Systems Biology

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    Protocols in Current Issue
    Computational Analysis and Phylogenetic Clustering of SARS-CoV-2 Genomes
    Authors:  Bani Jolly and Vinod Scaria, date: 04/20/2021, view: 2303, Q&A: 0
    [Abstract]

    COVID-19, the disease caused by the novel SARS-CoV-2 coronavirus, originated as an isolated outbreak in the Hubei province of China but soon created a global pandemic and is now a major threat to healthcare systems worldwide. Following the rapid human-to-human transmission of the infection, institutes around the world have made efforts to generate

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    HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets
    Authors:  Gaston Rozadilla, Jorgelina Moreiras Clemente and Christina B. McCarthy, date: 07/20/2020, view: 2174, Q&A: 0
    [Abstract] Data generated by metagenomic and metatranscriptomic experiments is both enormous and inherently noisy. When using taxonomy-dependent alignment-based methods to classify and label reads, the first step consists in performing homology searches against sequence databases. To obtain the most information from the samples, nucleotide sequences are ...
    Genome-wide Estimation of Evolutionary Distance and Phylogenetic Analysis of Homologous Genes
    Authors:  Meixia Zhao, Biao Zhang, Jianxin Ma and Damon Lisch, date: 12/05/2018, view: 4744, Q&A: 0
    [Abstract] Homologous genes, including paralogs and orthologs, are genes that share sequence homologies within or between different species. Homologous genes originate from a common origin through speciation, genetic duplication or horizontal gene transfer. Estimation of the sequence divergence of homologous genes help us to understand divergence time, which ...
    Extraction of DNA from Murine Fecal Pellets for Downstream Phylogenetic Microbiota Analysis by Next-generation Sequencing
    Authors:  Elien Eeckhout and Andy Wullaert, date: 02/05/2018, view: 8948, Q&A: 2
    [Abstract] Mouse models are widely used to evaluate the potential impact of the gut microbial composition on health and disease. Standardized protocols for sampling and storing murine feces, as well as for extracting DNA from these fecal pellets are needed to limit experimental variation between different studies. Both efficient lysis of the microbiota and ...
    Character-State Reconstruction to Infer Ancestral Protein-Protein Interaction Patterns
    Authors:  Florian Rümpler, Günter Theißen and Rainer Melzer, date: 08/20/2015, view: 10710, Q&A: 0
    [Abstract] Protein-protein interactions are at the core of a plethora of developmental, physiological and biochemical processes. Consequently, insights into the origin and evolutionary dynamics of protein-protein interactions may provide information on the constraints and dynamics of specific biomolecular circuits and their impact on the organismal ...



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