Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint

Research output: Contribution to journalArticlepeer-review

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Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint. / Henze, Richard; Mu, Chunyan; Puljiz, Mate; Kamaleson, Nishanthan; Huwald, Jan; Haslegrave, John; di Fenizio, Pietro Speroni; Parker, David; Good, Christopher; Rowe, Jonathan E; Ibrahim, Bashar; Dittrich, Peter.

In: Scientific Reports, Vol. 9, No. 1, 3902, 07.03.2019.

Research output: Contribution to journalArticlepeer-review

Harvard

Henze, R, Mu, C, Puljiz, M, Kamaleson, N, Huwald, J, Haslegrave, J, di Fenizio, PS, Parker, D, Good, C, Rowe, JE, Ibrahim, B & Dittrich, P 2019, 'Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint', Scientific Reports, vol. 9, no. 1, 3902. https://doi.org/10.1038/s41598-019-40648-w

APA

Henze, R., Mu, C., Puljiz, M., Kamaleson, N., Huwald, J., Haslegrave, J., di Fenizio, P. S., Parker, D., Good, C., Rowe, J. E., Ibrahim, B., & Dittrich, P. (2019). Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint. Scientific Reports, 9(1), [3902]. https://doi.org/10.1038/s41598-019-40648-w

Vancouver

Author

Henze, Richard ; Mu, Chunyan ; Puljiz, Mate ; Kamaleson, Nishanthan ; Huwald, Jan ; Haslegrave, John ; di Fenizio, Pietro Speroni ; Parker, David ; Good, Christopher ; Rowe, Jonathan E ; Ibrahim, Bashar ; Dittrich, Peter. / Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint. In: Scientific Reports. 2019 ; Vol. 9, No. 1.

Bibtex

@article{7de50207c31c410485419528fa7c05ad,
title = "Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint",
abstract = "The complexity of biological models makes methods for their analysis and understanding highly desirable. Here, we demonstrate the orchestration of various novel coarse-graining methods by applying them to the mitotic spindle assembly checkpoint. We begin with a detailed fine-grained spatial model in which individual molecules are simulated moving and reacting in a three-dimensional space. A sequence of manual and automatic coarse-grainings finally leads to the coarsest deterministic and stochastic models containing only four molecular species and four states for each kinetochore, respectively. We are able to relate each more coarse-grained level to a finer one, which allows us to relate model parameters between coarse-grainings and which provides a more precise meaning for the elements of the more abstract models. Furthermore, we discuss how organizational coarse-graining can be applied to spatial dynamics by showing spatial organizations during mitotic checkpoint inactivation. We demonstrate how these models lead to insights if the model has different {"}meaningful{"} behaviors that differ in the set of (molecular) species. We conclude that understanding, modeling and analyzing complex bio-molecular systems can greatly benefit from a set of coarse-graining methods that, ideally, can be automatically applied and that allow the different levels of abstraction to be related.",
author = "Richard Henze and Chunyan Mu and Mate Puljiz and Nishanthan Kamaleson and Jan Huwald and John Haslegrave and {di Fenizio}, {Pietro Speroni} and David Parker and Christopher Good and Rowe, {Jonathan E} and Bashar Ibrahim and Peter Dittrich",
year = "2019",
month = mar,
day = "7",
doi = "10.1038/s41598-019-40648-w",
language = "English",
volume = "9",
journal = "Scientific Reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

TY - JOUR

T1 - Multi-scale stochastic organization-oriented coarse-graining exemplified on the human mitotic checkpoint

AU - Henze, Richard

AU - Mu, Chunyan

AU - Puljiz, Mate

AU - Kamaleson, Nishanthan

AU - Huwald, Jan

AU - Haslegrave, John

AU - di Fenizio, Pietro Speroni

AU - Parker, David

AU - Good, Christopher

AU - Rowe, Jonathan E

AU - Ibrahim, Bashar

AU - Dittrich, Peter

PY - 2019/3/7

Y1 - 2019/3/7

N2 - The complexity of biological models makes methods for their analysis and understanding highly desirable. Here, we demonstrate the orchestration of various novel coarse-graining methods by applying them to the mitotic spindle assembly checkpoint. We begin with a detailed fine-grained spatial model in which individual molecules are simulated moving and reacting in a three-dimensional space. A sequence of manual and automatic coarse-grainings finally leads to the coarsest deterministic and stochastic models containing only four molecular species and four states for each kinetochore, respectively. We are able to relate each more coarse-grained level to a finer one, which allows us to relate model parameters between coarse-grainings and which provides a more precise meaning for the elements of the more abstract models. Furthermore, we discuss how organizational coarse-graining can be applied to spatial dynamics by showing spatial organizations during mitotic checkpoint inactivation. We demonstrate how these models lead to insights if the model has different "meaningful" behaviors that differ in the set of (molecular) species. We conclude that understanding, modeling and analyzing complex bio-molecular systems can greatly benefit from a set of coarse-graining methods that, ideally, can be automatically applied and that allow the different levels of abstraction to be related.

AB - The complexity of biological models makes methods for their analysis and understanding highly desirable. Here, we demonstrate the orchestration of various novel coarse-graining methods by applying them to the mitotic spindle assembly checkpoint. We begin with a detailed fine-grained spatial model in which individual molecules are simulated moving and reacting in a three-dimensional space. A sequence of manual and automatic coarse-grainings finally leads to the coarsest deterministic and stochastic models containing only four molecular species and four states for each kinetochore, respectively. We are able to relate each more coarse-grained level to a finer one, which allows us to relate model parameters between coarse-grainings and which provides a more precise meaning for the elements of the more abstract models. Furthermore, we discuss how organizational coarse-graining can be applied to spatial dynamics by showing spatial organizations during mitotic checkpoint inactivation. We demonstrate how these models lead to insights if the model has different "meaningful" behaviors that differ in the set of (molecular) species. We conclude that understanding, modeling and analyzing complex bio-molecular systems can greatly benefit from a set of coarse-graining methods that, ideally, can be automatically applied and that allow the different levels of abstraction to be related.

U2 - 10.1038/s41598-019-40648-w

DO - 10.1038/s41598-019-40648-w

M3 - Article

C2 - 30846816

VL - 9

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

IS - 1

M1 - 3902

ER -