---
_id: '5408'
abstract:
- lang: eng
text: "We consider two-player partial-observation stochastic games where player
1 has partial observation and player 2 has perfect observation. The winning condition
we study are omega-regular conditions specified as parity objectives. The qualitative
analysis problem given a partial-observation stochastic game and a parity objective
asks whether there is a strategy to ensure that the objective is satisfied with
probability 1 (resp. positive probability). While the qualitative analysis problems
are known to be undecidable even for very special cases of parity objectives,
they were shown to be decidable in 2EXPTIME under finite-memory strategies. We
improve the complexity and show that the qualitative analysis problems for partial-observation
stochastic parity games under finite-memory strategies are \r\nEXPTIME-complete;
and also establish optimal (exponential) memory bounds for finite-memory strategies
required for qualitative analysis. "
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: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Sumit
full_name: Nain, Sumit
last_name: Nain
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: Chatterjee K, Doyen L, Nain S, Vardi M. The Complexity of Partial-Observation
Stochastic Parity Games with Finite-Memory Strategies. IST Austria; 2013.
doi:10.15479/AT:IST-2013-141-v1-1
apa: Chatterjee, K., Doyen, L., Nain, S., & Vardi, M. (2013). The complexity
of partial-observation stochastic parity games with finite-memory strategies.
IST Austria. https://doi.org/10.15479/AT:IST-2013-141-v1-1
chicago: Chatterjee, Krishnendu, Laurent Doyen, Sumit Nain, and Moshe Vardi. The
Complexity of Partial-Observation Stochastic Parity Games with Finite-Memory Strategies.
IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-141-v1-1.
ieee: K. Chatterjee, L. Doyen, S. Nain, and M. Vardi, The complexity of partial-observation
stochastic parity games with finite-memory strategies. IST Austria, 2013.
ista: Chatterjee K, Doyen L, Nain S, Vardi M. 2013. The complexity of partial-observation
stochastic parity games with finite-memory strategies, IST Austria, 17p.
mla: Chatterjee, Krishnendu, et al. The Complexity of Partial-Observation Stochastic
Parity Games with Finite-Memory Strategies. IST Austria, 2013, doi:10.15479/AT:IST-2013-141-v1-1.
short: K. Chatterjee, L. Doyen, S. Nain, M. Vardi, The Complexity of Partial-Observation
Stochastic Parity Games with Finite-Memory Strategies, IST Austria, 2013.
date_created: 2018-12-12T11:39:10Z
date_published: 2013-09-12T00:00:00Z
date_updated: 2025-04-15T07:56:00Z
day: '12'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-141-v1-1
file:
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checksum: 226bc791124f8d3138379778ce834e86
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creator: system
date_created: 2018-12-12T11:53:16Z
date_updated: 2020-07-14T12:46:46Z
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file_name: IST-2013-141-v1+1_main-tech-rpt.pdf
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has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '141'
related_material:
record:
- id: '2213'
relation: later_version
status: public
status: public
title: The complexity of partial-observation stochastic parity games with finite-memory
strategies
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5409'
abstract:
- lang: eng
text: "The edit distance between two (untimed) traces is the minimum cost of a sequence
of edit operations (insertion, deletion, or substitution) needed to transform
one trace to the other. Edit distances have been extensively studied in the untimed
setting, and form the basis for approximate matching of sequences in different
domains such as coding theory, parsing, and speech recognition. \r\nIn this paper,
we lift the study of edit distances from untimed languages to the timed setting.
We define an edit distance between timed words which incorporates both the edit
distance between the untimed words and the absolute difference in timestamps.
Our edit distance between two timed words is computable in polynomial time. Further,
we show that the edit distance between a timed word and a timed language generated
by a timed automaton, defined as the edit distance between the word and the closest
word in the language, is PSPACE-complete. While computing the edit distance between
two timed automata is undecidable, we show that the approximate version, where
we decide if the edit distance between two timed automata is either less than
a given parameter or more than delta away from the parameter, for delta>0, can
be solved in exponential space and is EXPSPACE-hard. Our definitions and techniques
can be generalized to the setting of hybrid systems, and we show analogous decidability
results for rectangular automata."
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: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
citation:
ama: Chatterjee K, Ibsen-Jensen R, Majumdar R. Edit Distance for Timed Automata.
IST Austria; 2013. doi:10.15479/AT:IST-2013-144-v1-1
apa: Chatterjee, K., Ibsen-Jensen, R., & Majumdar, R. (2013). Edit distance
for timed automata. IST Austria. https://doi.org/10.15479/AT:IST-2013-144-v1-1
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Rupak Majumdar. Edit
Distance for Timed Automata. IST Austria, 2013. https://doi.org/10.15479/AT:IST-2013-144-v1-1.
ieee: K. Chatterjee, R. Ibsen-Jensen, and R. Majumdar, Edit distance for timed
automata. IST Austria, 2013.
ista: Chatterjee K, Ibsen-Jensen R, Majumdar R. 2013. Edit distance for timed automata,
IST Austria, 12p.
mla: Chatterjee, Krishnendu, et al. Edit Distance for Timed Automata. IST
Austria, 2013, doi:10.15479/AT:IST-2013-144-v1-1.
short: K. Chatterjee, R. Ibsen-Jensen, R. Majumdar, Edit Distance for Timed Automata,
IST Austria, 2013.
date_created: 2018-12-12T11:39:10Z
date_published: 2013-10-30T00:00:00Z
date_updated: 2024-10-21T06:02:53Z
day: '30'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-144-v1-1
file:
- access_level: open_access
checksum: 0f7633081ba8299c543322f0ad08571f
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:53:08Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5469'
file_name: IST-2013-144-v1+1_main.pdf
file_size: 336377
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file_date_updated: 2020-07-14T12:46:46Z
fulldoi: https://doi.org/10.15479/AT:IST-2013-144-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '12'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '144'
related_material:
record:
- id: '2216'
relation: later_version
status: public
status: public
title: Edit distance for timed automata
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5410'
abstract:
- lang: eng
text: "Board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only
in development of mathematical and logical skills, but also in emotional and social
development. In this paper, we address the problem of generating targeted starting
positions for such games. This can facilitate new approaches for bringing novice
players to mastery, and also leads to discovery of interesting game variants.
\r\nOur approach generates starting states of varying hardness levels for player
1 in a two-player board game, given rules of the board game, the desired number
of steps required for player 1 to win, and the expertise levels of the two players.
Our approach leverages symbolic methods and iterative simulation to efficiently
search the extremely large state space. We present experimental results that include
discovery of states of varying hardness levels for several simple grid-based board
games. Also, the presence of such states for standard game variants like Tic-Tac-Toe
on board size 4x4 opens up new games to be played that have not been played for
ages since the default start state is heavily biased. "
alternative_title:
- IST Austria Technical Report
author:
- first_name: Umair
full_name: Ahmed, Umair
last_name: Ahmed
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Sumit
full_name: Gulwani, Sumit
last_name: Gulwani
citation:
ama: Ahmed U, Chatterjee K, Gulwani S. Automatic Generation of Alternative Starting
Positions for Traditional Board Games. IST Austria; 2013. doi:10.15479/AT:IST-2013-146-v1-1
apa: Ahmed, U., Chatterjee, K., & Gulwani, S. (2013). Automatic generation
of alternative starting positions for traditional board games. IST Austria.
https://doi.org/10.15479/AT:IST-2013-146-v1-1
chicago: Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. Automatic Generation
of Alternative Starting Positions for Traditional Board Games. IST Austria,
2013. https://doi.org/10.15479/AT:IST-2013-146-v1-1.
ieee: U. Ahmed, K. Chatterjee, and S. Gulwani, Automatic generation of alternative
starting positions for traditional board games. IST Austria, 2013.
ista: Ahmed U, Chatterjee K, Gulwani S. 2013. Automatic generation of alternative
starting positions for traditional board games, IST Austria, 13p.
mla: Ahmed, Umair, et al. Automatic Generation of Alternative Starting Positions
for Traditional Board Games. IST Austria, 2013, doi:10.15479/AT:IST-2013-146-v1-1.
short: U. Ahmed, K. Chatterjee, S. Gulwani, Automatic Generation of Alternative
Starting Positions for Traditional Board Games, IST Austria, 2013.
date_created: 2018-12-12T11:39:10Z
date_published: 2013-12-03T00:00:00Z
date_updated: 2025-05-19T11:10:16Z
day: '03'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2013-146-v1-1
file:
- access_level: open_access
checksum: 409f3aaaf1184e4057b89cbb449dac80
content_type: application/pdf
creator: system
date_created: 2018-12-12T11:54:06Z
date_updated: 2020-07-14T12:46:46Z
file_id: '5528'
file_name: IST-2013-146-v1+1_main.pdf
file_size: 818189
relation: main_file
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fulldoi: https://doi.org/10.15479/AT:IST-2013-146-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: '13'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '146'
related_material:
record:
- id: '1481'
relation: later_version
status: public
status: public
title: Automatic generation of alternative starting positions for traditional board
games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '5747'
article_processing_charge: No
author:
- first_name: Cezara
full_name: Dragoi, Cezara
id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87
last_name: Dragoi
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Dragoi C, Gupta A, Henzinger TA. Automatic Linearizability Proofs of Concurrent
Objects with Cooperating Updates. In: Computer Aided Verification. Vol
8044. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg; 2013:174-190. doi:10.1007/978-3-642-39799-8_11'
apa: 'Dragoi, C., Gupta, A., & Henzinger, T. A. (2013). Automatic Linearizability
Proofs of Concurrent Objects with Cooperating Updates. In Computer Aided Verification
(Vol. 8044, pp. 174–190). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-39799-8_11'
chicago: 'Dragoi, Cezara, Ashutosh Gupta, and Thomas A Henzinger. “Automatic Linearizability
Proofs of Concurrent Objects with Cooperating Updates.” In Computer Aided Verification,
8044:174–90. CAV. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. https://doi.org/10.1007/978-3-642-39799-8_11.'
ieee: 'C. Dragoi, A. Gupta, and T. A. Henzinger, “Automatic Linearizability Proofs
of Concurrent Objects with Cooperating Updates,” in Computer Aided Verification,
vol. 8044, Berlin, Heidelberg: Springer Berlin Heidelberg, 2013, pp. 174–190.'
ista: 'Dragoi C, Gupta A, Henzinger TA. 2013.Automatic Linearizability Proofs of
Concurrent Objects with Cooperating Updates. In: Computer Aided Verification.
vol. 8044, 174–190.'
mla: Dragoi, Cezara, et al. “Automatic Linearizability Proofs of Concurrent Objects
with Cooperating Updates.” Computer Aided Verification, vol. 8044, Springer
Berlin Heidelberg, 2013, pp. 174–90, doi:10.1007/978-3-642-39799-8_11.
short: C. Dragoi, A. Gupta, T.A. Henzinger, in:, Computer Aided Verification, Springer
Berlin Heidelberg, Berlin, Heidelberg, 2013, pp. 174–190.
conference:
end_date: 2013-07-19
location: Saint Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
date_created: 2018-12-18T13:10:21Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2025-07-10T11:52:57Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-39799-8_11
ec_funded: 1
file:
- access_level: open_access
checksum: a901cc6b71db08b61c0d4c0cbacc6287
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T13:13:33Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5748'
file_name: 2013_CAV_Dragoi.pdf
file_size: 236480
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
fulldoi: https://doi.org/10.1007/978-3-642-39799-8_11
has_accepted_license: '1'
intvolume: ' 8044'
language:
- iso: eng
month: '08'
oa: 1
oa_version: None
page: 174-190
place: Berlin, Heidelberg
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: Computer Aided Verification
publication_identifier:
eisbn:
- '9783642397998'
eissn:
- 1611-3349
isbn:
- '9783642397981'
issn:
- 0302-9743
publication_status: published
publisher: Springer Berlin Heidelberg
pubrep_id: '195'
quality_controlled: '1'
scopus_import: '1'
series_title: CAV
status: public
title: Automatic Linearizability Proofs of Concurrent Objects with Cooperating Updates
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
OA_place: repository
OA_type: green
_id: '19995'
abstract:
- lang: eng
text: Markov decision processes (MDPs) and simple stochastic games (SSGs) provide
a rich mathematical framework to study many important problems related to probabilistic
systems. MDPs and SSGs with finite-horizon objectives, where the goal is to maximize
the probability to reach a target state in a given finite time, is a classical
and well-studied problem. In this work we consider the strategy complexity of
finite-horizon MDPs and SSGs. We show that for all ε > 0, the natural class of
counter-based strategies require at most log log/(1/ε) + n + 1 memory states,
and memory of size Omega(log log(1/ε) + n) is required, for ε-optimality, where
n is the number of states of the MDP (resp. SSG). Thus our bounds are asymptotically
optimal. We then study the periodic property of optimal strategies, and show a
sub-exponential lower bound on the period for optimal strategies.
acknowledgement: 'Work of the second author supported by the Sino-Danish Center for
the Theory of Interactive Computation, funded by the Danish National Research Foundation
and the National Science Foundation of China (under the grant 61061130540). The
second author acknowledge support from the Center for research in the Foundations
of Electronic Markets (CFEM), supported by the Danish Strategic Research Council.
The first author was supported by FWF Grant No P 23499-N23, FWF NFN Grant No S11407-N23
(RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 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: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
citation:
ama: 'Chatterjee K, Ibsen-Jensen R. Strategy complexity of finite-horizon Markov
decision processes and simple stochastic games. In: Mathematical and Engineering
Methods in Computer Science. Vol 7721. Springer Nature; 2013:106-117. doi:10.1007/978-3-642-36046-6_11'
apa: 'Chatterjee, K., & Ibsen-Jensen, R. (2013). Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games. In Mathematical and
Engineering Methods in Computer Science (Vol. 7721, pp. 106–117). Znojmo,
Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-642-36046-6_11'
chicago: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of
Finite-Horizon Markov Decision Processes and Simple Stochastic Games.” In Mathematical
and Engineering Methods in Computer Science, 7721:106–17. Springer Nature,
2013. https://doi.org/10.1007/978-3-642-36046-6_11.
ieee: K. Chatterjee and R. Ibsen-Jensen, “Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games,” in Mathematical and
Engineering Methods in Computer Science, Znojmo, Czech Republic, 2013, vol.
7721, pp. 106–117.
ista: 'Chatterjee K, Ibsen-Jensen R. 2013. Strategy complexity of finite-horizon
Markov decision processes and simple stochastic games. Mathematical and Engineering
Methods in Computer Science. MEMICS: Mathematical and Engineering Methods in Computer
Science, LNCS, vol. 7721, 106–117.'
mla: Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “Strategy Complexity of Finite-Horizon
Markov Decision Processes and Simple Stochastic Games.” Mathematical and Engineering
Methods in Computer Science, vol. 7721, Springer Nature, 2013, pp. 106–17,
doi:10.1007/978-3-642-36046-6_11.
short: K. Chatterjee, R. Ibsen-Jensen, in:, Mathematical and Engineering Methods
in Computer Science, Springer Nature, 2013, pp. 106–117.
conference:
end_date: 2012-10-28
location: Znojmo, Czech Republic
name: 'MEMICS: Mathematical and Engineering Methods in Computer Science'
start_date: 2012-10-25
corr_author: '1'
date_created: 2025-07-10T14:08:49Z
date_published: 2013-01-17T00:00:00Z
date_updated: 2025-09-23T09:24:13Z
day: '17'
department:
- _id: KrCh
doi: 10.1007/978-3-642-36046-6_11
ec_funded: 1
external_id:
arxiv:
- '1209.3617'
fulldoi: https://doi.org/10.1007/978-3-642-36046-6_11
intvolume: ' 7721'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1209.3617
month: '01'
oa: 1
oa_version: Preprint
page: 106-117
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Mathematical and Engineering Methods in Computer Science
publication_identifier:
eisbn:
- '9783642360466'
eissn:
- 1611-3349
isbn:
- '9783642360442'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategy complexity of finite-horizon Markov decision processes and simple
stochastic games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7721
year: '2013'
...
---
_id: '2009'
abstract:
- lang: eng
text: Traditional statistical methods for confidentiality protection of statistical
databases do not scale well to deal with GWAS databases especially in terms of
guarantees regarding protection from linkage to external information. The more
recent concept of differential privacy, introduced by the cryptographic community,
is an approach which provides a rigorous definition of privacy with meaningful
privacy guarantees in the presence of arbitrary external information, although
the guarantees may come at a serious price in terms of data utility. Building
on such notions, we propose new methods to release aggregate GWAS data without
compromising an individual’s privacy. We present methods for releasing differentially
private minor allele frequencies, chi-square statistics and p-values. We compare
these approaches on simulated data and on a GWAS study of canine hair length involving
685 dogs. We also propose a privacy-preserving method for finding genome-wide
associations based on a differentially-private approach to penalized logistic
regression.
article_processing_charge: No
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Aleksandra
full_name: Slavkovic, Aleksandra
last_name: Slavkovic
- first_name: Stephen
full_name: Fienberg, Stephen
last_name: Fienberg
citation:
ama: Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide
association studies. Journal of Privacy and Confidentiality . 2013;5(1):137-166.
doi:10.29012/jpc.v5i1.629
apa: Uhler, C., Slavkovic, A., & Fienberg, S. (2013). Privacy-preserving data
sharing for genome-wide association studies. Journal of Privacy and Confidentiality
. Carnegie Mellon University. https://doi.org/10.29012/jpc.v5i1.629
chicago: Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving
Data Sharing for Genome-Wide Association Studies.” Journal of Privacy and Confidentiality
. Carnegie Mellon University, 2013. https://doi.org/10.29012/jpc.v5i1.629.
ieee: C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing
for genome-wide association studies,” Journal of Privacy and Confidentiality
, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.
ista: Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for
genome-wide association studies. Journal of Privacy and Confidentiality . 5(1),
137–166.
mla: Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association
Studies.” Journal of Privacy and Confidentiality , vol. 5, no. 1, Carnegie
Mellon University, 2013, pp. 137–66, doi:10.29012/jpc.v5i1.629.
short: C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality 5
(2013) 137–166.
date_created: 2018-12-11T11:55:11Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2026-06-18T18:20:21Z
day: '01'
ddc:
- '000'
department:
- _id: CaUh
doi: 10.29012/jpc.v5i1.629
fulldoi: https://doi.org/10.29012/jpc.v5i1.629
intvolume: ' 5'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://repository.cmu.edu/jpc/vol5/iss1/6
month: '08'
oa: 1
oa_version: Published Version
page: 137 - 166
publication: 'Journal of Privacy and Confidentiality '
publication_status: published
publisher: Carnegie Mellon University
publist_id: '5067'
quality_controlled: '1'
status: public
title: Privacy-preserving data sharing for genome-wide association studies
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2013'
...
---
_id: '2010'
abstract:
- lang: eng
text: Many algorithms for inferring causality rely heavily on the faithfulness assumption.
The main justification for imposing this assumption is that the set of unfaithful
distributions has Lebesgue measure zero, since it can be seen as a collection
of hypersurfaces in a hypercube. However, due to sampling error the faithfulness
condition alone is not sufficient for statistical estimation, and strong-faithfulness
has been proposed and assumed to achieve uniform or high-dimensional consistency.
In contrast to the plain faithfulness assumption, the set of distributions that
is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly
large as we show in this paper. We study the strong-faithfulness condition from
a geometric and combinatorial point of view and give upper and lower bounds on
the Lebesgue measure of strong-faithful distributions for various classes of directed
acyclic graphs. Our results imply fundamental limitations for the PC-algorithm
and potentially also for other algorithms based on partial correlation testing
in the Gaussian case.
article_processing_charge: No
arxiv: 1
author:
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Garvesh
full_name: Raskutti, Garvesh
last_name: Raskutti
- first_name: Peter
full_name: Bühlmann, Peter
last_name: Bühlmann
- first_name: Bin
full_name: Yu, Bin
last_name: Yu
citation:
ama: Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption
in causal inference. The Annals of Statistics. 2013;41(2):436-463. doi:10.1214/12-AOS1080
apa: Uhler, C., Raskutti, G., Bühlmann, P., & Yu, B. (2013). Geometry of the
faithfulness assumption in causal inference. The Annals of Statistics.
Institute of Mathematical Statistics. https://doi.org/10.1214/12-AOS1080
chicago: Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry
of the Faithfulness Assumption in Causal Inference.” The Annals of Statistics.
Institute of Mathematical Statistics, 2013. https://doi.org/10.1214/12-AOS1080.
ieee: C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness
assumption in causal inference,” The Annals of Statistics, vol. 41, no.
2. Institute of Mathematical Statistics, pp. 436–463, 2013.
ista: Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness
assumption in causal inference. The Annals of Statistics. 41(2), 436–463.
mla: Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal
Inference.” The Annals of Statistics, vol. 41, no. 2, Institute of Mathematical
Statistics, 2013, pp. 436–63, doi:10.1214/12-AOS1080.
short: C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013)
436–463.
date_created: 2018-12-11T11:55:11Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2026-06-18T18:20:45Z
day: '01'
ddc:
- '500'
department:
- _id: CaUh
doi: 10.1214/12-AOS1080
external_id:
arxiv:
- '1207.0547'
isi:
- '000320488200002'
fulldoi: https://doi.org/10.1214/12-AOS1080
intvolume: ' 41'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: www.doi.org/10.1214/12-AOS1080
month: '04'
oa: 1
oa_version: Published Version
page: 436 - 463
publication: The Annals of Statistics
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '5066'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of the faithfulness assumption in causal inference
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2013'
...
---
_id: '10396'
abstract:
- lang: eng
text: Stimfit is a free cross-platform software package for viewing and analyzing
electrophysiological data. It supports most standard file types for cellular neurophysiology
and other biomedical formats. Its analysis algorithms have been used and validated
in several experimental laboratories. Its embedded Python scripting interface
makes Stimfit highly extensible and customizable.
article_number: '000010151520134181'
article_processing_charge: No
article_type: original
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: C.
full_name: Schmidt-Hieber, C.
last_name: Schmidt-Hieber
- first_name: S. J.
full_name: Guzman, S. J.
last_name: Guzman
citation:
ama: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 2013;58(SI-1-Track-G). doi:10.1515/bmt-2013-4181'
apa: 'Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., & Guzman, S. J. (2013).
Stimfit: A fast visualization and analysis environment for cellular neurophysiology.
Biomedical Engineering / Biomedizinische Technik. Graz, Austria: De Gruyter.
https://doi.org/10.1515/bmt-2013-4181'
chicago: 'Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit:
A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical
Engineering / Biomedizinische Technik. De Gruyter, 2013. https://doi.org/10.1515/bmt-2013-4181.'
ieee: 'A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A
fast visualization and analysis environment for cellular neurophysiology,” Biomedical
Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G. De Gruyter,
2013.'
ista: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.'
mla: 'Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment
for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik,
vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:10.1515/bmt-2013-4181.'
short: A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering
/ Biomedizinische Technik 58 (2013).
conference:
end_date: 2013-09-21
location: Graz, Austria
name: 'BMT: Biomedizinische Technik '
start_date: 2013-09-19
corr_author: '1'
date_created: 2021-12-01T14:35:35Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2025-09-30T07:31:23Z
day: '01'
ddc:
- '005'
- '610'
department:
- _id: PeJo
doi: 10.1515/bmt-2013-4181
external_id:
isi:
- '000497714000034'
pmid:
- '24042795'
file:
- access_level: open_access
checksum: cdfc5339b530a25d6079f7223f0b1f16
content_type: application/pdf
creator: schloegl
date_created: 2021-12-01T14:38:08Z
date_updated: 2021-12-01T14:38:08Z
file_id: '10397'
file_name: Schloegl_Abstract-BMT2013.pdf
file_size: 149825
relation: main_file
success: 1
file_date_updated: 2021-12-01T14:38:08Z
fulldoi: https://doi.org/10.1515/bmt-2013-4181
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: SI-1-Track-G
keyword:
- biomedical engineering
- data analysis
- free software
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Biomedical Engineering / Biomedizinische Technik
publication_identifier:
eissn:
- 1862-278X
issn:
- 0013-5585
publication_status: published
publisher: De Gruyter
quality_controlled: '1'
status: public
title: 'Stimfit: A fast visualization and analysis environment for cellular neurophysiology'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 58
year: '2013'
...
---
_id: '827'
abstract:
- lang: eng
text: As sessile organisms, plants have to be able to adapt to a continuously changing
environment. Plants that perceive some of these changes as stress signals activate
signaling pathways to modulate their development and to enable them to survive.
The complex responses to environmental cues are to a large extent mediated by
plant hormones that together orchestrate the final plant response. The phytohormone
cytokinin is involved in many plant developmental processes. Recently, it has
been established that cytokinin plays an important role in stress responses, but
does not act alone. Indeed, the hormonal control of plant development and stress
adaptation is the outcome of a complex network of multiple synergistic and antagonistic
interactions between various hormones. Here, we review the recent findings on
the cytokinin function as part of this hormonal network. We focus on the importance
of the crosstalk between cytokinin and other hormones, such as abscisic acid,
jasmonate, salicylic acid, ethylene, and auxin in the modulation of plant development
and stress adaptation. Finally, the impact of the current research in the biotechnological
industry will be discussed.
article_number: '451'
article_processing_charge: No
author:
- first_name: José
full_name: O'Brien, José
last_name: O'Brien
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: O’Brien J, Benková E. Cytokinin cross talking during biotic and abiotic stress
responses. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00451
apa: O’Brien, J., & Benková, E. (2013). Cytokinin cross talking during biotic
and abiotic stress responses. Frontiers in Plant Science. Frontiers Research
Foundation. https://doi.org/10.3389/fpls.2013.00451
chicago: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic
and Abiotic Stress Responses.” Frontiers in Plant Science. Frontiers Research
Foundation, 2013. https://doi.org/10.3389/fpls.2013.00451.
ieee: J. O’Brien and E. Benková, “Cytokinin cross talking during biotic and abiotic
stress responses,” Frontiers in Plant Science, vol. 4. Frontiers Research
Foundation, 2013.
ista: O’Brien J, Benková E. 2013. Cytokinin cross talking during biotic and abiotic
stress responses. Frontiers in Plant Science. 4, 451.
mla: O’Brien, José, and Eva Benková. “Cytokinin Cross Talking during Biotic and
Abiotic Stress Responses.” Frontiers in Plant Science, vol. 4, 451, Frontiers
Research Foundation, 2013, doi:10.3389/fpls.2013.00451.
short: J. O’Brien, E. Benková, Frontiers in Plant Science 4 (2013).
corr_author: '1'
date_created: 2018-12-11T11:48:43Z
date_published: 2013-11-19T00:00:00Z
date_updated: 2025-09-29T14:33:09Z
day: '19'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2013.00451
ec_funded: 1
external_id:
isi:
- '000331445200001'
file:
- access_level: open_access
checksum: fdc25ddd1bf9a99b99f662cdbafeddd4
content_type: application/pdf
creator: dernst
date_created: 2019-01-31T10:40:38Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5903'
file_name: 2013_FrontiersPlant_OBrien.pdf
file_size: 953299
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
fulldoi: https://doi.org/10.3389/fpls.2013.00451
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6821'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cytokinin cross talking during biotic and abiotic stress responses
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: 4
year: '2013'
...
---
_id: '828'
abstract:
- lang: eng
text: The plant root system is essential for providing anchorage to the soil, supplying
minerals and water, and synthesizing metabolites. It is a dynamic organ modulated
by external cues such as environmental signals, water and nutrients availability,
salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically,
after which they progress through discrete developmental stages which can be independently
controlled, providing a high level of plasticity during root system formation.
Within this review, main contributions are presented, from the classical forward
genetic screens to the more recent high-throughput approaches, combined with computer
model predictions, dissecting how LRs and thereby root system architecture is
established and developed.
article_number: '537'
article_processing_charge: No
author:
- first_name: Candela
full_name: Cuesta, Candela
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Cuesta C, Wabnik KT, Benková E. Systems approaches to study root architecture
dynamics. Frontiers in Plant Science. 2013;4. doi:10.3389/fpls.2013.00537
apa: Cuesta, C., Wabnik, K. T., & Benková, E. (2013). Systems approaches to
study root architecture dynamics. Frontiers in Plant Science. Frontiers
Research Foundation. https://doi.org/10.3389/fpls.2013.00537
chicago: Cuesta, Candela, Krzysztof T Wabnik, and Eva Benková. “Systems Approaches
to Study Root Architecture Dynamics.” Frontiers in Plant Science. Frontiers
Research Foundation, 2013. https://doi.org/10.3389/fpls.2013.00537.
ieee: C. Cuesta, K. T. Wabnik, and E. Benková, “Systems approaches to study root
architecture dynamics,” Frontiers in Plant Science, vol. 4. Frontiers Research
Foundation, 2013.
ista: Cuesta C, Wabnik KT, Benková E. 2013. Systems approaches to study root architecture
dynamics. Frontiers in Plant Science. 4, 537.
mla: Cuesta, Candela, et al. “Systems Approaches to Study Root Architecture Dynamics.”
Frontiers in Plant Science, vol. 4, 537, Frontiers Research Foundation,
2013, doi:10.3389/fpls.2013.00537.
short: C. Cuesta, K.T. Wabnik, E. Benková, Frontiers in Plant Science 4 (2013).
corr_author: '1'
date_created: 2018-12-11T11:48:43Z
date_published: 2013-12-26T00:00:00Z
date_updated: 2025-09-29T14:32:42Z
day: '26'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.3389/fpls.2013.00537
ec_funded: 1
external_id:
isi:
- '000331533500002'
file:
- access_level: open_access
checksum: 0185b3c4d7df9a94bd3ce5a66d213506
content_type: application/pdf
creator: dernst
date_created: 2019-01-31T10:36:43Z
date_updated: 2020-07-14T12:48:11Z
file_id: '5902'
file_name: 2013_FrontiersPlant_Cuesta.pdf
file_size: 710835
relation: main_file
file_date_updated: 2020-07-14T12:48:11Z
fulldoi: https://doi.org/10.3389/fpls.2013.00537
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: Frontiers in Plant Science
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6820'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Systems approaches to study root architecture dynamics
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: 4
year: '2013'
...
---
_id: '9459'
abstract:
- lang: eng
text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation
of transposable elements, but the reason for this is unknown. How DDM1 interacts
with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM),
which is thought to mediate plant asymmetric methylation through DRM enzymes,
is also unclear. Here, we show that most asymmetric methylation is facilitated
by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find
that heterochromatic sequences preferentially require DDM1 for DNA methylation
and that this preference depends on linker histone H1. RdDM is instead inhibited
by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together,
DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress
transposition and regulate the methylation and expression of genes. Our results
indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin
to allow stable silencing of transposable elements in cooperation with the RdDM
pathway.
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: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Ka
full_name: Thao, Ka
last_name: Thao
- first_name: Stacey L.
full_name: Harmer, Stacey L.
last_name: Harmer
- 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, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1
allows DNA methyltransferases to access H1-containing heterochromatin. Cell.
2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033
apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L.,
Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.02.033
chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor
Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis
Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing
Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033.
ieee: A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin,” Cell,
vol. 153, no. 1. Elsevier, pp. 193–205, 2013.
ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer
SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases
to access H1-containing heterochromatin. Cell. 153(1), 193–205.
mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA
Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol.
153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033.
short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K.
Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.
date_created: 2021-06-04T12:23:28Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2021-12-14T08:25:35Z
day: '28'
department:
- _id: DaZi
doi: 10.1016/j.cell.2013.02.033
extern: '1'
external_id:
pmid:
- '23540698'
fulldoi: https://doi.org/10.1016/j.cell.2013.02.033
intvolume: ' 153'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.02.033
month: '03'
oa: 1
oa_version: Published Version
page: 193-205
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to
access H1-containing heterochromatin
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 153
year: '2013'
...
---
_id: '9481'
abstract:
- lang: eng
text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo,
exhibits extensive localized DNA demethylation on maternally inherited chromosomes.
Demethylation mediates parent-of-origin–specific (imprinted) gene expression but
is apparently unnecessary for the extensive accumulation of maternally biased
small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related
monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation
is generally parent-of-origin specific is unknown. Imprinted expression of sRNA
also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing
of the Kitaake rice cultivar that enabled us to show that localized hypomethylation
in rice endosperm occurs solely on the maternal genome, preferring regions of
high DNA accessibility. Maternally expressed imprinted genes are enriched for
hypomethylation at putative promoter regions and transcriptional termini and paternally
expressed genes at promoters and gene bodies, mirroring our recent results in
A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are
dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are
expressed from both parental genomes and correlate with hypomethylation. Overlaps
between imprinted sRNA loci and imprinted genes expressed from opposite alleles
suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling
tissues primarily originate from small class II (cut-and-paste) transposable elements,
those in endosperm are more uniformly derived, including sequences from other
transposon classes, as well as genic and intergenic regions. Our data indicate
that the endosperm exhibits a unique pattern of sRNA expression and suggest that
localized hypomethylation of maternal endosperm DNA is conserved in flowering
plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Randy
full_name: Ruan, Randy
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: Pamela C
full_name: Ronald, Pamela C
last_name: Ronald
- 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: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and
small RNA is associated with localized hypomethylation of the maternal genome
in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939.
doi:10.1073/pnas.1306164110
apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald,
P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is
associated with localized hypomethylation of the maternal genome in rice endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1306164110
chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma,
Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted
Expression of Genes and Small RNA Is Associated with Localized Hypomethylation
of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA
is associated with localized hypomethylation of the maternal genome in rice endosperm,”
Proceedings of the National Academy of Sciences, vol. 110, no. 19. National
Academy of Sciences, pp. 7934–7939, 2013.
ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer
RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated
with localized hypomethylation of the maternal genome in rice endosperm. Proceedings
of the National Academy of Sciences. 110(19), 7934–7939.
mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA
Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 110, no. 19, National
Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.
short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald,
R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110
(2013) 7934–7939.
date_created: 2021-06-07T07:31:02Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-12-14T08:26:44Z
day: '07'
department:
- _id: DaZi
doi: 10.1073/pnas.1306164110
extern: '1'
external_id:
pmid:
- '23613580'
fulldoi: https://doi.org/10.1073/pnas.1306164110
intvolume: ' 110'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1306164110
month: '05'
oa: 1
oa_version: Published Version
page: 7934-7939
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: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 110
year: '2013'
...
---
_id: '9520'
abstract:
- lang: eng
text: Plants undergo alternation of generation in which reproductive cells develop
in the plant body ("sporophytic generation") and then differentiate into a multicellular
gamete-forming "gametophytic generation." Different populations of helper cells
assist in this transgenerational journey, with somatic tissues supporting early
development and single nurse cells supporting gametogenesis. New data reveal a
two-way relationship between early reproductive cells and their helpers involving
complex epigenetic and signaling networks determining cell number and fate. Later,
the egg cell plays a central role in specifying accessory cells, whereas in both
gametophytes, companion cells contribute non-cell-autonomously to the epigenetic
landscape of the gamete genomes.
article_processing_charge: No
article_type: review
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Hugh
full_name: Dickinson, Hugh
last_name: Dickinson
citation:
ama: 'Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ
cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014'
apa: 'Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across
generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2013.01.014'
chicago: 'Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across
Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier,
2013. https://doi.org/10.1016/j.devcel.2013.01.014.'
ieee: 'X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations:
Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3.
Elsevier, pp. 215–225, 2013.'
ista: 'Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations:
Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.'
mla: 'Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk
in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25,
doi:10.1016/j.devcel.2013.01.014.'
short: X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.
date_created: 2021-06-08T06:14:50Z
date_published: 2013-02-11T00:00:00Z
date_updated: 2023-05-08T11:00:59Z
day: '11'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.devcel.2013.01.014
extern: '1'
external_id:
pmid:
- '23410937'
fulldoi: https://doi.org/10.1016/j.devcel.2013.01.014
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2013.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 215-225
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A conversation across generations: Soma-germ cell crosstalk in plants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '9749'
abstract:
- lang: eng
text: Cooperative behavior, where one individual incurs a cost to help another,
is a wide spread phenomenon. Here we study direct reciprocity in the context of
the alternating Prisoner's Dilemma. We consider all strategies that can be implemented
by one and two-state automata. We calculate the payoff matrix of all pairwise
encounters in the presence of noise. We explore deterministic selection dynamics
with and without mutation. Using different error rates and payoff values, we observe
convergence to a small number of distinct equilibria. Two of them are uncooperative
strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium
is mixed and represents a cooperative alliance of several strategies, dominated
by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent
has cooperated; it defects once when the opponent has defected, but subsequently
Forgiver attempts to re-establish cooperation even if the opponent has defected
again. Forgiver is not an evolutionarily stable strategy, but the alliance, which
it rules, is asymptotically stable. For a wide range of parameter values the most
commonly observed outcome is convergence to the mixed equilibrium, dominated by
Forgiver. Our results show that although forgiving might incur a short-term loss
it can lead to a long-term gain. Forgiveness facilitates stable cooperation in
the presence of exploitation and noise.
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Zagorsky, Benjamin
last_name: Zagorsky
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating
prisoner’s dilemma . 2013. doi:10.1371/journal.pone.0080814.s001
apa: Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver
triumphs in alternating prisoner’s dilemma . Public Library of Science. https://doi.org/10.1371/journal.pone.0080814.s001
chicago: Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin
Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library
of Science, 2013. https://doi.org/10.1371/journal.pone.0080814.s001.
ieee: B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in
alternating prisoner’s dilemma .” Public Library of Science, 2013.
ista: Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating
prisoner’s dilemma , Public Library of Science, 10.1371/journal.pone.0080814.s001.
mla: Zagorsky, Benjamin, et al. Forgiver Triumphs in Alternating Prisoner’s Dilemma
. Public Library of Science, 2013, doi:10.1371/journal.pone.0080814.s001.
short: B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).
date_created: 2021-07-28T15:45:07Z
date_published: 2013-12-12T00:00:00Z
date_updated: 2025-09-29T14:30:03Z
day: '12'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0080814.s001
fulldoi: https://doi.org/10.1371/journal.pone.0080814.s001
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2247'
relation: used_in_publication
status: public
status: public
title: 'Forgiver triumphs in alternating prisoner''s dilemma '
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '9751'
abstract:
- lang: eng
text: High relatedness among interacting individuals has generally been considered
a precondition for the evolution of altruism. However, kin-selection theory also
predicts the evolution of altruism when relatedness is low, as long as the cost
of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence
for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding
to the attack of an obligately lytic phage by committing suicide in order to prevent
parasite transmission to nearby relatives. We found that bacterial suicide provides
large benefits to survivors at marginal costs to committers. The cost of suicide
was low because infected cells are moribund, rapidly dying upon phage infection,
such that no more opportunity for reproduction remains. As a consequence of its
marginal cost, host suicide was selectively favoured even when relatedness between
committers and survivors approached zero. Altogether, our findings demonstrate
that low-cost suicide can evolve with ease, represents an effective host-defence
strategy, and seems to be widespread among microbes. Moreover, low-cost suicide
might also occur in higher organisms as exemplified by infected social insect
workers leaving the colony to die in isolation.
article_processing_charge: No
author:
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
citation:
ama: 'Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness
is low: evidence from bacteria committing suicide upon phage infection. 2013.
doi:10.5061/dryad.b1q2n'
apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Data from: Altruism
can evolve when relatedness is low: evidence from bacteria committing suicide
upon phage infection. Dryad. https://doi.org/10.5061/dryad.b1q2n'
chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism
Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide
upon Phage Infection.” Dryad, 2013. https://doi.org/10.5061/dryad.b1q2n.'
ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection.” Dryad, 2013.'
ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection, Dryad, 10.5061/dryad.b1q2n.'
mla: 'Refardt, Dominik, et al. Data from: Altruism Can Evolve When Relatedness
Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection. Dryad,
2013, doi:10.5061/dryad.b1q2n.'
short: D. Refardt, T. Bergmiller, R. Kümmerli, (2013).
date_created: 2021-07-30T08:08:09Z
date_published: 2013-03-21T00:00:00Z
date_updated: 2025-09-29T13:41:12Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.b1q2n
fulldoi: https://doi.org/10.5061/dryad.b1q2n
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.b1q2n
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2853'
relation: used_in_publication
status: public
status: public
title: 'Data from: Altruism can evolve when relatedness is low: evidence from bacteria
committing suicide upon phage infection'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '9754'
abstract:
- lang: eng
text: Short-read sequencing technologies have in principle made it feasible to draw
detailed inferences about the recent history of any organism. In practice, however,
this remains challenging due to the difficulty of genome assembly in most organisms
and the lack of statistical methods powerful enough to discriminate among recent,
non-equilibrium histories. We address both the assembly and inference challenges.
We develop a bioinformatic pipeline for generating outgroup-rooted alignments
of orthologous sequence blocks from de novo low-coverage short-read data for a
small number of genomes, and show how such sequence blocks can be used to fit
explicit models of population divergence and admixture in a likelihood framework.
To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding
insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa,
was restricted during Pleistocene ice ages to a longitudinal series of southern
refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled
from a single genome from each of three major glacial refugia reveals support
for an unexpected history dominated by recent admixture. Despite the fact that
80% of the genome is affected by admixture during the last glacial cycle, we are
able to infer the deeper divergence history of these populations. These inferences
are robust to variation in block length, mutation model, and the sampling location
of individual genomes within refugia. This combination of de novo assembly and
numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.
article_processing_charge: No
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- 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: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
citation:
ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies. 2013.
doi:10.5061/dryad.r3r60'
apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013).
Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60'
chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey
Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low
Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.'
ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from:
Likelihood-based inference of population history from low coverage de novo genome
assemblies.” Dryad, 2013.'
ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies, Dryad,
10.5061/dryad.r3r60.'
mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population
History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.'
short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).
date_created: 2021-07-30T08:31:22Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2025-09-29T11:38:51Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.r3r60
fulldoi: https://doi.org/10.5061/dryad.r3r60
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.r3r60
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2170'
relation: used_in_publication
status: public
status: public
title: 'Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '6440'
abstract:
- lang: eng
text: In order to guarantee that each method of a data structure updates the logical
state exactly once, al-most all non-blocking implementations employ Compare-And-Swap
(CAS) based synchronization. For FIFO queue implementations this translates into concurrent enqueue or dequeue methods
competing among themselves to update the same variable, the tail or the head,
respectively, leading to high contention and poor scalability. Recent non-blocking
queue implementations try to alleviate high contentionby increasing the number
of contention points, all the while using CAS-based synchronization. Furthermore,
obtaining a wait-free implementation with competition is achieved by additional
synchronization which leads to further degradation of performance.In this paper
we formalize the notion of competitiveness of a synchronizing statement which
can beused as a measure for the scalability of concurrent implementations. We
present a new queue implementation, the Speculative Pairing (SP) queue, which,
as we show, decreases competitiveness by using Fetch-And-Increment (FAI) instead
of CAS. We prove that the SP queue is linearizable and lock-free.We also show
that replacing CAS with FAI leads to wait-freedom for dequeue methods without
an adverse effect on performance. In fact, our experiments suggest that the SP
queue can perform and scale better than the state-of-the-art queue implementations.
alternative_title:
- IST Austria Technical Report
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: Hannes
full_name: Payer, Hannes
last_name: Payer
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: Henzinger TA, Payer H, Sezgin A. Replacing Competition with Cooperation
to Achieve Scalable Lock-Free FIFO Queues . IST Austria; 2013. doi:10.15479/AT:IST-2013-124-v1-1
apa: Henzinger, T. A., Payer, H., & Sezgin, A. (2013). Replacing competition
with cooperation to achieve scalable lock-free FIFO queues . IST Austria.
https://doi.org/10.15479/AT:IST-2013-124-v1-1
chicago: Henzinger, Thomas A, Hannes Payer, and Ali Sezgin. Replacing Competition
with Cooperation to Achieve Scalable Lock-Free FIFO Queues . IST Austria,
2013. https://doi.org/10.15479/AT:IST-2013-124-v1-1.
ieee: T. A. Henzinger, H. Payer, and A. Sezgin, Replacing competition with cooperation
to achieve scalable lock-free FIFO queues . IST Austria, 2013.
ista: Henzinger TA, Payer H, Sezgin A. 2013. Replacing competition with cooperation
to achieve scalable lock-free FIFO queues , IST Austria, 23p.
mla: Henzinger, Thomas A., et al. Replacing Competition with Cooperation to Achieve
Scalable Lock-Free FIFO Queues . IST Austria, 2013, doi:10.15479/AT:IST-2013-124-v1-1.
short: T.A. Henzinger, H. Payer, A. Sezgin, Replacing Competition with Cooperation
to Achieve Scalable Lock-Free FIFO Queues , IST Austria, 2013.
date_created: 2019-05-13T14:13:27Z
date_published: 2013-06-13T00:00:00Z
date_updated: 2020-07-14T23:06:19Z
day: '13'
ddc:
- '000'
- '005'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2013-124-v1-1
file:
- access_level: open_access
checksum: a219ba4eada6cd62befed52262ee15d4
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T14:11:39Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6441'
file_name: 2013_TechRep_Henzinger.pdf
file_size: 549684
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
fulldoi: https://doi.org/10.15479/AT:IST-2013-124-v1-1
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '23'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '124'
status: public
title: 'Replacing competition with cooperation to achieve scalable lock-free FIFO
queues '
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '3116'
abstract:
- lang: eng
text: Multithreaded programs coordinate their interaction through synchronization
primitives like mutexes and semaphores, which are managed by an OS-provided resource
manager. We propose algorithms for the automatic construction of code-aware resource
managers for multithreaded embedded applications. Such managers use knowledge
about the structure and resource usage (mutex and semaphore usage) of the threads
to guarantee deadlock freedom and progress while managing resources in an efficient
way. Our algorithms compute managers as winning strategies in certain infinite
games, and produce a compact code description of these strategies. We have implemented
the algorithms in the tool Cynthesis. Given a multithreaded program in C, the
tool produces C code implementing a code-aware resource manager. We show in experiments
that Cynthesis produces compact resource managers within a few minutes on a set
of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business
Media, LLC.
acknowledgement: This research was supported in part by the National Science Foundation
CAREER award CCR-0132780, by the ONR grant N00014-02-1-0671, by the National Science
Foundation grants CCR-0427202 and CCR-0234690, and by the ARP award TO.030.MM.D.
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full_name: Chatterjee, Krishnendu
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- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Marco
full_name: Faella, Marco
last_name: Faella
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Vishwanath
full_name: Raman, Vishwanath
last_name: Raman
citation:
ama: Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. Code aware resource
management. Formal Methods in System Design. 2013;42(2):142-174. doi:10.1007/s10703-012-0170-4
apa: Chatterjee, K., De Alfaro, L., Faella, M., Majumdar, R., & Raman, V. (2013).
Code aware resource management. Formal Methods in System Design. Springer.
https://doi.org/10.1007/s10703-012-0170-4
chicago: Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Ritankar Majumdar,
and Vishwanath Raman. “Code Aware Resource Management.” Formal Methods in System
Design. Springer, 2013. https://doi.org/10.1007/s10703-012-0170-4.
ieee: K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, and V. Raman, “Code aware
resource management,” Formal Methods in System Design, vol. 42, no. 2.
Springer, pp. 142–174, 2013.
ista: Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. 2013. Code aware
resource management. Formal Methods in System Design. 42(2), 142–174.
mla: Chatterjee, Krishnendu, et al. “Code Aware Resource Management.” Formal
Methods in System Design, vol. 42, no. 2, Springer, 2013, pp. 142–74, doi:10.1007/s10703-012-0170-4.
short: K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, V. Raman, Formal Methods
in System Design 42 (2013) 142–174.
date_created: 2018-12-11T12:01:29Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2025-09-29T13:24:54Z
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---
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abstract:
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text: Cells in a developing embryo have no direct way of "measuring" their
physical position. Through a variety of processes, however, the expression levels
of multiple genes come to be correlated with position, and these expression levels
thus form a code for "positional information." We show how to measure
this information, in bits, using the gap genes in the Drosophila embryo as an
example. Individual genes carry nearly two bits of information, twice as much
as expected if the expression patterns consisted only of on/off domains separated
by sharp boundaries. Taken together, four gap genes carry enough information to
define a cell's location with an error bar of ~1% along the anterior-posterior
axis of the embryo. This precision is nearly enough for each cell to have a unique
identity, which is the maximum information the system can use, and is nearly constant
along the length of the embryo. We argue that this constancy is a signature of
optimality in the transmission of information from primary morphogen inputs to
the output of the gap gene network.
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last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Eric
full_name: Wieschaus, Eric
last_name: Wieschaus
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full_name: Gregor, Thomas
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- first_name: William
full_name: Bialek, William
last_name: Bialek
citation:
ama: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information,
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apa: Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., & Bialek, W. (2013).
Positional information, in bits. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315642110
chicago: Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William
Bialek. “Positional Information, in Bits.” PNAS. National Academy of Sciences,
2013. https://doi.org/10.1073/pnas.1315642110.
ieee: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional
information, in bits,” PNAS, vol. 110, no. 41. National Academy of Sciences,
pp. 16301–16308, 2013.
ista: Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information,
in bits. PNAS. 110(41), 16301–16308.
mla: Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol.
110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.
short: J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013)
16301–16308.
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date_published: 2013-10-08T00:00:00Z
date_updated: 2025-09-29T13:24:21Z
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ddc:
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doi: 10.1073/pnas.1315642110
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title: Positional information, in bits
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...
---
_id: '3321'
author:
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer
O, Cho K, Yokota H, eds. Encyclopedia of Systems Biology. Vol 3. Springer;
2013:1069-1069. doi:10.1007/978-1-4419-9863-7_604'
apa: Quadrianto, N., & Lampert, C. (2013). Kernel based learning. In W. Dubitzky,
O. Wolkenhauer, K. Cho, & H. Yokota (Eds.), Encyclopedia of Systems Biology
(Vol. 3, pp. 1069–1069). Springer. https://doi.org/10.1007/978-1-4419-9863-7_604
chicago: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In Encyclopedia
of Systems Biology, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho,
and Hiroki Yokota, 3:1069–1069. Springer, 2013. https://doi.org/10.1007/978-1-4419-9863-7_604.
ieee: N. Quadrianto and C. Lampert, “Kernel based learning,” in Encyclopedia
of Systems Biology, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota,
Eds. Springer, 2013, pp. 1069–1069.
ista: 'Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of
Systems Biology. vol. 3, 1069–1069.'
mla: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” Encyclopedia
of Systems Biology, edited by Werner Dubitzky et al., vol. 3, Springer, 2013,
pp. 1069–1069, doi:10.1007/978-1-4419-9863-7_604.
short: N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota
(Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069.
date_created: 2018-12-11T12:02:39Z
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- first_name: Hiroki
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