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    Journal: Genomics, Proteomics & Bioinformatics

    Volume 18, Issue 6

    627 -- 639Jun Yu. From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2
    640 -- 647Qi Liu, Shilei Zhao, Chengmin Shi, Shuhui Song, Sihui Zhu, Yankai Su, Wenming Zhao, Mingkun Li, Yiming Bao, Yongbiao Xue, Hua Chen 0010. Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters
    648 -- 663Xufei Teng, Qianpeng Li, Zhao Li, Yuansheng Zhang, Guangyi Niu, Jing-Fa Xiao, Jun Yu 0004, Zhang Zhang 0002, Shuhui Song. Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades
    664 -- 678Ting Li, Bing Chen, Pengcheng Yang, Depin Wang, Baozhen Du, Le Kang. Long Non-coding RNA Derived from lncRNA-mRNA Co-expression Networks Modulates the Locust Phase Change
    679 -- 695Yongxi Song, Jun Wang, Jingxu Sun, Xiaowan Chen, Jinxin Shi, Zhonghua Wu, Dehao Yu, Fei Zhang, Zhenning Wang. Screening of Potential Biomarkers for Gastric Cancer with Diagnostic Value Using Label-free Global Proteome Analysis
    696 -- 707Wang-Lin Liu, Mingyue Cheng, Jinman Li, Peng Zhang, Hang Fan, Qinghe Hu, Maozhen Han, Longxiang Su, Huaiwu He, Yigang Tong, Kang Ning 0001, Yun Long. Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock
    708 -- 720Ben Wang, Shiwei Zhu, Zuojing Liu, Hui Wei, Lu Zhang, Meibo He, Fei Pei, Jindong Zhang, Qinghua Sun, Liping Duan. Increased Expression of Colonic Mucosal Melatonin in Patients with Irritable Bowel Syndrome Correlated with Gut Dysbiosis
    721 -- 736Xizhan Xu, Zezheng Gao, Fuquan Yang, Yingying Yang, Liang Chen, Lin Han, Na Zhao, Jiayue Xu, Xinmiao Wang, Yue MaKiran Kumar Eepuri, Lian Shu, Xiaoxi Hu, Na Lyu, Yuanlong Pan, Baoli Zhu, Linhua Zhao, Xiaolin Tong, Jun Wang 0074. Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient Berberine
    737 -- 748Yafei Chang, Yisheng Jiang, Cui Li, Qin Wang, Feng Zhang, Cheng-Feng Qin, Qing-feng Wu, Jing Li, Zhiheng Xu. Different Gene Networks Are Disturbed by Zika Virus Infection in A Mouse Microcephaly Model
    749 -- 759Shuhui Song, Lina Ma, Dong Zou, Dongmei Tian, Cuiping Li, Junwei Zhu, Meili Chen, Anke Wang, Yingke Ma, Mengwei Li, Xufei Teng, Ying Cui, Guangya Duan, Mochen Zhang, Tong Jin, Chengmin Shi, Zhenglin Du, Yadong Zhang, Chuandong Liu, Rujiao Li, Jingyao Zeng, Lili Hao, Shuai Jiang, Hua Chen, Dali Han, Jing-Fa Xiao, Zhang Zhang 0002, Wenming Zhao, Yongbiao Xue, Yiming Bao. The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR
    760 -- 772Guocai Yao, Wenliang Zhang, Minglei Yang, Huan Yang, Jianbo Wang, Haiyue Zhang, Lai Wei, Zhi Xie, Weizhong Li 0001. MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes

    Volume 18, Issue 5

    489 -- 500Lindan Ji, Dongdong Wu, Haibing Xie, Binbin Yao, Yanming Chen, David M. Irwin, Dan Huang, Jin Xu, Nelson L. S. Tang, Yaping Zhang. Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity
    501 -- 515Kun Li, Yang Wu, Young Li, Qiaoni Yu, Zhigang Tian, Haiming Wei, Kun Qu. Landscape and Dynamics of the Transcriptional Regulatory Network During Natural Killer Cell Differentiation
    516 -- 524Jing Sun, Yanfang Zhang, Minhui Wang, Qian Guan, Xiujia Yang, Jin Xia Ou, Mingchen Yan, Chengrui Wang, Yan Zhang, Zhi-Hao Li, Chunhong Lan, Chen Mao, Hong-Wei Zhou, Bingtao Hao, Zhenhai Zhang. The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery
    525 -- 538Yidi Sun, Chen Li, Shichao Pang, Qianlan Yao, Luonan Chen, Yixue Li, Rong Zeng. Kinase-substrate Edge Biomarkers Provide A More Accurate Prognostic Prediction in ER-negative Breast Cancer
    539 -- 548Yan Jiang, Yanfei Wang, Xiaoting Hua, Yue Qu, Anton Y. Peleg, Yunsong Yu. Klebsiella pneumoniae
    549 -- 564Arup Panda, Tamir Tuller. Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins
    565 -- 581Song He, Yuqi Wen, Xiaoxi Yang, Zhen Liu, Xinyu Song, Xin Huang, Xiaochen Bo. PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion
    582 -- 592Bin Yu 0007, Cheng Chen, Hongyan Zhou, Bingqiang Liu, Qin Ma 0003. GTB-PPI: Predict Protein-protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting
    593 -- 600Md. Mehedi Hasan 0002, Mst. Shamima Khatun, Hiroyuki Kurata. iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features
    601 -- 612Jee Eun Kang, Antonio Ciampi, Mohamed Hijri. SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms
    613 -- 623Jee Eun Kang, Antonio Ciampi, Mohamed Hijri. SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi
    624 -- 625Jun Li 0051, Elizabeth A. Rettedal, Eric van der Helm, Mostafa Ellabaan, Gianni Panagiotou, Morten O. A. Sommer. Corrigendum to "Antibiotic Treatment Drives the Diversification of the Human Gut Resistome" [Genomics Proteomics Bioinformatics 17 (1) (2019) 39-51]

    Volume 18, Issue 4

    359 -- 370Zixiang Yan, Luzhang Ji, Xiangru Huo, Qianfeng Wang, Yuwen Zhang, Bo Wen. G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments
    371 -- 383Yuhuan Li, Qingyang Zhang, Guanshen Cui, Fang Zhao, Xin Tian, Baofa Sun, Ying Yang, Wei Li. 6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes
    384 -- 396Monika Hiller, Miriam Geissler, George Janssen, Peter van Veelen, Annemieke Aartsma-Rus, Pietro Spitali. The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells
    397 -- 414Zhi-Fang Gao, Zhuo Shen, Qing Chao, Hai-Yan Zheng, Xuan-Liang Ge, Tian-Cong Lu, Haiyan Zheng, Chun-Rong Qian, Bai-Chen Wang. Large-scale Proteomic and Phosphoproteomic Analyses of Maize Seedling Leaves During De-etiolation
    415 -- 429Shan Chi, Guoliang Wang, Tao Liu, Xumin Wang, Cui Liu, Yuemei Jin, Hongxin Yin, Xin Xu, Jun Yu 0004. Saccharina japonica
    430 -- 442Akash Srivastava, Emanuel Barth, Maria A. Ermolaeva, Madlen Guenther, Christiane Frahm, Manja Marz, Otto W. Witte. Tissue-specific Gene Expression Changes Are Associated with Aging in Mice
    443 -- 454Jun Wang, Xiaowen Chen, Funan He, Xiao Song, Shu Huang, Wucheng Yue, Yipei Chen, Zhixi Su, Chenghui Wang. Eriocheir sinensis
    455 -- 467Hongmei Luo, Jun Qian, Zhichao Xu, Wanjing Liu, Lei Xu, Ying Li, Jiang Xu, Jianhong Zhang, Xiaolan Xu, Chang Liu, Liu He, Jianqin Li, Chao Sun, Francis Martin, Jingyuan Song, Shilin Chen. Wolfiporia cocos Genome and Transcriptome Shed Light on the Formation of Its Edible and Medicinal Sclerotium
    468 -- 480Jun Wang, Xueying Xie, Junchao Shi, Wenjun He, Qi Chen 0010, Liang Chen, Wanjun Gu, Tong Zhou. Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma
    481 -- 487Ya-Wen Zhang, Cox Lwaka Tamba, Yang-Jun Wen, Pei Li, Wen-Long Ren, Yuan-Li Ni, Jun Gao, Yuan-Ming Zhang. mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies
    488 -- 0Yue-feng Wang, Qing Chao, Zhe Li 0018, Tian-Cong Lu, Hai-Yan Zheng, Cai-Feng Zhao, Zhuo Shen, Xiao-hui Li, Bai-Chen Wang. Corrigendum to "Large-scale Identification and Time-course Quantification of Ubiquitylation Events During Maize Seedling De-etiolation" [Genomics Proteomics Bioinformatics 17 (6) (2019) 603-622]

    Volume 18, Issue 3

    221 -- 229Jiantao Guan, Diego F. Garcia, Yun Zhou, Rudi Appels, Aili Li, Long Mao. Three Kingdoms
    230 -- 240Zhichao Xu, Ranran Gao, Xiangdong Pu, Rong Xu, Jiyong Wang, Sihao Zheng, Yan Zeng, Jun Chen, Chunnian He, Jingyuan Song. Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis
    241 -- 255Zijian Zhou, Yan Cao, Tao Li, Xinghao Wang, Jiafa Chen, Hang He, Wen Yao, Jianyu Wu, Huiyong Zhang. Fusarium verticillioides Ear Rot
    256 -- 270Jihong Hu, Tao Zeng, Qiongmei Xia, Liyu Huang, Yesheng Zhang, Chuanchao Zhang, Yan Zeng, Hui Liu, Shilai Zhang, Guangfu Huang, Wenting Wan, Yi Ding, Fengyi Hu, Congdang Yang, Luonan Chen, Wen Wang. Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis
    271 -- 288Jinwei Suo, Heng Zhang, Qi Zhao, Nan Zhang, Yongxue Zhang, Ying Li, Baohua Song, Juanjuan Yu, Jianguo Cao, Tai Wang, Ji Luo, Lihai Guo, Jun Ma, Xumin Zhang, Yimin She, Lianwei Peng, Weimin Ma, Siyi Guo, Shaojun Dai. -responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics
    289 -- 304Xiaohuang Lin, Mingkun Yang, Xin Liu, Zhongyi Cheng, Feng Ge. Synechocystis sp. PCC 6803
    305 -- 320Liya Zhu, Han Cheng, Guoqing Peng, Shuansuo Wang, Zhiguo Zhang, Erdong Ni, Xiangdong Fu, Chuxiong Zhuang, Zexian Liu, Hai Zhou. Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles
    321 -- 332Shi-Jian Zhang, Lei Liu, Ruolin Yang, Xiangfeng Wang. Gypsy Retrotransposons in Brassicaceae
    333 -- 340Jinpeng Wang, Jigao Yu, Pengchuan Sun, Chao Li, Xiaoming Song, Tianyu Lei, Yuxian Li, Jiaqing Yuan, Sangrong Sun, Hongling Ding, Xueqian Duan, Shaoqi Shen, Yanshuang Shen, Jing Li, Fanbo Meng, Yangqin Xie, Jianyu Wang, Yue Hou, Xiyin Wang. Paleo-polyploidization in Lycophytes
    341 -- 351Yuan Liang, Dengxue Lu, Sen Wang, YuHui Zhao, Shenghan Gao, Rongbing Han, Jun Yu 0004, Weili Zheng, Jianing Geng, Songnian Hu. Agrocybe cylindracea
    352 -- 358Peijing Zhang, Yongjing Liu, Hongjun Chen, Xianwen Meng, Jitong Xue, Kunsong Chen, Ming Chen 0005. CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants

    Volume 18, Issue 2

    91 -- 103Qingyu Chen 0001, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor. Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
    104 -- 119Tiansheng Zhu, Yi Zhu, Yue Xuan, Huanhuan Gao, Xue Cai, Sander R. Piersma, Thang V. Pham, Tim Schelfhorst, Richard R. G. D. Haas, Irene V. Bijnsdorp, Rui Sun, Liang Yue, Guan Ruan, Qiushi Zhang, Mo Hu, Yue Zhou, Winan J. Van Houdt, Tessa Y. S. Le Large, Tiannan Guo. DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
    120 -- 128Qiong Zhang, Wei Liu 0032, Hong-mei Zhang, Gui-Yan Xie, Ya-Ru Miao, Meng Xuan Xia, An-Yuan Guo. hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets
    129 -- 139Jian Zhao, Yan Li, Cong Wang, Haotian Zhang, Hao Zhang, Bin Jiang 0001, Xuejiang Guo, Xiaofeng Song. IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites
    140 -- 149Xiaoxu Yang, Changhong Yang, Xianing Zheng, Luoxing Xiong, Yutian Tao, Meng Wang, Adam Yongxin Ye, Qixi Wu, Yanmei Dou, Junyu Luo, Liping Wei, August Yue Huang. MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals
    150 -- 160Xiang Chen, Yi Guo, Xin Chen. iGMDR: Integrated Pharmacogenetic Resource Guide to Cancer Therapy and Research
    161 -- 172Jian Sang, Dong Zou, Zhennan Wang, Fan Wang, Yuansheng Zhang, Lin Xia, Zhaohua Li, Lina Ma, Mengwei Li, Bingxiang Xu, Xiaonan Liu, Shuangyang Wu, Lin Liu, Guangyi Niu, Man Li, Yingfeng Luo, Songnian Hu, Lili Hao, Zhang Zhang 0002. IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data
    173 -- 185Jun Yan, Dong Zou, Chen Li, Zhang Zhang 0002, Shuhui Song, Xiangfeng Wang. SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice
    186 -- 193Ningbo Chen, Weiwei Fu, Jianbang Zhao, Jiafei Shen, Qiuming Chen, Zhuqing Zheng, Hong Chen, Tad S. Sonstegard, Chuzhao Lei, Yu Jiang. BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures
    194 -- 207Wanshan Ning, Hao-Dong Xu, Peiran Jiang, Han Cheng, Wankun Deng, Yaping Guo, Yu Xue 0001. HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction
    208 -- 219Hui-Ju Kao, Van-Nui Nguyen, Kai-Yao Huang, Wen-Chi Chang, Tzong-Yi Lee. k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites

    Volume 18, Issue 1

    1 -- 4Zhang Zhang 0002, Shuhui Song, Jun Yu 0004, Wenming Zhao, Jingfa Xiao, Yiming Bao. The Elements of Data Sharing
    5 -- 15Wilson Wen Bin Goh, Limsoon Wong. The Birth of Bio-data Science: Trends, Expectations, and Applications
    16 -- 25Shahzina Kanwal, Xiangpeng Guo, Carl Ward, Giacomo Volpe, Baoming Qin, Miguel A. Esteban, Xichen Bao. Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency
    26 -- 40Ziyi Li, Binbin Wang, Shengqing Gu, Peng Jiang, Avinash Das Sahu, Chen-Hao Chen, Tong Han, Sailing Shi, Xiaoqing Wang, Nicole Traugh, Hailing Liu, Yin Liu, Qiu Wu, Myles Brown, Tengfei Xiao, Genevieve M. Boland, Xiaole Shirley Liu. CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma
    41 -- 51Xiao Han, Hanchen Liu, Zezhong Zhang, Wenlan Yang, Chunyan Wu, Xueying Liu, Fang Zhang, Baofa Sun, Yongliang Zhao, Guibin Jiang, Yun-Gui Yang, Wenjun Ding. 2.5-induced Mouse Pulmonary Fibrosis
    52 -- 64Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li 0052, Jiangning Song. Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information
    65 -- 71Peng Jia, Xiaofei Yang, Li Guo 0012, Bowen Liu, Jiadong Lin, Hao Liang, Jianyong Sun, Chengsheng Zhang, Kai Ye. MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
    72 -- 80Chenwei Wang, Hao-Dong Xu, Shaofeng Lin, Wankun Deng, Jiaqi Zhou 0003, Ying Zhang, Ying Shi, Di Peng, Yu Xue 0001. GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins
    81 -- 90Yongzhe Ren, Yang Zhang, Dandan Wang, Fengying Liu, Ying Fu, Shaohua Xiang, Li Su, Jiancheng Li, Heng Dai, Bingding Huang. SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples
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