Omics A Journal of Integrative Biology最新文献_第5页

Multiomics Integration Reveals Distinct miRNA-Mediated Regulatory Networks at the Transcript and Protein Levels in Idiopathic Pulmonary Fibrosis. 多组学整合揭示了特发性肺纤维化中转录物和蛋白质水平上不同的mirna介导的调节网络。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-09-01 Epub Date: 2026-07-10 DOI: 10.1177/15578100261467222

Min Kyung Kim, Seung Hyun Kim, Sung Woo Park, Jong-Uk Lee

{"title":"Multiomics Integration Reveals Distinct miRNA-Mediated Regulatory Networks at the Transcript and Protein Levels in Idiopathic Pulmonary Fibrosis.","authors":"Min Kyung Kim, Seung Hyun Kim, Sung Woo Park, Jong-Uk Lee","doi":"10.1177/15578100261467222","DOIUrl":"10.1177/15578100261467222","url":null,"abstract":"MicroRNAs (miRNAs) are key post-transcriptional regulators implicated in multilevel molecular dysregulation in idiopathic pulmonary fibrosis (IPF). However, their function is largely inferred from miRNA-mRNA associations, leaving protein-level consequences poorly defined. We performed an integrated multiomics analysis combining miRNA sequencing, RNA sequencing, and proteomic profiling of primary lung fibroblasts from patients with IPF and controls. Transcriptomic data were obtained from the Gene Expression Omnibus (GSE301181), and donor-matched proteomic data were deposited in Figshare. miRNA-mRNA correlations and miRNA-protein associations were evaluated through integrative correlation and interaction analyses, followed by functional enrichment and network modeling. Thirteen differentially expressed miRNAs were identified and showed widespread negative correlations with 710 differentially expressed genes. In contrast, proteomic integration identified a more restricted subset of 229 miRNA-associated differentially expressed proteins. Functional enrichment revealed broad distribution of miRNA-mRNA associations across extracellular matrix organization, immune signaling, and cell migration pathways, whereas miRNA-protein associations converged on a limited set of biological processes with higher enrichment ratios. Several miRNAs were linked to known fibrosis- and stress-related targets, supporting biological relevance. Together, these findings suggest that integrated protein-level analysis helps refine fibrosis-relevant miRNA regulatory programs in IPF fibroblasts and may improve biological interpretation of disease-associated molecular changes.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"541-550"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148423079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrative Biological Analysis of Histamine Depletion on Neuroinflammation, Dopamine D2 Receptor, and Glutamate in Experimental Tic Disorder. 组胺耗竭对实验性抽动障碍中神经炎症、多巴胺D2受体和谷氨酸的综合生物学分析。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-09-01 Epub Date: 2026-07-11 DOI: 10.1177/15578100261468080

Jing Zhang, Qianying Liu, Shuyao Chen, Ru Sun, Guizhi Xia

{"title":"Integrative Biological Analysis of Histamine Depletion on Neuroinflammation, Dopamine D2 Receptor, and Glutamate in Experimental Tic Disorder.","authors":"Jing Zhang, Qianying Liu, Shuyao Chen, Ru Sun, Guizhi Xia","doi":"10.1177/15578100261468080","DOIUrl":"10.1177/15578100261468080","url":null,"abstract":"Tic disorder (TD) is a common neurodevelopmental disorder in children. Acute histamine deficiency may be involved in the pathogenesis of TDs. In this study, we demonstrate that histamine depletion exacerbates tic-like behaviors in a rat model of TD. Sprague-Dawley rats were divided into control, TD model, TD plus saline, and TD plus α-fluoromethylhistidine (α-FMH) groups. TD was induced by intraperitoneal iminodipropionitrile, and α-FMH was administered intracerebroventricularly. Behavioral assessments showed that α-FMH treatment significantly increased stereotyped and motor behavior scores compared with TD groups (p < 0.05). Immunohistochemistry revealed marked microglial activation in the striatum of TD groups, which was exacerbated by histamine deficiency. Striatal IL-6 and TNF-α levels were elevated in all TD groups; IL-6 was significantly higher in the α-FMH group than in TD groups (p < 0.05). Striatal dopamine receptor D2 (DRD2) expression was also upregulated in TD groups, with the highest levels observed after histamine depletion (p < 0.05). Liquid chromatography-tandem mass spectrometry result showed that glutamate levels were significantly reduced in the α-FMH group compared to the TD-NaCl group (p < 0.05). No significant differences were observed in the levels of dopamine, serotonin, or acetylcholine between the TD-NaCl and TD-α-FMH groups. Overall, our findings suggest that acute histamine deficiency aggravates TD-related behaviors by promoting neuroinflammation and upregulating DRD2 expression, highlighting the therapeutic potential of targeting histamine signaling in TD.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"551-559"},"PeriodicalIF":2.0,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148423095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Apigenin Alleviates Ligamentum Flavum Ossification by Dual-Targeting CA9 and CDK6 and Modulating Calcium/PI3K-Akt Signaling. 芹菜素通过双靶向CA9和CDK6以及调节钙/PI3K-Akt信号通路缓解黄韧带骨化。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-08-22 DOI: 10.1177/15578100261479078

Yuanqun Zhang, Yihuang Chen, Guohao Liu, Huan Liu

{"title":"Apigenin Alleviates Ligamentum Flavum Ossification by Dual-Targeting CA9 and CDK6 and Modulating Calcium/PI3K-Akt Signaling.","authors":"Yuanqun Zhang, Yihuang Chen, Guohao Liu, Huan Liu","doi":"10.1177/15578100261479078","DOIUrl":"https://doi.org/10.1177/15578100261479078","url":null,"abstract":"While apigenin shows therapeutic potential for bone-related disorders like osteoporosis and osteoarthritis, its mechanisms in regulating ligamentum flavum ossification (OLF) are unclear. An integrated computational strategy combining network pharmacology, machine learning, and molecular docking was used to study apigenin's therapeutic potential for OLF. First, differential gene expression profiling was done using the GSE113212 dataset to find OLF-related differentially expressed genes. At the same time, apigenin's putative targets and bioactive components were collected from pharmacological databases and literature. Common targets between apigenin and OLF-related genes were identified by Venn diagram analysis. Then, the Metascape platform was used to analyze the functional enrichment of these overlapping targets, including Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes analyses. The results showed significant involvement in bone-metabolism and inflammatory-response biological processes and signaling pathways, especially the calcium and PI3K-Akt signaling pathways. A protein-protein interaction network was built with the STRING database and refined by machine-learning algorithms to find central therapeutic targets. Molecular docking analysis showed binding energies of <-5 kcal/mol between apigenin and core target proteins, indicating strong binding. Molecular dynamics simulations supported the stability and binding reliability of apigenin-target complexes. Overall, these results offer initial insights into how apigenin may modulate OLF, highlighting new therapeutic strategies and potential targets for OLF treatment.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"15578100261479078"},"PeriodicalIF":2.0,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148796395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phosphosite-Centric Association of MBD3 and NuRD Complex Based on Meta-Analysis of Global Human Phosphoproteome. 基于全球人类磷酸化蛋白组meta分析的MBD3和NuRD复合物的磷酸化中心关联。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-08-22 DOI: 10.1177/15578100261479165

Rachael Dsouza, Vaishnavi Gopalakrishnan, Leona Dcunha, Althaf Mahin, Athira Perunelly Gopalakrishnan, Samseera Ummar, Rajesh Raju, Sowmya Soman

{"title":"Phosphosite-Centric Association of MBD3 and NuRD Complex Based on Meta-Analysis of Global Human Phosphoproteome.","authors":"Rachael Dsouza, Vaishnavi Gopalakrishnan, Leona Dcunha, Althaf Mahin, Athira Perunelly Gopalakrishnan, Samseera Ummar, Rajesh Raju, Sowmya Soman","doi":"10.1177/15578100261479165","DOIUrl":"https://doi.org/10.1177/15578100261479165","url":null,"abstract":"Methyl-CpG-binding domain protein 3 (MBD3) is a member of the methyl-CpG-binding domain (MBD) family, which functions as a scaffold within the nucleosome remodeling and histone deacetylase complex (NuRD). MBD3 has been studied extensively in pluripotency and gene regulation, particularly through chromatin remodeling. Emerging evidence indicates the role MBD3 in cancer-related signaling pathways. Although MBD3 is detected to be highly phosphoregulated in various phosphoproteomic studies, the phosphoregulatory network of MBD3 remains largely unknown. To address this gap, a comprehensive analysis of MBD3 was performed using publicly available human cellular phosphoproteome datasets. Our study identified two phosphosites, S85 and S56, as the most frequently detected and differentially regulated across datasets. The S56 is situated within its MBD while the S85 site resides within the MBDa. Co-occurrence analysis revealed co-ordinated regulation between these predominant phosphosites. Focusing on the phosphoregulation of the NuRD complex proteins and their binary interactors that co-regulated with MBD3-predominant phosphosites, we constructed a protein-protein interaction network that highlights co-ordinated interactions between MBD3 phosphoregulated proteins with the NuRD complex. These findings provide the first phosphosite-centric view on MBD3 regulation, establishing a basis for future investigations into MBD3 phosphorylation and its implications in cancer.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"15578100261479165"},"PeriodicalIF":2.0,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148796400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Stage-Specific Gene Expression Profiles in Multiple Sclerosis Cortical Lesions Identified via Spatial Transcriptomics. 通过空间转录组学鉴定多发性硬化症皮质病变的阶段特异性基因表达谱。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-08-17 DOI: 10.1177/15578100261479076

Raquel Gasque-Rubio, Laura Cubas-Nuñez, Jéssica Castillo-Villalba, Lucía Casas-Hidalgo, Lorena Forés-Toribio, Sara Carratalá-Boscá, Jordi Tortosa-Carreres, Carmen Alcalá-Vicente, Carlos Quintanilla-Bordás, David Gorriz, Francisco Pérez-Miralles, Bonaventura Casanova

{"title":"Stage-Specific Gene Expression Profiles in Multiple Sclerosis Cortical Lesions Identified via Spatial Transcriptomics.","authors":"Raquel Gasque-Rubio, Laura Cubas-Nuñez, Jéssica Castillo-Villalba, Lucía Casas-Hidalgo, Lorena Forés-Toribio, Sara Carratalá-Boscá, Jordi Tortosa-Carreres, Carmen Alcalá-Vicente, Carlos Quintanilla-Bordás, David Gorriz, Francisco Pérez-Miralles, Bonaventura Casanova","doi":"10.1177/15578100261479076","DOIUrl":"https://doi.org/10.1177/15578100261479076","url":null,"abstract":"Multiple sclerosis (MS) is a chronic inflammatory disease characterized by demyelinating lesions in the central nervous system. While animal models have provided insights into lesion development, human-based studies remain limited. This study investigated the molecular landscape of gray matter lesions at different stages using spatial transcriptomics. Post-mortem cortical tissue from MS patients was analyzed to examine gene expression in lesions classified as early active, chronic active, or chronic inactive based on myelin integrity and macrophage/microglia activity. Distinct transcriptomic profiles were observed across lesion stages, although these findings should be considered exploratory given the limited sample size, with the early active category represented by a single lesion. The early active lesion showed increased expression of immune-related genes (e.g., HLA-DRA, CD68, CCL5) and enrichment of inflammatory and extracellular matrix remodeling pathways. Chronic active lesions showed enrichment of innate immune pathways, including Toll-like receptor and complement signaling, whereas chronic inactive lesions exhibited increased expression of heat shock proteins (HSPA1A, HSPA1B), and stress-response pathways. Control samples showed preserved neuronal and myelin gene expression. These findings provide preliminary insights into molecular processes that may be associated with MS lesion progression and may identify candidate biomarkers for future validation studies.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"15578100261479076"},"PeriodicalIF":2.0,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148760638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Vertical Multi-Target Design of Potential Staphylococcus aureus Respiratory Inhibitors: A Systematic in Silico Fragment-Based Approach. 潜在金黄色葡萄球菌呼吸抑制剂的垂直多靶点设计：基于硅碎片的系统方法。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-08-17 DOI: 10.1177/15578100261479161

Srimari Srikanth, Soundarya Priya Alexandar, Venkatasubramanian Ulaganathan

{"title":"Vertical Multi-Target Design of Potential Staphylococcus aureus Respiratory Inhibitors: A Systematic in Silico Fragment-Based Approach.","authors":"Srimari Srikanth, Soundarya Priya Alexandar, Venkatasubramanian Ulaganathan","doi":"10.1177/15578100261479161","DOIUrl":"https://doi.org/10.1177/15578100261479161","url":null,"abstract":"Multi-target drug design has emerged as a promising strategy to overcome the limitations of single-target drugs, particularly in combating infectious diseases that develop resistance through different mechanisms. Enzymes in the Menaquinone (MK) biosynthesis pathway of Staphylococcus aureus represent attractive targets for this approach, as they catalyze the sequential steps in the pathway, each of which processes a substrate intermediate that contains a thioester-coenzyme A or dicarboxylate moiety. Therefore, this acts as a vertical targeting strategy where multiple enzymes within the same pathway can be inhibited simultaneously. In this study, we provide the first systematic approach for vertical multi-target design. We used an in silico fragment-based approach to match the structural features of the active sites and identify common pharmacophoric elements, and screen for compounds that can simultaneously inhibit target enzymes within the MK pathway. Common fragments across the targets were identified through multi-target docking, and built compounds were prioritized using a geometric mean-based multi-target activity score. Structure-based pharmacophore modeling revealed a conserved Donor-Hydrophobic-Ring-Ring motif across all active sites. Molecular dynamics simulations supported the stability and multi-target potential of the identified compounds.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"15578100261479161"},"PeriodicalIF":2.0,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148761984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the ROS-Related Therapeutic Mechanism of Bushen Huoxue Decoction in Postmenopausal Osteoporosis through Transcriptomics and Network Pharmacology. 通过转录组学和网络药理学探讨补肾活血汤对绝经后骨质疏松症ros相关的治疗机制。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-08-01 Epub Date: 2026-06-11 DOI: 10.1177/15578100261458418

Li Yin, Xin Chen, Jianli Xu

{"title":"Exploring the ROS-Related Therapeutic Mechanism of Bushen Huoxue Decoction in Postmenopausal Osteoporosis through Transcriptomics and Network Pharmacology.","authors":"Li Yin, Xin Chen, Jianli Xu","doi":"10.1177/15578100261458418","DOIUrl":"10.1177/15578100261458418","url":null,"abstract":"Introduction: Postmenopausal osteoporosis (PMOP) involves bone loss and fracture risk, driven by estrogen deficiency, oxidative stress, immune dysregulation, and endocrine alterations. Bushen Huoxue Decoction is used for osteoporosis, but its mechanisms in PMOP are unclear.Methods: We integrated network pharmacology, transcriptomics, machine learning, molecular docking, molecular dynamics, and absorption, distribution, metabolism, excretion, and toxicity prediction. Reactive oxygen species (ROS)-related differentially expressed genes (ROS-DEGs) from gene expression omnibus datasets were assessed by enrichment, single-sample gene set enrichment analysis (ssGSEA), feature-gene selection, diagnostic modeling, external validation, and in silico binding analyses.Results: A total of 118 compounds and 489 targets were identified. ROS-DEGs were enriched in inflammation, cell death, and bone metabolism pathways, including TNF, NF-kappa B, MAPK, Ras, and metabolic pathways. ssGSEA revealed remodeling of immune-related transcriptional signatures rather than direct changes in immune-cell composition. Integration with herbal targets highlighted ABL1 and CYP1A1 as key nodes; the combined diagnostic model outperformed single genes and was supported by external validation in GSE7429 (B-cell context). Tanshinone IIA showed the strongest predicted binding to CYP1A1.Conclusion: Bushen Huoxue Decoction may mitigate PMOP through multicomponent, multitarget modulation of ROS, immune, and bone remodeling networks. ABL1 and CYP1A1, along with Ras and metabolic pathways, represent major mechanistic axes, providing prioritized targets for experimental validation.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"436-448"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148218876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Site-Specific Phosphoproteomics Uncovers Potential Regulatory Networks of NEK4 in DNA Damage Response and Cancer Progression. 位点特异性磷酸化蛋白质组学揭示了NEK4在DNA损伤反应和癌症进展中的潜在调控网络。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-08-01 Epub Date: 2026-06-24 DOI: 10.1177/15578100261461325

Spoorthi Sathish Kashipatna, Apoorva Pai, Leona Dcunha, Ummar Samseera, Athira Perunelly Gopalakrishnan, Athira C Rajeev, Rajesh Raju

{"title":"Site-Specific Phosphoproteomics Uncovers Potential Regulatory Networks of NEK4 in DNA Damage Response and Cancer Progression.","authors":"Spoorthi Sathish Kashipatna, Apoorva Pai, Leona Dcunha, Ummar Samseera, Athira Perunelly Gopalakrishnan, Athira C Rajeev, Rajesh Raju","doi":"10.1177/15578100261461325","DOIUrl":"10.1177/15578100261461325","url":null,"abstract":"NIMA-related kinase 4 (NEK4) is a serine/threonine kinase implicated in microtubule stabilization, cilia function, and DNA damage response (DDR), with emerging roles in cancer progression through context-dependent effects on proliferation, epithelial-to-mesenchymal transition (EMT), and metastasis. Despite its significance, site-specific phosphorylation dynamics of NEK4 remain underexplored. Here, we conducted a comprehensive computational phosphoproteomic analysis by curating Class-1 phosphosites from over 3800 public datasets, identifying NEK4 phosphosites, including four predominant sites (S563, S661, S461, S639) outside the kinase domain that exhibit high detection frequencies and differential regulation. Coregulation analysis revealed phosphosites in other proteins (PsOPs) that coordinate with these NEK4 sites, linking them to DDR pathways (e.g., via interactions with DNA-PK complex components), EMT signaling, microtubule organization, and mitochondrial function. Network mapping integrated predicted upstream kinases (e.g., CDK13, RPS6KA1/3), downstream substrates (e.g., MKI67, INCENP), and binary interactors (e.g., TMPO, RRP1B), highlighting NEK4's integration into cancer-associated networks involving cell cycle regulation, apoptosis, and autophagy. Functional enrichment underscored NEK4's potential in modulating genotoxic stress responses and tumorigenic reprogramming. These findings provide a phospho-centric framework for NEK4 signaling, positioning it as a therapeutic target in DDR-defective and EMT-driven cancers, and lay the groundwork for experimental validation of its site-specific roles.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"466-478"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148308966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Digital Resources for Traversing the Landscape of Human Aging: Databases, Key Computational Strategies, and Artificial Intelligence. 跨越人类老龄化景观的数字资源：数据库，关键计算策略和人工智能。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-08-01 Epub Date: 2026-06-08 DOI: 10.1177/15578100261457662

Aaysha Gupta, Sonam Chawla

{"title":"Digital Resources for Traversing the Landscape of Human Aging: Databases, Key Computational Strategies, and Artificial Intelligence.","authors":"Aaysha Gupta, Sonam Chawla","doi":"10.1177/15578100261457662","DOIUrl":"10.1177/15578100261457662","url":null,"abstract":"By 2050, nearly 20% of the global population will exceed 60 years old, experiencing compromised physiological and functional abilities, neurological disorders, and sarcopenia. Geroscience has evolved immensely through OMICS approaches and high-throughput technologies, generating massive datasets requiring efficient management, annotation, and storage. This highlights the need for user-friendly databases integrated with machine learning (ML) and artificial intelligence (AI). This review provides a comparative synthesis of the state-of-the-art databases on longevity genes, age-related signaling pathways, model organism phenotypes, and manually curated aging/antiaging experimental studies. We delineate the architecture, methodology, and functional features of contemporary geroscience databases, detailing the objectives, content, and dataset size, including multiomics information. Critically, these databases facilitate geriatric interventions: from biomarker discovery to drug repositioning, significantly impacting aging-associated conditions like muscle loss and Alzheimer's. In addition, we present updated insights into the increasing use of deep aging clocks and multiomics databases, coupled with ML- and AI-dependent analyses, fostering advanced dataset development. Interestingly, these tools are capable of dataset pattern recognition, predictive modeling, and the generation of research hypotheses. By bridging manually curated and AI-driven tools, this review offers a holistic view of the complementary strengths of aging databases, paving the way for the next generation of geroscience.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"421-435"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148199604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteogenomic Analysis of CDPK1 Mutant in Plasmodium falciparum. 恶性疟原虫CDPK1突变体的蛋白质基因组学分析。

IF 2 3区生物学

Omics A Journal of Integrative Biology Pub Date : 2026-08-01 Epub Date: 2026-06-16 DOI: 10.1177/15578100261461321

Nikita Choudhary, Akhila Balakrishna Rai, Thottethodi Subrahmanya Keshava Prasad, Shobha Dagamajalu

{"title":"Proteogenomic Analysis of CDPK1 Mutant in Plasmodium falciparum.","authors":"Nikita Choudhary, Akhila Balakrishna Rai, Thottethodi Subrahmanya Keshava Prasad, Shobha Dagamajalu","doi":"10.1177/15578100261461321","DOIUrl":"10.1177/15578100261461321","url":null,"abstract":"Malaria caused by Plasmodium falciparum remains a health burden worldwide due to drug resistance and limited treatment options. Calcium-dependent protein kinase 1 (CDPK1) plays a central role in parasite development and invasion, but the downstream molecular alterations that occur upon its disruption remain poorly understood. We present a proteogenomic-based data analysis pipeline for the reanalysis of the publicly available P. falciparum CDPK1 mutant dataset (PRIDE: PXD005207), integrating proteomic and phosphoproteomic data with six-frame genome translation. This led to the discovery of 24 new protein-coding genes, including 17 exonic and 7 intronic peptides, thereby enriching the current genome annotation. Several peptides, such as NILLTFDK, THNNNPQPNPQQK, and EVTSNFGNIR, mapped to previously unannotated genomic regions, which showed orthologous evidence in other Plasmodium species. The reanalysis of phosphoproteomics data identified 37 novel peptides that imply changes in phosphorylation signaling upon CDPK1 knockdown. The identification of conserved peptides like those associated with metacaspase and HSP70, indicates their potential roles in the survival and adaptation of parasites. Overall, this study highlights the potential of proteogenomics to improve genome annotation and reveal hidden coding regions of the P. falciparum genome. This provides new insights into kinase-regulated pathways and potential molecular targets for malaria control.","PeriodicalId":19530,"journal":{"name":"Omics A Journal of Integrative Biology","volume":" ","pages":"459-465"},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148258843","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0