@article{Yang2015,
  author = {Yang, Laurence and Tan, Justin and O'Brien, Edward J. and
    Monk, Jonathan and Kim, Donghyuk and Li, Howard J. and Charusantia, Pep
    and Ebrahim, Ali and Lloyd, Colton J. and Yurkovich, James T. and Du, Bin
    and Dr\"ager, Andreas and Thomas, Alex and Sun, Yuekai and Saunders, Michael A.
    and Palsson, Bernhard O.},
  title = {Systems biology definition of the core proteome of metabolism and
    expression is consistent with high-throughput data},
  journal = {Proceedings of the National Academy of Sciences},
  abstract = {Finding the minimal set of gene functions needed to sustain life
    is of both fundamental and practical importance. Minimal gene lists have
    been proposed using comparative genomics-based core proteome definitions.
    A definition of a core proteome that is supported by empirical data, is
    understood at the systems-level, and provides a basis for computing
    essential cell functions is lacking. Here, we use a systems biology-based
    genome-scale model of metabolism and expression to define a functional core
    proteome consisting of 356 gene products, accounting for 44\% of the
    \emph{Escherichia coli} proteome by mass based on proteomics data. This
    systems biology core proteome includes 212 genes not found in previous
    comparative genomics-based core proteome definitions, accounts for 65\% of
    known essential genes in \emph{E.~coli}, and has 78\% gene function overlap with
    minimal genomes (\emph{Buchnera aphidicola} and \emph{Mycoplasma genitalium}).
    Based on transcriptomics data across environmental and genetic backgrounds,
    the systems biology core proteome is significantly enriched in non-differentially
    expressed genes, and depleted in differentially expressed genes. Compared to
    the non-core, core gene expression levels are also similar across genetic
    backgrounds (two times higher Spearman rank correlation), and exhibit
    significantly more complex transcriptional and post-transcriptional regulatory
    features (40\% more transcription start sites per gene, 22\% longer 5'UTR).
    Thus, genome-scale systems biology approaches rigorously identify a
    functional core proteome needed to support growth. This framework, validated
    using high-throughput datasets, facilitates a mechanistic understanding of
    systems-level core proteome function through in silico models; it
    \emph{de facto} defines a paleome.},
  year = {2015},
  month = aug,
  url = {https://www.pnas.org/content/early/2015/08/05/1501384112},
  pdf = {https://www.pnas.org/content/early/2015/08/05/1501384112.full.pdf},
  doi = {10.1073/pnas.1501384112},
}