In Silico Biology最新文献_第6页

Towards a virtual C. elegans: a framework for simulation and visualization of the neuromuscular system in a 3D physical environment. 迈向虚拟秀丽隐杆线虫:在三维物理环境中模拟和可视化神经肌肉系统的框架。

In Silico Biology Pub Date : 2011-01-01 DOI: 10.3233/ISB-2012-0445

Andrey Palyanov, Sergey Khayrulin, Stephen D Larson, Alexander Dibert

{"title":"Towards a virtual C. elegans: a framework for simulation and visualization of the neuromuscular system in a 3D physical environment.","authors":"Andrey Palyanov, Sergey Khayrulin, Stephen D Larson, Alexander Dibert","doi":"10.3233/ISB-2012-0445","DOIUrl":"https://doi.org/10.3233/ISB-2012-0445","url":null,"abstract":"<p><p>The nematode C. elegans is the only animal with a known neuronal wiring diagram, or \"connectome\". During the last three decades, extensive studies of the C. elegans have provided wide-ranging data about it, but few systematic ways of integrating these data into a dynamic model have been put forward. Here we present a detailed demonstration of a virtual C. elegans aimed at integrating these data in the form of a 3D dynamic model operating in a simulated physical environment. Our current demonstration includes a realistic flexible worm body model, muscular system and a partially implemented ventral neural cord. Our virtual C. elegans demonstrates successful forward and backward locomotion when sending sinusoidal patterns of neuronal activity to groups of motor neurons. To account for the relatively slow propagation velocity and the attenuation of neuronal signals, we introduced \"pseudo neurons\" into our model to simulate simplified neuronal dynamics. The pseudo neurons also provide a good way of visualizing the nervous system's structure and activity dynamics.</p>","PeriodicalId":39379,"journal":{"name":"In Silico Biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3233/ISB-2012-0445","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30870652","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: 38

Hydrophobic tint of knot proteins 结蛋白的疏水性

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722034

P. Anto, S. N. Achuthsankar

引用次数: 0

Improving prediction of protein secondary structure using physicochemical properties of amino acids 利用氨基酸的理化性质改进蛋白质二级结构的预测

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722036

P. Chatterjee, Subhadip Basu, M. Nasipuri

{"title":"Improving prediction of protein secondary structure using physicochemical properties of amino acids","authors":"P. Chatterjee, Subhadip Basu, M. Nasipuri","doi":"10.1145/1722024.1722036","DOIUrl":"https://doi.org/10.1145/1722024.1722036","url":null,"abstract":"Protein Structure Prediction is important in the sense that it helps to extend knowledge about the understanding of protein structures and functions. The knowledge is essential for prediction of secondary structures of unknown proteins required for applications related to drug discovery. A novel technique for protein secondary structure prediction is presented here. In this work, two levels of multi-layer feed forward neural networks are used. In the first level network, sequence profiles from PSI-BLAST and physicochemical properties of amino acids are used for sequence to structure predictions. Confidence values of forming helix, sheet and coil, obtained from the first level network are then used with the second level network for structure to structure predictions. The overall prediction accuracy as obtained through experimentation is in the range of 75.58% to 77.48%. This method is trained and tested with nrDSSP datasets using four folds cross validation. It is also tested on target proteins of Critical Assessment of Protein Structure Prediction Experiment (CASP3) and achieves better results than PSIPRED over some target proteins.","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/10.1145/1722024.1722036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64107844","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: 9

Application of reactive GRASP to the biclustering of gene expression data 反应性GRASP在基因表达数据双聚类中的应用

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722041

Shyama Das, S. M. Idicula

{"title":"Application of reactive GRASP to the biclustering of gene expression data","authors":"Shyama Das, S. M. Idicula","doi":"10.1145/1722024.1722041","DOIUrl":"https://doi.org/10.1145/1722024.1722041","url":null,"abstract":"A bicluster in gene expression dataset is a subset of genes that exhibit similar expression patterns through a subset of conditions. In this work biclusters are identified in two steps. In the first step high quality bicluster seeds are generated using KMeans clustering algorithm. These seeds are then enlarged using Reactive Greedy Randomized Adaptive Search Procedure (RGRASP) which is a multi-start metaheuristic method in which there are two phases, construction and local search. The objective here is to identify biclusters of maximum size with MSR lower than a given threshold. Experiments are conducted on both Yeast and Human Lymphoma datasets. The Experimental results on the benchmark datasets demonstrate that RGRASP is capable of identifying high quality biclusters compared to many of the already existing biclustering algorithms. Compared to the already existing algorithm based on the same RGRASP metaheuristics biclusters with larger size and lower mean squared residue are obtained using this algorithm in Yeast dataset. Moreover in this study the RGRASP is applied for the first time to find biclusters from the Human Lymphoma dataset.","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/10.1145/1722024.1722041","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64107881","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

Fuzzy pattern extraction for classification of protein sequences 模糊模式提取在蛋白质序列分类中的应用

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722046

Abhijit J. Kulkarni, A. Noronha, Sasanka Roy, S. Angadi

引用次数: 2

Study of indole inhibitors to increase the affinity of hnps-PLA2 in inflammatory disease 吲哚抑制剂在炎性疾病中增加hnps-PLA2亲和力的研究

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722056

Amit Nagal, Swapnil R. Jaiswal, H. Yadav, M. Mohan, P. Ghosh

引用次数: 0

Finding motifs using harmony search 使用和声搜索寻找主题

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722072

Jyotshna Dongardive, Aarti Patil, A. Bir, S. Jamkhedkar, Siby Abraham

引用次数: 8

Biclustering gene expression data using KMeans-binary PSO hybrid 使用kmeans -二进制PSO杂交对基因表达数据进行双聚类

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722074

Shyama Das, S. M. Idicula

引用次数: 3

Cis regulatory module discovery in immune cell development 免疫细胞发育中Cis调控模块的发现

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722039

S. R. Ganakammal, M. Kaplan, N. Perumal

{"title":"Cis regulatory module discovery in immune cell development","authors":"S. R. Ganakammal, M. Kaplan, N. Perumal","doi":"10.1145/1722024.1722039","DOIUrl":"https://doi.org/10.1145/1722024.1722039","url":null,"abstract":"Transcriptional regulatory mechanisms are mediated by a set of transcription factors (TFs), which bind to a specific region (motifs or transcription factor binding sites, TFBS), on the target gene(s) leading to gene expression. Eukaryotic regulatory motifs, referred to as cis regulatory modules (CRMs), tend to co-occur near the regulated gene's transcription start site and provide the building blocks to transcriptional regulatory networks that model the relevant TF-TFBS interactions. Here, we study IL-12 stimulated transcriptional regulators in STAT4 mediated T helper 1 (Th1) cell development by focusing on the identification of TFBS and CRMs using a set of Stat4 ChIP-on-chip target genes. A region containing 2000 bases of Mus musculus sequences with the Stat4 binding site, derived from the ChIP-on-chip data, has been characterized for enrichment of other motifs and, thus CRMs. We find two such motifs, (NF-κB and PPARγ/RXR) being enriched in the Stat4 binding sequences compared to neighboring background sequences and sets of random sequences of equal size. Furthermore, these predicted CRMs were observed to be associated with biologically relevant target genes in the ChIP-on-chip data set by meaningful gene ontology annotations. These analyses will lead to a better understanding of transcriptional regulatory networks in IL-12 stimulated Stat4 mediated Th1 cell differentiation.","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/10.1145/1722024.1722039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"64107849","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

Complete enumeration of compact structural motifs in proteins 在蛋白质中紧凑结构基序的完整枚举

In Silico Biology Pub Date : 2010-02-15 DOI: 10.1145/1722024.1722047

Bhadrachalam Chitturi, D. Bein, N. Grishin

引用次数: 10