---
_id: '1164'
abstract:
- lang: eng
text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric
circles C1, … , Ck with common center c, and edges are drawn radially: every edge
intersects every circle centered at c at most once. G is radial planar if it has
a radial embedding, that is, a crossing-free radial drawing. If the vertices of
G are ordered or partitioned into ordered levels (as they are for leveled graphs),
we require that the assignment of vertices to circles corresponds to the given
ordering or leveling. A pair of edges e and f in a graph is independent if e and
f do not share a vertex. We show that a graph G is radial planar if G has a radial
drawing in which every two independent edges cross an even number of times; the
radial embedding has the same leveling as the radial drawing. In other words,
we establish the strong Hanani-Tutte theorem for radial planarity. This characterization
yields a very simple algorithm for radial planarity testing.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Michael
full_name: Pelsmajer, Michael
last_name: Pelsmajer
- first_name: Marcus
full_name: Schaefer, Marcus
last_name: Schaefer
citation:
ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity II. In:
Vol 9801. Springer; 2016:468-481. doi:10.1007/978-3-319-50106-2_36'
apa: 'Fulek, R., Pelsmajer, M., & Schaefer, M. (2016). Hanani-Tutte for radial
planarity II (Vol. 9801, pp. 468–481). Presented at the GD: Graph Drawing and
Network Visualization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_36'
chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte
for Radial Planarity II,” 9801:468–81. Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_36.
ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity
II,” presented at the GD: Graph Drawing and Network Visualization, Athens, Greece,
2016, vol. 9801, pp. 468–481.'
ista: 'Fulek R, Pelsmajer M, Schaefer M. 2016. Hanani-Tutte for radial planarity
II. GD: Graph Drawing and Network Visualization, LNCS, vol. 9801, 468–481.'
mla: Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity II. Vol. 9801,
Springer, 2016, pp. 468–81, doi:10.1007/978-3-319-50106-2_36.
short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2016, pp. 468–481.
conference:
end_date: 2016-09-21
location: Athens, Greece
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:29Z
date_published: 2016-12-08T00:00:00Z
date_updated: 2023-02-23T10:05:57Z
day: '08'
department:
- _id: UlWa
doi: 10.1007/978-3-319-50106-2_36
ec_funded: 1
external_id:
arxiv:
- '1608.08662'
intvolume: ' 9801'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1608.08662
month: '12'
oa: 1
oa_version: Preprint
page: 468 - 481
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6193'
quality_controlled: '1'
related_material:
record:
- id: '1113'
relation: later_version
status: public
- id: '1595'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hanani-Tutte for radial planarity II
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9801
year: '2016'
...
---
_id: '1165'
abstract:
- lang: eng
text: We show that c-planarity is solvable in quadratic time for flat clustered
graphs with three clusters if the combinatorial embedding of the underlying graph
is fixed. In simpler graph-theoretical terms our result can be viewed as follows.
Given a graph G with the vertex set partitioned into three parts embedded on a
2-sphere, our algorithm decides if we can augment G by adding edges without creating
an edge-crossing so that in the resulting spherical graph the vertices of each
part induce a connected sub-graph. We proceed by a reduction to the problem of
testing the existence of a perfect matching in planar bipartite graphs. We formulate
our result in a slightly more general setting of cyclic clustered graphs, i.e.,
the simple graph obtained by contracting each cluster, where we disregard loops
and multi-edges, is a cycle.
acknowledgement: "R. Fulek—The research leading to these results has received funding
from the People Programme (Marie Curie Actions) of the European Union’s Seventh
Framework Programme (FP7/2007-2013) under REA grant agreement no [291734].\r\nI
would like to thank Jan Kynčl and Dömötör Pálvölgyi for many comments and suggestions
that helped to improve the presentation of the result."
alternative_title:
- LNCS
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
citation:
ama: 'Fulek R. C-planarity of embedded cyclic c-graphs. In: Vol 9801. Springer;
2016:94-106. doi:10.1007/978-3-319-50106-2_8'
apa: 'Fulek, R. (2016). C-planarity of embedded cyclic c-graphs (Vol. 9801, pp.
94–106). Presented at the GD: Graph Drawing and Network Visualization, Athens,
Greece: Springer. https://doi.org/10.1007/978-3-319-50106-2_8'
chicago: Fulek, Radoslav. “C-Planarity of Embedded Cyclic c-Graphs,” 9801:94–106.
Springer, 2016. https://doi.org/10.1007/978-3-319-50106-2_8.
ieee: 'R. Fulek, “C-planarity of embedded cyclic c-graphs,” presented at the GD:
Graph Drawing and Network Visualization, Athens, Greece, 2016, vol. 9801, pp.
94–106.'
ista: 'Fulek R. 2016. C-planarity of embedded cyclic c-graphs. GD: Graph Drawing
and Network Visualization, LNCS, vol. 9801, 94–106.'
mla: Fulek, Radoslav. C-Planarity of Embedded Cyclic c-Graphs. Vol. 9801,
Springer, 2016, pp. 94–106, doi:10.1007/978-3-319-50106-2_8.
short: R. Fulek, in:, Springer, 2016, pp. 94–106.
conference:
end_date: 2016-09-21
location: Athens, Greece
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2016-09-19
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-08T00:00:00Z
date_updated: 2023-09-27T12:14:48Z
day: '08'
department:
- _id: UlWa
doi: 10.1007/978-3-319-50106-2_8
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1602.01346
month: '12'
oa: 1
oa_version: Preprint
page: 94 - 106
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication_status: published
publisher: Springer
publist_id: '6192'
quality_controlled: '1'
related_material:
record:
- id: '794'
relation: later_version
status: public
scopus_import: 1
status: public
title: C-planarity of embedded cyclic c-graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: '9801 '
year: '2016'
...
---
_id: '1166'
abstract:
- lang: eng
text: POMDPs are standard models for probabilistic planning problems, where an agent
interacts with an uncertain environment. We study the problem of almost-sure reachability,
where given a set of target states, the question is to decide whether there is
a policy to ensure that the target set is reached with probability 1 (almost-surely).
While in general the problem is EXPTIMEcomplete, in many practical cases policies
with a small amount of memory suffice. Moreover, the existing solution to the
problem is explicit, which first requires to construct explicitly an exponential
reduction to a belief-support MDP. In this work, we first study the existence
of observation-stationary strategies, which is NP-complete, and then small-memory
strategies. We present a symbolic algorithm by an efficient encoding to SAT and
using a SAT solver for the problem. We report experimental results demonstrating
the scalability of our symbolic (SAT-based) approach. © 2016, Association for
the Advancement of Artificial Intelligence (www.aaai.org). All rights reserved.
author:
- 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: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Jessica
full_name: Davies, Jessica
id: 378E0060-F248-11E8-B48F-1D18A9856A87
last_name: Davies
citation:
ama: 'Chatterjee K, Chmelik M, Davies J. A symbolic SAT based algorithm for almost
sure reachability with small strategies in pomdps. In: Proceedings of the Thirtieth
AAAI Conference on Artificial Intelligence. Vol 2016. AAAI Press; 2016:3225-3232.'
apa: 'Chatterjee, K., Chmelik, M., & Davies, J. (2016). A symbolic SAT based
algorithm for almost sure reachability with small strategies in pomdps. In Proceedings
of the Thirtieth AAAI Conference on Artificial Intelligence (Vol. 2016, pp.
3225–3232). Phoenix, AZ, USA: AAAI Press.'
chicago: Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. “A Symbolic
SAT Based Algorithm for Almost Sure Reachability with Small Strategies in Pomdps.”
In Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence,
2016:3225–32. AAAI Press, 2016.
ieee: K. Chatterjee, M. Chmelik, and J. Davies, “A symbolic SAT based algorithm
for almost sure reachability with small strategies in pomdps,” in Proceedings
of the Thirtieth AAAI Conference on Artificial Intelligence, Phoenix, AZ,
USA, 2016, vol. 2016, pp. 3225–3232.
ista: 'Chatterjee K, Chmelik M, Davies J. 2016. A symbolic SAT based algorithm for
almost sure reachability with small strategies in pomdps. Proceedings of the Thirtieth
AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence
vol. 2016, 3225–3232.'
mla: Chatterjee, Krishnendu, et al. “A Symbolic SAT Based Algorithm for Almost Sure
Reachability with Small Strategies in Pomdps.” Proceedings of the Thirtieth
AAAI Conference on Artificial Intelligence, vol. 2016, AAAI Press, 2016, pp.
3225–32.
short: K. Chatterjee, M. Chmelik, J. Davies, in:, Proceedings of the Thirtieth AAAI
Conference on Artificial Intelligence, AAAI Press, 2016, pp. 3225–3232.
conference:
end_date: 2016-02-17
location: Phoenix, AZ, USA
name: 'AAAI: Conference on Artificial Intelligence'
start_date: 2016-02-12
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-02T00:00:00Z
date_updated: 2023-02-23T12:26:41Z
day: '02'
department:
- _id: KrCh
- _id: ToHe
ec_funded: 1
intvolume: ' 2016'
language:
- iso: eng
month: '12'
oa_version: None
page: 3225 - 3232
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence
publication_status: published
publisher: AAAI Press
publist_id: '6191'
quality_controlled: '1'
related_material:
link:
- relation: table_of_contents
url: https://dl.acm.org/citation.cfm?id=3016355
record:
- id: '5443'
relation: earlier_version
status: public
status: public
title: A symbolic SAT based algorithm for almost sure reachability with small strategies
in pomdps
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1167'
abstract:
- lang: eng
text: Evolutionary pathways describe trajectories of biological evolution in the
space of different variants of organisms (genotypes). The probability of existence
and the number of evolutionary pathways that lead from a given genotype to a better-adapted
genotype are important measures of accessibility of local fitness optima and the
reproducibility of evolution. Both quantities have been studied in simple mathematical
models where genotypes are represented as binary sequences of two types of basic
units, and the network of permitted mutations between the genotypes is a hypercube
graph. However, it is unclear how these results translate to the biologically
relevant case in which genotypes are represented by sequences of more than two
units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the
mutational graph is not the hypercube. Here we investigate accessibility of the
best-adapted genotype in the general case of K > 2 units. Using computer generated
and experimental fitness landscapes we show that accessibility of the global fitness
maximum increases with K and can be much higher than for binary sequences. The
increase in accessibility comes from the increase in the number of indirect trajectories
exploited by evolution for higher K. As one of the consequences, the fraction
of genotypes that are accessible increases by three orders of magnitude when the
number of units K increases from 2 to 16 for landscapes of size N ∼ 106genotypes.
This suggests that evolution can follow many different trajectories on such landscapes
and the reconstruction of evolutionary pathways from experimental data might be
an extremely difficult task.
acknowledgement: MZ acknowledges the Polish National Science Centre grant no. DEC-2012/07/N/NZ2/00107.
BW was supported by the Scottish Government/Royal Society of Edinburgh Personal
Research Fellowship. We thank Marjon de Vos and Oliver Martin for critically reading
the manuscript.
article_number: e1005218
article_processing_charge: No
author:
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Zdzisław
full_name: Burda, Zdzisław
last_name: Burda
- first_name: Bartłomiej
full_name: Wacław, Bartłomiej
last_name: Wacław
citation:
ama: Zagórski MP, Burda Z, Wacław B. Beyond the hypercube evolutionary accessibility
of fitness landscapes with realistic mutational networks. PLoS Computational
Biology. 2016;12(12). doi:10.1371/journal.pcbi.1005218
apa: Zagórski, M. P., Burda, Z., & Wacław, B. (2016). Beyond the hypercube evolutionary
accessibility of fitness landscapes with realistic mutational networks. PLoS
Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005218
chicago: Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “Beyond the
Hypercube Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational
Networks.” PLoS Computational Biology. Public Library of Science, 2016.
https://doi.org/10.1371/journal.pcbi.1005218.
ieee: M. P. Zagórski, Z. Burda, and B. Wacław, “Beyond the hypercube evolutionary
accessibility of fitness landscapes with realistic mutational networks,” PLoS
Computational Biology, vol. 12, no. 12. Public Library of Science, 2016.
ista: Zagórski MP, Burda Z, Wacław B. 2016. Beyond the hypercube evolutionary accessibility
of fitness landscapes with realistic mutational networks. PLoS Computational Biology.
12(12), e1005218.
mla: Zagórski, Marcin P., et al. “Beyond the Hypercube Evolutionary Accessibility
of Fitness Landscapes with Realistic Mutational Networks.” PLoS Computational
Biology, vol. 12, no. 12, e1005218, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005218.
short: M.P. Zagórski, Z. Burda, B. Wacław, PLoS Computational Biology 12 (2016).
date_created: 2018-12-11T11:50:30Z
date_published: 2016-12-09T00:00:00Z
date_updated: 2023-02-23T14:11:22Z
day: '09'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1371/journal.pcbi.1005218
file:
- access_level: open_access
checksum: 84f44ae92866c52ff1ca8a574558dca7
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:08Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4926'
file_name: IST-2017-740-v1+1_journal.pcbi.1005218.pdf
file_size: 3822299
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 12'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6190'
pubrep_id: '740'
quality_controlled: '1'
related_material:
record:
- id: '9866'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Beyond the hypercube evolutionary accessibility of fitness landscapes with
realistic mutational networks
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: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 12
year: '2016'
...
---
_id: '1170'
abstract:
- lang: eng
text: The increasing complexity of dynamic models in systems and synthetic biology
poses computational challenges especially for the identification of model parameters.
While modularization of the corresponding optimization problems could help reduce
the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit
a simple decomposition of most biomolecular networks into subnetworks, or modules.
Drawing on ideas from network modularization and multiple-shooting optimization,
we present here a modular parameter identification approach that explicitly allows
for such interdependencies. Interfaces between our modules are given by the experimentally
measured molecular species. This definition allows deriving good (initial) estimates
for the inter-module communication directly from the experimental data. Given
these estimates, the states and parameter sensitivities of different modules can
be integrated independently. To achieve consistency between modules, we iteratively
adjust the estimates for inter-module communication while optimizing the parameters.
After convergence to an optimal parameter set---but not during earlier iterations---the
intermodule communication as well as the individual modules\' state dynamics agree
with the dynamics of the nonmodularized network. Our modular parameter identification
approach allows for easy parallelization; it can reduce the computational complexity
for larger networks and decrease the probability to converge to suboptimal local
minima. We demonstrate the algorithm\'s performance in parameter estimation for
two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling
pathway.
author:
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Jörg
full_name: Stelling, Jörg
last_name: Stelling
citation:
ama: Lang M, Stelling J. Modular parameter identification of biomolecular networks.
SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X
apa: Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular
networks. SIAM Journal on Scientific Computing. Society for Industrial
and Applied Mathematics . https://doi.org/10.1137/15M103306X
chicago: Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular
Networks.” SIAM Journal on Scientific Computing. Society for Industrial
and Applied Mathematics , 2016. https://doi.org/10.1137/15M103306X.
ieee: M. Lang and J. Stelling, “Modular parameter identification of biomolecular
networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society
for Industrial and Applied Mathematics , pp. B988–B1008, 2016.
ista: Lang M, Stelling J. 2016. Modular parameter identification of biomolecular
networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.
mla: Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular
Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society
for Industrial and Applied Mathematics , 2016, pp. B988–1008, doi:10.1137/15M103306X.
short: M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.
date_created: 2018-12-11T11:50:31Z
date_published: 2016-11-15T00:00:00Z
date_updated: 2021-01-12T06:48:49Z
day: '15'
ddc:
- '003'
- '518'
- '570'
- '621'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1137/15M103306X
file:
- access_level: local
checksum: 781bc3ffd30b2dd65b7727c5a285fc78
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:41Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5095'
file_name: IST-2017-811-v1+1_modular_parameter_identification.pdf
file_size: 871964
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 38'
issue: '6'
language:
- iso: eng
month: '11'
oa_version: Submitted Version
page: B988 - B1008
publication: SIAM Journal on Scientific Computing
publication_status: published
publisher: 'Society for Industrial and Applied Mathematics '
publist_id: '6186'
pubrep_id: '811'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modular parameter identification of biomolecular networks
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2016'
...
---
_id: '1171'
author:
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: 'Tkačik G. Understanding regulatory networks requires more than computing a
multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. 2016;17:166-167. doi:10.1016/j.plrev.2016.06.005'
apa: 'Tkačik, G. (2016). Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.06.005'
chicago: 'Tkačik, Gašper. “Understanding Regulatory Networks Requires More than
Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural
Features in Gene Regulatory Networks: From Biophysical Constraints to Biological
Function" by O. C. Martin et Al.” Physics of Life Reviews. Elsevier,
2016. https://doi.org/10.1016/j.plrev.2016.06.005.'
ieee: 'G. Tkačik, “Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al.,” Physics of Life Reviews, vol. 17. Elsevier, pp.
166–167, 2016.'
ista: 'Tkačik G. 2016. Understanding regulatory networks requires more than computing
a multitude of graph statistics: Comment on "Drivers of structural features
in gene regulatory networks: From biophysical constraints to biological function"
by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.'
mla: 'Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing
a Multitude of Graph Statistics: Comment on "Drivers of Structural Features
in Gene Regulatory Networks: From Biophysical Constraints to Biological Function"
by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016,
pp. 166–67, doi:10.1016/j.plrev.2016.06.005.'
short: G. Tkačik, Physics of Life Reviews 17 (2016) 166–167.
date_created: 2018-12-11T11:50:32Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2021-01-12T06:48:50Z
day: '01'
department:
- _id: GaTk
doi: 10.1016/j.plrev.2016.06.005
intvolume: ' 17'
language:
- iso: eng
month: '07'
oa_version: None
page: 166 - 167
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '6185'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Understanding regulatory networks requires more than computing a multitude
of graph statistics: Comment on "Drivers of structural features in gene regulatory
networks: From biophysical constraints to biological function" by O. C. Martin
et al.'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2016'
...
---
_id: '1172'
abstract:
- lang: eng
text: A central issue in cell biology is the physico-chemical basis of organelle
biogenesis in intracellular trafficking pathways, its most impressive manifestation
being the biogenesis of Golgi cisternae. At a basic level, such morphologically
and chemically distinct compartments should arise from an interplay between the
molecular transport and chemical maturation. Here, we formulate analytically tractable,
minimalist models, that incorporate this interplay between transport and chemical
progression in physical space, and explore the conditions for de novo biogenesis
of distinct cisternae. We propose new quantitative measures that can discriminate
between the various models of transport in a qualitative manner-this includes
measures of the dynamics in steady state and the dynamical response to perturbations
of the kind amenable to live-cell imaging.
acknowledgement: H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund
Thattai for critical discussions and suggestions.
article_number: '38840'
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Mustansir
full_name: Barma, Mustansir
last_name: Barma
- first_name: Madan
full_name: Rao, Madan
last_name: Rao
citation:
ama: Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 2016;6.
doi:10.1038/srep38840
apa: Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of
de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep38840
chicago: Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description
of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific
Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.
ieee: H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo
biogenesis and transport through Golgi-like cisternae,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.
mla: Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis
and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6,
38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.
short: H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:32Z
date_published: 2016-12-19T00:00:00Z
date_updated: 2021-01-12T06:48:50Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1038/srep38840
file:
- access_level: open_access
checksum: cb378732da885ea4959ec5b845fb6e52
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:56Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4977'
file_name: IST-2017-737-v1+1_srep38840.pdf
file_size: 760967
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6183'
pubrep_id: '737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonequilibrium description of de novo biogenesis and transport through Golgi-like
cisternae
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1177'
abstract:
- lang: eng
text: Boldyreva, Palacio and Warinschi introduced a multiple forking game as an
extension of general forking. The notion of (multiple) forking is a useful abstraction
from the actual simulation of cryptographic scheme to the adversary in a security
reduction, and is achieved through the intermediary of a so-called wrapper algorithm.
Multiple forking has turned out to be a useful tool in the security argument of
several cryptographic protocols. However, a reduction employing multiple forking
incurs a significant degradation of (Formula presented.) , where (Formula presented.)
denotes the upper bound on the underlying random oracle calls and (Formula presented.)
, the number of forkings. In this work we take a closer look at the reasons for
the degradation with a tighter security bound in mind. We nail down the exact
set of conditions for success in the multiple forking game. A careful analysis
of the cryptographic schemes and corresponding security reduction employing multiple
forking leads to the formulation of ‘dependence’ and ‘independence’ conditions
pertaining to the output of the wrapper in different rounds. Based on the (in)dependence
conditions we propose a general framework of multiple forking and a General Multiple
Forking Lemma. Leveraging (in)dependence to the full allows us to improve the
degradation factor in the multiple forking game by a factor of (Formula presented.).
By implication, the cost of a single forking involving two random oracles (augmented
forking) matches that involving a single random oracle (elementary forking). Finally,
we study the effect of these observations on the concrete security of existing
schemes employing multiple forking. We conclude that by careful design of the
protocol (and the wrapper in the security reduction) it is possible to harness
our observations to the full extent.
acknowledgement: "We are grateful to the anonymous reviewers for their insightful
comments. The\r\ndetailed reports helped us a lot to address the technical mistakes
as well as to improve the overall presentation of the paper."
author:
- first_name: Chethan
full_name: Kamath Hosdurg, Chethan
id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87
last_name: Kamath Hosdurg
- first_name: Sanjit
full_name: Chatterjee, Sanjit
last_name: Chatterjee
citation:
ama: 'Kamath Hosdurg C, Chatterjee S. A closer look at multiple-forking: Leveraging
(in)dependence for a tighter bound. Algorithmica. 2016;74(4):1321-1362.
doi:10.1007/s00453-015-9997-6'
apa: 'Kamath Hosdurg, C., & Chatterjee, S. (2016). A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound. Algorithmica. Springer.
https://doi.org/10.1007/s00453-015-9997-6'
chicago: 'Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking:
Leveraging (in)Dependence for a Tighter Bound.” Algorithmica. Springer,
2016. https://doi.org/10.1007/s00453-015-9997-6.'
ieee: 'C. Kamath Hosdurg and S. Chatterjee, “A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound,” Algorithmica, vol. 74,
no. 4. Springer, pp. 1321–1362, 2016.'
ista: 'Kamath Hosdurg C, Chatterjee S. 2016. A closer look at multiple-forking:
Leveraging (in)dependence for a tighter bound. Algorithmica. 74(4), 1321–1362.'
mla: 'Kamath Hosdurg, Chethan, and Sanjit Chatterjee. “A Closer Look at Multiple-Forking:
Leveraging (in)Dependence for a Tighter Bound.” Algorithmica, vol. 74,
no. 4, Springer, 2016, pp. 1321–62, doi:10.1007/s00453-015-9997-6.'
short: C. Kamath Hosdurg, S. Chatterjee, Algorithmica 74 (2016) 1321–1362.
date_created: 2018-12-11T11:50:33Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:48:52Z
day: '01'
department:
- _id: KrPi
doi: 10.1007/s00453-015-9997-6
intvolume: ' 74'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://eprint.iacr.org/2013/651
month: '04'
oa: 1
oa_version: Submitted Version
page: 1321 - 1362
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '6177'
quality_controlled: '1'
status: public
title: 'A closer look at multiple-forking: Leveraging (in)dependence for a tighter
bound'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2016'
...
---
_id: '1179'
abstract:
- lang: eng
text: "Computational notions of entropy have recently found many applications, including
leakage-resilient cryptography, deterministic encryption or memory delegation.
The two main types of results which make computational notions so useful are (1)
Chain rules, which quantify by how much the computational entropy of a variable
decreases if conditioned on some other variable (2) Transformations, which quantify
to which extend one type of entropy implies another.\r\n\r\nSuch chain rules and
transformations typically lose a significant amount in quality of the entropy,
and are the reason why applying these results one gets rather weak quantitative
security bounds. In this paper we for the first time prove lower bounds in this
context, showing that existing results for transformations are, unfortunately,
basically optimal for non-adaptive black-box reductions (and it’s hard to imagine
how non black-box reductions or adaptivity could be useful here.)\r\n\r\nA variable
X has k bits of HILL entropy of quality (ϵ,s)\r\nif there exists a variable Y
with k bits min-entropy which cannot be distinguished from X with advantage ϵ\r\n\r\nby
distinguishing circuits of size s. A weaker notion is Metric entropy, where we
switch quantifiers, and only require that for every distinguisher of size s, such
a Y exists.\r\n\r\nWe first describe our result concerning transformations. By
definition, HILL implies Metric without any loss in quality. Metric entropy often
comes up in applications, but must be transformed to HILL for meaningful security
guarantees. The best known result states that if a variable X has k bits of Metric
entropy of quality (ϵ,s)\r\n, then it has k bits of HILL with quality (2ϵ,s⋅ϵ2).
We show that this loss of a factor Ω(ϵ−2)\r\n\r\nin circuit size is necessary.
In fact, we show the stronger result that this loss is already necessary when
transforming so called deterministic real valued Metric entropy to randomised
boolean Metric (both these variants of Metric entropy are implied by HILL without
loss in quality).\r\n\r\nThe chain rule for HILL entropy states that if X has
k bits of HILL entropy of quality (ϵ,s)\r\n, then for any variable Z of length
m, X conditioned on Z has k−m bits of HILL entropy with quality (ϵ,s⋅ϵ2/2m). We
show that a loss of Ω(2m/ϵ) in circuit size necessary here. Note that this still
leaves a gap of ϵ between the known bound and our lower bound."
acknowledgement: "K. Pietrzak—Supported by the European Research Council consolidator
grant (682815-TOCNeT).\r\nM. Skórski—Supported by the National Science Center, Poland
(2015/17/N/ST6/03564)."
alternative_title:
- LNCS
author:
- first_name: Krzysztof Z
full_name: Pietrzak, Krzysztof Z
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Skorski
full_name: Maciej, Skorski
last_name: Maciej
citation:
ama: 'Pietrzak KZ, Maciej S. Pseudoentropy: Lower-bounds for chain rules and transformations.
In: Vol 9985. Springer; 2016:183-203. doi:10.1007/978-3-662-53641-4_8'
apa: 'Pietrzak, K. Z., & Maciej, S. (2016). Pseudoentropy: Lower-bounds for
chain rules and transformations (Vol. 9985, pp. 183–203). Presented at the TCC:
Theory of Cryptography Conference, Beijing, China: Springer. https://doi.org/10.1007/978-3-662-53641-4_8'
chicago: 'Pietrzak, Krzysztof Z, and Skorski Maciej. “Pseudoentropy: Lower-Bounds
for Chain Rules and Transformations,” 9985:183–203. Springer, 2016. https://doi.org/10.1007/978-3-662-53641-4_8.'
ieee: 'K. Z. Pietrzak and S. Maciej, “Pseudoentropy: Lower-bounds for chain rules
and transformations,” presented at the TCC: Theory of Cryptography Conference,
Beijing, China, 2016, vol. 9985, pp. 183–203.'
ista: 'Pietrzak KZ, Maciej S. 2016. Pseudoentropy: Lower-bounds for chain rules
and transformations. TCC: Theory of Cryptography Conference, LNCS, vol. 9985,
183–203.'
mla: 'Pietrzak, Krzysztof Z., and Skorski Maciej. Pseudoentropy: Lower-Bounds
for Chain Rules and Transformations. Vol. 9985, Springer, 2016, pp. 183–203,
doi:10.1007/978-3-662-53641-4_8.'
short: K.Z. Pietrzak, S. Maciej, in:, Springer, 2016, pp. 183–203.
conference:
end_date: 2016-11-03
location: Beijing, China
name: 'TCC: Theory of Cryptography Conference'
start_date: 2016-10-31
date_created: 2018-12-11T11:50:34Z
date_published: 2016-10-22T00:00:00Z
date_updated: 2021-01-12T06:48:53Z
day: '22'
department:
- _id: KrPi
doi: 10.1007/978-3-662-53641-4_8
ec_funded: 1
intvolume: ' 9985'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2016/159
month: '10'
oa: 1
oa_version: Preprint
page: 183 - 203
project:
- _id: 258AA5B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '682815'
name: Teaching Old Crypto New Tricks
publication_status: published
publisher: Springer
publist_id: '6175'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Pseudoentropy: Lower-bounds for chain rules and transformations'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9985
year: '2016'
...
---
_id: '1181'
abstract:
- lang: eng
text: 'This review accompanies a 2016 SFN mini-symposium presenting examples of
current studies that address a central question: How do neural stem cells (NSCs)
divide in different ways to produce heterogeneous daughter types at the right
time and in proper numbers to build a cerebral cortex with the appropriate size
and structure? We will focus on four aspects of corticogenesis: cytokinesis events
that follow apical mitoses of NSCs; coordinating abscission with delamination
from the apical membrane; timing of neurogenesis and its indirect regulation through
emergence of intermediate progenitors; and capacity of single NSCs to generate
the correct number and laminar fate of cortical neurons. Defects in these mechanisms
can cause microcephaly and other brain malformations, and understanding them is
critical to designing diagnostic tools and preventive and corrective therapies.'
acknowledgement: This work was supported by National Institutes of Health Grants R01NS089795
and R01NS098370 to H.T.G., R01NS076640 to N.D.D., and R01MH094589 and R01NS089777
to B.C., Academia Sinica AS-104-TPB09-2 to S.-J.C, European Union FP7-CIG618444
and Human Frontiers Science Program RGP0053 to S.H., and Fonds Léon Fredericq, from
the Fondation Médicale Reine Elisabeth, and from the Fonation Simone et Pierre Clerdent
to L.N. The authors apologize to colleagues whose work could not be cited due to
space limitations.
author:
- first_name: Noelle
full_name: Dwyer, Noelle
last_name: Dwyer
- first_name: Bin
full_name: Chen, Bin
last_name: Chen
- first_name: Shen
full_name: Chou, Shen
last_name: Chou
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Laurent
full_name: Nguyen, Laurent
last_name: Nguyen
- first_name: Troy
full_name: Ghashghaei, Troy
last_name: Ghashghaei
citation:
ama: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. Neural stem
cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior and
productivity. Journal of Neuroscience. 2016;36(45):11394-11401. doi:10.1523/JNEUROSCI.2359-16.2016'
apa: 'Dwyer, N., Chen, B., Chou, S., Hippenmeyer, S., Nguyen, L., & Ghashghaei,
T. (2016). Neural stem cells to cerebral cortex: Emerging mechanisms regulating
progenitor behavior and productivity. Journal of Neuroscience. Society
for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2359-16.2016'
chicago: 'Dwyer, Noelle, Bin Chen, Shen Chou, Simon Hippenmeyer, Laurent Nguyen,
and Troy Ghashghaei. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms
Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience.
Society for Neuroscience, 2016. https://doi.org/10.1523/JNEUROSCI.2359-16.2016.'
ieee: 'N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, and T. Ghashghaei,
“Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor
behavior and productivity,” Journal of Neuroscience, vol. 36, no. 45. Society
for Neuroscience, pp. 11394–11401, 2016.'
ista: 'Dwyer N, Chen B, Chou S, Hippenmeyer S, Nguyen L, Ghashghaei T. 2016. Neural
stem cells to cerebral cortex: Emerging mechanisms regulating progenitor behavior
and productivity. Journal of Neuroscience. 36(45), 11394–11401.'
mla: 'Dwyer, Noelle, et al. “Neural Stem Cells to Cerebral Cortex: Emerging Mechanisms
Regulating Progenitor Behavior and Productivity.” Journal of Neuroscience,
vol. 36, no. 45, Society for Neuroscience, 2016, pp. 11394–401, doi:10.1523/JNEUROSCI.2359-16.2016.'
short: N. Dwyer, B. Chen, S. Chou, S. Hippenmeyer, L. Nguyen, T. Ghashghaei, Journal
of Neuroscience 36 (2016) 11394–11401.
date_created: 2018-12-11T11:50:35Z
date_published: 2016-11-09T00:00:00Z
date_updated: 2021-01-12T06:48:54Z
day: '09'
department:
- _id: SiHi
doi: 10.1523/JNEUROSCI.2359-16.2016
intvolume: ' 36'
issue: '45'
language:
- iso: eng
month: '11'
oa_version: None
page: 11394 - 11401
project:
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '6172'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Neural stem cells to cerebral cortex: Emerging mechanisms regulating progenitor
behavior and productivity'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2016'
...
---
_id: '1182'
abstract:
- lang: eng
text: 'Balanced knockout tournaments are ubiquitous in sports competitions and are
also used in decisionmaking and elections. The traditional computational question,
that asks to compute a draw (optimal draw) that maximizes the winning probability
for a distinguished player, has received a lot of attention. Previous works consider
the problem where the pairwise winning probabilities are known precisely, while
we study how robust is the winning probability with respect to small errors in
the pairwise winning probabilities. First, we present several illuminating examples
to establish: (a) there exist deterministic tournaments (where the pairwise winning
probabilities are 0 or 1) where one optimal draw is much more robust than the
other; and (b) in general, there exist tournaments with slightly suboptimal draws
that are more robust than all the optimal draws. The above examples motivate the
study of the computational problem of robust draws that guarantee a specified
winning probability. Second, we present a polynomial-time algorithm for approximating
the robustness of a draw for sufficiently small errors in pairwise winning probabilities,
and obtain that the stated computational problem is NP-complete. We also show
that two natural cases of deterministic tournaments where the optimal draw could
be computed in polynomial time also admit polynomial-time algorithms to compute
robust optimal draws.'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. Robust draws in balanced knockout
tournaments. In: Vol 2016-January. AAAI Press; 2016:172-179.'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Tkadlec, J. (2016). Robust draws in
balanced knockout tournaments (Vol. 2016–January, pp. 172–179). Presented at the
IJCAI: International Joint Conference on Artificial Intelligence, New York, NY,
USA: AAAI Press.'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Josef Tkadlec. “Robust
Draws in Balanced Knockout Tournaments,” 2016–January:172–79. AAAI Press, 2016.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and J. Tkadlec, “Robust draws in balanced
knockout tournaments,” presented at the IJCAI: International Joint Conference
on Artificial Intelligence, New York, NY, USA, 2016, vol. 2016–January, pp. 172–179.'
ista: 'Chatterjee K, Ibsen-Jensen R, Tkadlec J. 2016. Robust draws in balanced knockout
tournaments. IJCAI: International Joint Conference on Artificial Intelligence
vol. 2016–January, 172–179.'
mla: Chatterjee, Krishnendu, et al. Robust Draws in Balanced Knockout Tournaments.
Vol. 2016–January, AAAI Press, 2016, pp. 172–79.
short: K. Chatterjee, R. Ibsen-Jensen, J. Tkadlec, in:, AAAI Press, 2016, pp. 172–179.
conference:
end_date: 2016-07-15
location: New York, NY, USA
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2016-07-09
date_created: 2018-12-11T11:50:35Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2023-02-21T10:04:26Z
day: '01'
department:
- _id: KrCh
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.05090v1
month: '01'
oa: 1
oa_version: Preprint
page: 172 - 179
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: AAAI Press
publist_id: '6171'
quality_controlled: '1'
related_material:
link:
- relation: table_of_contents
url: https://www.ijcai.org/proceedings/2016
scopus_import: 1
status: public
title: Robust draws in balanced knockout tournaments
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-January
year: '2016'
...
---
_id: '1183'
abstract:
- lang: eng
text: Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping
with other neurological conditions. We previously described abnormalities in the
branched-chain amino acid (BCAA) catabolic pathway as a cause of ASD. Here, we
show that the solute carrier transporter 7a5 (SLC7A5), a large neutral amino acid
transporter localized at the blood brain barrier (BBB), has an essential role
in maintaining normal levels of brain BCAAs. In mice, deletion of Slc7a5 from
the endothelial cells of the BBB leads to atypical brain amino acid profile, abnormal
mRNA translation, and severe neurological abnormalities. Furthermore, we identified
several patients with autistic traits and motor delay carrying deleterious homozygous
mutations in the SLC7A5 gene. Finally, we demonstrate that BCAA intracerebroventricular
administration ameliorates abnormal behaviors in adult mutant mice. Our data elucidate
a neurological syndrome defined by SLC7A5 mutations and support an essential role
for the BCAA in human brain function.
acknowledgement: "This work was supported by NICHD (P01HD070494) and SFARI (grant
275275) to J.G.G., and FWF (SFB35_3523) to G.N.\r\nWe thank A.C. Manzano, Mike Liu,
and F. Marr for technical assistance, and R. Shigemoto and the IST Austria Electron
Microscopy (EM) Facility for assistance. We acknowledge support from CIDR for genome-wide
SNP analysis (X01HG008823) and Broad Institute Center for Mendelian Disorders (UM1HG008900
to D. MacArthur), the Yale Center for Mendelian Disorders (U54HG006504 to M.G.),
the Gregory M. Kiez and Mehmet Kutman Foundation (M.G.), Italian Ministry of Instruction
University and Research (PON01_00937 to C.I.), and NIH (R01-GM108911 to A.S.). This
work was supported by NICHD (P01HD070494) and SFARI (grant 275275) to J.G.G., and
FWF (SFB35_3523) to G.N.\r\n\r\n#EMFacility"
article_processing_charge: No
article_type: original
author:
- first_name: Dora-Clara
full_name: Tarlungeanu, Dora-Clara
id: 2ABCE612-F248-11E8-B48F-1D18A9856A87
last_name: Tarlungeanu
- first_name: Elena
full_name: Deliu, Elena
id: 37A40D7E-F248-11E8-B48F-1D18A9856A87
last_name: Deliu
orcid: 0000-0002-7370-5293
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Majdi
full_name: Kara, Majdi
last_name: Kara
- first_name: Philipp
full_name: Janiesch, Philipp
last_name: Janiesch
- first_name: Mariafrancesca
full_name: Scalise, Mariafrancesca
last_name: Scalise
- first_name: Michele
full_name: Galluccio, Michele
last_name: Galluccio
- first_name: Mateja
full_name: Tesulov, Mateja
last_name: Tesulov
- first_name: Emanuela
full_name: Morelli, Emanuela
id: 3F4D1282-F248-11E8-B48F-1D18A9856A87
last_name: Morelli
- first_name: Fatma
full_name: Sönmez, Fatma
last_name: Sönmez
- first_name: Kaya
full_name: Bilgüvar, Kaya
last_name: Bilgüvar
- first_name: Ryuichi
full_name: Ohgaki, Ryuichi
last_name: Ohgaki
- first_name: Yoshikatsu
full_name: Kanai, Yoshikatsu
last_name: Kanai
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Seham
full_name: Esharif, Seham
last_name: Esharif
- first_name: Tawfeg
full_name: Ben Omran, Tawfeg
last_name: Ben Omran
- first_name: Meral
full_name: Topcu, Meral
last_name: Topcu
- first_name: Avner
full_name: Schlessinger, Avner
last_name: Schlessinger
- first_name: Cesare
full_name: Indiveri, Cesare
last_name: Indiveri
- first_name: Kent
full_name: Duncan, Kent
last_name: Duncan
- first_name: Ahmet
full_name: Caglayan, Ahmet
last_name: Caglayan
- first_name: Murat
full_name: Günel, Murat
last_name: Günel
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Tarlungeanu D-C, Deliu E, Dotter C, et al. Impaired amino acid transport at
the blood brain barrier is a cause of autism spectrum disorder. Cell. 2016;167(6):1481-1494.
doi:10.1016/j.cell.2016.11.013
apa: Tarlungeanu, D.-C., Deliu, E., Dotter, C., Kara, M., Janiesch, P., Scalise,
M., … Novarino, G. (2016). Impaired amino acid transport at the blood brain barrier
is a cause of autism spectrum disorder. Cell. Cell Press. https://doi.org/10.1016/j.cell.2016.11.013
chicago: Tarlungeanu, Dora-Clara, Elena Deliu, Christoph Dotter, Majdi Kara, Philipp
Janiesch, Mariafrancesca Scalise, Michele Galluccio, et al. “Impaired Amino Acid
Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.”
Cell. Cell Press, 2016. https://doi.org/10.1016/j.cell.2016.11.013.
ieee: D.-C. Tarlungeanu et al., “Impaired amino acid transport at the blood
brain barrier is a cause of autism spectrum disorder,” Cell, vol. 167,
no. 6. Cell Press, pp. 1481–1494, 2016.
ista: Tarlungeanu D-C, Deliu E, Dotter C, Kara M, Janiesch P, Scalise M, Galluccio
M, Tesulov M, Morelli E, Sönmez F, Bilgüvar K, Ohgaki R, Kanai Y, Johansen A,
Esharif S, Ben Omran T, Topcu M, Schlessinger A, Indiveri C, Duncan K, Caglayan
A, Günel M, Gleeson J, Novarino G. 2016. Impaired amino acid transport at the
blood brain barrier is a cause of autism spectrum disorder. Cell. 167(6), 1481–1494.
mla: Tarlungeanu, Dora-Clara, et al. “Impaired Amino Acid Transport at the Blood
Brain Barrier Is a Cause of Autism Spectrum Disorder.” Cell, vol. 167,
no. 6, Cell Press, 2016, pp. 1481–94, doi:10.1016/j.cell.2016.11.013.
short: D.-C. Tarlungeanu, E. Deliu, C. Dotter, M. Kara, P. Janiesch, M. Scalise,
M. Galluccio, M. Tesulov, E. Morelli, F. Sönmez, K. Bilgüvar, R. Ohgaki, Y. Kanai,
A. Johansen, S. Esharif, T. Ben Omran, M. Topcu, A. Schlessinger, C. Indiveri,
K. Duncan, A. Caglayan, M. Günel, J. Gleeson, G. Novarino, Cell 167 (2016) 1481–1494.
date_created: 2018-12-11T11:50:35Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2024-03-25T23:30:07Z
day: '01'
ddc:
- '576'
- '616'
department:
- _id: GaNo
doi: 10.1016/j.cell.2016.11.013
file:
- access_level: open_access
checksum: 7fe01ab12a6610d3db421e0136db2f77
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:44Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5030'
file_name: IST-2017-771-v1+1_Tarlungeanu_et_al._Final_edited.pdf
file_size: 73907957
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 167'
issue: '6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 1481 - 1494
project:
- _id: 25473368-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: F03523
name: Transmembrane Transporters in Health and Disease
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '6170'
pubrep_id: '771'
quality_controlled: '1'
related_material:
record:
- id: '395'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Impaired amino acid transport at the blood brain barrier is a cause of autism
spectrum disorder
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 167
year: '2016'
...
---
_id: '1184'
abstract:
- lang: eng
text: Across multicellular organisms, the costs of reproduction and self-maintenance
result in a life history trade-off between fecundity and longevity. Queens of
perennial social Hymenoptera are both highly fertile and long-lived, and thus,
this fundamental trade-off is lacking. Whether social insect males similarly evade
the fecundity/longevity trade-off remains largely unstudied. Wingless males of
the ant genus Cardiocondyla stay in their natal colonies throughout their relatively
long lives and mate with multiple female sexuals. Here, we show that Cardiocondyla
obscurior males that were allowed to mate with large numbers of female sexuals
had a shortened life span compared to males that mated at a low frequency or virgin
males. Although frequent mating negatively affects longevity, males clearly benefit
from a “live fast, die young strategy” by inseminating as many female sexuals
as possible at a cost to their own survival.
acknowledgement: 'German Science Foundation. Grant Number: SCHR 1135/2-1. We thank
M. Adam for handling part of the setups and J. Zoellner for behavioral observations.'
author:
- first_name: Sina
full_name: Metzler, Sina
id: 48204546-F248-11E8-B48F-1D18A9856A87
last_name: Metzler
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
citation:
ama: Metzler S, Heinze J, Schrempf A. Mating and longevity in ant males. Ecology
and Evolution. 2016;6(24):8903-8906. doi:10.1002/ece3.2474
apa: Metzler, S., Heinze, J., & Schrempf, A. (2016). Mating and longevity in
ant males. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.2474
chicago: Metzler, Sina, Jürgen Heinze, and Alexandra Schrempf. “Mating and Longevity
in Ant Males.” Ecology and Evolution. Wiley-Blackwell, 2016. https://doi.org/10.1002/ece3.2474.
ieee: S. Metzler, J. Heinze, and A. Schrempf, “Mating and longevity in ant males,”
Ecology and Evolution, vol. 6, no. 24. Wiley-Blackwell, pp. 8903–8906,
2016.
ista: Metzler S, Heinze J, Schrempf A. 2016. Mating and longevity in ant males.
Ecology and Evolution. 6(24), 8903–8906.
mla: Metzler, Sina, et al. “Mating and Longevity in Ant Males.” Ecology and Evolution,
vol. 6, no. 24, Wiley-Blackwell, 2016, pp. 8903–06, doi:10.1002/ece3.2474.
short: S. Metzler, J. Heinze, A. Schrempf, Ecology and Evolution 6 (2016) 8903–8906.
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:55Z
day: '01'
ddc:
- '576'
- '592'
department:
- _id: SyCr
doi: 10.1002/ece3.2474
file:
- access_level: open_access
checksum: 789026eb9e1be2a0da08376f29f569cf
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:12Z
date_updated: 2020-07-14T12:44:37Z
file_id: '5062'
file_name: IST-2017-736-v1+1_Metzler_et_al-2016-Ecology_and_Evolution.pdf
file_size: 328414
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 8903 - 8906
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6169'
pubrep_id: '736'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mating and longevity in ant males
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1185'
abstract:
- lang: eng
text: The developmental programme of the pistil is under the control of both auxin
and cytokinin. Crosstalk between these factors converges on regulation of the
auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription
factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length
and ovule number were reduced. PIN1 expression was also lower in the triple mutant
and the phenotypes could not be rescued by exogenous cytokinin application. pin1
complementation studies using genomic PIN1 constructs showed that the pistil phenotypes
were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without
this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating
the pivotal role of CRFs in auxin-cytokinin crosstalk.
acknowledgement: M.C. was funded by a PhD fellowship from the Università degli Studi
di Milano-Bicocca and from Ministero dell'Istruzione, dell'Università e della Ricerca
(MIUR) [MIUR-PRIN 2012]. L.C. is also supported by MIUR [MIUR-PRIN 2012]. We would
like to thank Andrew MacCabe and Edward Kiegle for editing the paper.
author:
- first_name: Mara
full_name: Cucinotta, Mara
last_name: Cucinotta
- first_name: Silvia
full_name: Manrique, Silvia
last_name: Manrique
- first_name: Andrea
full_name: Guazzotti, Andrea
last_name: Guazzotti
- first_name: Nadia
full_name: Quadrelli, Nadia
last_name: Quadrelli
- first_name: Marta
full_name: Mendes, Marta
last_name: Mendes
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Lucia
full_name: Colombo, Lucia
last_name: Colombo
citation:
ama: Cucinotta M, Manrique S, Guazzotti A, et al. Cytokinin response factors integrate
auxin and cytokinin pathways for female reproductive organ development. Development.
2016;143(23):4419-4424. doi:10.1242/dev.143545
apa: Cucinotta, M., Manrique, S., Guazzotti, A., Quadrelli, N., Mendes, M., Benková,
E., & Colombo, L. (2016). Cytokinin response factors integrate auxin and cytokinin
pathways for female reproductive organ development. Development. Company
of Biologists. https://doi.org/10.1242/dev.143545
chicago: Cucinotta, Mara, Silvia Manrique, Andrea Guazzotti, Nadia Quadrelli, Marta
Mendes, Eva Benková, and Lucia Colombo. “Cytokinin Response Factors Integrate
Auxin and Cytokinin Pathways for Female Reproductive Organ Development.” Development.
Company of Biologists, 2016. https://doi.org/10.1242/dev.143545.
ieee: M. Cucinotta et al., “Cytokinin response factors integrate auxin and
cytokinin pathways for female reproductive organ development,” Development,
vol. 143, no. 23. Company of Biologists, pp. 4419–4424, 2016.
ista: Cucinotta M, Manrique S, Guazzotti A, Quadrelli N, Mendes M, Benková E, Colombo
L. 2016. Cytokinin response factors integrate auxin and cytokinin pathways for
female reproductive organ development. Development. 143(23), 4419–4424.
mla: Cucinotta, Mara, et al. “Cytokinin Response Factors Integrate Auxin and Cytokinin
Pathways for Female Reproductive Organ Development.” Development, vol.
143, no. 23, Company of Biologists, 2016, pp. 4419–24, doi:10.1242/dev.143545.
short: M. Cucinotta, S. Manrique, A. Guazzotti, N. Quadrelli, M. Mendes, E. Benková,
L. Colombo, Development 143 (2016) 4419–4424.
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:48:56Z
day: '01'
department:
- _id: EvBe
doi: 10.1242/dev.143545
intvolume: ' 143'
issue: '23'
language:
- iso: eng
month: '12'
oa_version: None
page: 4419 - 4424
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6168'
quality_controlled: '1'
scopus_import: 1
status: public
title: Cytokinin response factors integrate auxin and cytokinin pathways for female
reproductive organ development
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 143
year: '2016'
...
---
_id: '1186'
abstract:
- lang: eng
text: The human pathogen Streptococcus pneumoniae is decorated with a special class
of surface-proteins known as choline-binding proteins (CBPs) attached to phosphorylcholine
(PCho) moieties from cell-wall teichoic acids. By a combination of X-ray crystallography,
NMR, molecular dynamics techniques and in vivo virulence and phagocytosis studies,
we provide structural information of choline-binding protein L (CbpL) and demonstrate
its impact on pneumococcal pathogenesis and immune evasion. CbpL is a very elongated
three-module protein composed of (i) an Excalibur Ca 2+ -binding domain -reported
in this work for the very first time-, (ii) an unprecedented anchorage module
showing alternate disposition of canonical and non-canonical choline-binding sites
that allows vine-like binding of fully-PCho-substituted teichoic acids (with two
choline moieties per unit), and (iii) a Ltp-Lipoprotein domain. Our structural
and infection assays indicate an important role of the whole multimodular protein
allowing both to locate CbpL at specific places on the cell wall and to interact
with host components in order to facilitate pneumococcal lung infection and transmigration
from nasopharynx to the lungs and blood. CbpL implication in both resistance against
killing by phagocytes and pneumococcal pathogenesis further postulate this surface-protein
as relevant among the pathogenic arsenal of the pneumococcus.
acknowledgement: We gratefully acknowledge Karsta Barnekow and Kristine Sievert-Giermann,
for technical assistance and Lothar Petruschka for in silico analysis (all Dept.
of Genetics, University of Greifswald). We are further grateful to the staff from
SLS synchrotron beamline for help in data collection. This work was supported by
grants from the Deutsche Forschungsgemeinschaft DFG GRK 1870 (to SH) and the Spanish
Ministry of Economy and Competitiveness (BFU2014-59389-P to JAH, CTQ2014-52633-P
to MB and SAF2012-39760-C02-02 to FG) and S2010/BMD-2457 (Community of Madrid to
JAH and FG).
article_number: '38094'
author:
- first_name: Javier
full_name: Gutierrez-Fernandez, Javier
id: 3D9511BA-F248-11E8-B48F-1D18A9856A87
last_name: Gutierrez-Fernandez
- first_name: Malek
full_name: Saleh, Malek
last_name: Saleh
- first_name: Martín
full_name: Alcorlo, Martín
last_name: Alcorlo
- first_name: Alejandro
full_name: Gómez Mejóa, Alejandro
last_name: Gómez Mejóa
- first_name: David
full_name: Pantoja Uceda, David
last_name: Pantoja Uceda
- first_name: Miguel
full_name: Treviño, Miguel
last_name: Treviño
- first_name: Franziska
full_name: Vob, Franziska
last_name: Vob
- first_name: Mohammed
full_name: Abdullah, Mohammed
last_name: Abdullah
- first_name: Sergio
full_name: Galán Bartual, Sergio
last_name: Galán Bartual
- first_name: Jolien
full_name: Seinen, Jolien
last_name: Seinen
- first_name: Pedro
full_name: Sánchez Murcia, Pedro
last_name: Sánchez Murcia
- first_name: Federico
full_name: Gago, Federico
last_name: Gago
- first_name: Marta
full_name: Bruix, Marta
last_name: Bruix
- first_name: Sven
full_name: Hammerschmidt, Sven
last_name: Hammerschmidt
- first_name: Juan
full_name: Hermoso, Juan
last_name: Hermoso
citation:
ama: Gutierrez-Fernandez J, Saleh M, Alcorlo M, et al. Modular architecture and
unique teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 2016;6. doi:10.1038/srep38094
apa: Gutierrez-Fernandez, J., Saleh, M., Alcorlo, M., Gómez Mejóa, A., Pantoja Uceda,
D., Treviño, M., … Hermoso, J. (2016). Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep38094
chicago: Gutierrez-Fernandez, Javier, Malek Saleh, Martín Alcorlo, Alejandro Gómez
Mejóa, David Pantoja Uceda, Miguel Treviño, Franziska Vob, et al. “Modular Architecture
and Unique Teichoic Acid Recognition Features of Choline-Binding Protein L CbpL
Contributing to Pneumococcal Pathogenesis.” Scientific Reports. Nature
Publishing Group, 2016. https://doi.org/10.1038/srep38094.
ieee: J. Gutierrez-Fernandez et al., “Modular architecture and unique teichoic
acid recognition features of choline-binding protein L CbpL contributing to pneumococcal
pathogenesis,” Scientific Reports, vol. 6. Nature Publishing Group, 2016.
ista: Gutierrez-Fernandez J, Saleh M, Alcorlo M, Gómez Mejóa A, Pantoja Uceda D,
Treviño M, Vob F, Abdullah M, Galán Bartual S, Seinen J, Sánchez Murcia P, Gago
F, Bruix M, Hammerschmidt S, Hermoso J. 2016. Modular architecture and unique
teichoic acid recognition features of choline-binding protein L CbpL contributing
to pneumococcal pathogenesis. Scientific Reports. 6, 38094.
mla: Gutierrez-Fernandez, Javier, et al. “Modular Architecture and Unique Teichoic
Acid Recognition Features of Choline-Binding Protein L CbpL Contributing to Pneumococcal
Pathogenesis.” Scientific Reports, vol. 6, 38094, Nature Publishing Group,
2016, doi:10.1038/srep38094.
short: J. Gutierrez-Fernandez, M. Saleh, M. Alcorlo, A. Gómez Mejóa, D. Pantoja
Uceda, M. Treviño, F. Vob, M. Abdullah, S. Galán Bartual, J. Seinen, P. Sánchez
Murcia, F. Gago, M. Bruix, S. Hammerschmidt, J. Hermoso, Scientific Reports 6
(2016).
date_created: 2018-12-11T11:50:36Z
date_published: 2016-12-05T00:00:00Z
date_updated: 2021-01-12T06:48:56Z
day: '05'
ddc:
- '576'
- '610'
department:
- _id: LeSa
doi: 10.1038/srep38094
file:
- access_level: open_access
checksum: e007d78b483bc59bf5ab98e9d42a6ec1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:18Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4804'
file_name: IST-2017-735-v1+1_srep38094.pdf
file_size: 2716045
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6167'
pubrep_id: '735'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modular architecture and unique teichoic acid recognition features of choline-binding
protein L CbpL contributing to pneumococcal pathogenesis
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1188'
abstract:
- lang: eng
text: "We consider a population dynamics model coupling cell growth to a diffusion
in the space of metabolic phenotypes as it can be obtained from realistic constraints-based
modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with
the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation
is solved for the steady state in the WKB\r\napproximation that maps it into the
ground state of a quantum particle in an\r\nAiry potential plus a centrifugal
term. We retrieve scaling laws for growth rate\r\nfluctuations and time response
with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal
populations can have a faster response\r\nto perturbations."
acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions)
of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant
agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011.
D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa
for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano
and Vera Luz Masoero for useful discussions, also late at night.
article_number: '123502'
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Davide
full_name: Masoero, Davide
last_name: Masoero
citation:
ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics:
Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f'
apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness
maximization, applied to metabolism & growth. Journal of Statistical
Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f'
chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy
Fitness Maximization, Applied to Metabolism & Growth.” Journal of
Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.'
ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth,” Journal of Statistical Mechanics:
Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.'
ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization,
applied to metabolism & growth. Journal of Statistical Mechanics: Theory
and Experiment. 2016(12), 123502.'
mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness
Maximization, Applied to Metabolism & Growth.” Journal of Statistical
Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016,
doi:10.1088/1742-5468/aa4e8f.'
short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and
Experiment 2016 (2016).'
date_created: 2018-12-11T11:50:37Z
date_published: 2016-12-30T00:00:00Z
date_updated: 2021-01-12T06:48:57Z
day: '30'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa4e8f
ec_funded: 1
intvolume: ' 2016'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1606.09048
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_status: published
publisher: IOPscience
publist_id: '6165'
quality_controlled: '1'
scopus_import: 1
status: public
title: Asymptotic analysis of noisy fitness maximization, applied to metabolism &
growth
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2016
year: '2016'
...
---
_id: '1193'
abstract:
- lang: eng
text: We consider the recent formulation of the Algorithmic Lovász Local Lemma [1],
[2] for finding objects that avoid "bad features", or "flaws".
It extends the Moser-Tardos resampling algorithm [3] to more general discrete
spaces. At each step the method picks a flaw present in the current state and
"resamples" it using a "resampling oracle" provided by the
user. However, it is less flexible than the Moser-Tardos method since [1], [2]
require a specific flaw selection rule, whereas [3] allows an arbitrary rule (and
thus can potentially be implemented more efficiently). We formulate a new "commutativity"
condition, and prove that it is sufficient for an arbitrary rule to work. It also
enables an efficient parallelization under an additional assumption. We then show
that existing resampling oracles for perfect matchings and permutations do satisfy
this condition. Finally, we generalize the precondition in [2] (in the case of
symmetric potential causality graphs). This unifies special cases that previously
were treated separately.
acknowledgement: European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant
agreement no 616160
article_number: '7782993'
article_processing_charge: No
arxiv: 1
author:
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Commutativity in the algorithmic Lovasz local lemma. In: Proceedings
- Annual IEEE Symposium on Foundations of Computer Science. Vol 2016-December.
IEEE; 2016. doi:10.1109/FOCS.2016.88'
apa: 'Kolmogorov, V. (2016). Commutativity in the algorithmic Lovasz local lemma.
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science
(Vol. 2016–December). New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/FOCS.2016.88'
chicago: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
In Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
Vol. 2016–December. IEEE, 2016. https://doi.org/10.1109/FOCS.2016.88.
ieee: V. Kolmogorov, “Commutativity in the algorithmic Lovasz local lemma,” in Proceedings
- Annual IEEE Symposium on Foundations of Computer Science, New Brunswick,
NJ, USA , 2016, vol. 2016–December.
ista: 'Kolmogorov V. 2016. Commutativity in the algorithmic Lovasz local lemma.
Proceedings - Annual IEEE Symposium on Foundations of Computer Science. FOCS:
Foundations of Computer Science vol. 2016–December, 7782993.'
mla: Kolmogorov, Vladimir. “Commutativity in the Algorithmic Lovasz Local Lemma.”
Proceedings - Annual IEEE Symposium on Foundations of Computer Science,
vol. 2016–December, 7782993, IEEE, 2016, doi:10.1109/FOCS.2016.88.
short: V. Kolmogorov, in:, Proceedings - Annual IEEE Symposium on Foundations of
Computer Science, IEEE, 2016.
conference:
end_date: 2016-09-11
location: 'New Brunswick, NJ, USA '
name: 'FOCS: Foundations of Computer Science'
start_date: 2016-09-09
date_created: 2018-12-11T11:50:38Z
date_published: 2016-12-15T00:00:00Z
date_updated: 2023-09-19T14:24:57Z
day: '15'
department:
- _id: VlKo
doi: 10.1109/FOCS.2016.88
ec_funded: 1
external_id:
arxiv:
- '1506.08547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1506.08547v7
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings - Annual IEEE Symposium on Foundations of Computer Science
publication_status: published
publisher: IEEE
publist_id: '6158'
quality_controlled: '1'
related_material:
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relation: later_version
status: public
scopus_import: 1
status: public
title: Commutativity in the algorithmic Lovasz local lemma
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2016-December
year: '2016'
...
---
_id: '1195'
abstract:
- lang: eng
text: 'The genetic analysis of experimentally evolving populations typically relies
on short reads from pooled individuals (Pool-Seq). While this method provides
reliable allele frequency estimates, the underlying haplotype structure remains
poorly characterized. With small population sizes and adaptive variants that start
from low frequencies, the interpretation of selection signatures in most Evolve
and Resequencing studies remains challenging. To facilitate the characterization
of selection targets, we propose a new approach that reconstructs selected haplotypes
from replicated time series, using Pool-Seq data. We identify selected haplotypes
through the correlated frequencies of alleles carried by them. Computer simulations
indicate that selected haplotype-blocks of several Mb can be reconstructed with
high confidence and low error rates, even when allele frequencies change only
by 20% across three replicates. Applying this method to real data from D. melanogaster
populations adapting to a hot environment, we identify a selected haplotype-block
of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations
by experimental haplotyping, demonstrating the power and accuracy of our haplotype
reconstruction from Pool-Seq data. We propose that the combination of allele frequency
estimates with haplotype information will provide the key to understanding the
dynamics of adaptive alleles. '
acknowledgement: "The authors thank all members of the Institute of Population\r\nGenetics
for discussion and support on the project and par-\r\nticularly N. Barghi for helpful
comments on earlier versions of\r\nthe manuscript. This work was supported
\ by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”."
author:
- first_name: Susan
full_name: Franssen, Susan
last_name: Franssen
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Christian
full_name: Schlötterer, Christian
last_name: Schlötterer
citation:
ama: Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected
during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184.
doi:10.1093/molbev/msw210
apa: Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of
haplotype-blocks selected during experimental evolution. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210
chicago: Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction
of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology
and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.
ieee: S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks
selected during experimental evolution.,” Molecular Biology and Evolution,
vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.
ista: Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks
selected during experimental evolution. Molecular Biology and Evolution. 34(1),
174–184.
mla: Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during
Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no.
1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.
short: S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution
34 (2016) 174–184.
date_created: 2018-12-11T11:50:39Z
date_published: 2016-10-03T00:00:00Z
date_updated: 2021-01-12T06:49:00Z
day: '03'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1093/molbev/msw210
ec_funded: 1
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date_created: 2018-12-12T10:16:38Z
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creator: system
date_created: 2018-12-12T10:16:38Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5227'
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has_accepted_license: '1'
intvolume: ' 34'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 174 - 184
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6155'
pubrep_id: '770'
quality_controlled: '1'
scopus_import: 1
status: public
title: Reconstruction of haplotype-blocks selected during experimental evolution.
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2016'
...
---
_id: '1197'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
acknowledgement: JSP was supported by a C.V. Starr Fellowship from the Starr Foundation
(http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation
(https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National
Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science
Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler
for helpful comments on the manuscript.
article_number: e1005855
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes
of the retinal population code. PLoS Computational Biology. 2016;12(11).
doi:10.1371/journal.pcbi.1005148
apa: Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2016). Error-robust modes of the retinal population code. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148
chicago: Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS
Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148.
ieee: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust
modes of the retinal population code,” PLoS Computational Biology, vol.
12, no. 11. Public Library of Science, 2016.
ista: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust
modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.
mla: Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.”
PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of
Science, 2016, doi:10.1371/journal.pcbi.1005148.
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational
Biology 12 (2016).
date_created: 2018-12-11T11:50:40Z
date_published: 2016-11-17T00:00:00Z
date_updated: 2023-02-23T14:05:40Z
day: '17'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005148
file:
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checksum: 47b08cbd4dbf32b25ba161f5f4b262cc
content_type: application/pdf
creator: kschuh
date_created: 2019-01-25T10:35:00Z
date_updated: 2020-07-14T12:44:38Z
file_id: '5884'
file_name: 2016_PLOS_Prentice.pdf
file_size: 4492021
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month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 254D1A94-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 25651-N26
name: Sensitivity to higher-order statistics in natural scenes
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6153'
quality_controlled: '1'
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scopus_import: 1
status: public
title: Error-robust modes of the retinal population code
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2016'
...
---
_id: '1200'
acknowledgement: C.H. acknowledges generous support from the ISTFELLOW program.
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Arne
full_name: Traulsen, Arne
last_name: Traulsen
citation:
ama: 'Hilbe C, Traulsen A. Only the combination of mathematics and agent based simulations
can leverage the full potential of evolutionary modeling: Comment on “Evolutionary
game theory using agent-based methods” by C. Adami, J. Schossau and A. Hintze.
Physics of Life Reviews. 2016;19:29-31. doi:10.1016/j.plrev.2016.10.004'
apa: 'Hilbe, C., & Traulsen, A. (2016). Only the combination of mathematics
and agent based simulations can leverage the full potential of evolutionary modeling:
Comment on “Evolutionary game theory using agent-based methods” by C. Adami, J.
Schossau and A. Hintze. Physics of Life Reviews. Elsevier. https://doi.org/10.1016/j.plrev.2016.10.004'
chicago: 'Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics
and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling:
Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J.
Schossau and A. Hintze.” Physics of Life Reviews. Elsevier, 2016. https://doi.org/10.1016/j.plrev.2016.10.004.'
ieee: 'C. Hilbe and A. Traulsen, “Only the combination of mathematics and agent
based simulations can leverage the full potential of evolutionary modeling: Comment
on ‘Evolutionary game theory using agent-based methods’ by C. Adami, J. Schossau
and A. Hintze,” Physics of Life Reviews, vol. 19. Elsevier, pp. 29–31,
2016.'
ista: 'Hilbe C, Traulsen A. 2016. Only the combination of mathematics and agent
based simulations can leverage the full potential of evolutionary modeling: Comment
on “Evolutionary game theory using agent-based methods” by C. Adami, J. Schossau
and A. Hintze. Physics of Life Reviews. 19, 29–31.'
mla: 'Hilbe, Christian, and Arne Traulsen. “Only the Combination of Mathematics
and Agent Based Simulations Can Leverage the Full Potential of Evolutionary Modeling:
Comment on ‘Evolutionary Game Theory Using Agent-Based Methods’ by C. Adami, J.
Schossau and A. Hintze.” Physics of Life Reviews, vol. 19, Elsevier, 2016,
pp. 29–31, doi:10.1016/j.plrev.2016.10.004.'
short: C. Hilbe, A. Traulsen, Physics of Life Reviews 19 (2016) 29–31.
date_created: 2018-12-11T11:50:40Z
date_published: 2016-12-01T00:00:00Z
date_updated: 2021-01-12T06:49:03Z
day: '01'
ddc:
- '530'
department:
- _id: KrCh
doi: 10.1016/j.plrev.2016.10.004
ec_funded: 1
file:
- access_level: open_access
checksum: 95e6dc78278334b99dacbf8822509364
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:02Z
date_updated: 2020-07-14T12:44:39Z
file_id: '4855'
file_name: IST-2017-798-v1+1_comment_adami.pdf
file_size: 171352
relation: main_file
file_date_updated: 2020-07-14T12:44:39Z
has_accepted_license: '1'
intvolume: ' 19'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Submitted Version
page: 29 - 31
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Physics of Life Reviews
publication_status: published
publisher: Elsevier
publist_id: '6150'
pubrep_id: '798'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Only the combination of mathematics and agent based simulations can leverage
the full potential of evolutionary modeling: Comment on “Evolutionary game theory
using agent-based methods” by C. Adami, J. Schossau and A. Hintze'
tmp:
image: /images/cc_by_nc_nd.png
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(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
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year: '2016'
...