Genomics, proteomics & bioinformatics最新文献_第5页

HemaCisDB: An Interactive Database for Analyzing Cis-Regulatory Elements Across Hematopoietic Malignancies. HemaCisDB：分析各种造血恶性肿瘤顺式调节元件的交互式数据库。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-26 DOI: 10.1093/gpbjnl/qzae088

Xinping Cai, Qianru Zhang, Bolin Liu, Lu Sun, Yuxuan Liu

{"title":"HemaCisDB: An Interactive Database for Analyzing Cis-Regulatory Elements Across Hematopoietic Malignancies.","authors":"Xinping Cai, Qianru Zhang, Bolin Liu, Lu Sun, Yuxuan Liu","doi":"10.1093/gpbjnl/qzae088","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae088","url":null,"abstract":"Noncoding cis-regulatory elements (CREs), such as transcriptional enhancers, are key regulators of gene expression programs. Accessible chromatin and H3K27ac are well-recognized markers for CREs associated with their biological function. Deregulation of CREs is commonly found in hematopoietic malignancies yet the extent to which CRE dysfunction contributes to pathophysiology remains incompletely understood. Here, we developed HemaCisDB, an interactive, comprehensive, and centralized online resource for CRE characterization across hematopoietic malignancies, serving as a useful resource for investigating the pathological roles of CREs in blood disorders. Currently, we collected 922 ATAC-seq, 190 DNase-seq, and 531 H3K27ac ChIP-seq datasets from patient samples and cell lines across different myeloid and lymphoid neoplasms. HemaCisDB provides comprehensive quality control metrics to assess ATAC-seq, DNase-seq, and H3K27ac ChIP-seq data quality. The analytic modules in HemaCisDB include transcription factor (TF) footprinting inference, super-enhancer identification, and core transcriptional regulatory circuitry analysis. Moreover, HemaCisDB also enables the study of TF binding dynamics by comparing TF footprints across different disease types or conditions via web-based interactive analysis. Together, HemaCisDB provides an interactive platform for CRE characterization to facilitate mechanistic studies of transcriptional regulation in hematopoietic malignancies. HemaCisDB is available at https://hemacisdb.chinablood.com.cn/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

COCOA: A Framework for Fine-scale Mapping Cell-type-specific Chromatin Compartments with Epigenomic Information. COCOA：利用表观基因组信息绘制细胞类型特异性染色质区室精细图谱的框架。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-26 DOI: 10.1093/gpbjnl/qzae091

Kai Li, Ping Zhang, Jinsheng Xu, Zi Wen, Junying Zhang, Zhike Zi, Li Li

{"title":"COCOA: A Framework for Fine-scale Mapping Cell-type-specific Chromatin Compartments with Epigenomic Information.","authors":"Kai Li, Ping Zhang, Jinsheng Xu, Zi Wen, Junying Zhang, Zhike Zi, Li Li","doi":"10.1093/gpbjnl/qzae091","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae091","url":null,"abstract":"Chromatin compartmentalization and epigenomic modification are crucial in cell differentiation and diseases development. However, precise mapping of chromatin compartmental patterns requires Hi-C or Micro-C data at high sequencing depth. Exploring the systematic relationship between epigenomic modifications and compartmental patterns remains challenging. To address these issues, we present COCOA, a deep neural network framework using convolution and attention mechanisms to infer fine-scale chromatin compartment patterns from six histone modification signals. COCOA extracts 1-D track features through bi-directional feature reconstruction after resolution-specific binning epigenomic signals. These track features are then cross-fused with contact features using an attention mechanism and transformed into chromatin compartment patterns through residual feature reduction. COCOA demonstrates accurate inference of chromatin compartmentalization at a fine-scale resolution and exhibits stable performance on test sets. Additionally, we explored the impact of histone modifications on chromatin compartmentalization prediction through in silico epigenomic perturbation experiments. Unlike obscure compartments observed with 1 kb resolution high-depth experimental data, COCOA generates clear and detailed compartmental patterns, highlighting its superior performance. Finally, we demonstrated that COCOA enables cell-type-specific prediction of unrevealed chromatin compartment patterns in various biological processes, making it an effective tool for gaining chromatin compartmentalization insights from epigenomics in diverse biological scenarios. The COCOA python code is publicly available at https://github.com/onlybugs/COCOA.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome Assembly and Winged fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses. 中国翅果基因组组装和翅果基因调控：来自基因组和转录组学分析的见解。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-12 DOI: 10.1093/gpbjnl/qzae087

Fangdong Geng, Xuedong Zhang, Jiayu Ma, Hengzhao Liu, Hang Ye, Fan Hao, Miaoqing Liu, Meng Dang, Huijuan Zhou, Mengdi Li, Peng Zhao

{"title":"Genome Assembly and Winged fruit Gene Regulation of Chinese Wingnut: Insights from Genomic and Transcriptomic Analyses.","authors":"Fangdong Geng, Xuedong Zhang, Jiayu Ma, Hengzhao Liu, Hang Ye, Fan Hao, Miaoqing Liu, Meng Dang, Huijuan Zhou, Mengdi Li, Peng Zhao","doi":"10.1093/gpbjnl/qzae087","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae087","url":null,"abstract":"The genomic basis and biology of winged fruit are interesting issues in ecological and evolutionary biology. Chinese wingnut (Pterocarya stenoptera) is an important garden and economic tree species in China. The genomic resources of this hardwood tree could provide advanced genomic studies of Juglandaceae and their evolutionary relationships. Here, we reported a high-quality reference genome of P. stenoptera (N50 = 35.15 Mb) and provided a comparative analysis of Juglandaceae genomes. Paralogous relationships among the 16 chromosomes of the Chinese wingnut genome revealed eight main duplications representing the subgenome. Molecular dating suggested that the most recent common ancestor of P. stenopetera and Cyclocarya paliurus diverged from Juglans around 56.7 million years ago (Mya). The expanded and contracted gene families were associated with cutin, suberine, and wax biosynthesis, cytochrome P450, and anthocyanin biosynthesis. We identified large inversion blocks between the P. stenoptera genome and its relatives, which are enriched in genes related lipid biosynthesis and metabolism, and starch and sucrose metabolism. The twenty-eight individuals were clearly clustered into three groups responding to three species, namely Pterocarya macroptera, Pterocarya hupehensis, and P. stenoptera, based on whole genome resequencing data. Morphological and gene expression analysis showed that CAD, COMT, LOX, and MADS-box play important roles during the five developmental stages of wingnuts. Our study highlights the evolutionary history of the P. stenoptera genome and supports P. stenoptera as an appropriate Juglandaceae model for studying winged fruits. These results provide a theoretical basis for the evolution, development, and diversity of woody plant winged fruits.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Novel IgG-IgM Autoantibody Panel Enhances Detection of Early-stage Lung Adenocarcinoma from Benign Nodules. 新型IgG-IgM自身抗体检测增强早期肺腺癌良性结节的检测。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-11 DOI: 10.1093/gpbjnl/qzae085

Rongrong Luo, Xiying Li, Ruyun Gao, Mengwei Yang, Juan Cai, Liyuan Dai, Nin Lou, Guangyu Fan, Haohua Zhu, Shasha Wang, Zhishang Zhang, Le Tang, Jiarui Yao, Di Wu, Yuankai Shi, Xiaohong Han

{"title":"Novel IgG-IgM Autoantibody Panel Enhances Detection of Early-stage Lung Adenocarcinoma from Benign Nodules.","authors":"Rongrong Luo, Xiying Li, Ruyun Gao, Mengwei Yang, Juan Cai, Liyuan Dai, Nin Lou, Guangyu Fan, Haohua Zhu, Shasha Wang, Zhishang Zhang, Le Tang, Jiarui Yao, Di Wu, Yuankai Shi, Xiaohong Han","doi":"10.1093/gpbjnl/qzae085","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae085","url":null,"abstract":"Autoantibodies hold promise for diagnosing lung cancer. However, their effectiveness in early-stage detection needs improvement. We investigated novel IgG and IgM autoantibodies for detection of early-stage lung adenocarcinoma (Early-LUAD) across three independent cohorts of 1246 individuals. A multi-step approach, including Human proteome microarray (HuProtTM) discovery, focused array verification, and ELISA validation, was conducted on 634 individuals with Early-LUAD (stage 0-I), 280 with benign lung disease (BLD), and 332 normal healthy controls (NHC). HuProtTM profiling discovered 417 IgG/IgM candidates, and focused array verified 32 autoantibodies with distinct distributions in Early-LUAD and BLD/NHC. A novel panel of 10 autoantibodies (ELAVL4-IgM, GDA-IgM, GIMAP4-IgM, GIMAP4-IgG, MGMT-IgM, UCHL1-IgM, DCTPP1-IgM, KCMF1-IgM, UCHL1-IgG, and WWP2-IgM) demonstrated a sensitivity of 70.5% and specificities of 77.0% or 80.0% in detecting Early-LUAD from BLD or NHC in ELISA validation. Positive predictive value for distinguishing Early-LUAD from BLD with nodules ≤ 8 mm, 9 ≤ IMD ≤ 20 mm, and > 20 mm significantly increased from 47.27%, 52.00% and 62.90% [low-dose computed tomography (LDCT) alone] to 79.17%, 71.13% and 87.88% (10-autoantibody panel with LDCT), respectively. The combined risk score (CRS), based on 10-autoantibody panel, sex, and imaging maximum diameter, effectively stratified risk for Early-LUAD. Individuals with scores 10-25 and > 25 indicated a higher risk of Early-LUAD compared to the reference (scores < 10), with adjusted odds ratios of 5.28 (95% CI:3.18-8.76) and 9.05 (95% CI:5.40-15.15), respectively. This novel panel of IgG and IgM autoantibodies offers a complementary approach to LDCT in distinguishing Early-LUAD from benign nodules.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants. MitoSort：利用内源性线粒体变异对汇集的单细胞基因组学数据进行稳健的解复用。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae073

Zhongjie Tang, Weixing Zhang, Peiyu Shi, Sijun Li, Xinhui Li, Yueming Li, Yicong Xu, Yaqing Shu, Zheng Hu, Jin Xu

{"title":"MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants.","authors":"Zhongjie Tang, Weixing Zhang, Peiyu Shi, Sijun Li, Xinhui Li, Yueming Li, Yicong Xu, Yaqing Shu, Zheng Hu, Jin Xu","doi":"10.1093/gpbjnl/qzae073","DOIUrl":"10.1093/gpbjnl/qzae073","url":null,"abstract":"Multiplexing across donors has emerged as a popular strategy to increase throughput, reduce costs, overcome technical batch effects, and improve doublet detection in single-cell genomic studies. To eliminate additional experimental steps, endogenous nuclear genome variants are used for demultiplexing pooled single-cell RNA sequencing (scRNA-seq) data by several computational tools. However, these tools have limitations when applied to single-cell sequencing methods that do not cover nuclear genomic regions well, such as single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq). Here, we demonstrate that mitochondrial germline variants are an alternative, robust, and computationally efficient endogenous barcode for sample demultiplexing. We propose MitoSort, a tool that uses mitochondrial germline variants to assign cells to their donor origins and identify cross-genotype doublets in single-cell genomic datasets. We evaluate its performance by using in silico pooled mitochondrial scATAC-seq (mtscATAC-seq) libraries and experimentally multiplexed data with cell hashtags. MitoSort achieves high accuracy and efficiency in genotype clustering and doublet detection for mtscATAC-seq data, addressing the limitations of current computational techniques tailored for scRNA-seq data. Moreover, MitoSort exhibits versatility, and can be applied to various single-cell sequencing approaches beyond mtscATAC-seq provided that the mitochondrial variants are reliably detected. Furthermore, we demonstrate the application of MitoSort in a case study where B cells from eight donors were pooled and assayed by single-cell multi-omics sequencing. Altogether, our results demonstrate the accuracy and efficiency of MitoSort, which enables reliable sample demultiplexing in various single-cell genomic applications. MitoSort is available at https://github.com/tangzhj/MitoSort.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11671100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484015","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

Virus Infection Induces Immune Gene Activation with CTCF-anchored Enhancers and Chromatin Interactions in Pig Genome. 病毒感染通过猪基因组中的 CTCF 锚定增强子和染色质相互作用诱导免疫基因激活

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae062

Jianhua Cao, Ruimin Ren, Xiaolong Li, Xiaoqian Zhang, Yan Sun, Xiaohuan Tian, Ru Liu, Xiangdong Liu, Yijun Ruan, Guoliang Li, Shuhong Zhao

{"title":"Virus Infection Induces Immune Gene Activation with CTCF-anchored Enhancers and Chromatin Interactions in Pig Genome.","authors":"Jianhua Cao, Ruimin Ren, Xiaolong Li, Xiaoqian Zhang, Yan Sun, Xiaohuan Tian, Ru Liu, Xiangdong Liu, Yijun Ruan, Guoliang Li, Shuhong Zhao","doi":"10.1093/gpbjnl/qzae062","DOIUrl":"10.1093/gpbjnl/qzae062","url":null,"abstract":"Chromatin organization is important for gene transcription in pig genome. However, its three-dimensional (3D) structure and dynamics are much less investigated than those in human. Here, we applied the long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) method to map the whole-genome chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) in porcine macrophage cells before and after polyinosinic-polycytidylic acid [Poly(I:C)] induction. Our results reveal that Poly(I:C) induction impacts the 3D genome organization in the 3D4/21 cells at the fine-scale chromatin loop level rather than at the large-scale domain level. Furthermore, our findings underscore the pivotal role of CTCF-anchored chromatin interactions in reshaping chromatin architecture during immune responses. Knockout of the CTCF-binding locus further confirms that the CTCF-anchored enhancers are associated with the activation of immune genes via long-range interactions. Notably, the ChIA-PET data also support the spatial relationship between single nucleotide polymorphisms (SNPs) and related gene transcription in 3D genome aspect. Our findings in this study provide new clues and potential targets to explore key elements related to diseases in pigs and are also likely to shed light on elucidating chromatin organization and dynamics underlying the process of mammalian infectious diseases.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11725346/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309474","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

Bioinformatic Resources for Exploring Human-virus Protein-protein Interactions Based on Binding Modes. 基于结合模式探索人类-病毒蛋白质-蛋白质相互作用的生物信息资源。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae075

Huimin Chen, Jiaxin Liu, Gege Tang, Gefei Hao, Guangfu Yang

引用次数: 0

The Genome Architecture of the Copepod Eurytemora carolleeae - the Highly Invasive Atlantic Clade of the Eurytemoraaffinis Species Complex. 桡足类 Eurytemora carolleeae 的基因组结构--E. affinis 种群中具有高度入侵性的大西洋支系。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae066

Zhenyong Du, Gregory Gelembiuk, Wynne Moss, Andrew Tritt, Carol Eunmi Lee

{"title":"The Genome Architecture of the Copepod Eurytemora carolleeae - the Highly Invasive Atlantic Clade of the Eurytemoraaffinis Species Complex.","authors":"Zhenyong Du, Gregory Gelembiuk, Wynne Moss, Andrew Tritt, Carol Eunmi Lee","doi":"10.1093/gpbjnl/qzae066","DOIUrl":"10.1093/gpbjnl/qzae066","url":null,"abstract":"Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as food sources for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genome architecture underlying the highly invasive and adaptive capacity of certain populations. Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage PacBio long-read and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome, consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb), was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transport-related gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transport-related genes and the significant clustering of these genes on each chromosome. This genome represents one of the most contiguous copepod genomes to date and is among the highest quality marine invertebrate genomes. As such, this genome provides an invaluable resource to help yield fundamental insights into the ability of this copepod to adapt to rapidly changing environments.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11706791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142335111","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

GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis. GP-Plotter：灵活的蛋白质组学数据光谱可视化，重点是糖蛋白组学分析。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae069

Zheng Fang, Mingming Dong, Hongqiang Qin, Mingliang Ye

{"title":"GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis.","authors":"Zheng Fang, Mingming Dong, Hongqiang Qin, Mingliang Ye","doi":"10.1093/gpbjnl/qzae069","DOIUrl":"10.1093/gpbjnl/qzae069","url":null,"abstract":"Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis. The visualization of fragment ions in mass spectrum provides strong evidence for peptide identification and modification localization. Here, we present an easy-to-use tool, named GP-Plotter, for ion annotation of tandem mass spectra and corresponding image output. Identification result files of common searching tools in the community and user-customized files are supported as input of GP-Plotter. Multiple display modes and parameter customization can be achieved in GP-Plotter to present annotated spectra of interest. Different image formats, especially vector graphic formats, are available for image generation which is favorable for data publication. Notably, GP-Plotter is also well-suited for the visualization and evaluation of glycopeptide spectrum assignments with comprehensive annotation of glycan fragment ions. With a user-friendly graphical interface, GP-Plotter is expected to be a universal visualization tool for the community. GP-Plotter has been implemented in the latest version of Glyco-Decipher (v1.0.4) and the standalone GP-Plotter software is also freely available at https://github.com/DICP-1809.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396283","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

Centromere Landscapes Resolved from Hundreds of Human Genomes. 从数百个人类基因组中解析中心粒景观

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae071

Shenghan Gao, Yimeng Zhang, Stephen J Bush, Bo Wang, Xiaofei Yang, Kai Ye

{"title":"Centromere Landscapes Resolved from Hundreds of Human Genomes.","authors":"Shenghan Gao, Yimeng Zhang, Stephen J Bush, Bo Wang, Xiaofei Yang, Kai Ye","doi":"10.1093/gpbjnl/qzae071","DOIUrl":"10.1093/gpbjnl/qzae071","url":null,"abstract":"High-fidelity (HiFi) sequencing has facilitated the assembly and analysis of the most repetitive region of the genome, the centromere. Nevertheless, our current understanding of human centromeres is based on a relatively small number of telomere-to-telomere assemblies, which have not yet captured its full diversity. In this study, we investigated the genomic diversity of human centromere higher order repeats (HORs) via both HiFi reads and haplotype-resolved assemblies from hundreds of samples drawn from ongoing pangenome-sequencing projects and reprocessed them via a novel HOR annotation pipeline, HiCAT-human. We used this wealth of data to provide a global survey of the centromeric HOR landscape; in particular, we found that 23 HORs presented significant copy number variability between populations. We detected three centromere genotypes with unbalanced population frequencies on chromosomes 5, 8, and 17. An inter-assembly comparison of HOR loci further revealed that while HOR array structures are diverse, they nevertheless tend to form a number of specific landscapes, each exhibiting different levels of HOR subunit expansion and possibly reflecting a cyclical evolutionary transition from homogeneous to nested structures and back.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11652271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484010","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