Systems Biology


    A Simple Protocol for Informative Visualization of Enriched Gene Ontology Terms
    Authors:  Titouan Bonnot, Morgane B. Gillard and Dawn H. Nagel, date: 11/20/2019, view: 8721, Q&A: 6
    In genome-scale datasets, Gene Ontology (GO) enrichment is a common analysis to highlight functions over-represented or under-represented in a subset of differentially expressed genes to elucidate the biological significance of the results. However, ...
    Hormone Treatments during Maize Vegetative and Reproductive Development
    Authors:  María Jazmín Abraham-Juárez and Harry Klein, date: 05/20/2019, view: 2260, Q&A: 0
    Plant hormones are a group of organic natural compounds that can influence physiological processes when present at low concentrations. Plant biologists frequently use exogenous hormone application to modify plant physiology or to rescue mutants with ...
    A Bioinformatics Pipeline for Whole Exome Sequencing: Overview of the Processing and Steps from Raw Data to Downstream Analysis
    Authors:  Narendra Meena, Praveen Mathur, Krishna Mohan Medicherla and Prashanth Suravajhala, date: 04/20/2018, view: 25223, Q&A: 0
    Recent advances in Next Generation Sequencing (NGS) technologies have given an impetus to find causality for rare genetic disorders. Since 2005 and aftermath of the human genome project, efforts have been made to understand the rare variants of ...
    Protein-ligand Binding Assay by Liquid Chromatography-Mass Spectrometry
    Author:  Xiyan Li, date: 08/20/2011, view: 15828, Q&A: 0
    Protein-small molecule binding coefficients are determined by quantitative LC-MS in this method. Traditional biochemical plot is consequently used to set up the binding curve between a known protein and a small molecule (<1000 da) to determine the affinity constant (kd) and the stoichiometry (bmax). da)="" to="" determine="" the="" affinity="" constant="" (kd)="" and="" the="" stoichiometry=""> ...
    Rabbit IgG Conjugation to Dynabeads
    Author:  Xiyan Li, date: 05/05/2011, view: 15752, Q&A: 1
    This method couples rabbit IgG (or any other proteins serve as affinity reagent) to the surface of magnetic beads (Brand name: Dynabeads). The amine and thiol groups of amino acid residues on the protein are covalently linked with the epoxy group on ...
    In-Solution Digestion Of Purified Yeast Protein For LC-MS
    Author:  Xiyan Li, date: 04/20/2011, view: 13956, Q&A: 0
    This method describes the preparation of total yeast protein extract for mass spectrometry analysis. The protein extract is digested by trypsin in a solution with strong denaturants. The digested sample is dried and re-constituted in a mixture ...
    Affinity Purification of Yeast Protein-interacting Metabolites for ESI-MS Analysis
    Author:  Xiyan Li, date: 04/20/2011, view: 14385, Q&A: 5
    The method described here can be used to discover in vivo protein-metabolite interactions. Metabolite-protein complexes are purified from yeast cell lysates by an affinity tag that recognizes the protein of interest. The protein-bound metabolites ...

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