292 Result(s)
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Protocol
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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Protocol
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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Protocol
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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Protocol
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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Protocol
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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Protocol
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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Protocol
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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Protocol
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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Protocol
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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Protocol
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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Protocol
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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Immunoinformatics and the in Silico Prediction of Immunogenicity
Immunoinformatics is the application of informatics techniques to molecules of the immune system. One of its principal goals is the effective prediction of immunogenicity, be that at the level of epitope, subu...
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Protocol
Useful Mass Spectrometry Programs Freely Available on the Internet
The intention with this chapter is to give an overview of a broad range of freely available programs on the internet which are useful for analyses of mass spectrometry data. The list is by no means a full list...
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Protocol
Organization of Proteomics Data With YassDB
In recent years the organization of mass spectrometry (MS) data obtained in large-scale proteomics projects became an important issue. This has catalyzed the development of a few different database schemes for...
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Protocol
The IMGT/HLA Database
The human leukocyte antigen (HLA) complex is located within the 6p21.3 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of t...
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Protocol
SYFPEITHI
Reverse immunology has been used for about 12 years in order to identify T-cell epitopes from pathogens or tumor-associated antigens. In this chapter, we discuss the advantages and pitfalls of T-cell epitope p...
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Protocol
Structural Basis for HLA-A2 Supertypes
The human leukocyte antigen (HLA) alleles are extremely polymorphic among ethnic population, and the peptide-binding specificity varies for different alleles in a combinatorial manner. However, it has been sug...
