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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 oligodendrocy...
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 compoun...
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 of t...
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 genomes vi...
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 quantificatio...
Source: Genomics, Proteomics and Bioinformatics - January 15, 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 application,...
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 clustering ...
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 quantificatio...
Source: Genomics, Proteomics and Bioinformatics - January 3, 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 cons...
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 characteris...
Source: Genomics, Proteomics and Bioinformatics - January 1, 2020 Category: Bioinformatics Source Type: research

Translational Informatics for Parkinson’s Disease: from Big Biomedical Data to Small Actionable Alterations
Publication date: Available online 28 November 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Bairong Shen, Yuxin Lin, Cheng Bi, Shengrong Zhou, Zhongchen Bai, Guangmin Zheng, Jing ZhouAbstractParkinson's disease (PD) is a common neurological disease in elderly people, and its morbidity and mortality are increasing with the advent of global ageing. The traditional paradigm of moving from small data to big data in biomedical research is shifting toward big data-based identification of small actionable alterations. To highlight the use of big data for precision PD medicine, we review PD big data and informatics ...
Source: Genomics, Proteomics and Bioinformatics - December 25, 2019 Category: Bioinformatics Source Type: research

In Memory of Vladimir B. Bajic (1952–2019)
Publication date: Available online 12 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Zhang Zhang, Jun Yu, Frank Eisenhaber, Xin Gao, Takashi Gojobori (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - December 14, 2019 Category: Bioinformatics Source Type: research

GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis
Publication date: Available online 5 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yadong Yang, Yang Sui, Bingbing Xie, Hongzhu Qu, Xiangdong FangAbstractGliomas are one of the most common types of brain cancers. Numerous efforts have been devoted to studying the mechanisms of glioma genesis and identifying biomarkers for diagnosis and treatment. To help further investigations, we present a comprehensive database named GliomaDB. GliomaDB includes 21,439 samples from 4304 patients and integrates genomic, transcriptomic, epigenomic, clinical, and gene-drug association data regarding glioblastoma multif...
Source: Genomics, Proteomics and Bioinformatics - December 5, 2019 Category: Bioinformatics Source Type: research

Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation
Publication date: Available online 5 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Le Wang, Yan Xia, Yu Chen, Rujia Dai, Wenying Qiu, Qingtuan Meng, Liz Kuney, Chao ChenAbstractNeuropsychiatric disorders affect hundreds of millions of patients and families worldwide. To decode the molecular framework of these diseases, many studies use human postmortem brain samples. These studies reveal brain-specific genetic and epigenetic patterns via high-throughput sequencing technologies. Identifying best practices for the collection of postmortem brain samples, analyzing such large amounts of sequencing data, ...
Source: Genomics, Proteomics and Bioinformatics - December 5, 2019 Category: Bioinformatics Source Type: research