---
_id: '9453'
abstract:
- lang: eng
text: Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis
thaliana endosperm by cytosine demethylation of the maternal genome mediated by
the DNA glycosylase DEMETER, but the extent of the methylation changes is not
known. Here, we show that virtually the entire endosperm genome is demethylated,
coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted
sequences. Mutation of DEMETER partially restores endosperm CG methylation to
levels found in other tissues, indicating that CG demethylation is specific to
maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation
of embryo transposable elements. Our findings demonstrate extensive reconfiguration
of the endosperm methylation landscape that likely reinforces transposon silencing
in the embryo.
article_processing_charge: No
article_type: original
author:
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis
endosperm. Science. 2009;324(5933):1451-1454. doi:10.1126/science.1172417
apa: Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer,
R. L., & Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1172417
chicago: Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams,
Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis
Endosperm.” Science. American Association for the Advancement of Science,
2009. https://doi.org/10.1126/science.1172417.
ieee: T.-F. Hsieh et al., “Genome-wide demethylation of Arabidopsis endosperm,”
Science, vol. 324, no. 5933. American Association for the Advancement of
Science, pp. 1451–1454, 2009.
ista: Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman
D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933),
1451–1454.
mla: Hsieh, Tzung-Fu, et al. “Genome-Wide Demethylation of Arabidopsis Endosperm.”
Science, vol. 324, no. 5933, American Association for the Advancement of
Science, 2009, pp. 1451–54, doi:10.1126/science.1172417.
short: T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer,
D. Zilberman, Science 324 (2009) 1451–1454.
date_created: 2021-06-04T08:55:41Z
date_published: 2009-06-12T00:00:00Z
date_updated: 2021-12-14T08:53:26Z
day: '12'
department:
- _id: DaZi
doi: 10.1126/science.1172417
extern: '1'
external_id:
pmid:
- '19520962'
intvolume: ' 324'
issue: '5933'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1451-1454
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide demethylation of Arabidopsis endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 324
year: '2009'
...
---
_id: '3675'
abstract:
- lang: eng
text: "Sex and recombination have long been seen as adaptations that facilitate
natural selection by generating favorable variations. If recombination is to aid
selection, there must be negative linkage disequilibria—favorable alleles must
be found together less often than expected by chance. These negative linkage disequilibria
can be generated directly by selection, but this must involve negative epistasis
of just the right strength, which is not expected, from either experiment or theory.
Random drift provides a more general source of negative associations: Favorable
mutations almost always arise on different genomes, and negative associations
tend to persist, precisely because they shield variation from selection.\r\n\r\nWe
can understand how recombination aids adaptation by determining the maximum possible
rate of adaptation. With unlinked loci, this rate increases only logarithmically
with the influx of favorable mutations. With a linear genome, a scaling argument
shows that in a large population, the rate of adaptive substitution depends only
on the expected rate in the absence of interference, divided by the total rate
of recombination. A two-locus approximation predicts an upper bound on the rate
of substitution, proportional to recombination rate.\r\n\r\nIf associations between
linked loci do impede adaptation, there can be substantial selection for modifiers
that increase recombination. Whether this can account for the maintenance of high
rates of sex and recombination depends on the extent of selection. It is clear
that the rate of species-wide substitutions is typically far too low to generate
appreciable selection for recombination. However, local sweeps within a subdivided
population may be effective."
acknowledgement: Royal Society and the Engineering and Physical Sciences for support
(GR/ T11753/01)
author:
- 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: 'Barton NH. Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195.
doi:10.1101/sqb.2009.74.030'
apa: Barton, N. H. (2009). Why sex and recombination? . In Cold Spring Harbor
Symposia on Quantitative Biology (Vol. 74, pp. 187–195). Cold Spring Harbor
Laboratory Press. https://doi.org/10.1101/sqb.2009.74.030
chicago: Barton, Nicholas H. “Why Sex and Recombination? .” In Cold Spring Harbor
Symposia on Quantitative Biology, 74:187–95. Cold Spring Harbor Laboratory
Press, 2009. https://doi.org/10.1101/sqb.2009.74.030.
ieee: N. H. Barton, “Why sex and recombination? ,” in Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–195.
ista: 'Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia
on Quantitative Biology. vol. 74, 187–195.'
mla: Barton, Nicholas H. “Why Sex and Recombination? .” Cold Spring Harbor Symposia
on Quantitative Biology, vol. 74, Cold Spring Harbor Laboratory Press, 2009,
pp. 187–95, doi:10.1101/sqb.2009.74.030.
short: N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold
Spring Harbor Laboratory Press, 2009, pp. 187–195.
date_created: 2018-12-11T12:04:33Z
date_published: 2009-11-10T00:00:00Z
date_updated: 2021-01-12T07:45:04Z
day: '10'
department:
- _id: NiBa
doi: 10.1101/sqb.2009.74.030
intvolume: ' 74'
language:
- iso: eng
month: '11'
oa_version: None
page: 187 - 195
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '2708'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Why sex and recombination? '
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2009'
...
---
_id: '3775'
abstract:
- lang: eng
text: There is a close analogy between statistical thermodynamics and the evolution
of allele frequencies under mutation, selection and random drift. Wright's formula
for the stationary distribution of allele frequencies is analogous to the Boltzmann
distribution in statistical physics. Population size, 2N, plays the role of the
inverse temperature, 1/kT, and determines the magnitude of random fluctuations.
Log mean fitness, View the MathML source, tends to increase under selection, and
is analogous to a (negative) energy; a potential function, U, increases under
mutation in a similar way. An entropy, SH, can be defined which measures the deviation
from the distribution of allele frequencies expected under random drift alone;
the sum View the MathML source gives a free fitness that increases as the population
evolves towards its stationary distribution. Usually, we observe the distribution
of a few quantitative traits that depend on the frequencies of very many alleles.
The mean and variance of such traits are analogous to observable quantities in
statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures
the volume of allele frequency space that is consistent with the observed trait
distribution. The stationary distribution of the traits is View the MathML source;
this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are
distinct, but converge when there are so many alleles that traits fluctuate close
to their expectations. Populations tend to evolve towards states that can be realised
in many ways (i.e., large SΩ), which may lead to a substantial drop below the
adaptive peak; we illustrate this point with a simple model of genetic redundancy.
This analogy with statistical thermodynamics brings together previous ideas in
a general framework, and justifies a maximum entropy approximation to the dynamics
of quantitative traits.
acknowledgement: "This work was supported by a Royal Society/Wolfson Award, and by
grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates,
H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments."
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: Jason
full_name: Coe, Jason
last_name: Coe
citation:
ama: Barton NH, Coe J. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 2009;259(2):317-324. doi:10.1016/j.jtbi.2009.03.019
apa: Barton, N. H., & Coe, J. (2009). On the application of statistical physics
to evolutionary biology. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2009.03.019
chicago: Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology. Elsevier, 2009.
https://doi.org/10.1016/j.jtbi.2009.03.019.
ieee: N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary
biology,” Journal of Theoretical Biology, vol. 259, no. 2. Elsevier, pp.
317–324, 2009.
ista: Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary
biology. Journal of Theoretical Biology. 259(2), 317–324.
mla: Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics
to Evolutionary Biology.” Journal of Theoretical Biology, vol. 259, no.
2, Elsevier, 2009, pp. 317–24, doi:10.1016/j.jtbi.2009.03.019.
short: N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.
date_created: 2018-12-11T12:05:06Z
date_published: 2009-07-21T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '21'
department:
- _id: NiBa
doi: 10.1016/j.jtbi.2009.03.019
intvolume: ' 259'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://hal.archives-ouvertes.fr/hal-00554594/document
month: '07'
oa: 1
oa_version: Submitted Version
page: 317 - 324
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '2452'
quality_controlled: '1'
scopus_import: 1
status: public
title: On the application of statistical physics to evolutionary biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 259
year: '2009'
...
---
_id: '3780'
abstract:
- lang: eng
text: Why are sinistral snails so rare? Two main hypotheses are that selection acts
against the establishment of new coiling morphs, because dextral and sinistral
snails have trouble mating, or else a developmental constraint prevents the establishment
of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in
which sinistrals are rare, and populations of Partula suturalis, in which sinistrals
are common, as well as a mathematical model, to understand the circumstances by
which new morphs evolve. The main finding is that the sinistral genotype is associated
with reduced egg viability in L. stagnalis, but in P. suturalis individuals of
sinistral and dextral genotype appear equally fecund, implying a lack of a constraint.
As positive frequency-dependent selection against the rare chiral morph in P.
suturalis also operates over a narrow range (< 3%), the results suggest a model
for chiral evolution in snails in which weak positive frequency-dependent selection
may be overcome by a negative frequency-dependent selection, such as reproductive
character displacement. In snails, there is not always a developmental constraint.
As the direction of cleavage, and thus the directional asymmetry of the entire
body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans,
sipunculids and nemerteans), it remains an open question as to whether this is
because of a constraint and/or because most taxa do not have a conspicuous external
asymmetry (like a shell) upon which selection can act.
acknowledgement: We owe a great debt to Jim Murray for his many contributions to the
study of Partula, in the field, in the laboratory, in the interpretation of data,
and in generating new ideas about evolution. With pleasure and respect we dedicate
this paper to him. Jim Murray played a leading role in making the collections used
here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with
collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift
of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund
Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis.
Comments from an anonymous referee, A. Richard Palmer and the editorial board improved
the manuscript. Work in the field was supported by the Royal Society, The Carnegie
Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research
Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society
and the University of Nottingham supported work in the laboratory.
author:
- first_name: Angus
full_name: Davison, Angus
last_name: Davison
- 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: Bryan
full_name: Clarke, Bryan
last_name: Clarke
citation:
ama: 'Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype
on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications
for the evolution of sinistral snails. Journal of Evolutionary Biology.
2009;22(8):1624-1635. doi:10.1111/j.1420-9101.2009.01770.x'
apa: 'Davison, A., Barton, N. H., & Clarke, B. (2009). The effect of chirality
phenotype and genotype on the fecundity and viability of Partula suturalis and
Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal
of Evolutionary Biology. Wiley. https://doi.org/10.1111/j.1420-9101.2009.01770.x'
chicago: 'Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality
Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and
Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” Journal
of Evolutionary Biology. Wiley, 2009. https://doi.org/10.1111/j.1420-9101.2009.01770.x.'
ieee: 'A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype
and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis:
Implications for the evolution of sinistral snails,” Journal of Evolutionary
Biology, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.'
ista: 'Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and
genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis:
Implications for the evolution of sinistral snails. Journal of Evolutionary Biology.
22(8), 1624–1635.'
mla: 'Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on
the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications
for the Evolution of Sinistral Snails.” Journal of Evolutionary Biology,
vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:10.1111/j.1420-9101.2009.01770.x.'
short: A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009)
1624–1635.
date_created: 2018-12-11T12:05:08Z
date_published: 2009-08-01T00:00:00Z
date_updated: 2021-01-12T07:52:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/j.1420-9101.2009.01770.x
file:
- access_level: open_access
checksum: f70c15c6ab9306121d4153a3be0d2346
content_type: application/pdf
creator: dernst
date_created: 2019-02-22T09:21:44Z
date_updated: 2020-07-14T12:46:15Z
file_id: '6044'
file_name: Davison_JEB_v31_2009.pdf
file_size: 2583812
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 22'
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 1624 - 1635
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley
publist_id: '2447'
pubrep_id: '553'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The effect of chirality phenotype and genotype on the fecundity and viability
of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral
snails'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2009'
...
---
_id: '3837'
abstract:
- lang: eng
text: In this paper we extend the work of Alfaro, Henzinger et al. on interface
theories for component-based design. Existing interface theories often fail to
capture functional relations between the inputs and outputs of an interface. For
example, a simple synchronous interface that takes as input a number n ≥ 0 and
returns, at the same time, as output n + 1, cannot be expressed in existing theories.
In this paper we provide a theory of relational interfaces, where such input-output
relations can be captured. Our theory supports synchronous interfaces, both stateless
and stateful. It includes explicit notions of environments and pluggability, and
satisfies fundamental properties such as preservation of refinement by composition,
and characterization of pluggability by refinement. We achieve these properties
by making reasonable restrictions on feedback loops in interface compositions.
acknowledgement: 'This work is supported by the Center for Hybrid and Embedded Software
Systems (CHESS) at UC Berkeley, which receives support from the National Science
Foundation (NSF awards #0720882 (CSR-EHS: PRET) and #0720841 (CSR-CPS)), the U.S.
Army Research Office (ARO #W911NF-07-2-0019), the U.S. Air Force Office of Scientific
Research (MURI #FA9550-06-0312), the Air Force Research Lab (AFRL), the State of
California Micro Program, and the following companies: Agilent, Bosch, Lockheed-Martin,
National Instruments, Thales and Toyota. This work is also supported by the COMBEST
and ArtistDesign projects of the European Union, and the Swiss National Science
Foundation. '
author:
- first_name: Stavros
full_name: Tripakis, Stavros
last_name: Tripakis
- first_name: Ben
full_name: Lickly, Ben
last_name: Lickly
- 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: Edward
full_name: Lee, Edward
last_name: Lee
citation:
ama: 'Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: EMSOFT
’09 Proceedings of the Seventh ACM International Conference on Embedded Software.
ACM; 2009:67-76. doi:10.1145/1629335.1629346'
apa: 'Tripakis, S., Lickly, B., Henzinger, T. A., & Lee, E. (2009). On relational
interfaces. In EMSOFT ’09 Proceedings of the seventh ACM international conference
on Embedded software (pp. 67–76). Grenoble, France: ACM. https://doi.org/10.1145/1629335.1629346'
chicago: Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On
Relational Interfaces.” In EMSOFT ’09 Proceedings of the Seventh ACM International
Conference on Embedded Software, 67–76. ACM, 2009. https://doi.org/10.1145/1629335.1629346.
ieee: S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,”
in EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded
software, Grenoble, France, 2009, pp. 67–76.
ista: 'Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces.
EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded
software. EMSOFT: Embedded Software , 67–76.'
mla: Tripakis, Stavros, et al. “On Relational Interfaces.” EMSOFT ’09 Proceedings
of the Seventh ACM International Conference on Embedded Software, ACM, 2009,
pp. 67–76, doi:10.1145/1629335.1629346.
short: S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings
of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp.
67–76.
conference:
end_date: 2009-10-16
location: Grenoble, France
name: 'EMSOFT: Embedded Software '
start_date: 2009-10-12
date_created: 2018-12-11T12:05:26Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1145/1629335.1629346
ec_funded: 1
file:
- access_level: open_access
checksum: 3a70e21527dfaad2f198549ae5710786
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:57Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5045'
file_name: IST-2012-70-v1+1_On_Relational_Interfaces.pdf
file_size: 310902
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 67 - 76
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication: EMSOFT '09 Proceedings of the seventh ACM international conference on
Embedded software
publication_status: published
publisher: ACM
publist_id: '2360'
pubrep_id: '70'
quality_controlled: '1'
status: public
title: On relational interfaces
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '3841'
abstract:
- lang: eng
text: 'We compare several languages for specifying Markovian population models such
as queuing networks and chemical reaction networks. These languages —matrix descriptions,
stochastic Petri nets, stoichiometric equations, stochastic process algebras,
and guarded command models— all describe continuous-time Markov chains, but they
differ according to important properties, such as compositionality, expressiveness
and succinctness, executability, ease of use, and the support they provide for
checking the well-formedness of a model and for analyzing a model. '
acknowledgement: This research was supported in part by the Excellence Cluster on
Multimodal Computing and Interaction and the Swiss National Science Foundation.
alternative_title:
- LNCS
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: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population
models. In: Vol 5797. Springer; 2009:3-23. doi:10.1007/978-3-642-04420-5_2'
apa: 'Henzinger, T. A., Jobstmann, B., & Wolf, V. (2009). Formalisms for specifying
Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability
Problems, Palaiseau, France: Springer. https://doi.org/10.1007/978-3-642-04420-5_2'
chicago: Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for
Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. https://doi.org/10.1007/978-3-642-04420-5_2.
ieee: 'T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian
population models,” presented at the RP: Reachability Problems, Palaiseau, France,
2009, vol. 5797, pp. 3–23.'
ista: 'Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian
population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.'
mla: Henzinger, Thomas A., et al. Formalisms for Specifying Markovian Population
Models. Vol. 5797, Springer, 2009, pp. 3–23, doi:10.1007/978-3-642-04420-5_2.
short: T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23.
conference:
end_date: 2009-09-25
location: Palaiseau, France
name: 'RP: Reachability Problems'
start_date: 2009-09-23
date_created: 2018-12-11T12:05:28Z
date_published: 2009-09-07T00:00:00Z
date_updated: 2023-02-23T11:24:49Z
day: '07'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-04420-5_2
file:
- access_level: open_access
checksum: df88431872586c773fbcfea37d7b36a2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:41Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4702'
file_name: IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf
file_size: 222840
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 5797'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 3 - 23
publication_status: published
publisher: Springer
publist_id: '2352'
pubrep_id: '67'
quality_controlled: '1'
related_material:
record:
- id: '3381'
relation: later_version
status: public
scopus_import: 1
status: public
title: Formalisms for specifying Markovian population models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5797
year: '2009'
...
---
_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: 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'
...
---
_id: '3844'
abstract:
- lang: eng
text: The Hierarchical Timing Language (HTL) is a real-time coordination language
for distributed control systems. HTL programs must be checked for well-formedness,
race freedom, transmission safety (schedulability of inter-host communication),
and time safety (schedulability of host computation). We present a modular abstract
syntax and semantics for HTL, modular checks of well-formedness, race freedom,
and transmission safety, and modular code distribution. Our contributions here
complement previous results on HTL time safety and modular code generation. Modularity
in HTL can be utilized in easy program composition as well as fast program analysis
and code generation, but also in so-called runtime patching, where program components
may be modified at runtime.
acknowledgement: Supported by the EU ArtistDesign Network of Excellence on Embedded
Systems Design, the EU project COMBEST, the Austrian Science Funds P18913-N15 and
V00125, and Fundacao para a Ciencia e Tecnologia funds SFRH/BD/29461/2006 and PTDC/EIA/71462/2006
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: Christoph
full_name: Kirsch, Christoph
last_name: Kirsch
- first_name: Eduardo
full_name: Marques, Eduardo
last_name: Marques
- first_name: Ana
full_name: Sokolova, Ana
last_name: Sokolova
citation:
ama: 'Henzinger TA, Kirsch C, Marques E, Sokolova A. Distributed, modular HTL. In:
IEEE; 2009:171-180. doi:10.1109/RTSS.2009.9'
apa: 'Henzinger, T. A., Kirsch, C., Marques, E., & Sokolova, A. (2009). Distributed,
modular HTL (pp. 171–180). Presented at the RTSS: Real-Time Systems Symposium,
Washington, DC, United States: IEEE. https://doi.org/10.1109/RTSS.2009.9'
chicago: Henzinger, Thomas A, Christoph Kirsch, Eduardo Marques, and Ana Sokolova.
“Distributed, Modular HTL,” 171–80. IEEE, 2009. https://doi.org/10.1109/RTSS.2009.9.
ieee: 'T. A. Henzinger, C. Kirsch, E. Marques, and A. Sokolova, “Distributed, modular
HTL,” presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United
States, 2009, pp. 171–180.'
ista: 'Henzinger TA, Kirsch C, Marques E, Sokolova A. 2009. Distributed, modular
HTL. RTSS: Real-Time Systems Symposium, 171–180.'
mla: Henzinger, Thomas A., et al. Distributed, Modular HTL. IEEE, 2009, pp.
171–80, doi:10.1109/RTSS.2009.9.
short: T.A. Henzinger, C. Kirsch, E. Marques, A. Sokolova, in:, IEEE, 2009, pp.
171–180.
conference:
end_date: 2009-12-04
location: Washington, DC, United States
name: 'RTSS: Real-Time Systems Symposium'
start_date: 2009-12-01
date_created: 2018-12-11T12:05:28Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:36Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1109/RTSS.2009.9
ec_funded: 1
file:
- access_level: open_access
checksum: b2b15a5ef71eb50d62eaa5aea7efd8c4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:56Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4655'
file_name: IST-2012-65-v1+1_Distributed_modular_Htl.pdf
file_size: 526458
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 171 - 180
project:
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: IEEE
publist_id: '2346'
pubrep_id: '65'
quality_controlled: '1'
status: public
title: Distributed, modular HTL
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '3870'
abstract:
- lang: eng
text: Games on graphs with omega-regular objectives provide a model for the control
and synthesis of reactive systems. Every omega-regular objective can be decomposed
into a safety part and a liveness part. The liveness part ensures that something
good happens “eventually.” Two main strengths of the classical, infinite-limit
formulation of liveness are robustness (independence from the granularity of transitions)
and simplicity (abstraction of complicated time bounds). However, the classical
liveness formulation suffers from the drawback that the time until something good
happens may be unbounded. A stronger formulation of liveness, so-called finitary
liveness, overcomes this drawback, while still retaining robustness and simplicity.
Finitary liveness requires that there exists an unknown, fixed bound b such that
something good happens within b transitions. While for one-shot liveness (reachability)
objectives, classical and finitary liveness coincide, for repeated liveness (Buchi)
objectives, the finitary formulation is strictly stronger. In this work we study
games with finitary parity and Streett objectives. We prove the determinacy of
these games, present algorithms for solving these games, and characterize the
memory requirements of winning strategies. We show that finitary parity games
can be solved in polynomial time, which is not known for infinitary parity games.
For finitary Streett games, we give an EXPTIME algorithm and show that the problem
is NP-hard. Our algorithms can be used, for example, for synthesizing controllers
that do not let the response time of a system increase without bound.
acknowledgement: "This research was supported in part by the AFOSR MURI grant F49620-00-1-0327,
the NSF grants CCR-0132780, CNS-0720884, and CCR- 225610, by the Swiss National
Science Foundation, by the COMBEST project of the European Union, and EU-TMR network
Games.\r\nWe thank anonymous reviewers for useful comments."
article_number: '1'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: Chatterjee K, Henzinger TA, Horn F. Finitary winning in omega-regular games.
ACM Transactions on Computational Logic (TOCL). 2009;11(1). doi:10.1145/1614431.1614432
apa: Chatterjee, K., Henzinger, T. A., & Horn, F. (2009). Finitary winning in
omega-regular games. ACM Transactions on Computational Logic (TOCL). ACM.
https://doi.org/10.1145/1614431.1614432
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Finitary
Winning in Omega-Regular Games.” ACM Transactions on Computational Logic (TOCL).
ACM, 2009. https://doi.org/10.1145/1614431.1614432.
ieee: K. Chatterjee, T. A. Henzinger, and F. Horn, “Finitary winning in omega-regular
games,” ACM Transactions on Computational Logic (TOCL), vol. 11, no. 1.
ACM, 2009.
ista: Chatterjee K, Henzinger TA, Horn F. 2009. Finitary winning in omega-regular
games. ACM Transactions on Computational Logic (TOCL). 11(1), 1.
mla: Chatterjee, Krishnendu, et al. “Finitary Winning in Omega-Regular Games.” ACM
Transactions on Computational Logic (TOCL), vol. 11, no. 1, 1, ACM, 2009,
doi:10.1145/1614431.1614432.
short: K. Chatterjee, T.A. Henzinger, F. Horn, ACM Transactions on Computational
Logic (TOCL) 11 (2009).
date_created: 2018-12-11T12:05:37Z
date_published: 2009-10-01T00:00:00Z
date_updated: 2021-01-12T07:52:50Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/1614431.1614432
ec_funded: 1
file:
- access_level: open_access
checksum: 139c4586d24f11e5da31fb3a0cf96ef4
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:08Z
date_updated: 2020-07-14T12:46:20Z
file_id: '5125'
file_name: IST-2012-53-v1+1_Finitary_winning_in_omega-regular_games.pdf
file_size: 180082
relation: main_file
file_date_updated: 2020-07-14T12:46:20Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication: ACM Transactions on Computational Logic (TOCL)
publication_status: published
publisher: ACM
publist_id: '2309'
pubrep_id: '53'
quality_controlled: '1'
scopus_import: 1
status: public
title: Finitary winning in omega-regular games
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2009'
...
---
_id: '3871'
abstract:
- lang: eng
text: 'Nondeterministic weighted automata are finite automata with numerical weights
oil transitions. They define quantitative languages 1, that assign to each word
v; a real number L(w). The value of ail infinite word w is computed as the maximal
value of all runs over w, and the value of a run as the supremum, limsup liminf,
limit average, or discounted sum of the transition weights. We introduce probabilistic
weighted antomata, in which the transitions are chosen in a randomized (rather
than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics),
the value of a word v) is the largest real v such that the runs over w have value
at least v with probability I (resp. positive probability). We study the classical
questions of automata theory for probabilistic weighted automata: emptiness and
universality, expressiveness, and closure under various operations oil languages.
For quantitative languages, emptiness university axe defined as whether the value
of some (resp. every) word exceeds a given threshold. We prove some, of these
questions to he decidable, and others undecidable. Regarding expressive power,
we show that probabilities allow its to define a wide variety of new classes of
quantitative languages except for discounted-sum automata, where probabilistic
choice is no more expressive than nondeterminism. Finally we live ail almost complete
picture of the closure of various classes of probabilistic weighted automata for
the following, provide, is operations oil quantitative languages: maximum, sum.
and numerical complement.'
acknowledgement: This research was supported in part by the Swiss National Science
Foundation under the Indo-Swiss Joint Research Programme, by the European Network
of Excellence on Embedded Systems Design (ArtistDesign), by the European projects
Combest, Quasimodo, and Gasics, by the PAI program Moves funded by the Belgian Federal
Government, and by the CFV (Federated Center in Verification ) funded by the F.R.S.-FNRS.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA. Probabilistic weighted automata. In:
Vol 5710. Springer; 2009:244-258. doi:10.1007/978-3-642-04081-8_17'
apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2009). Probabilistic weighted
automata (Vol. 5710, pp. 244–258). Presented at the CONCUR: Concurrency Theory,
Bologna, Italy: Springer. https://doi.org/10.1007/978-3-642-04081-8_17'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Probabilistic
Weighted Automata,” 5710:244–58. Springer, 2009. https://doi.org/10.1007/978-3-642-04081-8_17.
ieee: 'K. Chatterjee, L. Doyen, and T. A. Henzinger, “Probabilistic weighted automata,”
presented at the CONCUR: Concurrency Theory, Bologna, Italy, 2009, vol. 5710,
pp. 244–258.'
ista: 'Chatterjee K, Doyen L, Henzinger TA. 2009. Probabilistic weighted automata.
CONCUR: Concurrency Theory, LNCS, vol. 5710, 244–258.'
mla: Chatterjee, Krishnendu, et al. Probabilistic Weighted Automata. Vol.
5710, Springer, 2009, pp. 244–58, doi:10.1007/978-3-642-04081-8_17.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 244–258.
conference:
end_date: 2009-09-04
location: Bologna, Italy
name: 'CONCUR: Concurrency Theory'
start_date: 2009-09-01
date_created: 2018-12-11T12:05:37Z
date_published: 2009-09-01T00:00:00Z
date_updated: 2021-01-12T07:52:50Z
day: '01'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.1007/978-3-642-04081-8_17
ec_funded: 1
file:
- access_level: open_access
checksum: af973ddbcf131b8810c6bff2c055ff56
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:46Z
date_updated: 2020-07-14T12:46:20Z
file_id: '4771'
file_name: IST-2012-52-v1+1_Probabilistic_Weighted_Automata.pdf
file_size: 200161
relation: main_file
file_date_updated: 2020-07-14T12:46:20Z
has_accepted_license: '1'
intvolume: ' 5710'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 244 - 258
project:
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: Springer
publist_id: '2304'
pubrep_id: '52'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic weighted automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5710
year: '2009'
...
---
_id: '3968'
abstract:
- lang: eng
text: We describe an algorithm for segmenting three-dimensional medical imaging
data modeled as a continuous function on a 3-manifold. It is related to watershed
algorithms developed in image processing but is closer to its mathematical roots,
which are Morse theory and homological algebra. It allows for the implicit treatment
of an underlying mesh, thus combining the structural integrity of its mathematical
foundations with the computational efficiency of image processing.
acknowledgement: This research was partially supported by Geomagic, Inc., and by the
Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007
and HR0011-05-1-0057.
alternative_title:
- LNCS
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: 'Edelsbrunner H, Harer J. The persistent Morse complex segmentation of a 3-manifold.
In: Vol 5903. Springer; 2009:36-50. doi:10.1007/978-3-642-10470-1_4'
apa: 'Edelsbrunner, H., & Harer, J. (2009). The persistent Morse complex segmentation
of a 3-manifold (Vol. 5903, pp. 36–50). Presented at the 3DPH: Modelling the Physiological
Human, Zermatt, Switzerland: Springer. https://doi.org/10.1007/978-3-642-10470-1_4'
chicago: Edelsbrunner, Herbert, and John Harer. “The Persistent Morse Complex Segmentation
of a 3-Manifold,” 5903:36–50. Springer, 2009. https://doi.org/10.1007/978-3-642-10470-1_4.
ieee: 'H. Edelsbrunner and J. Harer, “The persistent Morse complex segmentation
of a 3-manifold,” presented at the 3DPH: Modelling the Physiological Human, Zermatt,
Switzerland, 2009, vol. 5903, pp. 36–50.'
ista: 'Edelsbrunner H, Harer J. 2009. The persistent Morse complex segmentation
of a 3-manifold. 3DPH: Modelling the Physiological Human, LNCS, vol. 5903, 36–50.'
mla: Edelsbrunner, Herbert, and John Harer. The Persistent Morse Complex Segmentation
of a 3-Manifold. Vol. 5903, Springer, 2009, pp. 36–50, doi:10.1007/978-3-642-10470-1_4.
short: H. Edelsbrunner, J. Harer, in:, Springer, 2009, pp. 36–50.
conference:
end_date: 2009-12-02
location: Zermatt, Switzerland
name: '3DPH: Modelling the Physiological Human'
start_date: 2009-11-29
date_created: 2018-12-11T12:06:10Z
date_published: 2009-11-17T00:00:00Z
date_updated: 2021-01-12T07:53:32Z
day: '17'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-10470-1_4
file:
- access_level: open_access
checksum: 11fc85bcc19bab1f020e706a4b8a4660
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:33Z
date_updated: 2020-07-14T12:46:21Z
file_id: '4694'
file_name: IST-2016-535-v1+1_2009-P-04-3ManifoldSegmentation.pdf
file_size: 165090
relation: main_file
file_date_updated: 2020-07-14T12:46:21Z
has_accepted_license: '1'
intvolume: ' 5903'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 36 - 50
publication_status: published
publisher: Springer
publist_id: '2160'
pubrep_id: '535'
quality_controlled: '1'
scopus_import: 1
status: public
title: The persistent Morse complex segmentation of a 3-manifold
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5903
year: '2009'
...
---
_id: '4136'
abstract:
- lang: eng
text: 'Populations living in a spatially and temporally changing environment can
adapt to the changing optimum and/or migrate toward favorable habitats. Here we
extend previous analyses with a static optimum to allow the environment to vary
in time as well as in space. The model follows both population dynamics and the
trait mean under stabilizing selection, and the outcomes can be understood by
comparing the loads due to genetic variance, dispersal, and temporal change. With
fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform
along the environmental gradient and that responds to the moving optimum as expected
for panmictic populations and when the spatial gradient is sufficiently steep,
and (2) a population with limited range that adapts more slowly than the environmental
optimum changes in both time and space; the population therefore becomes locally
extinct and migrates toward suitable habitat. We also use a population‐genetic
model with many loci to allow genetic variance to evolve, and we show that the
only solution now has uniform adaptation.'
article_processing_charge: No
article_type: original
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- 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: Glenn
full_name: Marion, Glenn
last_name: Marion
citation:
ama: 'Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and
time. American Naturalist. 2009;174(5):E186-E204. doi:10.1086/605958'
apa: 'Polechova, J., Barton, N. H., & Marion, G. (2009). Species’ range: Adaptation
in space and time. American Naturalist. University of Chicago Press. https://doi.org/10.1086/605958'
chicago: 'Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range:
Adaptation in Space and Time.” American Naturalist. University of Chicago
Press, 2009. https://doi.org/10.1086/605958.'
ieee: 'J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in
space and time,” American Naturalist, vol. 174, no. 5. University of Chicago
Press, pp. E186–E204, 2009.'
ista: 'Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space
and time. American Naturalist. 174(5), E186–E204.'
mla: 'Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” American
Naturalist, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204,
doi:10.1086/605958.'
short: J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.
date_created: 2018-12-11T12:07:09Z
date_published: 2009-11-05T00:00:00Z
date_updated: 2021-01-12T07:54:46Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1086/605958
external_id:
pmid:
- ' 19788353'
intvolume: ' 174'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.doi.org/10.1086/605958
month: '11'
oa: 1
oa_version: Published Version
page: E186 - E204
pmid: 1
publication: American Naturalist
publication_status: published
publisher: University of Chicago Press
publist_id: '1986'
pubrep_id: '552'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1086/659642
scopus_import: 1
status: public
title: 'Species'' range: Adaptation in space and time'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 174
year: '2009'
...
---
_id: '4231'
abstract:
- lang: eng
text: The evolution of quantitative characters depends on the frequencies of the
alleles involved, yet these frequencies cannot usually be measured. Previous groups
have proposed an approximation to the dynamics of quantitative traits, based on
an analogy with statistical mechanics. We present a modified version of that approach,
which makes the analogy more precise and applies quite generally to describe the
evolution of allele frequencies. We calculate explicitly how the macroscopic quantities
(i.e., quantities that depend on the quantitative trait) depend on evolutionary
forces, in a way that is independent of the microscopic details. We first show
that the stationary distribution of allele frequencies under drift, selection,
and mutation maximizes a certain measure of entropy, subject to constraints on
the expectation of observable quantities. We then approximate the dynamical changes
in these expectations, assuming that the distribution of allele frequencies always
maximizes entropy, conditional on the expected values. When applied to directional
selection on an additive trait, this gives a very good approximation to the evolution
of the trait mean and the genetic variance, when the number of mutations per generation
is sufficiently high (4Nμ > 1). We show how the method can be modified for
small mutation rates (4Nμ → 0). We outline how this method describes epistatic
interactions as, for example, with stabilizing selection.
acknowledgement: "N.B. was supported by the Engineering and Physical Sciences Research
Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to
Ellen Baake for helping to initiate this project and for her comments on this manuscript.
We also thank Michael Turelli for his comments on the manuscript and I. Pen for
discussions and support in this project. This project was a result of a collaboration
supported by the European Science Foundation grant “Integrating population genetics
and conservation biology.” "
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: Harold
full_name: De Vladar, Harold
last_name: De Vladar
citation:
ama: Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic
quantitative traits. Genetics. 2009;181(3):997-1011. doi:10.1534/genetics.108.099309
apa: Barton, N. H., & De Vladar, H. (2009). Statistical mechanics and the evolution
of polygenic quantitative traits. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.108.099309
chicago: Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the
Evolution of Polygenic Quantitative Traits.” Genetics. Genetics Society
of America, 2009. https://doi.org/10.1534/genetics.108.099309.
ieee: N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of
polygenic quantitative traits,” Genetics, vol. 181, no. 3. Genetics Society
of America, pp. 997–1011, 2009.
ista: Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic
quantitative traits. Genetics. 181(3), 997–1011.
mla: Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution
of Polygenic Quantitative Traits.” Genetics, vol. 181, no. 3, Genetics
Society of America, 2009, pp. 997–1011, doi:10.1534/genetics.108.099309.
short: N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.
date_created: 2018-12-11T12:07:44Z
date_published: 2009-03-01T00:00:00Z
date_updated: 2021-01-12T07:55:29Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.108.099309
intvolume: ' 181'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 997 - 1011
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '1882'
quality_controlled: '1'
scopus_import: 1
status: public
title: Statistical mechanics and the evolution of polygenic quantitative traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 181
year: '2009'
...
---
_id: '4242'
abstract:
- lang: eng
text: 'Felsenstein distinguished two ways by which selection can directly strengthen
isolation. First, a modifier that strengthens prezygotic isolation can be favored
everywhere. This fits with the traditional view of reinforcement as an adaptation
to reduce deleterious hybridization by strengthening assortative mating. Second,
selection can favor association between different incompatibilities, despite recombination.
We generalize this “two allele” model to follow associations among any number
of incompatibilities, which may include both assortment and hybrid inviability.
Our key argument is that this process, of coupling between incompatibilities,
may be quite different from the usual view of reinforcement: strong isolation
can evolve through the coupling of any kind of incompatibility, whether prezygotic
or postzygotic. Single locus incompatibilities become coupled because associations
between them increase the variance in compatibility, which in turn increases mean
fitness if there is positive epistasis. Multiple incompatibilities, each maintained
by epistasis, can become coupled in the same way. In contrast, a single-locus
incompatibility can become coupled with loci that reduce the viability of haploid
hybrids because this reduces harmful recombination. We obtain simple approximations
for the limits of tight linkage, and strong assortment, and show how assortment
alleles can invade through associations with other components of reproductive
isolation.'
acknowledgement: "This work was supported by a Royal Society/Wolfson Research Merit
award, and by a grant from the Natural Environment Research Council.\r\nWe are very
grateful for insightful comments from S. P. Otto, and for helpful suggestions from
the referees and the Associate Editor, Maria Servedio."
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: Maria
full_name: De Cara, Maria
last_name: De Cara
citation:
ama: Barton NH, De Cara M. The evolution of strong reproductive isolation. Evolution;
International Journal of Organic Evolution. 2009;63(5):1171-1190. doi:10.1111/j.1558-5646.2009.00622.x
apa: Barton, N. H., & De Cara, M. (2009). The evolution of strong reproductive
isolation. Evolution; International Journal of Organic Evolution. Wiley.
https://doi.org/10.1111/j.1558-5646.2009.00622.x
chicago: Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive
Isolation.” Evolution; International Journal of Organic Evolution. Wiley,
2009. https://doi.org/10.1111/j.1558-5646.2009.00622.x.
ieee: N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,”
Evolution; International Journal of Organic Evolution, vol. 63, no. 5.
Wiley, pp. 1171–1190, 2009.
ista: Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation.
Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.
mla: Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive
Isolation.” Evolution; International Journal of Organic Evolution, vol.
63, no. 5, Wiley, 2009, pp. 1171–90, doi:10.1111/j.1558-5646.2009.00622.x.
short: N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution
63 (2009) 1171–1190.
date_created: 2018-12-11T12:07:48Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:55:33Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2009.00622.x
file:
- access_level: open_access
checksum: 1920d2e25ef335833764256c1a47bbfb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:46Z
date_updated: 2020-07-14T12:46:25Z
file_id: '4903'
file_name: IST-2016-551-v1+1_BartonDeCaraRevNew.pdf
file_size: 720913
relation: main_file
- access_level: open_access
checksum: c1c51bbc10d4f328fc96fc5b0e5dc25d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:47Z
date_updated: 2020-07-14T12:46:25Z
file_id: '4904'
file_name: IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf
file_size: 290160
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 63'
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 1171 - 1190
publication: Evolution; International Journal of Organic Evolution
publication_status: published
publisher: Wiley
publist_id: '1866'
pubrep_id: '551'
quality_controlled: '1'
scopus_import: 1
status: public
title: The evolution of strong reproductive isolation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 63
year: '2009'
...
---
_id: '4542'
abstract:
- lang: eng
text: "Weighted automata are finite automata with numerical weights on transitions.
Nondeterministic weighted automata define quantitative languages L that assign
to each word w a real number L(w) computed as the maximal value of all runs over
w, and the value of a run r is a function of the sequence of weights that appear
along r. There are several natural functions to consider such as Sup, LimSup,
LimInf, limit average, and discounted sum of transition weights.\r\nWe introduce
alternating weighted automata in which the transitions of the runs are chosen
by two players in a turn-based fashion. Each word is assigned the maximal value
of a run that the first player can enforce regardless of the choices made by the
second player. We survey the results about closure properties, expressiveness,
and decision problems for nondeterministic weighted automata, and we extend these
results to alternating weighted automata.\r\nFor quantitative languages L 1 and
L 2, we consider the pointwise operations max(L 1,L 2), min(L 1,L 2), 1 − L 1,
and the sum L 1 + L 2. We establish the closure properties of all classes of alternating
weighted automata with respect to these four operations.\r\nWe next compare the
expressive power of the various classes of alternating and nondeterministic weighted
automata over infinite words. In particular, for limit average and discounted
sum, we show that alternation brings more expressive power than nondeterminism.\r\nFinally,
we present decidability results and open questions for the quantitative extension
of the classical decision problems in automata theory: emptiness, universality,
language inclusion, and language equivalence."
acknowledgement: This research was supported in part by the Swiss National Science
Foundation under the Indo-Swiss Joint Research Programme, by the European Network
of Excellence on Embedded Systems Design (ArtistDesign), by the European Combest,
Quasimodo, and Gasics projects, by the PAI program Moves funded by the Belgian Federal
Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA. Alternating weighted automata. In: Vol
5699. Springer; 2009:3-13. doi:10.1007/978-3-642-03409-1_2'
apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2009). Alternating weighted
automata (Vol. 5699, pp. 3–13). Presented at the FCT: Fundamentals of Computation
Theory, Wroclaw, Poland: Springer. https://doi.org/10.1007/978-3-642-03409-1_2'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Alternating
Weighted Automata,” 5699:3–13. Springer, 2009. https://doi.org/10.1007/978-3-642-03409-1_2.
ieee: 'K. Chatterjee, L. Doyen, and T. A. Henzinger, “Alternating weighted automata,”
presented at the FCT: Fundamentals of Computation Theory, Wroclaw, Poland, 2009,
vol. 5699, pp. 3–13.'
ista: 'Chatterjee K, Doyen L, Henzinger TA. 2009. Alternating weighted automata.
FCT: Fundamentals of Computation Theory, LNCS, vol. 5699, 3–13.'
mla: Chatterjee, Krishnendu, et al. Alternating Weighted Automata. Vol. 5699,
Springer, 2009, pp. 3–13, doi:10.1007/978-3-642-03409-1_2.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 3–13.
conference:
end_date: 2009-09-04
location: Wroclaw, Poland
name: 'FCT: Fundamentals of Computation Theory'
start_date: 2009-09-02
date_created: 2018-12-11T12:09:23Z
date_published: 2009-09-10T00:00:00Z
date_updated: 2021-01-12T07:59:34Z
day: '10'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1007/978-3-642-03409-1_2
ec_funded: 1
file:
- access_level: open_access
checksum: e8f53abb63579de3f2bff58b2a1188e2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:09Z
date_updated: 2020-07-14T12:46:31Z
file_id: '5126'
file_name: IST-2012-39-v1+1_Alternating_Weighted_Automata.pdf
file_size: 164428
relation: main_file
file_date_updated: 2020-07-14T12:46:31Z
has_accepted_license: '1'
intvolume: ' 5699'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 3 - 13
project:
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: Springer
publist_id: '180'
pubrep_id: '39'
quality_controlled: '1'
scopus_import: 1
status: public
title: Alternating weighted automata
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5699
year: '2009'
...
---
_id: '4543'
abstract:
- lang: eng
text: The synthesis of a reactive system with respect to all omega-regular specification
requires the solution of a graph game. Such games have been extended in two natural
ways. First, a game graph can be equipped with probabilistic choices between alternative
transitions, thus allowing the, modeling of uncertain behaviour. These are called
stochastic games. Second, a liveness specification can he strengthened to require
satisfaction within all unknown but bounded amount of time. These are called finitary
objectives. We study. for the first time, the, combination of Stochastic games
and finitary objectives. We characterize the requirements on optimal strategies
and provide algorithms for Computing the maximal achievable probability of winning
stochastic games with finitary parity or Street, objectives. Most notably the
set of state's from which a player can win with probability . for a finitary parity
objective can he computed in polynomial time even though no polynomial-time algorithm
is known in the nonfinitary case.
acknowledgement: This research was supported in part by the Swiss National Science
Foundation under the Indo-Swiss Joint Research Programme, by the European Network
of Excellence on Embedded Systems Design (ArtistDesign), and by the European project
Combest.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: 'Chatterjee K, Henzinger TA, Horn F. Stochastic games with finitary objectives.
In: Vol 5734. Springer; 2009:34-54. doi:10.1007/978-3-642-03816-7_4'
apa: 'Chatterjee, K., Henzinger, T. A., & Horn, F. (2009). Stochastic games
with finitary objectives (Vol. 5734, pp. 34–54). Presented at the MFCS: Mathematical
Foundations of Computer Science, High Tatras, Slovakia: Springer. https://doi.org/10.1007/978-3-642-03816-7_4'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Stochastic
Games with Finitary Objectives,” 5734:34–54. Springer, 2009. https://doi.org/10.1007/978-3-642-03816-7_4.
ieee: 'K. Chatterjee, T. A. Henzinger, and F. Horn, “Stochastic games with finitary
objectives,” presented at the MFCS: Mathematical Foundations of Computer Science,
High Tatras, Slovakia, 2009, vol. 5734, pp. 34–54.'
ista: 'Chatterjee K, Henzinger TA, Horn F. 2009. Stochastic games with finitary
objectives. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 5734,
34–54.'
mla: Chatterjee, Krishnendu, et al. Stochastic Games with Finitary Objectives.
Vol. 5734, Springer, 2009, pp. 34–54, doi:10.1007/978-3-642-03816-7_4.
short: K. Chatterjee, T.A. Henzinger, F. Horn, in:, Springer, 2009, pp. 34–54.
conference:
end_date: 2009-08-28
location: High Tatras, Slovakia
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2009-08-24
date_created: 2018-12-11T12:09:24Z
date_published: 2009-08-01T00:00:00Z
date_updated: 2021-01-12T07:59:35Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-03816-7_4
ec_funded: 1
intvolume: ' 5734'
language:
- iso: eng
month: '08'
oa_version: None
page: 34 - 54
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: Springer
publist_id: '178'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stochastic games with finitary objectives
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5734
year: '2009'
...
---
_id: '4545'
abstract:
- lang: eng
text: 'A stochastic game is a two-player game played oil a graph, where in each
state the successor is chosen either by One of the players, or according to a
probability distribution. We Survey Stochastic games with limsup and liminf objectives.
A real-valued re-ward is assigned to each state, and the value of all infinite
path is the limsup (resp. liminf) of all rewards along the path. The value of
a stochastic game is the maximal expected value of an infinite path that call
he achieved by resolving the decisions of the first player. We present the complexity
of computing values of Stochastic games and their subclasses, and the complexity,
of optimal strategies in such games. '
acknowledgement: This research was supported in part by the Swiss National Science
Foundation under the Indo-Swiss Joint Research Programme, by the European Network
of Excellence on Embedded Systems Design (ArtistDesign), by the European projects
COMBEST, Quasimodo, Gasics, by the PAI program Moves funded by the Belgian Federal
Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Chatterjee K, Doyen L, Henzinger TA. A survey of stochastic games with limsup
and liminf objectives. In: Vol 5556. Springer; 2009:1-15. doi:10.1007/978-3-642-02930-1_1'
apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2009). A survey of stochastic
games with limsup and liminf objectives (Vol. 5556, pp. 1–15). Presented at the
ICALP: Automata, Languages and Programming, Rhodos, Greece: Springer. https://doi.org/10.1007/978-3-642-02930-1_1'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey
of Stochastic Games with Limsup and Liminf Objectives,” 5556:1–15. Springer, 2009.
https://doi.org/10.1007/978-3-642-02930-1_1.
ieee: 'K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of stochastic games
with limsup and liminf objectives,” presented at the ICALP: Automata, Languages
and Programming, Rhodos, Greece, 2009, vol. 5556, pp. 1–15.'
ista: 'Chatterjee K, Doyen L, Henzinger TA. 2009. A survey of stochastic games with
limsup and liminf objectives. ICALP: Automata, Languages and Programming, LNCS,
vol. 5556, 1–15.'
mla: Chatterjee, Krishnendu, et al. A Survey of Stochastic Games with Limsup
and Liminf Objectives. Vol. 5556, Springer, 2009, pp. 1–15, doi:10.1007/978-3-642-02930-1_1.
short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 1–15.
conference:
end_date: 2009-07-12
location: Rhodos, Greece
name: 'ICALP: Automata, Languages and Programming'
start_date: 2009-07-05
date_created: 2018-12-11T12:09:24Z
date_published: 2009-06-24T00:00:00Z
date_updated: 2021-01-12T07:59:35Z
day: '24'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.1007/978-3-642-02930-1_1
ec_funded: 1
file:
- access_level: open_access
checksum: dabb6d24428a000254c95493d9c492e6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:11Z
date_updated: 2020-07-14T12:46:31Z
file_id: '4992'
file_name: IST-2012-38-v1+1_A_survey_of_stochastic_games_with_limsup_and_liminf_objectives.pdf
file_size: 187419
relation: main_file
file_date_updated: 2020-07-14T12:46:31Z
has_accepted_license: '1'
intvolume: ' 5556'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 1 - 15
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '215543'
name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: Springer
publist_id: '177'
pubrep_id: '38'
quality_controlled: '1'
scopus_import: 1
status: public
title: A survey of stochastic games with limsup and liminf objectives
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5556
year: '2009'
...
---
_id: '517'
article_processing_charge: No
author:
- 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: 'Barton NH. Identity and coalescence in structured populations: A commentary
on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics
Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683'
apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations:
A commentary on “Inbreeding coefficients and coalescence times” by Montgomery
Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683'
chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations:
A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery
Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.'
ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics
Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.'
ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics
Research. 89(5–6), 475–477.'
mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A
Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.”
Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008,
pp. 475–77, doi:10.1017/S0016672308009683.'
short: N.H. Barton, Genetics Research 89 (2008) 475–477.
date_created: 2018-12-11T11:46:55Z
date_published: 2008-10-29T00:00:00Z
date_updated: 2024-02-14T09:51:09Z
day: '29'
department:
- _id: NiBa
doi: 10.1017/S0016672308009683
intvolume: ' 89'
issue: 5-6
language:
- iso: eng
month: '10'
oa_version: None
page: 475 - 477
publication: Genetics Research
publication_status: published
publisher: Cambridge University Press
publist_id: '7302'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding
coefficients and coalescence times'' by Montgomery Slatkin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2008'
...
---
_id: '9457'
abstract:
- lang: eng
text: Eukaryotic chromatin is separated into functional domains differentiated by
posttranslational histone modifications, histone variants, and DNA methylation1–6.
Methylation is associated with repression of transcriptional initiation in plants
and animals, and is frequently found in transposable elements. Proper methylation
patterns are critical for eukaryotic development4,5, and aberrant methylation-induced
silencing of tumor suppressor genes is a common feature of human cancer7. In contrast
to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1
ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20.
How DNA methylation and H2A.Z influence transcription remains largely unknown.
Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation
are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of
DNA methylation in the bodies of actively transcribed genes and in methylated
transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses
and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition,
while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads
to genome-wide hypermethylation. Our findings indicate that DNA methylation can
influence chromatin structure and effect gene silencing by excluding H2A.Z, and
that H2A.Z protects genes from DNA methylation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA
methylation are mutually antagonistic chromatin marks. Nature. 2008;456(7218):125-129.
doi:10.1038/nature07324
apa: Zilberman, D., Coleman-Derr, D., Ballinger, T., & Henikoff, S. (2008).
Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature.
Springer Nature. https://doi.org/10.1038/nature07324
chicago: Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff.
“Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.”
Nature. Springer Nature, 2008. https://doi.org/10.1038/nature07324.
ieee: D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z
and DNA methylation are mutually antagonistic chromatin marks,” Nature,
vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.
ista: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z
and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218),
125–129.
mla: Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic
Chromatin Marks.” Nature, vol. 456, no. 7218, Springer Nature, 2008, pp.
125–29, doi:10.1038/nature07324.
short: D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008)
125–129.
date_created: 2021-06-04T11:49:32Z
date_published: 2008-11-06T00:00:00Z
date_updated: 2021-12-14T08:54:36Z
day: '06'
department:
- _id: DaZi
doi: 10.1038/nature07324
extern: '1'
external_id:
pmid:
- '18815594'
intvolume: ' 456'
issue: '7218'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/
month: '11'
oa: 1
oa_version: Submitted Version
page: 125-129
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 456
year: '2008'
...
---
_id: '9537'
abstract:
- lang: eng
text: DNA methylation is an ancient process found in all domains of life. Although
the enzymes that mediate methylation have remained highly conserved, DNA methylation
has been adapted for a variety of uses throughout evolution, including defense
against transposable elements and control of gene expression. Defects in DNA methylation
are linked to human diseases, including cancer. Methylation has been lost several
times in the course of animal and fungal evolution, thus limiting the opportunity
for study in common model organisms. In the past decade, plants have emerged as
a premier model system for genetic dissection of DNA methylation. A recent combination
of plant genetics with powerful genomic approaches has led to a number of exciting
discoveries and promises many more.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. The evolving functions of DNA methylation. Current Opinion
in Plant Biology. 2008;11(5):554-559. doi:10.1016/j.pbi.2008.07.004
apa: Zilberman, D. (2008). The evolving functions of DNA methylation. Current
Opinion in Plant Biology. Elsevier . https://doi.org/10.1016/j.pbi.2008.07.004
chicago: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current
Opinion in Plant Biology. Elsevier , 2008. https://doi.org/10.1016/j.pbi.2008.07.004.
ieee: D. Zilberman, “The evolving functions of DNA methylation,” Current Opinion
in Plant Biology, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.
ista: Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion
in Plant Biology. 11(5), 554–559.
mla: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” Current
Opinion in Plant Biology, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:10.1016/j.pbi.2008.07.004.
short: D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.
date_created: 2021-06-08T13:13:37Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-12-14T08:54:07Z
department:
- _id: DaZi
doi: 10.1016/j.pbi.2008.07.004
extern: '1'
external_id:
pmid:
- '18774331'
intvolume: ' 11'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 554-559
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolving functions of DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11
year: '2008'
...