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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 by ...
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 < 0.05). Use of the Protoarray platform uncovered over 300 novel autoAbs targeting a broad range of nuclear, cytoplasmic, and membrane antigens. Molecular interaction network analysis revealed that the antigens targeted by the autoAbs were most significantly enriched in ce...
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 the ...
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 (normal lung ...
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 six d...
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 problematic...
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 depressive di...
Source: Genomics, Proteomics and Bioinformatics - June 22, 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 conforming to stringent...
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′ un...
Source: Genomics, Proteomics and Bioinformatics - June 13, 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 13, 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 clusteri...
Source: Genomics, Proteomics and Bioinformatics - June 13, 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 typ...
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, the...
Source: Genomics, Proteomics and Bioinformatics - May 31, 2019 Category: Bioinformatics Source Type: research