122 Result(s)
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English
Biochemistry, general
Bioinformatics
Cell Biology
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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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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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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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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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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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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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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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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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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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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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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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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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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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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...
