Genomics, proteomics & bioinformatics最新文献_第3页

Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio. 使用纳米孔和PacBio进行长读元基因组测序的计算工具和资源。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-22 DOI: 10.1093/gpbjnl/qzaf075

Tianyuan Zhang, Mian Jiang, Hanzhou Li, Yunyun Gao, Salsabeel Yousuf, Kaimin Yu, Xinxin Yi, Jun Wang, Lulu Yang, Yong-Xin Liu

{"title":"Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio.","authors":"Tianyuan Zhang, Mian Jiang, Hanzhou Li, Yunyun Gao, Salsabeel Yousuf, Kaimin Yu, Xinxin Yi, Jun Wang, Lulu Yang, Yong-Xin Liu","doi":"10.1093/gpbjnl/qzaf075","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf075","url":null,"abstract":"In recent years, the field of shotgun metagenomics has witnessed remarkable advancements, primarily driven by the development and refinement of next-generation sequencing technologies, particularly long-read sequencing platforms such as Nanopore and PacBio. These platforms have significantly improved the ability to analyze microbial communities directly from environmental samples, providing valuable information on their composition, function, and dynamics without the need for pure cultivation. These technologies enhance metagenomic data assembly, annotation, and analysis by addressing longer reads, higher error rates, and complex data. In this review, we provide a comprehensive overview of the historical development of long-read metagenomics, highlighting significant landmarks and advancements. We also explore the diverse applications of long-read metagenomics, emphasizing its impact across various fields. Additionally, we summarize the essential computational resources, including software, databases, and packages, developed to enhance the efficiency and accuracy of metagenomic analysis. Finally, we provide a practical guide for the installation and use of notable software available on GitHub (https://github.com/zhangtianyuan666/LongMetagenome). Overall, this review assists the metagenomics community in exploring microbial life in unprecedented depth by providing a roadmap for successful resource utilization and emphasizing possibilities for innovation.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144984018","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

MedImg: An Integrated Database for Public Medical Image. MedImg：公共医学图像集成数据库。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-20 DOI: 10.1093/gpbjnl/qzaf068

Bitao Zhong, Rui Fan, Yue Ma, Xiangwen Ji, Qinghua Cui, Chunmei Cui

{"title":"MedImg: An Integrated Database for Public Medical Image.","authors":"Bitao Zhong, Rui Fan, Yue Ma, Xiangwen Ji, Qinghua Cui, Chunmei Cui","doi":"10.1093/gpbjnl/qzaf068","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf068","url":null,"abstract":"The advancements in deep learning algorithms for medical image analysis have garnered significant attention in recent years. While several studies show promising results, with models achieving or even surpassing human performance, translating these advancements into clinical practice is still accompanied by various challenges. A primary obstacle lies in the availability of large-scale, well-characterized datasets for validating the generalization of approaches. To address this challenge, we curated a diverse collection of medical image datasets from multiple public sources, containing 105 datasets and a total of 1,995,671 images. These images span 14 modalities, including X-ray, computed tomography, magnetic resonance imaging, optical coherence tomography, ultrasound, and endoscopy, and originate from 13 organs, such as the lung, brain, eye, and heart. Subsequently, we constructed an online database, MedImg, which incorporates and systematically organizes these medical images to facilitate data accessibility. MedImg serves as an intuitive and open-access platform for facilitating research in deep learning-based medical image analysis, accessible at https://www.cuilab.cn/medimg/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144984001","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-wide Genetic Mutations Accumulated in Pigs Genome-edited for Xenotransplantation and Their Filial Generation. 用于异种移植的猪基因组编辑中积累的全基因组基因突变及其后代。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-20 DOI: 10.1093/gpbjnl/qzaf071

Xueyun Huo, Xianhui Sun, Xiangyang Xing, Jing Lu, Jingjing Zhang, Yanyan Jiang, Xiao Zhu, Changlong Li, Jianyi Lv, Meng Guo, Lixue Cao, Xin Liu, Zhenwen Chen, Dengke Pan, Shunmin He, Chen Zhang, Xiaoyan Du

{"title":"Genome-wide Genetic Mutations Accumulated in Pigs Genome-edited for Xenotransplantation and Their Filial Generation.","authors":"Xueyun Huo, Xianhui Sun, Xiangyang Xing, Jing Lu, Jingjing Zhang, Yanyan Jiang, Xiao Zhu, Changlong Li, Jianyi Lv, Meng Guo, Lixue Cao, Xin Liu, Zhenwen Chen, Dengke Pan, Shunmin He, Chen Zhang, Xiaoyan Du","doi":"10.1093/gpbjnl/qzaf071","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf071","url":null,"abstract":"Although xenotransplantation has been revolutionized by the development of genome-edited pigs, it is still unknown whether these pigs and their offspring remain genomically stable. Here, we show that GGTA1-knockout (GTKO) pigs accumulated an average of 1205 genome-wide genetic mutations, and their filial 1 (F1) offspring contained an average of 18 de novo mutations compared with wild-type controls and their parents. The majority of mutations were in regions annotated as intergenic regions, without altering protein functions, and were not located at predicted off-target mutation sites. RNA-sequencing analysis and phenotype observations indicated that the accumulated mutations may have only a limited influence on GTKO pigs and most of the mutations in the GTKO pigs could be attributed to the electrotransfection of plasmids into cells. This is the first report that genetic mutations in genome-edited pigs are inherited stably by the next generation, providing a reference for the safe application and a standard approach to breed genome-edited pigs for xenotransplantation.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144983964","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

LncCE: Landscape of Cellularly-elevated lncRNAs in Single Cells Across Normal and Cancer Tissues. lncrna在正常和癌症组织中单细胞的表达。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-20 DOI: 10.1093/gpbjnl/qzaf069

Kang Xu, Yujie Liu, Chongwen Lv, Ya Luo, Jingyi Shi, Haozhe Zou, Weiwei Zhou, Dezhong Lv, Changbo Yang, Yongsheng Li, Juan Xu

{"title":"LncCE: Landscape of Cellularly-elevated lncRNAs in Single Cells Across Normal and Cancer Tissues.","authors":"Kang Xu, Yujie Liu, Chongwen Lv, Ya Luo, Jingyi Shi, Haozhe Zou, Weiwei Zhou, Dezhong Lv, Changbo Yang, Yongsheng Li, Juan Xu","doi":"10.1093/gpbjnl/qzaf069","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf069","url":null,"abstract":"Long non-coding RNAs (lncRNAs) have emerged as significant players in maintaining the morphology and function of tissues and cells. The precise regulatory effectiveness of lncRNAs is closely associated with the spatial expression patterns across tissues and cells. Here, we propose the Cellularly-Elevated LncRNA (LncCE) resource to systematically explore cellularly-elevated (CE) lncRNAs across normal and cancer tissues in single cells. LncCE encompasses 87,946 entries of CE lncRNAs of 149 cell types by analyzing 181 single-cell RNA sequencing datasets, involving 20 fetal normal tissues, 59 adult normal tissues, as well as 32 adult and five pediatric cancer tissues. Two main search options are provided via a given lncRNA name or cell type. The results emphasize both qualitative and quantitative expression features of lncRNAs across different cell types, co-expression with protein-coding genes, as well as their involvement in biological functions. In particular, LncCE provides quantitative figures for exhibiting lncRNA expression changes in cancers, compared to control samples, and clinical associations with patients' overall survival. Together, LncCE offers an extensive, quantitative, and user-friendly interface to create a CE expression atlas for lncRNAs across normal and cancer tissues at the single-cell level. The LncCE database is available at http://bio-bigdata.hrbmu.edu.cn/LncCE.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144983935","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

Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle. 牛体重调节变异的综合多组学分析。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-18 DOI: 10.1093/gpbjnl/qzaf067

Qunhao Niu, Jiayuan Wu, Tianyi Wu, Tianliu Zhang, Tianzhen Wang, Xu Zheng, Zhida Zhao, Ling Xu, Zezhao Wang, Bo Zhu, Lupei Zhang, Huijiang Gao, Geroge E Liu, Junya Li, Lingyang Xu

{"title":"Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle.","authors":"Qunhao Niu, Jiayuan Wu, Tianyi Wu, Tianliu Zhang, Tianzhen Wang, Xu Zheng, Zhida Zhao, Ling Xu, Zezhao Wang, Bo Zhu, Lupei Zhang, Huijiang Gao, Geroge E Liu, Junya Li, Lingyang Xu","doi":"10.1093/gpbjnl/qzaf067","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf067","url":null,"abstract":"Body weight is a polygenic trait with intricate inheritance patterns. Functional genomics enriched with multi-layer annotations offers essential resources for exploring the genetic architecture of complex traits. In this study, we undertook an extensive characterization of regulatory variants for body weight related traits in cattle using a multi-omics approach. First, we identified seven candidate genes through an integrative analysis of selective sweeps and multiple genome-wide association studies (GWAS) strategies using imputed whole-genome sequencing in a population of 1577 individuals. Subsequently, we uncovered 3340 eGenes [genes whose expression levels are significantly associated with genetic variants in expression quantitative trait locus (eQTL) studies] across 227 muscle samples. Transcriptome-wide association studies (TWAS) further revealed a total of 532 distinct candidate genes associated with body weight traits. Also, colocalization analyses unveiled 44 genes that were shared between eQTLs and GWAS. Moreover, our comprehensive analysis highlighted one target genomic region under positive selection with pleiotropic genes (LAP3, MED28, and NCAPG), and pinpointed a prioritized functional variant within the locus on Bos taurus autosome 6 (BTA6) with complex regulation for body weight by integrating GWAS, selective sweep, eQTL, TWAS, as well as epigenomic analysis and molecular validation. Additionally, convergent evolution analysis and phenome-wide association studies underscored the conservation of the locus across species. Our study provided a comprehensive understanding of the genetic regulation for body weight related traits through multi-omics analysis in cattle. Our findings contribute to unraveling the genetic mechanisms governing weight related traits and shed valuable light on the genetic improvement of farm animals.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144877545","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

Regulatory Genomic Circuitry of Brain Age by Integrative Functional Genomic Analyses. 通过综合功能基因组分析脑年龄的调控基因组电路。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-08 DOI: 10.1093/gpbjnl/qzaf064

Xingzhong Zhao, Anyi Yang, Jing Ding, Yucheng T Yang, Xing-Ming Zhao

{"title":"Regulatory Genomic Circuitry of Brain Age by Integrative Functional Genomic Analyses.","authors":"Xingzhong Zhao, Anyi Yang, Jing Ding, Yucheng T Yang, Xing-Ming Zhao","doi":"10.1093/gpbjnl/qzaf064","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf064","url":null,"abstract":"Brain age gap (BAG) is a valuable biomarker for evaluating brain healthy status and detecting age-associated cognitive degeneration. However, the genetic architecture of BAG and the underlying mechanisms are poorly understood. Here, we estimated brain age from magnetic resonance imaging with improved accuracy using our proposed adversarial convolution network (ACN), followed by applying the ACN model to an elder cohort from UK Biobank. The genetic heritability of BAG was significantly enriched in the regulatory regions and implicated in glial cells. We prioritized a set of BAG-associated genes, and further characterized their expression patterns across brain cell types and regions. Two BAG-associated genes, RUNX2 and KLF3, were found as associated with epigenetic clock and diverse aging-related biological pathways. Finally, two BAG-associated hub transcription factors, KLF3 and SOX10, were identified as regulators of pleiotropic risk genes from diverse brain disorders. Altogether, we improve the estimation of BAG, and identify BAG-associated genes and regulatory networks that are implicated in brain disorders.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839430","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

PreDigs: A Database of Context-specific Cell-type Markers and Precise Cell Subtypes for Digestive Cell Annotation. PreDigs：用于消化细胞注释的上下文特异性细胞类型标记和精确细胞亚型数据库。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-07 DOI: 10.1093/gpbjnl/qzaf066

Jiayue Meng, Mengyao Han, Yuwei Huang, Liang Li, Yuanhu Ju, Daqing Lv, Xiaoyi Chen, Liyun Yuan, Guoqing Zhang

{"title":"PreDigs: A Database of Context-specific Cell-type Markers and Precise Cell Subtypes for Digestive Cell Annotation.","authors":"Jiayue Meng, Mengyao Han, Yuwei Huang, Liang Li, Yuanhu Ju, Daqing Lv, Xiaoyi Chen, Liyun Yuan, Guoqing Zhang","doi":"10.1093/gpbjnl/qzaf066","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf066","url":null,"abstract":"Research on cell type markers helps investigators explore the diverse cellular compositions of gastrointestinal tumors. This enhances our understanding of tumor heterogeneity and its impact on disease progression and treatment response. However, integrating large-scale datasets and the lack of standardized cell type identification remain challenges. Here, we developed PreDigs, a user-friendly database of predicted signatures in digestive system, which offers 124 curated single-cell RNA sequencing datasets, covering over 3.4 million cells, all available for download. After unsupervised clustering, we unified the identification and naming of subtype labels, constructing a cell ontology tree with 142 cell types across eight hierarchical levels. Meanwhile, we calculated three different context-specific cell-type markers, including \"Cell Markers\", \"Subtype Markers\", and \"TPN Markers\", based on various application requirements within or across tissues. Through the integrated analysis of PreDigs data, we identified distinct cell subpopulations exclusive to tumors, one of which corresponds to tumor-specific endothelial cells. Additionally, PreDigs offers online cell annotation tools, allowing users to classify single cells with greater flexibility. PreDigs is accessible at https://www.biosino.org/predigs/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839429","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

Macrophage Response to Avirulent and Virulent Mycobacterium tuberculosis and Anti-TB Effects of Exosome Treatment. 巨噬细胞对无毒性和强毒性结核分枝杆菌的应答及外泌体治疗的抗结核作用。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-05 DOI: 10.1093/gpbjnl/qzaf065

Li Yang, Lingna Lyu, Cuidan Li, Xiuli Zhang, Yingjiao Ju, Ju Zhang, Jie Liu, Liya Yue, Nan Ding, Xiangli Zhang, Dandan Lu, Tingting Yang, Peihan Wang, Jie Wang, Xiaotong Wang, Sihong Xu, Yongjie Sheng, Chunlai Jiang, Jing Wang, Xin Hu, Tuohetaerbaike Bahetibieke, Zongde Zhang, Fei Chen

{"title":"Macrophage Response to Avirulent and Virulent Mycobacterium tuberculosis and Anti-TB Effects of Exosome Treatment.","authors":"Li Yang, Lingna Lyu, Cuidan Li, Xiuli Zhang, Yingjiao Ju, Ju Zhang, Jie Liu, Liya Yue, Nan Ding, Xiangli Zhang, Dandan Lu, Tingting Yang, Peihan Wang, Jie Wang, Xiaotong Wang, Sihong Xu, Yongjie Sheng, Chunlai Jiang, Jing Wang, Xin Hu, Tuohetaerbaike Bahetibieke, Zongde Zhang, Fei Chen","doi":"10.1093/gpbjnl/qzaf065","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf065","url":null,"abstract":"Tuberculosis (TB) returned as the leading cause of death from a single infectious agent in 2023. Human-macrophages and their secreted exosomes play important roles in combating invading Mycobacterium tuberculosis (Mtb). However, panoramic analysis of the underlying immune mechanism for infected macrophages, package mechanism and anti-TB effect of Mtb treated exosomes remain understood. Here we conducted comprehensive analyses of the macrophages infected with avirulent and virulent Mtb (H37Ra & H37Rv) and their exosomes through omics and phenotypic analyses. The results showed that H37Ra stimulated strong immune responses and apoptosis in macrophages to eliminate the invading Mtb, while H37Rv induced severe necrosis and immune escape for survival. Interestingly, our results suggest that macrophages kill Mtb in an interferon-gamma (IFN-γ) independent but simulative way, highlighting the central role of IFN signaling pathway in anti-TB response. Moreover, we observed selective transport of host and Mtb RNAs from macrophages to exosomes. Notably, H37Ra-treated exosomes displayed a higher anti-TB effect than H37Rv-treated exosomes due to some enriched pro-inflammation and immune escape related Mtb proteins in these two exosomes, respectively. Conclusively, our findings shed new light on the immune mechanism of macrophages in response to Mtb infection, offering a new TB treatment strategy and promising vaccine candidates.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144839428","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

ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration. ACE：单细胞镶嵌整合的通用对比学习框架。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-08-04 DOI: 10.1093/gpbjnl/qzaf062

Xuhua Yan, Jinmiao Chen, Ruiqing Zheng, Min Li

{"title":"ACE: A Versatile Contrastive Learning Framework for Single-cell Mosaic Integration.","authors":"Xuhua Yan, Jinmiao Chen, Ruiqing Zheng, Min Li","doi":"10.1093/gpbjnl/qzaf062","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf062","url":null,"abstract":"The integration of single-cell multi-omics datasets is critical for deciphering cellular heterogeneities. Mosaic integration, the most general integration task, poses a greater challenge regarding disparity in modality abundance across datasets. Here, we present Align and CompletE (ACE), a mosaic integration framework that assembles two types of strategies to handle this problem: modality alignment-based strategy (ACE-align) and regression-based strategy (ACE-spec). ACE-align utilizes a novel contrastive learning objective for explicit modality alignment to uncover the shared latent representations behind modalities. ACE-spec combines the modality alignment results and modality-specific representations to construct complete multi-omics representations for all datasets. Extensive experiments across various mosaic integration scenarios demonstrate the superiority of ACE's two strategies over existing methods. Application of ACE-spec to bi-modal and tri-modal integration scenarios showcases that ACE-spec is able to enhance the representation of cellular heterogeneities for datasets with incomplete modalities. The source code of ACE can be accessed at https://github.com/CSUBioGroup/ACE-main.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144777417","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

Whole Genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese. 10763名中国人的全基因组序列分析揭示了新的主观认知能力下降相关基因。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2025-07-29 DOI: 10.1093/gpbjnl/qzaf063

Mengying Wang, Liyang Sun, Xin Xu, Ruoqi Dai, Qilong Tan, Yun Zhu, Andi Xu, Weifang Zheng, Yuanxing Tu, Dan Zhou, Wenyuan Li, Xifeng Wu

{"title":"Whole Genome Sequence Analysis Revealed Novel Subjective Cognitive Decline-associated Genes in 10,763 Chinese.","authors":"Mengying Wang, Liyang Sun, Xin Xu, Ruoqi Dai, Qilong Tan, Yun Zhu, Andi Xu, Weifang Zheng, Yuanxing Tu, Dan Zhou, Wenyuan Li, Xifeng Wu","doi":"10.1093/gpbjnl/qzaf063","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzaf063","url":null,"abstract":"Subjective cognitive decline (SCD) is widely regarded as a potential preclinical stage of Alzheimer's disease (AD), yet its genetic basis remains poorly understood. To address this gap, we investigated genetic biomarkers associated with SCD using whole-genome sequencing (WGS) in 10,763 Chinese participants from the Healthy Zhejiang One Million People Cohort (HOPE Cohort). The discovery stage included 9284 samples, with 1479 samples used for validation. Using a two-stage design, we systematically investigated both common and rare variants associated with SCD. In rare variant analyses, we identified and replicated an association between the upstream region of SEPHS2 and SCD. SEPHS2 is involved in selenophosphate synthesis, and Mendelian randomization analysis showed its association with AD in both blood and brain cerebellum expression levels. Additionally, we identified CLVS2, which encodes a protein primarily expressed in neuronal cells, as a potential regulator for SCD based on missense rare variants. Multi-omics evidence suggests that both SEPHS2 and CLVS2 may play roles in neurodegenerative diseases. For common variants, we validated 8 known loci related to cognitive decline, 3 of which originated from the only existing SCD genetic study conducted under a migraine background. Overall, our WGS-based study fills the gap in SCD research by providing vital genetic evidence from an East Asian population and offers insights into the pathogenic mechanisms of SCD.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144746638","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