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ncbi refseq genome annotation  (DOE Systems Biology Knowledgebase)

 
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    Structured Review

    DOE Systems Biology Knowledgebase ncbi refseq genome annotation
    Overall process of the model reconstruction, refinement, and subsequent analysis/validation. Kbase, <t>NCBI</t> <t>RefSeq,</t> and ModelSEED database were used to reconstruct the initial model. After standard model curations, a high-quality GSM was ready to use. Later, condition-specific transcriptomics data were incorporated with GSM through E-flux algorithm, which resulted in five contextualized models. These models were used to find metabolic bottlenecks and persistence mechanism. K-mean clustering algorithm applied on the transcriptomics data revealed a global stress response mechanism. Thermodynamics and enzyme cost analysis, along with in vitro experimentation, reveal the regulatory role of pgm in CTL persistence.
    Ncbi Refseq Genome Annotation, supplied by DOE Systems Biology Knowledgebase, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ncbi refseq genome annotation/product/DOE Systems Biology Knowledgebase
    Average 90 stars, based on 1 article reviews
    ncbi refseq genome annotation - by Bioz Stars, 2026-03
    90/100 stars

    Images

    1) Product Images from "Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in Chlamydia trachomatis persistence"

    Article Title: Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in Chlamydia trachomatis persistence

    Journal: mSystems

    doi: 10.1128/msystems.00717-24

    Overall process of the model reconstruction, refinement, and subsequent analysis/validation. Kbase, NCBI RefSeq, and ModelSEED database were used to reconstruct the initial model. After standard model curations, a high-quality GSM was ready to use. Later, condition-specific transcriptomics data were incorporated with GSM through E-flux algorithm, which resulted in five contextualized models. These models were used to find metabolic bottlenecks and persistence mechanism. K-mean clustering algorithm applied on the transcriptomics data revealed a global stress response mechanism. Thermodynamics and enzyme cost analysis, along with in vitro experimentation, reveal the regulatory role of pgm in CTL persistence.
    Figure Legend Snippet: Overall process of the model reconstruction, refinement, and subsequent analysis/validation. Kbase, NCBI RefSeq, and ModelSEED database were used to reconstruct the initial model. After standard model curations, a high-quality GSM was ready to use. Later, condition-specific transcriptomics data were incorporated with GSM through E-flux algorithm, which resulted in five contextualized models. These models were used to find metabolic bottlenecks and persistence mechanism. K-mean clustering algorithm applied on the transcriptomics data revealed a global stress response mechanism. Thermodynamics and enzyme cost analysis, along with in vitro experimentation, reveal the regulatory role of pgm in CTL persistence.

    Techniques Used: Biomarker Discovery, In Vitro



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    Overall process of the model reconstruction, refinement, and subsequent analysis/validation. Kbase, <t>NCBI</t> <t>RefSeq,</t> and ModelSEED database were used to reconstruct the initial model. After standard model curations, a high-quality GSM was ready to use. Later, condition-specific transcriptomics data were incorporated with GSM through E-flux algorithm, which resulted in five contextualized models. These models were used to find metabolic bottlenecks and persistence mechanism. K-mean clustering algorithm applied on the transcriptomics data revealed a global stress response mechanism. Thermodynamics and enzyme cost analysis, along with in vitro experimentation, reveal the regulatory role of pgm in CTL persistence.
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    Overall process of the model reconstruction, refinement, and subsequent analysis/validation. Kbase, <t>NCBI</t> <t>RefSeq,</t> and ModelSEED database were used to reconstruct the initial model. After standard model curations, a high-quality GSM was ready to use. Later, condition-specific transcriptomics data were incorporated with GSM through E-flux algorithm, which resulted in five contextualized models. These models were used to find metabolic bottlenecks and persistence mechanism. K-mean clustering algorithm applied on the transcriptomics data revealed a global stress response mechanism. Thermodynamics and enzyme cost analysis, along with in vitro experimentation, reveal the regulatory role of pgm in CTL persistence.
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    Image Search Results


    Overall process of the model reconstruction, refinement, and subsequent analysis/validation. Kbase, NCBI RefSeq, and ModelSEED database were used to reconstruct the initial model. After standard model curations, a high-quality GSM was ready to use. Later, condition-specific transcriptomics data were incorporated with GSM through E-flux algorithm, which resulted in five contextualized models. These models were used to find metabolic bottlenecks and persistence mechanism. K-mean clustering algorithm applied on the transcriptomics data revealed a global stress response mechanism. Thermodynamics and enzyme cost analysis, along with in vitro experimentation, reveal the regulatory role of pgm in CTL persistence.

    Journal: mSystems

    Article Title: Metabolic model guided CRISPRi identifies a central role for phosphoglycerate mutase in Chlamydia trachomatis persistence

    doi: 10.1128/msystems.00717-24

    Figure Lengend Snippet: Overall process of the model reconstruction, refinement, and subsequent analysis/validation. Kbase, NCBI RefSeq, and ModelSEED database were used to reconstruct the initial model. After standard model curations, a high-quality GSM was ready to use. Later, condition-specific transcriptomics data were incorporated with GSM through E-flux algorithm, which resulted in five contextualized models. These models were used to find metabolic bottlenecks and persistence mechanism. K-mean clustering algorithm applied on the transcriptomics data revealed a global stress response mechanism. Thermodynamics and enzyme cost analysis, along with in vitro experimentation, reveal the regulatory role of pgm in CTL persistence.

    Article Snippet: To analyze the metabolism of CTL in different stress conditions, we reconstructed a GSM of CTL using the NCBI RefSeq genome annotation (KBase Genome ID: GCF_000068585.1) from KBase ( ).

    Techniques: Biomarker Discovery, In Vitro