worldwide. Monogenic inborn errors of immunity (IEIs) are traditionally defined as a heterogeneous group of rare inborn genetic diseases affecting the functioning of the immune system. Greater awareness has led to the clinical definition of 485 monogenic IEIs and whole exome sequencing (WES) is becoming increasingly relevant for IEI genetic diagnosis. The current protocol for IEI genetic studies includes manual filtering of the list of genes obtained as a WES read-out providing a short list of candidate genes. This procedure is time-consuming and can produce mistakes due to human error in manual filtering. IEIVariantFilter is a new web-based bioinformatics tool to speed up and refine the genetic diagnosis of IEI patients oriented for users in the biomedical field without needing bioinformatics expertise. IEIVariantFilter prioritizes genetic variants based on ranges of zygosity, the quality of reads, the predicted variant effect, and genes related to immunity, considering a consanguineous hypothesis whenever necessary. IEIVariantFilter facilitates gene and variant list prioritization, speeding up the identification of candidate disease-causing variants for validation by experimental studies. The software improves the genetic diagnosis of patients, thereby facilitating precision medicine and fast and proper treatment.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 2","pages":"lqaf069"},"PeriodicalIF":2.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175129","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

Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila. 从整合转录组数据集推断基因通路关联：嗜热四膜虫的交互式基因网络探索者。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2025-05-27 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf067

Michael A Bertagna, Lydia J Bright, Fei Ye, Yu-Yang Jiang, Debolina Sarkar, Ajay Pradhan, Santosh Kumar, Shan Gao, Aaron P Turkewitz, Lev M Z Tsypin

{"title":"Inferring gene-pathway associations from consolidated transcriptome datasets: an interactive gene network explorer for Tetrahymena thermophila.","authors":"Michael A Bertagna, Lydia J Bright, Fei Ye, Yu-Yang Jiang, Debolina Sarkar, Ajay Pradhan, Santosh Kumar, Shan Gao, Aaron P Turkewitz, Lev M Z Tsypin","doi":"10.1093/nargab/lqaf067","DOIUrl":"10.1093/nargab/lqaf067","url":null,"abstract":"Although an established model organism, Tetrahymena thermophila remains comparatively inaccessible to high throughput screens, and alternative bioinformatic approaches still rely on unconnected datasets and outdated algorithms. Here, we report a new approach to consolidating RNA-seq and microarray data based on a systematic exploration of parameters and computational controls, enabling us to infer functional gene associations from their co-expression patterns. To illustrate the power of this approach, we took advantage of new data regarding a previously studied pathway, the biogenesis of a secretory organelle called the mucocyst. Our untargeted clustering approach recovered over 80% of the genes that were previously verified to play a role in mucocyst biogenesis. Furthermore, we tested four new genes that we predicted to be mucocyst-associated based on their co-expression and found that knocking out each of them results in mucocyst secretion defects. We also found that our approach succeeds in clustering genes associated with several other cellular pathways that we evaluated based on prior literature. We present the Tetrahymena Gene Network Explorer (TGNE) as an interactive tool for genetic hypothesis generation and functional annotation in this organism and as a framework for building similar tools for other systems.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 2","pages":"lqaf067"},"PeriodicalIF":4.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162528","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

Methyl-Micro-C: simultaneous characterization of chromatin accessibility, interactions, and DNA methylation. 甲基微c：同时表征染色质可及性，相互作用，和DNA甲基化。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2025-05-27 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf060

Leonardo Gonzalez-Smith, Claire Stevens, Huan Cao, Zexun Wu, Suhn K Rhie

{"title":"Methyl-Micro-C: simultaneous characterization of chromatin accessibility, interactions, and DNA methylation.","authors":"Leonardo Gonzalez-Smith, Claire Stevens, Huan Cao, Zexun Wu, Suhn K Rhie","doi":"10.1093/nargab/lqaf060","DOIUrl":"10.1093/nargab/lqaf060","url":null,"abstract":"Epigenomes, characterized by patterns of different signatures such as chromatin accessibility, chromatin interactions, and DNA methylation, vary across cell types and play a pivotal role in regulating gene expression. By mapping these signatures, the underlying mechanisms of development and diseases can be uncovered. However, many canonical epigenetic methods focus on mapping only one signature. Simultaneous measurement of epigenetic signatures from the same cell or tissue provides significant benefits for research, especially when resources are limited, and precise analysis is essential. Here, we report a technique called Methyl-Micro-C (MMC), which simultaneously profiles chromatin accessibility, chromatin interactions, and DNA methylation in the same sample. MMC enhances the resolution of chromatin interactions and the coverage of CpGs by combining MNase-mediated fragmentation with enzymatic conversion. This technique allows for the profiling of three-dimensional epigenomes, capturing consistent chromatin accessibility, chromatin interactions, and DNA methylation signals in an efficient manner. It is also relatively straightforward, allowing researchers to implement and apply it easily.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 2","pages":"lqaf060"},"PeriodicalIF":4.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162530","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

TCRCluster: a novel approach to T-cell receptor latent featurization and clustering using contrastive learning-guided two-stage variational autoencoders. TCRCluster：一种使用对比学习引导的两阶段变分自编码器的t细胞受体潜在特征和聚类的新方法。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2025-05-27 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf065

Yat-Tsai Richie Wan, Morten Nielsen

{"title":"TCRCluster: a novel approach to T-cell receptor latent featurization and clustering using contrastive learning-guided two-stage variational autoencoders.","authors":"Yat-Tsai Richie Wan, Morten Nielsen","doi":"10.1093/nargab/lqaf065","DOIUrl":"10.1093/nargab/lqaf065","url":null,"abstract":"T cells play a vital role in adaptive immunity by targeting pathogen-infected or cancerous cells, but predicting their specificity remains challenging. Encoding T-cell receptor (TCR) sequences into informative feature spaces is therefore crucial for advancing specificity prediction and downstream applications. For this, we developed a variational autoencoder (VAE)-based model trained on paired TCR α-β chain data, incorporating all six complementarity-determining regions. A semi-supervised 'two-stage VAE' framework, integrating cosine triplet loss and a classifier, was found to further refine peptide-specific latent representations, outperforming sequence-based methods in specificity prediction. Clustering analyses leveraging our VAE latent space were evaluated using K-means, agglomerative clustering, and a novel graph-based method. Agglomerative clustering achieved the most biologically relevant results, balancing cluster purity and retention despite noise in TCR specificity annotations. We extended these insights to evaluate TCR repertoire data. Across datasets, VAE-based models outperformed sequence-based methods, particularly in retention metrics, with notable improvements in the SARS-CoV-2 repertoire dataset. Moreover, the cancer repertoire analysis highlighted the generalizability of our approach, where the model displayed high performance despite minimal similarity between the training and test data. Collectively, these results demonstrate the potential of VAE-based latent representations to offer a robust framework for prediction, clustering, and repertoire analysis.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 2","pages":"lqaf065"},"PeriodicalIF":4.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12107435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144162533","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

Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline. 免疫管道：一个全面和灵活的scRNA-seq和scTCR-seq数据分析管道。

IF 2.8

NAR Genomics and Bioinformatics Pub Date : 2025-05-19 eCollection Date: 2025-06-01 DOI: 10.1093/nargab/lqaf063

Panwen Wang, Yue Yu, Haidong Dong, Shuwen Zhang, Zhifu Sun, Hu Zeng, Patrizia Mondello, Jean-Pierre A Kocher, Junwen Wang, Yan W Asmann, Yi Lin, Ying Li

{"title":"Immunopipe: a comprehensive and flexible scRNA-seq and scTCR-seq data analysis pipeline.","authors":"Panwen Wang, Yue Yu, Haidong Dong, Shuwen Zhang, Zhifu Sun, Hu Zeng, Patrizia Mondello, Jean-Pierre A Kocher, Junwen Wang, Yan W Asmann, Yi Lin, Ying Li","doi":"10.1093/nargab/lqaf063","DOIUrl":"10.1093/nargab/lqaf063","url":null,"abstract":"Single-cell sequencing technologies provide us with information at the level of individual cells. Combining single-cell RNA-seq and single-cell TCR-seq profiling enables the exploration of cell heterogeneity and T-cell receptor repertoires simultaneously. Integrating both types of data can play a crucial role in enhancing our understanding of T-cell-mediated immunity and, in turn, facilitate the advancement of immunotherapy. Here, we present immunopipe, a comprehensive and flexible pipeline to perform integrated analysis of scRNA-seq and scTCR-seq data. In addition to the command line tool, we provide a user-friendly web interface for pipeline configuration and execution monitoring, benefiting researchers without extensive programming experience. With its comprehensive functionality and ease of use, immunopipe empowers researchers to uncover valuable insights from scRNA-seq and scTCR-seq data, ultimately advancing the understanding of immune responses and immunotherapy development.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 2","pages":"lqaf063"},"PeriodicalIF":2.8,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12086537/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102445","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