Corrigendum to “Antibiotic Treatment Drives the Diversification of the Human Gut Resistome” [Genomics Proteomics Bioinformatics 17 (1) (2019) 39–51]
Publication date: Available online 9 September 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jun Li, Elizabeth A. Rettedal, Eric van der Helm, Mostafa Ellabaan, Gianni Panagiotou, Morten O.A. Sommer (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - September 10, 2020 Category: Bioinformatics Source Type: research

iGMDR: Integrated Pharmacogenetic Resource Guide to Cancer Therapy and Research
Publication date: Available online 8 September 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xiang Chen, Yi Guo, Xin Chen (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - September 9, 2020 Category: Bioinformatics Source Type: research

MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals
Publication date: Available online 8 September 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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 (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - September 9, 2020 Category: Bioinformatics Source Type: research

Long Non-coding RNA Derived from lncRNA–mRNA Co-expression Networks Modulates the Locust Phase Change
Publication date: Available online 29 August 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Ting Li, Bing Chen, Pengcheng Yang, Depin Wang, Baozhen Du, Le Kang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - August 29, 2020 Category: Bioinformatics Source Type: research

HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction
Publication date: Available online 28 August 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Wanshan Ning, Haodong Xu, Peiran Jiang, Han Cheng, W.un Deng, Yaping Guo, Yu Xue (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - August 29, 2020 Category: Bioinformatics Source Type: research

hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets
Publication date: Available online 26 August 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Qiong Zhang, Wei Liu, Hong-Mei Zhang, Gui-Yan Xie, Ya-Ru Miao, Mengxuan Xia, An-Yuan Guo (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - August 26, 2020 Category: Bioinformatics Source Type: research

Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity
Publication date: Available online 19 August 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Lindan Ji, Dongdong Wu, Haibing Xie, Binbin Yao, Yanming Chen, David M. Irwin, Dan Huang, Jin Xu, Nelson L.S. Tang, Yaping Zhang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - August 19, 2020 Category: Bioinformatics Source Type: research

The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery
Publication date: Available online 19 August 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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 (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - August 19, 2020 Category: Bioinformatics Source Type: research

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
Publication date: Available online 12 August 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Tiansheng 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. Lelarge, Jacqueline Cloos, Anna Wojtuszkiewicz (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - August 13, 2020 Category: Bioinformatics Source Type: research

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]
Publication date: Available online 1 August 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yue-Feng Wang, Qing Chao, Zhe Li, Tian-Cong Lu, Hai-Yan Zheng, Cai-Feng Zhao, Zhuo Shen, Xiao-Hui Li, Bai-Chen Wang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - August 3, 2020 Category: Bioinformatics Source Type: research

From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2
Publication date: Available online 30 July 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jun Yu (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 31, 2020 Category: Bioinformatics Source Type: research

Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis
Publication date: Available online 28 July 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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 (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 29, 2020 Category: Bioinformatics Source Type: research

Na2CO3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics
Publication date: Available online 16 July 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jinwei Suo, Heng Zhang, Qi Zhao, Nan Zhang, Yongxue Zhang, Ying Li, Baohua Song, Juanjuan Yu, Jian'guo Cao, Tai Wang, Ji Luo, Lihai Guo, Jun Ma, Xumin Zhang, Yimin She, Lianwei Peng, Weimin Ma, Siyi Guo, Yuchen Miao, Sixue Chen (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 17, 2020 Category: Bioinformatics Source Type: research

IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data
Publication date: Available online 16 July 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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 (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 17, 2020 Category: Bioinformatics Source Type: research

Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters
Publication date: Available online 12 July 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Qi Liu, Shilei Zhao, Cheng-Min Shi, Shuhui Song, Sihui Zhu, Yankai Su, Wenming Zhao, Mingkun Li, Yiming Bao, Yongbiao Xue, Hua Chen (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 12, 2020 Category: Bioinformatics Source Type: research

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Publication date: Available online 9 July 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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 (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 9, 2020 Category: Bioinformatics Source Type: research

SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice
Publication date: Available online 30 June 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jun Yan, Dong Zou, Chen Li, Zhang Zhang, Shuhui Song, Xiangfeng Wang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 1, 2020 Category: Bioinformatics Source Type: research

SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites
Publication date: Available online 24 June 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Hui-Ju Kao, Van-Nui Nguyen, Kai-Yao Huang, Wen-Chi Chang, Tzong-Yi Lee (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - June 25, 2020 Category: Bioinformatics Source Type: research

The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms
Publication date: Available online 17 June 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jiantao Guan, Diego F. Garcia, Yun Zhou, Rudi Appels, Aili Li, Long Mao (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - June 18, 2020 Category: Bioinformatics Source Type: research

Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea
Publication date: Available online 17 June 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yuan Liang, Dengxue Lu, Sen Wang, Yuhui Zhao, Shenghan Gao, Rongbing Han, Jun Yu, Weili Zheng, Jianing Geng, Songnian Hu (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - June 18, 2020 Category: Bioinformatics Source Type: research

BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures
Publication date: Available online 12 June 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Ningbo Chen, Weiwei Fu, Jianbang Zhao, Jiafei Shen, Qiuming Chen, Zhuqing Zheng, Hong Chen, Tad S. Sonstegard, Chuzhao Lei, Yu Jiang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - June 13, 2020 Category: Bioinformatics Source Type: research

MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot
Publication date: Available online 10 June 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Zijian Zhou, Yan Cao, Tao Li, Xinghao Wang, Jiafa Chen, Hang He, Wen Yao, Jianyu Wu, Huiyong Zhang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - June 10, 2020 Category: Bioinformatics Source Type: research

IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites
Publication date: Available online 6 June 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jian Zhao, Yan Li, Cong Wang, Haotian Zhang, Hao Zhang, Bin Jiang, Xuejiang Guo, Xiaofeng Song (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - June 7, 2020 Category: Bioinformatics Source Type: research

Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency
Publication date: Available online 21 May 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Shahzina Kanwal, Xiangpeng Guo, Carl Ward, Giacomo Volpe, Baoming Qin, Miguel A. Esteban, Xichen Bao (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 21, 2020 Category: Bioinformatics Source Type: research

SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples
Publication date: Available online 16 May 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yongzhe Ren, Yang Zhang, Dandan Wang, Fengying Liu, Ying Fu, Shaohua Xiang, Li Su, Jiancheng Li, Heng Dai, Bingding Huang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 18, 2020 Category: Bioinformatics Source Type: research

The Birth of Bio-data Science: Trends, Expectations, and Applications
Publication date: Available online 16 May 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Wilson Wen Bin Goh, Limsoon Wong (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 16, 2020 Category: Bioinformatics Source Type: research

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information
Publication date: Available online 12 May 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Fuyi Li, Andre Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, A. Ian Smith, Tatiana Marquez-Lago, Jian Li, Jiangning Song (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 13, 2020 Category: Bioinformatics Source Type: research

CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma
Publication date: Available online 13 May 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Ziyi Li, Binbin Wang, Shengqing Gu, Peng Jiang, Avinash 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, X. Shirley Liu (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 13, 2020 Category: Bioinformatics Source Type: research

The Elements of Data Sharing
Publication date: Available online 28 April 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Zhang Zhang, Shuhui Song, Jun Yu, Wenming Zhao, Jingfa Xiao, Yiming Bao (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - April 29, 2020 Category: Bioinformatics Source Type: research

Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production
Publication date: Available online 26 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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, Jiang Hu, Depeng Wang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 27, 2020 Category: Bioinformatics Source Type: research

Multi-omics Analysis of Primary Cell Culture Models Reveals Genetic and Epigenetic Basis of Intratumoral Phenotypic Diversity
Publication date: Available online 20 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Sixue Liu, Zuyu Yang, Guanghao Li, Chunyan Li, Yanting Luo, Qiang Gong, Xin Wu, Tao Li, Zhiqian Zhang, Baocai Xing, Xiaolan Xu, Xuemei Lu (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 22, 2020 Category: Bioinformatics Source Type: research

GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins
Publication date: Available online 19 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Chenwei Wang, Haodong Xu, Shaofeng Lin, W.un Deng, Jiaqi Zhou, Ying Zhang, Ying Shi, Di Peng, Yu Xue (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 19, 2020 Category: Bioinformatics Source Type: research

Intriguing Origins of Protein Lysine Methylation: Influencing Cell Function Through Dynamic Methylation
Publication date: Available online 17 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Natalie Mezey, William C.S. Cho, Kyle K. Biggar (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 19, 2020 Category: Bioinformatics Source Type: research

Large-scale Identification and Time-course Quantification of Ubiquitylation Events During Maize Seedling De-etiolation
Publication date: Available online 14 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yue-Feng Wang, Qing Chao, Zhe Li, Tian-Cong Lu, Hai-Yan Zheng, Cai-Feng Zhao, Zhuo Shen, Xiao-Hui Li, Bai-Chen Wang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 14, 2020 Category: Bioinformatics Source Type: research

SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning
Publication date: Available online 13 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jack Hanson, Kuldip K. Paliwal, Thomas Litfin, Yaoqi Zhou (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 13, 2020 Category: Bioinformatics Source Type: research

A Computational Approach for Modeling the Allele Frequency Spectrum of Populations with Arbitrarily Varying Size
Publication date: Available online 13 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Hua Chen (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 13, 2020 Category: Bioinformatics Source Type: research

Meta-analysis Reveals Potential Influence of Oxidative Stress on the Airway Microbiomes of Cystic Fibrosis Patients
Publication date: Available online 12 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xing Shi, Zhancheng Gao, Qiang Lin, Liping Zhao, Qin Ma, Yu Kang, Jun Yu (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 13, 2020 Category: Bioinformatics Source Type: research

MSIsensor-pro: Fast, Accurate, and Matched-normal-sample-free Detection of Microsatellite Instability
Publication date: Available online 12 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Peng Jia, Xiaofei Yang, Li Guo, Bowen Liu, Jiadong Lin, Hao Liang, Jianyong Sun, Chengsheng Zhang, Kai Ye (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 13, 2020 Category: Bioinformatics Source Type: research

Epitranscriptomic 5-Methylcytosine Profile in PM2.5-induced Mouse Pulmonary Fibrosis
Publication date: Available online 3 March 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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 (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - March 4, 2020 Category: Bioinformatics Source Type: research

Schizophrenia-associated MicroRNA–Gene Interactions in the Dorsolateral Prefrontal Cortex
In this study, we integrate changes in cortical gene and miRNA expression to identify regulatory interactions and networks associated with the disorder. Gene expression analysis in post-mortem prefrontal dorsolateral cortex (BA 46) (n = 74 matched pairs of schizophrenia, schizoaffective, and control samples) was integrated with miRNA expression in the same cohort to identify gene–miRNA regulatory networks. A significant gene–miRNA interaction network was identified, including miR-92a, miR-495, and miR-134, which converged with differentially expressed genes in pathways involved in neurodevelopment and oligo...
Source: Genomics, Proteomics and Bioinformatics - February 14, 2020 Category: Bioinformatics Source Type: research

DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening
Publication date: Available online 6 February 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Fangping Wan, Yue Zhu, Hailin Hu, Antao Dai, Xiaoqing Cai, Ligong Chen, Haipeng Gong, Tian Xia, Dehua Yang, Mingwei Wang, Jianyang ZengAbstractAccurate identification of compound–protein interactions (CPIs) in silico may deepen our understanding of the underlying mechanisms of drug action and thus remarkably facilitate drug discovery and development. Conventional similarity- or docking-based computational methods for predicting CPIs rarely exploit latent features from currently available large-scale unlabeled...
Source: Genomics, Proteomics and Bioinformatics - February 7, 2020 Category: Bioinformatics Source Type: research

CircAST: Full-length Assembly and Quantification of Alternatively Spliced Isoforms in Circular RNAs
Publication date: Available online 31 January 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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 SongAbstractCircular RNAs (circRNAs), covalently closed continuous RNA loops, are generated from cognate linear RNAs through back splicing events, and alternative splicing events may generate different circRNA isoforms at the same locus. However, the challenges of reconstruction and quantification of alternatively spliced full-length circRNAs remain unresolved. On the basis ...
Source: Genomics, Proteomics and Bioinformatics - February 1, 2020 Category: Bioinformatics Source Type: research

MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs
Publication date: Available online 28 January 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Katharina Jasmin HoffAbstractNovel genomes are today often annotated by small consortia or individuals whose background is not from bioinformatics. This audience requires tools that are easy to use. Such need has been addressed by several genome annotation tools and pipelines. Visualizing resulting annotation is a crucial step of quality control. The UCSC Genome Browser is a powerful and popular genome visualization tool. Assembly Hubs, which can be hosted on any publicly available web server, allow browsing genome...
Source: Genomics, Proteomics and Bioinformatics - January 28, 2020 Category: Bioinformatics Source Type: research

CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression
Publication date: Available online 3 January 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xu-Kai Ma, Meng-Ran Wang, Chu-Xiao Liu, Rui Dong, Gordon G. Carmichael, Ling-Ling Chen, Li YangAbstractSequences of circular RNAs (circRNAs) produced from back-splicing of exon(s) completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction (BSJ) sites. Therefore, examination of global circRNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites, which is different from the quantific...
Source: Genomics, Proteomics and Bioinformatics - January 16, 2020 Category: Bioinformatics Source Type: research

shinyChromosome: An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes
Publication date: Available online 11 January 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yiming Yu, Wen Yao, Yuping Wang, Fangfang HuangAbstractNon-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes. Currently, there is no specialized graphical user interface (GUI) designed to produce non-circular whole genome diagrams, and the use of existing tools requires considerable coding effort from users. Moreover, such tools also require improvement, including the addition of new functionalities. To address these issues, we developed a new R/Shiny applicat...
Source: Genomics, Proteomics and Bioinformatics - January 11, 2020 Category: Bioinformatics Source Type: research

Gclust: A Parallel Clustering Tool for Microbial Genomic Data
Publication date: Available online 7 January 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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 NiuAbstractThe accelerating growth of the public microbial genomic data imposes substantial burden on the research community that uses such resources. Building databases for non-redundant reference sequences from massive microbial genomic data based on clustering analysis is essential. However, existing cluster...
Source: Genomics, Proteomics and Bioinformatics - January 8, 2020 Category: Bioinformatics Source Type: research

CIRCexplorer3-CLEAR: A Pipeline for Direct Comparison of Circular and Linear RNA Expression
Publication date: Available online 3 January 2020Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xu-Kai Ma, Meng-Ran Wang, Chu-Xiao Liu, Rui Dong, Gordon G. Carmichael, Ling-Ling Chen, Li YangAbstractSequences of circular RNAs (circRNAs) produced from back-splicing of exon(s) completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction (BSJ) sites. Therefore, examination of global circRNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites, which is different from the quantific...
Source: Genomics, Proteomics and Bioinformatics - January 4, 2020 Category: Bioinformatics Source Type: research

Identification of Cognitive Dysfunction in Patients with T2DM Using Whole Brain Functional Connectivity
Publication date: August 2019Source: Genomics, Proteomics & Bioinformatics, Volume 17, Issue 4Author(s): Zhenyu Liu, Jiangang Liu, Huijuan Yuan, Taiyuan Liu, Xingwei Cui, Zhenchao Tang, Yang Du, Meiyun Wang, Yusong Lin, Jie TianAbstractMajority of type 2 diabetes mellitus (T2DM) patients are highly susceptible to several forms of cognitive impairments, particularly dementia. However, the underlying neural mechanism of these cognitive impairments remains unclear. We aimed to investigate the correlation between whole brain resting state functional connections (RSFCs) and the cognitive status in 95 patients with T2DM. We ...
Source: Genomics, Proteomics and Bioinformatics - January 1, 2020 Category: Bioinformatics Source Type: research

Challenges of Processing and Analyzing Big Data in Mesoscopic Whole-brain Imaging
Publication date: August 2019Source: Genomics, Proteomics & Bioinformatics, Volume 17, Issue 4Author(s): Anan Li, Yue Guan, Hui Gong, Qingming Luo (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - January 1, 2020 Category: Bioinformatics Source Type: research

Application of Computational Biology to Decode Brain Transcriptomes
Publication date: August 2019Source: Genomics, Proteomics & Bioinformatics, Volume 17, Issue 4Author(s): Jie Li, Guang-Zhong WangAbstractThe rapid development of high-throughput sequencing technologies has generated massive valuable brain transcriptome atlases, providing great opportunities for systematically investigating gene expression characteristics across various brain regions throughout a series of developmental stages. Recent studies have revealed that the transcriptional architecture is the key to interpreting the molecular mechanisms of brain complexity. However, our knowledge of brain transcriptional charact...
Source: Genomics, Proteomics and Bioinformatics - January 1, 2020 Category: Bioinformatics Source Type: research