Advances and Applications in Bioinformatics and Chemistry最新文献

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A simple method for assessing the strength of evidence for association at the level of the whole gene. 一种在整个基因水平上评估关联证据强度的简单方法。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2008-01-01 Epub Date: 2008-11-17 DOI: 10.2147/aabc.s4095

David Curtis, Anna E Vine, Jo Knight

{"title":"A simple method for assessing the strength of evidence for association at the level of the whole gene.","authors":"David Curtis, Anna E Vine, Jo Knight","doi":"10.2147/aabc.s4095","DOIUrl":"10.2147/aabc.s4095","url":null,"abstract":"Introduction: It is expected that different markers may show different patterns of association with different pathogenic variants within a given gene. It would be helpful to combine the evidence implicating association at the level of the whole gene rather than just for individual markers or haplotypes. Doing this is complicated by the fact that different markers do not represent independent sources of information.Method: We propose combining the p values from all single locus and/or multilocus analyses of different markers according to the formula of Fisher, X = ∑(-2ln(p(i))), and then assessing the empirical significance of this statistic using permutation testing. We present an example application to 19 markers around the HTRA2 gene in a case-control study of Parkinson's disease.Results: Applying our approach shows that, although some individual tests produce low p values, overall association at the level of the gene is not supported.Discussion: Approaches such as this should be more widely used in assimilating the overall evidence supporting involvement of a gene in a particular disease. Information can be combined from biallelic and multiallelic markers and from single markers along with multimarker analyses. Single genes can be tested or results from groups of genes involved in the same pathway could be combined in order to test biologically relevant hypotheses. The approach has been implemented in a computer program called COMBASSOC which is made available for downloading.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"1 ","pages":"115-20"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30142649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. 一种结合基于结构的药物筛选和基于配体的筛选来提高命中率的方法。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2008-01-01 Epub Date: 2008-08-12 DOI: 10.2147/aabc.s3767

Katsumi Omagari, Daisuke Mitomo, Satoru Kubota, Haruki Nakamura, Yoshifumi Fukunishi

{"title":"A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening.","authors":"Katsumi Omagari, Daisuke Mitomo, Satoru Kubota, Haruki Nakamura, Yoshifumi Fukunishi","doi":"10.2147/aabc.s3767","DOIUrl":"https://doi.org/10.2147/aabc.s3767","url":null,"abstract":"We examined the procedures to combine two different in silico drug-screening results to achieve a high hit ratio. When the 3D structure of the target protein and some active compounds are known, both structure-based and ligand-based in silico screening methods can be applied. In the present study, the machine-learning score modification multiple target screening (MSM-MTS) method was adopted as a structure-based screening method, and the machine-learning docking score index (ML-DSI) method was adopted as a ligand-based screening method. To combine the predicted compound’s sets by these two screening methods, we examined the product of the sets (consensus set) and the sum of the sets. As a result, the consensus set achieved a higher hit ratio than the sum of the sets and than either individual predicted set. In addition, the current combination was shown to be robust enough for the structural diversities both in different crystal structure and in snapshot structures during molecular dynamics simulations.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"1 ","pages":"19-28"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s3767","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30141693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Binarization of medical images based on the recursive application of mean shift filtering : Another algorithm. 基于均值移位滤波递归应用的医学图像二值化:另一种算法。

Advances and Applications in Bioinformatics and Chemistry Pub Date : 2008-01-01 Epub Date: 2008-05-28 DOI: 10.2147/aabc.s3206

Roberto Rodríguez

{"title":"Binarization of medical images based on the recursive application of mean shift filtering : Another algorithm.","authors":"Roberto Rodríguez","doi":"10.2147/aabc.s3206","DOIUrl":"https://doi.org/10.2147/aabc.s3206","url":null,"abstract":"Binarization is often recognized to be one of the most important steps in most high-level image analysis systems, particularly for object recognition. Its precise functioning highly determines the performance of the entire system. According to many researchers, segmentation finishes when the observer's goal is satisfied. Experience has shown that the most effective methods continue to be the iterative ones. However, a problem with these algorithms is the stopping criterion. In this work, entropy is used as the stopping criterion when segmenting an image by recursively applying mean shift filtering. Of this way, a new algorithm is introduced for the binarization of medical images, where the binarization is carried out after the segmented image was obtained. The good performance of the proposed method; that is, the good quality of the binarization, is illustrated with several experimental results. In this paper a comparison was carried out among the obtained results with this new algorithm with respect to another developed by the author and collaborators previously and also with Otsu's method.","PeriodicalId":53584,"journal":{"name":"Advances and Applications in Bioinformatics and Chemistry","volume":"1 ","pages":"1-12"},"PeriodicalIF":0.0,"publicationDate":"2008-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2147/aabc.s3206","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30141691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 18

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