Advances in Bioinformatics最新文献_第9页

Network completion for static gene expression data. 网络完成静态基因表达数据。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-03-26 DOI: 10.1155/2014/382452

Natsu Nakajima, Tatsuya Akutsu

引用次数: 3

Comparative genomics of ten solanaceous plastomes. 十种茄属植物质体的比较基因组学研究。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-11-17 DOI: 10.1155/2014/424873

Harpreet Kaur, Bhupinder Pal Singh, Harpreet Singh, Avinash Kaur Nagpal

{"title":"Comparative genomics of ten solanaceous plastomes.","authors":"Harpreet Kaur, Bhupinder Pal Singh, Harpreet Singh, Avinash Kaur Nagpal","doi":"10.1155/2014/424873","DOIUrl":"https://doi.org/10.1155/2014/424873","url":null,"abstract":"Availability of complete plastid genomes of ten solanaceous species, Atropa belladonna, Capsicum annuum, Datura stramonium, Nicotiana sylvestris, Nicotiana tabacum, Nicotiana tomentosiformis, Nicotiana undulata, Solanum bulbocastanum, Solanum lycopersicum, and Solanum tuberosum provided us with an opportunity to conduct their in silico comparative analysis in depth. The size of complete chloroplast genomes and LSC and SSC regions of three species of Solanum is comparatively smaller than that of any other species studied till date (exception: SSC region of A. belladonna). AT content of coding regions was found to be less than noncoding regions. A duplicate copy of trnH gene in C. annuum and two alternative tRNA genes for proline in D. stramonium were observed for the first time in this analysis. Further, homology search revealed the presence of rps19 pseudogene and infA genes in A. belladonna and D. stramonium, a region identical to rps19 pseudogene in C. annum and orthologues of sprA gene in another six species. Among the eighteen intron-containing genes, 3 genes have two introns and 15 genes have one intron. The longest insertion was found in accD gene in C. annuum. Phylogenetic analysis using concatenated protein coding sequences gave two clades, one for Nicotiana species and another for Solanum, Capsicum, Atropa, and Datura. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2014 ","pages":"424873"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/424873","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32882185","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: 5

In Silico Screening of Mutated K-Ras Inhibitors from Malaysian Typhonium flagelliforme for Non-Small Cell Lung Cancer. 非小细胞肺癌中马来西亚鞭毛虫K-Ras抑制剂突变的计算机筛选。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-09-21 DOI: 10.1155/2014/431696

Ayesha Fatima, H F Yee

引用次数: 8

Computational Analysis Reveals the Association of Threonine 118 Methionine Mutation in PMP22 Resulting in CMT-1A. 计算分析揭示PMP22中苏氨酸118蛋氨酸突变导致CMT-1A的关联。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-10-20 DOI: 10.1155/2014/502618

Chundi Vinay Kumar, Rayapadi G Swetha, Anand Anbarasu, Sudha Ramaiah

引用次数: 86

A Hybrid Method for Endocardial Contour Extraction of Right Ventricle in 4-Slices from 3D Echocardiography Dataset. 三维超声心动图数据集4片右心室心内膜轮廓提取的混合方法。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-10-12 DOI: 10.1155/2014/207149

Faten A Dawood, Rahmita W Rahmat, Suhaini B Kadiman, Lili N Abdullah, Mohd D Zamrin

{"title":"A Hybrid Method for Endocardial Contour Extraction of Right Ventricle in 4-Slices from 3D Echocardiography Dataset.","authors":"Faten A Dawood, Rahmita W Rahmat, Suhaini B Kadiman, Lili N Abdullah, Mohd D Zamrin","doi":"10.1155/2014/207149","DOIUrl":"https://doi.org/10.1155/2014/207149","url":null,"abstract":"This paper presents a hybrid method to extract endocardial contour of the right ventricular (RV) in 4-slices from 3D echocardiography dataset. The overall framework comprises four processing phases. In Phase I, the region of interest (ROI) is identified by estimating the cavity boundary. Speckle noise reduction and contrast enhancement were implemented in Phase II as preprocessing tasks. In Phase III, the RV cavity region was segmented by generating intensity threshold which was used for once for all frames. Finally, Phase IV is proposed to extract the RV endocardial contour in a complete cardiac cycle using a combination of shape-based contour detection and improved radial search algorithm. The proposed method was applied to 16 datasets of 3D echocardiography encompassing the RV in long-axis view. The accuracy of experimental results obtained by the proposed method was evaluated qualitatively and quantitatively. It has been done by comparing the segmentation results of RV cavity based on endocardial contour extraction with the ground truth. The comparative analysis results show that the proposed method performs efficiently in all datasets with overall performance of 95% and the root mean square distances (RMSD) measure in terms of mean ± SD was found to be 2.21 ± 0.35 mm for RV endocardial contours. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2014 ","pages":"207149"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/207149","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32793842","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: 1

Secondary structure preferences of mn (2+) binding sites in bacterial proteins. 细菌蛋白中mn(2+)结合位点的二级结构偏好。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-03-17 DOI: 10.1155/2014/501841

Tatyana Aleksandrovna Khrustaleva

{"title":"Secondary structure preferences of mn (2+) binding sites in bacterial proteins.","authors":"Tatyana Aleksandrovna Khrustaleva","doi":"10.1155/2014/501841","DOIUrl":"https://doi.org/10.1155/2014/501841","url":null,"abstract":"3D structures of proteins with coordinated Mn(2+) ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn(2+) binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure \"beta strand-major binder-random coil\" is overrepresented around all the three major Mn(2+) binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn(2+) binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn(2+) ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn(2+) sites with at least one amino acid in the \"beta strand-major binder-random coil\" motif of secondary structure (77.88%) does not depend on genomic GC-content. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2014 ","pages":"501841"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/501841","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32301020","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: 8

Breast Cancer Nodes Detection Using Ultrasonic Microscale Subarrayed MIMO RADAR. 超声微尺度亚阵列MIMO雷达检测乳腺癌淋巴结。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-09-15 DOI: 10.1155/2014/797013

Attaphongse Taparugssanagorn, Siwaruk Siwamogsatham, Carlos Pomalaza-Ráez

引用次数: 1

Computational Studies of Beta Amyloid (Aβ42) with p75NTR Receptor: A Novel Therapeutic Target in Alzheimer's Disease. β -淀粉样蛋白(A - β42)与p75NTR受体的计算研究:阿尔茨海默病的新治疗靶点。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-11-11 DOI: 10.1155/2014/736378

Shine Devarajan, Jeya Sundara Sharmila

{"title":"Computational Studies of Beta Amyloid (Aβ42) with p75NTR Receptor: A Novel Therapeutic Target in Alzheimer's Disease.","authors":"Shine Devarajan, Jeya Sundara Sharmila","doi":"10.1155/2014/736378","DOIUrl":"https://doi.org/10.1155/2014/736378","url":null,"abstract":"Alzheimer's disease is a neurodegenerative disorder characterized by the accumulation of beta amyloid plaques (Aβ) which can induce neurite degeneration and progressive dementia. It has been identified that neuronal apoptosis is induced by binding of Aβ42 to pan neurotrophin receptor (p75NTR) and gave the possibility that beta amyloid oligomer is a ligand for p75NTR. However, the atomic contact point responsible for molecular interactions and conformational changes of the protein upon binding was not studied in detail. In view of this, we conducted a molecular docking and simulation study to investigate the binding behaviour of Aβ42 monomer with p75NTR ectodomain. Furthermore, we proposed a p75NTR-ectodomain-Aβ42 complex model. Our data revealed that, Aβ42 specifically recognizes CRD1 and CRD2 domains of the receptor and formed a \"cap\" like structure at the N-terminal of receptor which is stabilized by a network of hydrogen bonds. These findings are supported by molecular dynamics simulation that Aβ42 showed distinct structural alterations at N- and C-terminal regions due to the influence of the receptor binding site. Overall, the present study gives more structural insight on the molecular interactions of beta amyloid protein involved in the activation of p75NTR receptor. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2014 ","pages":"736378"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/736378","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32882186","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: 9

Multiplex degenerate primer design for targeted whole genome amplification of many viral genomes. 多种病毒基因组全基因组扩增的多重退化引物设计。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-08-03 DOI: 10.1155/2014/101894

Shea N Gardner, Crystal J Jaing, Maher M Elsheikh, José Peña, David A Hysom, Monica K Borucki

{"title":"Multiplex degenerate primer design for targeted whole genome amplification of many viral genomes.","authors":"Shea N Gardner, Crystal J Jaing, Maher M Elsheikh, José Peña, David A Hysom, Monica K Borucki","doi":"10.1155/2014/101894","DOIUrl":"https://doi.org/10.1155/2014/101894","url":null,"abstract":"Background. Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results. A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions. This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family. ","PeriodicalId":39059,"journal":{"name":"Advances in Bioinformatics","volume":"2014 ","pages":"101894"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/101894","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32613607","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: 13

An In Silico Approach towards the Prediction of Druglikeness Properties of Inhibitors of Plasminogen Activator Inhibitor1. 纤溶酶原激活物抑制剂药物相似性预测的计算机方法[j]。

Advances in Bioinformatics Pub Date : 2014-01-01 Epub Date: 2014-12-15 DOI: 10.1155/2014/385418

Umadevi Subramanian, Ashok Sivapunniyam, Ayyasamy Pudukadu Munusamy, Rajakumar Sundaram

引用次数: 4