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ORCIDGenomics, Proteomics & Bioinformatics, Volume 18
Volume 18, Number 1, February 2020
- Zhang Zhang
, Shuhui Song, Jun Yu, Wenming Zhao, Jing-Fa Xiao, Yiming Bao:
The Elements of Data Sharing. 1-4 - Wilson Wen Bin Goh, Limsoon Wong:
The Birth of Bio-data Science: Trends, Expectations, and Applications. 5-15
- Shahzina 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. 16-25
- Ziyi 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. 26-40 - Xiao Han, Hanchen Liu, Zezhong Zhang, Wenlan Yang, Chunyan Wu, Xueying Liu, Fang Zhang, Baofa Sun, Yongliang Zhao, Guibin Jiang, Yun-Gui Yang, Wenjun Ding:
Epitranscriptomic 5-Methylcytosine Profile in PM2.5-induced Mouse Pulmonary Fibrosis. 41-51 - Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li, Jiangning Song:
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. 52-64
- Peng Jia, Xiaofei Yang, Li Guo, 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. 65-71
- Chenwei Wang, Hao-Dong Xu, Shaofeng Lin, Wankun Deng, Jiaqi Zhou, Ying Zhang, Ying Shi, Di Peng, Yu Xue:
GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins. 72-80
- Yongzhe 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. 81-90
Volume 18, Number 2, April 2020
- Qingyu Chen, 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. 91-103
- Tiansheng Zhu, Yi Zhu, Yue Xuan, Huanhuan Gao, Xue Cai, Sander R. Piersma, Thang Viet 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. 104-119
- Qiong Zhang, Wei Liu, 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. 120-128 - Jian Zhao, Yan Li, Cong Wang, Haotian Zhang, Hao Zhang, Bin Jiang, Xuejiang Guo, Xiaofeng Song:
IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. 129-139 - Xiaoxu 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. 140-149 - Xiang Chen, Yi Guo, Xin Chen:
iGMDR: Integrated Pharmacogenetic Resource Guide to Cancer Therapy and Research. 150-160 - Jian 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:
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. 161-172 - Jun Yan, Dong Zou, Chen Li, Zhang Zhang, Shuhui Song, Xiangfeng Wang:
SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice. 173-185 - Ningbo 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. 186-193
- Wanshan Ning, Hao-Dong Xu, Peiran Jiang, Han Cheng, Wankun Deng, Yaping Guo, Yu Xue:
HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction. 194-207 - Hui-Ju Kao, Van-Nui Nguyen, Kai-Yao Huang, Wen-Chi Chang, Tzong-Yi Lee:
SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. 208-219
Volume 18, Number 3, June 2020
- Jiantao Guan, Diego F. Garcia, Yun Zhou, Rudi Appels, Aili Li, Long Mao:
The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms. 221-229
- Zhichao Xu, Ranran Gao, Xiangdong Pu, Rong Xu, Jiyong Wang, Sihao Zheng, Yan Zeng, Jun Chen, Chunnian He, Jingyuan Song:
Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis. 230-240 - Zijian Zhou, Yan Cao, Tao Li, Xinghao Wang, Jiafa Chen, Hang He, Wen Yao, Jianyu Wu, Huiyong Zhang:
MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot. 241-255 - Jihong 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. 256-270 - Jinwei 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:
Na2CO3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics. 271-288 - Xiaohuang Lin, Mingkun Yang, Xin Liu, Zhongyi Cheng, Feng Ge:
Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp. PCC 6803. 289-304 - Liya 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. 305-320 - Shi-Jian Zhang, Lei Liu, Ruolin Yang, Xiangfeng Wang:
Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae. 321-332 - Jinpeng 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, Jin Zhang, Xianchun Zhang, Xiuqing Li, Andrew H. Paterson, Xiyin Wang:
Paleo-polyploidization in Lycophytes. 333-340
- Yuan Liang, Dengxue Lu, Sen Wang, Yuhui Zhao, Shenghan Gao, Rongbing Han, Jun Yu, Weili Zheng, Jianing Geng, Songnian Hu:
Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea. 341-351
- Peijing Zhang, Yongjing Liu, Hongjun Chen, Xianwen Meng, Jitong Xue, Kunsong Chen, Ming Chen:
CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants. 352-358
Volume 18, Number 4, August 2020
- Zixiang Yan, Luzhang Ji, Xiangru Huo, Qianfeng Wang, Yuwen Zhang, Bo Wen:
G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments. 359-370 - Yuhuan Li, Qingyang Zhang, Guanshen Cui, Fang Zhao, Xin Tian, Baofa Sun, Ying Yang, Wei Li:
m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes. 371-383 - Monika Hiller, Miriam Geissler, George Janssen, Peter A. van Veelen, Annemieke Aartsma-Rus, Pietro Spitali:
The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells. 384-396 - Zhi-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. 397-414 - Shan Chi, Guoliang Wang, Tao Liu, Xumin Wang, Cui Liu, Yuemei Jin, Hongxin Yin, Xin Xu, Jun Yu:
Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica. 415-429 - Akash 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. 430-442 - Jun Wang, Xiaowen Chen, Funan He, Xiao Song, Shu Huang, Wucheng Yue, Yipei Chen, Zhixi Su, Chenghui Wang:
Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis. 443-454 - Hongmei 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:
The Wolfiporia cocos Genome and Transcriptome Shed Light on the Formation of Its Edible and Medicinal Sclerotium. 455-467 - Jun Wang, Xueying Xie, Junchao Shi, Wenjun He, Qi Chen, Liang Chen, Wanjun Gu, Tong Zhou:
Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma. 468-480 - Ya-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. 481-487
- Yue-Feng Wang, Qing Chao, Zhe Li, 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]. 488
Volume 18, Number 5, October 2020
- Lindan 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. 489-500 - Kun 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. 501-515 - Jing 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. 516-524 - Yidi 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. 525-538 - Yan Jiang, Yanfei Wang, Xiaoting Hua, Yue Qu, Anton Y. Peleg, Yunsong Yu:
Pooled Plasmid Sequencing Reveals the Relationship Between Mobile Genetic Elements and Antimicrobial Resistance Genes in Clinically Isolated Klebsiella pneumoniae. 539-548 - Arup Panda, Tamir Tuller:
Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins. 549-564
- Song He, Yuqi Wen, Xiaoxi Yang, Zhen Liu, Xinyu Song, Xin Huang, Xiaochen Bo:
PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion. 565-581 - Bin Yu, Cheng Chen, Hongyan Zhou, Bingqiang Liu, Qin Ma:
GTB-PPI: Predict Protein-protein Interactions Based on L1-regularized Logistic Regression and Gradient Tree Boosting. 582-592 - Md. Mehedi Hasan, Mst. Shamima Khatun, Hiroyuki Kurata:
iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features. 593-600
- Jee Eun Kang, Antonio Ciampi, Mohamed Hijri:
SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms. 601-612 - Jee Eun Kang, Antonio Ciampi, Mohamed Hijri:
SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi. 613-623
- Jun Li, 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]. 624-625
Volume 18, Number 6, December 2020
- Jun Yu:
From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2. 627-639
- Qi Liu, Shilei Zhao, Chengmin Shi, Shuhui Song, Sihui Zhu, Yankai Su, Wenming Zhao, Mingkun Li, Yiming Bao, Yongbiao Xue, Hua Chen:
Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters. 640-647 - Xufei Teng, Qianpeng Li, Zhao Li, Yuansheng Zhang, Guangyi Niu, Jing-Fa Xiao, Jun Yu, Zhang Zhang, Shuhui Song:
Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades. 648-663 - Ting 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. 664-678 - Yongxi 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. 679-695 - Wang-Lin Liu, Mingyue Cheng, Jinman Li, Peng Zhang, Hang Fan, Qinghe Hu, Maozhen Han, Longxiang Su, Huaiwu He, Yigang Tong, Kang Ning, Yun Long:
Classification of the Gut Microbiota of Patients in Intensive Care Units During Development of Sepsis and Septic Shock. 696-707 - Ben 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. 708-720 - Xizhan Xu, Zezheng Gao, Fuquan Yang, Yingying Yang, Liang Chen, Lin Han, Na Zhao, Jiayue Xu, Xinmiao Wang, Yue Ma, Kiran Kumar Eepuri, Lian Shu, Xiaoxi Hu, Na Lyu, Yuanlong Pan, Baoli Zhu, Linhua Zhao, Xiaolin Tong, Jun Wang:
Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient Berberine. 721-736
- Yafei 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. 737-748
- Shuhui 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, Wenming Zhao, Yongbiao Xue, Yiming Bao:
The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR. 749-759 - Guocai Yao, Wenliang Zhang, Minglei Yang, Huan Yang, Jianbo Wang, Haiyue Zhang, Lai Wei, Zhi Xie, Weizhong Li:
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes. 760-772
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