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

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 informat...
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 mu...
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 da...
Source: Genomics, Proteomics and Bioinformatics - December 5, 2019 Category: Bioinformatics Source Type: research

Big Data and the Brain: Peeking at the Future
Publication date: Available online 4 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Hongzhu Qu, Hongxing Lei, Xiangdong Fang (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - December 4, 2019 Category: Bioinformatics Source Type: research

Functional Neuroimaging in the New Era of Big Data
Publication date: Available online 4 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xiang Li, Ning Guo, Quanzheng LiAbstractThe field of functional neuroimaging has substantially advanced as a big data science in the past decade, thanks to international collaborative projects and community efforts. Here we conducted a literature review on functional neuroimaging, with focus on three general challenges in big data tasks: data collection and sharing, data infrastructure construction, and data analysis methods. The review covers a wide range of literature types including perspectives, database descri...
Source: Genomics, Proteomics and Bioinformatics - December 4, 2019 Category: Bioinformatics Source Type: research

Machine Learning to Detect Alzheimer’s Disease from Circulating Non-coding RNAs
Publication date: Available online 4 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Nicole Ludwig, Tobias Fehlmann, Fabian Kern, Manfred Gogol, Walter Maetzler, Stephanie Deutscher, Simone Gurlit, Claudia Schulte, Anna-Katharina von Thaler, Christian Deuschle, Florian Metzger, Daniela Berg, Ulrike Suenkel, Verena Keller, Christina Backes, Hans-Peter Lenhof, Eckart Meese, Andreas KellerAbstractBlood-borne small non-coding (sncRNAs) are among the prominent candidates for blood-based diagnostic tests. Often, high-throughput approaches are applied to discover biomarker signatures. These have to be val...
Source: Genomics, Proteomics and Bioinformatics - December 4, 2019 Category: Bioinformatics Source Type: research

PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders
Publication date: Available online 4 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Guan Ning Lin, Sijia Guo, Xian Tan, Weidi Wang, Wei Qian, Weichen Song, Jingru Wang, Shunying Yu, Zhen Wang, Donghong Cui, Han WangAbstractDe novo variants (DNVs) are one of the most significant contributors to severe early-onset genetic disorders such as autism spectrum disorder, intellectual disability, and other developmental and neuropsychiatric (DNP) disorders. Presently, a plethora of DNVs have been identified using next-generation sequencing, and many efforts have been made to understand their impact at the ...
Source: Genomics, Proteomics and Bioinformatics - December 4, 2019 Category: Bioinformatics Source Type: research

Challenges to Processing and Analyzing Big Data in Mesoscopic Whole-brain Imaging
Publication date: Available online 2 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Anan Li, Yue Guan, Hui Gong, Qingming Luo (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - December 4, 2019 Category: Bioinformatics Source Type: research

How Big Data and High-performance Computing Drive Brain Science
Publication date: Available online 2 December 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Shanyu Chen, Zhipeng He, Xinyin Han, Xiaoyu He, Ruilin Li, Haidong Zhu, Dan Zhao, Chuangchuang Dai, Yu Zhang, Zhonghua Lu, Xuebin Chi, Beifang NiuAbstractBrain science accelerates the study of intelligence and behavior, contributes fundamental insights into human cognition, and offers prospective treatments for brain disease. Faced with the challenges posed by imaging technologies and deep learning computational models, big data and high-performance computing (HPC) play essential roles in studying brain function, b...
Source: Genomics, Proteomics and Bioinformatics - December 4, 2019 Category: Bioinformatics Source Type: research

Identification of T2DM Patients Associated Cognitive Dysfunction Using Whole Brain Functional Connectivity
Publication date: Available online 28 November 2019Source: Genomics, Proteomics & BioinformaticsAuthor(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. W...
Source: Genomics, Proteomics and Bioinformatics - November 29, 2019 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 informat...
Source: Genomics, Proteomics and Bioinformatics - November 29, 2019 Category: Bioinformatics Source Type: research

VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants
Publication date: Available online 22 November 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Eddie Ip, Gavin Chapman, David Winlaw, Sally L. Dunwoodie, Eleni GiannoulatouAbstractNext-generation sequencing (NGS) technologies generate thousands to millions of genetic variants per sample. Identification of potential disease-causal variants is labor intensive as it relies on filtering using various annotation metrics and consideration of multiple pathogenicity prediction scores. We have developed VPOT (variant prioritization ordering tool), a python-based command line tool that allows researchers to create a ...
Source: Genomics, Proteomics and Bioinformatics - November 24, 2019 Category: Bioinformatics Source Type: research

I3: A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data
Publication date: Available online 23 November 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Yun Tan, Lulu Jiang, Kankan Wang, Hai FangAbstractWe propose a computational workflow (I3) for intuitive integrative interpretation of complex genetic data mainly building on the self-organising principle. We illustrate the use in interpreting genetics of gene expression and understanding genetic regulators of protein phenotypes, particularly in conjunction with information from human population genetics and/or evolutionary history of human genes. We reveal that loss-of-function intolerant genes tend to be deplete...
Source: Genomics, Proteomics and Bioinformatics - November 24, 2019 Category: Bioinformatics Source Type: research

Deep Learning Deciphers Protein–RNA Interaction
Publication date: Available online 23 November 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Ming Li (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - November 24, 2019 Category: Bioinformatics Source Type: research

Application of Computational Biology for Decoding Brain Transcriptomes
Publication date: Available online 23 October 2019Source: Genomics, Proteomics & BioinformaticsAuthor(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 charac...
Source: Genomics, Proteomics and Bioinformatics - October 24, 2019 Category: Bioinformatics Source Type: research

Deciphering Brain Complexity Using Single-cell Sequencing
Publication date: Available online 3 October 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Quanhua Mu, Yiyun Chen, Jiguang WangAbstractThe human brain contains billions of highly differentiated and interconnected cells that form intricate neural networks and collectively control the physical activities and high-level cognitive functions, such as memory, decision-making, and social behavior. Big data is required to decipher the complexity of cell types, as well as connectivity and functions of the brain. The newly developed single-cell sequencing technology, which provides a comprehensive landscape of brai...
Source: Genomics, Proteomics and Bioinformatics - October 4, 2019 Category: Bioinformatics Source Type: research

Mapping Genome Variants Sheds Light on Genetic and Phenotypic Differentiation in Chinese
Publication date: Available online 9 September 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Li Guo, Kai Ye (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - September 10, 2019 Category: Bioinformatics Source Type: research

Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions
In this report, we tested the antisera-antigen interaction using serum samples from patients with inclusion body myositis (IBM). Tripartite motif containing 21 (TRIM21) was identified as a potentially new IBM autoantigen. We also expanded the application of PLATO-BC to identify protein interactions for JQ1, single ubiquitin peptide, and NS5 protein of Zika virus. From PLATO-BC analyses, we identified new protein interactions for these “bait” molecules. We demonstrate that Ewing sarcoma breakpoint region 1 (EWSR1) binds to JQ1 and their interactions may interrupt the EWSR1 association with acetylated histone H4....
Source: Genomics, Proteomics and Bioinformatics - September 6, 2019 Category: Bioinformatics Source Type: research

Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome
Publication date: Available online 5 September 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): 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, Yaqiang Hong, Lili DongAbstractTo unravel the genetic mechanisms of disease and physiological traits, it requires comprehensive sequencing analysis of large sample size in Chinese populations. Here, we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative (CASPMI) project launched...
Source: Genomics, Proteomics and Bioinformatics - September 6, 2019 Category: Bioinformatics Source Type: research

Novel Autoantibodies Related to Cell Death and DNA Repair Pathways in Systemic Lupus Erythematosus
In this study, a commercial platform bearing 9400 antigens (Protoarray) was used to identify autoAbs that were significantly elevated in the sera of SLE patients. By comparing the autoAb profiles of SLE patients with those of healthy controls, we identified 437 IgG and 1213 IgM autoAbs that the expression levels were significantly increased in SLE (P
Source: Genomics, Proteomics and Bioinformatics - September 6, 2019 Category: Bioinformatics Source Type: research

Proteomics Analysis of Lipid Droplets from the Oleaginous Alga Chromochloris zofingiensis Reveals Novel Proteins for Lipid Metabolism
Publication date: Available online 5 September 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xiaofei Wang, Hehong Wei, Xuemei Mao, Jin LiuAbstractChromochloris zofingiensis represents an industrially relevant and unique green alga, given its capability of synthesizing triacylglycerol (TAG) and astaxanthin simultaneously for storage in lipid droplets (LDs). To further decipher lipid metabolism, the nitrogen deprivation (ND)-induced LDs from C. zofingiensis were isolated, purified, and subjected to proteomic analysis. Intriguingly, many C. zofingiensis LD proteins had no orthologs present in LD proteome of ...
Source: Genomics, Proteomics and Bioinformatics - September 6, 2019 Category: Bioinformatics Source Type: research

Characterization of Distinct T Cell Receptor Repertoires in Tumor and Distant Non-tumor Tissues from Lung Cancer Patients
Publication date: Available online 31 August 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xiang Wang, Botao Zhang, Yikun Yang, Jiawei Zhu, Shujun Cheng, Yousheng Mao, Lin Feng, Ting XiaoAbstractT cells and T cell receptors (TCRs) play pivotal roles in adaptive immune responses against tumors. The development of next-generation sequencing technologies has enabled the analysis of the TCRβ repertoire usage. Given the scarce investigations on the TCR repertoire in lung cancer tissues, in this study, we analyzed TCRβ repertoires in lung cancer tissues and the matched distant non-tumor lung tissues (...
Source: Genomics, Proteomics and Bioinformatics - September 1, 2019 Category: Bioinformatics Source Type: research

C3: Consensus Cancer Driver Gene Caller
Publication date: Available online 26 August 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Chen-Yu Zhu, Chi Zhou, Yun-Qin Chen, Ai-Zong Shen, Zong-Ming Guo, Zhao-Yi Yang, Xiang-Yun Ye, Shen Qu, Jia Wei, Qi LiuAbstractNext-generation sequencing has allowed identification of millions of somatic mutations in human cancer cells. A key challenge in interpreting cancer genomes is to distinguish drivers of cancer development among available genetic mutations. To address this issue, we present the first web-based application, consensus cancer driver gene caller (C3), to identify the consensus driver genes using s...
Source: Genomics, Proteomics and Bioinformatics - August 28, 2019 Category: Bioinformatics Source Type: research

gFACs: Gene Filtering, Analysis, and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks
Publication date: Available online 19 August 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Madison Caballero, Jill WegrzynAbstractPublished genomes frequently contain erroneous gene models that represent issues associated with identification of open reading frames, start sites, splice sites, and related structural features. The source of these inconsistencies is often traced back to integration across text file formats designed to describe long read alignments and predicted gene structures. In addition, the majority of gene prediction frameworks do not provide robust downstream filtering to remove problem...
Source: Genomics, Proteomics and Bioinformatics - August 20, 2019 Category: Bioinformatics Source Type: research

That’s A Scientist Should Do—A Dialog with Tomas Lindahl
Publication date: Available online 16 July 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Shanshan Xie, Yuxia Jiao (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 24, 2019 Category: Bioinformatics Source Type: research

That’s A Scientist Should Do — A Dialog with Tomas Lindahl
Publication date: Available online 16 July 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Shanshan Xie, Yuxia Jiao (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - July 17, 2019 Category: Bioinformatics Source Type: research

Chronic Food Antigen-specific IgG-mediated Hypersensitivity Reaction as A Risk Factor for Adolescent Depressive Disorder
Publication date: Available online 21 June 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Ran Tao, Zhicheng Fu, Lijun XiaoAbstractMajor depressive disorder (MDD) is the most common nonfatal disease burden worldwide. Systemic chronic low-grade inflammation has been reported to be associated with MDD progression by affecting monoaminergic and glutamatergic neurotransmission. However, whether various proinflammatory cytokines are abnormally elevated before the first episode of depression is still largely unclear. Here, we evaluated 184 adolescent patients who were experiencing their first episode of depressiv...
Source: Genomics, Proteomics and Bioinformatics - June 23, 2019 Category: Bioinformatics Source Type: research

Single-cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation
We present the first comprehensive portrait of single-cell level transcriptional and cytokine signatures of anti-CD19/4-1BB/CD28/CD3ζ CAR-T cells upon antigen-specific stimulation. Both CD4+ helper T (TH) cells and CD8+ cytotoxic CAR-T cells are equally effective in directly killing target tumor cells and their cytotoxic activity is associated with the elevation of a range of TH1 and TH2 signature cytokines, e.g., interferon γ, tumor necrotic factor α, interleukin 5 (IL5), and IL13, as confirmed by the expression of master transcription factor genes TBX21 and GATA3. However, rather than conformin...
Source: Genomics, Proteomics and Bioinformatics - June 21, 2019 Category: Bioinformatics Source Type: research

Global Quantitative Mapping of Enhancers in Rice by STARR-seq
Publication date: Available online 13 June 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jialei Sun, Na He, Longjian Niu, Yingzhang Huang, Wei Shen, Yuedong Zhang, Li Li, Chunhui HouAbstractEnhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5&p...
Source: Genomics, Proteomics and Bioinformatics - June 14, 2019 Category: Bioinformatics Source Type: research

Transcriptome and Regulatory Network Analyses of CD19-CAR-T Immunotherapy for B-ALL
In this study, we reported the transcriptome profiles of bone marrow cells in four B-cell acute lymphoblastic leukemia (B-ALL) patients before and after CD19-specific CAR-T therapy. CD19-CAR-T therapy remarkably reduced the number of leukemia cells, and three patients achieved bone marrow remission (minimal residual disease negative). The efficacy of CD19-CAR-T therapy on B-ALL was positively correlated with the abundance of CAR and immune cell subpopulations, e.g., CD8+ T cells and natural killer (NK) cells, in the bone marrow. Additionally, CD19-CAR-T therapy mainly influenced the expression of genes linked to cell cycle...
Source: Genomics, Proteomics and Bioinformatics - June 14, 2019 Category: Bioinformatics Source Type: research

SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data
Publication date: Available online 13 June 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xianwen Ren, Liangtao Zheng, Zemin ZhangAbstractClustering is a prevalent analytical means to analyze single cell RNA sequencing (scRNA-seq) data but the rapidly expanding data volume can make this process computationally challenging. New methods for both accurate and efficient clustering are of pressing needs. Here we proposed Spearman subsampling-clustering-classification (SSCC), a new clustering framework based on random projection and feature construction, for large-scale scRNA-seq data. SSCC greatly improves clus...
Source: Genomics, Proteomics and Bioinformatics - June 14, 2019 Category: Bioinformatics Source Type: research

H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development
Publication date: Available online 11 June 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xiaolong Chen, Youqiong Ye, Liang Gu, Jin Sun, Yanhua Du, Wen-Ju Liu, Wei Li, Xiaobai Zhang, Cizhong JiangAbstractDrosophila neural development undergoes extensive chromatin remodeling and precise epigenetic regulation. However, the roles of chromatin remodeling in establishment and maintenance of cell identity during cell fate transition remain enigmatic. Here, we compared the changes in gene expression, as well as the dynamics of nucleosome positioning and key histone modifications between the four major neural cell...
Source: Genomics, Proteomics and Bioinformatics - June 12, 2019 Category: Bioinformatics Source Type: research

m6A Regulates Neurogenesis and Neuronal Development by Modulating Histone Methyltransferase Ezh2
Publication date: Available online 30 May 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Junchen Chen, Yi-Chang Zhang, Chunmin Huang, Hui Shen, Baofa Sun, Xuejun Cheng, Yu-Jie Zhang, Yun-Gui Yang, Qiang Shu, Ying Yang, Xuekun LiAbstractN6-methyladenosine (m6A), catalyzed by the methyltransferase complex consisting of Mettl3 and Mettl14, is the most abundant RNA modification in mRNAs and participates in diverse biological processes. However, the roles and precise mechanisms of m6A modification in regulating neuronal development and adult neurogenesis remain unclear. Here, we examined the function of Mettl3,...
Source: Genomics, Proteomics and Bioinformatics - May 31, 2019 Category: Bioinformatics Source Type: research

Acknowledgments to Reviewers 2018
Publication date: February 2019Source: Genomics, Proteomics & Bioinformatics, Volume 17, Issue 1Author(s): (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 18, 2019 Category: Bioinformatics Source Type: research

9. 1st before inside back cover-Acknowledgements to Peer Reviewers 2018 E
Publication date: February 2019Source: Genomics, Proteomics & Bioinformatics, Volume 17, Issue 1Author(s): (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 15, 2019 Category: Bioinformatics Source Type: research

Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates
Publication date: Available online 14 May 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Valentina Galata, Cédric C. 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 KellerAbstractEmerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We...
Source: Genomics, Proteomics and Bioinformatics - May 15, 2019 Category: Bioinformatics Source Type: research

Deep Learning Deepens the Analysis of Alternative Splicing
Publication date: Available online 14 May 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Xudong Zou, Xin Gao, Wei Chen (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - May 15, 2019 Category: Bioinformatics Source Type: research

Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name
Publication date: Available online 7 May 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Huiyan Sun, Liang Chen, Sha Cao, Yanchun Liang, Ying XuAbstractIt has been observed that both cancer tissue cells and normal proliferating cells (NPCs) have the Warburg effect. Our goal here is to demonstrate that they do this for different reasons. To accomplish this, we have analyzed the transcriptomic data of over 7000 cancer and control tissues of 14 cancer types in TCGA and data of five NPC types in GEO. Our analyses reveal that NPCs accumulate large quantities of ATPs produced by the respiration process before sta...
Source: Genomics, Proteomics and Bioinformatics - May 7, 2019 Category: Bioinformatics Source Type: research

GPA: A Microbial Genetic Polymorphisms Assignments Tool in Metagenomic Analysis by Bayesian Estimation
Publication date: Available online 23 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Jiarui Li, Pengcheng Du, Adam Yongxin Ye, Yuanyuan Zhang, Chuan Song, Hui Zeng, Chen ChenAbstractIdentifying antimicrobial resistant (AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing (NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify gene...
Source: Genomics, Proteomics and Bioinformatics - May 1, 2019 Category: Bioinformatics Source Type: research

The Fast Track for Microbiome Research
Publication date: Available online 26 April 2019Source: Genomics, Proteomics & BioinformaticsAuthor(s): Kang Ning, Yigang Tong (Source: Genomics, Proteomics and Bioinformatics)
Source: Genomics, Proteomics and Bioinformatics - April 28, 2019 Category: Bioinformatics Source Type: research

Effects of Proton Pump Inhibitors on the Gastrointestinal Microbiota in Gastroesophageal Reflux Disease
We examined the association between the PPI usage and the microbiota present in gastric mucosal and fecal samples from GERD patients and healthy controls (HCs) using 16S rRNA gene sequencing. GERD patients taking PPIs were further divided into short-term and long- term PPI user groups. We showed that PPI administration lowered the relative bacterial diversity of the gastric microbiota in GERD patients. Compared to the non-PPI-user and HC groups, higher abundances of Planococcaceae, Oxalobacteraceae, and Sphingomonadaceae were found in the gastric microbiota from the PPI-user group. In addition, the Methylophilus genus was ...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment
We examined the relationships between gut microbiome profiles of ASD children and those of their mothers, and evaluated the clinical discriminatory power of discovered bacterial biomarkers. Gut microbiome was profiled and evaluated by 16S ribosomal RNA gene sequencing in stool samples of 59 mother–child pairs of ASD children and 30 matched mother–child pairs of healthy children. Significant differences were observed in the gut microbiome composition between ASD and healthy children in our Chinese cohort. Several unique bacterial biomarkers, such as Alcaligenaceae and Acinetobacter, were identified. Mothers of A...
Source: Genomics, Proteomics and Bioinformatics - April 25, 2019 Category: Bioinformatics Source Type: research