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Construction of a CRISPR-based paired-sgRNA library for chromosomal deletion of long non-coding RNAs 基于CRISPR的配对sgRNA文库的构建用于长非编码RNA的染色体缺失
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2020-03-01 DOI: 10.1007/s40484-020-0194-5
Minzhen Tao, Qiaochu Mu, Yurui Zhang, Zhen Xie
{"title":"Construction of a CRISPR-based paired-sgRNA library for chromosomal deletion of long non-coding RNAs","authors":"Minzhen Tao, Qiaochu Mu, Yurui Zhang, Zhen Xie","doi":"10.1007/s40484-020-0194-5","DOIUrl":"https://doi.org/10.1007/s40484-020-0194-5","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 1","pages":"31-42"},"PeriodicalIF":3.1,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0194-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41852931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Combination of versatile platforms for the development of synthetic biology 合成生物学发展的多功能平台组合
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2020-03-01 DOI: 10.1007/s40484-020-0197-2
Baizhu Chen, Zhuojun Dai
{"title":"Combination of versatile platforms for the development of synthetic biology","authors":"Baizhu Chen, Zhuojun Dai","doi":"10.1007/s40484-020-0197-2","DOIUrl":"https://doi.org/10.1007/s40484-020-0197-2","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 1","pages":"4-10"},"PeriodicalIF":3.1,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0197-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45721415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor ZokorDB:高原鼢鼠非编码元件的组织特异性调控网络注释
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2020-03-01 DOI: 10.1007/s40484-020-0195-4
Jingxue Xin, Junjun Hao, Lang Chen, Tao Zhang, Lei Li, Luonan Chen, Wenming Zhao, Xuemei Lu, Peng Shi, Yong Wang
{"title":"ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor","authors":"Jingxue Xin, Junjun Hao, Lang Chen, Tao Zhang, Lei Li, Luonan Chen, Wenming Zhao, Xuemei Lu, Peng Shi, Yong Wang","doi":"10.1007/s40484-020-0195-4","DOIUrl":"https://doi.org/10.1007/s40484-020-0195-4","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 1","pages":"43-50"},"PeriodicalIF":3.1,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0195-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48873282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Multi-chain Fudan-CCDC model for COVID-19-a revisit to Singapore's case. covid -19多链复旦- ccdc模式——对新加坡案例的重新审视。
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2020-01-01 Epub Date: 2020-11-23 DOI: 10.1007/s40484-020-0224-3
Hanshuang Pan, Nian Shao, Yue Yan, Xinyue Luo, Shufen Wang, Ling Ye, Jin Cheng, Wenbin Chen
{"title":"Multi-chain Fudan-CCDC model for COVID-19-a revisit to Singapore's case.","authors":"Hanshuang Pan,&nbsp;Nian Shao,&nbsp;Yue Yan,&nbsp;Xinyue Luo,&nbsp;Shufen Wang,&nbsp;Ling Ye,&nbsp;Jin Cheng,&nbsp;Wenbin Chen","doi":"10.1007/s40484-020-0224-3","DOIUrl":"https://doi.org/10.1007/s40484-020-0224-3","url":null,"abstract":"<p><strong>Background: </strong>COVID-19 has been impacting on the whole world critically and constantly since late December 2019. Rapidly increasing infections has raised intense worldwide attention. How to model the evolution of COVID-19 effectively and efficiently is of great significance for prevention and control.</p><p><strong>Methods: </strong>We propose the multi-chain Fudan-CCDC model based on the original single-chain model in [Shao et al. 2020] to describe the evolution of COVID-19 in Singapore. Multi-chains can be considered as the superposition of several single chains with different characteristics. We identify the parameters of models by minimizing the penalty function.</p><p><strong>Results: </strong>The numerical simulation results exhibit the multi-chain model performs well on data fitting. Though unsteady the increments are, they could still fall within the range of _30% fluctuation from simulation results.</p><p><strong>Conclusion: </strong>The multi-chain Fudan-CCDC model provides an effective way to early detect the appearance of imported infectors and super spreaders and forecast a second outbreak. It can also explain the data from those countries where the single-chain model shows deviation from the data.</p>","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 4","pages":"325-335"},"PeriodicalIF":3.1,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0224-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38312867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Differential methylation analysis for bisulfite sequencing using DSS. DSS对亚硫酸盐序列的差异甲基化分析。
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2019-12-31 Epub Date: 2019-12-15 DOI: 10.1007/s40484-019-0183-8
Hao Feng, Hao Wu
{"title":"Differential methylation analysis for bisulfite sequencing using DSS.","authors":"Hao Feng,&nbsp;Hao Wu","doi":"10.1007/s40484-019-0183-8","DOIUrl":"https://doi.org/10.1007/s40484-019-0183-8","url":null,"abstract":"<p><p>Bisulfite sequencing (BS-seq) technology measures DNA methylation at single nucleotide resolution. A key task in BS-seq data analysis is to identify differentially methylation (DM) under different conditions. Here we provide a tutorial for BS-seq DM analysis using Bioconductor package DSS. DSS uses a beta-binomial model to characterize the sequence counts from BS-seq, and implements rigorous statistical method for hypothesis testing. It provides flexible functionalities for a variety of DM analyses.</p>","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"7 4","pages":"327-334"},"PeriodicalIF":3.1,"publicationDate":"2019-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-019-0183-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38979346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 13
International Workshop on Applications of Probability and Statistics to Biology, July 11–13, 2019 概率论和统计学在生物学中的应用国际研讨会，2019年7月11-13日
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2019-12-20 DOI: 10.1007/s40484-019-0182-9
Minghua Deng, Jianfeng Feng, Hong Qian, Lin Wan, Fengzhu Sun
{"title":"International Workshop on Applications of Probability and Statistics to Biology, July 11–13, 2019","authors":"Minghua Deng, Jianfeng Feng, Hong Qian, Lin Wan, Fengzhu Sun","doi":"10.1007/s40484-019-0182-9","DOIUrl":"https://doi.org/10.1007/s40484-019-0182-9","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 1","pages":"177-186"},"PeriodicalIF":3.1,"publicationDate":"2019-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-019-0182-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42598989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Emerging deep learning methods for single-cell RNA-seq data analysis 用于单细胞RNA-seq数据分析的新兴深度学习方法
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2019-12-01 DOI: 10.1007/s40484-019-0189-2
Jie Zheng, Ke Wang
{"title":"Emerging deep learning methods for single-cell RNA-seq data analysis","authors":"Jie Zheng, Ke Wang","doi":"10.1007/s40484-019-0189-2","DOIUrl":"https://doi.org/10.1007/s40484-019-0189-2","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"7 1","pages":"247 - 254"},"PeriodicalIF":3.1,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-019-0189-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44179762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 25
A survey of some tensor analysis techniques for biological systems 生物系统张量分析技术综述
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2019-12-01 DOI: 10.1007/s40484-019-0186-5
Farzane Yahyanejad, R. Albert, B. Dasgupta
{"title":"A survey of some tensor analysis techniques for biological systems","authors":"Farzane Yahyanejad, R. Albert, B. Dasgupta","doi":"10.1007/s40484-019-0186-5","DOIUrl":"https://doi.org/10.1007/s40484-019-0186-5","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"7 1","pages":"266 - 277"},"PeriodicalIF":3.1,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-019-0186-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46061971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Molecular modeling studies of repandusinic acid as potent small molecule for hepatitis B virus through molecular docking and ADME analysis 通过分子对接和ADME分析，研究鼠戊二酸作为乙型肝炎病毒强效小分子的分子模型
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2019-12-01 DOI: 10.1007/s40484-019-0179-4
V. Subramaniyan, R. Sekar, A. Praveenkumar, Rajalakshmi Selvam
{"title":"Molecular modeling studies of repandusinic acid as potent small molecule for hepatitis B virus through molecular docking and ADME analysis","authors":"V. Subramaniyan, R. Sekar, A. Praveenkumar, Rajalakshmi Selvam","doi":"10.1007/s40484-019-0179-4","DOIUrl":"https://doi.org/10.1007/s40484-019-0179-4","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"7 1","pages":"302 - 312"},"PeriodicalIF":3.1,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-019-0179-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45397737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 4
WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning WEDeepT3:基于词嵌入和深度学习的III型分泌效应预测
IF 3.1 4区 生物学
Quantitative Biology Pub Date : 2019-12-01 DOI: 10.1007/s40484-019-0184-7
Xiaofeng Fu, Yang Yang
{"title":"WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning","authors":"Xiaofeng Fu, Yang Yang","doi":"10.1007/s40484-019-0184-7","DOIUrl":"https://doi.org/10.1007/s40484-019-0184-7","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"7 1","pages":"293 - 301"},"PeriodicalIF":3.1,"publicationDate":"2019-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-019-0184-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48921667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
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