Systems Biology

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    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: 444, 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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    Sample Preparation and Integrative Data Analysis of a Droplet-based Single-Cell ATAC-sequencing Using Murine Thymic Epithelial Cells

    Accessible chromatin regions modulate gene expression by acting as cis-regulatory elements. Understanding the epigenetic landscape by mapping accessible regions of DNA is therefore imperative to decipher mechanisms of gene regulation under

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    A Cartographic Tool to Predict Disease Risk-associated Pseudo-Dynamic Networks from Tissue-specific Gene Expression
    Authors:  Chixiang Chen, Biyi Shen, Lijun Zhang, Tonghui Yu, Ming Wang and Rongling Wu, date: 01/05/2023, view: 200, Q&A: 0

    Understanding how genes are differentially expressed across tissues is key to reveal the etiology of human diseases. Genes are never expressed in isolation, but rather co-expressed in a community; thus, they co-act through intricate but

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    Efficient Generation of Genome-wide Libraries for Protein–ligand Screens Using Gibson Assembly
    Authors:  Tamara Sternlieb, Mira Loock, Mengjin Gao and Igor Cestari, date: 11/20/2022, view: 731, Q&A: 0

    Genome-wide screens using yeast or phage displays are powerful tools for identifying protein–ligand interactions, including drug or vaccine targets, ligand receptors, or protein–protein interactions. However, assembling libraries

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    Proteome Integral Solubility Alteration (PISA) Assay in Mammalian Cells for Deep, High-Confidence, and High-Throughput Target Deconvolution

    Chemical proteomics focuses on the drug–target–phenotype relationship for target deconvolution and elucidation of the mechanism of action—key and bottleneck in drug development and repurposing. Majorly due to the limits of using

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    Chromosome Scaffolding of Diploid Genomes Using ALLHiC
    Authors:  Yi-Bin Wang and Xing-Tan Zhang, date: 09/20/2022, view: 167, Q&A: 0

    High-throughput chromosome conformation capture (Hi-C) technology has become an economical and robust tool for generating a chromosome-scale assembly. However, high-quality chromosome scaffoldings are limited by the number of short and chimeric

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    GO/KEGG Enrichment Analysis on Gene Lists from Rice (Oryza Sativa)
    Author:  Yahui Li, date: 06/20/2022, view: 841, 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

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    ATAC-Seq of a Single Myofiber from Mus musculus
    Authors:  Korin Sahinyan, Darren M. Blackburn and Vahab D. Soleimani, date: 06/20/2022, view: 2144, 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

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    Protocol for Initiating and Monitoring Bumble Bee Microcolonies with Bombus impatiens (Hymenoptera: Apidae)
    Author:  David M. Lehmann, date: 06/20/2022, view: 1774, 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

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    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: 464, 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

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