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Bioinformatics
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Protocol
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Mining Biomedical Data Using MetaMap Transfer (MMTx) and the Unified Medical Language System (UMLS)
Detailed instruction is described for map** unstructured, free text data into common biomedical concepts (drugs, diseases, anatomy, and so on) found in the Unified Medical Language System using MetaMap Trans...
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Proteomic Data Exchange and Storage
The ever increasing volumes of proteomic data now being produced by laboratories across the world have resulted in major issues in data storage and accessibility. The further demands of multilaboratory initiat...
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Construction of Simple and Efficient DNA Vector-Based Short Hairpin RNA Expression Systems for Specific Gene Silencing in Mammalian Cells
RNA interference (RNAi) is an evolutionarily conserved mechanism of posttranscriptional gene silencing induced by introducing the double-stranded RNAs (dsRNAs) into cells. Recent progress in RNAi-based gene-si...
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Conditional Targeting
Tissue specific gene knockouts using Cre recombinase can have broad applicability in murine disease models of cardiovascular disease. The Cre system has been shown to have broad experimental versatility for bo...
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Assaying Calpain Activity
The calpains represent a well-conserved family of intracellular proteases that exhibit broad substrate specificity and consequently influence many cellular processes. Calpain activity regulates the turnover of...
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Microarray Technology for Use in Molecular Epidemiology
Microarrays are a powerful laboratory tool for the simultaneous assessment of the activity of thousands genes. Remarkable advances in biological sample collection, preparation and automation of hybridization h...
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Sequence Handling by Sequence Analysis Toolbox v1.0
The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that...
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Predicting DNA Duplex Stability on Oligonucleotide Arrays
DNA duplex stability on oligonucleotide microarray was calculated using recently developed electrostatic theory of on-array hybridization thermodynamics. In this method, the first step is to finding the enthal...
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Nonlinear Predictive Modeling of MHC Class II-Peptide Binding Using Bayesian Neural Networks
Methods for predicting the binding affinity of peptides to the MHC have become more sophisticated in the past 5–10 years. It is possible to use computational quantitative structure-activity methods to build mo...
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Predicting Virulence Factors of Immunological Interest
In this chapter, three prediction servers used for predicting virulence factors, bacterial toxins, and neurotoxins have been described. VICMpred server predicts the functional proteins of gram-negative bacteri...
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A Bacterial/Yeast Merged Two-Hybrid System
The yeast two-hybrid system is a useful tool for identifying new protein-protein interactions, and for the dissection of previously identified interactions. An important issue in protein-interaction studies is...
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Adeno-Associated Viral Vector-Delivered Hypoxia-Inducible Gene Expression in Ischemic Hearts
This chapter describes a system using adeno-associated viral (AAV) vector to deliver hypoxia-inducible gene expression to ischemic hearts. The hypoxia induction of gene expression in this system is based on th...
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Microarray Data Analysis
Microarray analysis results in the gathering of massive amounts of information concerning gene expression profiles of different cells and experimental conditions. Analyzing these data can often be a quagmire, ...
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A Microarray-Based Method to Profile Global microRNA Expression in Human and Mouse
The microRNAs (or miRNAs) are small noncoding RNAs (21—25 nt) that are processed from large hairpin RNA precursors and are believed to be involved in a wide range of developmental and cellular processes, by ei...
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Analysis of Comparative Genomic Hybridization Data on cDNA Microarrays
We present a detailed method to analyze DNA copy number data generated on cDNA microarrays. A web interface is made available for those steps in the workflow that are not typically used in gene expression anal...
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In Silico Gene Selection for Custom Oligonucleotide Microarray Design
A method for systematically selecting the large number of sequences needed to custom design an oligonucleotide microarray was presented. This approach uses a Perl script to query sequence databases with gene l...
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Prediction Methods for B-cell Epitopes
In this chapter, two prediction servers of linear B-cell epiotpes have been described; (i) BcePred, based on physico-chemical properties that include hydrophilicity, flexibility/mobility, accessibility, polari...
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Engineering Cys2His2 Zinc Finger Domains Using a Bacterial Cell-Based Two-Hybrid Selection System
Synthetic Cys2His2 zinc finger domains with novel DNA-binding specificities can be identified from large randomized libraries using selection methodologies such as phage display. It has been previously demonst...
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Online Analysis of Microarray Data Using Artificial Neural Networks
Herein we have set forth a detailed method to analyze microarray data using artificial neural networks (ANN) for the purpose of classification, diagnosis, or prognosis. All aspects of this analysis can be carr...
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Progression-Associated Genes in Astrocytoma Identified by Novel Microarray Gene Expression Data Reanalysis
Astrocytoma is graded as pilocytic (WHO grade I), diffuse (WHO grade II), anaplastic (WHO grade III), and glioblastoma multiforme (WHO grade IV). The progression from low- to high-grade astrocytoma is associat...
