系统生物学

分类

    现刊
    Reference-free Association Mapping from Sequencing Reads Using k-mers
    利用k-mers进行测序读取的无参考关联映射
    作者:Zakaria Mehrab, Jaiaid Mobin, Ibrahim Asadullah Tahmid, Lior Pachter and Atif Rahman日期:11/05/2020,浏览量:2629,Q&A: 0
    [Abstract] Association mapping is the process of linking phenotypes with genotypes. In genome wide association studies (GWAS), individuals are first genotyped using microarrays or by aligning sequenced reads to reference genomes. However, both these approaches rely on reference genomes which limits their application to organisms with no or incomplete ...
    Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria
    细菌转录起始位点的差异RNA序列全基因组鉴定
    作者:Ramón Cervantes-Rivera and Andrea Puhar日期:09/20/2020,浏览量:2713,Q&A: 0
    [Abstract] Gene transcription in bacteria often starts some nucleotides upstream of the start codon. Identifying the specific Transcriptional Start Site (TSS) is essential for genetic manipulation, as in many cases upstream of the start codon there are sequence elements that are involved in gene expression regulation. Taken into account the classical gene ...
    Extraction and 16S rRNA Sequence Analysis of Microbiomes Associated with Rice Roots
    水稻根系相关微生物群落的分离及其16S rRNA序列分析
    作者:Joseph Edwards, Christian Santos-Medellín and Venkatesan Sundaresan日期:06/20/2018,浏览量:11585,Q&A: 0
    [Abstract] Plant roots associate with a wide diversity of bacteria and archaea across the root-soil spectrum. The rhizosphere microbiota, the communities of microbes in the soil adjacent to the root, can contain up to 10 billion bacterial cells per gram of soil (Raynaud and Nunan, 2014) and can play important roles for the fitness of the host plant. Subsets ...
    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 ...
    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:7563,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:7867,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 ...
    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:8797,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 ...
    Chromosome Dosage Analysis in Plants Using Whole Genome Sequencing
    采用全基因组测序法进行染色体剂量分析
    作者:Ek Han Tan, Luca Comai and Isabelle M. Henry日期:07/05/2016,浏览量:9511,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 ...
    Protocol for the Generation of a Transcription Factor Open Reading Frame Collection (TFome)
    转录因子开放阅读框收集(Tfome)的生成方法
    [Abstract] The construction of a physical collection of open reading frames (ORFeomes) for genes of any model organism is a useful tool for the exploration of gene function, gene regulation, and protein-protein interaction. Here we describe in detail a protocol that has been used to develop the first collection of transcription factor (TF) and co-regulator ...
    Human, Bacterial and Fungal Amplicon Collection and Processing for Sequencing
    人、细菌和真菌扩增子的采集、处理并测序
    作者:Julia Oh日期:05/20/2015,浏览量:10733,Q&A: 3
    [Abstract] Sequencing taxonomic marker genes is a powerful tool to interrogate the composition of microbial communities. For example, bacterial and fungal community composition can be evaluated in parallel using the 16S ribosomal RNA gene for bacteria or the internal transcribed spacer region in fungi. These are conserved regions that are universal to a ...