系统生物学

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    现刊
    BRIDGE: An Open Platform for Reproducible Protein-Ligand Simulations and Free Energy of Binding Calculations
    BRIDGE:一个可重复的蛋白质配体模拟和结合自由能计算的开放平台
    作者:Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo日期:09/05/2020,浏览量:753,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
    BRIDGE:一个可重复的蛋白质配体模拟和结合自由能计算的开放平台
    作者:Tharindu Senapathi, Christopher B. Barnett and Kevin J. Naidoo日期:09/05/2020,浏览量:753,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
    骨髓衍生巨噬细胞的代谢组学和脂质组学分析
    作者:Gretchen L. Seim, Steven V. John and Jing Fan日期:07/20/2020,浏览量: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
    HoSeIn:整合来自宏基因组和元转录组序列数据集的各种同源性搜索结果的工作流
    作者:Gaston Rozadilla, Jorgelina Moreiras Clemente and Christina B. McCarthy日期:07/20/2020,浏览量: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
    Oligo-dT磁珠用于Illumina测序平台的低成本和可复用的完整mRNA-Seq文库制备方法
    作者:Makoto Kashima, Ayumi Deguchi, Ayumi Tezuka and Atsushi J. Nagano日期:06/20/2020,浏览量:1300,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
    HIV-CRISPR:一种CRISPR/Cas9筛选HIV复制相关基因的方法
    作者:Ferdinand Roesch and Molly OhAinle日期:05/05/2020,浏览量: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
    基于模板的蛋白质结构精确预测的机器学习序列比对
    作者:Shuichiro Makigaki and Takashi Ishida日期:05/05/2020,浏览量:1090,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
    激光捕获显微解剖小鼠棒状细胞的昼夜节律基因分析
    作者:Zhenguang Zhang and Andrew Loudon日期:04/20/2020,浏览量:959,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
    树冠中光合氮分配的最适生物信息学评估实验:温室黄瓜应用实例
    作者:Yi-Chen Pao, Tsu-Wei Chen, Dany Pascal Moualeu-Ngangue and Hartmut Stützel日期:03/20/2020,浏览量:1174,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
    延迟交替任务用于研究大鼠空间工作记忆和长期记忆
    作者:Megi Hoxha and Marta Sabariego日期:03/05/2020,浏览量:1344,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
    鳃组织mRNA 提取用于RNA测序
    作者:Jukka-Pekka Verta and Felicity Jones日期:03/05/2020,浏览量: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 ...