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ORCIDGenomics, Proteomics & Bioinformatics, Volume 17
Volume 17, Number 1, February 2019
- Kang Ning
, Yigang Tong:
The Fast Track for Microbiome Research. 1-3
- Mingyue Cheng, Kang Ning:
Stereotypes About Enterotype: the Old and New Ideas. 4-12 - Lu Zhuang, Haihua Chen, Sheng Zhang, Jiahui Zhuang, Qiuping Li, Zhichun Feng:
Intestinal Microbiota in Early Life and Its Implications on Childhood Health. 13-25
- Ning 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. 26-38 - Jun Li, 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. 39-51 - Yi-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, Yunsheng Yang:
Effects of Proton Pump Inhibitors on the Gastrointestinal Microbiota in Gastroesophageal Reflux Disease. 52-63 - Xiaofeng Song, Liang Zhong, Na Lyu, Fei Liu, Boxing Li, Yanan Hao, Yong Xue, Jing Li, Yuqing Feng, Yue Ma, Yongfei Hu, Baoli Zhu:
Inulin Can Alleviate Metabolism Disorders in ob/ob Mice by Partially Restoring Leptin-related Pathways Mediated by Gut Microbiota. 64-75 - Maozhen 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. 76-90 - Xiaoqing 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. 91-105 - Jiarui 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. 106-117
Volume 17, Number 2, April 2019
- Xiaotian 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. 119-128
- Iva Xhangolli, Burak Dura, GeeHee Lee, Dongjoo Kim, Yang Xiao, Rong Fan:
Single-cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation. 129-139 - Jialei 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. 140-153 - Junchen Chen, Yi-Chang Zhang, Chunmin Huang, Hui Shen, Baofa Sun, Xuejun Cheng, Yu-Jie Zhang, Yun-Gui Yang, Qiang Shu, Ying Yang, Xuekun Li:
m6A Regulates Neurogenesis and Neuronal Development by Modulating Histone Methyltransferase Ezh2. 154-168 - Valentina Galata, Cedric Christian Laczny, Christina Backes, Georg Hemmrich-Stanisak, Susanne Schmolke, Andre Franke, Eckart Meese, Mathias Herrmann, Lutz von Müller, Achim Plum, Rolf Müller, Cord Stähler, Andreas E. Posch, Andreas Keller:
Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11, 087 Clinical Isolates. 169-182 - Ran Tao, Zhicheng Fu, Lijun Xiao:
Chronic Food Antigen-specific IgG-mediated Hypersensitivity Reaction as A Risk Factor for Adolescent Depressive Disorder. 183-189
- Qiong 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. 190-200
- Xianwen Ren, Liangtao Zheng, Zemin Zhang:
SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data. 201-210 - Qian Liu, Qiang Hu, Song Yao, Marilyn L. Kwan, Janise M. Roh, Hua Zhao, Christine B. Ambrosone, Lawrence H. Kushi, Song Liu, Qianqian Zhu:
SeqSQC: A Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data. 211-218
- Xudong Zou, Xin Gao, Wei Chen:
Deep Learning Deepens the Analysis of Alternative Splicing. 219-221
Volume 17, Number 3, June 2019
- Shanshan Xie, Yuxia Jiao:
That's A Scientist Should Do - A Dialog with Tomas Lindahl. 223-225
- Li Guo, Kai Ye:
Mapping Genome Variants Sheds Light on Genetic and Phenotypic Differentiation in Chinese. 226-228
- Zhenglin Du, Liang Ma, Hongzhu Qu, Wei Chen, Bing Zhang, 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:
Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome. 229-247 - Hui 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. 248-259 - Xiaofei Wang, Hehong Wei, Xuemei Mao, Jin Liu:
Proteomics Analysis of Lipid Droplets from the Oleaginous Alga Chromochloris zofingiensis Reveals Novel Proteins for Lipid Metabolism. 260-272 - Huiyan Sun, Liang Chen, Sha Cao, Yanchun Liang, Ying Xu:
Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name. 273-286 - Xiang 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. 287-296
- Xiaolong Chen, Youqiong Ye, Liang Gu, Jin Sun, Yanhua Du, Wen-Ju Liu, Wei Li, Xiaobai Zhang, Cizhong Jiang:
H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development. 297-304
- Madison Caballero, Jill L. Wegrzyn:
gFACs: Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks. 305-310 - Chen-Yu Zhu, Chi Zhou, Yun-Qin Chen, Ai-Zong Shen, Zong-Ming Guo, Zhao-Yi Yang, Xiangyun Ye, Shen Qu, Jia Wei, Qi Liu:
C3: Consensus Cancer Driver Gene Caller. 311-318 - Weili 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. 319-331
Volume 17, Number 4, August 2019
- Hongzhu Qu, Hongxing Lei, Xiangdong Fang:
Big Data and the Brain: Peeking at the Future. 333-336
- Anan Li, Yue Guan, Hui Gong, Qingming Luo:
Challenges of Processing and Analyzing Big Data in Mesoscopic Whole-brain Imaging. 337-343
- Quanhua Mu, Yiyun Chen, Jiguang Wang:
Deciphering Brain Complexity Using Single-cell Sequencing. 344-366 - Jie Li, Guang-Zhong Wang:
Application of Computational Biology to Decode Brain Transcriptomes. 367-380 - Shanyu 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. 381-392 - Xiang Li, Ning Guo, Quanzheng Li:
Functional Neuroimaging in the New Era of Big Data. 393-401 - Le 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. 402-414 - Bairong 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. 415-429
- Nicole Ludwig, 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. 430-440 - Zhenyu Liu, Jiangang Liu, Huijuan Yuan, Taiyuan Liu, Xingwei Cui, Zhenchao Tang, Yang Du, Meiyun Wang, Yusong Lin, Jie Tian:
Identification of Cognitive Dysfunction in Patients with T2DM Using Whole Brain Functional Connectivity. 441-452
- Guan Ning Lin, Sijia Guo, Xian Tan, Weidi Wang, Wei Qian, Weichen Song, Jingru Wang, Shunying Yu, Zhen Wang, Donghong Cui, Han Wang:
PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders. 453-464 - Yadong Yang, Yang Sui, Bingbing Xie, Hongzhu Qu, Xiangdong Fang:
GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis. 465-471
Volume 17, Number 5, October 2019
- Zhang Zhang, Jun Yu, Frank Eisenhaber, Xin Gao, Takashi Gojobori:
In Memory of Vladimir B. Bajic (1952-2019). 473-474
- Ming Li:
Deep Learning Deciphers Protein-RNA Interaction. 475-477
- Fangping Wan, Yue Zhu, Hailin Hu, Antao Dai, Xiaoqing Cai, Ligong Chen, Haipeng Gong, Tian Xia, Dehua Yang, Ming-Wei Wang, Jianyang Zeng:
DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening. 478-495
- Ruilin Li, Xiaoyu He, Chuangchuang Dai, Haidong Zhu, Xianyu Lang, Wei Chen, 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. 496-502 - Yun Tan, Lulu Jiang, Kankan Wang, Hai Fang:
I3: A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data. 503-510
- Xu-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. 511-521 - Jing Wu, Yan Li, Cheng Wang, Yiqiang Cui, Tianyi Xu, Chang Wang, Xiao Wang, Jiahao Sha, Bin Jiang, Kai Wang, Zhibin Hu, Xuejiang Guo, Xiaofeng Song:
CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs. 522-534 - Yiming Yu, Wen Yao, Yuping Wang, Fangfang Huang:
shinyChromosome: An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes. 535-539 - Eddie Ip, Gavin Chapman, David S. Winlaw, Sally L. Dunwoodie, Eleni Giannoulatou:
VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants. 540-545 - Katharina Jasmin Hoff:
MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs. 546-549
Volume 17, Number 6, December 2019
- Natalie Mezey, William C. S. Cho, Kyle K. Biggar:
Intriguing Origins of Protein Lysine Methylation: Influencing Cell Function Through Dynamic Methylation. 551-557
- Lin 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:
Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production. 558-575 - Sixue 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. 576-589 - Xing 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. 590-602 - Yue-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. 603-622
- Danielle M. Santarelli, Adam P. Carroll, Heath M. Cairns, Paul A. Tooney, Murray J. Cairns:
Schizophrenia-associated MicroRNA-Gene Interactions in the Dorsolateral Prefrontal Cortex. 623-634
- Hua Chen:
A Computational Approach for Modeling the Allele Frequency Spectrum of Populations with Arbitrarily Varying Size. 635-644 - Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou:
SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning. 645-656
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