Systems Biology


    Computational Analysis of Plasma Lipidomics from Mice Fed Standard Chow and Ketogenic Diet
    Authors:  Amy L. Seufert, James W. Hickman, Jaewoo Choi and Brooke A. Napier, date: 09/20/2023, view: 119, Q&A: 0

    Dietary saturated fatty acids (SFAs) are upregulated in the blood circulation following digestion. A variety of circulating lipid species have been implicated in metabolic and inflammatory diseases; however, due to the extreme variability in serum

    Controlled Level of Contamination Coupled to Deep Sequencing (CoLoC-seq) Probes the Global Localisation Topology of Organelle Transcriptomes
    Authors:  Anna Smirnova, Damien Jeandard and Alexandre Smirnov, date: 09/20/2023, view: 69, Q&A: 0

    Information on RNA localisation is essential for understanding physiological and pathological processes, such as gene expression, cell reprogramming, host–pathogen interactions, and signalling pathways involving RNA transactions at the level

    T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
    Authors:  Massimo Andreatta, Paul Gueguen, Nicholas Borcherding and Santiago J. Carmona, date: 08/20/2023, view: 1025, Q&A: 0

    T cells are endowed with T-cell antigen receptors (TCR) that give them the capacity to recognize specific antigens and mount antigen-specific adaptive immune responses. Because TCR sequences are distinct in each naïve T cell, they serve as

    Chromatin-RNA in situ Reverse Transcription Sequencing (CRIST-seq) Approach to Profile the Non-coding RNA Interaction Network
    Authors:  Shilin Zhang, Xue Wen, Lei Zhou, Hui Li, Wei Li, Andrew R. Hoffman, Ji-Fan Hu and Jiuwei Cui, date: 07/20/2023, view: 404, Q&A: 0

    Non-coding RNAs (ncRNAs) are defined as RNAs that do not encode proteins, but many ncRNAs do have the ability to regulate gene expression. These ncRNAs play a critical role in the epigenetic regulation of various physiological and pathological

    Lipidomics Workflow for Analyzing Lipid Profiles Using Multiple Reaction Monitoring (MRM) in Liver Homogenate of Mice with Non-alcoholic Steatohepatitis (NASH)

    Non-alcoholic steatohepatitis (NASH) is a condition characterized by inflammation and hepatic injury/fibrosis caused by the accumulation of ectopic fats in the liver. Recent advances in lipidomics have allowed the identification and characterization

    Revised iCLIP-seq Protocol for Profiling RNA–protein Interaction Sites at Individual Nucleotide Resolution in Living Cells
    Authors:  Syed Nabeel-Shah and Jack F. Greenblatt, date: 06/05/2023, view: 1042, Q&A: 0

    Individual nucleotide resolution UV cross-linking and immunoprecipitation followed by high-throughput sequencing (iCLIP-seq) is a powerful technique that is used to identify RNA-binding proteins’ (RBP) binding sites on target RNAs and to

    Metagenomic Protocol (From Quality Control to Mapping) for Metagenome-assembled Genomes Using Anvi’o
    Authors:  Soumyadev Sarkar, Tanner Richie and Sonny T. M. Lee, date: 05/20/2023, view: 69, Q&A: 0

    Synapses provide the main route of signal transduction within neuronal networks. Many factors regulate critical synaptic functions. These include presynaptic calcium channels, triggering neurotransmitter release, and postsynaptic ionotropic

    Visualizing, Binning, and Refining of Metagenome-assembled Genomes (MAGs) with Anvi’o
    Authors:  Soumyadev Sarkar, Tanner Richie and Sonny T. M. Lee, date: 05/20/2023, view: 159, Q&A: 0

    High throughput ‘omics technologies generate huge datasets that need to be properly analyzed in order to decipher the biological implications. The workflow of handling such datasets must be user friendly to facilitate rapid analysis. Here, we

    Rapid Multiplexed Flow Cytometric Validation of CRISPRi sgRNAs in Tissue Culture
    Authors:  John S. Chorba, Vivian Q. Xia, Geoffrey A. Smith and Arun Padmanabhan, date: 01/20/2023, view: 720, Q&A: 0

    Genome-wide CRISPR-based screening is a powerful tool in forward genetics, enabling biologic discovery by linking a desired phenotype to a specific genetic perturbation. However, hits from a genome-wide screen require individual validation to


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