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Determining In Vivo Phosphorylation Sites Using Mass Spectrometry

Abstract Table of Contents Materials Figures Literature Cited Abstract Phosphorylation is the most studied protein post?translational modification (PTM) in biological systems, since it controls cell growt

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RASL‐seq for Massively Parallel and Quantitative Analysis of Gene Expression

Abstract Table of Contents Materials Figures Literature Cited Abstract Large?scale, quantitative analysis of gene expression can be accomplished by microarray or RNA?seq analysis. While these methods are

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Searching for Non‐B DNA‐Forming Motifs Using nBMST (Non‐B DNA Motif Search Tool)

Abstract Table of Contents Materials Figures Literature Cited Abstract This unit describes basic protocols on using the non?B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form

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Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy

Abstract Table of Contents Materials Figures Literature Cited Abstract Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a larg

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Using Galaxy to Perform Large‐Scale Interactive Data Analyses

Abstract Table of Contents Figures Literature Cited Abstract Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high?throughput data resources to be ana

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Using the KEGG Database Resource

Abstract Table of Contents Figures Literature Cited Abstract KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding the functions and utilities of cells and organisms from both high?level and genomic

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Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) Compliant Manuscript Using the International Society for Advancement of

Abstract Table of Contents Materials Figures Literature Cited Abstract FlowRepository.org is a Web?based flow cytometry data repository provided by the International Society for Advancement of Cytometry (

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Mining the Salivary Proteome with Grating‐Coupled Surface Plasmon Resonance Imaging and Surface Plasmon Coupled Emission Microarrays

Abstract Table of Contents Materials Figures Literature Cited Abstract Biological indicators have numerous and widespread utility in personalized medicine, but the measurement of these indicators also pos

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Metallomics Using Inductively Coupled Plasma Mass Spectrometry

Abstract Table of Contents Materials Figures Literature Cited Abstract Inductively Coupled Plasma Mass Spectrometry (ICP?MS) is a highly sensitive elemental analysis technique that has been widely applied

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Dealing with the Data Deluge: Handling the Multitude of Chemical Biology Data Sources

Abstract Table of Contents Figures Literature Cited Abstract Over the last 20 years, there has been an explosion in the amount and type of biological and chemical data that has been made publicly available in a variety of online databases.

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Selecting, Acquiring, and Using Small Molecule Libraries for High‐Throughput Screening

Abstract Table of Contents Figures Literature Cited Abstract The selection, acquisition, and use of high?quality small molecule libraries for screening is an essential aspect of drug discovery and chemical biology programs. Screening libra

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Genotyping in the Cloud with Crossbow

Abstract Table of Contents Figures Literature Cited Abstract Crossbow is a scalable, portable, and automatic cloud computing tool for identifying SNPs from high?coverage, short?read resequencing data. It is built on Apache Hadoop, an imple

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Using ProHits to Store, Annotate, and Analyze Affinity Purification–Mass Spectrometry (AP‐MS) Data

Abstract Table of Contents Materials Figures Literature Cited Abstract Affinity purification coupled with mass spectrometry (AP?MS) is a robust technique used to identify protein?protein interactions. Wit

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Analyzing Protein‐Protein Interactions from Affinity Purification‐Mass Spectrometry Data with SAINT

Abstract Table of Contents Materials Figures Literature Cited Abstract Significance Analysis of INTeractome (SAINT) is a software package for scoring protein?protein interactions based on label?free quant

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The Human Gene Mutation Database (HGMD) and Its Exploitation in the Fields of Personalized Genomics and Molecular Evolution

Abstract Table of Contents Figures Literature Cited Abstract The Human Gene Mutation Database (HGMD) constitutes a comprehensive core collection of data on germ?line mutations in nuclear genes underlying or associated with human inherited

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A Survey of Copy‐Number Variation Detection Tools Based on High‐Throughput Sequencing Data

Abstract Table of Contents Figures Literature Cited Abstract Copy?number variation (CNV) is a major class of genomic variation with potentially important functional consequences in both normal and diseased populations. Remarkable advances

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Protein Databases on the Internet

Abstract Table of Contents Figures Literature Cited Abstract Protein databases have become a crucial part of modern biology. Huge amounts of data for protein structures, functions, and particularly sequences are being generated. Searching

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Byonic: Advanced Peptide and Protein Identification Software

Abstract Table of Contents Figures Literature Cited Abstract Byonic is the name of a software package for peptide and protein identification by tandem mass spectrometry. This software, which has only recently become commercially available,

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PatternLab: From Mass Spectra to Label‐Free Differential Shotgun Proteomics

Abstract Table of Contents Figures Literature Cited Abstract PatternLab for proteomics is a self?contained computational environment for analyzing shotgun proteomic data. Recent improvements incorporate modules to facilitate the computatio

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Using the Wash U Epigenome Browser to Examine Genome‐Wide Sequencing Data

Abstract Table of Contents Figures Literature Cited Abstract This unit describes the Wash U Epigenome Browser, a next?generation genomic data visualization system. The Browser currently hosts ENCODE and Roadmap Epigenomics data for human a

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