Systems Biology


    GO/KEGG Enrichment Analysis on Gene Lists from Rice (Oryza Sativa)
    Author:  Yahui Li, date: 06/20/2022, view: 81, Q&A: 0

    In RNA-seq data analysis, functional enrichment analysis on genes has become a routine. Many enrichment analysis software and web-applications have emerged. However, gene annotation information is only easily accessible for the most well-studied

    ATAC-Seq of a Single Myofiber from Mus musculus
    Authors:  Korin Sahinyan, Darren M. Blackburn and Vahab D. Soleimani, date: 06/20/2022, view: 1225, Q&A: 0

    Chromatin accessibility is a key determinant of gene expression that can be altered under different physiological and disease conditions. Skeletal muscle is made up of myofibers that are highly plastic and adaptive. Therefore, assessing the

    Protocol for Initiating and Monitoring Bumble Bee Microcolonies with Bombus impatiens (Hymenoptera: Apidae)
    Author:  David M. Lehmann, date: 06/20/2022, view: 1107, Q&A: 0

    Populations of some bumble bee species are in decline, prompting the need to better understand bumble bee biology and for assessing the effects of environmental stressors on these important pollinators. Microcolonies have been successfully used for

    Identification of Expression QTL by QTLtools in a Rice Recombinant Inbred Line Population
    Authors:  Feng Xiong, Hu Zhao and Weibo Xie, date: 06/20/2022, view: 122, Q&A: 0

    Expression QTL (eQTL) analysis assesses the association between the expression levels of target genes and genotypes of genetic markers to identify loci that regulate the expression of target genes. eQTL results can be used to construct genetic

    A Molecular Cloning and Sanger Sequencing-based Protocol for Detecting Site-specific DNA Methylation
    Authors:  Wei Guo, Anthony Cannon and Damon Lisch, date: 05/05/2022, view: 692, Q&A: 1

    DNA methylation is a conserved chemical modification, by which methyl groups are added to the cytosine of DNA molecules. Methylation can influence gene expression without changing the sequence of a particular gene. This epigenetic effect is an

    Method for Analysing Protein Structure of SARS-COV-2 M Protein for Possible Clues Regarding Virion Stability, Longevity and Transmission
    Authors:  Saam Hasan and Muhammad Maqsud Hossain, date: 05/05/2022, view: 170, Q&A: 0

    The Severe Acute Respiratory Syndrome Coronavirus 2 or SARS-CoV-2 has been the causative agent behind the 2020 global pandemic. With the numbers infected rising well above a 2.7 million and confirmed deaths above 122,000 as of 25th April 2020, it

    circFL-seq, A Full-length circRNA Sequencing Method
    Authors:  Zelin Liu and Ence Yang, date: 04/20/2022, view: 986, Q&A: 1

    Due to overlapping sequences with linear cognates, identifying internal sequences of circular RNA (circRNA) remains a challenge. Recently, we have developed a full-length circRNA sequencing method (circFL-seq) and computational pipeline, to profile

    Whole-genome Methylation Analysis of APOBEC Enzyme-converted DNA (~5 kb) by Nanopore Sequencing

    In recent years, DNA methylation research has been accelerated by the advent of nanopore sequencers. However, read length has been limited by the constraints of base conversion using the bisulfite method, making analysis of chromatin content

    Enrichment of Tyrosine Phosphorylated Peptides for Quantitative Mass Spectrometry Analysis of RTK Signaling Dynamics
    Authors:  Vidyasiri Vemulapalli, Stephen C. Blacklow, Steven P. Gygi and Alison Erickson, date: 02/05/2022, view: 1218, Q&A: 0

    Cells sense and respond to mitogens by activating a cascade of signaling events, primarily mediated by tyrosine phosphorylation (pY). Because of its key roles in cellular homeostasis, deregulation of this signaling is often linked to oncogenesis. To

    Subcellular RNA-seq for the Analysis of the Dendritic and Somatic Transcriptomes of Single Neurons
    Authors:  Julio D. Perez and Erin M. Schuman, date: 01/05/2022, view: 1545, Q&A: 0

    In neurons, local translation in dendritic and axonal compartments allows for the fast and on-demand modification of the local proteome. As the last few years have witnessed dramatic advancements in our appreciation of the brain’s neuronal


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