Searching journal content for articles similar to Kim and Tidor 13 (7): 1706.

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  1. LETTER: Principles of transcriptional regulation and evolution of the metabolic system in E. coli
    • Aswin S.N. Seshasayee,
    • Gillian M. Fraser,
    • M. Madan Babu,
    • and Nicholas M. Luscombe
    Genome Res. January 2009 19: 79-91; Published in Advance October 3, 2008, doi:10.1101/gr.079715.108
    ...a wide range of small-molecule products from a limited set of precursor molecules; and (3) the central/energy subsystem is situated between catabolic and anabolic pathways, generating ATP and biosynthetic precursors. We studied this by testing for differences in the numbers of TFs that regulate genes...
  2. Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
    • Georgi K. Marinov,
    • Benjamin Doughty,
    • Anshul Kundaje,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
    ...be associated with replication initiation.Chromatin accessibility correlates with transcriptional activity in BacteriovoraxOur next step was to characterize the relationship between chromatin accessibility and transcriptional activity in Bacteriovorax as well as their dynamics upon large-scale gene expression...
  3. Method: Control of fluxes in metabolic networks
    • Georg Basler,
    • Zoran Nikoloski,
    • Abdelhalim Larhlimi,
    • Albert-László Barabási,
    • and Yang-Yu Liu
    Genome Res. July 2016 26: 956-968; Published in Advance May 19, 2016, doi:10.1101/gr.202648.115
    ..., such as the identification of bottlenecks within subsystems of metabolism. This may help reveal novel targets for metabolic engineering applications, such as optimizing the microbial production of chemicals. In this regard, our framework differs from the classical metabolic control analysis (MCA) (Heinrich and Schuster 1996...
  4. Methods: Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
    • Nitin Gupta,
    • Stephen Tanner,
    • Navdeep Jaitly,
    • Joshua N. Adkins,
    • Mary Lipton,
    • Robert Edwards,
    • Margaret Romine,
    • Andrei Osterman,
    • Vineet Bafna,
    • Richard D. Smith,
    • and Pavel A. Pevzner
    Genome Res. September 2007 17: 1362-1377; Published in Advance August 9, 2007, doi:10.1101/gr.6427907
    ...active. A subsystem involved with the utilization of chitin and N-acetyglucosamine provides a remarkable example of correlation between the observed coverage and expected phenotype. Most of the genes recently implicated in the respective regulon in S. oneidensis ( Yang et al. 2006 ) display very low...
  5. REVIEW: Synthetic biology projects in vitro
    • Anthony C. Forster and
    • George M. Church
    Genome Res. January 2007 17: 1-6; Published in Advance December 6, 2006, doi:10.1101/gr.5776007
    ...conditions, efficiency of translation, control and integration of subsystems, and cosegregation of genes with their products. Nevertheless, this biochemical approach has advantages over the genetic approach ( Hutchison et al. 1999 ) of enabling system-by-system debugging to attain self-replication, being...
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