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《医学前沿(英文)》 2015年 第9卷 第3期 页码 322-330 doi: 10.1007/s11684-015-0408-9
This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.
Exploring the cancer genome in the era of next-generation sequencing
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《医学前沿(英文)》 2012年 第6卷 第1期 页码 48-55 doi: 10.1007/s11684-012-0182-x
The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.
关键词: next-generation sequencing cancer genome whole genome sequencing exome transcriptome
《医学前沿(英文)》 页码 889-906 doi: 10.1007/s11684-023-0994-x
关键词: primary central nervous system lymphoma whole-genome sequencing TMSB4X copy number variation gene mutation
Exome sequencing greatly expedites the progressive research of Mendelian diseases
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《医学前沿(英文)》 2014年 第8卷 第1期 页码 42-57 doi: 10.1007/s11684-014-0303-9
The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.
关键词: genetics whole-exome sequencing Mendelian disease disease gene
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《医学前沿(英文)》 2018年 第12卷 第1期 页码 23-33 doi: 10.1007/s11684-017-0607-7
Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics. Bacterial whole-genome sequencing and bioinformatic computing allow genotyping to satisfy the requirements of epidemiological study in disease control. In this review, we outline the significance and summarize the roles of bacterial genome sequencing in the context of bacterial disease control and prevention. We discuss the applications of bacterial genome sequencing in outbreak detection, source tracing, transmission mode discovery, and new epidemic clone identification. Wide applications of genome sequencing and data sharing in infectious disease surveillance networks will considerably promote outbreak detection and early warning to prevent the dissemination of bacterial diseases.
关键词: genome sequencing genomic epidemiology bacteria surveillance infectious diseases
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《医学前沿(英文)》 2016年 第10卷 第1期 页码 61-75 doi: 10.1007/s11684-016-0436-0
The latent expression pattern of Epstein-Barr Virus (EBV) genes in nasopharyngeal carcinoma (NPC) has been extensively investigated, and the expression of several lytic genes in NPC has been reported. However, comprehensive information through EBV transcriptome analysis in NPC is limited. We performed paired-end RNA-seq to systematically and comprehensively characterize the expression of EBV genes in NPC tissue and C666-1 NPC cell line, which consistently carries EBV. In addition to the transcripts restricted to type II latency infection, the type III latency EBNA3s genes and a substantial number of lytic genes, such as BZLF1, BRLF1, and BMRF1, were detected through RNA-seq and were further verified in C666-1 cells and NPC tissue through real-time PCR. We also performed clustering analysis to classify NPC patient groups in terms of EBV gene expression, which presented two subtypes of NPC samples. Results revealed interesting patterns of EBV gene expression in NPC patients. This clustering was correlated with many signaling pathways, such as those related to heterotrimeric G-protein signaling, inflammation mediated by chemokine and cytokine signaling, ribosomes, protein metabolism, influenza infection, and ECM-receptor interaction. Our combined findings suggested that the expression of EBV genes in NPC is restricted not only to type II latency genes but also to type III latency and lytic genes. This study provided further insights into the potential role of EBV in the development of NPC.
关键词: Epstein-Barr virus paired-end transcriptome sequencing latency genes lytic genes nasopharyngeal carcinoma
Plastic materials and water sources actively select and shape wastewater plastispheres over time
《环境科学与工程前沿(英文)》 2022年 第16卷 第11期 doi: 10.1007/s11783-022-1580-1
● Wastewater MPs exhibited resistomes and therefore health threats.
关键词: Microplastics Whole-genome metagenomic sequencing Plastisphere Plastic degradation MHETase
A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome
《医学前沿(英文)》 2023年 第17卷 第2期 页码 330-338 doi: 10.1007/s11684-022-0933-2
关键词: Clouston syndrome whole exome sequencing GJB6 gene novel variant unique phenotype
Transcriptome resources and genome-wide marker development for Japanese larch (
Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG
《农业科学与工程前沿(英文)》 2014年 第1卷 第1期 页码 77-84 doi: 10.15302/J-FASE-2014010
关键词: Larix transcriptome age wood formation somatic embryogenesis molecular marker
《医学前沿(英文)》 doi: 10.1007/s11684-023-1029-3
关键词: tumor prognosis molecular Microbiome subsets determine center analysis microbiome transcriptome data
《农业科学与工程前沿(英文)》 2021年 第8卷 第2期
Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.
《工程管理前沿(英文)》 页码 439-454 doi: 10.1007/s42524-022-0211-7
关键词: megaproject organizational evolution whole lifecycle management project management team
Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI
《农业科学与工程前沿(英文)》 2018年 第5卷 第2期 页码 214-225 doi: 10.15302/J-FASE-2018219
关键词: anthocyanin gene expression mutant purple-fleshed sweet potato transcriptome
Cell surface protein engineering for high-performance whole-cell catalysts
Hajime Nakatani,Katsutoshi Hori
《化学科学与工程前沿(英文)》 2017年 第11卷 第1期 页码 46-57 doi: 10.1007/s11705-017-1609-3
关键词: cell surface engineering surface display whole-cell catalysts bioprocess
单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞 Article
张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟
《工程(英文)》 2022年 第17卷 第10期 页码 161-169 doi: 10.1016/j.eng.2021.05.009
了解重症新型冠状病毒肺炎(COVID-19)患者单核细胞的免疫学特征(包括与纤维化相关的特征)对了解疾病的重症化机制和阻止疾病恶化至关重要。本研究共纳入7名COVID-19患者(包括3名重症/危重症患者和4名普通型患者)和6名健康对照者。采集7名COVID-19患者不同疾病时期外周血样本,包括重症/危重症时期血样3例,轻症时期血样4例,康复期血样7例。将以上血样和6例健康对照者血样进行单细胞转录组测序分析。本研究发现在COVID-19重症/危重症时期,单核细胞发生显著变化。单核细胞在外周血单个核细胞中占比增加,多样性却显著降低。同时本研究发现两个新的COVID-19重症疾病特异性单核细胞亚群:Mono 0和Mono 5。这两个亚群表达amphiregulin(AREG)、epiregulin(EREG)和细胞因子基因IL-18,KEGG分析显示富集的ErbB信号通路,这两个亚群可能具有促纤维化和促炎的特征。进一步分析发现Mono 0和Mono 5发生代谢改变,包括糖酵解/糖异生的增加和HIF-1信号通路的增加。本研究同时发现一个疾病重症前期取得的样本显示出与重症/危重症时期样本相似的单核细胞UMAP图谱。本研究发现了两种新的COVID-19重症疾病特异性单核细胞亚群,可作为重症COVID-19的潜在预测因子和治疗靶点。
标题 作者 时间 类型 操作
TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways
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期刊论文
Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing
期刊论文
Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the
null
期刊论文
Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptomesequencing
null
期刊论文
Plastic materials and water sources actively select and shape wastewater plastispheres over time
期刊论文
A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome
期刊论文
Transcriptome resources and genome-wide marker development for Japanese larch (
Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG
期刊论文
clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome
期刊论文
METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN
期刊论文
Organizational evolution of project management teams over the whole lifecycle of megaprojects: Case study
期刊论文
Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular
Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI
期刊论文
Cell surface protein engineering for high-performance whole-cell catalysts
Hajime Nakatani,Katsutoshi Hori
期刊论文