---
_id: '513'
abstract:
- lang: eng
text: 'We present an experimental setup that creates a shear flow with zero mean
advection velocity achieved by counterbalancing the nonzero streamwise pressure
gradient by moving boundaries, which generates plane Couette-Poiseuille flow.
We obtain experimental results in the transitional regime for this flow. Using
flow visualization, we characterize the subcritical transition to turbulence in
Couette-Poiseuille flow and show the existence of turbulent spots generated by
a permanent perturbation. Due to the zero mean advection velocity of the base
profile, these turbulent structures are nearly stationary. We distinguish two
regions of the turbulent spot: the active turbulent core, which is characterized
by waviness of the streaks similar to traveling waves, and the surrounding region,
which includes in addition the weak undisturbed streaks and oblique waves at the
laminar-turbulent interface. We also study the dependence of the size of these
two regions on Reynolds number. Finally, we show that the traveling waves move
in the downstream (Poiseuille) direction.'
article_number: '043904'
author:
- first_name: Lukasz
full_name: Klotz, Lukasz
id: 2C9AF1C2-F248-11E8-B48F-1D18A9856A87
last_name: Klotz
orcid: 0000-0003-1740-7635
- first_name: Grégoire M
full_name: Lemoult, Grégoire M
id: 4787FE80-F248-11E8-B48F-1D18A9856A87
last_name: Lemoult
- first_name: Idalia
full_name: Frontczak, Idalia
last_name: Frontczak
- first_name: Laurette
full_name: Tuckerman, Laurette
last_name: Tuckerman
- first_name: José
full_name: Wesfreid, José
last_name: Wesfreid
citation:
ama: 'Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence.
Physical Review Fluids. 2017;2(4). doi:10.1103/PhysRevFluids.2.043904'
apa: 'Klotz, L., Lemoult, G. M., Frontczak, I., Tuckerman, L., & Wesfreid, J.
(2017). Couette-Poiseuille flow experiment with zero mean advection velocity:
Subcritical transition to turbulence. Physical Review Fluids. American
Physical Society. https://doi.org/10.1103/PhysRevFluids.2.043904'
chicago: 'Klotz, Lukasz, Grégoire M Lemoult, Idalia Frontczak, Laurette Tuckerman,
and José Wesfreid. “Couette-Poiseuille Flow Experiment with Zero Mean Advection
Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids.
American Physical Society, 2017. https://doi.org/10.1103/PhysRevFluids.2.043904.'
ieee: 'L. Klotz, G. M. Lemoult, I. Frontczak, L. Tuckerman, and J. Wesfreid, “Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence,”
Physical Review Fluids, vol. 2, no. 4. American Physical Society, 2017.'
ista: 'Klotz L, Lemoult GM, Frontczak I, Tuckerman L, Wesfreid J. 2017. Couette-Poiseuille
flow experiment with zero mean advection velocity: Subcritical transition to turbulence.
Physical Review Fluids. 2(4), 043904.'
mla: 'Klotz, Lukasz, et al. “Couette-Poiseuille Flow Experiment with Zero Mean Advection
Velocity: Subcritical Transition to Turbulence.” Physical Review Fluids,
vol. 2, no. 4, 043904, American Physical Society, 2017, doi:10.1103/PhysRevFluids.2.043904.'
short: L. Klotz, G.M. Lemoult, I. Frontczak, L. Tuckerman, J. Wesfreid, Physical
Review Fluids 2 (2017).
date_created: 2018-12-11T11:46:54Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2021-01-12T08:01:16Z
day: '01'
department:
- _id: BjHo
doi: 10.1103/PhysRevFluids.2.043904
intvolume: ' 2'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.02619
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Fluids
publication_status: published
publisher: American Physical Society
publist_id: '7306'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Couette-Poiseuille flow experiment with zero mean advection velocity: Subcritical
transition to turbulence'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2017'
...
---
_id: '520'
abstract:
- lang: eng
text: Cyanobacteria are mostly engineered to be sustainable cell-factories by genetic
manipulations alone. Here, by modulating the concentration of allosteric effectors,
we focus on increasing product formation without further burdening the cells with
increased expression of enzymes. Resorting to a novel 96-well microplate cultivation
system for cyanobacteria, and using lactate-producing strains of Synechocystis
PCC6803 expressing different l-lactate dehydrogenases (LDH), we titrated the effect
of 2,5-anhydro-mannitol supplementation. The latter acts in cells as a nonmetabolizable
analogue of fructose 1,6-bisphosphate, a known allosteric regulator of one of
the tested LDHs. In this strain (SAA023), we achieved over 2-fold increase of
lactate productivity. Furthermore, we observed that as carbon is increasingly
deviated during growth toward product formation, there is an increased fixation
rate in the population of spontaneous mutants harboring an impaired production
pathway. This is a challenge in the development of green cell factories, which
may be countered by the incorporation in biotechnological processes of strategies
such as the one pioneered here.
article_type: letter_note
author:
- first_name: Wei
full_name: Du, Wei
last_name: Du
- first_name: Andreas
full_name: Angermayr, Andreas
id: 4677C796-F248-11E8-B48F-1D18A9856A87
last_name: Angermayr
orcid: 0000-0001-8619-2223
- first_name: Joeri
full_name: Jongbloets, Joeri
last_name: Jongbloets
- first_name: Douwe
full_name: Molenaar, Douwe
last_name: Molenaar
- first_name: Herwig
full_name: Bachmann, Herwig
last_name: Bachmann
- first_name: Klaas
full_name: Hellingwerf, Klaas
last_name: Hellingwerf
- first_name: Filipe
full_name: Branco Dos Santos, Filipe
last_name: Branco Dos Santos
citation:
ama: Du W, Angermayr A, Jongbloets J, et al. Nonhierarchical flux regulation exposes
the fitness burden associated with lactate production in Synechocystis sp. PCC6803.
ACS Synthetic Biology. 2017;6(3):395-401. doi:10.1021/acssynbio.6b00235
apa: Du, W., Angermayr, A., Jongbloets, J., Molenaar, D., Bachmann, H., Hellingwerf,
K., & Branco Dos Santos, F. (2017). Nonhierarchical flux regulation exposes
the fitness burden associated with lactate production in Synechocystis sp. PCC6803.
ACS Synthetic Biology. American Chemical Society. https://doi.org/10.1021/acssynbio.6b00235
chicago: Du, Wei, Andreas Angermayr, Joeri Jongbloets, Douwe Molenaar, Herwig Bachmann,
Klaas Hellingwerf, and Filipe Branco Dos Santos. “Nonhierarchical Flux Regulation
Exposes the Fitness Burden Associated with Lactate Production in Synechocystis
Sp. PCC6803.” ACS Synthetic Biology. American Chemical Society, 2017. https://doi.org/10.1021/acssynbio.6b00235.
ieee: W. Du et al., “Nonhierarchical flux regulation exposes the fitness
burden associated with lactate production in Synechocystis sp. PCC6803,” ACS
Synthetic Biology, vol. 6, no. 3. American Chemical Society, pp. 395–401,
2017.
ista: Du W, Angermayr A, Jongbloets J, Molenaar D, Bachmann H, Hellingwerf K, Branco
Dos Santos F. 2017. Nonhierarchical flux regulation exposes the fitness burden
associated with lactate production in Synechocystis sp. PCC6803. ACS Synthetic
Biology. 6(3), 395–401.
mla: Du, Wei, et al. “Nonhierarchical Flux Regulation Exposes the Fitness Burden
Associated with Lactate Production in Synechocystis Sp. PCC6803.” ACS Synthetic
Biology, vol. 6, no. 3, American Chemical Society, 2017, pp. 395–401, doi:10.1021/acssynbio.6b00235.
short: W. Du, A. Angermayr, J. Jongbloets, D. Molenaar, H. Bachmann, K. Hellingwerf,
F. Branco Dos Santos, ACS Synthetic Biology 6 (2017) 395–401.
date_created: 2018-12-11T11:46:56Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2021-01-12T08:01:21Z
day: '17'
department:
- _id: ToBo
doi: 10.1021/acssynbio.6b00235
external_id:
pmid:
- '27936615'
intvolume: ' 6'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 395 - 401
pmid: 1
publication: ACS Synthetic Biology
publication_identifier:
issn:
- '21615063'
publication_status: published
publisher: American Chemical Society
publist_id: '7298'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonhierarchical flux regulation exposes the fitness burden associated with
lactate production in Synechocystis sp. PCC6803
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '521'
abstract:
- lang: eng
text: Let X and Y be proper metric spaces. We show that a coarsely n-to-1 map f:X→Y
induces an n-to-1 map of Higson coronas. This viewpoint turns out to be successful
in showing that the classical dimension raising theorems hold in large scale;
that is, if f:X→Y is a coarsely n-to-1 map between proper metric spaces X and
Y then asdim(Y)≤asdim(X)+n−1. Furthermore we introduce coarsely open coarsely
n-to-1 maps, which include the natural quotient maps via a finite group action,
and prove that they preserve the asymptotic dimension.
author:
- first_name: Kyle
full_name: Austin, Kyle
last_name: Austin
- first_name: Ziga
full_name: Virk, Ziga
id: 2E36B656-F248-11E8-B48F-1D18A9856A87
last_name: Virk
citation:
ama: Austin K, Virk Z. Higson compactification and dimension raising. Topology
and its Applications. 2017;215:45-57. doi:10.1016/j.topol.2016.10.005
apa: Austin, K., & Virk, Z. (2017). Higson compactification and dimension raising.
Topology and Its Applications. Elsevier. https://doi.org/10.1016/j.topol.2016.10.005
chicago: Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.”
Topology and Its Applications. Elsevier, 2017. https://doi.org/10.1016/j.topol.2016.10.005.
ieee: K. Austin and Z. Virk, “Higson compactification and dimension raising,” Topology
and its Applications, vol. 215. Elsevier, pp. 45–57, 2017.
ista: Austin K, Virk Z. 2017. Higson compactification and dimension raising. Topology
and its Applications. 215, 45–57.
mla: Austin, Kyle, and Ziga Virk. “Higson Compactification and Dimension Raising.”
Topology and Its Applications, vol. 215, Elsevier, 2017, pp. 45–57, doi:10.1016/j.topol.2016.10.005.
short: K. Austin, Z. Virk, Topology and Its Applications 215 (2017) 45–57.
date_created: 2018-12-11T11:46:56Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2021-01-12T08:01:21Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.topol.2016.10.005
intvolume: ' 215'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.03954v1
month: '01'
oa: 1
oa_version: Submitted Version
page: 45 - 57
publication: Topology and its Applications
publication_identifier:
issn:
- '01668641'
publication_status: published
publisher: Elsevier
publist_id: '7299'
quality_controlled: '1'
status: public
title: Higson compactification and dimension raising
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 215
year: '2017'
...
---
_id: '534'
abstract:
- lang: eng
text: We investigate the complexity of finding an embedded non-orientable surface
of Euler genus g in a triangulated 3-manifold. This problem occurs both as a natural
question in low-dimensional topology, and as a first non-trivial instance of embeddability
of complexes into 3-manifolds. We prove that the problem is NP-hard, thus adding
to the relatively few hardness results that are currently known in 3-manifold
topology. In addition, we show that the problem lies in NP when the Euler genus
g is odd, and we give an explicit algorithm in this case.
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin
full_name: Burton, Benjamin
last_name: Burton
- first_name: Arnaud N
full_name: De Mesmay, Arnaud N
id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87
last_name: De Mesmay
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Burton B, de Mesmay AN, Wagner U. Finding non-orientable surfaces in 3-Manifolds.
Discrete & Computational Geometry. 2017;58(4):871-888. doi:10.1007/s00454-017-9900-0
apa: Burton, B., de Mesmay, A. N., & Wagner, U. (2017). Finding non-orientable
surfaces in 3-Manifolds. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-017-9900-0
chicago: Burton, Benjamin, Arnaud N de Mesmay, and Uli Wagner. “Finding Non-Orientable
Surfaces in 3-Manifolds.” Discrete & Computational Geometry. Springer,
2017. https://doi.org/10.1007/s00454-017-9900-0.
ieee: B. Burton, A. N. de Mesmay, and U. Wagner, “Finding non-orientable surfaces
in 3-Manifolds,” Discrete & Computational Geometry, vol. 58, no. 4.
Springer, pp. 871–888, 2017.
ista: Burton B, de Mesmay AN, Wagner U. 2017. Finding non-orientable surfaces in
3-Manifolds. Discrete & Computational Geometry. 58(4), 871–888.
mla: Burton, Benjamin, et al. “Finding Non-Orientable Surfaces in 3-Manifolds.”
Discrete & Computational Geometry, vol. 58, no. 4, Springer, 2017,
pp. 871–88, doi:10.1007/s00454-017-9900-0.
short: B. Burton, A.N. de Mesmay, U. Wagner, Discrete & Computational Geometry
58 (2017) 871–888.
date_created: 2018-12-11T11:47:01Z
date_published: 2017-06-09T00:00:00Z
date_updated: 2023-02-21T17:01:34Z
day: '09'
department:
- _id: UlWa
doi: 10.1007/s00454-017-9900-0
external_id:
arxiv:
- '1602.07907'
intvolume: ' 58'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.07907
month: '06'
oa: 1
oa_version: Preprint
page: 871 - 888
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '7283'
quality_controlled: '1'
related_material:
record:
- id: '1379'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Finding non-orientable surfaces in 3-Manifolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2017'
...
---
_id: '538'
abstract:
- lang: ger
text: 'Optogenetik und Photopharmakologie ermöglichen präzise räumliche und zeitliche
Kontrolle von Proteinwechselwirkung und -funktion in Zellen und Tieren. Optogenetische
Methoden, die auf grünes Licht ansprechen und zum Trennen von Proteinkomplexen
geeignet sind, sind nichtweitläufig verfügbar, würden jedoch mehrfarbige Experimente
zur Beantwortung von biologischen Fragestellungen ermöglichen. Hier demonstrieren
wir die Verwendung von Cobalamin(Vitamin B12)-bindenden Domänen von bakteriellen
CarH-Transkriptionsfaktoren zur Grünlicht-induzierten Dissoziation von Rezeptoren.
Fusioniert mit dem Fibroblasten-W achstumsfaktor-Rezeptor 1 führten diese im Dunkeln
in kultivierten Zellen zu Signalaktivität durch Oligomerisierung, welche durch
Beleuchten umgehend aufgehoben wurde. In Zebrafischembryonen, die einen derartigen
Rezeptor exprimieren, ermöglichte grünes Licht die Kontrolle über abnormale Signalaktivität
während der Embryonalentwicklung. '
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
- first_name: Manuela
full_name: Stadler, Manuela
last_name: Stadler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Martin
full_name: Distel, Martin
last_name: Distel
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Grünlicht-induzierte
Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte Chemie.
2017;129(16):4679-4682. doi:10.1002/ange.201611998
apa: Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak,
H. L. (2017). Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende
Domänen. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201611998
chicago: Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel,
and Harald L Janovjak. “Grünlicht-Induzierte Rezeptorinaktivierung Durch Cobalamin-Bindende
Domänen.” Angewandte Chemie. Wiley, 2017. https://doi.org/10.1002/ange.201611998.
ieee: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak,
“Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen,”
Angewandte Chemie, vol. 129, no. 16. Wiley, pp. 4679–4682, 2017.
ista: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017.
Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angewandte
Chemie. 129(16), 4679–4682.
mla: Kainrath, Stephanie, et al. “Grünlicht-Induzierte Rezeptorinaktivierung Durch
Cobalamin-Bindende Domänen.” Angewandte Chemie, vol. 129, no. 16, Wiley,
2017, pp. 4679–82, doi:10.1002/ange.201611998.
short: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak,
Angewandte Chemie 129 (2017) 4679–4682.
date_created: 2018-12-11T11:47:02Z
date_published: 2017-05-20T00:00:00Z
date_updated: 2021-01-12T08:01:33Z
day: '20'
ddc:
- '571'
department:
- _id: CaGu
- _id: HaJa
doi: 10.1002/ange.201611998
ec_funded: 1
file:
- access_level: open_access
checksum: d66fee867e7cdbfa3fe276c2fb0778bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:24Z
date_updated: 2020-07-14T12:46:39Z
file_id: '5007'
file_name: IST-2018-932-v1+1_Kainrath_et_al-2017-Angewandte_Chemie.pdf
file_size: 1668557
relation: main_file
file_date_updated: 2020-07-14T12:46:39Z
has_accepted_license: '1'
intvolume: ' 129'
issue: '16'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 4679 - 4682
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Angewandte Chemie
publication_status: published
publisher: Wiley
publist_id: '7279'
pubrep_id: '932'
quality_controlled: '1'
status: public
title: Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2017'
...
---
_id: '540'
abstract:
- lang: eng
text: RNA-dependent RNA polymerases (RdRps) play a key role in the life cycle of
RNA viruses and impact their immunobiology. The arenavirus lymphocytic choriomeningitis
virus (LCMV) strain Clone 13 provides a benchmark model for studying chronic infection.
A major genetic determinant for its ability to persist maps to a single amino
acid exchange in the viral L protein, which exhibits RdRp activity, yet its functional
consequences remain elusive. To unravel the L protein interactions with the host
proteome, we engineered infectious L protein-tagged LCMV virions by reverse genetics.
A subsequent mass-spectrometric analysis of L protein pulldowns from infected
human cells revealed a comprehensive network of interacting host proteins. The
obtained LCMV L protein interactome was bioinformatically integrated with known
host protein interactors of RdRps from other RNA viruses, emphasizing interconnected
modules of human proteins. Functional characterization of selected interactors
highlighted proviral (DDX3X) as well as antiviral (NKRF, TRIM21) host factors.
To corroborate these findings, we infected Trim21-/-mice with LCMV and found impaired
virus control in chronic infection. These results provide insights into the complex
interactions of the arenavirus LCMV and other viral RdRps with the host proteome
and contribute to a better molecular understanding of how chronic viruses interact
with their host.
article_number: e1006758
author:
- first_name: Kseniya
full_name: Khamina, Kseniya
last_name: Khamina
- first_name: Alexander
full_name: Lercher, Alexander
last_name: Lercher
- first_name: Michael
full_name: Caldera, Michael
last_name: Caldera
- first_name: Christopher
full_name: Schliehe, Christopher
last_name: Schliehe
- first_name: Bojan
full_name: Vilagos, Bojan
last_name: Vilagos
- first_name: Mehmet
full_name: Sahin, Mehmet
last_name: Sahin
- first_name: Lindsay
full_name: Kosack, Lindsay
last_name: Kosack
- first_name: Anannya
full_name: Bhattacharya, Anannya
last_name: Bhattacharya
- first_name: Peter
full_name: Májek, Peter
last_name: Májek
- first_name: Alexey
full_name: Stukalov, Alexey
last_name: Stukalov
- first_name: Roberto
full_name: Sacco, Roberto
id: 42C9F57E-F248-11E8-B48F-1D18A9856A87
last_name: Sacco
- first_name: Leo
full_name: James, Leo
last_name: James
- first_name: Daniel
full_name: Pinschewer, Daniel
last_name: Pinschewer
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Andreas
full_name: Bergthaler, Andreas
last_name: Bergthaler
citation:
ama: Khamina K, Lercher A, Caldera M, et al. Characterization of host proteins interacting
with the lymphocytic choriomeningitis virus L protein. PLoS Pathogens.
2017;13(12). doi:10.1371/journal.ppat.1006758
apa: Khamina, K., Lercher, A., Caldera, M., Schliehe, C., Vilagos, B., Sahin, M.,
… Bergthaler, A. (2017). Characterization of host proteins interacting with the
lymphocytic choriomeningitis virus L protein. PLoS Pathogens. Public Library
of Science. https://doi.org/10.1371/journal.ppat.1006758
chicago: Khamina, Kseniya, Alexander Lercher, Michael Caldera, Christopher Schliehe,
Bojan Vilagos, Mehmet Sahin, Lindsay Kosack, et al. “Characterization of Host
Proteins Interacting with the Lymphocytic Choriomeningitis Virus L Protein.” PLoS
Pathogens. Public Library of Science, 2017. https://doi.org/10.1371/journal.ppat.1006758.
ieee: K. Khamina et al., “Characterization of host proteins interacting with
the lymphocytic choriomeningitis virus L protein,” PLoS Pathogens, vol.
13, no. 12. Public Library of Science, 2017.
ista: Khamina K, Lercher A, Caldera M, Schliehe C, Vilagos B, Sahin M, Kosack L,
Bhattacharya A, Májek P, Stukalov A, Sacco R, James L, Pinschewer D, Bennett K,
Menche J, Bergthaler A. 2017. Characterization of host proteins interacting with
the lymphocytic choriomeningitis virus L protein. PLoS Pathogens. 13(12), e1006758.
mla: Khamina, Kseniya, et al. “Characterization of Host Proteins Interacting with
the Lymphocytic Choriomeningitis Virus L Protein.” PLoS Pathogens, vol.
13, no. 12, e1006758, Public Library of Science, 2017, doi:10.1371/journal.ppat.1006758.
short: K. Khamina, A. Lercher, M. Caldera, C. Schliehe, B. Vilagos, M. Sahin, L.
Kosack, A. Bhattacharya, P. Májek, A. Stukalov, R. Sacco, L. James, D. Pinschewer,
K. Bennett, J. Menche, A. Bergthaler, PLoS Pathogens 13 (2017).
date_created: 2018-12-11T11:47:03Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:48Z
day: '01'
ddc:
- '576'
- '616'
department:
- _id: GaNo
doi: 10.1371/journal.ppat.1006758
file:
- access_level: open_access
checksum: 1aa20f19a1e90664fadce6e7d5284fdc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:26Z
date_updated: 2020-07-14T12:46:44Z
file_id: '4944'
file_name: IST-2018-931-v1+1_journal.ppat.1006758.pdf
file_size: 4106772
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file_date_updated: 2020-07-14T12:46:44Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '12'
language:
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month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Pathogens
publication_identifier:
issn:
- '15537366'
publication_status: published
publisher: Public Library of Science
publist_id: '7276'
pubrep_id: '931'
quality_controlled: '1'
scopus_import: 1
status: public
title: Characterization of host proteins interacting with the lymphocytic choriomeningitis
virus L protein
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '466'
abstract:
- lang: eng
text: 'We consider Markov decision processes (MDPs) with multiple limit-average
(or mean-payoff) objectives. There exist two different views: (i) the expectation
semantics, where the goal is to optimize the expected mean-payoff objective, and
(ii) the satisfaction semantics, where the goal is to maximize the probability
of runs such that the mean-payoff value stays above a given vector. We consider
optimization with respect to both objectives at once, thus unifying the existing
semantics. Precisely, the goal is to optimize the expectation while ensuring the
satisfaction constraint. Our problem captures the notion of optimization with
respect to strategies that are risk-averse (i.e., ensure certain probabilistic
guarantee). Our main results are as follows: First, we present algorithms for
the decision problems which are always polynomial in the size of the MDP. We also
show that an approximation of the Pareto-curve can be computed in time polynomial
in the size of the MDP, and the approximation factor, but exponential in the number
of dimensions. Second, we present a complete characterization of the strategy
complexity (in terms of memory bounds and randomization) required to solve our
problem. '
article_number: '15'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Zuzana
full_name: Křetínská, Zuzana
last_name: Křetínská
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: Chatterjee K, Křetínská Z, Kretinsky J. Unifying two views on multiple mean-payoff
objectives in Markov decision processes. Logical Methods in Computer Science.
2017;13(2). doi:10.23638/LMCS-13(2:15)2017
apa: Chatterjee, K., Křetínská, Z., & Kretinsky, J. (2017). Unifying two views
on multiple mean-payoff objectives in Markov decision processes. Logical Methods
in Computer Science. International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(2:15)2017
chicago: Chatterjee, Krishnendu, Zuzana Křetínská, and Jan Kretinsky. “Unifying
Two Views on Multiple Mean-Payoff Objectives in Markov Decision Processes.” Logical
Methods in Computer Science. International Federation of Computational Logic,
2017. https://doi.org/10.23638/LMCS-13(2:15)2017.
ieee: K. Chatterjee, Z. Křetínská, and J. Kretinsky, “Unifying two views on multiple
mean-payoff objectives in Markov decision processes,” Logical Methods in Computer
Science, vol. 13, no. 2. International Federation of Computational Logic,
2017.
ista: Chatterjee K, Křetínská Z, Kretinsky J. 2017. Unifying two views on multiple
mean-payoff objectives in Markov decision processes. Logical Methods in Computer
Science. 13(2), 15.
mla: Chatterjee, Krishnendu, et al. “Unifying Two Views on Multiple Mean-Payoff
Objectives in Markov Decision Processes.” Logical Methods in Computer Science,
vol. 13, no. 2, 15, International Federation of Computational Logic, 2017, doi:10.23638/LMCS-13(2:15)2017.
short: K. Chatterjee, Z. Křetínská, J. Kretinsky, Logical Methods in Computer Science
13 (2017).
date_created: 2018-12-11T11:46:38Z
date_published: 2017-07-03T00:00:00Z
date_updated: 2023-02-23T12:26:16Z
day: '03'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.23638/LMCS-13(2:15)2017
ec_funded: 1
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checksum: bfa405385ec6229ad5ead89ab5751639
content_type: application/pdf
creator: system
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date_updated: 2020-07-14T12:46:33Z
file_id: '5354'
file_name: IST-2018-957-v1+1_2017_Chatterjee_Unifying_two.pdf
file_size: 511832
relation: main_file
file_date_updated: 2020-07-14T12:46:33Z
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issue: '2'
language:
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license: https://creativecommons.org/licenses/by-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
project:
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call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2590DB08-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '701309'
name: Atomic-Resolution Structures of Mitochondrial Respiratory Chain Supercomplexes
(H2020)
publication: Logical Methods in Computer Science
publication_identifier:
issn:
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publisher: International Federation of Computational Logic
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scopus_import: 1
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title: Unifying two views on multiple mean-payoff objectives in Markov decision processes
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: journal_article
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volume: 13
year: '2017'
...
---
_id: '467'
abstract:
- lang: eng
text: Recently there has been a significant effort to handle quantitative properties
in formal verification and synthesis. While weighted automata over finite and
infinite words provide a natural and flexible framework to express quantitative
properties, perhaps surprisingly, some basic system properties such as average
response time cannot be expressed using weighted automata or in any other known
decidable formalism. In this work, we introduce nested weighted automata as a
natural extension of weighted automata, which makes it possible to express important
quantitative properties such as average response time. In nested weighted automata,
a master automaton spins off and collects results from weighted slave automata,
each of which computes a quantity along a finite portion of an infinite word.
Nested weighted automata can be viewed as the quantitative analogue of monitor
automata, which are used in runtime verification. We establish an almost-complete
decidability picture for the basic decision problems about nested weighted automata
and illustrate their applicability in several domains. In particular, nested weighted
automata can be used to decide average response time properties.
article_number: '31'
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: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Otop J. Nested weighted automata. ACM Transactions
on Computational Logic (TOCL). 2017;18(4). doi:10.1145/3152769
apa: Chatterjee, K., Henzinger, T. A., & Otop, J. (2017). Nested weighted automata.
ACM Transactions on Computational Logic (TOCL). ACM. https://doi.org/10.1145/3152769
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted
Automata.” ACM Transactions on Computational Logic (TOCL). ACM, 2017. https://doi.org/10.1145/3152769.
ieee: K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted automata,” ACM
Transactions on Computational Logic (TOCL), vol. 18, no. 4. ACM, 2017.
ista: Chatterjee K, Henzinger TA, Otop J. 2017. Nested weighted automata. ACM Transactions
on Computational Logic (TOCL). 18(4), 31.
mla: Chatterjee, Krishnendu, et al. “Nested Weighted Automata.” ACM Transactions
on Computational Logic (TOCL), vol. 18, no. 4, 31, ACM, 2017, doi:10.1145/3152769.
short: K. Chatterjee, T.A. Henzinger, J. Otop, ACM Transactions on Computational
Logic (TOCL) 18 (2017).
date_created: 2018-12-11T11:46:38Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-02-23T12:26:19Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/3152769
ec_funded: 1
external_id:
arxiv:
- '1606.03598'
intvolume: ' 18'
issue: '4'
language:
- iso: eng
main_file_link:
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url: https://arxiv.org/abs/1606.03598
month: '12'
oa: 1
oa_version: Preprint
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- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ACM Transactions on Computational Logic (TOCL)
publication_identifier:
issn:
- '15293785'
publication_status: published
publisher: ACM
publist_id: '7354'
quality_controlled: '1'
related_material:
record:
- id: '1656'
relation: earlier_version
status: public
- id: '5415'
relation: earlier_version
status: public
- id: '5436'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Nested weighted automata
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2017'
...
---
_id: '465'
abstract:
- lang: eng
text: 'The edit distance between two words w 1 , w 2 is the minimal number of word
operations (letter insertions, deletions, and substitutions) necessary to transform
w 1 to w 2 . The edit distance generalizes to languages L 1 , L 2 , where the
edit distance from L 1 to L 2 is the minimal number k such that for every word
from L 1 there exists a word in L 2 with edit distance at most k . We study the
edit distance computation problem between pushdown automata and their subclasses.
The problem of computing edit distance to a pushdown automaton is undecidable,
and in practice, the interesting question is to compute the edit distance from
a pushdown automaton (the implementation, a standard model for programs with recursion)
to a regular language (the specification). In this work, we present a complete
picture of decidability and complexity for the following problems: (1) deciding
whether, for a given threshold k , the edit distance from a pushdown automaton
to a finite automaton is at most k , and (2) deciding whether the edit distance
from a pushdown automaton to a finite automaton is finite. '
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: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Jan
full_name: Otop, Jan
last_name: Otop
citation:
ama: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown
automata. Logical Methods in Computer Science. 2017;13(3). doi:10.23638/LMCS-13(3:23)2017
apa: Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2017).
Edit distance for pushdown automata. Logical Methods in Computer Science.
International Federation of Computational Logic. https://doi.org/10.23638/LMCS-13(3:23)2017
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. “Edit Distance for Pushdown Automata.” Logical Methods in Computer Science.
International Federation of Computational Logic, 2017. https://doi.org/10.23638/LMCS-13(3:23)2017.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance
for pushdown automata,” Logical Methods in Computer Science, vol. 13, no.
3. International Federation of Computational Logic, 2017.
ista: Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2017. Edit distance for
pushdown automata. Logical Methods in Computer Science. 13(3).
mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” Logical
Methods in Computer Science, vol. 13, no. 3, International Federation of Computational
Logic, 2017, doi:10.23638/LMCS-13(3:23)2017.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Logical Methods
in Computer Science 13 (2017).
date_created: 2018-12-11T11:46:37Z
date_published: 2017-09-13T00:00:00Z
date_updated: 2023-02-23T12:26:25Z
day: '13'
ddc:
- '004'
department:
- _id: KrCh
- _id: ToHe
doi: 10.23638/LMCS-13(3:23)2017
ec_funded: 1
file:
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checksum: 08041379ba408d40664f449eb5907a8f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:37Z
date_updated: 2020-07-14T12:46:33Z
file_id: '5090'
file_name: IST-2015-321-v1+1_main.pdf
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date_updated: 2020-07-14T12:46:33Z
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language:
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month: '09'
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oa_version: Published Version
project:
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call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
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call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
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call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: Logical Methods in Computer Science
publication_identifier:
issn:
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publication_status: published
publisher: International Federation of Computational Logic
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title: Edit distance for pushdown automata
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short: CC BY-ND (4.0)
type: journal_article
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volume: 13
year: '2017'
...
---
_id: '512'
abstract:
- lang: eng
text: 'The fixation probability is the probability that a new mutant introduced
in a homogeneous population eventually takes over the entire population. The fixation
probability is a fundamental quantity of natural selection, and known to depend
on the population structure. Amplifiers of natural selection are population structures
which increase the fixation probability of advantageous mutants, as compared to
the baseline case of well-mixed populations. In this work we focus on symmetric
population structures represented as undirected graphs. In the regime of undirected
graphs, the strongest amplifier known has been the Star graph, and the existence
of undirected graphs with stronger amplification properties has remained open
for over a decade. In this work we present the Comet and Comet-swarm families
of undirected graphs. We show that for a range of fitness values of the mutants,
the Comet and Cometswarm graphs have fixation probability strictly larger than
the fixation probability of the Star graph, for fixed population size and at the
limit of large populations, respectively. '
article_number: '82'
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- 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: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. Amplification on undirected
population structures: Comets beat stars. Scientific Reports. 2017;7(1).
doi:10.1038/s41598-017-00107-w'
apa: 'Pavlogiannis, A., Tkadlec, J., Chatterjee, K., & Nowak, M. (2017). Amplification
on undirected population structures: Comets beat stars. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/s41598-017-00107-w'
chicago: 'Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin
Nowak. “Amplification on Undirected Population Structures: Comets Beat Stars.”
Scientific Reports. Nature Publishing Group, 2017. https://doi.org/10.1038/s41598-017-00107-w.'
ieee: 'A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, “Amplification
on undirected population structures: Comets beat stars,” Scientific Reports,
vol. 7, no. 1. Nature Publishing Group, 2017.'
ista: 'Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2017. Amplification on
undirected population structures: Comets beat stars. Scientific Reports. 7(1),
82.'
mla: 'Pavlogiannis, Andreas, et al. “Amplification on Undirected Population Structures:
Comets Beat Stars.” Scientific Reports, vol. 7, no. 1, 82, Nature Publishing
Group, 2017, doi:10.1038/s41598-017-00107-w.'
short: A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Scientific Reports
7 (2017).
date_created: 2018-12-11T11:46:53Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2023-02-23T12:26:57Z
day: '06'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1038/s41598-017-00107-w
ec_funded: 1
file:
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checksum: 7d05cbdd914e194a019c0f91fb64e9a8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:35Z
date_updated: 2020-07-14T12:46:36Z
file_id: '5357'
file_name: IST-2018-938-v1+1_2017_Pavlogiannis_Amplification_on.pdf
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has_accepted_license: '1'
intvolume: ' 7'
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
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
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call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Scientific Reports
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issn:
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publisher: Nature Publishing Group
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- id: '5449'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'Amplification on undirected population structures: Comets beat stars'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2017'
...