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Genomics, 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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