---
_id: '2718'
abstract:
- lang: eng
text: Even though both population and quantitative genetics, and evolutionary computation,
deal with the same questions, they have developed largely independently of each
other. I review key results from each field, emphasising those that apply independently
of the (usually unknown) relation between genotype and phenotype. The infinitesimal
model provides a simple framework for predicting the response of complex traits
to selection, which in biology has proved remarkably successful. This allows one
to choose the schedule of population sizes and selection intensities that will
maximise the response to selection, given that the total number of individuals
realised, C = ∑t Nt, is constrained. This argument shows that for an additive
trait (i.e., determined by the sum of effects of the genes), the optimum population
size and the maximum possible response (i.e., the total change in trait mean)
are both proportional to √C.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: 'Barton NH, Paixao T. Can quantitative and population genetics help us understand
evolutionary computation? In: Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation. ACM; 2013:1573-1580. doi:10.1145/2463372.2463568'
apa: 'Barton, N. H., & Paixao, T. (2013). Can quantitative and population genetics
help us understand evolutionary computation? In Proceedings of the 15th annual
conference on Genetic and evolutionary computation (pp. 1573–1580). Amsterdam,
Netherlands: ACM. https://doi.org/10.1145/2463372.2463568'
chicago: Barton, Nicholas H, and Tiago Paixao. “Can Quantitative and Population
Genetics Help Us Understand Evolutionary Computation?” In Proceedings of the
15th Annual Conference on Genetic and Evolutionary Computation, 1573–80. ACM,
2013. https://doi.org/10.1145/2463372.2463568.
ieee: N. H. Barton and T. Paixao, “Can quantitative and population genetics help
us understand evolutionary computation?,” in Proceedings of the 15th annual
conference on Genetic and evolutionary computation, Amsterdam, Netherlands,
2013, pp. 1573–1580.
ista: 'Barton NH, Paixao T. 2013. Can quantitative and population genetics help
us understand evolutionary computation? Proceedings of the 15th annual conference
on Genetic and evolutionary computation. GECCO: Genetic and evolutionary computation
conference, 1573–1580.'
mla: Barton, Nicholas H., and Tiago Paixao. “Can Quantitative and Population Genetics
Help Us Understand Evolutionary Computation?” Proceedings of the 15th Annual
Conference on Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–80,
doi:10.1145/2463372.2463568.
short: N.H. Barton, T. Paixao, in:, Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation, ACM, 2013, pp. 1573–1580.
conference:
end_date: 2013-07-10
location: Amsterdam, Netherlands
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2013-07-06
corr_author: '1'
date_created: 2018-12-11T11:59:14Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2024-10-09T20:55:12Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2463372.2463568
ec_funded: 1
file:
- access_level: open_access
checksum: 9d9be9090ce5c20766e0eb076ace5b98
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:38Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5159'
file_name: IST-2016-564-v1+1_NickGECCO_2013_1_-1.pdf
file_size: 475844
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 1573 - 1580
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Proceedings of the 15th annual conference on Genetic and evolutionary
computation
publication_status: published
publisher: ACM
publist_id: '4174'
pubrep_id: '564'
quality_controlled: '1'
scopus_import: 1
status: public
title: Can quantitative and population genetics help us understand evolutionary computation?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2719'
abstract:
- lang: eng
text: Prediction of the evolutionary process is a long standing problem both in
the theory of evolutionary biology and evolutionary computation (EC). It has long
been realized that heritable variation is crucial to both the response to selection
and the success of genetic algorithms. However, not all variation contributes
in the same way to the response. Quantitative genetics has developed a large body
of work trying to estimate and understand how different components of the variance
in fitness in the population contribute to the response to selection. We illustrate
how to apply some concepts of quantitative genetics to the analysis of genetic
algorithms. In particular, we derive estimates for the short term prediction of
the response to selection and we use variance decomposition to gain insight on
local aspects of the landscape. Finally, we propose a new population based genetic
algorithm that uses these methods to improve its operation.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Paixao T, Barton NH. A variance decomposition approach to the analysis of
genetic algorithms. In: Proceedings of the 15th Annual Conference on Genetic
and Evolutionary Computation. ACM; 2013:845-852. doi:10.1145/2463372.2463470'
apa: 'Paixao, T., & Barton, N. H. (2013). A variance decomposition approach
to the analysis of genetic algorithms. In Proceedings of the 15th annual conference
on Genetic and evolutionary computation (pp. 845–852). Amsterdam, Netherlands:
ACM. https://doi.org/10.1145/2463372.2463470'
chicago: Paixao, Tiago, and Nicholas H Barton. “A Variance Decomposition Approach
to the Analysis of Genetic Algorithms.” In Proceedings of the 15th Annual Conference
on Genetic and Evolutionary Computation, 845–52. ACM, 2013. https://doi.org/10.1145/2463372.2463470.
ieee: T. Paixao and N. H. Barton, “A variance decomposition approach to the analysis
of genetic algorithms,” in Proceedings of the 15th annual conference on Genetic
and evolutionary computation, Amsterdam, Netherlands, 2013, pp. 845–852.
ista: 'Paixao T, Barton NH. 2013. A variance decomposition approach to the analysis
of genetic algorithms. Proceedings of the 15th annual conference on Genetic and
evolutionary computation. GECCO: Genetic and evolutionary computation conference,
845–852.'
mla: Paixao, Tiago, and Nicholas H. Barton. “A Variance Decomposition Approach to
the Analysis of Genetic Algorithms.” Proceedings of the 15th Annual Conference
on Genetic and Evolutionary Computation, ACM, 2013, pp. 845–52, doi:10.1145/2463372.2463470.
short: T. Paixao, N.H. Barton, in:, Proceedings of the 15th Annual Conference on
Genetic and Evolutionary Computation, ACM, 2013, pp. 845–852.
conference:
end_date: 2013-07-10
location: Amsterdam, Netherlands
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2013-07-06
corr_author: '1'
date_created: 2018-12-11T11:59:15Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2024-10-09T20:55:12Z
day: '01'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2463372.2463470
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 845 - 852
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Proceedings of the 15th annual conference on Genetic and evolutionary
computation
publication_status: published
publisher: ACM
publist_id: '4173'
quality_controlled: '1'
scopus_import: 1
status: public
title: A variance decomposition approach to the analysis of genetic algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2720'
abstract:
- lang: eng
text: 'Knowledge of the rate and fitness effects of mutations is essential for understanding
the process of evolution. Mutations are inherently difficult to study because
they are rare and are frequently eliminated by natural selection. In the ciliate
Tetrahymena thermophila, mutations can accumulate in the germline genome without
being exposed to selection. We have conducted a mutation accumulation (MA) experiment
in this species. Assuming that all mutations are deleterious and have the same
effect, we estimate that the deleterious mutation rate per haploid germline genome
per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that
germline mutations decrease fitness by s = 11% when expressed in a homozygous
state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially
recessive on average (h = 0.26; 95% CI: –0.022, 0.62) and that the rate of lethal
mutations is <10% of the deleterious mutation rate. Comparisons between the
observed evolutionary responses in the germline and somatic genomes and the results
from individual-based simulations of MA suggest that the two genomes have similar
mutational parameters. These are the first estimates of the deleterious mutation
rate and fitness effects from the eukaryotic supergroup Chromalveolata and are
within the range of those of other eukaryotes.'
article_processing_charge: No
author:
- first_name: Hongan
full_name: Long, Hongan
last_name: Long
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Ricardo
full_name: Azevedo, Ricardo
last_name: Azevedo
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Long H, Paixao T, Azevedo R, Zufall R. Accumulation of spontaneous mutations
in the ciliate Tetrahymena thermophila. Genetics. 2013;195(2):527-540.
doi:10.1534/genetics.113.153536
apa: Long, H., Paixao, T., Azevedo, R., & Zufall, R. (2013). Accumulation of
spontaneous mutations in the ciliate Tetrahymena thermophila. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.113.153536
chicago: Long, Hongan, Tiago Paixao, Ricardo Azevedo, and Rebecca Zufall. “Accumulation
of Spontaneous Mutations in the Ciliate Tetrahymena Thermophila.” Genetics.
Genetics Society of America, 2013. https://doi.org/10.1534/genetics.113.153536.
ieee: H. Long, T. Paixao, R. Azevedo, and R. Zufall, “Accumulation of spontaneous
mutations in the ciliate Tetrahymena thermophila,” Genetics, vol. 195,
no. 2. Genetics Society of America, pp. 527–540, 2013.
ista: Long H, Paixao T, Azevedo R, Zufall R. 2013. Accumulation of spontaneous mutations
in the ciliate Tetrahymena thermophila. Genetics. 195(2), 527–540.
mla: Long, Hongan, et al. “Accumulation of Spontaneous Mutations in the Ciliate
Tetrahymena Thermophila.” Genetics, vol. 195, no. 2, Genetics Society of
America, 2013, pp. 527–40, doi:10.1534/genetics.113.153536.
short: H. Long, T. Paixao, R. Azevedo, R. Zufall, Genetics 195 (2013) 527–540.
date_created: 2018-12-11T11:59:15Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2025-09-29T14:08:19Z
day: '01'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1534/genetics.113.153536
ec_funded: 1
external_id:
isi:
- '000325286200020'
pmid:
- '23934880'
intvolume: ' 195'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781978/
month: '10'
oa: 1
oa_version: Submitted Version
page: 527-540
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '4172'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accumulation of spontaneous mutations in the ciliate Tetrahymena thermophila
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 195
year: '2013'
...
---
_id: '2853'
abstract:
- lang: eng
text: High relatedness among interacting individuals has generally been considered
a precondition for the evolution of altruism. However, kin-selection theory also
predicts the evolution of altruism when relatedness is low, as long as the cost
of the altruistic act is minor compared with its benefit. Here, we demonstrate
evidence for a low-cost altruistic act in bacteria. We investigated Escherichia
coli responding to the attack of an obligately lytic phage by committing suicide
in order to prevent parasite transmission to nearby relatives. We found that bacterial
suicide provides large benefits to survivors at marginal costs to committers.
The cost of suicide was low, because infected cells are moribund, rapidly dying
upon phage infection, such that no more opportunity for reproduction remains.
As a consequence of its marginal cost, host suicide was selectively favoured even
when relatedness between committers and survivors approached zero. Altogether,
our findings demonstrate that low-cost suicide can evolve with ease, represents
an effective host-defence strategy, and seems to be widespread among microbes.
Moreover, low-cost suicide might also occur in higher organisms as exemplified
by infected social insect workers leaving the colony to die in isolation.
article_processing_charge: No
article_type: original
author:
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
citation:
ama: 'Refardt D, Bergmiller T, Kümmerli R. Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection. Proceedings
of the Royal Society of London Series B Biological Sciences. 2013;280(1759).
doi:10.1098/rspb.2012.3035'
apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Altruism can evolve
when relatedness is low: Evidence from bacteria committing suicide upon phage
infection. Proceedings of the Royal Society of London Series B Biological Sciences.
The Royal Society. https://doi.org/10.1098/rspb.2012.3035'
chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can
Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon
Phage Infection.” Proceedings of the Royal Society of London Series B Biological
Sciences. The Royal Society, 2013. https://doi.org/10.1098/rspb.2012.3035.'
ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 280, no.
1759. The Royal Society, 2013.'
ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness
is low: Evidence from bacteria committing suicide upon phage infection. Proceedings
of the Royal Society of London Series B Biological Sciences. 280(1759).'
mla: 'Refardt, Dominik, et al. “Altruism Can Evolve When Relatedness Is Low: Evidence
from Bacteria Committing Suicide upon Phage Infection.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 280, no. 1759,
The Royal Society, 2013, doi:10.1098/rspb.2012.3035.'
short: D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society
of London Series B Biological Sciences 280 (2013).
corr_author: '1'
date_created: 2018-12-11T11:59:56Z
date_published: 2013-05-22T00:00:00Z
date_updated: 2025-09-29T13:41:12Z
day: '22'
department:
- _id: CaGu
doi: 10.1098/rspb.2012.3035
external_id:
isi:
- '000317482100005'
pmid:
- '23516238'
intvolume: ' 280'
isi: 1
issue: '1759'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619501/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
publication_status: published
publisher: The Royal Society
publist_id: '3939'
quality_controlled: '1'
related_material:
record:
- id: '9751'
relation: research_data
status: public
scopus_import: '1'
status: public
title: 'Altruism can evolve when relatedness is low: Evidence from bacteria committing
suicide upon phage infection'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 280
year: '2013'
...
---
_id: '9751'
abstract:
- lang: eng
text: High relatedness among interacting individuals has generally been considered
a precondition for the evolution of altruism. However, kin-selection theory also
predicts the evolution of altruism when relatedness is low, as long as the cost
of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence
for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding
to the attack of an obligately lytic phage by committing suicide in order to prevent
parasite transmission to nearby relatives. We found that bacterial suicide provides
large benefits to survivors at marginal costs to committers. The cost of suicide
was low because infected cells are moribund, rapidly dying upon phage infection,
such that no more opportunity for reproduction remains. As a consequence of its
marginal cost, host suicide was selectively favoured even when relatedness between
committers and survivors approached zero. Altogether, our findings demonstrate
that low-cost suicide can evolve with ease, represents an effective host-defence
strategy, and seems to be widespread among microbes. Moreover, low-cost suicide
might also occur in higher organisms as exemplified by infected social insect
workers leaving the colony to die in isolation.
article_processing_charge: No
author:
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
citation:
ama: 'Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness
is low: evidence from bacteria committing suicide upon phage infection. 2013.
doi:10.5061/dryad.b1q2n'
apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Data from: Altruism
can evolve when relatedness is low: evidence from bacteria committing suicide
upon phage infection. Dryad. https://doi.org/10.5061/dryad.b1q2n'
chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism
Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide
upon Phage Infection.” Dryad, 2013. https://doi.org/10.5061/dryad.b1q2n.'
ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection.” Dryad, 2013.'
ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection, Dryad, 10.5061/dryad.b1q2n.'
mla: 'Refardt, Dominik, et al. Data from: Altruism Can Evolve When Relatedness
Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection. Dryad,
2013, doi:10.5061/dryad.b1q2n.'
short: D. Refardt, T. Bergmiller, R. Kümmerli, (2013).
date_created: 2021-07-30T08:08:09Z
date_published: 2013-03-21T00:00:00Z
date_updated: 2025-09-29T13:41:12Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.b1q2n
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.b1q2n
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2853'
relation: used_in_publication
status: public
status: public
title: 'Data from: Altruism can evolve when relatedness is low: evidence from bacteria
committing suicide upon phage infection'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '499'
abstract:
- lang: eng
text: Exposure of an isogenic bacterial population to a cidal antibiotic typically
fails to eliminate a small fraction of refractory cells. Historically, fractional
killing has been attributed to infrequently dividing or nondividing "persisters."
Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium
smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although
persistence in these studies was characterized by stable numbers of cells, this
apparent stability was actually a dynamic state of balanced division and death.
Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic
pulses that were negatively correlated with cell survival. These behaviors may
reflect epigenetic effects, because KatG pulsing and death were correlated between
sibling cells. Selection of lineages characterized by infrequent KatG pulsing
could allow nonresponsive adaptation during prolonged drug exposure.
article_processing_charge: No
author:
- first_name: Yurichi
full_name: Wakamoto, Yurichi
last_name: Wakamoto
- first_name: Neraaj
full_name: Dhar, Neraaj
last_name: Dhar
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Katrin
full_name: Schneider, Katrin
last_name: Schneider
- first_name: François
full_name: Signorino Gelo, François
last_name: Signorino Gelo
- first_name: Stanislas
full_name: Leibler, Stanislas
last_name: Leibler
- first_name: John
full_name: Mckinney, John
last_name: Mckinney
citation:
ama: Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed
mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858
apa: Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler,
S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858
chicago: Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François
Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of
Antibiotic-Stressed Mycobacteria.” Science. American Association for the
Advancement of Science, 2013. https://doi.org/10.1126/science.1229858.
ieee: Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,”
Science, vol. 339, no. 6115. American Association for the Advancement of
Science, pp. 91–95, 2013.
ista: Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney
J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115),
91–95.
mla: Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”
Science, vol. 339, no. 6115, American Association for the Advancement of
Science, 2013, pp. 91–95, doi:10.1126/science.1229858.
short: Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler,
J. Mckinney, Science 339 (2013) 91–95.
date_created: 2018-12-11T11:46:48Z
date_published: 2013-01-04T00:00:00Z
date_updated: 2025-09-30T07:29:30Z
day: '04'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1126/science.1229858
external_id:
isi:
- '000312985800059'
intvolume: ' 339'
isi: 1
issue: '6115'
language:
- iso: eng
month: '01'
oa_version: None
page: 91 - 95
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7321'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic persistence of antibiotic-stressed mycobacteria
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 339
year: '2013'
...
---
_id: '2943'
abstract:
- lang: eng
text: We examine whether the Escherichia coli chromosome is folded into a self-adherent
nucleoprotein complex, or alternately is a confined but otherwise unconstrained
self-avoiding polymer. We address this through in vivo visualization, using an
inducible GFP fusion to the nucleoid-associated protein Fis to non-specifically
decorate the entire chromosome. For a range of different growth conditions, the
chromosome is a compact structure that does not fill the volume of the cell, and
which moves from the new pole to the cell centre. During rapid growth, chromosome
segregation occurs well before cell division, with daughter chromosomes coupled
by a thin inter-daughter filament before complete segregation, whereas during
slow growth chromosomes stay adjacent until cell division occurs. Image correlation
analysis indicates that sub-nucleoid structure is stable on a 1min timescale,
comparable to the timescale for redistribution time measured for GFP-Fis after
photobleaching. Optical deconvolution and writhe calculation analysis indicate
that the nucleoid has a large-scale coiled organization rather than being an amorphous
mass. Our observations are consistent with the chromosome having a self-adherent
filament organization.
acknowledgement: We thank Professor Philippe Cluzel and Mr Lance Min for providing
advice and materials. Jeannette Chau provided technical support. Work at NU was
supported by NSF Grants DMR-0715099, MCB-1022117, DMR-1206868, DMR-0520513 and DMR-1121262
(NU-MRSEC), by NIH-NCI Grant U54CA143869-01 (NU-PS-OC) and by the Chicago Biomedical
Consortium with support from the Searle Funds at the Chicago Community Trust. Work
at UCLA was supported by NIH Grant GM038509.
article_processing_charge: No
author:
- first_name: Nastaran
full_name: Hadizadeh Yazdi, Nastaran
last_name: Hadizadeh Yazdi
- 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: Reid
full_name: Johnson, Reid
last_name: Johnson
- first_name: John
full_name: Marko, John
last_name: Marko
citation:
ama: Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. Variation of the folding and
dynamics of the Escherichia coli chromosome with growth conditions. Molecular
Microbiology. 2012;86(6):1318-1333. doi:10.1111/mmi.12071
apa: Hadizadeh Yazdi, N., Guet, C. C., Johnson, R., & Marko, J. (2012). Variation
of the folding and dynamics of the Escherichia coli chromosome with growth conditions.
Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.12071
chicago: Hadizadeh Yazdi, Nastaran, Calin C Guet, Reid Johnson, and John Marko.
“Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with
Growth Conditions.” Molecular Microbiology. Wiley-Blackwell, 2012. https://doi.org/10.1111/mmi.12071.
ieee: N. Hadizadeh Yazdi, C. C. Guet, R. Johnson, and J. Marko, “Variation of the
folding and dynamics of the Escherichia coli chromosome with growth conditions,”
Molecular Microbiology, vol. 86, no. 6. Wiley-Blackwell, pp. 1318–1333,
2012.
ista: Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. 2012. Variation of the folding
and dynamics of the Escherichia coli chromosome with growth conditions. Molecular
Microbiology. 86(6), 1318–1333.
mla: Hadizadeh Yazdi, Nastaran, et al. “Variation of the Folding and Dynamics of
the Escherichia Coli Chromosome with Growth Conditions.” Molecular Microbiology,
vol. 86, no. 6, Wiley-Blackwell, 2012, pp. 1318–33, doi:10.1111/mmi.12071.
short: N. Hadizadeh Yazdi, C.C. Guet, R. Johnson, J. Marko, Molecular Microbiology
86 (2012) 1318–1333.
date_created: 2018-12-11T12:00:28Z
date_published: 2012-11-09T00:00:00Z
date_updated: 2025-09-30T08:13:13Z
day: '09'
department:
- _id: CaGu
doi: 10.1111/mmi.12071
external_id:
isi:
- '000312557000005'
intvolume: ' 86'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://europepmc.org/articles/pmc3524407
month: '11'
oa: 1
oa_version: Submitted Version
page: 1318 - 1333
publication: Molecular Microbiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3790'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Variation of the folding and dynamics of the Escherichia coli chromosome with
growth conditions
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 86
year: '2012'
...
---
_id: '3130'
abstract:
- lang: eng
text: 'Essential genes code for fundamental cellular functions required for the
viability of an organism. For this reason, essential genes are often highly conserved
across organisms. However, this is not always the case: orthologues of genes that
are essential in one organism are sometimes not essential in other organisms or
are absent from their genomes. This suggests that, in the course of evolution,
essential genes can be rendered nonessential. How can a gene become non-essential?
Here we used genetic manipulation to deplete the products of 26 different essential
genes in Escherichia coli. This depletion results in a lethal phenotype, which
could often be rescued by the overexpression of a non-homologous, non-essential
gene, most likely through replacement of the essential function. We also show
that, in a smaller number of cases, the essential genes can be fully deleted from
the genome, suggesting that complete functional replacement is possible. Finally,
we show that essential genes whose function can be replaced in the laboratory
are more likely to be non-essential or not present in other taxa. These results
are consistent with the notion that patterns of evolutionary conservation of essential
genes are influenced by their compensability-that is, by how easily they can be
functionally replaced, for example through increased expression of other genes.'
acknowledgement: We thank Alex Boehm for discussions and comments.
article_number: e1002803
article_processing_charge: No
author:
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
- first_name: Olin
full_name: Silander, Olin
last_name: Silander
citation:
ama: Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation
of essential genes correlate with their compensability. PLoS Genetics.
2012;8(6). doi:10.1371/journal.pgen.1002803
apa: Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary
conservation of essential genes correlate with their compensability. PLoS Genetics.
Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803
chicago: Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary
Conservation of Essential Genes Correlate with Their Compensability.” PLoS
Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803.
ieee: T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation
of essential genes correlate with their compensability,” PLoS Genetics,
vol. 8, no. 6. Public Library of Science, 2012.
ista: Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation
of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.
mla: Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential
Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no.
6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803.
short: T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).
corr_author: '1'
date_created: 2018-12-11T12:01:34Z
date_published: 2012-06-28T00:00:00Z
date_updated: 2025-09-30T07:57:16Z
day: '28'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1002803
external_id:
isi:
- '000305961000055'
file:
- access_level: open_access
checksum: f8506fb579eda6fc5613ba9bf421b86a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:52Z
date_updated: 2020-07-14T12:46:01Z
file_id: '4973'
file_name: IST-2015-386-v1+1_journal.pgen.1002803.pdf
file_size: 2674138
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '3567'
pubrep_id: '386'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Patterns of evolutionary conservation of essential genes correlate with their
compensability
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2012'
...
---
_id: '3136'
abstract:
- lang: eng
text: 'Continuous-time Markov chains (CTMC) with their rich theory and efficient
simulation algorithms have been successfully used in modeling stochastic processes
in diverse areas such as computer science, physics, and biology. However, systems
that comprise non-instantaneous events cannot be accurately and efficiently modeled
with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that
allows for the specification of a lower bound on the time interval between an
event''s initiation and its completion, and we propose an algorithm for the computation
of their behavior. Our algorithm effectively decomposes the computation into two
stages: a pure CTMC governs event initiations while a deterministic process guarantees
lower bounds on event completion times. Furthermore, from the nature of delayed
CTMCs, we obtain a parallelized version of our algorithm. We use our formalism
to model genetic regulatory circuits (biological systems where delayed events
are common) and report on the results of our numerical algorithm as run on a cluster.
We compare performance and accuracy of our results with results obtained by using
pure CTMCs. © 2012 Springer-Verlag.'
acknowledgement: This work was supported by the ERC Advanced Investigator grant on
Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.
alternative_title:
- LNCS
author:
- 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: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- 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: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time
Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309.
doi:10.1007/978-3-642-31424-7_24'
apa: 'Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., & Sezgin, A. (2012).
Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358,
pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA,
USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_24'
chicago: Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and
Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,”
7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24.
ieee: 'C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed
continuous time Markov chains for genetic regulatory circuits,” presented at the
CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.'
ista: 'Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous
time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification,
LNCS, vol. 7358, 294–309.'
mla: Guet, Calin C., et al. Delayed Continuous Time Markov Chains for Genetic
Regulatory Circuits. Vol. 7358, Springer, 2012, pp. 294–309, doi:10.1007/978-3-642-31424-7_24.
short: C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer,
2012, pp. 294–309.
conference:
end_date: 2012-07-13
location: Berkeley, CA, USA
name: 'CAV: Computer Aided Verification'
start_date: 2012-07-07
corr_author: '1'
date_created: 2018-12-11T12:01:36Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2024-10-09T20:54:47Z
day: '01'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-642-31424-7_24
ec_funded: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 294 - 309
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '3561'
quality_controlled: '1'
scopus_import: 1
status: public
title: Delayed continuous time Markov chains for genetic regulatory circuits
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: '7358 '
year: '2012'
...
---
_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.'
article_processing_charge: No
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. IEEE ACM Transactions on Computational Biology and Bioinformatics.
2012;10(2):310-322. doi:10.1109/TCBB.2012.91
apa: Henzinger, T. A., & Mateescu, M. (2012). The propagation approach for computing
biochemical reaction networks. IEEE ACM Transactions on Computational Biology
and Bioinformatics. IEEE. https://doi.org/10.1109/TCBB.2012.91
chicago: Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for
Computing Biochemical Reaction Networks.” IEEE ACM Transactions on Computational
Biology and Bioinformatics. IEEE, 2012. https://doi.org/10.1109/TCBB.2012.91.
ieee: T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical
reaction networks,” IEEE ACM Transactions on Computational Biology and Bioinformatics,
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.” IEEE ACM Transactions on Computational Biology
and Bioinformatics, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:10.1109/TCBB.2012.91.
short: T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology
and Bioinformatics 10 (2012) 310–322.
corr_author: '1'
date_created: 2018-12-11T11:56:52Z
date_published: 2012-07-03T00:00:00Z
date_updated: 2025-09-29T14:17:43Z
day: '03'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/TCBB.2012.91
ec_funded: 1
external_id:
isi:
- '000323504100006'
pmid:
- '22778152'
intvolume: ' 10'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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. Biophysical Journal. 2011;101(10):2336-2340.
doi:10.1016/j.bpj.2011.09.040
apa: Park, H., Oikonomou, P., Guet, C. C., & Cluzel, P. (2011). Noise underlies
switching behavior of the bacterial flagellum. Biophysical Journal. Elsevier.
https://doi.org/10.1016/j.bpj.2011.09.040
chicago: Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise
Underlies Switching Behavior of the Bacterial Flagellum.” Biophysical Journal.
Elsevier, 2011. https://doi.org/10.1016/j.bpj.2011.09.040.
ieee: H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching
behavior of the bacterial flagellum,” Biophysical Journal, 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.” Biophysical Journal, vol. 101, no. 10, Elsevier, 2011, pp.
2336–40, doi:10.1016/j.bpj.2011.09.040.
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: 2025-09-30T09:26:28Z
day: '16'
department:
- _id: CaGu
doi: 10.1016/j.bpj.2011.09.040
external_id:
isi:
- '000297143500008'
pmid:
- '22098731'
intvolume: ' 101'
isi: 1
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
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., & 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. Lumpability Abstractions of Rule-Based Systems.
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: 2025-09-30T07:50:34Z
day: '30'
ddc:
- '570'
department:
- _id: ToHe
- _id: CaGu
external_id:
arxiv:
- '1011.0496'
file:
- access_level: open_access
checksum: eaaba991a86fff37606b0eb5196878e8
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record:
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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:10.1109/QEST.2010.33'
apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & 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. https://doi.org/10.1109/QEST.2010.33'
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. https://doi.org/10.1109/QEST.2010.33.'
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. SABRE: A Tool for the Stochastic Analysis of Biochemical
Reaction Networks. IEEE, 2010, pp. 193–94, doi:10.1109/QEST.2010.33.'
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:
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creator: system
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file_id: '4726'
file_name: IST-2012-63-v1+1_SABRE-A_tool_for_the_stochastic_analysis_of_biochemical_reaction_networks.pdf
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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:10.1109/HiBi.2009.23'
apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & 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.
https://doi.org/10.1109/HiBi.2009.23'
chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE,
2009. https://doi.org/10.1109/HiBi.2009.23.
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. Fast Adaptive Uniformization of the Chemical Master
Equation. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:10.1109/HiBi.2009.23.
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: 2025-09-30T09:54:51Z
day: '30'
ddc:
- '000'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/HiBi.2009.23
external_id:
isi:
- '000275038300017'
file:
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language:
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month: '10'
oa: 1
oa_version: Submitted Version
page: 118 - 127
publication_status: published
publisher: IEEE
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title: Fast adaptive uniformization of the chemical master equation
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2009'
...