Handbook of Research on Computational and Systems Biology最新文献

A New Approach for Sequence Analysis: Illustrating an Expanded Bioinformatics View through Exploring Properties of the Prestin Protein 序列分析的新方法:通过探索Prestin蛋白的特性来阐述扩展的生物信息学观点

Handbook of Research on Computational and Systems Biology Pub Date : 2011-12-01 DOI: 10.4018/978-1-60960-491-2.ch009

K. Dempsey, Benjamin Currall, R. Hallworth, H. Ali

{"title":"A New Approach for Sequence Analysis: Illustrating an Expanded Bioinformatics View through Exploring Properties of the Prestin Protein","authors":"K. Dempsey, Benjamin Currall, R. Hallworth, H. Ali","doi":"10.4018/978-1-60960-491-2.ch009","DOIUrl":"https://doi.org/10.4018/978-1-60960-491-2.ch009","url":null,"abstract":"Understanding the structure-function relationship of proteins offers the key to biological processes, and can offer knowledge for better investigation of matters with widespread impact, such as pathological disease and drug intervention. This relationship is dictated at the simplest level by the primary protein sequence. Since useful structures and functions are conserved within biology, a sequence with known structure-function relationship can be compared to related sequences to aid in novel structure-function prediction. Sequence analysis provides a means for suggesting evolutionary relationships, and inferring structural or functional similarity. It is crucial to consider these parameters while comparing sequences as they influence both the algorithms used and the implications of the results. For example, proteins that are closely related on an evolutionary time scale may have very similar structure, but entirely different functions. In contrast, proteins which have undergone convergent evolution may have dissimilar primary structure, but perform similar functions. This chapter details how the aspects of evolution, structure, and function can be taken into account when performing sequence analysis, and proposes an expansion on traditional approaches resulting in direct improvement of said analysis. This model is applied to a case study in the prestin protein and shows that the proposed approach provides a better understanding of input and output and can improve the performance of sequence analysis by means of motif detection software. Kathryn Dempsey University of Nebraska at Omaha, USA & University of Nebraska Medical Center, USA Benjamin Currall Creighton University, USA Richard Hallworth Creighton University, USA Hesham Ali University of Nebraska at Omaha, USA & University of Nebraska Medical Center, USA DOI: 10.4018/978-1-4666-3604-0.ch079","PeriodicalId":254251,"journal":{"name":"Handbook of Research on Computational and Systems Biology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130761593","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: 11

Connecting Microbial Population Genetics with Microbial Pathogenesis Engineering Microfluidic Cell Arrays for High-throughput Interrogation of Host-Pathogen Interaction 连接微生物群体遗传学与微生物发病机理工程的微流控细胞阵列高通量询问宿主-病原体相互作用

Handbook of Research on Computational and Systems Biology Pub Date : 2011-12-01 DOI: 10.4018/978-1-60960-491-2.ch023

P. Sethu, K. Putty, Y. Lian, A. Kalia

{"title":"Connecting Microbial Population Genetics with Microbial Pathogenesis Engineering Microfluidic Cell Arrays for High-throughput Interrogation of Host-Pathogen Interaction","authors":"P. Sethu, K. Putty, Y. Lian, A. Kalia","doi":"10.4018/978-1-60960-491-2.ch023","DOIUrl":"https://doi.org/10.4018/978-1-60960-491-2.ch023","url":null,"abstract":"A bacterial species typically includes heterogeneous collections of genetically diverse isolates. How genetic diversity within bacterial populations influences the clinical outcome of infection remains mostly indeterminate. In part, this is due to a lack of technologies that can enable contemporaneous systemslevel interrogation of host-pathogen interaction using multiple, genetically diverse bacterial strains. This chapter presents a prototype microfluidic cell array (MCA) that allows simultaneous elucidation of molecular events during infection of human cells in a semi-automated fashion. It shows that infection of human cells with up to sixteen genetically diverse bacterial isolates can be studied simultaneously. The versatility of MCAs is enhanced by incorporation of a gradient generator that allows interrogation of host-pathogen interaction under four different concentrations of any given environmental variable at the same time. Availability of high throughput MCAs should foster studies that can determine how differences in bacterial gene pools and concentration-dependent environmental variables affect the outcome of host-pathogen interaction.","PeriodicalId":254251,"journal":{"name":"Handbook of Research on Computational and Systems Biology","volume":"202 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2011-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131472648","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: 2

Ethics and Privacy Considerations for Systems Biology Applications in Predictive and Personalized Medicine 在预测性和个性化医学中系统生物学应用的伦理和隐私考虑

Handbook of Research on Computational and Systems Biology Pub Date : 2011-12-01 DOI: 10.4018/978-1-60960-491-2.ch001

J. Chen, Heng Xu, Pan Shi, Adam Culbertson, E. Meslin

引用次数: 7

Mechanical Models of Cell Adhesion Incorporating Nonlinear Behavior and Stochastic Rupture of the Bonds: Concepts and Preliminary Results 结合非线性行为和随机断裂的细胞粘附力学模型:概念和初步结果

Handbook of Research on Computational and Systems Biology Pub Date : 1900-01-01 DOI: 10.4018/978-1-60960-491-2.ch027

J. Ganghoffer

{"title":"Mechanical Models of Cell Adhesion Incorporating Nonlinear Behavior and Stochastic Rupture of the Bonds: Concepts and Preliminary Results","authors":"J. Ganghoffer","doi":"10.4018/978-1-60960-491-2.ch027","DOIUrl":"https://doi.org/10.4018/978-1-60960-491-2.ch027","url":null,"abstract":"The rolling of a single biological cell is analysed using modelling of the local kinetics of successive attachment and detachment of bonds occurring at the interface between a single cell and the wall of an ECM (extracellular matrix). Those kinetics correspond to a succession of creations and ruptures of ligand-receptor molecular connections under the combined effects of mechanical, physical (both specific and non-specific), and chemical external interactions. A three-dimensional model of the interfacial molecular rupture and adhesion kinetic events is developed in the present contribution. From a mechanical point of view, this chapter works under the assumption that the cell-wall interface is composed of two elastic shells, namely the wall and the cell membrane, linked by rheological elements representing the molecular bonds. Both the time and space fluctuations of several parameters related to the mutual affinity of ligands and receptors are described by stochastic field theory; especially, the individual rupture limits of the bonds are modelled in Fourier space from the spectral distribution of power. The bonds","PeriodicalId":254251,"journal":{"name":"Handbook of Research on Computational and Systems Biology","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123040633","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: 3

Dynamic Modeling and Parameter Identification for Biological Networks: Application to the DNA Damage and Repair Processes 生物网络的动态建模和参数识别:在DNA损伤和修复过程中的应用

Handbook of Research on Computational and Systems Biology Pub Date : 1900-01-01 DOI: 10.4018/978-1-60960-491-2.ch021

F. Bianconi, G. Lillacci, P. Valigi

{"title":"Dynamic Modeling and Parameter Identification for Biological Networks: Application to the DNA Damage and Repair Processes","authors":"F. Bianconi, G. Lillacci, P. Valigi","doi":"10.4018/978-1-60960-491-2.ch021","DOIUrl":"https://doi.org/10.4018/978-1-60960-491-2.ch021","url":null,"abstract":"DNA damage and repair processes are key cellular phenomena that are being intensely studied because of their implications in the onset and therapy of cancer. This chapter introduces a general dynamic model of gene expression, and proposes a genetic network modeling framework based on the interconnection of a continuous-time model and a hybrid model. This strategy is applied to a network built around the p53 gene and protein, which detects DNA damage and activates the downstream nucleotide excision repair (NER) network, which carries out the actual repair tasks. Then, two different parameter identification techniques are presented for the proposed models. One is based on a least squares procedure, which treats the signals provided by a high gain observer; the other one is based on a Mixed Extended Kalman Filter. Prior to the estimation phase, identifiability and sensitivity analyses are used to determine which parameters can be and/or should be estimated. The procedures are tested and compared by means of data obtained by in silico experiments. DOI: 10.4018/978-1-60960-491-2.ch021","PeriodicalId":254251,"journal":{"name":"Handbook of Research on Computational and Systems Biology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117224080","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: 5

Network-Driven Analysis Methods and their Application to Drug Discovery 网络驱动分析方法及其在药物发现中的应用

Handbook of Research on Computational and Systems Biology Pub Date : 1900-01-01 DOI: 10.4018/978-1-60960-491-2.ch013

D. Ziemek, C. Brockel

引用次数: 1

Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis 基于基因组分析鉴定新型次生代谢物生物合成途径的计算方法

Handbook of Research on Computational and Systems Biology Pub Date : 1900-01-01 DOI: 10.4018/978-1-60960-491-2.ch018

S. Anand, D. Mohanty

{"title":"Computational Methods for Identification of Novel Secondary Metabolite Biosynthetic Pathways by Genome Analysis","authors":"S. Anand, D. Mohanty","doi":"10.4018/978-1-60960-491-2.ch018","DOIUrl":"https://doi.org/10.4018/978-1-60960-491-2.ch018","url":null,"abstract":"Secondary metabolites belonging to polyketide and nonribosomal peptide families constitute a major class of natural products with diverse biological functions and a variety of pharmaceutically important properties. Experimental studies have shown that the biosynthetic machinery for polyketide and nonribosomal peptides involves multi-functional megasynthases like Polyketide Synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) which utilize a thiotemplate mechanism similar to that for fatty acid biosynthesis. Availability of complete genome sequences for an increasing number of microbial organisms has provided opportunities for using in silico genome mining to decipher the secondary metabolite natural product repertoire encoded by these organisms. Therefore, in recent years there have been major advances in development of computational methods which can analyze genome sequences to identify genes involved in secondary metabolite biosynthesis and help in deciphering the putative chemical structures of their biosynthetic products based on analysis of the sequence and structural features of the proteins encoded by these genes. These computational methods for deciphering the secondary metabolite biosynthetic code essentially involve identification of various catalytic domains present in DOI: 10.4018/978-1-60960-491-2.ch018","PeriodicalId":254251,"journal":{"name":"Handbook of Research on Computational and Systems Biology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132322704","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: 18

Finding Attractors on a Folding Energy Landscape 在折叠能量格局中寻找吸引子

Handbook of Research on Computational and Systems Biology Pub Date : 1900-01-01 DOI: 10.4018/978-1-60960-491-2.ch025

W. Ndifon, J. Dushoff

引用次数: 2

Visualization of Protein 3D Structures in 'Double-Centroid' Reduced Representation: Application to Ligand Binding Site Modeling and Screening “双质心”简化表示中蛋白质三维结构的可视化:在配体结合位点建模和筛选中的应用

Handbook of Research on Computational and Systems Biology Pub Date : 1900-01-01 DOI: 10.4018/978-1-60960-491-2.ch026

V. M. Reyes, Vrunda Sheth

{"title":"Visualization of Protein 3D Structures in 'Double-Centroid' Reduced Representation: Application to Ligand Binding Site Modeling and Screening","authors":"V. M. Reyes, Vrunda Sheth","doi":"10.4018/978-1-60960-491-2.ch026","DOIUrl":"https://doi.org/10.4018/978-1-60960-491-2.ch026","url":null,"abstract":"This article is of two parts: (a) the development of a protein reduced representation and its implementation in a Web server; and (b) the use of the reduced protein representation in the modeling of the binding site of a given ligand and the screening for the model in other protein 3D structures. Current methods of reduced protein 3D structure representation such as the Cα trace method not only lack essential molecular detail, but also ignore the chemical properties of the component amino acid side chains. This chapter describes a reduced protein 3D structure representation called “double-centroid reduced representation” and presents a visualization tool called the “DCRR Web Server” that graphically displays a protein 3D structure in DCRR along with non-covalent intraand intermolecular hydrogen bonding and van der Waals interactions. In the DCRR model, each amino acid residue is represented as two points: the centroid of the backbone atoms and that of the side chain atoms; in the visualization Web server, they and the non-bonded interactions are color-coded for easy identification. The visualization tool in this chapter is implemented in MATLAB and is the first for a reduced protein representation as well as one that simultaneously displays non-covalent interactions in the molecule. The DCRR model reduces the atomicity of the protein structure by ~75% while capturing the essential chemical properties of the component amino acids. The second half of this chapter describes the application of this reduced representation to the modeling and screening of ligand binding sites using a data model termed the “tetrahedral motif.” This type of ligand binding site modeling and screening presents a novel type of pharmacophore modeling and screening, one that depends on a reduced protein representation. DOI: 10.4018/978-1-4666-3604-0.ch059","PeriodicalId":254251,"journal":{"name":"Handbook of Research on Computational and Systems Biology","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124685899","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: 16

Granger Causality: Its Foundation and Applications in Systems Biology 格兰杰因果关系:其基础及其在系统生物学中的应用

Handbook of Research on Computational and Systems Biology Pub Date : 1900-01-01 DOI: 10.4018/978-1-60960-491-2.ch022

Tian Ge, Jianfeng Feng

引用次数: 1