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ORCIDGenomics, Proteomics & Bioinformatics, Volume 16
Volume 16, Number 1, February 2018
- Leroy E. Hood
:
Lessons Learned as President of the Institute for Systems Biology (2000-2018). 1-9
- Yueqiang Wang, Yue Shen, Ying Gu, Shida Zhu, Ye Yin:
Genome Writing: Current Progress and Related Applications. 10-16 - Chensi Cao, Feng Liu, Hai Tan, Deshou Song, Wenjie Shu, Weizhong Li, Yiming Zhou, Xiaochen Bo, Zhi Xie:
Deep Learning and Its Applications in Biomedicine. 17-32 - Changting Meng, Chunmei Bai, Thomas D. Brown, Leroy E. Hood, Qiang Tian:
Human Gut Microbiota and Gastrointestinal Cancer. 33-49 - Yan Chen, Guangping Li, Ming-Lin Liu:
Microvesicles as Emerging Biomarkers and Therapeutic Targets in Cardiometabolic Diseases. 50-62 - Manuel Mauricio Goez, Maria C. Torres-Madronero, Sarah Röthlisberger, Edilson Delgado-Trejos:
Preprocessing of 2-Dimensional Gel Electrophoresis Images Applied to Proteomic Analysis: A Review. 63-72
- Johana A. Luna Coronell, Khulan Sergelen, Philipp Hofer, István Gyurján, Stefanie Brezina, Peter Hettegger, Gernot Leeb, Karl Mach, Andrea Gsur, Andreas Weinhäusel:
The Immunome of Colon Cancer: Functional In Silico Analysis of Antigenic Proteins Deduced from IgG Microarray Profiling. 73-84
Volume 16, Number 2, April 2018
Review
- Jinbo Huang, Ping Yin:
Structural Insights into N6-methyladenosine (m6A) Modification in the Transcriptome. 85-98 - Shanhui Liao, Hongbin Sun, Chao Xu:
YTH Domain: A Family of N6-methyladenosine (m6A) Readers. 99-107 - Liming Ma, Zirui Liang, Hui Zhou, Liang-Hu Qu:
Applications of RNA Indexes for Precision Oncology in Breast Cancer. 108-119 - Ke Wu, Juan He, Wenchen Pu, Yong Peng:
The Role of Exportin-5 in MicroRNA Biogenesis and Cancer. 120-126
- Yuan Zhou, Qinghua Cui:
Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m6A Modification. 127-135
- Jiaqi Gu, Ming Wang, Yang Yang, Ding Qiu, Yiqun Zhang, Jinbiao Ma, Yu Zhou, Gregory J. Hannon, Yang Yu:
GoldCLIP: Gel-omitted Ligation-dependent CLIP. 136-143
- Junchao Shi, Eun-A Ko, Kenton M. Sanders, Qi Chen, Tong Zhou:
SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA- and tRNA-derived Small RNAs. 144-151
Volume 16, Number 3, June 2018
- Chi Zhang, Guifang Jia:
Reversible RNA Modification N1-methyladenosine (m1A) in mRNA and tRNA. 155-161
- Andreas Keller, Tobias Fehlmann, Nicole Ludwig, Mustafa Kahraman, Thomas Laufer, Christina Backes, Claus Vogelmeier, Caroline Diener, Frank Biertz, Christian Herr, Rudolf A. Jörres, Hans-Peter Lenhof, Eckart Meese, Robert Bals:
Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development. 162-171 - Yajing Chu, Zhigang Zhao, David Wayne Sant, Ganqian Zhu, Sarah M. Greenblatt, Lin Liu, Jinhuan Wang, Zeng Cao, Jeanette Cheng Tho, Shi Chen, Xiaochen Liu, Peng Zhang, Jaroslaw P. Maciejewski, Stephen Nimer, Gaofeng Wang, Weiping Yuan, Feng-Chun Yang, Mingjiang Xu:
Tet2 Regulates Osteoclast Differentiation by Interacting with Runx1 and Maintaining Genomic 5-Hydroxymethylcytosine (5hmC). 172-186 - Ji Zhang, Xiao Han, Chunchun Gao, Yurong Xing, Zheng Qi, Ruijuan Liu, Yueqin Wang, Xiaojian Zhang, Yun-Gui Yang, Xiangnan Li, Baofa Sun, Xin Tian:
5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer. 187-199 - Chunmei Cui, Weili Yang, Jiangcheng Shi, Yong Zhou, Jichun Yang, Qinghua Cui, Yuan Zhou:
Identification and Analysis of Human Sex-biased MicroRNAs. 200-211
- Erin L. Crowgey, Jennifer T. Wyffels, Patrick M. Osborn, Thomas T. Wood, Laura E. Edsberg:
A Systems Biology Approach for Studying Heterotopic Ossification: Proteomic Analysis of Clinical Serum and Tissue Samples. 212-220
Volume 16, Number 4, August 2018
Preface
- Zhang Zhang, Yu Xue, Fangqing Zhao:
Bioinformatics Commons: The Cornerstone of Life and Health Sciences. 223-225 - Rui Dong, Xu-Kai Ma, Guo-Wei Li, Li Yang:
CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison. 226-233 - Qing Huan, Yuliang Zhang, Shaohuan Wu, Wenfeng Qian:
HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation. 234-243 - Hao-Dong Xu, Yongbo Wang, Shaofeng Lin, Wankun Deng, Di Peng, Qinghua Cui, Yu Xue:
PTMD: A Database of Human Disease-associated Post-translational Modifications. 244-251 - Guanting Lu, Xiaowen Hao, Wei-Hua Chen, Shijie Mu:
GAAD: A Gene and Autoimmiune Disease Association Database. 252-261 - Linna Peng, Sijin Cheng, Yuan Lin, Qionghua Cui, Yingying Luo, Jiahui Chu, Mingming Shao, Wenyi Fan, Yamei Chen, Ai Lin, Yiyi Xi, Yanxia Sun, Lei Zhang, Chao Zhang, Wen Tan, Ge Gao, Chen Wu, Dongxin Lin:
CCGD-ESCC: A Comprehensive Database for Genetic Variants Associated with Esophageal Squamous Cell Carcinoma in Chinese Population. 262-268 - Qiuyu Lian, Shicheng Wang, Guchao Zhang, Dongfang Wang, Guijuan Luo, Jing Tang, Lei Chen, Jin Gu:
HCCDB: A Database of Hepatocellular Carcinoma Expression Atlas. 269-275 - Jingcheng Wu, Wenyi Zhao, Binbin Zhou, Zhixi Su, Xun Gu, Zhan Zhou, Shuqing Chen:
TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis. 276-282 - Huan Qi, Zhenhong Jiang, Kang Zhang, Shiping Yang, Fei He, Ziding Zhang:
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. 283-293
- Yubin Xie, Xiaotong Luo, Yupeng Li, Li Chen, Wenbin Ma, Junjiu Huang, Jun Cui, Yong Zhao, Yu Xue, Zhixiang Zuo, Jian Ren:
DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning. 294-306
Volume 16, Number 5, October 2018
Editorial
- Jun Yu:
A Scientist Guerilla Fighter in the Frontiers of Bioinformatics - In Memory of Bailin Hao. 307-309 - Guanghong Zuo, Ji Qi, Bailin Hao:
Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree. 310-319
- Dongfang Wang, Jin Gu:
VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder. 320-331 - Dimitrios Kleftogiannis, Haitham Ashoor, Vladimir B. Bajic:
TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers. 332-341 - Stefano Perna, Pietro Pinoli, Stefano Ceri, Limsoon Wong:
TICA: Transcriptional Interaction and Coregulation Analyzer. 342-353 - Shi-Jian Zhang, Peiqi Meng, Jieni Zhang, Peizeng Jia, Jiuxiang Lin, Xiangfeng Wang, Feng Chen, Xiaoxing Wei:
Machine Learning Models for Genetic Risk Assessment of Infants with Non-syndromic Orofacial Cleft. 354-364
- Riccardo Calandrelli, Qiuyang Wu, Jihong Guan, Sheng Zhong:
GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. 365-372 - Wanfei Liu, Shuangyang Wu, Qiang Lin, Shenghan Gao, Feng Ding, Xiaowei Zhang, Hasan Awad Aljohi, Jun Yu, Songnian Hu:
RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes. 373-381 - Qidi Feng, Dongsheng Lu, Shuhua Xu:
AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals. 382-385
Volume 16, Number 6, December 2018
- Ding Tang, Zhukuan Cheng:
From Basic Research to Molecular Breeding - Chinese Scientists Play A Central Role in Boosting World Rice Production. 389-392 - Haiyang Wang, Xing Wang Deng:
Development of the "Third-Generation" Hybrid Rice in China. 393-396
- Shuhui Song, Dongmei Tian, Zhang Zhang, Songnian Hu, Jun Yu:
Rice Genomics: over the Past Two Decades and into the Future. 397-404 - Tanyaradzwa Rodgers Ngara, Houjin Zhang:
Recent Advances in Function-based Metagenomic Screening. 405-415
- Wenfang Zhou, Mojie Duan, Weitao Fu, Jinping Pang, Qin Tang, Huiyong Sun, Lei Xu, Shan Chang, Dan Li, Tingjun Hou:
Discovery of Novel Androgen Receptor Ligands by Structure-based Virtual Screening and Bioassays. 416-427 - Lianzhong Zhang, Zhenzhen Wang, Ruifeng Shi, Xuefei Zhu, Jiahui Zhou, Bin Peng, Xingzhi Xu:
RNF126 Quenches RNF168 Function in the DNA Damage Response. 428-438 - Shangang Jia, Kyla Morton, Chi Zhang, David Holding:
An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants. 439-450
- Zhen Chen, Ningning He, Yu Huang, Wen Tao Qin, Xuhan Liu, Lei Li:
Integration of A Deep Learning Classifier with A Random Forest Approach for Predicting Malonylation Sites. 451-459
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