---
_id: '12199'
abstract:
- lang: eng
text: The four microsporangia of the flowering plant anther develop from archesporial
cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes
are surrounded by concentric monolayers of tapetal, middle layer and endothecial
cells. How this intricate array of tissues, each containing relatively few cells,
is established in an organ possessing no formal meristems is poorly understood.
We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES
1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually
for plants, tapetal cells are specified very early in development, and are subsequently
stimulated to proliferate by a receptor-like kinase (RLK) complex that includes
EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand
result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly,
these cells continue to develop, isolated at the locular periphery. Mutant and
wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the
periphery of mutant locules becomes occupied by microsporocytes. However, induction
of late expression of EMS1 in the few tapetal initials in ems1 plants results
in their proliferation to generate a functional tapetum, and this proliferation
suppresses microsporocyte number. Our experiments also show that integrity of
the tapetal monolayer is crucial for the maintenance of the polarity of divisions
within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the
context of tissue development in complex plant organs, where constancy in size,
shape and cell number is crucial.
acknowledgement: 'We thank the following for providing mutant lines and reagents:
Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines
and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable
help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing
Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance.
We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the
research was funded by Oxford University through a Clarendon Scholarship to X.F.,
with additional financial support from Magdalen College (Oxford).'
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis
anther. Development. 2010;137(14):2409-2416. doi:10.1242/dev.049320
apa: Feng, X., & Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation
in the Arabidopsis anther. Development. The Company of Biologists. https://doi.org/10.1242/dev.049320
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation
in the Arabidopsis Anther.” Development. The Company of Biologists, 2010.
https://doi.org/10.1242/dev.049320.
ieee: X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation
in the Arabidopsis anther,” Development, vol. 137, no. 14. The Company
of Biologists, pp. 2409–2416, 2010.
ista: Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in
the Arabidopsis anther. Development. 137(14), 2409–2416.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation
in the Arabidopsis Anther.” Development, vol. 137, no. 14, The Company
of Biologists, 2010, pp. 2409–16, doi:10.1242/dev.049320.
short: X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.
date_created: 2023-01-16T09:21:54Z
date_published: 2010-07-15T00:00:00Z
date_updated: 2023-05-08T10:57:11Z
day: '15'
department:
- _id: XiFe
doi: 10.1242/dev.049320
extern: '1'
external_id:
pmid:
- '20570940'
intvolume: ' 137'
issue: '14'
keyword:
- Developmental Biology
- Molecular Biology
- Anther Tapetum
- Arabidopsis
- Cell Fate Establishment
- EMS1
- Reproductive Cell Lineage
language:
- iso: eng
month: '07'
oa_version: None
page: 2409-2416
pmid: 1
publication: Development
publication_identifier:
issn:
- 1477-9129
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tapetal cell fate, lineage and proliferation in the Arabidopsis anther
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2010'
...
---
_id: '12200'
abstract:
- lang: eng
text: Key steps in the evolution of the angiosperm anther include the patterning
of the concentrically organized microsporangium and the incorporation of four
such microsporangia into a leaf-like structure. Mutant studies in the model plant
Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the
cell lineages culminating in the different cell types present in the microsporangium
(the microsporocytes, the tapetum, and the middle and endothecial layers), and
(ii) some of the genes responsible for specifying their fates. However, the processes
that confer polarity on the developing anther and position the microsporangia
within it remain unclear. Certainly, data from a range of experimental strategies
suggest that hormones play a central role in establishing polarity and the patterning
of the anther initial, and may be responsible for locating the microsporangia.
But the fact that microsporangia were originally positioned externally suggests
that their development is likely to be autonomous, perhaps with the reproductive
cells generating signals controlling the growth and division of the investing
anther epidermis. These possibilities are discussed in the context of the expression
of genes which initiate and maintain male and female reproductive development,
and in the perspective of our current views of anther evolution.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Cell–cell interactions during patterning of the Arabidopsis
anther. Biochemical Society Transactions. 2010;38(2):571-576. doi:10.1042/bst0380571
apa: Feng, X., & Dickinson, H. G. (2010). Cell–cell interactions during patterning
of the Arabidopsis anther. Biochemical Society Transactions. Portland
Press Ltd. https://doi.org/10.1042/bst0380571
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning
of the Arabidopsis Anther.” Biochemical Society Transactions. Portland
Press Ltd., 2010. https://doi.org/10.1042/bst0380571.
ieee: X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of
the Arabidopsis anther,” Biochemical Society Transactions, vol.
38, no. 2. Portland Press Ltd., pp. 571–576, 2010.
ista: Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the
Arabidopsis anther. Biochemical Society Transactions. 38(2), 571–576.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning
of the Arabidopsis Anther.” Biochemical Society Transactions, vol.
38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:10.1042/bst0380571.
short: X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.
date_created: 2023-01-16T09:22:18Z
date_published: 2010-03-22T00:00:00Z
date_updated: 2023-05-08T10:57:59Z
day: '22'
department:
- _id: XiFe
doi: 10.1042/bst0380571
extern: '1'
external_id:
pmid:
- '20298223'
intvolume: ' 38'
issue: '2'
keyword:
- Biochemistry
- Anther Development
- Arabidopsis
- Cell Fate
- Microsporangium
- Polarity
- Receptor Kinase
language:
- iso: eng
month: '03'
oa_version: None
page: 571-576
pmid: 1
publication: Biochemical Society Transactions
publication_identifier:
issn:
- 0300-5127
- 1470-8752
publication_status: published
publisher: Portland Press Ltd.
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell–cell interactions during patterning of the Arabidopsis anther
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2010'
...
---
_id: '3303'
abstract:
- lang: eng
text: 'Biological traits result in part from interactions between different genetic
loci. This can lead to sign epistasis, in which a beneficial adaptation involves
a combination of individually deleterious or neutral mutations; in this case,
a population must cross a “fitness valley” to adapt. Recombination can assist
this process by combining mutations from different individuals or retard it by
breaking up the adaptive combination. Here, we analyze the simplest fitness valley,
in which an adaptation requires one mutation at each of two loci to provide a
fitness benefit. We present a theoretical analysis of the effect of recombination
on the valley-crossing process across the full spectrum of possible parameter
regimes. We find that low recombination rates can speed up valley crossing relative
to the asexual case, while higher recombination rates slow down valley crossing,
with the transition between the two regimes occurring when the recombination rate
between the loci is approximately equal to the selective advantage provided by
the adaptation. In large populations, if the recombination rate is high and selection
against single mutants is substantial, the time to cross the valley grows exponentially
with population size, effectively meaning that the population cannot acquire the
adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing
time by up to several orders of magnitude relative to that in an asexual population. '
acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate
Fellowship and European Research Council grant 250152 (to D.B.W.) and by National
Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many
ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer
for their helpful suggestions. "
article_processing_charge: No
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus
last_name: Feldman
- first_name: Daniel
full_name: Fisher, Daniel
last_name: Fisher
citation:
ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual
populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240
apa: Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley
crossing in sexual populations. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.110.123240
chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley
Crossing in Sexual Populations.” Genetics. Genetics Society of America,
2010. https://doi.org/10.1534/genetics.110.123240.
ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing
in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of
America, pp. 1389–1410, 2010.
ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing
in sexual populations. Genetics. 186(4), 1389–1410.
mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.”
Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410,
doi:10.1534/genetics.110.123240.
short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.
corr_author: '1'
date_created: 2018-12-11T12:02:33Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2025-09-30T09:47:59Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.110.123240
ec_funded: 1
external_id:
isi:
- '000285297000025'
intvolume: ' 186'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1389 - 1410
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: '3337'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The rate of fitness-valley crossing in sexual populations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 186
year: '2010'
...
---
_id: '14983'
abstract:
- lang: eng
text: 'This chapter tackles a difficult challenge: presenting signal processing
material to non-experts. This chapter is meant to be comprehensible to people
who have some math background, including a course in linear algebra and basic
statistics, but do not specialize in mathematics, engineering, or related fields.
Some formulas assume the reader is familiar with matrices and basic matrix operations,
but not more advanced material. Furthermore, we tried to make the chapter readable
even if you skip the formulas. Nevertheless, we include some simple methods to
demonstrate the basics of adaptive data processing, then we proceed with some
advanced methods that are fundamental in adaptive signal processing, and are likely
to be useful in a variety of applications. The advanced algorithms are also online
available [30]. In the second part, these techniques are applied to some real-world
BCI data.'
acknowledgement: This work was supported by the EU grants “BrainCom” (FP6-2004-Mobility-5
Grant No 024259) and “Multi-adaptive BCI” (MEIF-CT-2006 Grant No 040666). Furthermore,
we thank Matthias Krauledat for fruitful discussions and tools for generating Fig.
5.
alternative_title:
- The Frontiers Collection
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Carmen
full_name: Vidaurre, Carmen
last_name: Vidaurre
- first_name: Klaus-Robert
full_name: Müller, Klaus-Robert
last_name: Müller
citation:
ama: 'Schlögl A, Vidaurre C, Müller K-R. Adaptive Methods in BCI Research - An Introductory
Tutorial. In: Graimann B, Pfurtscheller G, Allison B, eds. Brain-Computer Interfaces.
1st ed. FRONTCOLL. Berlin, Heidelberg: Springer; 2010:331-355. doi:10.1007/978-3-642-02091-9_18'
apa: 'Schlögl, A., Vidaurre, C., & Müller, K.-R. (2010). Adaptive Methods in
BCI Research - An Introductory Tutorial. In B. Graimann, G. Pfurtscheller, &
B. Allison (Eds.), Brain-Computer Interfaces (1st ed., pp. 331–355). Berlin,
Heidelberg: Springer. https://doi.org/10.1007/978-3-642-02091-9_18'
chicago: 'Schlögl, Alois, Carmen Vidaurre, and Klaus-Robert Müller. “Adaptive Methods
in BCI Research - An Introductory Tutorial.” In Brain-Computer Interfaces,
edited by Bernhard Graimann, Gert Pfurtscheller, and Brendan Allison, 1st ed.,
331–55. FRONTCOLL. Berlin, Heidelberg: Springer, 2010. https://doi.org/10.1007/978-3-642-02091-9_18.'
ieee: 'A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research
- An Introductory Tutorial,” in Brain-Computer Interfaces, 1st ed., B.
Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer,
2010, pp. 331–355.'
ista: 'Schlögl A, Vidaurre C, Müller K-R. 2010.Adaptive Methods in BCI Research
- An Introductory Tutorial. In: Brain-Computer Interfaces. The Frontiers Collection,
, 331–355.'
mla: Schlögl, Alois, et al. “Adaptive Methods in BCI Research - An Introductory
Tutorial.” Brain-Computer Interfaces, edited by Bernhard Graimann et al.,
1st ed., Springer, 2010, pp. 331–55, doi:10.1007/978-3-642-02091-9_18.
short: A. Schlögl, C. Vidaurre, K.-R. Müller, in:, B. Graimann, G. Pfurtscheller,
B. Allison (Eds.), Brain-Computer Interfaces, 1st ed., Springer, Berlin, Heidelberg,
2010, pp. 331–355.
corr_author: '1'
date_created: 2024-02-14T09:56:00Z
date_published: 2010-09-06T00:00:00Z
date_updated: 2024-10-21T06:03:06Z
day: '06'
department:
- _id: ScienComp
doi: 10.1007/978-3-642-02091-9_18
edition: '1'
editor:
- first_name: Bernhard
full_name: Graimann, Bernhard
last_name: Graimann
- first_name: Gert
full_name: Pfurtscheller, Gert
last_name: Pfurtscheller
- first_name: Brendan
full_name: Allison, Brendan
last_name: Allison
language:
- iso: eng
month: '09'
oa_version: None
page: 331-355
place: Berlin, Heidelberg
publication: Brain-Computer Interfaces
publication_identifier:
eisbn:
- '9783642020919'
isbn:
- '9783642020902'
issn:
- 1612-3018
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
series_title: FRONTCOLL
status: public
title: Adaptive Methods in BCI Research - An Introductory Tutorial
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '10908'
abstract:
- lang: eng
text: We present ABC, a software tool for automatically computing symbolic upper
bounds on the number of iterations of nested program loops. The system combines
static analysis of programs with symbolic summation techniques to derive loop
invariant relations between program variables. Iteration bounds are obtained from
the inferred invariants, by replacing variables with bounds on their greatest
values. We have successfully applied ABC to a large number of examples. The derived
symbolic bounds express non-trivial polynomial relations over loop variables.
We also report on results to automatically infer symbolic expressions over harmonic
numbers as upper bounds on loop iteration counts.
acknowledgement: This work was supported in part by the Swiss NSF. The fourth author
is supported by an FWF Hertha Firnberg Research grant (T425-N23).
article_processing_charge: No
author:
- first_name: Régis
full_name: Blanc, Régis
last_name: Blanc
- 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: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
citation:
ama: 'Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation
for loops. In: Clarke EM, Voronkov A, eds. Logic for Programming, Artificial
Intelligence, and Reasoning. Vol 6355. LNCS. Berlin, Heidelberg: Springer
Nature; 2010:103-118. doi:10.1007/978-3-642-17511-4_7'
apa: 'Blanc, R., Henzinger, T. A., Hottelier, T., & Kovács, L. (2010). ABC:
Algebraic Bound Computation for loops. In E. M. Clarke & A. Voronkov (Eds.),
Logic for Programming, Artificial Intelligence, and Reasoning (Vol. 6355,
pp. 103–118). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-17511-4_7'
chicago: 'Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács.
“ABC: Algebraic Bound Computation for Loops.” In Logic for Programming, Artificial
Intelligence, and Reasoning, edited by Edmund M Clarke and Andrei Voronkov,
6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. https://doi.org/10.1007/978-3-642-17511-4_7.'
ieee: 'R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound
Computation for loops,” in Logic for Programming, Artificial Intelligence,
and Reasoning, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.'
ista: 'Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound
Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning.
LPAR: Logic for Programming, Artificial Intelligence and ReasoningLNCS vol. 6355,
103–118.'
mla: 'Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” Logic
for Programming, Artificial Intelligence, and Reasoning, edited by Edmund
M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:10.1007/978-3-642-17511-4_7.'
short: R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov
(Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer
Nature, Berlin, Heidelberg, 2010, pp. 103–118.
conference:
end_date: 2010-05-01
location: Dakar, Senegal
name: 'LPAR: Logic for Programming, Artificial Intelligence and Reasoning'
start_date: 2010-04-25
corr_author: '1'
date_created: 2022-03-21T08:14:35Z
date_published: 2010-05-01T00:00:00Z
date_updated: 2025-09-30T09:51:13Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-17511-4_7
editor:
- first_name: Edmund M
full_name: Clarke, Edmund M
last_name: Clarke
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
external_id:
isi:
- '000309668000007'
intvolume: ' 6355'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://infoscience.epfl.ch/record/186096
month: '05'
oa: 1
oa_version: Submitted Version
page: 103-118
place: Berlin, Heidelberg
publication: Logic for Programming, Artificial Intelligence, and Reasoning
publication_identifier:
eisbn:
- '9783642175114'
eissn:
- 1611-3349
isbn:
- '9783642175107'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: 'ABC: Algebraic Bound Computation for loops'
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6355
year: '2010'
...
---
_id: '10909'
abstract:
- lang: eng
text: We address the problem of localizing homology classes, namely, finding the
cycle representing a given class with the most concise geometric measure. We focus
on the volume measure, that is, the 1-norm of a cycle. Two main results are presented.
First, we prove the problem is NP-hard to approximate within any constant factor.
Second, we prove that for homology of dimension two or higher, the problem is
NP-hard to approximate even when the Betti number is O(1). A side effect is the
inapproximability of the problem of computing the nonbounding cycle with the smallest
volume, and computing cycles representing a homology basis with the minimal total
volume. We also discuss other geometric measures (diameter and radius) and show
their disadvantages in homology localization. Our work is restricted to homology
over the ℤ2 field.
acknowledgement: Partially supported by the Austrian Science Fund under grantFSP-S9103-N04
and P20134-N13.
article_processing_charge: No
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
citation:
ama: 'Chen C, Freedman D. Hardness results for homology localization. In: Proceedings
of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for
Industrial and Applied Mathematics; 2010:1594-1604. doi:10.1137/1.9781611973075.129'
apa: 'Chen, C., & Freedman, D. (2010). Hardness results for homology localization.
In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms
(pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied
Mathematics. https://doi.org/10.1137/1.9781611973075.129'
chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
1594–1604. Society for Industrial and Applied Mathematics, 2010. https://doi.org/10.1137/1.9781611973075.129.
ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” in
Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
Austin, TX, United States, 2010, pp. 1594–1604.
ista: 'Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings
of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium
on Discrete Algorithms, 1594–1604.'
mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:10.1137/1.9781611973075.129.
short: C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium
on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010,
pp. 1594–1604.
conference:
end_date: 2010-01-19
location: Austin, TX, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2010-01-17
corr_author: '1'
date_created: 2022-03-21T08:24:07Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2025-09-30T09:22:32Z
day: '01'
department:
- _id: HeEd
doi: 10.1137/1.9781611973075.129
language:
- iso: eng
month: '02'
oa_version: None
page: 1594-1604
publication: Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- '9781611973075'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '3267'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Hardness results for homology localization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '2409'
abstract:
- lang: eng
text: "Background: The availability of many gene alignments with overlapping taxon
sets raises the question of which strategy is the best to infer species phylogenies
from multiple gene information. Methods and programs abound that use the gene
alignment in different ways to reconstruct the species tree. In particular, different
methods combine the original data at different points along the way from the underlying
sequences to the final tree. Accordingly, they are classified into superalignment,
supertree and medium-level approaches. Here, we present a simulation study to
compare different methods from each of these three approaches.\r\n\r\nResults:
We observe that superalignment methods usually outperform the other approaches
over a wide range of parameters including sparse data and gene-specific evolutionary
parameters. In the presence of high incongruency among gene trees, however, other
combination methods show better performance than the superalignment approach.
Surprisingly, some supertree and medium-level methods exhibit, on average, worse
results than a single gene phylogeny with complete taxon information.\r\n\r\nConclusions:
For some methods, using the reconstructed gene tree as an estimation of the species
tree is superior to the combination of incomplete information. Superalignment
usually performs best since it is less susceptible to stochastic error. Supertree
methods can outperform superalignment in the presence of gene-tree conflict."
acknowledgement: Financial support from the Wiener Wissenschafts-, Forschungs- and
Technologiefonds (WWTF) is greatly appreciated. A.v.H. acknowledges support from
the German Research Foundation (DFG, SPP-1174).
article_number: '37'
article_processing_charge: No
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Heiko
full_name: Schmidt, Heiko
last_name: Schmidt
- first_name: Arndt
full_name: Von Haeseler, Arndt
last_name: Von Haeseler
citation:
ama: Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets. Algorithms for Molecular Biology.
2010;5(1). doi:10.1186/1748-7188-5-37
apa: Kupczok, A., Schmidt, H., & Von Haeseler, A. (2010). Accuracy of phylogeny
reconstruction methods combining overlapping gene data sets. Algorithms for
Molecular Biology. BioMed Central. https://doi.org/10.1186/1748-7188-5-37
chicago: Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny
Reconstruction Methods Combining Overlapping Gene Data Sets.” Algorithms for
Molecular Biology. BioMed Central, 2010. https://doi.org/10.1186/1748-7188-5-37.
ieee: A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets,” Algorithms for Molecular Biology,
vol. 5, no. 1. BioMed Central, 2010.
ista: Kupczok A, Schmidt H, Von Haeseler A. 2010. Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets. Algorithms for Molecular Biology.
5(1), 37.
mla: Kupczok, Anne, et al. “Accuracy of Phylogeny Reconstruction Methods Combining
Overlapping Gene Data Sets.” Algorithms for Molecular Biology, vol. 5,
no. 1, 37, BioMed Central, 2010, doi:10.1186/1748-7188-5-37.
short: A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology
5 (2010).
date_created: 2018-12-11T11:57:30Z
date_published: 2010-12-06T00:00:00Z
date_updated: 2025-09-30T09:48:29Z
day: '06'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1748-7188-5-37
external_id:
isi:
- '000286183400001'
file:
- access_level: open_access
checksum: e2497285388bc4da629bafb46662eb43
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:16Z
date_updated: 2020-07-14T12:45:40Z
file_id: '4739'
file_name: IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf
file_size: 723929
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
publication: Algorithms for Molecular Biology
publication_status: published
publisher: BioMed Central
publist_id: '4517'
pubrep_id: '939'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Accuracy of phylogeny reconstruction methods combining overlapping gene data
sets
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: 5
year: '2010'
...
---
_id: '9452'
abstract:
- lang: eng
text: Eukaryotic cytosine methylation represses transcription but also occurs in
the bodies of active genes, and the extent of methylation biology conservation
is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that
gene body methylation is conserved between plants and animals, whereas selective
methylation of transposons is not. We show that methylation of plant transposons
in the CHG context extends to green algae and that exclusion of histone H2A.Z
from methylated DNA is conserved between plants and animals, and we present evidence
for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant
DNA methylation systems are mosaics of conserved and derived features, and indicate
that gene body methylation is an ancient property of eukaryotic genomes.
article_processing_charge: No
article_type: original
author:
- first_name: 'Assaf '
full_name: 'Zemach, Assaf '
last_name: Zemach
- first_name: Ivy E.
full_name: McDaniel, Ivy E.
last_name: McDaniel
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis
of eukaryotic DNA methylation. Science. 2010;328(5980):916-919. doi:10.1126/science.1186366
apa: Zemach, A., McDaniel, I. E., Silva, P., & Zilberman, D. (2010). Genome-wide
evolutionary analysis of eukaryotic DNA methylation. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.1186366
chicago: Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide
Evolutionary Analysis of Eukaryotic DNA Methylation.” Science. American
Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1186366.
ieee: A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary
analysis of eukaryotic DNA methylation,” Science, vol. 328, no. 5980. American
Association for the Advancement of Science, pp. 916–919, 2010.
ista: Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary
analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.
mla: Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA
Methylation.” Science, vol. 328, no. 5980, American Association for the
Advancement of Science, 2010, pp. 916–19, doi:10.1126/science.1186366.
short: A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.
date_created: 2021-06-04T08:26:08Z
date_published: 2010-05-14T00:00:00Z
date_updated: 2021-12-14T08:35:37Z
day: '14'
department:
- _id: DaZi
doi: 10.1126/science.1186366
extern: '1'
external_id:
pmid:
- '20395474 '
intvolume: ' 328'
issue: '5980'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa_version: None
page: 916-919
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 evolutionary analysis of eukaryotic DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 328
year: '2010'
...
---
_id: '9485'
abstract:
- lang: eng
text: 'Cytosine methylation silences transposable elements in plants, vertebrates,
and fungi but also regulates gene expression. Plant methylation is catalyzed by
three families of enzymes, each with a preferred sequence context: CG, CHG (H
= A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis
thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally
hypomethylated in the CG context while retaining high non-CG methylation. Global
methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition
remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all
sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas
CG hypomethylation is localized. CHH methylation of small transposable elements
is increased in embryos, suggesting that endosperm demethylation enhances transposon
silencing. Genes preferentially expressed in endosperm, including those coding
for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated
in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm
biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is
conserved among angiosperms and has a profound effect on gene expression in cereal
crops.'
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Pedro
full_name: Silva, Pedro
last_name: Silva
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Bradley
full_name: Dotson, Bradley
last_name: Dotson
- first_name: Matthew D.
full_name: Brooks, Matthew D.
last_name: Brooks
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes
in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734.
doi:10.1073/pnas.1009695107
apa: Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M.
D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice
endosperm. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1009695107
chicago: Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley
Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates
Genes in Rice Endosperm.” Proceedings of the National Academy of Sciences.
National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107.
ieee: A. Zemach et al., “Local DNA hypomethylation activates genes in rice
endosperm,” Proceedings of the National Academy of Sciences, vol. 107,
no. 43. National Academy of Sciences, pp. 18729–18734, 2010.
ista: Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D.
2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings
of the National Academy of Sciences. 107(43), 18729–18734.
mla: Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 107, no. 43, National
Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107.
short: A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D.
Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.
date_created: 2021-06-07T09:31:01Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-12-14T08:40:02Z
day: '26'
department:
- _id: DaZi
doi: 10.1073/pnas.1009695107
extern: '1'
external_id:
pmid:
- '20937895'
intvolume: ' 107'
issue: '43'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1009695107
month: '10'
oa: 1
oa_version: Published Version
page: 18729-18734
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Local DNA hypomethylation activates genes in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 107
year: '2010'
...
---
_id: '9489'
abstract:
- lang: eng
text: Cytosine methylation is an ancient process with conserved enzymology but diverse
biological functions that include defense against transposable elements and regulation
of gene expression. Here we will discuss the evolution and biological significance
of eukaryotic DNA methylation, the likely drivers of that evolution, and major
remaining mysteries.
article_processing_charge: No
article_type: review
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit
of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007
apa: Zemach, A., & Zilberman, D. (2010). Evolution of eukaryotic DNA methylation
and the pursuit of safer sex. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2010.07.007
chicago: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007.
ieee: A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the
pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp.
R780–R785, 2010.
ista: Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the
pursuit of safer sex. Current Biology. 20(17), R780–R785.
mla: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation
and the Pursuit of Safer Sex.” Current Biology, vol. 20, no. 17, Elsevier,
2010, pp. R780–85, doi:10.1016/j.cub.2010.07.007.
short: A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.
date_created: 2021-06-07T09:45:27Z
date_published: 2010-09-14T00:00:00Z
date_updated: 2021-12-14T08:52:34Z
day: '14'
department:
- _id: DaZi
doi: 10.1016/j.cub.2010.07.007
extern: '1'
external_id:
pmid:
- '20833323'
intvolume: ' 20'
issue: '17'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2010.07.007
month: '09'
oa: 1
oa_version: Published Version
page: R780-R785
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of eukaryotic DNA methylation and the pursuit of safer sex
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 20
year: '2010'
...
---
_id: '9764'
article_processing_charge: No
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- 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: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the
drift load. 2010. doi:10.1371/journal.pbio.1000429.s003
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010.
https://doi.org/10.1371/journal.pbio.1000429.s003.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis
and the drift load.” Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis
and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003.
mla: Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.s003.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).
date_created: 2021-08-02T09:45:39Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2025-09-30T09:42:52Z
day: '20'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '3779'
relation: used_in_publication
status: public
status: public
title: Heterosis and the drift load
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2010'
...
---
_id: '474'
abstract:
- lang: eng
text: 'Classical models of gene flow fail in three ways: they cannot explain large-scale
patterns; they predict much more genetic diversity than is observed; and they
assume that loosely linked genetic loci evolve independently. We propose a new
model that deals with these problems. Extinction events kill some fraction of
individuals in a region. These are replaced by offspring from a small number of
parents, drawn from the preexisting population. This model of evolution forwards
in time corresponds to a backwards model, in which ancestral lineages jump to
a new location if they are hit by an event, and may coalesce with other lineages
that are hit by the same event. We derive an expression for the identity in allelic
state, and show that, over scales much larger than the largest event, this converges
to the classical value derived by Wright and Malécot. However, rare events that
cover large areas cause low genetic diversity, large-scale patterns, and correlations
in ancestry between unlinked loci.'
acknowledgement: This work has made use of the resources provided by the Edinburgh
Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative.
NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant
EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.
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
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: 'Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization
in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715.
doi:10.1111/j.1558-5646.2010.01019.x'
apa: 'Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography. Evolution.
Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x'
chicago: 'Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model
for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.”
Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.'
ieee: 'N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography,” Evolution,
vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.'
ista: 'Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and
recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9),
2701–2715.'
mla: 'Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization
in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no.
9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.'
short: N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.
corr_author: '1'
date_created: 2018-12-11T11:46:40Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2025-09-30T09:50:22Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2010.01019.x
external_id:
isi:
- '000281636400017'
intvolume: ' 64'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 2701 - 2715
publication: Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2780'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A new model for extinction and recolonization in two dimensions: Quantifying
phylogeography'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 64
year: '2010'
...
---
_id: '488'
abstract:
- lang: eng
text: 'Streaming string transducers [1] define (partial) functions from input strings
to output strings. A streaming string transducer makes a single pass through the
input string and uses a finite set of variables that range over strings from the
output alphabet. At every step, the transducer processes an input symbol, and
updates all the variables in parallel using assignments whose right-hand-sides
are concatenations of output symbols and variables with the restriction that a
variable can be used at most once in a right-hand-side expression. It has been
shown that streaming string transducers operating on strings over infinite data
domains are of interest in algorithmic verification of list-processing programs,
as they lead to PSPACE decision procedures for checking pre/post conditions and
for checking semantic equivalence, for a well-defined class of heap-manipulating
programs. In order to understand the theoretical expressiveness of streaming transducers,
we focus on streaming transducers processing strings over finite alphabets, given
the existence of a robust and well-studied class of "regular" transductions
for this case. Such regular transductions can be defined either by two-way deterministic
finite-state transducers, or using a logical MSO-based characterization. Our main
result is that the expressiveness of streaming string transducers coincides exactly
with this class of regular transductions. '
alternative_title:
- LIPIcs
article_processing_charge: No
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
citation:
ama: 'Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:10.4230/LIPIcs.FSTTCS.2010.1'
apa: 'Alur, R., & Cerny, P. (2010). Expressiveness of streaming string transducers
(Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology
and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1'
chicago: Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,”
8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1.
ieee: 'R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented
at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science,
Chennai, India, 2010, vol. 8, pp. 1–12.'
ista: 'Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS:
Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol.
8, 1–12.'
mla: Alur, Rajeev, and Pavol Cerny. Expressiveness of Streaming String Transducers.
Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:10.4230/LIPIcs.FSTTCS.2010.1.
short: R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2010, pp. 1–12.
conference:
end_date: 2010-12-18
location: Chennai, India
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
start_date: 2010-12-15
corr_author: '1'
date_created: 2018-12-11T11:46:45Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2025-09-30T09:49:32Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.FSTTCS.2010.1
external_id:
isi:
- '000310361000001'
file:
- access_level: open_access
checksum: 5845be5aa19791830f7407d8853f2df0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:29Z
date_updated: 2020-07-14T12:46:35Z
file_id: '4690'
file_name: IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf
file_size: 492344
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 1 - 12
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '7331'
pubrep_id: '948'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Expressiveness of streaming string transducers
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2010'
...
---
_id: '489'
abstract:
- lang: eng
text: 'Graph games of infinite length are a natural model for open reactive processes:
one player represents the controller, trying to ensure a given specification,
and the other represents a hostile environment. The evolution of the system depends
on the decisions of both players, supplemented by chance. In this work, we focus
on the notion of randomised strategy. More specifically, we show that three natural
definitions may lead to very different results: in the most general cases, an
almost-surely winning situation may become almost-surely losing if the player
is only allowed to use a weaker notion of strategy. In more reasonable settings,
translations exist, but they require infinite memory, even in simple cases. Finally,
some traditional problems becomes undecidable for the strongest type of strategies.'
alternative_title:
- EPTCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Julien
full_name: Cristau, Julien
last_name: Cristau
- first_name: Claire
full_name: David, Claire
last_name: David
- first_name: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: 'Cristau J, David C, Horn F. How do we remember the past in randomised strategies?
In: Proceedings of GandALF 2010. Vol 25. Open Publishing Association; 2010:30-39.
doi:10.4204/EPTCS.25.7'
apa: 'Cristau, J., David, C., & Horn, F. (2010). How do we remember the past
in randomised strategies? In Proceedings of GandALF 2010 (Vol. 25, pp.
30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. https://doi.org/10.4204/EPTCS.25.7'
chicago: Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the
Past in Randomised Strategies?” In Proceedings of GandALF 2010, 25:30–39.
Open Publishing Association, 2010. https://doi.org/10.4204/EPTCS.25.7.
ieee: J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised
strategies?,” in Proceedings of GandALF 2010, Minori, Amalfi Coast, Italy,
2010, vol. 25, pp. 30–39.
ista: 'Cristau J, David C, Horn F. 2010. How do we remember the past in randomised
strategies? Proceedings of GandALF 2010. GandALF: Games, Automata, Logic, and
Formal Verification, EPTCS, vol. 25, 30–39.'
mla: Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies?”
Proceedings of GandALF 2010, vol. 25, Open Publishing Association, 2010,
pp. 30–39, doi:10.4204/EPTCS.25.7.
short: J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing
Association, 2010, pp. 30–39.
conference:
end_date: 2010-06-18
location: Minori, Amalfi Coast, Italy
name: 'GandALF: Games, Automata, Logic, and Formal Verification'
start_date: 2010-06-17
corr_author: '1'
date_created: 2018-12-11T11:46:45Z
date_published: 2010-06-09T00:00:00Z
date_updated: 2025-06-11T08:14:27Z
day: '09'
department:
- _id: KrCh
doi: 10.4204/EPTCS.25.7
external_id:
arxiv:
- '1006.1404'
intvolume: ' 25'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1006.1404
month: '06'
oa: 1
oa_version: Published Version
page: 30 - 39
publication: Proceedings of GandALF 2010
publication_status: published
publisher: Open Publishing Association
publist_id: '7332'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How do we remember the past in randomised strategies?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2010'
...
---
_id: '533'
abstract:
- lang: eng
text: Any programming error that can be revealed before compiling a program saves
precious time for the programmer. While integrated development environments already
do a good job by detecting, e.g., data-flow abnormalities, current static analysis
tools suffer from false positives ("noise") or require strong user interaction.
We propose to avoid this deficiency by defining a new class of errors. A program
fragment is doomed if its execution will inevitably fail, regardless of which
state it is started in. We use a formal verification method to identify such errors
fully automatically and, most significantly, without producing noise. We report
on experiments with a prototype tool.
article_processing_charge: No
author:
- first_name: Jochen
full_name: Hoenicke, Jochen
last_name: Hoenicke
- first_name: Kari
full_name: Leino, Kari
last_name: Leino
- first_name: Andreas
full_name: Podelski, Andreas
last_name: Podelski
- first_name: Martin
full_name: Schäf, Martin
last_name: Schäf
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
citation:
ama: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. Formal
Methods in System Design. 2010;37(2-3):171-199. doi:10.1007/s10703-010-0102-0
apa: Hoenicke, J., Leino, K., Podelski, A., Schäf, M., & Wies, T. (2010). Doomed
program points. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-010-0102-0
chicago: Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas
Wies. “Doomed Program Points.” Formal Methods in System Design. Springer,
2010. https://doi.org/10.1007/s10703-010-0102-0.
ieee: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program
points,” Formal Methods in System Design, vol. 37, no. 2–3. Springer, pp.
171–199, 2010.
ista: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points.
Formal Methods in System Design. 37(2–3), 171–199.
mla: Hoenicke, Jochen, et al. “Doomed Program Points.” Formal Methods in System
Design, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:10.1007/s10703-010-0102-0.
short: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in
System Design 37 (2010) 171–199.
corr_author: '1'
date_created: 2018-12-11T11:47:01Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2025-09-30T09:48:58Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/s10703-010-0102-0
external_id:
isi:
- '000286631700004'
intvolume: ' 37'
isi: 1
issue: 2-3
language:
- iso: eng
month: '12'
oa_version: None
page: 171 - 199
publication: Formal Methods in System Design
publication_status: published
publisher: Springer
publist_id: '7284'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Doomed program points
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2010'
...
---
_id: '5388'
abstract:
- lang: eng
text: "We present an algorithmic method for the synthesis of concurrent programs
that are optimal with respect to quantitative performance measures. The input
consists of a sequential sketch, that is, a program that does not contain synchronization
constructs, and of a parametric performance model that assigns costs to actions
such as locking, context switching, and idling. The quantitative synthesis problem
is to automatically introduce synchronization constructs into the sequential sketch
so that both correctness is guaranteed and worst-case (or average-case) performance
is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe
show that for worst-case performance, the problem can be modeled\r\nas a 2-player
graph game with quantitative (limit-average) objectives, and\r\nfor average-case
performance, as a 2 1/2 -player graph game (with probabilistic transitions). In
both cases, the optimal correct program is derived from an optimal strategy in
the corresponding quantitative game. We prove that the respective game problems
are computationally expensive (NP-complete), and present several techniques that
overcome the theoretical difficulty in cases of concurrent programs of practical
interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic
syn- thesis of programs that access a concurrent list. For certain parameter val-
ues, our method automatically synthesizes various classical synchronization schemes
for implementing a concurrent list, such as fine-grained locking or a lazy algorithm.
For other parameter values, a new, hybrid synchronization style is synthesized,
which uses both the lazy approach and coarse-grained locks (instead of standard
fine-grained locks). The trade-off occurs because while fine-grained locking tends
to decrease the cost that is due to waiting for locks, it increases cache size
requirements."
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Rohit
full_name: Singh, Rohit
last_name: Singh
citation:
ama: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. Quantitative
Synthesis for Concurrent Programs. IST Austria; 2010. doi:10.15479/AT:IST-2010-0004
apa: Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., & Singh,
R. (2010). Quantitative synthesis for concurrent programs. IST Austria.
https://doi.org/10.15479/AT:IST-2010-0004
chicago: Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna,
and Rohit Singh. Quantitative Synthesis for Concurrent Programs. IST Austria,
2010. https://doi.org/10.15479/AT:IST-2010-0004.
ieee: K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, Quantitative
synthesis for concurrent programs. IST Austria, 2010.
ista: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative
synthesis for concurrent programs, IST Austria, 17p.
mla: Chatterjee, Krishnendu, et al. Quantitative Synthesis for Concurrent Programs.
IST Austria, 2010, doi:10.15479/AT:IST-2010-0004.
short: K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative
Synthesis for Concurrent Programs, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-10-07T00:00:00Z
date_updated: 2025-04-15T08:12:00Z
day: '07'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2010-0004
file:
- access_level: open_access
checksum: da38782d2388a6fa32109d10bb9bad67
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:53Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5515'
file_name: IST-2010-0004_IST-2010-0004.pdf
file_size: 429101
relation: main_file
file_date_updated: 2020-07-14T12:46:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '24'
related_material:
record:
- id: '3366'
relation: later_version
status: public
status: public
title: Quantitative synthesis for concurrent programs
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5389'
abstract:
- lang: eng
text: Boolean notions of correctness are formalized by preorders on systems. Quantitative
measures of correctness can be formalized by real-valued distance functions between
systems, where the distance between implementation and specification provides
a measure of “fit” or “desirability.” We extend the simulation preorder to the
quantitative setting, by making each player of a simulation game pay a certain
price for her choices. We use the resulting games with quantitative objectives
to define three different simulation distances. The correctness distance measures
how much the specification must be changed in order to be satisfied by the implementation.
The coverage distance measures how much the im- plementation restricts the degrees
of freedom offered by the specification. The robustness distance measures how
much a system can deviate from the implementation description without violating
the specification. We consider these distances for safety as well as liveness
specifications. The distances can be computed in polynomial time for safety specifications,
and for liveness specifications given by weak fairness constraints. We show that
the distance functions satisfy the triangle inequality, that the distance between
two systems does not increase under parallel composition with a third system,
and that the distance between two systems can be bounded from above and below
by distances between abstractions of the two systems. These properties suggest
that our simulation distances provide an appropriate basis for a quantitative
theory of discrete systems. We also demonstrate how the robustness distance can
be used to measure how many transmission errors are tolerated by error correcting
codes.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
citation:
ama: Cerny P, Henzinger TA, Radhakrishna A. Simulation Distances. IST Austria;
2010. doi:10.15479/AT:IST-2010-0003
apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances.
IST Austria. https://doi.org/10.15479/AT:IST-2010-0003
chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. Simulation
Distances. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0003.
ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, Simulation distances.
IST Austria, 2010.
ista: Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria,
24p.
mla: Cerny, Pavol, et al. Simulation Distances. IST Austria, 2010, doi:10.15479/AT:IST-2010-0003.
short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria,
2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2025-09-30T07:46:05Z
day: '04'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0003
file:
- access_level: open_access
checksum: 284ded99764e32a583a8ea83fcea254b
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:25Z
date_updated: 2020-07-14T12:46:42Z
file_id: '5547'
file_name: IST-2010-0003_IST-2010-0003.pdf
file_size: 367246
relation: main_file
file_date_updated: 2020-07-14T12:46:42Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '24'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '25'
related_material:
record:
- id: '4393'
relation: later_version
status: public
- id: '3249'
relation: later_version
status: public
status: public
title: Simulation distances
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5390'
abstract:
- lang: eng
text: The class of ω regular languages provide a robust specification language in
verification. Every ω-regular condition 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. In this work we consider the finitary parity and Streett (fairness)
conditions. We present the topological, automata-theoretic and logical characterization
of finitary languages defined by finitary parity and Streett conditions. We (a)
show that the finitary parity and Streett languages are Σ2-complete; (b) present
a complete characterization of the expressive power of various classes of automata
with finitary and infinitary conditions (in particular we show that non-deterministic
finitary parity and Streett automata cannot be determinized to deterministic finitary
parity or Streett automata); and (c) show that the languages defined by non-deterministic
finitary parity automata exactly characterize the star-free fragment of ωB-regular
languages.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Nathanaël
full_name: Fijalkow, Nathanaël
last_name: Fijalkow
citation:
ama: Chatterjee K, Fijalkow N. Topological, Automata-Theoretic and Logical Characterization
of Finitary Languages. IST Austria; 2010. doi:10.15479/AT:IST-2010-0002
apa: Chatterjee, K., & Fijalkow, N. (2010). Topological, automata-theoretic
and logical characterization of finitary languages. IST Austria. https://doi.org/10.15479/AT:IST-2010-0002
chicago: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic
and Logical Characterization of Finitary Languages. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0002.
ieee: K. Chatterjee and N. Fijalkow, Topological, automata-theoretic and logical
characterization of finitary languages. IST Austria, 2010.
ista: Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical
characterization of finitary languages, IST Austria, 21p.
mla: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic
and Logical Characterization of Finitary Languages. IST Austria, 2010, doi:10.15479/AT:IST-2010-0002.
short: K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization
of Finitary Languages, IST Austria, 2010.
date_created: 2018-12-12T11:39:03Z
date_published: 2010-06-04T00:00:00Z
date_updated: 2020-07-14T23:04:41Z
day: '04'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2010-0002
file:
- access_level: open_access
checksum: 283d3604d76dd4d5161585d4c8625fbe
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:10Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5532'
file_name: IST-2010-0002_IST-2010-0002.pdf
file_size: 395662
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '21'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '26'
status: public
title: Topological, automata-theoretic and logical characterization of finitary languages
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '5391'
abstract:
- lang: eng
text: Concurrent data structures with fine-grained synchronization are notoriously
difficult to implement correctly. The difficulty of reasoning about these implementations
does not stem from the number of variables or the program size, but rather from
the large number of possible interleavings. These implementations are therefore
prime candidates for model checking. We introduce an algorithm for verifying linearizability
of singly-linked heap-based concurrent data structures. We consider a model consisting
of an unbounded heap where each node consists an element from an unbounded data
domain, with a restricted set of operations for testing and updating pointers
and data elements. Our main result is that linearizability is decidable for programs
that invoke a fixed number of methods, possibly in parallel. This decidable fragment
covers many of the common implementation techniques — fine-grained locking, lazy
synchronization, and lock-free synchronization. We also show how the technique
can be used to verify optimistic implementations with the help of programmer annotations.
We developed a verification tool CoLT and evaluated it on a representative sample
of Java implementations of the concurrent set data structure. The tool verified
linearizability of a number of implementations, found a known error in a lock-free
imple- mentation and proved that the corrected version is linearizable.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Arjun
full_name: Radhakrishna, Arjun
id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
last_name: Radhakrishna
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
- first_name: Swarat
full_name: Chaudhuri, Swarat
last_name: Chaudhuri
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
citation:
ama: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model Checking
of Linearizability of Concurrent List Implementations. IST Austria; 2010.
doi:10.15479/AT:IST-2010-0001
apa: Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., & Alur, R. (2010).
Model checking of linearizability of concurrent list implementations. IST
Austria. https://doi.org/10.15479/AT:IST-2010-0001
chicago: Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and
Rajeev Alur. Model Checking of Linearizability of Concurrent List Implementations.
IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0001.
ieee: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, Model
checking of linearizability of concurrent list implementations. IST Austria,
2010.
ista: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking
of linearizability of concurrent list implementations, IST Austria, 27p.
mla: Cerny, Pavol, et al. Model Checking of Linearizability of Concurrent List
Implementations. IST Austria, 2010, doi:10.15479/AT:IST-2010-0001.
short: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking
of Linearizability of Concurrent List Implementations, IST Austria, 2010.
date_created: 2018-12-12T11:39:04Z
date_published: 2010-04-19T00:00:00Z
date_updated: 2024-10-21T06:03:05Z
day: '19'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2010-0001
file:
- access_level: open_access
checksum: 986645caad7dd85a6a091488f6c646dc
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:44Z
date_updated: 2020-07-14T12:46:43Z
file_id: '5505'
file_name: IST-2010-0001_IST-2010-0001.pdf
file_size: 372286
relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '27'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '27'
related_material:
record:
- id: '4390'
relation: later_version
status: public
status: public
title: Model checking of linearizability of concurrent list implementations
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3604'
abstract:
- lang: eng
text: We investigated temporal changes in hybridization and introgression between
native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on
the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples
of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that
either the proportion of recent hybrids, or the levels of introgression had changed
over the study period. Nevertheless, in one population where the two species have
been in contact since ∼1970, 44% of individuals sampled during the study were
hybrids. This suggests that hybridization between these species can proceed fairly
rapidly. By analysing the number of alleles that have introgressed from polymorphic
red deer into the genetically homogenous sika population, we reconstructed the
haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization
events could account for all the recently hybridized sika-like individuals found
across a large section of the Peninsula. Although we demonstrate that low rates
of F1 hybridization can lead to substantial introgression, the progress of hybridization
and introgression appears to be unpredictable over the short timescales.
article_processing_charge: No
author:
- first_name: Helen
full_name: Senn, Helen
last_name: Senn
- first_name: Simon
full_name: Goodman, Simon
last_name: Goodman
- first_name: Graeme
full_name: Swanson, Graeme
last_name: Swanson
- 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: Josephine
full_name: Pemberton, Josephine
last_name: Pemberton
citation:
ama: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal
changes in hybridisation and introgression between invasive sika (Cervus nippon)
and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular
Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x
apa: Senn, H., Goodman, S., Swanson, G., Barton, N. H., & Pemberton, J. (2010).
Investigating temporal changes in hybridisation and introgression between invasive
sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula,
Scotland. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x
chicago: Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine
Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression
between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on
the Kintyre Peninsula, Scotland.” Molecular Ecology. Wiley-Blackwell, 2010.
https://doi.org/10.1111/j.1365-294X.2009.04497.x.
ieee: H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating
temporal changes in hybridisation and introgression between invasive sika (Cervus
nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,”
Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010.
ista: Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating
temporal changes in hybridisation and introgression between invasive sika (Cervus
nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland.
Molecular Ecology. 19(5), 910–924.
mla: Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression
between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on
the Kintyre Peninsula, Scotland.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell,
2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x.
short: H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology
19 (2010) 910–924.
date_created: 2018-12-11T12:04:12Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2025-09-30T09:47:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1365-294X.2009.04497.x
external_id:
isi:
- '000274550100008'
intvolume: ' 19'
isi: 1
issue: '5'
language:
- iso: eng
month: '03'
oa_version: None
page: 910 - 924
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2779'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Investigating temporal changes in hybridisation and introgression between invasive
sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula,
Scotland
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 19
year: '2010'
...