Systems Biology


    Protocols in Current Issue
    Transient Expression Assay in NahG Arabidopsis Plants Using Agrobacterium tumefaciens
    Authors:  Pepe Cana-Quijada, Eduardo R. Bejarano, Rosa Lozano-Durán and Tábata Rosas-Díaz, date: 06/20/2018, view: 1119, Q&A: 0
    [Abstract] Agrobacterium-mediated transient expression has greatly contributed to research in molecular plant biology but has low efficiency and inconsistency in Arabidopsis thaliana (Arabidopsis). Here, we describe a simple, efficient and fast protocol to make transient gene expression in NahG Arabidopsis plants using ...
    Synthetic Genetic Interaction (CRISPR-SGI) Profiling in Caenorhabditis elegans
    Authors:  John A. Calarco and Adam D. Norris, date: 03/05/2018, view: 1501, 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), ...
    Protocol for Molecular Dynamics Simulations of Proteins
    Authors:  MNV Prasad Gajula, Anuj Kumar and Johny Ijaq, date: 12/05/2016, view: 8225, Q&A: 0
    [Abstract] Molecular dynamics (MD) simulations have become one of the most important tools in understanding the behavior of bio-molecules on nanosecond to microsecond time scales. In this protocol, we provide a general approach and standard setup protocol for MD simulations by using the Gromacs MD suite.
    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: 4628, 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 ...
    Character-State Reconstruction to Infer Ancestral Protein-Protein Interaction Patterns
    Authors:  Florian Rümpler, Günter Theißen and Rainer Melzer, date: 08/20/2015, view: 5931, Q&A: 0
    [Abstract] Protein-protein interactions are at the core of a plethora of developmental, physiological and biochemical processes. Consequently, insights into the origin and evolutionary dynamics of protein-protein interactions may provide information on the constraints and dynamics of specific biomolecular circuits and their impact on the organismal ...
    A Conceptual Outline for Omics Experiments Using Bioinformatics Analogies
    Authors:  Prashanth Suravajhala and Jeffrey W. Bizzaro, date: 02/05/2015, view: 6231, 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: 5504, 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: 9047, 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 ...