Systems Biology

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    Protocols in Current Issue
    Synthetic Genetic Interaction (CRISPR-SGI) Profiling in Caenorhabditis elegans
    Authors:  John A. Calarco and Adam D. Norris, date: 03/05/2018, view: 3639, Q&A: 0
    [Abstract] Genetic interaction screens are a powerful methodology to establish novel roles for genes and elucidate functional connections between genes. Such studies have been performed to great effect in single-cell organisms such as yeast and E. coli (Schuldiner et al., 2005; Butland et al., 2008; Costanzo et al., 2010), ...
    Computational Identification of MicroRNA-targeted Nucleotide-binding Site-leucine-rich Repeat Genes in Plants
    Authors:  Zhu-Qing Shao, Yan-Mei Zhang, Bin Wang and Jian-Qun Chen, date: 11/05/2015, view: 6159, Q&A: 0
    [Abstract] Plant genomes harbor dozens to hundreds of nucleotide-binding site-leucine-rich repeat (NBS-LRR, NBS for short) type disease resistance genes (Shao et al., 2014; Zhang et al., 2015). Proper regulation of these genes is important for normal growth of plants by reducing unnecessary fitness costs in the absence of pathogen ...
    A Conceptual Outline for Omics Experiments Using Bioinformatics Analogies
    Authors:  Prashanth Suravajhala and Jeffrey W. Bizzaro, date: 02/05/2015, view: 7917, Q&A: 0
    [Abstract] Hypothetical proteins (HP) are those that are not characterized in the laboratory and so remain “orphaned” in genomic databases. In recent times there has been a lot of progress in characterizing HPs in the laboratory. Various methods, such as sequence capture and Next Generation Sequencing (NGS), have been used to rapidly identify HP functions ...
    SGR-based Reporter to Assay Plant Transcription Factor-promoter Interactions
    Authors:  Shisong Ma and Savithramma Dinesh-Kumar, date: 08/20/2014, view: 7291, Q&A: 0
    [Abstract] We developed an in vivo method to assay plant transcription factor (TF)–promoter interactions using the transient expression system in Nicotiana benthamiana (N. benthamiana) plants. The system uses the Arabidopsis stay green (SGR) gene as a reporter. Induction of SGR expression in N. ...
    Gene Networks Based on the Graphical Gaussian Model
    Author:  Shisong Ma, date: 02/20/2012, view: 10983, Q&A: 1
    [Abstract] This protocol describes how to build a gene network based on the graphical Gaussian model (GGM) from large scale microarray data. GGM uses partial correlation coefficient (pcor) to infer co-expression relationship between genes. Compared to the traditional Pearson’ correlation coefficient, partial correlation is a better measurement of direct ...



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