292 Result(s)
within
English
Bioinformatics
Cell Biology
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Protocol
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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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Interpretation of Collision-Induced Fragmentation Tandem Mass Spectra of Posttranslationally Modified Peptides
Tandem collision-induced dissociation (CID) mass spectrometry (MS) provides a sensitive means of analyzing the amino acid sequence of peptides. Modern MS instrumentation is capable of rapidly generating many t...
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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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Extracting Monoisotopic Single-Charge Peaks From Liquid Chromatography-Electrospray Ionization-Mass Spectrometry
Peak extraction from raw data is the first step in analysis of mass spectrometry (MS) data. The quality of this procedure is very important because it affects the quality of all subsequent analysis, such as da...
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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...
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Association Analysis for Large-Scale Gene Set Data
High-throughput experiments in biology often produce sets of genes of potential interests. Some of those gene sets might be of considerable size. Therefore, computer-assisted analysis is necessary for the biol...
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Separation of Cell-Cell Adhesion Complexes by Differential Centrifugation
The number of proteins found associated with cell-cell adhesion substructures is growing rapidly. Based on potential protein-protein interactions, complex protein networks at cell-cell contacts can be modeled....
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ArrayPlex SA
Automated target preparation for gene expression analysis eliminates the time-consuming and labor-intensive manual process, which is error prone and diverts scientists from value added activities. Target prepa...
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Toward the Prediction of Class I and II Mouse Major Histocompatibility Complex-Peptide-Binding Affinity
Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide–major histocompatibility complex (MHC)-binding affinity based on ...
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In Silico Prediction of Peptide-MHC Binding Affinity Using SVRMHC
The binding between peptide epitopes and major histocompatibility complex (MHC) proteins is a major event in the cellular immune response. Accurate prediction of the binding between short peptides and class I ...
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Quantitative Proteomics by Stable Isotope Labeling and Mass Spectrometry
The goal of quantitative proteomics is to systematically study static state or perturbation-induced changes in protein profile. Most of the recently developed mass spectrometry (MS)-based quantitative proteomi...
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Analysis of Focal Adhesions and Cytoskeleton by Custom Microarray
Focal adhesions and the cell cytoskeleton (intermediate filaments, microfilaments, microtubules) are involved in mechanotransduction—both direct (transduction of mechanical forces to the nucleus) and indirect ...
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From Promoter Analysis to Transcriptional Regulatory Network Prediction Using PAINT
Highly parallel gene-expression analysis has led to analysis of gene regulation, in particular coregulation, at a system level. Promoter analysis and interaction network toolset (PAINT) was developed to provid...
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Analysis of Leukocyte Migration Through Monolayers of Cultured Endothelial Cells
In this chapter methods are described for analyzing the adhesion and migration of isolated leukocytes on endothelial cell monolayers that have been cultured on different substrates and treated with cytokines. ...
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Quality Considerations and Selection of Surface Chemistry for Glass-Based DNA, Peptide, Antibody, Carbohydrate, and Small Molecule Microarrays
The complexity of workflows for the production of high quality microarrays asks for the careful evaluation and implementation of materials and methods. As a cornerstone of the whole microarray process, the mic...
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Identification of Small Molecule Targets on Functional Protein Microarrays
Small molecules, such as metabolites and hormones, interact with proteins to regulate numerous biological pathways, which are often aberrant in disease. Small molecule drugs have been successfully exploited to...
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Implementing the Modular MHC Model for Predicting Peptide Binding
The challenge of predicting which peptide sequences bind to which major histocompatibility complex (MHC) molecules has been met with various computational techniques. Scoring matrices, hidden Markov models, an...
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A Practical Guide to Structure-Based Prediction of MHC-Binding Peptides
The binding of bound peptide ligands to major histocompatibility complex (MHC) molecules plays a key role in the activation of normal immune responses and is an intricate theoretical problem that remains unsol...
