---
_id: '2302'
abstract:
- lang: eng
  text: 'We introduce propagation models (PMs), a formalism able to express several
    kinds of equations that describe the behavior of biochemical reaction networks.
    Furthermore, we introduce the propagation abstract data type (PADT), which separates
    concerns regarding different numerical algorithms for the transient analysis of
    biochemical reaction networks from concerns regarding their implementation, thus
    allowing for portable and efficient solutions. The state of a propagation abstract
    data type is given by a vector that assigns mass values to a set of nodes, and
    its (next) operator propagates mass values through this set of nodes. We propose
    an approximate implementation of the (next) operator, based on threshold abstraction,
    which propagates only "significant" mass values and thus achieves a
    compromise between efficiency and accuracy. Finally, we give three use cases for
    propagation models: the chemical master equation (CME), the reaction rate equation
    (RRE), and a hybrid method that combines these two equations. These three applications
    use propagation models in order to propagate probabilities and/or expected values
    and variances of the model''s variables.'
author:
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Maria
  full_name: Mateescu, Maria
  id: 3B43276C-F248-11E8-B48F-1D18A9856A87
  last_name: Mateescu
citation:
  ama: Henzinger TA, Mateescu M. The propagation approach for computing biochemical
    reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>.
    2012;10(2):310-322. doi:<a href="https://doi.org/10.1109/TCBB.2012.91">10.1109/TCBB.2012.91</a>
  apa: Henzinger, T. A., &#38; Mateescu, M. (2012). The propagation approach for computing
    biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology
    and Bioinformatics</i>. IEEE. <a href="https://doi.org/10.1109/TCBB.2012.91">https://doi.org/10.1109/TCBB.2012.91</a>
  chicago: Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for
    Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational
    Biology and Bioinformatics</i>. IEEE, 2012. <a href="https://doi.org/10.1109/TCBB.2012.91">https://doi.org/10.1109/TCBB.2012.91</a>.
  ieee: T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical
    reaction networks,” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>,
    vol. 10, no. 2. IEEE, pp. 310–322, 2012.
  ista: Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical
    reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics.
    10(2), 310–322.
  mla: Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing
    Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology
    and Bioinformatics</i>, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:<a href="https://doi.org/10.1109/TCBB.2012.91">10.1109/TCBB.2012.91</a>.
  short: T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology
    and Bioinformatics 10 (2012) 310–322.
date_created: 2018-12-11T11:56:52Z
date_published: 2012-07-03T00:00:00Z
date_updated: 2021-01-12T06:56:38Z
day: '03'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/TCBB.2012.91
ec_funded: 1
external_id:
  pmid:
  - '22778152'
intvolume: '        10'
issue: '2'
language:
- iso: eng
month: '07'
oa_version: None
page: 310 - 322
pmid: 1
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
publication: IEEE ACM Transactions on Computational Biology and Bioinformatics
publication_status: published
publisher: IEEE
publist_id: '4625'
quality_controlled: '1'
scopus_import: 1
status: public
title: The propagation approach for computing biochemical reaction networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2012'
...
---
_id: '6496'
abstract:
- lang: eng
  text: We report the switching behavior of the full bacterial flagellum system that
    includes the filament and the motor in wild-type Escherichia coli cells. In sorting
    the motor behavior by the clockwise bias, we find that the distributions of the
    clockwise (CW) and counterclockwise (CCW) intervals are either exponential or
    nonexponential with long tails. At low bias, CW intervals are exponentially distributed
    and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and
    CCW intervals are mainly exponentially distributed. A simple model suggests that
    these two distinct switching behaviors are governed by the presence of signaling
    noise within the chemotaxis network. Low noise yields exponentially distributed
    intervals, whereas large noise yields nonexponential behavior with long tails.
    These drastically different motor statistics may play a role in optimizing bacterial
    behavior for a wide range of environmental conditions.
article_processing_charge: No
author:
- first_name: Heungwon
  full_name: Park, Heungwon
  last_name: Park
- first_name: Panos
  full_name: Oikonomou, Panos
  last_name: Oikonomou
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Philippe
  full_name: Cluzel, Philippe
  last_name: Cluzel
citation:
  ama: Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior
    of the bacterial flagellum. <i>Biophysical Journal</i>. 2011;101(10):2336-2340.
    doi:<a href="https://doi.org/10.1016/j.bpj.2011.09.040">10.1016/j.bpj.2011.09.040</a>
  apa: Park, H., Oikonomou, P., Guet, C. C., &#38; Cluzel, P. (2011). Noise underlies
    switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.bpj.2011.09.040">https://doi.org/10.1016/j.bpj.2011.09.040</a>
  chicago: Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise
    Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>.
    Elsevier, 2011. <a href="https://doi.org/10.1016/j.bpj.2011.09.040">https://doi.org/10.1016/j.bpj.2011.09.040</a>.
  ieee: H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching
    behavior of the bacterial flagellum,” <i>Biophysical Journal</i>, vol. 101, no.
    10. Elsevier, pp. 2336–2340, 2011.
  ista: Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior
    of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.
  mla: Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial
    Flagellum.” <i>Biophysical Journal</i>, vol. 101, no. 10, Elsevier, 2011, pp.
    2336–40, doi:<a href="https://doi.org/10.1016/j.bpj.2011.09.040">10.1016/j.bpj.2011.09.040</a>.
  short: H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011)
    2336–2340.
date_created: 2019-05-28T11:54:29Z
date_published: 2011-11-16T00:00:00Z
date_updated: 2021-04-16T11:54:49Z
day: '16'
department:
- _id: CaGu
doi: 10.1016/j.bpj.2011.09.040
external_id:
  pmid:
  - '22098731'
intvolume: '       101'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/
month: '11'
oa: 1
oa_version: Published Version
page: 2336-2340
pmid: 1
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Noise underlies switching behavior of the bacterial flagellum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2011'
...
---
_id: '3719'
abstract:
- lang: eng
  text: The induction of a signaling pathway is characterized by transient complex
    formation and mutual posttranslational modification of proteins. To faithfully
    capture this combinatorial process in a math- ematical model is an important challenge
    in systems biology. Exploiting the limited context on which most binding and modification
    events are conditioned, attempts have been made to reduce the com- binatorial
    complexity by quotienting the reachable set of molecular species, into species
    aggregates while preserving the deterministic semantics of the thermodynamic limit.
    Recently we proposed a quotienting that also preserves the stochastic semantics
    and that is complete in the sense that the semantics of individual species can
    be recovered from the aggregate semantics. In this paper we prove that this quotienting
    yields a sufficient condition for weak lumpability and that it gives rise to a
    backward Markov bisimulation between the original and aggregated transition system.
    We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.
acknowledgement: Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL
  ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National
  Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support
  from SystemsX.ch, the Swiss Initiative in Systems Biology.
alternative_title:
- EPTCS
arxiv: 1
author:
- first_name: Jérôme
  full_name: Feret, Jérôme
  last_name: Feret
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Heinz
  full_name: Koeppl, Heinz
  last_name: Koeppl
- first_name: Tatjana
  full_name: Petrov, Tatjana
  id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
  last_name: Petrov
  orcid: 0000-0002-9041-0905
citation:
  ama: 'Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based
    systems. In: Vol 40. Open Publishing Association; 2010:142-161.'
  apa: 'Feret, J., Henzinger, T. A., Koeppl, H., &#38; Petrov, T. (2010). Lumpability
    abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC:
    Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open
    Publishing Association.'
  chicago: Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability
    Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.
  ieee: 'J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions
    of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically
    Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.'
  ista: 'Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions
    of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process
    Calculi, EPTCS, vol. 40, 142–161.'
  mla: Feret, Jérôme, et al. <i>Lumpability Abstractions of Rule-Based Systems</i>.
    Vol. 40, Open Publishing Association, 2010, pp. 142–61.
  short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association,
    2010, pp. 142–161.
conference:
  end_date: 2010-08-23
  location: Jena, Germany
  name: 'MECBIC: Membrane Computing and Biologically Inspired Process Calculi'
  start_date: 2010-08-23
date_created: 2018-12-11T12:04:47Z
date_published: 2010-10-30T00:00:00Z
date_updated: 2023-02-23T11:15:19Z
day: '30'
ddc:
- '570'
department:
- _id: ToHe
- _id: CaGu
external_id:
  arxiv:
  - '1011.0496'
file:
- access_level: open_access
  checksum: eaaba991a86fff37606b0eb5196878e8
  content_type: application/pdf
  creator: kschuh
  date_created: 2019-01-31T12:09:09Z
  date_updated: 2020-07-14T12:46:14Z
  file_id: '5904'
  file_name: Lumpability_abstractions_of_rule-based_systems.pdf
  file_size: 907155
  relation: main_file
file_date_updated: 2020-07-14T12:46:14Z
has_accepted_license: '1'
intvolume: '        40'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 142-161
publication_status: published
publisher: Open Publishing Association
publist_id: '2511'
quality_controlled: '1'
related_material:
  record:
  - id: '3168'
    relation: later_version
    status: public
scopus_import: 1
status: public
title: Lumpability abstractions of rule-based systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 40
year: '2010'
...
---
_id: '3847'
abstract:
- lang: eng
  text: The importance of stochasticity within biological systems has been shown repeatedly
    during the last years and has raised the need for efficient stochastic tools.
    We present SABRE, a tool for stochastic analysis of biochemical reaction networks.
    SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation
    algorithm for computing transient solutions of biochemical reaction networks.
    Biochemical reactions networks represent biological systems studied at a molecular
    level and these reactions can be modeled as transitions of a Markov chain. SABRE
    accepts as input the formalism of guarded commands, which it interprets either
    as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic
    mode, SABRE may also perform a deterministic analysis by directly computing a
    mean-field approximation of the system under study. We illustrate the different
    functionalities of SABRE by means of biological case studies.
author:
- first_name: Frédéric
  full_name: Didier, Frédéric
  last_name: Didier
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Maria
  full_name: Mateescu, Maria
  last_name: Mateescu
- first_name: Verena
  full_name: Wolf, Verena
  last_name: Wolf
citation:
  ama: 'Didier F, Henzinger TA, Mateescu M, Wolf V. SABRE: A tool for the stochastic
    analysis of biochemical reaction networks. In: IEEE; 2010:193-194. doi:<a href="https://doi.org/10.1109/QEST.2010.33">10.1109/QEST.2010.33</a>'
  apa: 'Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2010). SABRE:
    A tool for the stochastic analysis of biochemical reaction networks (pp. 193–194).
    Presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA:
    IEEE. <a href="https://doi.org/10.1109/QEST.2010.33">https://doi.org/10.1109/QEST.2010.33</a>'
  chicago: 'Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
    “SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,”
    193–94. IEEE, 2010. <a href="https://doi.org/10.1109/QEST.2010.33">https://doi.org/10.1109/QEST.2010.33</a>.'
  ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “SABRE: A tool for
    the stochastic analysis of biochemical reaction networks,” presented at the QEST:
    Quantitative Evaluation of Systems, Williamsburg, USA, 2010, pp. 193–194.'
  ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. SABRE: A tool for the stochastic
    analysis of biochemical reaction networks. QEST: Quantitative Evaluation of Systems,
    193–194.'
  mla: 'Didier, Frédéric, et al. <i>SABRE: A Tool for the Stochastic Analysis of Biochemical
    Reaction Networks</i>. IEEE, 2010, pp. 193–94, doi:<a href="https://doi.org/10.1109/QEST.2010.33">10.1109/QEST.2010.33</a>.'
  short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.
conference:
  end_date: 2010-09-18
  location: Williamsburg, USA
  name: 'QEST: Quantitative Evaluation of Systems'
  start_date: 2010-09-15
date_created: 2018-12-11T12:05:29Z
date_published: 2010-10-14T00:00:00Z
date_updated: 2021-01-12T07:52:37Z
day: '14'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/QEST.2010.33
file:
- access_level: open_access
  checksum: 38707b149d2174f01be406e794ffa849
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:09:03Z
  date_updated: 2020-07-14T12:46:17Z
  file_id: '4726'
  file_name: IST-2012-63-v1+1_SABRE-A_tool_for_the_stochastic_analysis_of_biochemical_reaction_networks.pdf
  file_size: 433824
  relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 193 - 194
publication_status: published
publisher: IEEE
publist_id: '2339'
pubrep_id: '63'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'SABRE: A tool for the stochastic analysis of biochemical reaction networks'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3843'
abstract:
- lang: eng
  text: "Within systems biology there is an increasing interest in the stochastic
    behavior of biochemical reaction networks. An appropriate stochastic description
    is provided by the chemical master equation, which represents a continuous- time
    Markov chain (CTMC).\r\nStandard Uniformization (SU) is an efficient method for
    the transient analysis of CTMCs. For systems with very different time scales,
    such as biochemical reaction networks, SU is computationally expensive. In these
    cases, a variant of SU, called adaptive uniformization (AU), is known to reduce
    the large number of iterations needed by SU. The additional difficulty of AU is
    that it requires the solution of a birth process.\r\nIn this paper we present
    an on-the-fly variant of AU, where we improve the original algorithm for AU at
    the cost of a small approximation error. By means of several examples, we show
    that our approach is particularly well-suited for biochemical reaction networks."
acknowledgement: This research has been partially funded by the Swiss National Science
  Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal
  Computing and Interaction at Saarland University.
article_processing_charge: No
author:
- first_name: Frédéric
  full_name: Didier, Frédéric
  last_name: Didier
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Maria
  full_name: Mateescu, Maria
  id: 3B43276C-F248-11E8-B48F-1D18A9856A87
  last_name: Mateescu
- first_name: Verena
  full_name: Wolf, Verena
  last_name: Wolf
citation:
  ama: 'Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of
    the chemical master equation. In: Vol 4. IEEE; 2009:118-127. doi:<a href="https://doi.org/10.1109/HiBi.2009.23">10.1109/HiBi.2009.23</a>'
  apa: 'Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2009). Fast adaptive
    uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented
    at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE.
    <a href="https://doi.org/10.1109/HiBi.2009.23">https://doi.org/10.1109/HiBi.2009.23</a>'
  chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
    “Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE,
    2009. <a href="https://doi.org/10.1109/HiBi.2009.23">https://doi.org/10.1109/HiBi.2009.23</a>.
  ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization
    of the chemical master equation,” presented at the HIBI: High-Performance Computational
    Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.'
  ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization
    of the chemical master equation. HIBI: High-Performance Computational Systems
    Biology vol. 4, 118–127.'
  mla: Didier, Frédéric, et al. <i>Fast Adaptive Uniformization of the Chemical Master
    Equation</i>. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:<a href="https://doi.org/10.1109/HiBi.2009.23">10.1109/HiBi.2009.23</a>.
  short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.
conference:
  end_date: 2009-10-16
  location: Trento, Italy
  name: 'HIBI: High-Performance Computational Systems Biology'
  start_date: 2009-10-14
date_created: 2018-12-11T12:05:28Z
date_published: 2009-10-30T00:00:00Z
date_updated: 2023-02-23T11:45:05Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/HiBi.2009.23
file:
- access_level: open_access
  checksum: 9a3bde48f43203991a0b3c6a277c2f5b
  content_type: application/pdf
  creator: dernst
  date_created: 2020-05-19T16:33:55Z
  date_updated: 2020-07-14T12:46:17Z
  file_id: '7874'
  file_name: 2009_HIBI_Didier.pdf
  file_size: 222890
  relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: '         4'
issue: '6'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 118 - 127
publication_status: published
publisher: IEEE
publist_id: '2348'
quality_controlled: '1'
related_material:
  record:
  - id: '3842'
    relation: later_version
    status: public
scopus_import: 1
status: public
title: Fast adaptive uniformization of the chemical master equation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2009'
...