International Journal of Computational Biology and Drug Design最新文献_第10页

Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis. 基于语义距离和模糊聚类方法的基因功能分类:参考集评价和重叠分析。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-09-24 DOI: 10.1504/IJCBDD.2012.049207

Marie-Dominique Devignes, Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch

{"title":"Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis.","authors":"Marie-Dominique Devignes, Sidahmed Benabderrahmane, Malika Smaïl-Tabbone, Amedeo Napoli, Olivier Poch","doi":"10.1504/IJCBDD.2012.049207","DOIUrl":"https://doi.org/10.1504/IJCBDD.2012.049207","url":null,"abstract":"Functional classification aims at grouping genes according to their molecular function or the biological process they participate in. Evaluating the validity of such unsupervised gene classification remains a challenge given the variety of distance measures and classification algorithms that can be used. We evaluate here functional classification of genes with the help of reference sets: KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways and Pfam clans. These sets represent ground truth for any distance based on GO (Gene Ontology) biological process and molecular function annotations respectively. Overlaps between clusters and reference sets are estimated by the F-score method. We test our previously described IntelliGO semantic distance with hierarchical and fuzzy C-means clustering and we compare results with the state-of-the-art DAVID (Database for Annotation Visualisation and Integrated Discovery) functional classification method. Finally, study of best matching clusters to reference sets leads us to propose a set-difference method for discovering missing information.","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"5 3-4","pages":"245-60"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2012.049207","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30932659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 10

3D QSAR CoMFA/CoMSIA and docking studies on azole dione derivatives, as anti-cancer inhibitors. 三维QSAR CoMFA/CoMSIA与唑类二酮衍生物抗癌抑制剂的对接研究。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-07-31 DOI: 10.1504/IJCBDD.2012.048280

Rohith Kumar Anugolu, Shravan Kumar Gunda, Shaik Mahmood

引用次数: 2

Genome wide search for identification of potential drug targets in Bacillus anthracis. 全基因组搜索鉴定炭疽芽孢杆菌的潜在药物靶点。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-07-31 DOI: 10.1504/IJCBDD.2012.048311

Ravi V Gutlapalli, Jyothsna L Ambaru, Pavani Darla, K R S Sambasiva Rao

{"title":"Genome wide search for identification of potential drug targets in Bacillus anthracis.","authors":"Ravi V Gutlapalli, Jyothsna L Ambaru, Pavani Darla, K R S Sambasiva Rao","doi":"10.1504/IJCBDD.2012.048311","DOIUrl":"https://doi.org/10.1504/IJCBDD.2012.048311","url":null,"abstract":"With the heightened interest in Bacillus anthracis as a potential biological threat agent, novel drug targets identification is of great importance in drug discovery. This study considered a genome-wide approach to identify 270 non-redundant, non-human homologous genes and 103 essential genes of the bacteria as putative drug targets. Sub-cellular localisation of each drug target was annotated using PSORTb 3.0 and confirmation by a hybrid support vector machine analysis identified 16 membrane-bound genes with reliability index ≥4. SPAAN analysis predicted 3 adhesion-like proteins and BLAST against the MEROPS database identified 7 peptidases with inhibitors. As a case study, a homology model was built for the ptsG gene using Modeller 9v8. The work reported here identified a small subset of potential drug targets involved in vital aspects of the metabolism of pathogen, persistence, virulence and cell wall biosynthesis. Thus, this manifold workflow can speed up the process of drug target discovery.","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"5 2","pages":"164-79"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2012.048311","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30805593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data. 基于蛋白质序列特征和结构域-结构域相互作用数据的疾病相关非单核苷酸多态性鉴定

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-09-24 DOI: 10.1504/IJCBDD.2012.049204

Rui Jiang, Mingxin Gan, Jiaxin Wu

{"title":"Identification of disease-related nsSNPs via the integration of protein sequence features and domain-domain interaction data.","authors":"Rui Jiang, Mingxin Gan, Jiaxin Wu","doi":"10.1504/IJCBDD.2012.049204","DOIUrl":"https://doi.org/10.1504/IJCBDD.2012.049204","url":null,"abstract":"Recent studies have suggested the common disease-rare variant (CD-RV) hypothesis in the mapping of disease-related genetic variants and have proposed a number of statistical methods to detect associations between rare variants and human inherited diseases. However, most of these methods take the selection of functional variants as a preliminary step in order to maximise the power of statistical tests. To meet this end, we put forward a filtration approach to identify genetic variants that are potentially associated with a query disease of interest from the perspective of one-class novelty learning. We propose to prioritise candidate non-synonymous single nucleotide polymorphisms (nsSNPs) relying on the integrated use of two sequence conservation properties of amino acids calculated from multiple sequence alignment of protein sequences and one functional similarity measure derived from domain-domain interaction data. We show the power of this approach in the detection of disease-related nsSNP via large-scale leave-one-out cross-validation experiments.","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"5 3-4","pages":"206-21"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2012.049204","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30932657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Associating functional groups to multiple clinical types using combined t-test scores and contingency-based measures: a study on breast cancer genes. 使用联合t检验分数和基于偶然性的措施将功能群与多种临床类型联系起来:一项关于乳腺癌基因的研究。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-09-24 DOI: 10.1504/IJCBDD.2012.049208

Noha A Yousri, Dalal M Elkaffash

{"title":"Associating functional groups to multiple clinical types using combined t-test scores and contingency-based measures: a study on breast cancer genes.","authors":"Noha A Yousri, Dalal M Elkaffash","doi":"10.1504/IJCBDD.2012.049208","DOIUrl":"https://doi.org/10.1504/IJCBDD.2012.049208","url":null,"abstract":"Stemming from the need to score relations between functional groups of genes and multiple clinical types associated with a tumour, this study proposes to use contingency-based measures to quantify such relations. It aims at reflecting a relative measure of association within a specific set of functional groups, and a specific set of clinical statuses. The proposed methodology is based on extracting features (scores) from expression sets that relate genes to multiple cancer subtypes (clinical statuses), and use those features (scores) to associate cancer subtypes with functional groups. It proposes combining t-test scores at several levels of cancer statuses' differentiation to calculate such gene features. It also proposes using contingency based measures as Jaccard and F-measure to associate gene functional groups to multiple cancer subtypes/statuses. Variations from the original Jaccard measure are proposed to reflect scores of genes' relations to classes/groups rather than using binary relations. The core objective of the experimental study is to identify the functional categories of genes that mark the change in lymph node status under each of oestrogen receptor positive and negative statuses in breast cancer expression sets.","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"5 3-4","pages":"261-83"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2012.049208","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30932660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Axonal transport analysis using Multitemporal Association Tracking. 利用多时相关联跟踪进行轴突运输分析。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-03-21 DOI: 10.1504/IJCBDD.2012.045950

Mark R Winter, Cheng Fang, Gary Banker, Badrinath Roysam, Andrew R Cohen

引用次数: 41

Research on segmentation of dorsal diencephalon and ventral midbrain of zebrafish embryo based on active contour model. 基于活动轮廓模型的斑马鱼胚胎背间脑和腹中脑分割研究。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-03-21 DOI: 10.1504/IJCBDD.2012.045948

Tao Wu, Jianfeng Lu, Yanting Lu, Jingyu Yang

引用次数: 1

Systems biology approaches in biological and biomedical research: opportunities and challenges. 生物和生物医学研究中的系统生物学方法:机遇与挑战。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-09-24 DOI: 10.1504/IJCBDD.2012

Zhongming Zhao, Rui Jiang, Huiru Zheng

引用次数: 1

Network-based approaches for extending the Wnt signalling pathway and identifying context-specific sub-networks. 扩展Wnt信号通路和识别上下文特定子网络的基于网络的方法。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-09-24 DOI: 10.1504/IJCBDD.2012.049203

Sudipto Saha, Theodore Roman, Alex Galante, Mehmet Koyutürk, Robert M Ewing

引用次数: 2

Peptide sequence tag generation for tandem mass spectra containing post-translational modifications. 包含翻译后修饰的串联质谱的肽序列标签生成。

International Journal of Computational Biology and Drug Design Pub Date : 2012-01-01 Epub Date: 2012-09-24 DOI: 10.1504/IJCBDD.2012.049209

Hui Li, Chunmei Liu

引用次数: 0