Genes & Diseases最新文献_第3页

The hidden Markov model and its applications in bioinformatics analysis 隐马尔可夫模型及其在生物信息学分析中的应用

IF 9.4 2区医学

Genes & Diseases Pub Date : 2025-06-22 DOI: 10.1016/j.gendis.2025.101729

Yingnan Ma , Haiyan Chen , Jingxuan Kang , Xuying Guo , Chen Sun , Jing Xu , Junxian Tao , Siyu Wei , Yu Dong , Hongsheng Tian , Wenhua Lv , Zhe Jia , Shuo Bi , Zhenwei Shang , Chen Zhang , Hongchao Lv , Yongshuai Jiang , Mingming Zhang

{"title":"The hidden Markov model and its applications in bioinformatics analysis","authors":"Yingnan Ma , Haiyan Chen , Jingxuan Kang , Xuying Guo , Chen Sun , Jing Xu , Junxian Tao , Siyu Wei , Yu Dong , Hongsheng Tian , Wenhua Lv , Zhe Jia , Shuo Bi , Zhenwei Shang , Chen Zhang , Hongchao Lv , Yongshuai Jiang , Mingming Zhang","doi":"10.1016/j.gendis.2025.101729","DOIUrl":"10.1016/j.gendis.2025.101729","url":null,"abstract":"<div><div>Big biological data contains a large amount of life science information, yet extracting meaningful insights from this data remains a complex challenge. The hidden Markov model (HMM), a statistical model widely utilized in machine learning, has proven effective in addressing various problems in bioinformatics. Despite its broad applicability, a more detailed and comprehensive discussion is needed regarding the specific ways in which HMMs are employed in this field. This review provides an overview of the HMM, including its fundamental concepts, the three canonical problems associated with it, and the relevant algorithms used for their resolution. The discussion emphasizes the model's significant applications in bioinformatics, particularly in areas such as transmembrane protein prediction, gene discovery, sequence alignment, CpG island detection, and copy number variation analysis. Finally, the strengths and limitations of the HMM are discussed, and its prospects in bioinformatics are predicted. HMMs can play a pivotal role in addressing complex biological problems and advancing our understanding of biological sequences and systems. This review can provide bioinformatics researchers with comprehensive information on HMM and guide their work.</div></div>","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"13 1","pages":"Article 101729"},"PeriodicalIF":9.4,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The specific hallmarks, emerging roles, key mechanisms, and clinical applications of intra-tumoral microbiota in human cancers 肿瘤内微生物群在人类癌症中的具体特征、新角色、关键机制和临床应用

IF 9.4 2区医学

Genes & Diseases Pub Date : 2025-06-22 DOI: 10.1016/j.gendis.2025.101733

Tingting Zhao , Na Sun , Jun Ding , Zaihui Peng , Fei Han , Xiaowei Qi

{"title":"The specific hallmarks, emerging roles, key mechanisms, and clinical applications of intra-tumoral microbiota in human cancers","authors":"Tingting Zhao , Na Sun , Jun Ding , Zaihui Peng , Fei Han , Xiaowei Qi","doi":"10.1016/j.gendis.2025.101733","DOIUrl":"10.1016/j.gendis.2025.101733","url":null,"abstract":"<div><div>Intra-tumoral microbes have been revealed to exist in many cancer types, attracting widespread attention. The significance of intra-tumoral microbes is becoming increasingly apparent in various aspects of human cancers, encompassing cancer initiation, progression, metastasis, diagnostic approaches, prognostic evaluations, and therapeutic interventions. Despite the considerable focus dedicated to this topic by numerous scholars, a comprehensive analysis of intra-tumoral microbiota is still lacking in human cancers. Especially, identifying specific microbial hallmarks in the occurrence and development of cancer and different cancers remains the central task for investigators. This review focuses on the identification and analysis of distinct attributes and noteworthy characteristics exhibited by intra-tumoral microbiota across various types of cancer. The potential mechanisms of intra-tumoral microbiota action, as well as the significance of the microbiome in the diagnosis and prognosis of cancer, are systematically summarized. The capacity of intra-tumoral microbes to regulate cancer treatment with a focus on the relevant microbial species, and the possibility of targeting the microbiota to improve treatment effectiveness while preventing toxicity, are specifically highlighted. Lastly, the challenges, limitations, and prospects of intra-tumoral microbes in further study and clinical application, including prognostic, diagnostic, and therapeutic applications, are discussed in cancers. This review provides a systematic summary of the specific characteristics, molecular mechanisms, therapeutic effects, and diagnostic and prognostic values of intra-tumoral microbiota in different cancers, which will help improve the diagnosis, treatment, and prognosis of tumor patients and offer new ideas for achieving precise treatment of cancer with intra-tumoral microbiota.</div></div>","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"13 1","pages":"Article 101733"},"PeriodicalIF":9.4,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145155777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CALR accelerates the growth of liver cancer cells by enhancing telomere activity via ARAF CALR通过ARAF增强端粒活性，加速肝癌细胞的生长

IF 9.4 2区医学

Genes & Diseases Pub Date : 2025-06-14 DOI: 10.1016/j.gendis.2025.101715

Sijie Xie , Xiaoxue Jiang , Xinlei Liu, Shuting Song, Liyan Wang, Shujie Li, Dongdong Lu

引用次数: 0

Corrigendum to “Pan-cancer analysis of MET mutation and its association with the efficacy of immune checkpoint blockade” [Genes & Dis 12 (2025) 101450] “MET突变的泛癌分析及其与免疫检查点阻断疗效的关系”的勘误表[基因与疾病12 (2025)101450]

IF 9.4 2区医学

Genes & Diseases Pub Date : 2025-06-13 DOI: 10.1016/j.gendis.2025.101726

Lijin Chen , Yingying Li , Hong Zhao , Jinyuan Huang , Huimeng Yan , Xiaoyan Lin , Bin Zhao

引用次数: 0

Forward genetics identifies HN1L/JPT2 as a novel carboplatin resistance gene in ovarian cancer 正向遗传学鉴定HN1L/JPT2是卵巢癌中新的卡铂耐药基因

IF 9.4 2区医学

Genes & Diseases Pub Date : 2025-06-13 DOI: 10.1016/j.gendis.2025.101720

Han Wei , Aishat Motolani , Kenneth P. Nephew , Guanglong Jiang , Faranak Alipourgivi , Steven Sun , Xiumei Huang , Mateusz Opyrchal , George Sandusky , Yunlong Liu , Tao Lu

引用次数: 0

Role of angiogenesis-related lncRNAs in tumor microenvironment and prognosis of lung adenocarcinoma 血管生成相关lncrna在肺腺癌肿瘤微环境及预后中的作用

IF 6.9 2区医学

Genes & Diseases Pub Date : 2025-06-11 DOI: 10.1016/j.gendis.2025.101700

Lifeng Li , Yaqi Yang , Mengle Peng , Zhirui Fan , Xiaoran Duan , Ruyue Xue , Xuefeng Lv , Ming Cheng , Jie Zhao

引用次数: 0

Emerging roles and therapeutic implications of lipid droplet protein perilipin 2 in liver disease 脂滴蛋白perilipin 2在肝脏疾病中的新作用和治疗意义

IF 9.4 2区医学

Genes & Diseases Pub Date : 2025-06-07 DOI: 10.1016/j.gendis.2025.101712

Xuwen Xiang , Jing Chen , Lin Che

引用次数: 0

TLR4 interaction with PIEZO1 facilitates the 5-HT-mediated intestinal motility dysfunction in offspring mice induced by LPS exposure during pregnancy TLR4与PIEZO1的相互作用促进了5- ht介导的妊娠期LPS暴露诱导的子代小鼠肠道运动功能障碍

IF 6.9 2区医学

Genes & Diseases Pub Date : 2025-06-05 DOI: 10.1016/j.gendis.2025.101707

Ruifang Luo , Yuan Miao , Riqiang Hu , Fang Lin , Junyan Yan , Ting Yang , Lu Xiao , Zhujun Sun , Yuting Wang , Jie Chen

{"title":"TLR4 interaction with PIEZO1 facilitates the 5-HT-mediated intestinal motility dysfunction in offspring mice induced by LPS exposure during pregnancy","authors":"Ruifang Luo , Yuan Miao , Riqiang Hu , Fang Lin , Junyan Yan , Ting Yang , Lu Xiao , Zhujun Sun , Yuting Wang , Jie Chen","doi":"10.1016/j.gendis.2025.101707","DOIUrl":"10.1016/j.gendis.2025.101707","url":null,"abstract":"<div><div>Several factors during pregnancy, such as changes in serotonin (5-HT) levels, can affect intestinal function in offspring mice. The role of 5-HT in regulating intestinal motility after lipopolysaccharide (LPS) exposure during pregnancy is unclear. In this study, <em>Tlr4</em><sup>fl/fl</sup> and <em>Tlr4</em><sup>▵IEC</sup> mice were injected with LPS or phosphate-buffered saline during pregnancy to obtain prenatal LPS-exposed or non-exposed offspring mice. Changes in intestinal morphology, motility, and the TLR4 and 5-HT signaling pathways were examined in male offspring mice. The role of TLR4 in regulating 5-HT secretion was investigated in the BON-1 enterochromaffin cell line. In the prenatal LPS-exposed <em>Tlr4</em><sup>fl/fl</sup> group, offspring mice exhibited colonic mucosal injury and faster intestinal motility, but these effects were absent when TLR4 was knocked out in intestinal epithelial cells. The TLR4 and 5-HT signaling pathways were activated in the colon of prenatal LPS-exposed <em>Tlr4</em><sup>fl/fl</sup> offspring mice but were inactivated in prenatal LPS-exposed <em>Tlr4</em> knockout offspring mice. In BON-1 cells, TLR4 interacted with the calcium ion channel PIEZO1, causing calcium influx and promoting 5-HT secretion. This process was disrupted by the TLR4 inhibitor TAK242. LPS exposure during pregnancy affected intestinal motility in offspring mice by activating TLR4 pathways in the colon and increasing 5-HT secretion from enterochromaffin cells. The effects of LPS on the intestine might be explained by the interaction between TLR4 and PIEZO1, suggesting that TLR4 is related to abnormal intestinal motility in offspring mice exposed to LPS during pregnancy.</div></div>","PeriodicalId":12689,"journal":{"name":"Genes & Diseases","volume":"12 5","pages":"Article 101707"},"PeriodicalIF":6.9,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144314140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The roles of cell cycle proteins in regulating the tumor immune microenvironment 细胞周期蛋白在调节肿瘤免疫微环境中的作用

IF 9.4 2区医学

Genes & Diseases Pub Date : 2025-06-04 DOI: 10.1016/j.gendis.2025.101706

Qingbo Zhu, Xiaoli Wei, Ziting Qu, Lili Lu, Yiyin Zhang, Hua Wang

引用次数: 0

Response to Shen et al to rapid communication “Fact or fiction: Exploring resident mesenchymal stem cells in abdominal aortic aneurysm from multiple perspectives” Shen等人对快速交流的回应“事实或虚构：从多角度探索腹主动脉瘤中的常驻间充质干细胞”

IF 9.4 2区医学

Genes & Diseases Pub Date : 2025-06-03 DOI: 10.1016/j.gendis.2025.101703

Carmen Ciavarella, Francesco Alviano, Gianandrea Pasquinelli

引用次数: 0