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Kinetic models of hematopoietic differentiation

Olariu, Victor LU and Peterson, Carsten LU (2019) In Wiley interdisciplinary reviews. Systems biology and medicine 11(1). p.1424-1424
Abstract

As cell and molecular biology is becoming increasingly quantitative, there is an upsurge of interest in mechanistic modeling at different levels of resolution. Such models mostly concern kinetics and include gene and protein interactions as well as cell population dynamics. The final goal of these models is to provide experimental predictions, which is now taking on. However, even without matured predictions, kinetic models serve the purpose of compressing a plurality of experimental results into something that can empower the data interpretation, and importantly, suggesting new experiments by turning "knobs" in silico. Once formulated, kinetic models can be executed in terms of molecular rate equations for concentrations or by... (More)

As cell and molecular biology is becoming increasingly quantitative, there is an upsurge of interest in mechanistic modeling at different levels of resolution. Such models mostly concern kinetics and include gene and protein interactions as well as cell population dynamics. The final goal of these models is to provide experimental predictions, which is now taking on. However, even without matured predictions, kinetic models serve the purpose of compressing a plurality of experimental results into something that can empower the data interpretation, and importantly, suggesting new experiments by turning "knobs" in silico. Once formulated, kinetic models can be executed in terms of molecular rate equations for concentrations or by stochastic simulations when only a limited number of copies are involved. Developmental processes, in particular those of stem and progenitor cell commitments, are not only topical but also particularly suitable for kinetic modeling due to the finite number of key genes involved in cellular decisions. Stem and progenitor cell commitment processes have been subject to intense experimental studies over the last decade with some emphasis on embryonic and hematopoietic stem cells. Gene and protein interactions governing these processes can be modeled by binary Boolean rules or by continuous-valued models with interactions set by binding strengths. Conceptual insights along with tested predictions have emerged from such kinetic models. Here we review kinetic modeling efforts applied to stem cell developmental systems with focus on hematopoiesis. We highlight the future challenges including multi-scale models integrating cell dynamical and transcriptional models. This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Developmental Biology > Stem Cell Biology and Regeneration.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
energy landscapes, hematopoiesis, rate equations, reprogramming, stem cells, stochastic simulations, systems biology
in
Wiley interdisciplinary reviews. Systems biology and medicine
volume
11
issue
1
pages
1424 - 1424
publisher
John Wiley and Sons Inc.
external identifiers
  • scopus:85058732767
DOI
10.1002/wsbm.1424
language
English
LU publication?
yes
id
42cb2294-1156-41a5-a75d-8016f6dc541f
date added to LUP
2019-01-02 13:26:25
date last changed
2019-10-15 06:53:13
@article{42cb2294-1156-41a5-a75d-8016f6dc541f,
  abstract     = {<p>As cell and molecular biology is becoming increasingly quantitative, there is an upsurge of interest in mechanistic modeling at different levels of resolution. Such models mostly concern kinetics and include gene and protein interactions as well as cell population dynamics. The final goal of these models is to provide experimental predictions, which is now taking on. However, even without matured predictions, kinetic models serve the purpose of compressing a plurality of experimental results into something that can empower the data interpretation, and importantly, suggesting new experiments by turning "knobs" in silico. Once formulated, kinetic models can be executed in terms of molecular rate equations for concentrations or by stochastic simulations when only a limited number of copies are involved. Developmental processes, in particular those of stem and progenitor cell commitments, are not only topical but also particularly suitable for kinetic modeling due to the finite number of key genes involved in cellular decisions. Stem and progenitor cell commitment processes have been subject to intense experimental studies over the last decade with some emphasis on embryonic and hematopoietic stem cells. Gene and protein interactions governing these processes can be modeled by binary Boolean rules or by continuous-valued models with interactions set by binding strengths. Conceptual insights along with tested predictions have emerged from such kinetic models. Here we review kinetic modeling efforts applied to stem cell developmental systems with focus on hematopoiesis. We highlight the future challenges including multi-scale models integrating cell dynamical and transcriptional models. This article is categorized under: Models of Systems Properties and Processes &gt; Mechanistic Models Developmental Biology &gt; Stem Cell Biology and Regeneration.</p>},
  author       = {Olariu, Victor and Peterson, Carsten},
  keyword      = {energy landscapes,hematopoiesis,rate equations,reprogramming,stem cells,stochastic simulations,systems biology},
  language     = {eng},
  number       = {1},
  pages        = {1424--1424},
  publisher    = {John Wiley and Sons Inc.},
  series       = {Wiley interdisciplinary reviews. Systems biology and medicine},
  title        = {Kinetic models of hematopoietic differentiation},
  url          = {http://dx.doi.org/10.1002/wsbm.1424},
  volume       = {11},
  year         = {2019},
}