1,720,961 research outputs found
Incorporating sequence motifs to improve accuracy of predicting transcription factor binding sites using ChIP-seq data
No full text染色質免疫沉澱定序技術，是用來尋找特定蛋白，例如轉錄因子，與其調控的基因一種方法，藉由這種技術我們可以大略的知道轉錄因子在人體DNA片段上的位置，然而這些被找到的轉錄因子結合位點的準確率尚未曾有研究做過系統性的討論。因此，本論文裡用TRANSFAC資料庫提供之已知的轉錄因子結合位點，針對染色質免疫沉澱技術鑑定之不同信心程度(FDR)下的轉錄因子結合位點進行整體性的預測表現評估，並輔以序列特徵資訊，增進其預測準確度。本論文使用了ENCODE資料庫的染色免疫沉澱資料來進行分析，且挑選了擁有不同細胞株的轉錄因子來做比較，整體而言，各個細胞株的結果顯示，經由ChIP-seq鑑定出的峰值區中，約六成會包含至少一個該特定轉錄因子的轉錄因子結合位。此外，本論文發現利用模序探勘所得之序列特徵結合ChIP-seq峰值區的資訊去預測轉錄因子結合位，經觀察確實可增加預測轉錄因子結合位的準確率，然而，使用不同FDR信心程度與不同的序列特徵，將會影響轉錄因子結合位的準確率。本論文之研究結果點出單純使用染色質免疫沉澱技術預測轉錄因子結合位點的缺陷，並提出序列特徵有助於改善預測結果，而可作為未來相關生物資訊預測方法之重要基礎。Transcription factors (TF) regulate gene expression in living organisms and influence multiple biological processes. Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that have been widely used to find transcription factor binding sites (TFBSs) of a specific TF among the DNA sequences of a genome. However, the accuracy of the TFBSs identified by ChIP-seq has not been systematically evaluated. In this regard, this thesis utilized TFBS information provided by the TRANSFAC database to validate the TFBSs identified by using ChIP-seq only with multiple false discovery rate (FDR). Moreover, in this thesis, a method incorporating de novo motif discovery was proposed to improve the performance of the predicted TFBSs. ChIP-seq data sampled from different cell lines was collected from ENCODE database. In general, ~60% of the peak regions identified by using the ChIP-seq only with a strict FDR cutoff (FDR = 0) contained at least one TFBS of the specific TF across multiple cell lines. In addition, by our proposed method, the prediction accuracy was improved and better than the results using ChIP-seq alone, though it was observed that the improved levels were affected by the used FDR cutoffs and discovered motifs. In conclusion, this thesis identified the accuracy problem of the ChIP-seq platform by observing from the data in a large scale, and address this issue by proposing a method incorporating de novo motif discovery. The observed results can serve as an important foundation for developing bioinformatics tools on TFBS prediction in future
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Fig. 2 in Out of the Pan- Himalaya: Evolutionary history of the Paeoniaceae revealed by phylogenomics
No full textFig. 2. Divergence times from BEAST analysis and biogeographical events in the evolutionary by RASP based on 25 regions of 20 nuclear loci from 52 individuals of all wild peony BEAST. Nodes where dispersals or vicariances occurred are number‐labelled and detailsPublished as part of Zhou, Shi- Liang, Xu, Chao, Liu, Jing, Yu, Yan, Wu, Ping, Cheng, Tao & Hong, De-Yuan, 2021, Out of the Pan- Himalaya: Evolutionary history of the Paeoniaceae revealed by phylogenomics, pp. 1170-1188 in Journal of Systematics and Evolution 59 (6) on page 1176, DOI: 10.1111/jse.12688, http://zenodo.org/record/788894
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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