Jiachun Lü

Guangzhou Medical University

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Co-Authors

Yifeng Zhou

First Affiliated Hospital of Xinxiang Medical University

143

Siqi Wu

First Affiliated Hospital of Xiamen University

Yirong Wang

Soochow University

Jian Zheng

Lanzhou University of Technology

Shenghua Zhang

Peking University

Yibin Deng

Guangxi Center for Disease Prevention and Control

Jieqiong Deng

Soochow University

Binbin Guo

Soochow University

Fanrong Li

Soochow University

Zheng Zhang

Soochow University

Cooperative Institutions

Guangzhou Medical University

199

Sun Yat-sen University

102

Nanjing Medical University

100

Chinese Academy of Medical Sciences & Peking Union Medical College

Huazhong University of Science and Technology

First Affiliated Hospital of Guangzhou Medical University

Shanghai Jiao Tong University

Peking University

Soochow University

Sichuan University

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Additional file 9 of An EMT-related genes signature as a prognostic biomarker for patients with endometrial cancer

Figshare (2023)

Yonghui Yu Yiwen Zhang Zhi Li Yongshun Dong Hongmei Huang

Additional file 9.

Signature (topology)

Gene signature

10.6084/m9.figshare.24159553

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The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing

Briefings in Functional Genomics (2018)

YongKiat Wee Salma Begum Bhyan Yining Liu Jiachun Lü Xiaoyan Li

The application of third-generation sequencing (TGS) technology in genetics and genomics have provided opportunities to categorize and explore the individual genomic landscapes and mutations relevant for diagnosis and therapy using whole genome sequencing and de novo genome assembly. In general, the emerging TGS technology can produce high quality long reads for the determination of overlapping reads and transcript isoforms. However, this technology still faces challenges such as the accuracy for the identification of nucleotide bases and high error rates. Here, we surveyed 39 TGS-related tools for de novo assembly and genome analysis to identify the differences among their characteristics, such as the required input, the interaction with the user, sequencing platforms, type of reads, error models, the possibility of introducing coverage bias, the simulation of genomic variants and outputs provided. The decision trees are summarized to help researchers to find out the most suitable tools to analyze the TGS data. Our comprehensive survey and evaluation of computational features of existing methods for TGS may provide a valuable guideline for researchers.

Sequence assembly

Identification

10.1093/bfgp/ely037

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Citations (40)

Figure S1 from Sequence Variation in Mature MicroRNA-499 Confers Unfavorable Prognosis of Lung Cancer Patients Treated with Platinum-Based Chemotherapy

Fuman Qiu Lei Yang Xiaoxuan Ling Rongrong Yang Xiaorong Yang

Figure S1. Genotyping of SNPs in the microRNAs by the TaqMan assay.

Sequence (biology)

Variation (astronomy)

10.1158/1078-0432.22461858.v1

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Table S3 from Sequence Variation in Mature MicroRNA-499 Confers Unfavorable Prognosis of Lung Cancer Patients Treated with Platinum-Based Chemotherapy

Fuman Qiu Lei Yang Xiaoxuan Ling Rongrong Yang Xiaorong Yang

Table S3. Sequence of primers used in real time RT-PCR analysis.

Sequence (biology)

Table (database)

10.1158/1078-0432.22461837

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Supplementary Figure 2 from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation

Shenghua Zhang Zheng Zhang Xiaolong Liu Yibin Deng Jian Zheng

Related to Figure 2

10.1158/1541-7786.23710290.v1

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Supplementary Table 1 from LncRNA-Encoded Micropeptide ACLY-BP Drives Lipid Deposition and Cell Proliferation in Clear Cell Renal Cell Carcinoma via Maintenance of ACLY Acetylation

Shenghua Zhang Zheng Zhang Xiaolong Liu Yibin Deng Jian Zheng

Primary clinical and histological characteristics of 67 study patients

10.1158/1541-7786.23710278.v1

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Long noncoding RNA PANDAR inhibits the development of lung cancer by regulating autophagy and apoptosis pathways

Journal of Cancer (2020)

Lan Zhang Yuanhang Wang Shengyuan Xia Lei Yang Di Wu

Background: LncRNAs has been shown to play important roles in the progression of lung cancer, but it remains poorly understood whether lncRNAs affect the occurrence and development of lung cancer by regulating autophagy and apoptosis levels. Here, we investigated the roles of PANDAR in NSCLC. Materials and Methods: The expression profile and clinical application of PANDAR and its possible target gene BECN1 were tested in 276 cases of lung cancer tissues. Through some actual experiments, we explored functions of PANDAR about proliferation, apoptosis and autophagy of NSCLC cells in vitro. Results: PANDAR was found to downregulate both in lung cancer tissues and cell lines compared with corresponding controls (P < 0.05 for all), which was related to tumor stage (P < 0.05). Moreover, autophagy related gene BECN1 was also downregulated in lung cancer tissues comparison with normal tissues (P < 0.01), and there was a significant positive correlation between PANDAR and BECN1 levels (r = 0.789, P < 0.001). So, the high expression of PANDAR increased BECN1 expression levels and impaired the proliferation of NSCLC cell lines in vitro. Furthermore study showed PANDAR could regulate cell autophagy and apoptosis levels. Conclusion: These results indicated lncRNA PANDAR was a tumor suppressor and can inhibit NSCLC cell proliferation by activating autophagy and apoptosis pathways via upregulation of BECN1 expression.

BECN1

10.7150/jca.45291

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Citations (16)

Additional file 1 of The evidence of indirect transmission of SARS-CoV-2 reported in Guangzhou, China

Figshare (2020)

Chaojun Xie Hongjun Zhao Kuibiao Li Zhoubin Zhang Xiaoxiao Lu

Additional file 1: Table S1. The outcome of whole blood samples tested. Table S2. The outcome of throat swabs tested.

2019-20 coronavirus outbreak

10.6084/m9.figshare.12768653

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Supplementary Figure Legend from A Sequence Polymorphism in miR-608 Predicts Recurrence after Radiotherapy for Nasopharyngeal Carcinoma

Jian Zheng Jieqiong Deng Mang Xiao Lei Yang Liyuan Zhang

PDF file - 64K

Legend

Sequence (biology)

10.1158/0008-5472.22402473.v1

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CircLRP6 Regulation of ZEB1 via miR-455 Is Involved in the Epithelial-Mesenchymal Transition During Arsenite-Induced Malignant Transformation of Human Keratinocytes

Toxicological Sciences (2017)

Junchao Xue Chao Chen Fei Luo Xueli Pan Hui Xu

Circular RNAs (circRNAs), a class of noncoding RNAs generated from pre-mRNAs, participate in the regulation of tumorigenesis. The mechanism for regulation, however, is unclear. Here, to determine whether circRNAs are involved in arsenite-induced epithelial-mesenchymal transition (EMT) and malignant transformation in human keratinocyte (HaCaT) cells, the up-regulation of circLRP6 was confirmed in arsenite-transformed HaCaT (T-HaCaT) cells. In HaCaT cells, circLRP6 acted as an microRNA (miR)-455 sponge. For these cells, chronic exposure to arsenite caused an increase of circLRP6 and the transcription factor ZEB1, which induced the EMT. miR-455 suppressed the expression of ZEB1. Further, in T-HaCaT cells, knockdown of circLRP6 with siRNA inhibited ZEB1 expression, but cotransfection with circLRP6 siRNA and an miR-455 inhibitor reversed this inhibition. These results suggest that, in HaCaT cells, arsenite increases circLRP6 levels, which act as a sponge for miR-455 and up-regulate the miR-455 target, ZEB1, which subsequently induces the EMT, thus promoting malignant transformation. Thus, for HaCaT cells chronically exposed to arsenite, circLRP6 via miR-455 regulation of ZEB1 is involved in the EMT during malignant transformation. The results establish a previously unknown mechanism for arsenite-induced carcinogenesis.

HaCaT

Malignant Transformation

10.1093/toxsci/kfx269

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Citations (39)