International Journal of Bioinformatics Research and Applications最新文献_第10页

A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments. 间隙生物序列比对极值(Gumbel)参数的直接计算方法。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.059517

Terrance Quinn, Zachariah Sinkala

引用次数: 0

Structure, evolution and virtual screening of NDM-1 strain from Kolkata. 加尔各答NDM-1菌株的结构、演变和虚拟筛选。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.060761

Ganesh Chandra Sahoo, Mukta Rani, Yousuf Ansari, Chanda Jha, Sindhuprava Rana, Manas Ranjan Dikhit, Kanhu Charan Moharana, Rakesh Kumar, Pradeep Das

{"title":"Structure, evolution and virtual screening of NDM-1 strain from Kolkata.","authors":"Ganesh Chandra Sahoo, Mukta Rani, Yousuf Ansari, Chanda Jha, Sindhuprava Rana, Manas Ranjan Dikhit, Kanhu Charan Moharana, Rakesh Kumar, Pradeep Das","doi":"10.1504/IJBRA.2014.060761","DOIUrl":"https://doi.org/10.1504/IJBRA.2014.060761","url":null,"abstract":"β-lactam antibiotics are utilised to treat bacterial infection. β-lactamase enzymes (EC 3.5.2.6) are produced by several bacteria and are responsible for their resistance to β-lactam antibiotics like penicillin, cephamycins and carbapenems. New Delhi Metallo-β-lactamase (NDM-1) is a gene that makes bacteria resistant to β-lactam antibiotics. Preparing a compound against NDM-1 will require additional investment and development by drug manufacturers as the current antibiotics will not treat patients with NDM-1 resistance. NDM-1 of Kolkata showed convergent-type evolution with other NDM-1 producing strains. The modelled structure exhibited α-β-α barrel-type domain along with Zn metallo-β-lactamase N-terminal domain. Compounds belonging to cephalosporins (relatively resistant to β-lactamase) and other antibiotics ceftaroline, ceftobiprole, piperacillin, penamecillin, azidocillin, cefonicid, tigecycline and colistin have exhibited better binding affinity with the modelled NDM-1. ","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2014.060761","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32312953","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: 6

Texture-based medical image retrieval in compressed domain using compressive sensing. 基于压缩感知的压缩域医学图像纹理检索。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.059519

Kuldeep Yadav, Avi Srivastava, Ankush Mittal, M A Ansari

引用次数: 12

Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data. 从DNA序列数据中划分细菌生态型的算法的准确性和效率。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.062992

Juan Carlos Francisco, Frederick M Cohan, Danny Krizanc

{"title":"Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data.","authors":"Juan Carlos Francisco, Frederick M Cohan, Danny Krizanc","doi":"10.1504/IJBRA.2014.062992","DOIUrl":"https://doi.org/10.1504/IJBRA.2014.062992","url":null,"abstract":"Identification of closely related, ecologically distinct populations of bacteria would benefit microbiologists working in many fields including systematics, epidemiology and biotechnology. Several laboratories have recently developed algorithms aimed at demarcating such 'ecotypes'. We examine the ability of four of these algorithms to correctly identify ecotypes from sequence data. We tested the algorithms on synthetic sequences, with known history and habitat associations, generated under the stable ecotype model and on data from Bacillus strains isolated from Death Valley where previous work has confirmed the existence of multiple ecotypes. We found that one of the algorithms (ecotype simulation) performs significantly better than the others (AdaptML, GMYC, BAPS) in both instances. Unfortunately, it was also shown to be the least efficient of the four. While ecotype simulation is the most accurate, it is by a large margin the slowest of the algorithms tested. Attempts at improving its efficiency are underway. ","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2014.062992","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32476019","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: 7

Vectorial total variation regularisation of orientation distribution functions in diffusion weighted MRI. 扩散加权MRI中方向分布函数的矢量总变分正则化。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.058781

Yuyuan Ouyang, Yunmei Chen, Ying Wu

引用次数: 6

DNA-algorithm for timetable problem. 时间表问题的dna算法。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.059520

Igor Yu Popov, Anastasiya V Vorobyova, Irina V Blinova

引用次数: 1

Effects of rooting via out-groups on in-group topology in phylogeny. 系统发育中外群生根对内群拓扑结构的影响。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.062993

Margareta Ackerman, Daniel G Brown, David Loker

引用次数: 0

Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements. 寻找一致、稳定的RNA序列局部最优结构及其在发现核糖开关元件中的应用。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.062997

Yuan Li, Cuncong Zhong, Shaojie Zhang

{"title":"Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.","authors":"Yuan Li, Cuncong Zhong, Shaojie Zhang","doi":"10.1504/IJBRA.2014.062997","DOIUrl":"https://doi.org/10.1504/IJBRA.2014.062997","url":null,"abstract":"Many non-coding RNAs (ncRNAs) can fold into alternate native structures and perform different biological functions. The computational prediction of an ncRNA's alternate native structures can be conducted by analysing the ncRNA's energy landscape. Previously, we have developed a computational approach, RNASLOpt, to predict alternate native structures for a single RNA. In this paper, in order to improve the accuracy of the prediction, we incorporate structural conservation information among a family of related ncRNA sequences to the prediction. We propose a comparative approach, RNAConSLOpt, to produce all possible consensus SLOpt stack configurations that are conserved on the consensus energy landscape of a family of related ncRNAs. Benchmarking tests show that RNAConSLOpt can reduce the number of candidate structures compared with RNASLOpt, and can predict ncRNAs' alternate native structures accurately. Moreover, an application of the proposed pipeline to bacteria in Bacillus genus has discovered several novel riboswitch candidates. ","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2014.062997","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32476476","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

Discovering rare behaviours in stochastic differential equations using decision procedures: applications to a minimal cell cycle model. 利用决策程序发现随机微分方程中的罕见行为:在最小细胞周期模型中的应用。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.062999

Arup Kumar Ghosh, Faraz Hussain, Susmit Jha, Christopher J Langmead, Sumit Kumar Jha

{"title":"Discovering rare behaviours in stochastic differential equations using decision procedures: applications to a minimal cell cycle model.","authors":"Arup Kumar Ghosh, Faraz Hussain, Susmit Jha, Christopher J Langmead, Sumit Kumar Jha","doi":"10.1504/IJBRA.2014.062999","DOIUrl":"https://doi.org/10.1504/IJBRA.2014.062999","url":null,"abstract":"Stochastic Differential Equation (SDE) models are used to describe the dynamics of complex systems with inherent randomness. The primary purpose of these models is to study rare but interesting or important behaviours, such as the formation of a tumour. Stochastic simulations are the most common means for estimating (or bounding) the probability of rare behaviours, but the cost of simulations increases with the rarity of events. To address this problem, we introduce a new algorithm specifically designed to quantify the likelihood of rare behaviours in SDE models. Our approach relies on temporal logics for specifying rare behaviours of interest, and on the ability of bit-vector decision procedures to reason exhaustively about fixed-precision arithmetic. We apply our algorithm to a minimal parameterised model of the cell cycle, and take Brownian noise into account while investigating the likelihood of irregularities in cell size and time between cell divisions. ","PeriodicalId":35444,"journal":{"name":"International Journal of Bioinformatics Research and Applications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1504/IJBRA.2014.062999","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32476478","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 experimental comparison of PMSprune and other algorithms for motif search. PMSprune与其他基序搜索算法的实验比较。

International Journal of Bioinformatics Research and Applications Pub Date : 2014-01-01 DOI: 10.1504/IJBRA.2014.065242

Dolly Sharma, Sanguthevar Rajasekaran, Sudipta Pathak

引用次数: 5