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    Protocol

    Predicting Pseudouridine Sites with Porpoise

    is a ubiquitous modification and plays a crucial role in many biological processes. However, it remains a challenging task to identify sites using expensive and time-consuming experimental research. To th...

    Xudong Guo, Fuyi Li, Jiangning Song in Computational Epigenomics and Epitranscriptomics (2023)

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    Protocol

    Quantitative Analysis of Directional Neural Crest Cell Migration

    The neural crest is a highly migratory cell population that evolved in vertebrates. Born at the lateral borders of the neural plate, neural crest cells migrate long distances along defined paths and contribute...

    Shuyi Nie in Cell Polarity Signaling (2022)

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    Protocol

    Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL

    Among various types of protein post-translational modifications (PTMs), lysine PTMs play an important role in regulating a wide range of functions and biological processes. Due to the generation and accumulat...

    Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li in Computational Methods for Predicting Post-… (2022)

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    Protocol

    Experimental and Computational Workflow for RNA Sequencing in Mycobacterium tuberculosis : From Total RNA to Differentially Expressed Genes

    RNA sequencing (RNAseq) in bacteria has become a transformative tool for many applications, including the identification of mechanisms that contribute to pathogenesis, environmental adaptation, and drug respon...

    Shuyi Ma, Richard M. Jones Jr., Natalie S. Gleason in Mycobacteria Protocols (2021)

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    Protocol

    Fabrication and Electrospinning of 3D Biodegradable Poly-l-Lactic Acid (PLLA) Nanofibers for Clinical Application

    Poly-l-lactic acid (PLLA) is a biodegradable synthetic polyester synthesized by polymerization or polycondensation. PLLA hydrolytically degrades into lactic acid, a biocompatible metabolic by-product, making it s...

    Balasundari Ramesh, Kotturathu Mammen Cherian in Stem Cell Nanotechnology (2020)

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    Protocol

    Analysis of Mitochondrial Markers of Programmed Cell Death

    Mitochondria play a crucial role in programmed cell death (PCD) in plants. In most cases of mitochondria-dependent PCD, cytochrome c (Cyt c) released from mitochondria due to the opening of mitochondrial perme...

    Dong **ao, Huyi He, Wen**g Huang, Thet Lwin Oo, Aiqin Wang in Plant Programmed Cell Death (2018)