In Silico Biology最新文献_第7页

An integrated model for visualizing biclusters from gene expression data and PPI networks 从基因表达数据和PPI网络中可视化双聚类的集成模型

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722052

Ahmet Emre Aladağ, C. Erten, Melih Sözdinler

引用次数: 2

Quantification and segmentation of progenitor cells in time-lapse microscopy 延时显微镜下祖细胞的定量和分割

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722071

R. Suresh, N. Jayalakshmi

引用次数: 3

Gene identification in Phytophthora capsici through expressed sequence tags 辣椒疫霉基因序列标记的基因鉴定

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722043

N. Reena, A. Chandrasekar, A. Riju, P. Nima, S. Eapen, M. Anandaraj

{"title":"Gene identification in Phytophthora capsici through expressed sequence tags","authors":"N. Reena, A. Chandrasekar, A. Riju, P. Nima, S. Eapen, M. Anandaraj","doi":"10.1145/1722024.1722043","DOIUrl":"https://doi.org/10.1145/1722024.1722043","url":null,"abstract":"Expressed Sequence Tags (ESTs) are a rich source of information for gene discovery. In this paper, we describe the annotation of ESTs of Phytophthora capsici whose complete genome is not yet available. P. capsici is an Oomycete plant pathogen capable of infecting wide range of plants including cucumber, squash, melons, pumpkin, pepper, tomato and eggplant. In India it causes severe economic losses in black pepper, chillies and cocoa. Towards the understanding of gene function in P. capsici, we undertook the functional annotation of ESTs available at NCBI. A total of 56,457 ESTs were downloaded from NCBI and assembled into 5966 contigs. Functional categorization of these ESTs was performed using database similarity search. By functional analysis, we estimated that 84.73% of transcripts encode significant proteins. The most prominent sequences corresponds to members of metabolic pathways, avirulence-associated protein, beta-tubulin, calcium/calmodulin dependent protein kinase 3, catalase, endo-1, 4-betaglucanase, cyst germination specific acidic repeat protein precursor, elicitin-like protein, glucanase inhibitor protein, heat shock protein, Kazal-like serine protease inhibitor, mitogen-activated protein kinase, ribosomal protein, serine/threonine kinase, syntaxin and ubiquitin. This EST-gene discovery information can be used to design sequence specific markers for P. capsici identification.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/1722024.1722043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64107885","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

Machine learning support for kidney transplantation decision making 机器学习支持肾移植决策

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722079

F. Reinaldo, Md. Anishur Rahman, Carlos F. Alves, A. Malucelli, Rui Camacho

引用次数: 6

Human Pol II promoter prediction by using nucleotide property composition features 利用核苷酸性质组成特征预测人类Pol II启动子

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722050

Wen-Lin Huang, C. Tung, Shinn-Ying Ho

{"title":"Human Pol II promoter prediction by using nucleotide property composition features","authors":"Wen-Lin Huang, C. Tung, Shinn-Ying Ho","doi":"10.1145/1722024.1722050","DOIUrl":"https://doi.org/10.1145/1722024.1722050","url":null,"abstract":"RNA polymerase II (Pol II) promoter is a key region that regulates differential transcription of protein coding genes. The identification of the RNA polymerase II (Pol II) promoter is one of the most challenging problems in genome annotation. Though many promoter prediction methods and tools have been developed, they have not yet extracted informative features from large-scale DNA sequences to improve predictive accuracy. A prediction method ProPolyII, which involves mining informative nucleotide property composition (NPC) features, is proposed to design a support vector machine-based classifier. An existing data set HumP (1872 human promoters and 1870 non-promoters) is used to evaluate ProPolyII for promoter prediction. ProPolyII yields 70 informative NPC features with training and test accuracies of 99.1% and 95.1%, respectively. The 70 NPC features consist of 46 4-mer motifs, 3 nucleotide properties and 21 global descriptors. The accuracies are better than those of Prom-Machine (94.9% and 91.1%) and M1 (97.4% and 93.6%) which uses top 128 4-mer motifs and 36 global descriptors, respectively. The high predictive performance indicates that ProPolyII can be beneficial in the identification of promoters comparative to other methods.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/1722024.1722050","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64108262","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

sRNA associated genomic islands in Salmonella spp. 沙门氏菌sRNA相关的基因组岛。

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722058

J. Sridhar, K. Kavitha

引用次数: 0

Comparative sequence and structural analyses of neuroserpin: the serine protease inhibitor family 丝氨酸蛋白酶抑制剂家族neuroserpin的比较序列和结构分析

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722031

Kuchi Srikeerthana, P. De Causmaecker

{"title":"Comparative sequence and structural analyses of neuroserpin: the serine protease inhibitor family","authors":"Kuchi Srikeerthana, P. De Causmaecker","doi":"10.1145/1722024.1722031","DOIUrl":"https://doi.org/10.1145/1722024.1722031","url":null,"abstract":"Neuroserpin, a clade of serine proteinase inhibitors (serpins) is a selective inhibitor of tissue-type plasminogen activator (tPA) and usually has more than 220 residues. The crystal structure of native human neuroserpin has been reported by Sayaka et al., [17] at 2.1 Å resolution. The native fold of neuroserpin is composed of a five stranded β-sheet A and a mobile helical reactive center loop (RCL). The structure also contains an omega loop (Ω-loop), which contributes to the inhibition of tPA and a helix 'F' that plays an important role in folding, complex formation and polymerization.\u0000 In this study, we identify new members of the neuroserpin family by comparative sequence analyses, and we analyze the conservation of the reactive center loop, the omega loop, the helix 'F' and other consensus residues, in the newly found relatives, which differ from the consensus sequences of other clades of serpins. By comparative structural analyses of neuroserpin with its structurally similar proteins, we reveal the structural patterns and the stabilizing interactions, that are unique among the members of neuroserpin family.","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2010-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/1722024.1722031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64108040","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

Computational design of soluble variants of transmembrane proteins: an information theoretic approach 跨膜蛋白可溶性变异体的计算设计:一种信息理论方法

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722033

Jishnu Das

引用次数: 0

Identifying human miRNA targets with a genetic algorithm 用遗传算法鉴定人类miRNA靶点

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722059

Kalle Karhu, S. Khuri, Juho Mäkinen, J. Tarhio

引用次数: 3

Evolving fragments to lead molecules 将碎片进化成先导分子

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722061

Soumi Sengupta, S. Bandyopadhyay

引用次数: 1