International Journal of Computational Biology and Drug Design最新文献_第4页

Inference of hierarchical regulatory network of TCF7L2 binding sites in MCF7 cell line MCF7细胞系TCF7L2结合位点分级调控网络的推断

International Journal of Computational Biology and Drug Design Pub Date : 2016-02-29 DOI: 10.1504/IJCBDD.2016.074990

Yao Wang, Rui Wang, V. Jin

引用次数: 2

A Framework for 3D Vessel Analysis using Whole Slide Images of Liver Tissue Sections. 利用肝组织切片全切片图像进行三维血管分析的框架。

International Journal of Computational Biology and Drug Design Pub Date : 2016-01-01 DOI: 10.1504/IJCBDD.2016.074983

Yanhui Liang, Fusheng Wang, Darren Treanor, Derek Magee, Nick Roberts, George Teodoro, Yangyang Zhu, Jun Kong

{"title":"A Framework for 3D Vessel Analysis using Whole Slide Images of Liver Tissue Sections.","authors":"Yanhui Liang, Fusheng Wang, Darren Treanor, Derek Magee, Nick Roberts, George Teodoro, Yangyang Zhu, Jun Kong","doi":"10.1504/IJCBDD.2016.074983","DOIUrl":"10.1504/IJCBDD.2016.074983","url":null,"abstract":"Three-dimensional (3D) high resolution microscopic images have high potential for improving the understanding of both normal and disease processes where structural changes or spatial relationship of disease features are significant. In this paper, we develop a complete framework applicable to 3D pathology analytical imaging, with an application to whole slide images of sequential liver slices for 3D vessel structure analysis. The analysis workflow consists of image registration, segmentation, vessel cross-section association, interpolation, and volumetric rendering. To identify biologically-meaningful correspondence across adjacent slides, we formulate a similarity function for four association cases. The optimal solution is then obtained by constrained Integer Programming. We quantitatively and qualitatively compare our vessel reconstruction results with human annotations. Validation results indicate a satisfactory concordance as measured both by region-based and distance-based metrics. These results demonstrate a promising 3D vessel analysis framework for whole slide images of liver tissue sections.","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"9 1-2 1","pages":"102-119"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66715638","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

In silico phylogenetic analysis of Vibrio cholerae isolates based on three housekeeping genes. 基于三个管家基因的霍乱弧菌分离株的计算机系统发育分析。

International Journal of Computational Biology and Drug Design Pub Date : 2015-01-01 Epub Date: 2015-04-13 DOI: 10.1504/IJCBDD.2015.068789

Tayebeh Farhadi, Navid Nezafat, Younes Ghasemi

{"title":"In silico phylogenetic analysis of Vibrio cholerae isolates based on three housekeeping genes.","authors":"Tayebeh Farhadi, Navid Nezafat, Younes Ghasemi","doi":"10.1504/IJCBDD.2015.068789","DOIUrl":"https://doi.org/10.1504/IJCBDD.2015.068789","url":null,"abstract":"Vibrio cholera, a gram-negative bacterium, has been categorised into clinical and environmental species. Phylogenetic studies have been performed to investigate the relationships of the V. cholerae populations in worldwide. In this study, phylogenetic relationship between V. cholerae isolates from Iran and other regions of the world was determined, based on three housekeeping genes analysis. Results for Iranian strains showed that congruency of asd and hlyA phylogenetic trees were remarkably higher than recA tree. Iranian strains displayed 2-3%, 1-14% and 3-5% deference in asd, hlyA and recA nucleotide sequences, respectively. Sequence similarity degrees were variable between Iranian and other region's strains. Furthermore, the non-congruence in the phylogeny of the pathogenic clones in cladograms is probably due to horizontal gene transfer. Finally, results of this study suggest that monitoring of surface waters for housekeeping genes of V. cholerae in the cholera endemic areas may be valuable for forecasting the expected cholera outbreaks. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"8 1","pages":"62-74"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2015.068789","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33214303","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

In silico prediction of anti-malarial hit molecules based on machine learning methods. 基于机器学习方法的抗疟疾分子的计算机预测。

International Journal of Computational Biology and Drug Design Pub Date : 2015-01-01 Epub Date: 2015-04-13 DOI: 10.1504/IJCBDD.2015.068783

Madhulata Kumari, Subhash Chandra

引用次数: 5

Binding mode analysis of anti-influenza drugs in H1N1 (2009) and H5N1 influenza A virus and designing of potential H1N1 inhibitors. 抗流感药物在H1N1(2009)和H5N1甲型流感病毒中的结合模式分析及潜在H1N1抑制剂的设计

International Journal of Computational Biology and Drug Design Pub Date : 2015-01-01 Epub Date: 2015-04-13 DOI: 10.1504/IJCBDD.2015.068753

Kh Dhanachandra Singh, Palani Kirubakaran, Selvaraman Nagamani, Muthusamy Karthikeyan

{"title":"Binding mode analysis of anti-influenza drugs in H1N1 (2009) and H5N1 influenza A virus and designing of potential H1N1 inhibitors.","authors":"Kh Dhanachandra Singh, Palani Kirubakaran, Selvaraman Nagamani, Muthusamy Karthikeyan","doi":"10.1504/IJCBDD.2015.068753","DOIUrl":"https://doi.org/10.1504/IJCBDD.2015.068753","url":null,"abstract":"The main goal of this study is to understand the molecular-level interactions of neuraminidase inhibitor. The molecular docking, molecular dynamics and binding energy calculation analyses were carried out and the results revealed that the 150-cavitiy in the active site may play an important role in binding of drugs. Free energy calculations revealed that electrostatic interaction is more favourable for Oseltamivir interaction with H1N1 and van der Waals interaction is more favourable for H5N1, whereas Zanamivir favours the electrostatic interaction in both the strains (H1N1 and H5N1). Energy-optimised pharmacophore mapping was created using Oseltamivir drug. The pharmacophore model contained two hydrogen-bond acceptor and two hydrogen bond donor sites. Using these pharmacophore features, we screened a compound database to find a potential ligand that could inhibit the H1N1 protein. The current research will pave the way to find potent neuraminidase inhibitors against H1N1 (2009) strain. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"8 1","pages":"1-18"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2015.068753","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33214299","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: 2

A novel formulation of veggies with potent anti-migraine activity. 一种具有有效抗偏头痛活性的新型蔬菜配方。

International Journal of Computational Biology and Drug Design Pub Date : 2015-01-01 Epub Date: 2015-04-13 DOI: 10.1504/IJCBDD.2015.068787

Mohit M Jain, Nirmala Kumari, Geeta Rai

引用次数: 9

A novel formulation of veggies with potent liver detoxifying activity. 一种新型的蔬菜配方，具有强大的肝脏排毒活性。

International Journal of Computational Biology and Drug Design Pub Date : 2015-01-01 Epub Date: 2015-04-13 DOI: 10.1504/IJCBDD.2015.068792

Mohit M Jain, Nirmala Kumari, Geeta Rai

引用次数: 0

Natural flavonoid derivatives as oral human epidermoid carcinoma cell inhibitors. 天然类黄酮衍生物作为口服人表皮样癌细胞抑制剂。

International Journal of Computational Biology and Drug Design Pub Date : 2015-01-01 Epub Date: 2015-04-13 DOI: 10.1504/IJCBDD.2015.068782

Shravan Kumar Gunda, Sofia Florence Kongaleti, Mahmood Shaik

引用次数: 9

A comparison of microRNA sequencing reproducibility and noise reduction using mirVana and TRIzol isolation methods. mirVana和TRIzol分离方法对microRNA测序可重复性和降噪效果的比较。

International Journal of Computational Biology and Drug Design Pub Date : 2014-01-01 Epub Date: 2014-05-28 DOI: 10.1504/IJCBDD.2014.061642

Yan Guo, Amma Bosompem, Xu Zhong, Travis Clark, Yu Shyr, Annette S Kim

引用次数: 12

Combining multiple clusterings of chemical structures using cluster-based similarity partitioning algorithm. 利用基于聚类的相似性划分算法组合化学结构的多个聚类。

International Journal of Computational Biology and Drug Design Pub Date : 2014-01-01 Epub Date: 2014-01-09 DOI: 10.1504/IJCBDD.2014.058584

Faisal Saeed, Naomie Salim, Ammar Abdo

{"title":"Combining multiple clusterings of chemical structures using cluster-based similarity partitioning algorithm.","authors":"Faisal Saeed, Naomie Salim, Ammar Abdo","doi":"10.1504/IJCBDD.2014.058584","DOIUrl":"https://doi.org/10.1504/IJCBDD.2014.058584","url":null,"abstract":"Many types of clustering techniques for chemical structures have been used in the literature, but it is known that any single method will not always give the best results for all types of applications. Recent work on consensus clustering methods is motivated because of the successes of combining multiple classifiers in many areas and the ability of consensus clustering to improve the robustness, novelty, consistency and stability of individual clusterings. In this paper, the Cluster-based Similarity Partitioning Algorithm (CSPA) was examined for improving the quality of chemical structures clustering. The effectiveness of clustering was evaluated based on the ability to separate active from inactive molecules in each cluster and the results were compared with the Ward's clustering method. The chemical dataset MDL Drug Data Report (MDDR) database was used for experiments. The results, obtained by combining multiple clusterings, showed that the consensus clustering method can improve the robustness, novelty and stability of chemical structures clustering. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"7 1","pages":"31-44"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2014.058584","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32032367","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: 5