132 Result(s)
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Bioinformatics
Cell Biology
Human Genetics
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Protocol
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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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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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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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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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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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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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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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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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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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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...
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Searching and Map** of B-Cell Epitopes in Bcipep Database
One of the major challenges in the field of subunit vaccine design is to identify the antigenic regions in an antigen, which can activate B cell. These antigenic regions are called B-cell epitopes. In this cha...
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Grou** of Class I HLA Alleles Using Electrostatic Distribution Maps of the Peptide Binding Grooves
Human leukocyte antigen (HLA) molecules involved in immune function by binding to short peptides (8–20 residues) have different sequences in different individuals belonging to distinct ethnic population. Hence...
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The Classification of HLA Supertypes by GRID/CPCA and Hierarchical Clustering Methods
Biological experiments often produce enormous amount of data, which are usually analyzed by data clustering. Cluster analysis refers to statistical methods that are used to assign data with similar properties ...
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Protein Chip for Detection of DNA Mutations
A large number of human genetic diseases, bacterial drug resistances, and single-nucleotide polymorphisms are caused by gene mutations. Rapid and high-throughput mutation detection methods are urgently demande...
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Application of Machine Learning Techniques in Predicting MHC Binders
The machine learning techniques are playing a vital role in the field of immunoinformatics. In the past, a number of methods have been developed for predicting major histocompatibility complex (MHC)-binding pe...
