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Single-cell Immune Landscape of Human Recurrent Miscarriage Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2021-01-19 Feiyang Wang; Wentong Jia; Mengjie Fan; Xuan Shao; Zhilang Li; Yongjie Liu; Yeling Ma; Yu-Xia Li; Rong Li; Qiang Tu; Yan-Ling Wang
Successful pregnancy in placental mammals substantially depends on the establishment of maternal immune tolerance to the semi-allogenic fetus. Disorders in this process are tightly associated with adverse pregnancy outcomes including recurrent miscarriage (RM). However, an in-depth understanding of the systematic and decidual immune environment in RM remains largely lacking. In this study, we utilized
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Kinase–substrate Edge Biomarkers Provide A More Accurate Prognostic Prediction in ER-negative Breast Cancer Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2021-01-13 Yidi Sun; Chen Li; Shichao Pang; Qianlan Yao; Luonan Chen; Yixue Li; Rong Zeng
The estrogen receptor (ER)-negative breast cancer subtype is aggressive with few treatment options available. To identify specific prognostic factors for ER-negative breast cancer, this study included 705,740 and 1034 breast invasive cancer patients from the Surveillance, Epidemiology, and End Results (SEER) and The Cancer Genome Atlas (TCGA) databases, respectively. To identify key kinase–substrate
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MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2021-01-06 Guocai Yao; Wenliang Zhang; Minglei Yang; Huan Yang; Jianbo Wang; Haiyue Zhang; Lai Wei; Zhi Xie; Weizhong Li
Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating
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Different Gene Networks are Disturbed by Zika Virus Infection in a Mouse Microcephaly Model Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2021-01-06 Yafei Chang; Yisheng Jiang; Cui Li; Qin Wang; Feng Zhang; Cheng-Feng Qin; Qing-Feng Wu; Jing Li; Zhiheng Xu
The association of Zika virus (ZIKV) infection with microcephaly has raised alarm worldwide. Their causal link has been confirmed in different animal models infected by ZIKV. However, the molecular mechanisms underlying ZIKV pathogenesis are far from clear. Hence, we performed global gene expression analysis of ZIKV-infected mouse brains to unveil the biological and molecular networks underpinning
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Comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-11-04 Zhichao Xu; Ranran Gao; Xiangdong Pu; Rong Xu; Jiyong Wang; Sihao Zheng; Yan Zeng; Jun Chen; Chunnian He; Jingyuan Song
Scutellaria baicalensis (S. baicalensis) and Scutellaria barbata (S. barbata) are common medicinal plants of the Lamiaceae family. Both produce specific flavonoid compounds, including baicalein, scutellarein, norwogonin, and wogonin, as well as their glycosides, which exhibit antioxidant and antitumor activities. Here, we report chromosome-level genome assemblies of S. baicalensis and S. barbata with
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Characterization of Lysine Monomethylome and Methyltransferase in Model Cyanobacterium Synechocystis sp. PCC 6803 Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-10-30 Xiaohuang Lin; Mingkun Yang; Xin Liu; Zhongyi Cheng; Feng Ge
Protein lysine methylation is a prevalent post-translational modification (PTM) and plays critical roles in all domains of life. However, its extent and function in photosynthetic organisms are still largely unknown. Cyanobacteria are a large group of prokaryotes that carry out oxygenic photosynthesis and are applied extensively in studies of photosynthetic mechanisms and environmental adaptation.
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Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-11-02 Liya Zhu; Han Cheng; Guoqing Peng; Shuansuo Wang; Zhiguo Zhang; Erdong Ni; Xiangdong Fu; Chuxiong Zhuang; Zexian Liu; Hai Zhou
Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest
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Genome Size Evolution Mediated by Gypsy Retrotransposons in Brassicaceae Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-10-31 Shi-Jian Zhang; Lei Liu; Ruolin Yang; Xiangfeng Wang
The dynamic activity of transposable elements (TEs) contributes to the vast diversity of genome size and architecture among plants. Here, we examined the genomic distribution and transposition activity of long terminal repeat retrotransposons (LTR-RTs) in Arabidopsis thaliana (Ath) and three of its relatives, Arabidopsis lyrata (Aly), Eutrema salsugineum (Esa), and Schrenkiella parvula (Spa), in Brassicaceae
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Paleo-polyploidization in Lycophytes Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-11-04 Jinpeng Wang; Jigao Yu; Pengchuan Sun; Chao Li; Xiaoming Song; Tianyu Lei; Yuxian Li; Jiaqing Yuan; Sangrong Sun; Hongling Ding; Xueqian Duan; Shaoqi Shen; Yanshuang Shen; Jing Li; Fanbo Meng; Yangqin Xie; Jianyu Wang; Yue Hou; Xiyin Wang
Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring approximately 13–15 million years ago (MYA) and another
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CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-11-04 Peijing Zhang; Yongjing Liu; Hongjun Chen; Xianwen Meng; Jitong Xue; Kunsong Chen; Ming Chen
The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods
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Pooled Plasmid Sequencing Reveals the Relationship Between Mobile Genetic Elements and Antimicrobial Resistance Genes in Clinically Isolated Klebsiella pneumoniae Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-30 Yan Jiang; Yanfei Wang; Xiaoting Hua; Yue Qu; Anton Y. Peleg; Yunsong Yu
Plasmids remain important microbial components mediating the horizontal gene transfer (HGT) and dissemination of antimicrobial resistance. To systematically explore the relationship between mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), a novel strategy using single-molecule real time (SMRT) sequencing was developed. This approach was applied to pooled conjugative plasmids
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Landscape and Dynamics of the Transcriptional Regulatory Network During Natural Killer Cell Differentiation Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-30 Kun Li; Yang Wu; Young Li; Qiaoni Yu; Zhigang Tian; Haiming Wei; Kun Qu
Natural killer (NK) cells are essential in controlling cancer and infection. However, little is known about the dynamics of the transcriptional regulatory machinery during NK cell differentiation. In this study, we applied assay of transposase accessible chromatin with sequencing (ATAC-seq) technique in a home-developed in vitro NK cell differentiation system. Analysis of ATAC-seq data illustrated
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Large-scale Proteomic and Phosphoproteomic Analysis of Maize Seedling Leaves During De-etiolation Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-30 Zhi-Fang Gao; Zhuo Shen; Qing Chao; Zhen Yan; Xuan-Liang Ge; Tiancong Lu; Haiyan Zheng; Chun-Rong Qian; Bai-Chen Wang
De-etiolation consists of a series of developmental and physiological changes that a plant undergoes in response to light. During this process light, an important environmental signal, triggers the inhibition of mesocotyl elongation and the production of photosynthetically active chloroplasts, and etiolated leaves transition from the “sink” stage to the “source” stage. De-etiolation has been extensively
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The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-28 Shuhui Song; Lina Ma; Dong Zou; Dongmei Tian; Cuiping Li; Junwei Zhu; Meili Chen; Anke Wang; Yingke Ma; Mengwei Li; Xufei Teng; Ying Cui; Guangya Duan; Mochen Zhang; Tong Jin; Chengmin Shi; Zhenglin Du; Yadong Zhang; Yiming Bao
On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added
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The Wolfiporia cocos Genome and Transcriptome Shed Light on the Formation of Its Edible and Medicinal Sclerotium Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-24 Hongmei Luo; Jun Qian; Zhichao Xu; Wanjing Liu; Lei Xu; Ying Li; Jiang Xu; Jianhong Zhang; Xiaolan Xu; Chang Liu; Liu He; Jianqin Li; Chao Sun; Francis Martin; Jingyuan Song; Shilin Chen
Wolfiporia cocos (F. A. Wolf) has been praised as a food delicacy and medicine for centuries in China. Here, we present the genome and transcriptome of the Chinese strain CGMCC5.78 of W. cocos. High-confidence functional prediction was made for 9277 genes among the 10,908 total predicted gene models in the W. cocos genome. Up to 2838 differentially expressed genes (DEGs) were identified to be related
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Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient Berberine Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-24 Xizhan Xu; Zezheng Gao; Fuquan Yang; Yingying Yang; Liang Chen; Lin Han; Na Zhao; Jiayue Xu; Xinmiao Wang; Yue Ma; Lian Shu; Xiaoxi Hu; Na Lyu; Yuanlong Pan; Baoli Zhu; Linhua Zhao; Xiaolin Tong; Jun Wang
Gegen Qinlian Decoction (GQD), a traditional Chinese medicine (TCM) formula, has long been used for the treatment of common metabolic diseases, including type 2 diabetes mellitus. However, the main limitation of its wider application is ingredient complexity of this formula. Thus, it is critically important to identify the major active ingredients of GQD and to illustrate mechanisms underlying its
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Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-24 Qianhui Huang; Yu Liu; Yuheng Du; Lana X. Garmire
Annotating cell types is a critical step in single-cell RNA sequencing (scRNA-seq) data analysis. Some supervised or semi-supervised classification methods have recently emerged to enable automated cell type identification. However, comprehensive evaluations of these methods are lacking. Moreover, it is not clear whether some classification methods originally designed for analyzing other bulk omics
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scLM: Automatic Detection of Consensus Gene Clusters Across Multiple Single-cell Datasets Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-24 Qianqian Song; Jing Su; Lance D. Miller; Wei Zhang
In gene expression profiling studies, including single-cell RNA-seq (scRNA-seq) analyses, the identification and characterization of co-expressed genes provides critical information on cell identity and function. Gene co-expression clustering in scRNA-seq data presents certain challenges. We show that commonly used methods for single cell data are not capable of identifying co-expressed genes accurately
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SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-18 JeeEun Kang; Antonio Ciampi; Mohamed Hijri
Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that play key roles in plant growth and soil fertility. They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores. Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia, resulting in a metagenome when whole-genome sequencing (WGS) data are obtained from sequencing
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SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-18 Jee Eun Kang; Antonio Ciampi; Mohamed Hijri
In this article, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes Position-Specific Function (SeSaMe PS Function), for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi. The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from
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mrMLM v4.0: An R Platform for Multi-locus Genome-wide Association Studies Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-18 Ya-Wen Zhang; Cox Lwaka Tamba; Yang-Jun Wen; Pei Li; Wen-Long Ren; Yuan-Li Ni; Jun Gao; Yuan-Ming Zhang
Previous studies reported that some important loci are missed in single-locus genome-wide association studies (GWAS), especially because of the large phenotypic error in field experiments. To solve this issue, multi-locus GWAS methods have been recommended. However, only a few software packages for multi-locus GWAS are available. Therefore, we developed an R software named mrMLM v4.0. This software
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Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-18 Jun Wang; Xiaowen Chen; Funan He; Xiao Song; Shu Huang; Wucheng Yue; Yipei Chen; Zhixi Su; Chenghui Wang
Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in Crustacea. Functional analysis, although essential, has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, transcriptome sequencing was conducted on 59 samples representing diverse developmental stages (fertilized eggs, zoea, megalopa, three sub-stages of larvae, juvenile crabs
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Denoising Autoencoder, a Deep Learning Algorithm, Aids the Identification of a Novel Molecular Signature of Lung Adenocarcinoma Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-18 Jun Wang; Xueying Xie; Junchao Shi; Wenjun He; Qi Chen; Liang Chen; Wanjun Gu; Tong Zhou
Precise biomarker development is a key step in disease management. However, most of the published biomarkers were derived from a relatively small number of samples with supervised approaches. Recent advances in unsupervised machine learning promise to leverage very large datasets for making better predictions of disease biomarkers. Denoising autoencoder (DA) is one of the unsupervised deep learning
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Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-18 Arup Panda; Tamir Tuller
Intrinsically disordered proteins (IDPs) are an important class of proteins in all domains of life for their functional importance. However, how nature has shaped the disorder potential of prokaryotic and eukaryotic proteins is still not clearly known. Randomly generated sequences are free of any selective constraints thus these sequences are commonly used as null models. Considering different types
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The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-16 Monika Hiller; Miriam Geissler; George Janssen; Peter van Veelen; Annemieke Aartsma-Rus; Pietro Spitali
Muscle formation is a coordinated process driven by extensive gene expression changes where single cells fuse together to form multinucleated muscle fibers. Newly synthesized mRNAs are then regulated by RNA binding proteins (RBPs), affecting post-transcriptional transcript metabolism. Here, we determined how large-scale gene expression changes affect the catalog of RBPs by studying proliferating and
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Tissue-specific Gene Expression Changes Are Associated with Aging in Mice Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-11 Akash Srivastava; Emanuel Barth; Maria A. Ermolaeva; Madlen Guenther; Christiane Frahm; Manja Marz; Otto W. Witte
Aging is a complex process that can be characterized by functional and cognitive decline in an individual. Aging can be assessed based on the functional capacity of vital organs and their intricate interactions with one another. Thus, the nature of aging can be described by focusing on a specific organ and an individual itself. However, to fully understand the complexity of aging, one must investigate
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Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-08 Grace E. Lidgerwood; Anne Senabouth; Casey J.A. Smith-Anttila; Vikkitharan Gnanasambandapillai; Dominik C. Kaczorowski; Daniela Amann-Zalcenstein; Erica L. Fletcher; Shalin H. Naik; Alex W. Hewitt; Joseph E. Powell; Alice Pébay
Human pluripotent stem cell (hPSC)-derived progenies are immature versions of cells, presenting a potential limitation to the accurate modelling of diseases associated with maturity or age. Hence, it is important to characterise how closely cells used in culture resemble their native counterparts. In order to select appropriate time points of retinal pigment epithelium (RPE) cultures that reflect native
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G9a/GLP-Sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-12-05 Zixiang Yan; Luzhang Ji; Xiangru Huo; Qianfeng Wang; Yuwen Zhang; Bo Wen
In the nucleus, chromatin is folded into hierarchical architecture that is tightly linked to various nuclear functions. However, the underlying molecular mechanisms that confer these architectures remain incompletely understood. Here, we investigated the functional roles of H3 lysine 9 dimethylation (H3K9me2), one of the abundant histone modifications, in three-dimensional (3D) genome organization
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Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-11-25 Shan Chi; Guoliang Wang; Tao Liu; Xumin Wang; Cui Liu; Yuemei Jin; Hongxin Yin; Xin Xu; Jun Yu
As a carbon-storage compound and osmoprotectant in brown algae, mannitol is synthesized and then accumulated at high levels in Saccharina japonica (Sja); however, the underlying control mechanisms have not been studied. Our analysis of genomic and transcriptomic data from Sja shows that mannitol metabolism is a cyclic pathway composed of four distinct steps. A mannitol-1-phosphate dehydrogenase (M1PDH2)
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m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-11-05 Yuhuan Li; Qingyang Zhang; Guanshen Cui; Fang Zhao; Xin Tian; Bao-Fa Sun; Ying Yang; Wei Li
N6-methyladenosine (m6A) is one of the most abundant modifications on mRNAs and plays important roles in various biological processes. The formation of m6A is catalyzed by a methyltransferase complex (MTC) containing a key factor methyltransferase-like 3 (Mettl3). However, the functions of Mettl3 and m6A modification in hepatic lipid and glucose metabolism remain unclear. Here, we showed that both
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hTFtarget: A Comprehensive Database for Regulations of Human Transcription Factors and Their Targets. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-08-26 Qiong Zhang,Wei Liu,Hong-Mei Zhang,Gui-Yan Xie,Ya-Ru Miao,Mengxuan Xia,An-Yuan Guo
Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF–target regulatory relationships is a key step for revealing functions of TFs and their regulations on gene expression. The accumulated data of chromatin immunoprecipitation sequencing (ChIP-seq) provide great opportunities to discover the TF–target regulations across different conditions
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MosaicBase: A Knowledgebase of Postzygotic Mosaic Variants in Noncancer Disease-related and Healthy Human Individuals. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-09-08 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
Mosaic variants resulting from postzygotic mutations are prevalent in the human genome and play important roles in human diseases. However, except for cancer-related variants, there is no collection of postzygotic mosaic variants in noncancer disease-related and healthy individuals. Here, we present MosaicBase, a comprehensive database that includes 6698 mosaic variants related to 266 noncancer diseases
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iGMDR: Integrated Pharmacogenetic Resource Guide to Cancer Therapy and Research. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-09-08 Xiang Chen,Yi Guo,Xin Chen
Current pharmacogenetic studies have obtained many genetic models that can predict the therapeutic efficacy of anticancer drugs. Although some of these models are of crucial importance and have been used in clinical practice, these very valuable models have not been well adopted into cancer research to promote the development of cancer therapies due to the lack of integration and standards for the
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HybridSucc: A Hybrid-learning Architecture for General and Species-specific Succinylation Site Prediction. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-08-28 Wanshan Ning,Haodong Xu,Peiran Jiang,Han Cheng,Wankun Deng,Yaping Guo,Yu Xue
As an important protein acylation modification, lysine succinylation (Ksucc) is involved in diverse biological processes, and participates in human tumorigenesis. Here, we collected 26,243 non-redundant known Ksucc sites from 13 species as the benchmark data set, combined 10 types of informative features, and implemented a hybrid-learning architecture by integrating deep-learning and conventional machine-learning
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iLBE for Computational Identification of Linear B-cell Epitopes by Integrating Sequence and Evolutionary Features Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-10-22 Md. Mehedi Hasan; Mst. Shamima Khatun; Hiroyuki Kurata
Linear B-cell epitopes are critically important for immunological applications, such as vaccine design, immunodiagnostic test, antibody production, as well as disease diagnosis and therapy. The accurate identification of linear B-cell epitopes remains challenging despite several decades of research. In this work, we have developed a novel predictor, Identification of B-Cell Epitope (iLBE), by integrating
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PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-10-17 Song He; Yuqi Wen; Xiaoxi Yang; Zhen Liu; Xinyu Song; Xin Huang; Xiaochen Bo
The accumulation of various types of drug informatics data and computational approaches for drug repositioning can accelerate pharmaceutical research and development. However, the integration of multi-dimensional drug data for precision repositioning remains a pressing challenge. Here, we propose a systematic framework named PIMD to predict drug therapeutic properties by integrating multi-dimensional
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Corrigendum to "Antibiotic Treatment Drives the Diversification of the Human Gut Resistome" [Genomics Proteomics Bioinformatics 17 (1) (2019) 39-51]. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-09-08 Jun Li,Elizabeth A Rettedal,Eric van der Helm,Mostafa Ellabaan,Gianni Panagiotou,Morten O A Sommer
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Long Non-coding RNA Derived from lncRNA-mRNA Co-expression Networks Modulates the Locust Phase Change. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-08-29 Ting Li,Bing Chen,Pengcheng Yang,Depin Wang,Baozhen Du,Le Kang
Long non-coding RNAs (lncRNAs) regulate various biological processes ranging from gene expression to animal behavior. Although protein-coding genes, microRNAs, and neuropeptides play important roles in the regulation of phenotypic plasticity in migratory locust, empirical studies on the function of lncRNAs in this process remain limited. Here, we applied high-throughput RNA-seq to compare the expression
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The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-08-19 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
Identification of genetic variants via high-throughput sequencing (HTS) technologies has been essential for both fundamental and clinical studies. However, to what extent the genome sequence composition affects variant calling remains unclear. In this study, we identified 63,897 multi-copy sequences (MCSs) with a minimum length of 300 bp, each of which occurs at least twice in the human genome. The
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Ambient Temperature is A Strong Selective Factor Influencing Human Development and Immunity. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-08-19 Lindan Ji,Dongdong Wu,Haibing Xie,Binbin Yao,Yanming Chen,David M Irwin,Dan Huang,Jin Xu,Nelson L S Tang,Yaping Zhang
Solar energy, which is essential for the origin and evolution of all life forms on Earth, can be objectively recorded as attributes such as climatic ambient temperature (CAT), ultraviolet radiation (UVR), and sunlight duration (SD). These attributes have specific geographical variations and may cause different adaptation traits. However, the adaptation profile of each attribute and the selective role
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DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-08-12 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 Le Large,Jacqueline Cloos,Anna Wojtuszkiewicz,Danijela Koppers-Lalic,Franziska Böttger,Chantal Scheepbouwer,Ruud H Brakenhoff,Geert J L H van Leenders,Jan N M Ijzermans,John W M Martens
To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted
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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]. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-08-01 Yue-Feng Wang,Qing Chao,Zhe Li,Tian-Cong Lu,Hai-Yan Zheng,Cai-Feng Zhao,Zhuo Shen,Xiao-Hui Li,Bai-Chen Wang
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From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-07-30 Jun Yu
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Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-05-21 Shahzina Kanwal,Xiangpeng Guo,Carl Ward,Giacomo Volpe,Baoming Qin,Miguel A Esteban,Xichen Bao
The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions. This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome. Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long non-coding RNAs
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Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-07-28 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
Significantly increasing crop yield is a major and worldwide challenge for food supply and security. It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide. Yet, the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery. Here, we systematically collected the transcriptome data for seven key tissues at different developmental
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Na2CO3-responsive Photosynthetic and ROS Scavenging Mechanisms in Chloroplasts of Alkaligrass Revealed by Phosphoproteomics. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-07-16 Jinwei Suo,Heng Zhang,Qi Zhao,Nan Zhang,Yongxue Zhang,Ying Li,Baohua Song,Juanjuan Yu,Jianguo Cao,Tai Wang,Ji Luo,Lihai Guo,Jun Ma,Xumin Zhang,Yimin She,Lianwei Peng,Weimin Ma,Siyi Guo,Yuchen Miao,Sixue Chen,Zhi Qin,Shaojun Dai
Alkali-salinity exerts severe osmotic, ionic, and high-pH stresses to plants. To understand the alkali-salinity responsive mechanisms underlying photosynthetic modulation and reactive oxygen species (ROS) homeostasis, physiological and diverse quantitative proteomics analyses of alkaligrass (Puccinellia tenuiflora) under Na2CO3 stress were conducted. In addition, Western blot, real-time PCR, and transgenic
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IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-07-16 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
Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp
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Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-07-12 Qi Liu,Shilei Zhao,Cheng-Min Shi,Shuhui Song,Sihui Zhu,Yankai Su,Wenming Zhao,Mingkun Li,Yiming Bao,Yongbiao Xue,Hua Chen
A novel RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the ongoing outbreak of coronavirus disease 2019 (COVID-19). Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19. However, due to extensive sampling bias and existence of infection clusters during the epidemic spread, direct applications
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Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-07-09 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
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SR4R: An Integrative SNP Resource for Genomic Breeding and Population Research in Rice. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-06-30 Jun Yan,Dong Zou,Chen Li,Zhang Zhang,Shuhui Song,Xiangfeng Wang
The information commons for rice (IC4R) database is a collection of 18 million single nucleotide polymorphisms (SNPs) identified by resequencing of 5152 rice accessions. Although IC4R offers ultra-high density rice variation map, these raw SNPs are not readily usable for the public. To satisfy different research utilizations of SNPs for population genetics, evolutionary analysis, association studies
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SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-06-24 Hui-Ju Kao,Van-Nui Nguyen,Kai-Yao Huang,Wen-Chi Chang,Tzong-Yi Lee
Protein succinylation is a biochemical reaction in which a succinyl group (-CO-CH2-CH2-CO-) is attached to the lysine residue of a protein molecule. Lysine succinylation plays important regulatory roles in living cells. However, studies in this field are limited by the difficulty in experimentally identifying the substrate site specificity of lysine succinylation. To facilitate this process, several
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The Battle to Sequence the Bread Wheat Genome: A Tale of the Three Kingdoms. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-06-17 Jiantao Guan,Diego F Garcia,Yun Zhou,Rudi Appels,Aili Li,Long Mao
In the year 2018, the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop, the common wheat. Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature. A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries, taking a conventional strategy similar to that for sequencing
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Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-06-17 Yuan Liang,Dengxue Lu,Sen Wang,Yuhui Zhao,Shenghan Gao,Rongbing Han,Jun Yu,Weili Zheng,Jianing Geng,Songnian Hu
Agrocybe cylindracea, an edible mushroom, is widely cultivated for its abundance of nutrients and flavor, and many of its metabolites are reported to have beneficial roles, such as medicinal effects on tumors and chronical illnesses. However, the lack of genomic information has hindered further molecular studies on this fungus. Here, we present a genome assembly of A. cylindracea together with comparative
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BGVD: An Integrated Database for Bovine Sequencing Variations and Selective Signatures. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-06-12 Ningbo Chen,Weiwei Fu,Jianbang Zhao,Jiafei Shen,Qiuming Chen,Zhuqing Zheng,Hong Chen,Tad S Sonstegard,Chuzhao Lei,Yu Jiang
Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD)
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MicroRNAs Are Involved in Maize Immunity Against Fusarium verticillioides Ear Rot. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-06-10 Zijian Zhou,Yan Cao,Tao Li,Xinghao Wang,Jiafa Chen,Hang He,Wen Yao,Jianyu Wu,Huiyong Zhang
Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the most common diseases affecting maize production worldwide. FER results in severe yield losses and grain contamination with health-threatening mycotoxins. Although most studies to date have focused on comprehensive analysis of gene regulation in maize during defense responses against F. verticillioides infection, less is known about
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IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-06-06 Jian Zhao,Yan Li,Cong Wang,Haotian Zhang,Hao Zhang,Bin Jiang,Xuejiang Guo,Xiaofeng Song
Internal ribosome entry sites (IRESs) are functional RNA elements that can directly recruit ribosomes to an internal position of the mRNA in a cap-independent manner to initiate translation. Recently, IRES elements have attracted much attention for their critical roles in various processes including translation initiation of a new type of RNA, circular RNA (circRNA), with no 5′ cap to support classical
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The Birth of Bio-data Science: Trends, Expectations, and Applications. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-05-16 Wilson Wen Bin Goh,Limsoon Wong
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SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-05-16 Yongzhe Ren,Yang Zhang,Dandan Wang,Fengying Liu,Ying Fu,Shaohua Xiang,Li Su,Jiancheng Li,Heng Dai,Bingding Huang
Accurate detection of low frequency mutations from plasma cell-free DNA in blood using targeted next generation sequencing technology has shown promising benefits in clinical settings. Duplex sequencing technology is the most commonly used approach in liquid biopsies. Unique molecular identifiers are attached to each double-stranded DNA template, followed by production of low-error consensus sequences
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CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma. Genom. Proteom. Bioinform. (IF 7.051) Pub Date : 2020-05-13 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
BRAF is a serine/threonine kinase that harbors activating mutations in ∼7% of human malignancies and ∼60% of melanomas. Despite initial clinical responses to BRAF inhibitors, patients frequently develop drug resistance. To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma, we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired