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Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer
《Genomics, Proteomics & Bioinformatics》2024年第4期99-117,共19页Rou Zhang Meng Hu Yu Liu Wanmeng Li Zhiqiang Xu Siyu He Ying Lu Yanqiu Gong Xiuxuan Wang Shan Hai Shuangqing Li Shiqian Qi Yuan Li Yang Shu Dan Du Huiyuan Zhang Heng Xu Zongguang Zhou Peng Lei Hai-Ning Chen Lunzhi Dai 
supported by the National Key R&D Program of China(Grant No.2022YFA1303200);the National Natural Science Foundation of China(Grant Nos.82073221,31870826,and 82073246);the Sichuan Provincial Science and Technology Project(Grant No.2021YFS0134);the National Clinical Research Center for Geriatrics of West China Hospital(Grant No.Z2021JC005);the 135 Project for Disciplines of Excellence of West China Hospital(Grant Nos.ZYYC23013,ZYYC23025,ZYGD20006,and 2016105).
Magnesium(Mg)deficiency is associated with increased risk and malignancy in colorectal cancer(CRC),yet the underlying mechanisms remain elusive.Here,we used genomic,proteomic,and phosphoproteomic data to elucidate the...
关键词：Magnesium deficiency Colorectal cancer Genome instability Tumor metastasis Phosphorylation. 
The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers
《Genomics, Proteomics & Bioinformatics》2023年第3期619-631,共13页Sijia Wu Zhiwei Fan Pora Kim Liyu Huang Xiaobo Zhou 
supported by the National Natural Science Foundation of China(Grant No.62002270);the Fundamental Research Funds for the Central Universities,the Natural Science Foundation of Shaanxi Province of China(Grant No.2020JQ-332);the China Postdoctoral Science Foundation(Grant No.2018M643583);the National Natural Science Foundation of China(Grant No.82227802);the National Key R&D Program of China(Grant No.2017YFA0205202);partially funded by the National Natural Science Foundation of China(Grant No.61672422).
Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse cancers.However,the comprehensive map for functional A...
关键词：A-to-I RNA editing Cancer Protein recoding Alternative splicing MicroRNA regulation 
iHypoxia:An Integrative Database of Protein Expression Dynamics in Response to Hypoxia in Animals被引量：2
《Genomics, Proteomics & Bioinformatics》2023年第2期267-277,共11页Ze-Xian Liu Panqin Wang Qingfeng Zhang Shihua Li Yuxin Zhang Yutong Guo Chongchong Jia Tian Shao Lin Li Han Cheng Zhenlong Wang 
supported by grants from the National Key R&D Program of China(Grant No.2021YFA1302100 to Ze-Xian Liu);the National Natural Science Foundation of China(Grant No.U2004152 to Zhenlong Wang,Grant Nos.81972239 and 91953123 to Ze-Xian Liu);the Fostering Fund of Fundamental Research for Young Teachers of Zhengzhou University,China(Grant No.JC21343016 to Han Cheng);the Program for Guangdong Introducing Innovative and Entrepreneurial Teams,China(Grant No.2017ZT07S096 to Ze-Xian Liu);the Tip-Top Scientific and Technical Innovative Youth Talents of Guangdong Special Support Program,China(Grant No.2019TQ05Y351 to Ze-Xian Liu).
Mammals have evolved mechanisms to sense hypoxia and induce hypoxic responses.Recently,high-throughput techniques have greatly promoted global studies of protein expression changes during hypoxia and the identificatio...
关键词：HYPOXIA Expression dynamics Low-throughput experiment High-throughput experiment Functional annotation 
Integrative Proteomic Analysis of Multiple Posttranslational Modifications in Inflammatory Response被引量：1
《Genomics, Proteomics & Bioinformatics》2022年第1期163-176,共14页Feiyang Ji Menghao Zhou Huihui Zhu Zhengyi Jiang Qirui Li Xiaoxi Ouyang Yiming Lv Sainan Zhang Tian Wu Lanjuan Li 
supported by the National Key R&D Program of China(Grant Nos.2016YFC1101304/3 and 2017YFC1200100);the National Natural Science Foundation of China(Grant No.81400589);the National S&T Major Project,China(Grant No.2017ZX10202202-001-008);the Science Fund for Creative Research Groups of the National Natural Science Foundation,China(Grant No.81721091)。
Posttranslational modifications(PTMs)of proteins,particularly acetylation,phosphorylation,and ubiquitination,play critical roles in the host innate immune response.PTMs’dynamic changes and the crosstalk among them ar...
关键词：PROTEOME CROSSTALK Inflammation LIPOPOLYSACCHARIDE MACROPHAGE 
Integrative Multi-omics Landscape of Non-structural Protein 3 of Severe Acute Respiratory Syndrome Coronaviruses
《Genomics, Proteomics & Bioinformatics》2021年第5期707-726,共20页Ruona Shi Zhenhuan Feng Xiaofei Zhang 
supported by the Guangdong Science and Technology Project,China(Grant Nos.2018B030306047 and 2020B1212060052);the National Natural Science Foundation of China(Grant Nos.31770889 and 31801180);the Guangzhou Science and Technology Project,China(Grant No.201904010469);the Guangzhou Regenerative Medicine and Health Guangdong Laboratory project,China(Grant No.2018GZR110104003)。
The coronavirus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection is currently a global pandemic.Extensive investigations have been performed to study the clinical an...
关键词：NSP3 SARS-CoV-2 SARS-COV Multi-omics MITOCHONDRIA 
Integrative Analysis of Genome,3D Genome,and Transcriptome Alterations of Clinical Lung Cancer Samples被引量：1
《Genomics, Proteomics & Bioinformatics》2021年第5期741-753,共13页Tingting Li Ruifeng Li Xuan Dong Lin Shi Miao Lin Ting Peng Pengze Wu Yuting Liu Xiaoting Li Xuheng He Xu Han Bin Kang Yinan Wang Zhiheng Liu Qing Chen Yue Shen Mingxiang Feng Xiangdong Wang Duojiao Wu Jian Wang Cheng Li 
supported by the National Natural Science Foundation of China(Grant No.31871266);the National Key R&D Program of China(Grant No.2016YFA0100103);the National Natural Science Foundation of China Key Research Grant(Grant No.71532001);supported by funding from Shenzhen Municipal Government of China(Grant No.DRC-SZ[2016]884)。
Genomic studies of cancer cell alterations,such as mutations,copy number variations(CNVs),and translocations,greatly promote our understanding of the genesis and development of cancers.However,the 3D genome architectu...
关键词：Lung cancer 3D genome Copy number variation Clinical sample Integrative genomic analysis 
From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-seq Data
《Genomics, Proteomics & Bioinformatics》2021年第4期519-521,共3页Ya Cui Jason Sheng Li Wei Li 
supported by the National Institutes of Health,United States,to Wei Li(Grant Nos.R01HG007538,R01CA193466,and R01CA228140)。
Underlying the regulation of mammalian gene expression at the level of transcription is the structure and modifications of chromatin. Understanding the twisting structures of DNA wrapped around histones and their high...
关键词：CLOSER LYING modification 
RePhine: An Integrative Method for Identification of Drug Response-related Transcriptional Regulators
《Genomics, Proteomics & Bioinformatics》2021年第4期534-548,共15页Xujun Wang Zhengtao Zhang Wenyi Qin Shiyi Liu Cong Liu Georgi ZGenchev Lijian Hui Hongyu Zhao Hui Lu 
supported by the National Key R&D Program of China(2018YFC0910500);the Neil Shen’s SJTU Medical Research Fund;the SJTU-Yale Collaborative Research Seed Fund;the National Natural Science Foundation of China(Grant Nos.31370751 and 31728012);the Shanghai Municipal Commission of Health and Family Planning(Grant No.20144Y0179);the Science and Technology Commission of Shanghai Municipality(STCSM)(Grant No.17DZ 22512000);the Shanghai Municipal Science and Technology Major Project(Grant No.2018SHZDZX01);the Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence(LCNBI);ZJLab。
Transcriptional regulators(TRs)participate in essential processes in cancer pathogenesis and are critical therapeutic targets.Identification of drug response-related TRs from cell line-based compound screening data is...
关键词：PHARMACOGENOMICS CHIP-SEQ Transcriptional regulator BRAF inhibitor resistance Drug resistance 
PIMD:An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion被引量：1
《Genomics, Proteomics & Bioinformatics》2020年第5期565-581,共17页Song He Yuqi Wen Xiaoxi Yang Zhen Liu Xinyu Song Xin Huang Xiaochen Bo 
supported by the National Natural Science Foundation of China(Grant No.U1435222);the Program of International Sci-Tech Cooperation,China(Grant No.2014DFB30020)。
The accumulation of various types of drug informatics data and computational approaches for drug repositioning can accelerate pharmaceutical research and development.However,the integration of multi-dimensional drug d...
关键词：Drug repositioning Drug similarity network Multiple characterization fusion Network pharmacology Drug discovery 
SR4R:An Integrative SNP Resource for Genomic Breeding and Population Research in Rice被引量：6
《Genomics, Proteomics & Bioinformatics》2020年第2期173-185,共13页Jun Yan Dong Zou Chen Li Zhang Zhang Shuhui Song Xiangfeng Wang 
supported by the National Natural Science Foundation of China(Grant No.31871706);the Department of Agriculture of Guangdong Province(2018-36);Science and Technology Program of Guangdong Province(Grant No.2019B030316006);The Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDA24040201);the Youth Innovation Promotion Association of the Chinese Academy of Sciences(Grant No.2017141)
The information commons for rice(IC4 R)database is a collection of 18 million single nucleotide polymorphisms(SNPs)identified by resequencing of 5152 rice accessions.Although IC4 R offers ultra-high density rice varia...
关键词：RICE SNP Database HAPMAP Panel 
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