International Journal of Computational Biology and Drug Design最新文献_第8页

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-02-21 DOI: 10.1504/IJCBDD.2013.052205

Guoqing Li, Di Wu, Shuning Wang, Jing Sun, Diansheng Xu, Zhiwei Cao

引用次数: 0

Breast tomosynthesis imaging configuration analysis. 乳腺断层合成成像构型分析。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-07-30 DOI: 10.1504/IJCBDD.2013.055460

Cleveland E Rayford, Weihua Zhou, Ying Chen

{"title":"Breast tomosynthesis imaging configuration analysis.","authors":"Cleveland E Rayford, Weihua Zhou, Ying Chen","doi":"10.1504/IJCBDD.2013.055460","DOIUrl":"https://doi.org/10.1504/IJCBDD.2013.055460","url":null,"abstract":"Traditional two-dimensional (2D) X-ray mammography is the most commonly used method for breast cancer diagnosis. Recently, a three-dimensional (3D) Digital Breast Tomosynthesis (DBT) system has been invented, which is likely to challenge the current mammography technology. The DBT system provides stunning 3D information, giving physicians increased detail of anatomical information, while reducing the chance of false negative screening. In this research, two reconstruction algorithms, Back Projection (BP) and Shift-And-Add (SAA), were used to investigate and compare View Angle (VA) and the number of projection images (N) with parallel imaging configurations. In addition, in order to better determine which method displayed better-quality imaging, Modulation Transfer Function (MTF) analyses were conducted with both algorithms, ultimately producing results which improve upon better breast cancer detection. Research studies find evidence that early detection of the disease is the best way to conquer breast cancer, and earlier detection results in the increase of life span for the affected person. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"6 3","pages":"255-62"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2013.055460","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31620030","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

Multi-view spectral clustering and its chemical application. 多视点光谱聚类及其化学应用。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-02-21 DOI: 10.1504/IJCBDD.2013.052200

Adeshola A Adefioye, Xinhai Liu, Bart De Moor

引用次数: 3

Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution. 泊松分布下 RNA-seq 数据差异表达分析的样本量计算

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-09-30 DOI: 10.1504/IJCBDD.2013.056830

Chung-I Li, Pei-Fang Su, Yan Guo, Yu Shyr

{"title":"Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution.","authors":"Chung-I Li, Pei-Fang Su, Yan Guo, Yu Shyr","doi":"10.1504/IJCBDD.2013.056830","DOIUrl":"10.1504/IJCBDD.2013.056830","url":null,"abstract":"Sample size determination is an important issue in the experimental design of biomedical research. Because of the complexity of RNA-seq experiments, however, the field currently lacks a sample size method widely applicable to differential expression studies utilising RNA-seq technology. In this report, we propose several methods for sample size calculation for single-gene differential expression analysis of RNA-seq data under Poisson distribution. These methods are then extended to multiple genes, with consideration for addressing the multiple testing problem by controlling false discovery rate. Moreover, most of the proposed methods allow for closed-form sample size formulas with specification of the desired minimum fold change and minimum average read count, and thus are not computationally intensive. Simulation studies to evaluate the performance of the proposed sample size formulas are presented; the results indicate that our methods work well, with achievement of desired power. Finally, our sample size calculation methods are applied to three real RNA-seq data sets. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"6 4","pages":"358-75"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874726/pdf/nihms536263.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31777251","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

Colony size optimisation in colony-based laser imaging for microbial source tracking. 基于菌落的微生物源跟踪激光成像中的菌落大小优化。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-07-30 DOI: 10.1504/IJCBDD.2013.055459

Hao Gong, Bin Chen, Xu Zhang, Charles C Tseng

{"title":"Colony size optimisation in colony-based laser imaging for microbial source tracking.","authors":"Hao Gong, Bin Chen, Xu Zhang, Charles C Tseng","doi":"10.1504/IJCBDD.2013.055459","DOIUrl":"https://doi.org/10.1504/IJCBDD.2013.055459","url":null,"abstract":"The colony-based laser scatter imaging provides a convincing solution to microbial source tracking. The optical scattering patterns of bacterial colonies are tightly correlated to the corresponding growth patterns. This relationship is manifested as the development of optical scattering patterns with the increment of colony size. An investigation was conducted into this relationship and the optimal range of colony size for improving the accuracy of microbial source tracking technique. All the bacterial samples from five host species were cultivated under the same conditions. The optical scattering patterns were recorded for the average colony diameter from 0.1 mm to 1.5 mm, using a bench top laser imaging system. Gabor wavelet was utilised to encode image signatures. Fuzzy-C-means was employed to cluster the colony patterns from the same host species. The experimental results demonstrate that the optimal range of the colony diameters is 0.8-1.0 mm. The corresponding identification rate of microbial source tracking is >80%. ","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":"6 3","pages":"234-43"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2013.055459","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31620028","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

An iterative searching and ranking algorithm for prioritising pharmacogenomics genes. 药物基因组学基因优先排序的迭代搜索和排序算法。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-02-21 DOI: 10.1504/IJCBDD.2013.052199

Rong Xu, Quanqiu Wang

引用次数: 0

Querying highly similar sequences. 查询高度相似的序列。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-02-21 DOI: 10.1504/IJCBDD.2013.052206

Carl Barton, Mathieu Giraud, Costas S Iliopoulos, Thierry Lecroq, Laurent Mouchard, Solon P Pissis

引用次数: 3

Engineering modelling and imaging technologies in biomedical research fields. 生物医学研究领域的工程建模和成像技术。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-07-30 DOI: 10.1504/IJCBDD.2013

Jun Qin, Nazeih M Botros, Ying Chen

引用次数: 3

Analysing molecular polar surface descriptors to predict blood-brain barrier permeation. 分析分子极性表面描述符预测血脑屏障渗透。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-02-21 DOI: 10.1504/IJCBDD.2013.052195

Sergey Shityakov, Winfried Neuhaus, Thomas Dandekar, Carola Förster

{"title":"Analysing molecular polar surface descriptors to predict blood-brain barrier permeation.","authors":"Sergey Shityakov, Winfried Neuhaus, Thomas Dandekar, Carola Förster","doi":"10.1504/IJCBDD.2013.052195","DOIUrl":"https://doi.org/10.1504/IJCBDD.2013.052195","url":null,"abstract":"Molecular polar surface (PS) descriptors are very useful parameters in prediction of drug transport properties. They could be also used to investigate the blood-brain barrier (BBB) permeation rate for various chemical compounds. In this study, a dataset of drugs (n = 19) from various pharmacological groups was studied to estimate their potential properties to permeate across the BBB. Experimental logBB data were available as steady-state distribution values of the in vivo rat model for these molecules. Including accurate calculation of the electrostatic potential maps, polar surface descriptors, such as a two-dimensional polar surface area (2D-PSA), topological polar surface area (TPSA) and three-dimensional polar surface area or polar area (3D-PSA; PA) were measured and analysed. We report the strong correlation of these descriptors with logBB values for the prediction of BBB permeation using the linear partial least squares (PLS) fitting technique. The 3D-PSA descriptor showed the best fit to logBB values with R² = 0.92 and RMSD = 0.29 (p-value < 0.0001). The obtained results demonstrate that all descriptors bear high predictive powers and could provide an efficient strategy to envisage the pharmacokinetic properties of chemical compounds to permeate across the BBB at an early stage of the drug development process.","PeriodicalId":39227,"journal":{"name":"International Journal of Computational Biology and Drug Design","volume":" ","pages":"146-56"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJCBDD.2013.052195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31254180","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: 56

Transform-invariant feature based functional MR image registration and neural activity modelling. 基于变换不变特征的功能性MR图像配准与神经活动建模。

International Journal of Computational Biology and Drug Design Pub Date : 2013-01-01 Epub Date: 2013-07-30 DOI: 10.1504/IJCBDD.2013.055456

Jiaqi Gong, Qi Hao, Fei Hu

引用次数: 0