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    Journal: Genomics, Proteomics & Bioinformatics

    Volume 17, Issue 6

    551 -- 557Natalie Mezey, William C. S. Cho, Kyle K. Biggar. Intriguing Origins of Protein Lysine Methylation: Influencing Cell Function Through Dynamic Methylation
    558 -- 575Lin Zhang, Meilan Liu, Hongxu Long, Wei Dong, Asher Pasha, Eddi Esteban, Wenying Li, Xiaoming Yang, Ze Li, Aixia Song, Duo Ran, Guang Zhao, Yanling Zeng, Hao Chen, Ming Zou, Jingjing Li, Fan Liang, Meili Xie, Xiaofeng Tan. Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production
    576 -- 589Sixue Liu, Zuyu Yang, Guanghao Li, Chunyan Li, Yanting Luo, Qiang Gong, Xin Wu, Tao Li, Zhiqian Zhang, Baocai Xing, Xiaolan Xu, Xuemei Lu. Multi-omics Analysis of Primary Cell Culture Models Reveals Genetic and Epigenetic Basis of Intratumoral Phenotypic Diversity
    590 -- 602Xing Shi, Zhancheng Gao, Qiang Lin, Liping Zhao, Qin Ma, Yu Kang, Jun Yu. Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients
    603 -- 622Yue-feng Wang, Qing Chao, Zhe Li, Tian-Cong Lu, Hai-Yan Zheng, Cai-Feng Zhao, Zhuo Shen, Xiao-hui Li, Bai-Chen Wang. Large-scale Identification and Time-course Quantification of Ubiquitylation Events During Maize Seedling De-etiolation
    623 -- 634Danielle M. Santarelli, Adam P. Carroll, Heath M. Cairns, Paul A. Tooney, Murray J. Cairns. Schizophrenia-associated MicroRNA-Gene Interactions in the Dorsolateral Prefrontal Cortex
    635 -- 644Hua Chen. A Computational Approach for Modeling the Allele Frequency Spectrum of Populations with Arbitrarily Varying Size
    645 -- 656Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou. SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning

    Volume 17, Issue 5

    473 -- 474Zhang Zhang 0002, Jun Yu 0004, Frank Eisenhaber, Xin Gao 0001, Takashi Gojobori. In Memory of Vladimir B. Bajic (1952-2019)
    475 -- 477Ming Li 0001. -RNA Interaction
    478 -- 495Fangping Wan, Yue Zhu, Hailin Hu, Antao Dai, Xiaoqing Cai, Ligong Chen, Haipeng Gong, Tian Xia, Dehua Yang, Ming-wei Wang, Jianyang Zeng. in silico Drug Screening
    496 -- 502Ruilin Li, Xiaoyu He, Chuangchuang Dai, Haidong Zhu, Xianyu Lang, Wei Chen 0033, Xiaodong Li, Dan Zhao, Yu Zhang, Xinyin Han, Tie Niu, Yi Zhao, Rongqiang Cao, Rong He, Zhonghua Lu, Xuebin Chi, Weizhong Li, Beifang Niu. Gclust: A Parallel Clustering Tool for Microbial Genomic Data
    503 -- 510Yun Tan, Lulu Jiang, Kankan Wang, Hai Fang. I3: A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data
    511 -- 521Xu-Kai Ma, Meng-Ran Wang, Chu-Xiao Liu, Rui Dong, Gordon G. Carmichael, Ling-Ling Chen, Li Yang. CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression
    522 -- 534Jing Wu, Yan Li, Cheng Wang, Yiqiang Cui, Tianyi Xu, Chang Wang, Xiao Wang 0016, Jiahao Sha, Bin Jiang 0001, Kai Wang, Zhibin Hu, Xuejiang Guo, Xiaofeng Song. CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs
    535 -- 539Yiming Yu, Wen Yao, Yuping Wang, Fangfang Huang. shinyChromosome: An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes
    540 -- 545Eddie Ip, Gavin Chapman, David Winlaw, Sally L. Dunwoodie, Eleni Giannoulatou. VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants
    546 -- 549Katharina Jasmin Hoff. MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs

    Volume 17, Issue 4

    333 -- 336Hongzhu Qu, Hongxing Lei, Xiangdong Fang. Big Data and the Brain: Peeking at the Future
    337 -- 343Anan Li, Yue Guan, Hui Gong, Qingming Luo. Challenges of Processing and Analyzing Big Data in Mesoscopic Whole-brain Imaging
    344 -- 366Quanhua Mu, Yiyun Chen, Jiguang Wang. Deciphering Brain Complexity Using Single-cell Sequencing
    367 -- 380Jie Li, Guang-Zhong Wang. Application of Computational Biology to Decode Brain Transcriptomes
    381 -- 392Shanyu Chen, Zhipeng He, Xinyin Han, Xiaoyu He, Ruilin Li, Haidong Zhu, Dan Zhao, Chuangchuang Dai, Yu Zhang, Zhonghua Lu, Xuebin Chi, Beifang Niu. How Big Data and High-performance Computing Drive Brain Science
    393 -- 401Xiang Li 0001, Ning Guo, Quanzheng Li. Functional Neuroimaging in the New Era of Big Data
    402 -- 414Le Wang, Yan Xia, Yu Chen, Rujia Dai, Wenying Qiu, Qingtuan Meng, Liz Kuney, Chao Chen. Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation
    415 -- 429Bairong Shen, Yuxin Lin, Cheng Bi, Shengrong Zhou, Zhongchen Bai, Guangmin Zheng, Jing Zhou. Translational Informatics for Parkinson's Disease: from Big Biomedical Data to Small Actionable Alterations
    430 -- 440Nicole Ludwig 0001, Tobias Fehlmann, Fabian Kern, Manfred Gogol, Walter Maetzler, Stephanie Deutscher, Simone Gurlit, Claudia Schulte, Anna-Katharina von Thaler, Christian Deuschle, Florian G. Metzger, Daniela Berg, Ulrike Suenkel, Verena Keller, Christina Backes, Hans-Peter Lenhof, Eckart Meese, Andreas Keller. Machine Learning to Detect Alzheimer's Disease from Circulating Non-coding RNAs
    441 -- 452Zhenyu Liu, Jiangang Liu, Huijuan Yuan, Taiyuan Liu, Xingwei Cui, Zhenchao Tang, Yang Du, Meiyun Wang, Yusong Lin, Jie Tian 0001. Identification of Cognitive Dysfunction in Patients with T2DM Using Whole Brain Functional Connectivity
    453 -- 464Guan Ning Lin, Sijia Guo, Xian Tan, Weidi Wang, Wei Qian, Weichen Song, Jingru Wang, Shunying Yu, Zhen Wang 0015, Donghong Cui, Han Wang. De Novo Variant Knowledge Base for Developmental Disorders
    465 -- 471Yadong Yang, Yang Sui, Bingbing Xie, Hongzhu Qu, Xiangdong Fang. GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis

    Volume 17, Issue 3

    223 -- 225Shanshan Xie, Yuxia Jiao. That's A Scientist Should Do - A Dialog with Tomas Lindahl
    226 -- 228Li Guo, Kai Ye. Mapping Genome Variants Sheds Light on Genetic and Phenotypic Differentiation in Chinese
    229 -- 247Zhenglin Du, Liang Ma, Hongzhu Qu, Wei Chen, Bing Zhang 0007, Xi Lu, Weibo Zhai, Xin Sheng, Yongqiao Sun, Wenjie Li, Meng Lei, Qiuhui Qi, Na Yuan, Shuo Shi, Jingyao Zeng, Jinyue Wang, Yadong Yang, Qi Liu, Changqing Zeng. De Novo Assembly of A Northern Han Genome
    248 -- 259Hui Luo, Ling Wang, Ding Bao, Li Wang, Hongjun Zhao, Yun Lian, Mei Yan, Chandra Mohan, Quan-Zhen Li. Novel Autoantibodies Related to Cell Death and DNA Repair Pathways in Systemic Lupus Erythematosus
    260 -- 272Xiaofei Wang, Hehong Wei, Xuemei Mao, Jin Liu. Chromochloris zofingiensis Reveals Novel Proteins for Lipid Metabolism
    273 -- 286Huiyan Sun, Liang Chen, Sha Cao, Yanchun Liang 0001, Ying Xu. Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name
    287 -- 296Xiang Wang, Botao Zhang, Yikun Yang, Jiawei Zhu, Shujun Cheng, Yousheng Mao, Lin Feng, Ting Xiao. Characterization of Distinct T Cell Receptor Repertoires in Tumor and Distant Non-tumor Tissues from Lung Cancer Patients
    297 -- 304Xiaolong Chen, Youqiong Ye, Liang Gu, Jin Sun, Yanhua Du, Wen-Ju Liu, Wei Li, Xiaobai Zhang, Cizhong Jiang. Drosophila Neuroglial Development
    305 -- 310Madison Caballero, Jill L. Wegrzyn. gFACs: Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks
    311 -- 318Chen-Yu Zhu, Chi Zhou, Yun-Qin Chen, Ai-Zong Shen, Zong-Ming Guo, Zhao-Yi Yang, Xiangyun Ye, Shen Qu, Jia Wei, Qi Liu. 3: Consensus Cancer Driver Gene Caller
    319 -- 331Weili Kong, Tsuyoshi Hayashi, Guillaume Fiches, Qikai Xu, Mamie Z. Li, Jianwen Que, Shuai Liu, Wei Zhang, Jun Qi, Netty Santoso, Stephen J. Elledge, Jian Zhu. Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions

    Volume 17, Issue 2

    119 -- 128Xiaotian Wu, Shiqi Mao, Yachen Ying, Christopher J. Krueger, Antony K. Chen. Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR-based Platforms
    129 -- 139Iva Xhangolli, Burak Dura, GeeHee Lee, Dongjoo Kim, Yang Xiao, Rong Fan. H2 Response Independent of Differentiation
    140 -- 153Jialei Sun, Na He, Longjian Niu, Yingzhang Huang, Wei Shen, Yuedong Zhang, Li Li, Chunhui Hou. Global Quantitative Mapping of Enhancers in Rice by STARR-seq
    154 -- 168Junchen Chen, Yi-Chang Zhang, Chunmin Huang, Hui Shen, Baofa Sun, Xuejun Cheng, Yu-Jie Zhang, Yun-Gui Yang, Qiang Shu, Ying Yang, Xuekun Li. 6A Regulates Neurogenesis and Neuronal Development by Modulating Histone Methyltransferase Ezh2
    169 -- 182Valentina Galata, Cedric Christian Laczny, Christina Backes, Georg Hemmrich-Stanisak, Susanne Schmolke, Andre Franke, Eckart Meese, Mathias Herrmann, Lutz von Müller, Achim Plum, Rolf Müller 0002, Cord Stähler, Andreas E. Posch, Andreas Keller. Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11, 087 Clinical Isolates
    183 -- 189Ran Tao, Zhicheng Fu, Lijun Xiao. Chronic Food Antigen-specific IgG-mediated Hypersensitivity Reaction as A Risk Factor for Adolescent Depressive Disorder
    190 -- 200Qiong Zhang, Hui Hu, Si-Yi Chen, Chun-Jie Liu, Fei-Fei Hu, Jianming Yu, Yaohui Wu, An-Yuan Guo. Transcriptome and Regulatory Network Analyses of CD19-CAR-T Immunotherapy for B-ALL
    201 -- 210Xianwen Ren, Liangtao Zheng, Zemin Zhang. SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data
    211 -- 218Qian Liu, Qiang Hu, Song Yao, Marilyn L. Kwan, Janise M. Roh, Hua Zhao, Christine B. Ambrosone, Lawrence H. Kushi, Song Liu, Qianqian Zhu. Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data
    219 -- 221Xudong Zou, Xin Gao, Wei Chen. Deep Learning Deepens the Analysis of Alternative Splicing

    Volume 17, Issue 1

    1 -- 3Kang Ning, Yigang Tong. The Fast Track for Microbiome Research
    4 -- 12Mingyue Cheng, Kang Ning. Stereotypes About Enterotype: the Old and New Ideas
    13 -- 25Lu Zhuang, Haihua Chen, Sheng Zhang, Jiahui Zhuang, Qiuping Li, Zhichun Feng. Intestinal Microbiota in Early Life and Its Implications on Childhood Health
    26 -- 38Ning Li, Junjie Yang, Jiaming Zhang, Cheng Liang, Ying Wang, Bin Chen, Changying Zhao, Jingwen Wang, Guangye Zhang, Dongmei Zhao, Yi Liu, Lehai Zhang, Jun Yang, Guimei Li, Zhongtao Gai, Lei Zhang, Guoping Zhao. Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment
    39 -- 51Jun Li 0051, Elizabeth A. Rettedal, Eric van der Helm, Mostafa Ellabaan, Gianni Panagiotou, Morten O. A. Sommer. Antibiotic Treatment Drives the Diversification of the Human Gut Resistome
    52 -- 63Yi-Chao Shi, Shun-Tian Cai, Yaping Tian, Hui-Jun Zhao, Yan Bing Zhang, Jing Chen, Rong-Rong Ren, Xi Luo, Li-Hua Peng, Gang Sun, Yun-Sheng Yang. Effects of Proton Pump Inhibitors on the Gastrointestinal Microbiota in Gastroesophageal Reflux Disease
    64 -- 75Xiaofeng Song, Liang Zhong, Na Lyu, Fei Liu, Boxing Li, Yanan Hao, Yong Xue, Jing Li, Yuqing Feng, Yue Ma, Yongfei Hu, Baoli Zhu. ob/ob Mice by Partially Restoring Leptin-related Pathways Mediated by Gut Microbiota
    76 -- 90Maozhen Han, Melissa Dsouza, Chunyu Zhou, Hongjun Li, Junqian Zhang, Chaoyun Chen, Qi Yao, Chaofang Zhong, Hao Zhou, Jack A. Gilbert, Zhi Wang, Kang Ning. Agricultural Risk Factors Influence Microbial Ecology in Honghu Lake
    91 -- 105Xiaoqing Jiang, Xin Li, Longshu Yang, Chunhong Liu, Qi Wang, Weilai Chi, Huaiqiu Zhu. How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes
    106 -- 117Jiarui Li, Pengcheng Du, Adam Yongxin Ye, Yuanyuan Zhang, Chuan Song, Hui Zeng, Chen Chen. GPA: A Microbial Genetic Polymorphisms Assignments Tool in Metagenomic Analysis by Bayesian Estimation
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