Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.
K. Takahashi, S. Arjunan, and M. Tomita.
FEBS Lett. 579 (8): 1783--1788 (March 2005)

How cells utilize intracellular spatial features to optimize their signaling characteristics is still not clearly understood. The physical distance between the cell-surface receptor and the gene expression machinery, fast reactions, and slow protein diffusion coefficients are some of the properties that contribute to their intricacy. This article reviews computational frameworks that can help biologists to elucidate the implications of space in signaling pathways. We argue that intracellular macromolecular crowding is an important modeling issue, and describe how recent simulation methods can reproduce this phenomenon in either implicit, semi-explicit or fully explicit representation.

URL: http://dx.doi.org/10.1016/j.febslet.2005.01.072
DOI: 10.1016/j.febslet.2005.01.072
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@article{Taka_2005_1783,
  abstract = {How cells utilize intracellular spatial features to optimize their
	signaling characteristics is still not clearly understood. The physical
	distance between the cell-surface receptor and the gene expression
	machinery, fast reactions, and slow protein diffusion coefficients
	are some of the properties that contribute to their intricacy. This
	article reviews computational frameworks that can help biologists
	to elucidate the implications of space in signaling pathways. We
	argue that intracellular macromolecular crowding is an important
	modeling issue, and describe how recent simulation methods can reproduce
	this phenomenon in either implicit, semi-explicit or fully explicit
	representation.},
  added-at = {2009-06-03T11:20:58.000+0200},
  author = {Takahashi, Kouichi and Arjunan, Satya Nanda Vel and Tomita, Masaru},
  biburl = {https://www.bibsonomy.org/bibtex/22631c6fb19e30f1dab97e0929aa16bf8/hake},
  description = {The whole bibliography file I use.},
  doi = {10.1016/j.febslet.2005.01.072},
  file = {Taka_2005_1783.pdf:Taka_2005_1783.pdf:PDF},
  interhash = {3f171ac9cbce00698553a38a7c50445b},
  intrahash = {2631c6fb19e30f1dab97e0929aa16bf8},
  journal = {F{EBS} Lett.},
  keywords = {15763552 Adolescent, Adrenal Adult, Aged, Algorithms, Animals, Antibodies, Antineutrophil Biology, C4b, Capillaries, Child, Combined Complement Computational Computer Cortex Cytapheresis, Cytoplasmic, Factor-alpha, Factors, Female, Follow-Up Fragments, Glomerulonephritis, Glomerulus, Gov't, Graft Hormones, Humans, Interleukin-1, Interleukin-10, Intracellular Kidney Kidney, Male, Methylprednisolone, Middle Modality Models, Necrosis Non-U.S. Nonparametric, Outcome, Peptide Processes, Rejection, Research Signal Simulation, Space, Statistics, Stochastic Studies, Support, Survival, Theoretical, Therapy, Time Transduction, Transplantation, Treatment Tubules, Tumor Vasculitis,},
  month = Mar,
  number = 8,
  pages = {1783--1788},
  pii = {S0014-5793(05)00185-7},
  pmid = {15763552},
  timestamp = {2009-06-03T11:21:33.000+0200},
  title = {Space in systems biology of signaling pathways--towards intracellular
	molecular crowding in silico.},
  url = {http://dx.doi.org/10.1016/j.febslet.2005.01.072},
  volume = 579,
  year = 2005
}

%0 Journal Article
%1 Taka_2005_1783
%A Takahashi, Kouichi
%A Arjunan, Satya Nanda Vel
%A Tomita, Masaru
%D 2005
%J FEBS Lett.
%K 15763552 Adolescent, Adrenal Adult, Aged, Algorithms, Animals, Antibodies, Antineutrophil Biology, C4b, Capillaries, Child, Combined Complement Computational Computer Cortex Cytapheresis, Cytoplasmic, Factor-alpha, Factors, Female, Follow-Up Fragments, Glomerulonephritis, Glomerulus, Gov't, Graft Hormones, Humans, Interleukin-1, Interleukin-10, Intracellular Kidney Kidney, Male, Methylprednisolone, Middle Modality Models, Necrosis Non-U.S. Nonparametric, Outcome, Peptide Processes, Rejection, Research Signal Simulation, Space, Statistics, Stochastic Studies, Support, Survival, Theoretical, Therapy, Time Transduction, Transplantation, Treatment Tubules, Tumor Vasculitis,
%N 8
%P 1783--1788
%R 10.1016/j.febslet.2005.01.072
%T Space in systems biology of signaling pathways--towards intracellular
	molecular crowding in silico.
%U http://dx.doi.org/10.1016/j.febslet.2005.01.072
%V 579
%X How cells utilize intracellular spatial features to optimize their
	signaling characteristics is still not clearly understood. The physical
	distance between the cell-surface receptor and the gene expression
	machinery, fast reactions, and slow protein diffusion coefficients
	are some of the properties that contribute to their intricacy. This
	article reviews computational frameworks that can help biologists
	to elucidate the implications of space in signaling pathways. We
	argue that intracellular macromolecular crowding is an important
	modeling issue, and describe how recent simulation methods can reproduce
	this phenomenon in either implicit, semi-explicit or fully explicit
	representation.

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Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.
K. Takahashi, S. Arjunan, and M. Tomita.
FEBS Lett. 579 (8): 1783--1788 (March 2005)

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Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.K. Takahashi, S. Arjunan, and M. Tomita. FEBS Lett. 579 (8): 1783--1788 (March 2005)

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Cite this publication

Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico.
K. Takahashi, S. Arjunan, and M. Tomita.
FEBS Lett. 579 (8): 1783--1788 (March 2005)