Quantitative Biology最新文献

{"title":"Transcriptome-wide association studies: a view from Mendelian randomization","authors":"Huanhuan Zhu, Xiang Zhou","doi":"10.1007/s40484-020-0207-4","DOIUrl":"https://doi.org/10.1007/s40484-020-0207-4","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":"1-15"},"PeriodicalIF":3.1,"publicationDate":"2020-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0207-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45821382","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}

{"title":"Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins.","authors":"Jianan Lin,&nbsp;Zhengqing Ouyang","doi":"10.1007/s40484-020-0206-5","DOIUrl":"https://doi.org/10.1007/s40484-020-0206-5","url":null,"abstract":"<p><strong>Background: </strong>RNA binding proteins (RBPs) play essential roles in the regulation of RNA metabolism. Recent studies have disclosed that RBPs achieve their functions via binding to their targets in a position-dependent pattern on RNAs. However, few studies have systematically addressed the associations between the RBP's functions and their positional binding preferences.</p><p><strong>Methods: </strong>Here, we present large-scale analyses on the functional targets of human RBPs by integrating the enhanced cross-linking and immunoprecipitation followed by sequencing (eCLIP-seq) datasets and the shRNA knockdown followed by RNA-seq datasets that are deposited in the integrated ENCyclopedia of DNA Elements in the human genome (ENCODE) data portal.</p><p><strong>Results: </strong>We found that (1) binding to the translation termination site and the 3'untranslated region is important to most human RBPs in the RNA decay regulation; (2) RBPs' binding and regulation follow a cell-type specific pattern.</p><p><strong>Conclusions: </strong>These analysis results show the strong relationship between the binding position and the functions of RBPs, which provides novel insights into the RBPs' regulation mechanisms.</p>","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 2","pages":"119-129"},"PeriodicalIF":3.1,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0206-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39150713","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}

{"title":"A censored-Poisson model based approach to the analysis of RNA-seq data","authors":"Xing Chen, Y. Lai","doi":"10.1007/s40484-020-0208-3","DOIUrl":"https://doi.org/10.1007/s40484-020-0208-3","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":"1-17"},"PeriodicalIF":3.1,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0208-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47639660","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}

{"title":"Prediction and differential analysis of RNA secondary structure","authors":"Bo Yuan, Yao Lu, Q. Zhang, Lin Hou","doi":"10.1007/s40484-020-0205-6","DOIUrl":"https://doi.org/10.1007/s40484-020-0205-6","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":"1-10"},"PeriodicalIF":3.1,"publicationDate":"2020-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0205-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47773580","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}

{"title":"Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data","authors":"Rongbin Zheng, Xin Dong, Changxin Wan, Xiaoying Shi, Xiaoyan Zhang, Clifford A. Meyer","doi":"10.1007/s40484-020-0204-7","DOIUrl":"https://doi.org/10.1007/s40484-020-0204-7","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 1","pages":"267-276"},"PeriodicalIF":3.1,"publicationDate":"2020-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0204-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48020516","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}

{"title":"Applications of probability and statistics in cancer genomics","authors":"Xiaotu Ma, Sasi Arunachalam, Yanling Liu","doi":"10.1007/s40484-020-0203-8","DOIUrl":"https://doi.org/10.1007/s40484-020-0203-8","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":"1-14"},"PeriodicalIF":3.1,"publicationDate":"2020-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0203-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45840074","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}

{"title":"Infrared imageries of human body activated by teas indicate the existence of meridian system","authors":"Wenli Jin, Yi Tao, Chen Wang, Lufei Wang, Xue Ao, Mingjie Su, Binwei Hu, Yuxiao Ouyang, Jiaxing Liu, Hui Li","doi":"10.21203/rs.3.rs-20030/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-20030/v1","url":null,"abstract":"\u0000 BackgroundHuman meridian (Jingluo) system was hypothesized by traditional Chinese medicine (TCM) for thousands of years. In this hypothesis, there believed to be twelve formal meridian channels going through respective organs, carrying fluid and energy, and laying thermal effects. Some treatments based on meridians have been proved effective. However, existence of meridians has never been confirmed. The infrared photograph was employed to display the picture to the meridians since 1970. Unfortunately, no satisfactory results have been obtained. We think that only when a certain meridian is activated will there be thermal effect for successful infrared photograph.Methods We selected thirteen types of tea out of the herbs to activate the hypothesized twelve meridians for imagery taking. We collected 42 volunteers to drink teas and take infrared imageries in thirteen days. After every tea was drunk, infrared imageries of the human bodies were taken immediately. The highest temperatures of the fingers, palms, and above the organs were derived from the imageries. The averages and standard deviations of the standardized data of volunteers were calculated. Significances of the temperature difference among the body areas after drinking different teas were evaluated. ResultsWe found that the temperatures of the organs and fingers possibly connected by twelve hypothesized meridians rose together significantly, i.e., the thumbs and lung after white teas, index fingers and colon after blue teas, middle fingers and thymus after dark black teas, ring fingers and gallbladder after red black teas, little fingers and heart after yellow teas. The temperature distribution on the human bodies exhibited twelve patterns following the meridian hypothesis. Infrared imageries showed quite clear shapes of the organs activated by the teas, e.g., heart and kidneys by yellow teas, thymus by dark black teas, lungs and spleen by white teas, gallbladder and thyroid by red black teas, etc. Some high temperature lines also matched the hypothetic meridians. ConclusionsOur work displayed the imageries of the possible meridians for the first time, and proved with data that different foods may activate different organs following the meridian hypothesis, shedding light on a possible new method of targeted drug designs.","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":""},"PeriodicalIF":3.1,"publicationDate":"2020-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45278489","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}

{"title":"A pan-cancer integrative pathway analysis of multi-omics data","authors":"Henry Linder, Yuping Zhang","doi":"10.1007/s40484-019-0185-6","DOIUrl":"https://doi.org/10.1007/s40484-019-0185-6","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":"1-13"},"PeriodicalIF":3.1,"publicationDate":"2020-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-019-0185-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45967454","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}

{"title":"Chao Tang: a self-motivated scientist pursues interdisciplinary excellence","authors":"Ya-Yuan Huang, Yimeng Ye, Jiang Zhang","doi":"10.1007/s40484-020-0198-1","DOIUrl":"https://doi.org/10.1007/s40484-020-0198-1","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 1","pages":"1-3"},"PeriodicalIF":3.1,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0198-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46843924","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}

{"title":"Quantifying E2F1 protein dynamics in single cells.","authors":"Bernard Mathey-Prevot,&nbsp;Bao-Tran Parker,&nbsp;Carolyn Im,&nbsp;Cierra Hong,&nbsp;Peng Dong,&nbsp;Guang Yao,&nbsp;Lingchong You","doi":"10.1007/s40484-019-0193-6","DOIUrl":"https://doi.org/10.1007/s40484-019-0193-6","url":null,"abstract":"<p><strong>Background: </strong>E2F1 protein, a major effector of the Rb/E2F pathway plays a central role in regulating cell-fate decisions involved in proliferation, apoptosis, and differentiation. Its expression is highly dynamic and tightly modulated through a combination of transcriptional, translational and posttranslational controls. However, the mechanisms by which its expression and activity can promote different cellular outcomes remain to be fully elucidated. To better document E2F1 expression in live cells, we have engineered a series of fluorescent E2F1 protein reporters that quantitatively capture E2F1 protein dynamics.</p><p><strong>Methods: </strong>Reporter constructs, under the control of the mouse or human E2F1 proximal promoter, were designed to express an E2F1-Venus fusion protein incapable of binding DNA. In addition, constructs either included or excluded the 3' untranslated region (3'UTR) of the <i>E2F1</i> gene. These constructs were introduced into fibroblasts and epithelial cells, and expression of the fusion reporter protein was validated and quantified in single cells using live imaging.</p><p><strong>Results: </strong>In all cases, expression of the reporter protein effectively recapitulated the behavior of E2F1 under various conditions, including cell cycle progression and genotoxic stress. No or little fluorescent signal of the reporter was detected in G₀, but as the cycle progressed, expression of the reporter protein steadily increased in the nucleus, peaking a few hours before cell division, but declining to baseline 2-3 h prior to the onset of mitosis. The absence of the E2F1 3'UTR in the constructs led to considerably higher steady-state levels of the fusion protein, which although normally regulated, exhibited a slightly less complex dynamic profile during the cell cycle or genotoxic stress. Lastly, the presence or absence of Rb failed to impact the overall detection and levels of the reporter proteins.</p><p><strong>Conclusions: </strong>Our validated E2F1 protein reporters complement nicely other reporters of the Rb/E2F pathway and provide a unique tool to follow the complex dynamics of E2F1 expression in real time in single cells.</p>","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 1","pages":"20-30"},"PeriodicalIF":3.1,"publicationDate":"2020-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-019-0193-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38047393","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}