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系统生物学

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    现刊
    Brief Protocol for EDGE Bioinformatics: Analyzing Microbial and Metagenomic NGS Data
    EDGE生物信息学工具简要使用方法:分析微生物和宏基因组学下一代测序数据
    [Abstract] Next-generation sequencing (NGS) offers unparalleled resolution for untargeted organism detection and characterization. However, the majority of NGS analysis programs require users to be proficient in programming and command-line interfaces. EDGE bioinformatics was developed to offer scientists with little to no bioinformatics expertise a ...
    Low-input Capture-C: A Chromosome Conformation Capture Assay to Analyze Chromatin Architecture in Small Numbers of Cells
    低样品量Capture-C:采用染色体构象采集分析法分析少量细胞中的染色质结构
    作者:A. Marieke Oudelaar, Damien J. Downes, James O.J. Davies and Jim R. Hughes日期:12/05/2017,浏览量:901,Q&A: 0
    [Abstract] Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This protocol describes two new low-input Capture-C approaches that can generate high-quality 3C interaction profiles from 10,000-20,000 cells, depending on the ...
    Lipidomic Analysis of Caenorhabditis elegans Embryos
    秀丽隐杆线虫胚胎的脂质组学分析
    作者:Hung-Chi Yang, Cheng-Yu Hung, Yi-Yun Pan, Szecheng J Lo and Daniel Tsun-Yee Chiu日期:09/20/2017,浏览量:992,Q&A: 0
    [Abstract] Metabolomic is an emerging field of system biology. Lipidomic, a branch of metabolomic, aims to characterize lipophilic metabolites in biological systems. Caenorhabditis elegans (C. elegans) is a genetically tractable and versatile animal model for novel discovery of lipid metabolism. In addition, C. elegans embryo is ...
    Cell Type-specific Metabolic Labeling of Proteins with Azidonorleucine in Drosophila
    果蝇中含叠氮正亮氨酸蛋白质的细胞类型特异性代谢标记
    [Abstract] Advanced mass spectrometry technology has pushed proteomic analyses to the forefront of biological and biomedical research. Limitations of proteomic approaches now often remain with sample preparations rather than with the sensitivity of protein detection. However, deciphering proteomes and their context-dependent dynamics in subgroups of ...
    Validating Candidate Congenital Heart Disease Genes in Drosophila
    果蝇中候选先天性心脏病基因的验证
    作者:Jun-yi Zhu, Yulong Fu, Adam Richman and Zhe Han日期:06/20/2017,浏览量:1331,Q&A: 0
    [Abstract] Genomic sequencing efforts can implicate large numbers of genes and de novo mutations as potential disease risk factors. A high throughput in vivo model system to validate candidate gene association with pathology is therefore useful. We present such a system employing Drosophila to validate candidate congenital heart ...
    A Method to Convert mRNA into a Guide RNA (gRNA) Library without Requiring Previous Bioinformatics Knowledge of the Organism
    不需预知生物体生物信息学条件下将其mRNA转化为向导RNA(gRNA)库的方法
    作者:Hiroshi Arakawa日期:05/20/2017,浏览量:1773,Q&A: 0
    [Abstract] While the diversity of species represents a diversity of special biological abilities, many of the genes that encode those special abilities in a variety of species are untouched, leaving an untapped gold mine of genetic information; however, despite current advances in genome bioinformatics, annotation of that genetic information is incomplete in ...
    Next-generation Sequencing of the DNA Virome from Fecal Samples
    粪便样本中DNA病毒组的下一代测序法
    作者:Cynthia L. Monaco and Douglas S. Kwon日期:03/05/2017,浏览量:2292,Q&A: 0
    [Abstract] Herein we describe a detailed protocol for DNA virome analysis of low input human stool samples (Monaco et al., 2016). This protocol is divided into four main steps: 1) stool samples are pulverized to evenly distribute microbial matter; 2) stool is enriched for virus-like particles and DNA is extracted by phenol-chloroform; 3) purified ...
    Bioinformatic Analysis for Profiling Drug-induced Chromatin Modification Landscapes in Mouse Brain Using ChlP-seq Data
    利用ChIP-seq数据分析药物诱导小鼠大脑中染色质修饰发生改变的生物信息学方法
    作者:Yong-Hwee Eddie Loh, Jian Feng, Eric Nestler and Li Shen日期:02/05/2017,浏览量:2354,Q&A: 0
    [Abstract] Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a powerful technology to profile genome-wide chromatin modification patterns and is increasingly being used to study the molecular mechanisms of brain diseases such as drug addiction. This protocol discusses the typical procedures involved in ChIP-seq data ...
    Protocol for Molecular Dynamics Simulations of Proteins
    蛋白质的分子动力学模拟方案
    作者:MNV Prasad Gajula, Anuj Kumar and Johny Ijaq日期:12/05/2016,浏览量:4541,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.
    Sequencing of Ebola Virus Genomes Using Nanopore Technology
    采用纳米孔技术对埃博拉病毒测序
    作者:Thomas Hoenen日期:11/05/2016,浏览量:2573,Q&A: 0
    [Abstract] Sequencing of virus genomes during disease outbreaks can provide valuable information for diagnostics, epidemiology, and evaluation of potential countermeasures. However, particularly in remote areas logistical and technical challenges can be significant. Nanopore sequencing provides an alternative to classical Sanger and next-generation ...