---
_id: '4543'
abstract:
- lang: eng
  text: The synthesis of a reactive system with respect to all omega-regular specification
    requires the solution of a graph game. Such games have been extended in two natural
    ways. First, a game graph can be equipped with probabilistic choices between alternative
    transitions, thus allowing the, modeling of uncertain behaviour. These are called
    stochastic games. Second, a liveness specification can he strengthened to require
    satisfaction within all unknown but bounded amount of time. These are called finitary
    objectives. We study. for the first time, the, combination of Stochastic games
    and finitary objectives. We characterize the requirements on optimal strategies
    and provide algorithms for Computing the maximal achievable probability of winning
    stochastic games with finitary parity or Street, objectives. Most notably the
    set of state's from which a player can win with probability . for a finitary parity
    objective can he computed in polynomial time even though no polynomial-time algorithm
    is known in the nonfinitary case.
acknowledgement: This research was supported in part by the Swiss National Science
  Foundation under the Indo-Swiss Joint Research Programme, by the European Network
  of Excellence on Embedded Systems Design (ArtistDesign), and by the European project
  Combest.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Florian
  full_name: Horn, Florian
  id: 37327ACE-F248-11E8-B48F-1D18A9856A87
  last_name: Horn
citation:
  ama: 'Chatterjee K, Henzinger TA, Horn F. Stochastic games with finitary objectives.
    In: Vol 5734. Springer; 2009:34-54. doi:<a href="https://doi.org/10.1007/978-3-642-03816-7_4">10.1007/978-3-642-03816-7_4</a>'
  apa: 'Chatterjee, K., Henzinger, T. A., &#38; Horn, F. (2009). Stochastic games
    with finitary objectives (Vol. 5734, pp. 34–54). Presented at the MFCS: Mathematical
    Foundations of Computer Science, High Tatras, Slovakia: Springer. <a href="https://doi.org/10.1007/978-3-642-03816-7_4">https://doi.org/10.1007/978-3-642-03816-7_4</a>'
  chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Stochastic
    Games with Finitary Objectives,” 5734:34–54. Springer, 2009. <a href="https://doi.org/10.1007/978-3-642-03816-7_4">https://doi.org/10.1007/978-3-642-03816-7_4</a>.
  ieee: 'K. Chatterjee, T. A. Henzinger, and F. Horn, “Stochastic games with finitary
    objectives,” presented at the MFCS: Mathematical Foundations of Computer Science,
    High Tatras, Slovakia, 2009, vol. 5734, pp. 34–54.'
  ista: 'Chatterjee K, Henzinger TA, Horn F. 2009. Stochastic games with finitary
    objectives. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 5734,
    34–54.'
  mla: Chatterjee, Krishnendu, et al. <i>Stochastic Games with Finitary Objectives</i>.
    Vol. 5734, Springer, 2009, pp. 34–54, doi:<a href="https://doi.org/10.1007/978-3-642-03816-7_4">10.1007/978-3-642-03816-7_4</a>.
  short: K. Chatterjee, T.A. Henzinger, F. Horn, in:, Springer, 2009, pp. 34–54.
conference:
  end_date: 2009-08-28
  location: High Tatras, Slovakia
  name: 'MFCS: Mathematical Foundations of Computer Science'
  start_date: 2009-08-24
date_created: 2018-12-11T12:09:24Z
date_published: 2009-08-01T00:00:00Z
date_updated: 2021-01-12T07:59:35Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-642-03816-7_4
ec_funded: 1
intvolume: '      5734'
language:
- iso: eng
month: '08'
oa_version: None
page: 34 - 54
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '215543'
  name: COMponent-Based Embedded Systems design Techniques
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '214373'
  name: Design for Embedded Systems
publication_status: published
publisher: Springer
publist_id: '178'
quality_controlled: '1'
scopus_import: 1
status: public
title: Stochastic games with finitary objectives
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5734
year: '2009'
...
---
_id: '4545'
abstract:
- lang: eng
  text: 'A stochastic game is a two-player game played oil a graph, where in each
    state the successor is chosen either by One of the players, or according to a
    probability distribution. We Survey Stochastic games with limsup and liminf objectives.
    A real-valued re-ward is assigned to each state, and the value of all infinite
    path is the limsup (resp. liminf) of all rewards along the path. The value of
    a stochastic game is the maximal expected value of an infinite path that call
    he achieved by resolving the decisions of the first player. We present the complexity
    of computing values of Stochastic games and their subclasses, and the complexity,
    of optimal strategies in such games. '
acknowledgement: This research was supported in part by the Swiss National Science
  Foundation under the Indo-Swiss Joint Research Programme, by the European Network
  of Excellence on Embedded Systems Design (ArtistDesign), by the European projects
  COMBEST, Quasimodo, Gasics, by the PAI program Moves funded by the Belgian Federal
  Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Laurent
  full_name: Doyen, Laurent
  last_name: Doyen
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
citation:
  ama: 'Chatterjee K, Doyen L, Henzinger TA. A survey of stochastic games with limsup
    and liminf objectives. In: Vol 5556. Springer; 2009:1-15. doi:<a href="https://doi.org/10.1007/978-3-642-02930-1_1">10.1007/978-3-642-02930-1_1</a>'
  apa: 'Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). A survey of stochastic
    games with limsup and liminf objectives (Vol. 5556, pp. 1–15). Presented at the
    ICALP: Automata, Languages and Programming, Rhodos, Greece: Springer. <a href="https://doi.org/10.1007/978-3-642-02930-1_1">https://doi.org/10.1007/978-3-642-02930-1_1</a>'
  chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey
    of Stochastic Games with Limsup and Liminf Objectives,” 5556:1–15. Springer, 2009.
    <a href="https://doi.org/10.1007/978-3-642-02930-1_1">https://doi.org/10.1007/978-3-642-02930-1_1</a>.
  ieee: 'K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of stochastic games
    with limsup and liminf objectives,” presented at the ICALP: Automata, Languages
    and Programming, Rhodos, Greece, 2009, vol. 5556, pp. 1–15.'
  ista: 'Chatterjee K, Doyen L, Henzinger TA. 2009. A survey of stochastic games with
    limsup and liminf objectives. ICALP: Automata, Languages and Programming, LNCS,
    vol. 5556, 1–15.'
  mla: Chatterjee, Krishnendu, et al. <i>A Survey of Stochastic Games with Limsup
    and Liminf Objectives</i>. Vol. 5556, Springer, 2009, pp. 1–15, doi:<a href="https://doi.org/10.1007/978-3-642-02930-1_1">10.1007/978-3-642-02930-1_1</a>.
  short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 1–15.
conference:
  end_date: 2009-07-12
  location: Rhodos, Greece
  name: 'ICALP: Automata, Languages and Programming'
  start_date: 2009-07-05
date_created: 2018-12-11T12:09:24Z
date_published: 2009-06-24T00:00:00Z
date_updated: 2021-01-12T07:59:35Z
day: '24'
ddc:
- '000'
- '005'
department:
- _id: KrCh
doi: 10.1007/978-3-642-02930-1_1
ec_funded: 1
file:
- access_level: open_access
  checksum: dabb6d24428a000254c95493d9c492e6
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T10:13:11Z
  date_updated: 2020-07-14T12:46:31Z
  file_id: '4992'
  file_name: IST-2012-38-v1+1_A_survey_of_stochastic_games_with_limsup_and_liminf_objectives.pdf
  file_size: 187419
  relation: main_file
file_date_updated: 2020-07-14T12:46:31Z
has_accepted_license: '1'
intvolume: '      5556'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 1 - 15
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '215543'
  name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: Springer
publist_id: '177'
pubrep_id: '38'
quality_controlled: '1'
scopus_import: 1
status: public
title: A survey of stochastic games with limsup and liminf objectives
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5556
year: '2009'
...
---
_id: '4569'
abstract:
- lang: eng
  text: "Most specification languages express only qualitative constraints. However,
    among two implementations that satisfy a given specification, one may be preferred
    to another. For example, if a specification asks that every request is followed
    by a response, one may prefer an implementation that generates responses quickly
    but does not generate unnecessary responses. We use quantitative properties to
    measure the “goodness” of an implementation. Using games with corresponding quantitative
    objectives, we can synthesize “optimal” implementations, which are preferred among
    the set of possible implementations that satisfy a given specification.\r\nIn
    particular, we show how automata with lexicographic mean-payoff conditions can
    be used to express many interesting quantitative properties for reactive systems.
    In this framework, the synthesis of optimal implementations requires the solution
    of lexicographic mean-payoff games (for safety requirements), and the solution
    of games with both lexicographic mean-payoff and parity objectives (for liveness
    requirements). We present algorithms for solving both kinds of novel graph games."
acknowledgement: This research was supported by the Swiss National Science Foundation
  (Indo-Swiss Research Program and NCCR MICS) and the European Union projects COMBEST
  and COCONUT.
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Roderick
  full_name: Bloem, Roderick
  last_name: Bloem
- first_name: Krishnendu
  full_name: Chatterjee, Krishnendu
  id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
  last_name: Chatterjee
  orcid: 0000-0002-4561-241X
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Barbara
  full_name: Jobstmann, Barbara
  last_name: Jobstmann
citation:
  ama: 'Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. Better quality in synthesis
    through quantitative objectives. In: Vol 5643. Springer; 2009:140-156. doi:<a
    href="https://doi.org/10.1007/978-3-642-02658-4_14">10.1007/978-3-642-02658-4_14</a>'
  apa: 'Bloem, R., Chatterjee, K., Henzinger, T. A., &#38; Jobstmann, B. (2009). Better
    quality in synthesis through quantitative objectives (Vol. 5643, pp. 140–156).
    Presented at the CAV: Computer Aided Verification, Grenoble, France: Springer.
    <a href="https://doi.org/10.1007/978-3-642-02658-4_14">https://doi.org/10.1007/978-3-642-02658-4_14</a>'
  chicago: Bloem, Roderick, Krishnendu Chatterjee, Thomas A Henzinger, and Barbara
    Jobstmann. “Better Quality in Synthesis through Quantitative Objectives,” 5643:140–56.
    Springer, 2009. <a href="https://doi.org/10.1007/978-3-642-02658-4_14">https://doi.org/10.1007/978-3-642-02658-4_14</a>.
  ieee: 'R. Bloem, K. Chatterjee, T. A. Henzinger, and B. Jobstmann, “Better quality
    in synthesis through quantitative objectives,” presented at the CAV: Computer
    Aided Verification, Grenoble, France, 2009, vol. 5643, pp. 140–156.'
  ista: 'Bloem R, Chatterjee K, Henzinger TA, Jobstmann B. 2009. Better quality in
    synthesis through quantitative objectives. CAV: Computer Aided Verification, LNCS,
    vol. 5643, 140–156.'
  mla: Bloem, Roderick, et al. <i>Better Quality in Synthesis through Quantitative
    Objectives</i>. Vol. 5643, Springer, 2009, pp. 140–56, doi:<a href="https://doi.org/10.1007/978-3-642-02658-4_14">10.1007/978-3-642-02658-4_14</a>.
  short: R. Bloem, K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009,
    pp. 140–156.
conference:
  end_date: 2009-07-02
  location: Grenoble, France
  name: 'CAV: Computer Aided Verification'
  start_date: 2009-06-26
date_created: 2018-12-11T12:09:31Z
date_published: 2009-06-19T00:00:00Z
date_updated: 2021-01-12T07:59:46Z
day: '19'
department:
- _id: KrCh
doi: 10.1007/978-3-642-02658-4_14
ec_funded: 1
external_id:
  arxiv:
  - '0904.2638'
intvolume: '      5643'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://arxiv.org/abs/0904.2638
month: '06'
oa: 1
oa_version: Preprint
page: 140 - 156
project:
- _id: 25EFB36C-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '215543'
  name: COMponent-Based Embedded Systems design Techniques
publication_status: published
publisher: Springer
publist_id: '141'
quality_controlled: '1'
status: public
title: Better quality in synthesis through quantitative objectives
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 5643
year: '2009'
...
---
_id: '5392'
abstract:
- lang: eng
  text: We consider probabilistic automata on infinite words with acceptance defined
    by safety, reachability, Büchi, coBüchi and limit-average conditions. We consider
    quantitative and qualitative decision problems. We present extensions and adaptations
    of proofs of [GO09] and present a precise characterization of the decidability
    and undecidability frontier of the quantitative and qualitative decision problems.
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
citation:
  ama: 'Chatterjee K. <i>Probabilistic Automata on Infinite Words: Decidability and
    Undecidability Results</i>. IST Austria; 2009. doi:<a href="https://doi.org/10.15479/AT:IST-2009-0004">10.15479/AT:IST-2009-0004</a>'
  apa: 'Chatterjee, K. (2009). <i>Probabilistic automata on infinite words: Decidability
    and undecidability results</i>. IST Austria. <a href="https://doi.org/10.15479/AT:IST-2009-0004">https://doi.org/10.15479/AT:IST-2009-0004</a>'
  chicago: 'Chatterjee, Krishnendu. <i>Probabilistic Automata on Infinite Words: Decidability
    and Undecidability Results</i>. IST Austria, 2009. <a href="https://doi.org/10.15479/AT:IST-2009-0004">https://doi.org/10.15479/AT:IST-2009-0004</a>.'
  ieee: 'K. Chatterjee, <i>Probabilistic automata on infinite words: Decidability
    and undecidability results</i>. IST Austria, 2009.'
  ista: 'Chatterjee K. 2009. Probabilistic automata on infinite words: Decidability
    and undecidability results, IST Austria, 17p.'
  mla: 'Chatterjee, Krishnendu. <i>Probabilistic Automata on Infinite Words: Decidability
    and Undecidability Results</i>. IST Austria, 2009, doi:<a href="https://doi.org/10.15479/AT:IST-2009-0004">10.15479/AT:IST-2009-0004</a>.'
  short: 'K. Chatterjee, Probabilistic Automata on Infinite Words: Decidability and
    Undecidability Results, IST Austria, 2009.'
date_created: 2018-12-12T11:39:04Z
date_published: 2009-11-02T00:00:00Z
date_updated: 2023-02-23T11:45:44Z
day: '02'
ddc:
- '005'
department:
- _id: KrCh
doi: 10.15479/AT:IST-2009-0004
file:
- access_level: open_access
  checksum: fb7563150231325b00b1718d956f687b
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T11:54:08Z
  date_updated: 2020-07-14T12:46:43Z
  file_id: '5530'
  file_name: IST-2009-0004_IST-2009-0004.pdf
  file_size: 311065
  relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '17'
publication_identifier:
  issn:
  - 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '28'
related_material:
  record:
  - id: '3857'
    relation: later_version
    status: public
status: public
title: 'Probabilistic automata on infinite words: Decidability and undecidability
  results'
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '5393'
abstract:
- lang: eng
  text: Gist is a tool that (a) solves the qualitative analysis problem of turn-based
    probabilistic games with ω-regular objectives; and (b) synthesizes reasonable
    environment assumptions for synthesis of unrealizable specifications. Our tool
    provides efficient implementations of several reduction based techniques to solve
    turn-based probabilistic games, and uses the analysis of turn-based probabilistic
    games for synthesizing environment assumptions for unrealizable specifications.
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: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Barbara
  full_name: Jobstmann, Barbara
  last_name: Jobstmann
- first_name: Arjun
  full_name: Radhakrishna, Arjun
  id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87
  last_name: Radhakrishna
citation:
  ama: 'Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. <i>Gist: A Solver
    for Probabilistic Games</i>. IST Austria; 2009. doi:<a href="https://doi.org/10.15479/AT:IST-2009-0003">10.15479/AT:IST-2009-0003</a>'
  apa: 'Chatterjee, K., Henzinger, T. A., Jobstmann, B., &#38; Radhakrishna, A. (2009).
    <i>Gist: A solver for probabilistic games</i>. IST Austria. <a href="https://doi.org/10.15479/AT:IST-2009-0003">https://doi.org/10.15479/AT:IST-2009-0003</a>'
  chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Arjun
    Radhakrishna. <i>Gist: A Solver for Probabilistic Games</i>. IST Austria, 2009.
    <a href="https://doi.org/10.15479/AT:IST-2009-0003">https://doi.org/10.15479/AT:IST-2009-0003</a>.'
  ieee: 'K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, <i>Gist:
    A solver for probabilistic games</i>. IST Austria, 2009.'
  ista: 'Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. 2009. Gist: A solver
    for probabilistic games, IST Austria, 12p.'
  mla: 'Chatterjee, Krishnendu, et al. <i>Gist: A Solver for Probabilistic Games</i>.
    IST Austria, 2009, doi:<a href="https://doi.org/10.15479/AT:IST-2009-0003">10.15479/AT:IST-2009-0003</a>.'
  short: 'K. Chatterjee, T.A. Henzinger, B. Jobstmann, A. Radhakrishna, Gist: A Solver
    for Probabilistic Games, IST Austria, 2009.'
date_created: 2018-12-12T11:39:05Z
date_published: 2009-10-09T00:00:00Z
date_updated: 2023-02-23T12:09:01Z
day: '09'
ddc:
- '000'
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2009-0003
file:
- access_level: open_access
  checksum: 49551ac552915b17593a14c993845274
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T11:52:58Z
  date_updated: 2020-07-14T12:46:43Z
  file_id: '5459'
  file_name: IST-2009-0003_IST-2009-0003.pdf
  file_size: 386866
  relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
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: '29'
related_material:
  record:
  - id: '4388'
    relation: later_version
    status: public
status: public
title: 'Gist: A solver for probabilistic games'
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '5394'
abstract:
- lang: eng
  text: We consider two-player games played on graphs with request-response and finitary
    Streett objectives. We show these games are PSPACE-hard, improving the previous
    known NP-hardness. We also improve the lower bounds on memory required by the
    winning strategies for the players.
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: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Florian
  full_name: Horn, Florian
  id: 37327ACE-F248-11E8-B48F-1D18A9856A87
  last_name: Horn
citation:
  ama: Chatterjee K, Henzinger TA, Horn F. <i>Improved Lower Bounds for Request-Response
    and Finitary Streett Games</i>. IST Austria; 2009. doi:<a href="https://doi.org/10.15479/AT:IST-2009-0002">10.15479/AT:IST-2009-0002</a>
  apa: Chatterjee, K., Henzinger, T. A., &#38; Horn, F. (2009). <i>Improved lower
    bounds for request-response and finitary Streett games</i>. IST Austria. <a href="https://doi.org/10.15479/AT:IST-2009-0002">https://doi.org/10.15479/AT:IST-2009-0002</a>
  chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. <i>Improved
    Lower Bounds for Request-Response and Finitary Streett Games</i>. IST Austria,
    2009. <a href="https://doi.org/10.15479/AT:IST-2009-0002">https://doi.org/10.15479/AT:IST-2009-0002</a>.
  ieee: K. Chatterjee, T. A. Henzinger, and F. Horn, <i>Improved lower bounds for
    request-response and finitary Streett games</i>. IST Austria, 2009.
  ista: Chatterjee K, Henzinger TA, Horn F. 2009. Improved lower bounds for request-response
    and finitary Streett games, IST Austria, 11p.
  mla: Chatterjee, Krishnendu, et al. <i>Improved Lower Bounds for Request-Response
    and Finitary Streett Games</i>. IST Austria, 2009, doi:<a href="https://doi.org/10.15479/AT:IST-2009-0002">10.15479/AT:IST-2009-0002</a>.
  short: K. Chatterjee, T.A. Henzinger, F. Horn, Improved Lower Bounds for Request-Response
    and Finitary Streett Games, IST Austria, 2009.
date_created: 2018-12-12T11:39:05Z
date_published: 2009-09-09T00:00:00Z
date_updated: 2020-07-14T23:07:47Z
day: '09'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2009-0002
file:
- access_level: open_access
  checksum: 1c50a9723fbae1b2c46d18138968efb3
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T11:53:50Z
  date_updated: 2020-07-14T12:46:43Z
  file_id: '5511'
  file_name: IST-2009-0002_IST-2009-0002.pdf
  file_size: 238091
  relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '11'
publication_identifier:
  issn:
  - 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '30'
status: public
title: Improved lower bounds for request-response and finitary Streett games
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '5395'
abstract:
- lang: eng
  text: 'We study observation-based strategies for partially-observable Markov decision
    processes (POMDPs) with omega-regular objectives. An observation-based strategy
    relies on partial information about the history of a play, namely, on the past
    sequence of observa- tions. We consider the qualitative analysis problem: given
    a POMDP with an omega-regular objective, whether there is an observation-based
    strategy to achieve the objective with probability 1 (almost-sure winning), or
    with positive probability (positive winning). Our main results are twofold. First,
    we present a complete picture of the computational complexity of the qualitative
    analysis of POMDPs with parity objectives (a canonical form to express omega-regular
    objectives) and its subclasses. Our contribution consists in establishing several
    upper and lower bounds that were not known in literature. Second, we present optimal
    bounds (matching upper and lower bounds) on the memory required by pure and randomized
    observation-based strategies for the qualitative analysis of POMDPs with parity
    objectives and its subclasses.'
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: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
citation:
  ama: Chatterjee K, Doyen L, Henzinger TA. <i>Qualitative Analysis of Partially-Observable
    Markov Decision Processes</i>. IST Austria; 2009. doi:<a href="https://doi.org/10.15479/AT:IST-2009-0001">10.15479/AT:IST-2009-0001</a>
  apa: Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). <i>Qualitative analysis
    of partially-observable Markov decision processes</i>. IST Austria. <a href="https://doi.org/10.15479/AT:IST-2009-0001">https://doi.org/10.15479/AT:IST-2009-0001</a>
  chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. <i>Qualitative
    Analysis of Partially-Observable Markov Decision Processes</i>. IST Austria, 2009.
    <a href="https://doi.org/10.15479/AT:IST-2009-0001">https://doi.org/10.15479/AT:IST-2009-0001</a>.
  ieee: K. Chatterjee, L. Doyen, and T. A. Henzinger, <i>Qualitative analysis of partially-observable
    Markov decision processes</i>. IST Austria, 2009.
  ista: Chatterjee K, Doyen L, Henzinger TA. 2009. Qualitative analysis of partially-observable
    Markov decision processes, IST Austria, 20p.
  mla: Chatterjee, Krishnendu, et al. <i>Qualitative Analysis of Partially-Observable
    Markov Decision Processes</i>. IST Austria, 2009, doi:<a href="https://doi.org/10.15479/AT:IST-2009-0001">10.15479/AT:IST-2009-0001</a>.
  short: K. Chatterjee, L. Doyen, T.A. Henzinger, Qualitative Analysis of Partially-Observable
    Markov Decision Processes, IST Austria, 2009.
date_created: 2018-12-12T11:39:05Z
date_published: 2009-09-09T00:00:00Z
date_updated: 2023-02-23T11:45:39Z
day: '09'
ddc:
- '005'
department:
- _id: KrCh
- _id: ToHe
doi: 10.15479/AT:IST-2009-0001
file:
- access_level: open_access
  checksum: 04d9cc065cc19598a4e8631c47f1a562
  content_type: application/pdf
  creator: system
  date_created: 2018-12-12T11:53:25Z
  date_updated: 2020-07-14T12:46:43Z
  file_id: '5486'
  file_name: IST-2009-0001_IST-2009-0001.pdf
  file_size: 342088
  relation: main_file
file_date_updated: 2020-07-14T12:46:43Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '20'
publication_identifier:
  issn:
  - 2664-1690
publication_status: published
publisher: IST Austria
pubrep_id: '31'
related_material:
  record:
  - id: '3855'
    relation: later_version
    status: public
status: public
title: Qualitative analysis of partially-observable Markov decision processes
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2009'
...
---
_id: '9453'
abstract:
- lang: eng
  text: Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis
    thaliana endosperm by cytosine demethylation of the maternal genome mediated by
    the DNA glycosylase DEMETER, but the extent of the methylation changes is not
    known. Here, we show that virtually the entire endosperm genome is demethylated,
    coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted
    sequences. Mutation of DEMETER partially restores endosperm CG methylation to
    levels found in other tissues, indicating that CG demethylation is specific to
    maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation
    of embryo transposable elements. Our findings demonstrate extensive reconfiguration
    of the endosperm methylation landscape that likely reinforces transposon silencing
    in the embryo.
article_processing_charge: No
article_type: original
author:
- first_name: Tzung-Fu
  full_name: Hsieh, Tzung-Fu
  last_name: Hsieh
- first_name: Christian A.
  full_name: Ibarra, Christian A.
  last_name: Ibarra
- first_name: Pedro
  full_name: Silva, Pedro
  last_name: Silva
- first_name: Assaf
  full_name: Zemach, Assaf
  last_name: Zemach
- first_name: Leor
  full_name: Eshed-Williams, Leor
  last_name: Eshed-Williams
- first_name: Robert L.
  full_name: Fischer, Robert L.
  last_name: Fischer
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis
    endosperm. <i>Science</i>. 2009;324(5933):1451-1454. doi:<a href="https://doi.org/10.1126/science.1172417">10.1126/science.1172417</a>
  apa: Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer,
    R. L., &#38; Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm.
    <i>Science</i>. American Association for the Advancement of Science. <a href="https://doi.org/10.1126/science.1172417">https://doi.org/10.1126/science.1172417</a>
  chicago: Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams,
    Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis
    Endosperm.” <i>Science</i>. American Association for the Advancement of Science,
    2009. <a href="https://doi.org/10.1126/science.1172417">https://doi.org/10.1126/science.1172417</a>.
  ieee: T.-F. Hsieh <i>et al.</i>, “Genome-wide demethylation of Arabidopsis endosperm,”
    <i>Science</i>, vol. 324, no. 5933. American Association for the Advancement of
    Science, pp. 1451–1454, 2009.
  ista: Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman
    D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933),
    1451–1454.
  mla: Hsieh, Tzung-Fu, et al. “Genome-Wide Demethylation of Arabidopsis Endosperm.”
    <i>Science</i>, vol. 324, no. 5933, American Association for the Advancement of
    Science, 2009, pp. 1451–54, doi:<a href="https://doi.org/10.1126/science.1172417">10.1126/science.1172417</a>.
  short: T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer,
    D. Zilberman, Science 324 (2009) 1451–1454.
date_created: 2021-06-04T08:55:41Z
date_published: 2009-06-12T00:00:00Z
date_updated: 2021-12-14T08:53:26Z
day: '12'
department:
- _id: DaZi
doi: 10.1126/science.1172417
extern: '1'
external_id:
  pmid:
  - '19520962'
intvolume: '       324'
issue: '5933'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1451-1454
pmid: 1
publication: Science
publication_identifier:
  eissn:
  - 1095-9203
  issn:
  - 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide demethylation of Arabidopsis endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 324
year: '2009'
...
---
_id: '517'
article_processing_charge: No
author:
- first_name: Nicholas H
  full_name: Barton, Nicholas H
  id: 4880FE40-F248-11E8-B48F-1D18A9856A87
  last_name: Barton
  orcid: 0000-0002-8548-5240
citation:
  ama: 'Barton NH. Identity and coalescence in structured populations: A commentary
    on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. <i>Genetics
    Research</i>. 2008;89(5-6):475-477. doi:<a href="https://doi.org/10.1017/S0016672308009683">10.1017/S0016672308009683</a>'
  apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations:
    A commentary on “Inbreeding coefficients and coalescence times” by Montgomery
    Slatkin. <i>Genetics Research</i>. Cambridge University Press. <a href="https://doi.org/10.1017/S0016672308009683">https://doi.org/10.1017/S0016672308009683</a>'
  chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations:
    A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery
    Slatkin.” <i>Genetics Research</i>. Cambridge University Press, 2008. <a href="https://doi.org/10.1017/S0016672308009683">https://doi.org/10.1017/S0016672308009683</a>.'
  ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary
    on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” <i>Genetics
    Research</i>, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.'
  ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary
    on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics
    Research. 89(5–6), 475–477.'
  mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A
    Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.”
    <i>Genetics Research</i>, vol. 89, no. 5–6, Cambridge University Press, 2008,
    pp. 475–77, doi:<a href="https://doi.org/10.1017/S0016672308009683">10.1017/S0016672308009683</a>.'
  short: N.H. Barton, Genetics Research 89 (2008) 475–477.
date_created: 2018-12-11T11:46:55Z
date_published: 2008-10-29T00:00:00Z
date_updated: 2024-02-14T09:51:09Z
day: '29'
department:
- _id: NiBa
doi: 10.1017/S0016672308009683
intvolume: '        89'
issue: 5-6
language:
- iso: eng
month: '10'
oa_version: None
page: 475 - 477
publication: Genetics Research
publication_status: published
publisher: Cambridge University Press
publist_id: '7302'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding
  coefficients and coalescence times'' by Montgomery Slatkin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2008'
...
---
_id: '9457'
abstract:
- lang: eng
  text: Eukaryotic chromatin is separated into functional domains differentiated by
    posttranslational histone modifications, histone variants, and DNA methylation1–6.
    Methylation is associated with repression of transcriptional initiation in plants
    and animals, and is frequently found in transposable elements. Proper methylation
    patterns are critical for eukaryotic development4,5, and aberrant methylation-induced
    silencing of tumor suppressor genes is a common feature of human cancer7. In contrast
    to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1
    ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20.
    How DNA methylation and H2A.Z influence transcription remains largely unknown.
    Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation
    are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of
    DNA methylation in the bodies of actively transcribed genes and in methylated
    transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses
    and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition,
    while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads
    to genome-wide hypermethylation. Our findings indicate that DNA methylation can
    influence chromatin structure and effect gene silencing by excluding H2A.Z, and
    that H2A.Z protects genes from DNA methylation.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Devin
  full_name: Coleman-Derr, Devin
  last_name: Coleman-Derr
- first_name: Tracy
  full_name: Ballinger, Tracy
  last_name: Ballinger
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA
    methylation are mutually antagonistic chromatin marks. <i>Nature</i>. 2008;456(7218):125-129.
    doi:<a href="https://doi.org/10.1038/nature07324">10.1038/nature07324</a>
  apa: Zilberman, D., Coleman-Derr, D., Ballinger, T., &#38; Henikoff, S. (2008).
    Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>.
    Springer Nature. <a href="https://doi.org/10.1038/nature07324">https://doi.org/10.1038/nature07324</a>
  chicago: Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff.
    “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.”
    <i>Nature</i>. Springer Nature, 2008. <a href="https://doi.org/10.1038/nature07324">https://doi.org/10.1038/nature07324</a>.
  ieee: D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z
    and DNA methylation are mutually antagonistic chromatin marks,” <i>Nature</i>,
    vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.
  ista: Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z
    and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218),
    125–129.
  mla: Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic
    Chromatin Marks.” <i>Nature</i>, vol. 456, no. 7218, Springer Nature, 2008, pp.
    125–29, doi:<a href="https://doi.org/10.1038/nature07324">10.1038/nature07324</a>.
  short: D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008)
    125–129.
date_created: 2021-06-04T11:49:32Z
date_published: 2008-11-06T00:00:00Z
date_updated: 2021-12-14T08:54:36Z
day: '06'
department:
- _id: DaZi
doi: 10.1038/nature07324
extern: '1'
external_id:
  pmid:
  - '18815594'
intvolume: '       456'
issue: '7218'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/
month: '11'
oa: 1
oa_version: Submitted Version
page: 125-129
pmid: 1
publication: Nature
publication_identifier:
  eissn:
  - 1476-4687
  issn:
  - 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 456
year: '2008'
...
---
_id: '9537'
abstract:
- lang: eng
  text: DNA methylation is an ancient process found in all domains of life. Although
    the enzymes that mediate methylation have remained highly conserved, DNA methylation
    has been adapted for a variety of uses throughout evolution, including defense
    against transposable elements and control of gene expression. Defects in DNA methylation
    are linked to human diseases, including cancer. Methylation has been lost several
    times in the course of animal and fungal evolution, thus limiting the opportunity
    for study in common model organisms. In the past decade, plants have emerged as
    a premier model system for genetic dissection of DNA methylation. A recent combination
    of plant genetics with powerful genomic approaches has led to a number of exciting
    discoveries and promises many more.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Zilberman D. The evolving functions of DNA methylation. <i>Current Opinion
    in Plant Biology</i>. 2008;11(5):554-559. doi:<a href="https://doi.org/10.1016/j.pbi.2008.07.004">10.1016/j.pbi.2008.07.004</a>
  apa: Zilberman, D. (2008). The evolving functions of DNA methylation. <i>Current
    Opinion in Plant Biology</i>. Elsevier . <a href="https://doi.org/10.1016/j.pbi.2008.07.004">https://doi.org/10.1016/j.pbi.2008.07.004</a>
  chicago: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” <i>Current
    Opinion in Plant Biology</i>. Elsevier , 2008. <a href="https://doi.org/10.1016/j.pbi.2008.07.004">https://doi.org/10.1016/j.pbi.2008.07.004</a>.
  ieee: D. Zilberman, “The evolving functions of DNA methylation,” <i>Current Opinion
    in Plant Biology</i>, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.
  ista: Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion
    in Plant Biology. 11(5), 554–559.
  mla: Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” <i>Current
    Opinion in Plant Biology</i>, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:<a
    href="https://doi.org/10.1016/j.pbi.2008.07.004">10.1016/j.pbi.2008.07.004</a>.
  short: D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.
date_created: 2021-06-08T13:13:37Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-12-14T08:54:07Z
department:
- _id: DaZi
doi: 10.1016/j.pbi.2008.07.004
extern: '1'
external_id:
  pmid:
  - '18774331'
intvolume: '        11'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 554-559
pmid: 1
publication: Current Opinion in Plant Biology
publication_identifier:
  issn:
  - 1369-5266
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolving functions of DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 11
year: '2008'
...
---
_id: '12201'
abstract:
- lang: eng
  text: The development of plant lateral organs is interesting because, although many
    of the same genes seem to be involved in the early growth of primordia, completely
    different gene combinations are required for the complete development of organs
    such as leaves and stamens. Thus, the genes common to the development of most
    organs, which generally form and polarize the primordial ‘envelope’, must at some
    stage interact with those that ‘install’ the functional content of the organ –
    in the case of the stamen, the four microsporangia. Although distinct genetic
    pathways of organ initiation, polarity establishment and setting up the reproductive
    cell line can readily be recognized, they do not occur sequentially. Rather, they
    are activated early and run in parallel. There is evidence for continuing crosstalk
    between these pathways.
acknowledgement: X.F. holds a Clarendon Scholarship from the University of Oxford.
  We thank Angela Hay and Jill Harrison for helpful advice and discussion.
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. Packaging the male germline in plants. <i>Trends in Genetics</i>.
    2007;23(10):503-510. doi:<a href="https://doi.org/10.1016/j.tig.2007.08.005">10.1016/j.tig.2007.08.005</a>
  apa: Feng, X., &#38; Dickinson, H. G. (2007). Packaging the male germline in plants.
    <i>Trends in Genetics</i>. Elsevier BV. <a href="https://doi.org/10.1016/j.tig.2007.08.005">https://doi.org/10.1016/j.tig.2007.08.005</a>
  chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”
    <i>Trends in Genetics</i>. Elsevier BV, 2007. <a href="https://doi.org/10.1016/j.tig.2007.08.005">https://doi.org/10.1016/j.tig.2007.08.005</a>.
  ieee: X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” <i>Trends
    in Genetics</i>, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007.
  ista: Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends
    in Genetics. 23(10), 503–510.
  mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”
    <i>Trends in Genetics</i>, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:<a
    href="https://doi.org/10.1016/j.tig.2007.08.005">10.1016/j.tig.2007.08.005</a>.
  short: X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.
date_created: 2023-01-16T09:22:44Z
date_published: 2007-10-01T00:00:00Z
date_updated: 2023-05-08T10:58:47Z
department:
- _id: XiFe
doi: 10.1016/j.tig.2007.08.005
extern: '1'
external_id:
  pmid:
  - '17825943'
intvolume: '        23'
issue: '10'
keyword:
- Genetics
language:
- iso: eng
month: '10'
oa_version: None
page: 503-510
pmid: 1
publication: Trends in Genetics
publication_identifier:
  issn:
  - 0168-9525
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
scopus_import: '1'
status: public
title: Packaging the male germline in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2007'
...
---
_id: '9487'
abstract:
- lang: eng
  text: Cytosine DNA methylation is considered to be a stable epigenetic mark, but
    active demethylation has been observed in both plants and animals. In Arabidopsis
    thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines
    from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation
    by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic
    background. However, the extent and function of demethylation by DEMETER-LIKE
    (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we
    mapped DNA methylation in mutant and WT plants and identified 179 loci actively
    demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA
    hypermethylation. Reintroducing WT DML genes restores most loci to the normal
    pattern of methylation, although at some loci, hypermethylated epialleles persist.
    Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation
    by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the
    overall distribution of WT DNA methylation. Our results show that demethylation
    by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis
    genome to protect genes from potentially deleterious methylation.
article_processing_charge: No
article_type: original
author:
- first_name: Jon
  full_name: Penterman, Jon
  last_name: Penterman
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Jin Hoe
  full_name: Huh, Jin Hoe
  last_name: Huh
- first_name: Tracy
  full_name: Ballinger, Tracy
  last_name: Ballinger
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
- first_name: Robert L.
  full_name: Fischer, Robert L.
  last_name: Fischer
citation:
  ama: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA
    demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy
    of Sciences</i>. 2007;104(16):6752-6757. doi:<a href="https://doi.org/10.1073/pnas.0701861104">10.1073/pnas.0701861104</a>
  apa: Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &#38;
    Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. <i>Proceedings
    of the National Academy of Sciences</i>. National Academy of Sciences. <a href="https://doi.org/10.1073/pnas.0701861104">https://doi.org/10.1073/pnas.0701861104</a>
  chicago: Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven
    Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.”
    <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences,
    2007. <a href="https://doi.org/10.1073/pnas.0701861104">https://doi.org/10.1073/pnas.0701861104</a>.
  ieee: J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L.
    Fischer, “DNA demethylation in the Arabidopsis genome,” <i>Proceedings of the
    National Academy of Sciences</i>, vol. 104, no. 16. National Academy of Sciences,
    pp. 6752–6757, 2007.
  ista: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007.
    DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy
    of Sciences. 104(16), 6752–6757.
  mla: Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings
    of the National Academy of Sciences</i>, vol. 104, no. 16, National Academy of
    Sciences, 2007, pp. 6752–57, doi:<a href="https://doi.org/10.1073/pnas.0701861104">10.1073/pnas.0701861104</a>.
  short: J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer,
    Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.
date_created: 2021-06-07T09:38:21Z
date_published: 2007-04-17T00:00:00Z
date_updated: 2021-12-14T08:55:12Z
day: '17'
department:
- _id: DaZi
doi: 10.1073/pnas.0701861104
extern: '1'
external_id:
  pmid:
  - '17409185'
intvolume: '       104'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1073/pnas.0701861104
month: '04'
oa: 1
oa_version: Published Version
page: 6752-6757
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: DNA demethylation in the Arabidopsis genome
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 104
year: '2007'
...
---
_id: '9504'
article_processing_charge: No
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Zilberman D. <i>The Human Promoter Methylome</i>. Vol 39. Nature Publishing
    Group; 2007:442-443. doi:<a href="https://doi.org/10.1038/ng0407-442">10.1038/ng0407-442</a>
  apa: Zilberman, D. (2007). <i>The human promoter methylome</i>. <i>Nature Genetics</i>
    (Vol. 39, pp. 442–443). Nature Publishing Group. <a href="https://doi.org/10.1038/ng0407-442">https://doi.org/10.1038/ng0407-442</a>
  chicago: Zilberman, Daniel. <i>The Human Promoter Methylome</i>. <i>Nature Genetics</i>.
    Vol. 39. Nature Publishing Group, 2007. <a href="https://doi.org/10.1038/ng0407-442">https://doi.org/10.1038/ng0407-442</a>.
  ieee: D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature
    Publishing Group, 2007, pp. 442–443.
  ista: Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.
  mla: Zilberman, Daniel. “The Human Promoter Methylome.” <i>Nature Genetics</i>,
    vol. 39, no. 4, Nature Publishing Group, 2007, pp. 442–43, doi:<a href="https://doi.org/10.1038/ng0407-442">10.1038/ng0407-442</a>.
  short: D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.
date_created: 2021-06-07T12:08:24Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-12-14T08:55:46Z
day: '01'
department:
- _id: DaZi
doi: 10.1038/ng0407-442
extern: '1'
external_id:
  pmid:
  - '17392803'
intvolume: '        39'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 442-443
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
status: public
title: The human promoter methylome
type: other_academic_publication
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2007'
...
---
_id: '9524'
abstract:
- lang: eng
  text: Cytosine methylation is the most common covalent modification of DNA in eukaryotes.
    DNA methylation has an important role in many aspects of biology, including development
    and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive
    restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies.
    Combining these techniques with DNA microarrays and high-throughput sequencing
    has made the mapping of DNA methylation feasible on a genome-wide scale. Here
    we discuss recent developments and future directions for identifying and mapping
    methylation, in an effort to help colleagues to identify the approaches that best
    serve their research interests.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns.
    <i>Development</i>. 2007;134(22):3959-3965. doi:<a href="https://doi.org/10.1242/dev.001131">10.1242/dev.001131</a>
  apa: Zilberman, D., &#38; Henikoff, S. (2007). Genome-wide analysis of DNA methylation
    patterns. <i>Development</i>. The Company of Biologists. <a href="https://doi.org/10.1242/dev.001131">https://doi.org/10.1242/dev.001131</a>
  chicago: Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation
    Patterns.” <i>Development</i>. The Company of Biologists, 2007. <a href="https://doi.org/10.1242/dev.001131">https://doi.org/10.1242/dev.001131</a>.
  ieee: D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,”
    <i>Development</i>, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965,
    2007.
  ista: Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns.
    Development. 134(22), 3959–3965.
  mla: Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation
    Patterns.” <i>Development</i>, vol. 134, no. 22, The Company of Biologists, 2007,
    pp. 3959–65, doi:<a href="https://doi.org/10.1242/dev.001131">10.1242/dev.001131</a>.
  short: D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.
date_created: 2021-06-08T06:29:50Z
date_published: 2007-11-15T00:00:00Z
date_updated: 2021-12-14T08:57:58Z
day: '15'
department:
- _id: DaZi
doi: 10.1242/dev.001131
extern: '1'
external_id:
  pmid:
  - '17928417'
intvolume: '       134'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1242/dev.001131
month: '11'
oa: 1
oa_version: Published Version
page: 3959-3965
pmid: 1
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
  issn:
  - 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of DNA methylation patterns
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 134
year: '2007'
...
---
_id: '9505'
abstract:
- lang: eng
  text: 'Cytosine methylation, a common form of DNA modification that antagonizes
    transcription, is found at transposons and repeats in vertebrates, plants and
    fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana
    genome at high resolution. DNA methylation covers transposons and is present within
    a large fraction of A. thaliana genes. Methylation within genes is conspicuously
    biased away from gene ends, suggesting a dependence on RNA polymerase transit.
    Genic methylation is strongly influenced by transcription: moderately transcribed
    genes are most likely to be methylated, whereas genes at either extreme are least
    likely. In turn, transcription is influenced by methylation: short methylated
    genes are poorly expressed, and loss of methylation in the body of a gene leads
    to enhanced transcription. Our results indicate that genic transcription and DNA
    methylation are closely interwoven processes.'
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Mary
  full_name: Gehring, Mary
  last_name: Gehring
- first_name: Robert K.
  full_name: Tran, Robert K.
  last_name: Tran
- first_name: Tracy
  full_name: Ballinger, Tracy
  last_name: Ballinger
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis
    of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation
    and transcription. <i>Nature Genetics</i>. 2006;39(1):61-69. doi:<a href="https://doi.org/10.1038/ng1929">10.1038/ng1929</a>
  apa: Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., &#38; Henikoff, S.
    (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers
    an interdependence between methylation and transcription. <i>Nature Genetics</i>.
    Nature Publishing Group. <a href="https://doi.org/10.1038/ng1929">https://doi.org/10.1038/ng1929</a>
  chicago: Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven
    Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers
    an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>.
    Nature Publishing Group, 2006. <a href="https://doi.org/10.1038/ng1929">https://doi.org/10.1038/ng1929</a>.
  ieee: D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide
    analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
    methylation and transcription,” <i>Nature Genetics</i>, vol. 39, no. 1. Nature
    Publishing Group, pp. 61–69, 2006.
  ista: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide
    analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
    methylation and transcription. Nature Genetics. 39(1), 61–69.
  mla: Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA
    Methylation Uncovers an Interdependence between Methylation and Transcription.”
    <i>Nature Genetics</i>, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69,
    doi:<a href="https://doi.org/10.1038/ng1929">10.1038/ng1929</a>.
  short: D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics
    39 (2006) 61–69.
date_created: 2021-06-07T12:19:31Z
date_published: 2006-11-26T00:00:00Z
date_updated: 2021-12-14T09:02:51Z
day: '26'
department:
- _id: DaZi
doi: 10.1038/ng1929
extern: '1'
external_id:
  pmid:
  - '17128275'
intvolume: '        39'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 61-69
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - 1546-1718
  issn:
  - 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence
  between methylation and transcription
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2006'
...
---
_id: '9491'
abstract:
- lang: eng
  text: Cytosine DNA methylation in vertebrates is widespread, but methylation in
    plants is found almost exclusively at transposable elements and repetitive DNA
    [1]. Within regions of methylation, methylcytosines are typically found in CG,
    CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian
    Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and
    asymmetric sites appears to be maintained at each cell cycle by other mechanisms.
    We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters
    found at scattered sites throughout the genome. These clusters lack non-CG methylation
    and are preferentially found in genes, although they are relatively deficient
    toward the 5′ end. CG methylation clusters are present in lines derived from different
    accessions and in mutants that eliminate de novo methylation, indicating that
    CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine
    is mutagenic, the appearance of CG methylation clusters over evolutionary time
    predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G
    trinucleotides within transcribed regions. This is exactly what we find, implying
    that CG methylation clusters have contributed profoundly to plant gene evolution.
    We suggest that CG methylation clusters silence cryptic promoters that arise sporadically
    within transcription units.
article_processing_charge: No
article_type: original
author:
- first_name: Robert K.
  full_name: Tran, Robert K.
  last_name: Tran
- first_name: Jorja G.
  full_name: Henikoff, Jorja G.
  last_name: Henikoff
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Renata F.
  full_name: Ditt, Renata F.
  last_name: Ditt
- first_name: Steven E.
  full_name: Jacobsen, Steven E.
  last_name: Jacobsen
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation
    profiling identifies CG methylation clusters in Arabidopsis genes. <i>Current
    Biology</i>. 2005;15(2):154-159. doi:<a href="https://doi.org/10.1016/j.cub.2005.01.008">10.1016/j.cub.2005.01.008</a>
  apa: Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E.,
    &#38; Henikoff, S. (2005). DNA methylation profiling identifies CG methylation
    clusters in Arabidopsis genes. <i>Current Biology</i>. Elsevier. <a href="https://doi.org/10.1016/j.cub.2005.01.008">https://doi.org/10.1016/j.cub.2005.01.008</a>
  chicago: Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven
    E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation
    Clusters in Arabidopsis Genes.” <i>Current Biology</i>. Elsevier, 2005. <a href="https://doi.org/10.1016/j.cub.2005.01.008">https://doi.org/10.1016/j.cub.2005.01.008</a>.
  ieee: R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and
    S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in
    Arabidopsis genes,” <i>Current Biology</i>, vol. 15, no. 2. Elsevier, pp. 154–159,
    2005.
  ista: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005.
    DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes.
    Current Biology. 15(2), 154–159.
  mla: Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation
    Clusters in Arabidopsis Genes.” <i>Current Biology</i>, vol. 15, no. 2, Elsevier,
    2005, pp. 154–59, doi:<a href="https://doi.org/10.1016/j.cub.2005.01.008">10.1016/j.cub.2005.01.008</a>.
  short: R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff,
    Current Biology 15 (2005) 154–159.
date_created: 2021-06-07T10:24:30Z
date_published: 2005-01-26T00:00:00Z
date_updated: 2021-12-14T09:12:26Z
day: '26'
department:
- _id: DaZi
doi: 10.1016/j.cub.2005.01.008
extern: '1'
external_id:
  pmid:
  - '15668172 '
intvolume: '        15'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.cub.2005.01.008
month: '01'
oa: 1
oa_version: Published Version
page: 154-159
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: DNA methylation profiling identifies CG methylation clusters in Arabidopsis
  genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2005'
...
---
_id: '9514'
abstract:
- lang: eng
  text: "Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In
    Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases
    with distinct substrate specificities and different modes of action. Targeting
    of cytosine methylation at selected loci has been found to sometimes involve histone
    H3 methylation and small interfering (si)RNAs. However, the relationship between
    different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe
    used a microarray-based profiling method to explore the involvement of Arabidopsis
    CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP)
    and an Argonaute-related siRNA silencing component (AGO4) in methylating target
    loci. We found that KYP targets are also CMT3 targets, suggesting that histone
    methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar
    proximal distributions that correspond to the overall distribution of transposable
    elements of all types, whereas DRM targets are distributed more distally along
    the chromosome. We find an inverse relationship between element size and loss
    of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the
    targets of both DNA methylation and histone H3K9 methylation pathways are transposable
    elements genome-wide, irrespective of element type and position. Our findings
    also suggest that RNA-directed DNA methylation is required to silence isolated
    elements that may be too small to be maintained in a silent state by a chromatin-based
    mechanism alone. Thus, parallel pathways would be needed to maintain silencing
    of transposable elements."
article_number: R90
article_processing_charge: No
article_type: original
author:
- first_name: Robert K.
  full_name: Tran, Robert K.
  last_name: Tran
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Cecilia
  full_name: de Bustos, Cecilia
  last_name: de Bustos
- first_name: Renata F.
  full_name: Ditt, Renata F.
  last_name: Ditt
- first_name: Jorja G.
  full_name: Henikoff, Jorja G.
  last_name: Henikoff
- first_name: Anders M.
  full_name: Lindroth, Anders M.
  last_name: Lindroth
- first_name: Jeffrey
  full_name: Delrow, Jeffrey
  last_name: Delrow
- first_name: Tom
  full_name: Boyle, Tom
  last_name: Boyle
- first_name: Samson
  full_name: Kwong, Samson
  last_name: Kwong
- first_name: Terri D.
  full_name: Bryson, Terri D.
  last_name: Bryson
- first_name: Steven E.
  full_name: Jacobsen, Steven E.
  last_name: Jacobsen
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate
    to maintain DNA methylation of small transposable elements in Arabidopsis. <i>Genome
    Biology</i>. 2005;6(11). doi:<a href="https://doi.org/10.1186/gb-2005-6-11-r90">10.1186/gb-2005-6-11-r90</a>
  apa: Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth,
    A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain
    DNA methylation of small transposable elements in Arabidopsis. <i>Genome Biology</i>.
    Springer Nature. <a href="https://doi.org/10.1186/gb-2005-6-11-r90">https://doi.org/10.1186/gb-2005-6-11-r90</a>
  chicago: Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja
    G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways
    Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.”
    <i>Genome Biology</i>. Springer Nature, 2005. <a href="https://doi.org/10.1186/gb-2005-6-11-r90">https://doi.org/10.1186/gb-2005-6-11-r90</a>.
  ieee: R. K. Tran <i>et al.</i>, “Chromatin and siRNA pathways cooperate to maintain
    DNA methylation of small transposable elements in Arabidopsis,” <i>Genome Biology</i>,
    vol. 6, no. 11. Springer Nature, 2005.
  ista: Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow
    J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA
    pathways cooperate to maintain DNA methylation of small transposable elements
    in Arabidopsis. Genome Biology. 6(11), R90.
  mla: Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain
    DNA Methylation of Small Transposable Elements in Arabidopsis.” <i>Genome Biology</i>,
    vol. 6, no. 11, R90, Springer Nature, 2005, doi:<a href="https://doi.org/10.1186/gb-2005-6-11-r90">10.1186/gb-2005-6-11-r90</a>.
  short: R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth,
    J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome
    Biology 6 (2005).
date_created: 2021-06-07T13:12:41Z
date_published: 2005-10-19T00:00:00Z
date_updated: 2021-12-14T09:09:41Z
day: '19'
department:
- _id: DaZi
doi: 10.1186/gb-2005-6-11-r90
extern: '1'
external_id:
  pmid:
  - '16277745'
intvolume: '         6'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1186/gb-2005-6-11-r90
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
  eissn:
  - 1465-6906
  issn:
  - 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin and siRNA pathways cooperate to maintain DNA methylation of small
  transposable elements in Arabidopsis
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2005'
...
---
_id: '9529'
abstract:
- lang: eng
  text: Eukaryotic organisms have the remarkable ability to inherit states of gene
    activity without altering the underlying DNA sequence. This epigenetic inheritance
    can persist over thousands of years, providing an alternative to genetic mutations
    as a substrate for natural selection. Epigenetic inheritance might be propagated
    by differences in DNA methylation, post-translational histone modifications, and
    deposition of histone variants. Mounting evidence also indicates that small interfering
    RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining
    states of gene activity. Much of the epigenetic machinery of many organisms, including
    Arabidopsis, appears to be directed at silencing viruses and transposable elements,
    with epigenetic regulation of endogenous genes being mostly derived from such
    processes.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: 'Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective
    silence. <i>Current Opinion in Genetics and Development</i>. 2005;15(5):557-562.
    doi:<a href="https://doi.org/10.1016/j.gde.2005.07.002">10.1016/j.gde.2005.07.002</a>'
  apa: 'Zilberman, D., &#38; Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis:
    Selective silence. <i>Current Opinion in Genetics and Development</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.gde.2005.07.002">https://doi.org/10.1016/j.gde.2005.07.002</a>'
  chicago: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis:
    Selective Silence.” <i>Current Opinion in Genetics and Development</i>. Elsevier,
    2005. <a href="https://doi.org/10.1016/j.gde.2005.07.002">https://doi.org/10.1016/j.gde.2005.07.002</a>.'
  ieee: 'D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective
    silence,” <i>Current Opinion in Genetics and Development</i>, vol. 15, no. 5.
    Elsevier, pp. 557–562, 2005.'
  ista: 'Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective
    silence. Current Opinion in Genetics and Development. 15(5), 557–562.'
  mla: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis:
    Selective Silence.” <i>Current Opinion in Genetics and Development</i>, vol. 15,
    no. 5, Elsevier, 2005, pp. 557–62, doi:<a href="https://doi.org/10.1016/j.gde.2005.07.002">10.1016/j.gde.2005.07.002</a>.'
  short: D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15
    (2005) 557–562.
date_created: 2021-06-08T09:05:56Z
date_published: 2005-10-01T00:00:00Z
date_updated: 2021-12-14T09:13:13Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2005.07.002
extern: '1'
external_id:
  pmid:
  - '16085410'
intvolume: '        15'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 557-562
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
  issn:
  - 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Epigenetic inheritance in Arabidopsis: Selective silence'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2005'
...
---
_id: '12203'
abstract:
- lang: eng
  text: 'Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis
    of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide
    biosynthesis. Here we reported for the first time the cloning of a new full-length
    cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length
    cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained
    a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis
    showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal,
    which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed
    that GbGGPPS was a member of polyprenyltransferases with two highly conserved
    aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated
    that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm
    GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.'
acknowledgement: This study was financially supported by China National High-Tech
  “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences,
  Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic
  tree.
article_processing_charge: No
article_type: original
author:
- first_name: Zhihua
  full_name: Liao, Zhihua
  last_name: Liao
- first_name: Min
  full_name: Chen, Min
  last_name: Chen
- first_name: Yifu
  full_name: Gong, Yifu
  last_name: Gong
- first_name: Liang
  full_name: Guo, Liang
  last_name: Guo
- first_name: Qiumin
  full_name: Tan, Qiumin
  last_name: Tan
- first_name: Xiaoqi
  full_name: Feng, Xiaoqi
  id: e0164712-22ee-11ed-b12a-d80fcdf35958
  last_name: Feng
  orcid: 0000-0002-4008-1234
- first_name: Xiaofen
  full_name: Sun, Xiaofen
  last_name: Sun
- first_name: Feng
  full_name: Tan, Feng
  last_name: Tan
- first_name: Kexuan
  full_name: Tang, Kexuan
  last_name: Tang
citation:
  ama: Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene
    from Ginkgo biloba, which intermediates the biosynthesis of the key precursor
    for ginkgolides. <i>DNA Sequence</i>. 2004;15(2):153-158. doi:<a href="https://doi.org/10.1080/10425170410001667348">10.1080/10425170410001667348</a>
  apa: Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004).
    A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
    the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. Informa
    UK Limited. <a href="https://doi.org/10.1080/10425170410001667348">https://doi.org/10.1080/10425170410001667348</a>
  chicago: Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng,
    Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase
    Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor
    for Ginkgolides.” <i>DNA Sequence</i>. Informa UK Limited, 2004. <a href="https://doi.org/10.1080/10425170410001667348">https://doi.org/10.1080/10425170410001667348</a>.
  ieee: Z. Liao <i>et al.</i>, “A new geranylgeranyl Diphosphate synthase gene from
    Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,”
    <i>DNA Sequence</i>, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.
  ista: Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004.
    A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
    the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.
  mla: Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo
    Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.”
    <i>DNA Sequence</i>, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:<a
    href="https://doi.org/10.1080/10425170410001667348">10.1080/10425170410001667348</a>.
  short: Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang,
    DNA Sequence 15 (2004) 153–158.
date_created: 2023-01-16T09:24:50Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-05-08T10:58:29Z
department:
- _id: XiFe
doi: 10.1080/10425170410001667348
extern: '1'
external_id:
  pmid:
  - '15352294'
intvolume: '        15'
issue: '2'
keyword:
- Endocrinology
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
oa_version: None
page: 153-158
pmid: 1
publication: DNA Sequence
publication_identifier:
  issn:
  - 1042-5179
publication_status: published
publisher: Informa UK Limited
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
  the biosynthesis of the key precursor for ginkgolides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2004'
...