Systems Biology

Categories

    Protocols in Current Issue
    BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
    Authors:  Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo, date: 09/05/2020, view: 757, Q&A: 0
    Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein ...
    BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
    Authors:  Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo, date: 09/05/2020, view: 757, Q&A: 0
    [Abstract] Protein-ligand binding prediction is central to the drug-discovery process. This often follows an analysis of genomics data for protein targets and then protein structure discovery. However, the complexity of performing reproducible protein conformational analysis and ligand binding calculations, using vetted methods and protocols can be a ...
    Metabolomic and Lipidomic Analysis of Bone Marrow Derived Macrophages
    Authors:  Gretchen L. Seim, Steven V. John and Jing Fan, date: 07/20/2020, view: 650, Q&A: 0
    [Abstract] Macrophages are highly plastic immune cells that are capable of adopting a wide array of functional phenotypes in response to environmental stimuli. The changes in macrophage function are often supported and regulated by changes in cellular metabolism. Capturing a comprehensive picture of metabolism is vital for understanding the role of metabolic ...
    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: 443, 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 ...
    Low-cost and Multiplexable Whole mRNA-Seq Library Preparation Method with Oligo-dT Magnetic Beads for Illumina Sequencing Platforms
    Authors:  Makoto Kashima, Ayumi Deguchi, Ayumi Tezuka and Atsushi J. Nagano, date: 06/20/2020, view: 1306, Q&A: 0
    [Abstract] RNA-Seq is a powerful method for transcriptome analysis used in varied field of biology. Although several commercial products and hand-made protocols enable us to prepare RNA-Seq library from total RNA, their cost are still expensive. Here, we established a low-cost and multiplexable whole mRNA-Seq library preparation method for illumine ...
    HIV-CRISPR: A CRISPR/Cas9 Screening Method to Identify Genes Affecting HIV Replication
    Authors:  Ferdinand Roesch and Molly OhAinle, date: 05/05/2020, view: 1050, Q&A: 0
    [Abstract] Screening with CRISPR/Cas9 technology has already led to significant discoveries in the fields of cancer biology, cell biology and virology. Because of the relatively low false discovery rates and the ability to perform high-throughput, pooled approaches, it has rapidly become the assay of choice for screening studies, including whole-genome ...
    Sequence Alignment Using Machine Learning for Accurate Template-based Protein Structure Prediction
    Authors:  Shuichiro Makigaki and Takashi Ishida, date: 05/05/2020, view: 1091, Q&A: 0
    [Abstract] Template-based modeling, the process of predicting the tertiary structure of a protein by using homologous protein structures, is useful when good templates can be available. Indeed, modern homology detection methods can find remote homologs with high sensitivity. However, the accuracy of template-based models generated from the ...
    Circadian Gene Profiling in Laser Capture Microdissected Mouse Club Cells
    Authors:  Zhenguang Zhang and Andrew Loudon, date: 04/20/2020, view: 960, Q&A: 0
    [Abstract] Cell heterogeneity is high in tissues like lung. Research conducted on pure population of cells usually offers more insights than bulk tissues, such as circadian clock work. In this protocol, we provide a detailed work flow on how to do circadian clock study by RNA seq in laser capture micro-dissected mouse lung club cells. The method uses frozen ...
    Experiments for in silico evaluation of Optimality of Photosynthetic Nitrogen Distribution and Partitioning in the Canopy: an Example Using Greenhouse Cucumber Plants
    Authors:  Yi-Chen Pao, Tsu-Wei Chen, Dany Pascal Moualeu-Ngangue and Hartmut Stützel, date: 03/20/2020, view: 1175, Q&A: 0
    [Abstract] Acclimation of leaf traits to fluctuating environments is a key mechanism to maximize fitness. One of the most important strategies in acclimation to changing light is to maintain efficient utilization of nitrogen in the photosynthetic apparatus by continuous modifications of between-leaf distribution along the canopy depth and within-leaf ...
    Delayed Alternation Task for the Study of Spatial Working and Long Term Memory in Rats
    Authors:  Megi Hoxha and Marta Sabariego, date: 03/05/2020, view: 1348, Q&A: 0
    [Abstract] Memory systems can hold previously presented information for several seconds, bridging gaps between discontinuous events. It has been previously demonstrated that the hippocampus and the medial entorhinal cortex (mEC) are necessary for memory retention over delay intervals in alternation tasks. Here we describe the delayed alternation task, a ...
    mRNA Extraction from Gill Tissue for RNA-sequencing
    Authors:  Jukka-Pekka Verta and Felicity Jones, date: 03/05/2020, view: 1158, Q&A: 0
    [Abstract] Adaptation is thought to proceed in part through spatial and temporal changes in gene expression. Fish species such as the threespine stickleback are powerful vertebrate models to study the genetic architecture of adaptive changes in gene expression since divergent adaptation to different environments is common, they are abundant and easy to study ...



    We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.