Systems Biology


    Protocols in Current Issue
    Lipidomic Analysis of Caenorhabditis elegans Embryos
    Authors:  Hung-Chi Yang, Cheng-Yu Hung, Yi-Yun Pan, Szecheng J Lo and Daniel Tsun-Yee Chiu, date: 09/20/2017, view: 418, 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
    [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
    Authors:  Jun-yi Zhu, Yulong Fu, Adam Richman and Zhe Han, date: 06/20/2017, view: 814, 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
    Author:  Hiroshi Arakawa, date: 05/20/2017, view: 1145, 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
    Authors:  Cynthia L. Monaco and Douglas S. Kwon, date: 03/05/2017, view: 1616, 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
    Authors:  Yong-Hwee Eddie Loh, Jian Feng, Eric Nestler and Li Shen, date: 02/05/2017, view: 1701, 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
    Authors:  MNV Prasad Gajula, Anuj Kumar and Johny Ijaq, date: 12/05/2016, view: 3239, 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
    Author:  Thomas Hoenen, date: 11/05/2016, view: 1985, 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 ...
    Metabolite Profiling of Mature Arabidopsis thaliana Seeds Using Gas Chromatography-Mass Spectrometry (GC-MS)
    Authors:  Hagai Cohen, Ifat Matityahu and Rachel Amir, date: 11/05/2016, view: 2143, Q&A: 0
    [Abstract] Metabolite profiling using gas chromatography-mass spectrometry (GC-MS) permits the annotation and quantification of a relatively wide variety of metabolites, covering a wide range of biochemical groups of metabolites. Lisec et al. (2006) established a method for GC-MS profiling in plants. Based on this protocol, we provide here a ...
    Chromosome Dosage Analysis in Plants Using Whole Genome Sequencing
    Authors:  Ek Han Tan, Luca Comai and Isabelle M. Henry, date: 07/05/2016, view: 2674, Q&A: 0
    [Abstract] Relative chromosome dosage, i.e., increases or decreases in the number of copies of specific chromosome regions in one sample versus another, can be determined using aligned read-counts from Illumina sequencing (Henry et al., 2010). The following protocol was used to identify the different classes of aneuploids that ...