Quantitative Biology最新文献

{"title":"Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data.","authors":"Lin Wan,&nbsp;Xin Kang,&nbsp;Jie Ren,&nbsp;Fengzhu Sun","doi":"10.1007/s40484-020-0200-y","DOIUrl":"https://doi.org/10.1007/s40484-020-0200-y","url":null,"abstract":"<p><strong>Background: </strong>Markov chains (MC) have been widely used to model molecular sequences. The estimations of MC transition matrix and confidence intervals of the transition probabilities from long sequence data have been intensively studied in the past decades. In next generation sequencing (NGS), a large amount of short reads are generated. These short reads can overlap and some regions of the genome may not be sequenced resulting in a new type of data. Based on NGS data, the transition probabilities of MC can be estimated by moment estimators. However, the classical asymptotic distribution theory for MC transition probability estimators based on long sequences is no longer valid.</p><p><strong>Methods: </strong>In this study, we present the asymptotic distributions of several statistics related to MC based on NGS data. We show that, after scaling by the effective coverage <i>d</i> defined in a previous study by the authors, these statistics based on NGS data approximate to the same distributions as the corresponding statistics for long sequences.</p><p><strong>Results: </strong>We apply the asymptotic properties of these statistics for finding the theoretical confidence regions for MC transition probabilities based on NGS short reads data. We validate our theoretical confidence intervals using both simulated data and real data sets, and compare the results with those by the parametric bootstrap method.</p><p><strong>Conclusions: </strong>We find that the asymptotic distributions of these statistics and the theoretical confidence intervals of transition probabilities based on NGS data given in this study are highly accurate, providing a powerful tool for NGS data analysis.</p>","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"8 2","pages":"143-154"},"PeriodicalIF":3.1,"publicationDate":"2020-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0200-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39185013","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":"DNA sequencing using nanopores and kinetic proofreading","authors":"X. Ling","doi":"10.1007/s40484-020-0201-x","DOIUrl":"https://doi.org/10.1007/s40484-020-0201-x","url":null,"abstract":"","PeriodicalId":45660,"journal":{"name":"Quantitative Biology","volume":"1 1","pages":"1-8"},"PeriodicalIF":3.1,"publicationDate":"2020-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s40484-020-0201-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49224985","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":"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}