---
_id: '1604'
abstract:
- lang: eng
text: We consider the quantitative analysis problem for interprocedural control-flow
graphs (ICFGs). The input consists of an ICFG, a positive weight function that
assigns every transition a positive integer-valued number, and a labelling of
the transitions (events) as good, bad, and neutral events. The weight function
assigns to each transition a numerical value that represents ameasure of how good
or bad an event is. The quantitative analysis problem asks whether there is a
run of the ICFG where the ratio of the sum of the numerical weights of good events
versus the sum of weights of bad events in the long-run is at least a given threshold
(or equivalently, to compute the maximal ratio among all valid paths in the ICFG).
The quantitative analysis problem for ICFGs can be solved in polynomial time,
and we present an efficient and practical algorithm for the problem. We show that
several problems relevant for static program analysis, such as estimating the
worst-case execution time of a program or the average energy consumption of a
mobile application, can be modeled in our framework. We have implemented our algorithm
as a tool in the Java Soot framework. We demonstrate the effectiveness of our
approach with two case studies. First, we show that our framework provides a sound
approach (no false positives) for the analysis of inefficiently-used containers.
Second, we show that our approach can also be used for static profiling of programs
which reasons about methods that are frequently invoked. Our experimental results
show that our tool scales to relatively large benchmarks, and discovers relevant
and useful information that can be used to optimize performance of the programs.
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis.
Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 2015;50(1):539-551.
doi:10.1145/2676726.2676968
apa: 'Chatterjee, K., Pavlogiannis, A., & Velner, Y. (2015). Quantitative interprocedural
analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . Mumbai, India:
ACM. https://doi.org/10.1145/2676726.2676968'
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative
Interprocedural Analysis.” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT
. ACM, 2015. https://doi.org/10.1145/2676726.2676968.
ieee: K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural
analysis,” Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50,
no. 1. ACM, pp. 539–551, 2015.
ista: Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural
analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551.
mla: Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” Proceedings
of the 42nd Annual ACM SIGPLAN-SIGACT , vol. 50, no. 1, ACM, 2015, pp. 539–51,
doi:10.1145/2676726.2676968.
short: K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual
ACM SIGPLAN-SIGACT 50 (2015) 539–551.
conference:
end_date: 2015-01-17
location: Mumbai, India
name: 'SIGPLAN: Symposium on Principles of Programming Languages'
start_date: 2015-01-15
date_created: 2018-12-11T11:52:59Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '01'
department:
- _id: KrCh
doi: 10.1145/2676726.2676968
ec_funded: 1
intvolume: ' 50'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 539 - 551
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _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: 'Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT '
publication_identifier:
isbn:
- 978-1-4503-3300-9
publication_status: published
publisher: ACM
publist_id: '5563'
pubrep_id: '523'
quality_controlled: '1'
related_material:
record:
- id: '5445'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Quantitative interprocedural analysis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2015'
...
---
_id: '1605'
abstract:
- lang: eng
text: Multiaffine hybrid automata (MHA) represent a powerful formalism to model
complex dynamical systems. This formalism is particularly suited for the representation
of biological systems which often exhibit highly non-linear behavior. In this
paper, we consider the problem of parameter identification for MHA. We present
an abstraction of MHA based on linear hybrid automata, which can be analyzed by
the SpaceEx model checker. This abstraction enables a precise handling of time-dependent
properties. We demonstrate the potential of our approach on a model of a genetic
regulatory network and a myocyte model.
acknowledgement: This work was partly supported by the European Research Council (ERC)
under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23,
S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by
the German Research Foundation (DFG) as part of the Transregional Collaborative
Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR
14 AVACS, http://www.avacs.org/).
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Grégory
full_name: Batt, Grégory
last_name: Batt
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Radu
full_name: Grosu, Radu
last_name: Grosu
citation:
ama: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based
parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35.
doi:10.1007/978-3-319-26287-1_2'
apa: 'Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu,
R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol.
9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa,
Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2'
chicago: Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui
Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,”
9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2.
ieee: 'S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu,
“Abstraction-based parameter synthesis for multiaffine systems,” presented at
the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.'
ista: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based
parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference,
LNCS, vol. 9434, 19–35.'
mla: Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine
Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2.
short: S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:,
Springer, 2015, pp. 19–35.
conference:
end_date: 2015-11-19
location: Haifa, Israel
name: 'HVC: Haifa Verification Conference'
start_date: 2015-11-17
date_created: 2018-12-11T11:52:59Z
date_published: 2015-11-28T00:00:00Z
date_updated: 2021-01-12T06:51:56Z
day: '28'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.1007/978-3-319-26287-1_2
ec_funded: 1
file:
- access_level: open_access
checksum: 3aab260f3f34641d622030ba22645b3e
content_type: application/pdf
creator: dernst
date_created: 2020-05-15T08:43:19Z
date_updated: 2020-07-14T12:45:05Z
file_id: '7851'
file_name: 2015_LNCS_Bogomolov.pdf
file_size: 1053207
relation: main_file
file_date_updated: 2020-07-14T12:45:05Z
has_accepted_license: '1'
intvolume: ' 9434'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 19 - 35
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication_status: published
publisher: Springer
publist_id: '5561'
quality_controlled: '1'
scopus_import: 1
status: public
title: Abstraction-based parameter synthesis for multiaffine systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9434
year: '2015'
...
---
_id: '1606'
abstract:
- lang: eng
text: 'In this paper, we present the first steps toward a runtime verification framework
for monitoring hybrid and cyber-physical systems (CPS) development tools based
on randomized differential testing. The development tools include hybrid systems
reachability analysis tools, model-based development environments like Simulink/Stateflow
(SLSF), etc. First, hybrid automaton models are randomly generated. Next, these
hybrid automaton models are translated to a number of different tools (currently,
SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using
the HyST source transformation and translation tool. Then, the hybrid automaton
models are executed in the different tools and their outputs are parsed. The final
step is the differential comparison: the outputs of the different tools are compared.
If the results do not agree (in the sense that an analysis or verification result
from one tool does not match that of another tool, ignoring timeouts, etc.), a
candidate bug is flagged and the model is saved for future analysis by the user.
The process then repeats and the monitoring continues until the user terminates
the process. We present preliminary results that have been useful in identifying
a few bugs in the analysis methods of different development tools, and in an earlier
version of HyST.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Luan
full_name: Nguyen, Luan
last_name: Nguyen
- first_name: Christian
full_name: Schilling, Christian
last_name: Schilling
- first_name: Sergiy
full_name: Bogomolov, Sergiy
id: 369D9A44-F248-11E8-B48F-1D18A9856A87
last_name: Bogomolov
orcid: 0000-0002-0686-0365
- first_name: Taylor
full_name: Johnson, Taylor
last_name: Johnson
citation:
ama: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid
analysis tools. In: 6th International Conference. Vol 9333. Springer Nature;
2015:281-286. doi:10.1007/978-3-319-23820-3_19'
apa: 'Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Runtime
verification for hybrid analysis tools. In 6th International Conference
(Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. https://doi.org/10.1007/978-3-319-23820-3_19'
chicago: Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson.
“Runtime Verification for Hybrid Analysis Tools.” In 6th International Conference,
9333:281–86. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-23820-3_19.
ieee: L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification
for hybrid analysis tools,” in 6th International Conference, Vienna, Austria,
2015, vol. 9333, pp. 281–286.
ista: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification
for hybrid analysis tools. 6th International Conference. RV: Runtime Verification,
LNCS, vol. 9333, 281–286.'
mla: Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” 6th
International Conference, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:10.1007/978-3-319-23820-3_19.
short: L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International
Conference, Springer Nature, 2015, pp. 281–286.
conference:
end_date: 2015-09-25
location: Vienna, Austria
name: 'RV: Runtime Verification'
start_date: 2015-09-22
date_created: 2018-12-11T11:52:59Z
date_published: 2015-11-15T00:00:00Z
date_updated: 2022-02-01T14:52:59Z
day: '15'
department:
- _id: ToHe
doi: 10.1007/978-3-319-23820-3_19
ec_funded: 1
intvolume: ' 9333'
language:
- iso: eng
month: '11'
oa_version: None
page: 281 - 286
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 6th International Conference
publication_identifier:
isbn:
- 978-3-319-23819-7
publication_status: published
publisher: Springer Nature
publist_id: '5562'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Runtime verification for hybrid analysis tools
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9333
year: '2015'
...
---
_id: '1607'
abstract:
- lang: eng
text: We consider the core algorithmic problems related to verification of systems
with respect to three classical quantitative properties, namely, the mean-payoff
property, the ratio property, and the minimum initial credit for energy property.
The algorithmic problem given a graph and a quantitative property asks to compute
the optimal value (the infimum value over all traces) from every node of the graph.
We consider graphs with constant treewidth, and it is well-known that the control-flow
graphs of most programs have constant treewidth. Let n denote the number of nodes
of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W
the largest absolute value of the weights. Our main theoretical results are as
follows. First, for constant treewidth graphs we present an algorithm that approximates
the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ))
and linear space, as compared to the classical algorithms that require quadratic
time. Second, for the ratio property we present an algorithm that for constant
treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output
is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)).
Third, for the minimum initial credit problem we show that (i) for general graphs
the problem can be solved in O(n2⋅m) time and the associated decision problem
can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and
O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present
an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W))
bound. We have implemented some of our algorithms and show that they present a
significant speedup on standard benchmarks.
acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Microsoft faculty fellows award.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Rasmus
full_name: Ibsen-Jensen, Rasmus
id: 3B699956-F248-11E8-B48F-1D18A9856A87
last_name: Ibsen-Jensen
orcid: 0000-0003-4783-0389
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative
verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157.
doi:10.1007/978-3-319-21690-4_9'
apa: 'Chatterjee, K., Ibsen-Jensen, R., & Pavlogiannis, A. (2015). Faster algorithms
for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157).
Presented at the CAV: Computer Aided Verification, San Francisco, CA, USA: Springer.
https://doi.org/10.1007/978-3-319-21690-4_9'
chicago: Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis.
“Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,”
9206:140–57. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_9.
ieee: 'K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for
quantitative verification in constant treewidth graphs,” presented at the CAV:
Computer Aided Verification, San Francisco, CA, USA, 2015, vol. 9206, pp. 140–157.'
ista: 'Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for
quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification,
LNCS, vol. 9206, 140–157.'
mla: Chatterjee, Krishnendu, et al. Faster Algorithms for Quantitative Verification
in Constant Treewidth Graphs. Vol. 9206, Springer, 2015, pp. 140–57, doi:10.1007/978-3-319-21690-4_9.
short: K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp.
140–157.
conference:
end_date: 2015-07-24
location: San Francisco, CA, USA
name: 'CAV: Computer Aided Verification'
start_date: 2015-07-18
date_created: 2018-12-11T11:52:59Z
date_published: 2015-07-16T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '16'
department:
- _id: KrCh
doi: 10.1007/978-3-319-21690-4_9
ec_funded: 1
intvolume: ' 9206'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.07384
month: '07'
oa: 1
oa_version: Preprint
page: 140 - 157
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'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '5560'
quality_controlled: '1'
related_material:
record:
- id: '5430'
relation: earlier_version
status: public
- id: '5437'
relation: earlier_version
status: public
- id: '821'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Faster algorithms for quantitative verification in constant treewidth graphs
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 9206
year: '2015'
...
---
_id: '1609'
abstract:
- lang: eng
text: The synthesis problem asks for the automatic construction of a system from
its specification. In the traditional setting, the system is “constructed from
scratch” rather than composed from reusable components. However, this is rare
in practice, and almost every non-trivial software system relies heavily on the
use of libraries of reusable components. Recently, Lustig and Vardi introduced
dataflow and controlflow synthesis from libraries of reusable components. They
proved that dataflow synthesis is undecidable, while controlflow synthesis is
decidable. The problem of controlflow synthesis from libraries of probabilistic
components was considered by Nain, Lustig and Vardi, and was shown to be decidable
for qualitative analysis (that asks that the specification be satisfied with probability
1). Our main contribution for controlflow synthesis from probabilistic components
is to establish better complexity bounds for the qualitative analysis problem,
and to show that the more general quantitative problem is undecidable. For the
qualitative analysis, we show that the problem (i) is EXPTIME-complete when the
specification is given as a deterministic parity word automaton, improving the
previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games
hard, when the specification is given directly as a parity condition on the components,
improving the previously known EXPTIME upper bound.
acknowledgement: 'This research was supported by Austrian Science Fund (FWF) Grant
No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph
Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF
Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program
Engineering”, by BSF grant 9800096, and by gift from Intel.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Moshe
full_name: Vardi, Moshe
last_name: Vardi
citation:
ama: 'Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic
components. In: 42nd International Colloquium. Vol 9135. Springer Nature;
2015:108-120. doi:10.1007/978-3-662-47666-6_9'
apa: 'Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis
from probabilistic components. In 42nd International Colloquium (Vol. 9135,
pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9'
chicago: Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity
of Synthesis from Probabilistic Components.” In 42nd International Colloquium,
9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9.
ieee: K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic
components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol.
9135, pp. 108–120.
ista: 'Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic
components. 42nd International Colloquium. ICALP: Automata, Languages and Programming,
LNCS, vol. 9135, 108–120.'
mla: Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic
Components.” 42nd International Colloquium, vol. 9135, Springer Nature,
2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9.
short: K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer
Nature, 2015, pp. 108–120.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:00Z
date_published: 2015-06-20T00:00:00Z
date_updated: 2022-02-01T15:04:44Z
day: '20'
department:
- _id: KrCh
doi: 10.1007/978-3-662-47666-6_9
ec_funded: 1
intvolume: ' 9135'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1502.04844
month: '06'
oa: 1
oa_version: Preprint
page: 108 - 120
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: 42nd International Colloquium
publication_identifier:
isbn:
- 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5557'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The complexity of synthesis from probabilistic components
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '1610'
abstract:
- lang: eng
text: The edit distance between two words w1, w2 is the minimal number of word operations
(letter insertions, deletions, and substitutions) necessary to transform w1 to
w2. The edit distance generalizes to languages L1,L2, where the edit distance
is the minimal number k such that for every word from L1 there exists a word in
L2 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 pushdown automata 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
deciding whether, for a given threshold k, the edit distance from a pushdown automaton
to a finite automaton is at most k.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: 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
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
citation:
ama: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown
automata. In: 42nd International Colloquium. Vol 9135. Springer Nature;
2015:121-133. doi:10.1007/978-3-662-47666-6_10'
apa: 'Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., & Otop, J. (2015).
Edit distance for pushdown automata. In 42nd International Colloquium (Vol.
9135, pp. 121–133). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_10'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan
Otop. “Edit Distance for Pushdown Automata.” In 42nd International Colloquium,
9135:121–33. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_10.
ieee: K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance
for pushdown automata,” in 42nd International Colloquium, Kyoto, Japan,
2015, vol. 9135, no. Part II, pp. 121–133.
ista: 'Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for
pushdown automata. 42nd International Colloquium. ICALP: Automata, Languages and
Programming, LNCS, vol. 9135, 121–133.'
mla: Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” 42nd
International Colloquium, vol. 9135, no. Part II, Springer Nature, 2015, pp.
121–33, doi:10.1007/978-3-662-47666-6_10.
short: K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International
Colloquium, Springer Nature, 2015, pp. 121–133.
conference:
end_date: 2015-07-10
location: Kyoto, Japan
name: 'ICALP: Automata, Languages and Programming'
start_date: 2015-07-06
date_created: 2018-12-11T11:53:01Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-02-23T12:26:24Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-662-47666-6_10
ec_funded: 1
external_id:
arxiv:
- '1504.08259'
intvolume: ' 9135'
issue: Part II
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1504.08259
month: '07'
oa: 1
oa_version: None
page: 121 - 133
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _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: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: 42nd International Colloquium
publication_identifier:
isbn:
- 978-3-662-47665-9
publication_status: published
publisher: Springer Nature
publist_id: '5556'
pubrep_id: '321'
quality_controlled: '1'
related_material:
record:
- id: '465'
relation: later_version
status: public
- id: '5438'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Edit distance for pushdown automata
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 9135
year: '2015'
...
---
_id: '1611'
abstract:
- lang: eng
text: Biosensors for signaling molecules allow the study of physiological processes
by bringing together the fields of protein engineering, fluorescence imaging,
and cell biology. Construction of genetically encoded biosensors generally relies
on the availability of a binding "core" that is both specific and stable,
which can then be combined with fluorescent molecules to create a sensor. However,
binding proteins with the desired properties are often not available in nature
and substantial improvement to sensors can be required, particularly with regard
to their durability. Ancestral protein reconstruction is a powerful protein-engineering
tool able to generate highly stable and functional proteins. In this work, we
sought to establish the utility of ancestral protein reconstruction to biosensor
development, beginning with the construction of an l-arginine biosensor. l-arginine,
as the immediate precursor to nitric oxide, is an important molecule in many physiological
contexts including brain function. Using a combination of ancestral reconstruction
and circular permutation, we constructed a Förster resonance energy transfer (FRET)
biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity,
with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was
highly robust, enabling accurate l-arginine measurement at physiological temperatures.
We established that cpFLIPR is compatible with two-photon excitation fluorescence
microscopy and report l-arginine concentrations in brain tissue.
author:
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Johanna
full_name: Radziejewski, Johanna
last_name: Radziejewski
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive
arginine biosensor through ancestral protein reconstruction. Protein Science.
2015;24(9):1412-1422. doi:10.1002/pro.2721
apa: Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak,
H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor
through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721
chicago: Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski,
Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of
a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.”
Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721.
ieee: J. Whitfield et al., “Construction of a robust and sensitive arginine
biosensor through ancestral protein reconstruction,” Protein Science, vol.
24, no. 9. Wiley, pp. 1412–1422, 2015.
ista: Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger
C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor
through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422.
mla: Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor
through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no.
9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721.
short: J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak,
C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422.
date_created: 2018-12-11T11:53:01Z
date_published: 2015-09-01T00:00:00Z
date_updated: 2021-01-12T06:52:00Z
day: '01'
department:
- _id: HaJa
doi: 10.1002/pro.2721
external_id:
pmid:
- '26061224'
intvolume: ' 24'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/
month: '09'
oa: 1
oa_version: Submitted Version
page: 1412 - 1422
pmid: 1
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Protein Science
publication_status: published
publisher: Wiley
publist_id: '5555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Construction of a robust and sensitive arginine biosensor through ancestral
protein reconstruction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2015'
...
---
_id: '1614'
abstract:
- lang: eng
text: 'GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively
control the activity of large neuron populations by their wide axonal arborizations.
It is generally assumed that the output of one PII to its target cells is strong
and rapid. Here, we show that, unexpectedly, both strength and time course of
PII-mediated perisomatic inhibition change with distance between synaptically
connected partners in the rodent hippocampus. Synaptic signals become weaker due
to lower contact numbers and decay more slowly with distance, very likely resulting
from changes in GABAA receptor subunit composition. When distance-dependent synaptic
inhibition is introduced to a rhythmically active neuronal network model, randomly
driven principal cell assemblies are strongly synchronized by the PIIs, leading
to higher precision in principal cell spike times than in a network with uniform
synaptic inhibition. '
author:
- first_name: Michael
full_name: Strüber, Michael
last_name: Strüber
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic
inhibition depend on distance between synaptically connected cells. PNAS.
2015;112(4):1220-1225. doi:10.1073/pnas.1412996112
apa: Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of
perisomatic GABAergic inhibition depend on distance between synaptically connected
cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112
chicago: Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration
of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected
Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112.
ieee: M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic
GABAergic inhibition depend on distance between synaptically connected cells,”
PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015.
ista: Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic
GABAergic inhibition depend on distance between synaptically connected cells.
PNAS. 112(4), 1220–1225.
mla: Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition
Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112,
no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112.
short: M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225.
date_created: 2018-12-11T11:53:02Z
date_published: 2015-01-27T00:00:00Z
date_updated: 2021-01-12T06:52:01Z
day: '27'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.1073/pnas.1412996112
ec_funded: 1
external_id:
pmid:
- '25583495'
file:
- access_level: open_access
checksum: 6703309a1f58493cf5a704211fb6ebed
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T07:52:40Z
date_updated: 2020-07-14T12:45:07Z
file_id: '5838'
file_name: 2015_PNAS_Strueber.pdf
file_size: 1280860
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 112'
issue: '4'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 1220 - 1225
pmid: 1
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5552'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strength and duration of perisomatic GABAergic inhibition depend on distance
between synaptically connected cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2015'
...
---
_id: '1383'
abstract:
- lang: eng
text: In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi
network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has
impeded our understanding of how the pH homeostasis within the plant TGN/EE controls
exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3
(det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly
impairing secretion and recycling of the brassinosteroid receptor and the cellulose
synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized
V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency
defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility.
Thus, our results provide strong evidence that acidification of the TGN/EE, but
not of the vacuole, is indispensable for functional secretion and recycling in
plants.
article_number: '15094'
article_processing_charge: No
article_type: original
author:
- first_name: Luo
full_name: Yu, Luo
last_name: Yu
- first_name: Stefan
full_name: Scholl, Stefan
last_name: Scholl
- first_name: Anett
full_name: Doering, Anett
last_name: Doering
- first_name: Zhang
full_name: Yi, Zhang
last_name: Yi
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Lutz
full_name: Neumetzler, Lutz
last_name: Neumetzler
- first_name: Praveen
full_name: Krishnamoorthy, Praveen
last_name: Krishnamoorthy
- first_name: Isabelle
full_name: Van Houtte, Isabelle
last_name: Van Houtte
- first_name: Evelien
full_name: Mylle, Evelien
last_name: Mylle
- first_name: Volker
full_name: Bischoff, Volker
last_name: Bischoff
- first_name: Samantha
full_name: Vernhettes, Samantha
last_name: Vernhettes
- first_name: Johan
full_name: Winne, Johan
last_name: Winne
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: York
full_name: Stierhof, York
last_name: Stierhof
- first_name: Karin
full_name: Schumacher, Karin
last_name: Schumacher
- first_name: Staffan
full_name: Persson, Staffan
last_name: Persson
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Yu L, Scholl S, Doering A, et al. V-ATPase activity in the TGN/EE is required
for exocytosis and recycling in Arabidopsis. Nature Plants. 2015;1(7).
doi:10.1038/nplants.2015.94
apa: Yu, L., Scholl, S., Doering, A., Yi, Z., Irani, N., Di Rubbo, S., … Russinova,
E. (2015). V-ATPase activity in the TGN/EE is required for exocytosis and recycling
in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/nplants.2015.94
chicago: Yu, Luo, Stefan Scholl, Anett Doering, Zhang Yi, Niloufer Irani, Simone
Di Rubbo, Lutz Neumetzler, et al. “V-ATPase Activity in the TGN/EE Is Required
for Exocytosis and Recycling in Arabidopsis.” Nature Plants. Nature Publishing
Group, 2015. https://doi.org/10.1038/nplants.2015.94.
ieee: L. Yu et al., “V-ATPase activity in the TGN/EE is required for exocytosis
and recycling in Arabidopsis,” Nature Plants, vol. 1, no. 7. Nature Publishing
Group, 2015.
ista: Yu L, Scholl S, Doering A, Yi Z, Irani N, Di Rubbo S, Neumetzler L, Krishnamoorthy
P, Van Houtte I, Mylle E, Bischoff V, Vernhettes S, Winne J, Friml J, Stierhof
Y, Schumacher K, Persson S, Russinova E. 2015. V-ATPase activity in the TGN/EE
is required for exocytosis and recycling in Arabidopsis. Nature Plants. 1(7),
15094.
mla: Yu, Luo, et al. “V-ATPase Activity in the TGN/EE Is Required for Exocytosis
and Recycling in Arabidopsis.” Nature Plants, vol. 1, no. 7, 15094, Nature
Publishing Group, 2015, doi:10.1038/nplants.2015.94.
short: L. Yu, S. Scholl, A. Doering, Z. Yi, N. Irani, S. Di Rubbo, L. Neumetzler,
P. Krishnamoorthy, I. Van Houtte, E. Mylle, V. Bischoff, S. Vernhettes, J. Winne,
J. Friml, Y. Stierhof, K. Schumacher, S. Persson, E. Russinova, Nature Plants
1 (2015).
date_created: 2018-12-11T11:51:42Z
date_published: 2015-07-06T00:00:00Z
date_updated: 2021-01-12T06:50:18Z
day: '06'
department:
- _id: JiFr
doi: 10.1038/nplants.2015.94
external_id:
pmid:
- '27250258'
intvolume: ' 1'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4905525/
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '5827'
quality_controlled: '1'
scopus_import: 1
status: public
title: V-ATPase activity in the TGN/EE is required for exocytosis and recycling in
Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2015'
...
---
_id: '1399'
abstract:
- lang: eng
text: This thesis is concerned with the computation and approximation of intrinsic
volumes. Given a smooth body M and a certain digital approximation of it, we develop
algorithms to approximate various intrinsic volumes of M using only measurements
taken from its digital approximations. The crucial idea behind our novel algorithms
is to link the recent theory of persistent homology to the theory of intrinsic
volumes via the Crofton formula from integral geometry and, in particular, via
Euler characteristic computations. Our main contributions are a multigrid convergent
digital algorithm to compute the first intrinsic volume of a solid body in R^n
as well as an appropriate integration pipeline to approximate integral-geometric
integrals defined over the Grassmannian manifold.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Florian
full_name: Pausinger, Florian
id: 2A77D7A2-F248-11E8-B48F-1D18A9856A87
last_name: Pausinger
orcid: 0000-0002-8379-3768
citation:
ama: Pausinger F. On the approximation of intrinsic volumes. 2015.
apa: Pausinger, F. (2015). On the approximation of intrinsic volumes. Institute
of Science and Technology Austria.
chicago: Pausinger, Florian. “On the Approximation of Intrinsic Volumes.” Institute
of Science and Technology Austria, 2015.
ieee: F. Pausinger, “On the approximation of intrinsic volumes,” Institute of Science
and Technology Austria, 2015.
ista: Pausinger F. 2015. On the approximation of intrinsic volumes. Institute of
Science and Technology Austria.
mla: Pausinger, Florian. On the Approximation of Intrinsic Volumes. Institute
of Science and Technology Austria, 2015.
short: F. Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science
and Technology Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2023-09-07T11:41:25Z
day: '01'
degree_awarded: PhD
department:
- _id: HeEd
language:
- iso: eng
month: '06'
oa_version: None
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5808'
related_material:
record:
- id: '1662'
relation: part_of_dissertation
status: public
- id: '1792'
relation: part_of_dissertation
status: public
- id: '2255'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
title: On the approximation of intrinsic volumes
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1400'
abstract:
- lang: eng
text: Cancer results from an uncontrolled growth of abnormal cells. Sequentially
accumulated genetic and epigenetic alterations decrease cell death and increase
cell replication. We used mathematical models to quantify the effect of driver
gene mutations. The recently developed targeted therapies can lead to dramatic
regressions. However, in solid cancers, clinical responses are often short-lived
because resistant cancer cells evolve. We estimated that approximately 50 different
mutations can confer resistance to a typical targeted therapeutic agent. We find
that resistant cells are likely to be present in expanded subclones before the
start of the treatment. The dominant strategy to prevent the evolution of resistance
is combination therapy. Our analytical results suggest that in most patients,
dual therapy, but not monotherapy, can result in long-term disease control. However,
long-term control can only occur if there are no possible mutations in the genome
that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous
therapy with two drugs is much more likely to result in long-term disease control
than sequential therapy with the same drugs. To improve our understanding of the
underlying subclonal evolution we reconstruct the evolutionary history of a patient's
cancer from next-generation sequencing data of spatially-distinct DNA samples.
Using a quantitative measure of genetic relatedness, we found that pancreatic
cancers and their metastases demonstrated a higher level of relatedness than that
expected for any two cells randomly taken from a normal tissue. This minimal amount
of genetic divergence among advanced lesions indicates that genetic heterogeneity,
when quantitatively defined, is not a fundamental feature of the natural history
of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics
finds evidence for seeding patterns of metastases and can directly be used to
discover rules governing the evolution of solid malignancies to transform cancer
into a more predictable disease.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
citation:
ama: Reiter J. The subclonal evolution of cancer. 2015.
apa: Reiter, J. (2015). The subclonal evolution of cancer. Institute of Science
and Technology Austria.
chicago: Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science
and Technology Austria, 2015.
ieee: J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology
Austria, 2015.
ista: Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and
Technology Austria.
mla: Reiter, Johannes. The Subclonal Evolution of Cancer. Institute of Science
and Technology Austria, 2015.
short: J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology
Austria, 2015.
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:44Z
day: '01'
degree_awarded: PhD
department:
- _id: KrCh
language:
- iso: eng
month: '04'
oa_version: None
page: '183'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5807'
related_material:
record:
- id: '1709'
relation: part_of_dissertation
status: public
- id: '2000'
relation: part_of_dissertation
status: public
- id: '2247'
relation: part_of_dissertation
status: public
- id: '2816'
relation: part_of_dissertation
status: public
- id: '2858'
relation: part_of_dissertation
status: public
- id: '3157'
relation: part_of_dissertation
status: public
- id: '3260'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: The subclonal evolution of cancer
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1401'
abstract:
- lang: eng
text: 'The human ability to recognize objects in complex scenes has driven research
in the computer vision field over couple of decades. This thesis focuses on the
object recognition task in images. That is, given the image, we want the computer
system to be able to predict the class of the object that appears in the image.
A recent successful attempt to bridge semantic understanding of the image perceived
by humans and by computers uses attribute-based models. Attributes are semantic
properties of the objects shared across different categories, which humans and
computers can decide on. To explore the attribute-based models we take a statistical
machine learning approach, and address two key learning challenges in view of
object recognition task: learning augmented attributes as mid-level discriminative
feature representation, and learning with attributes as privileged information.
Our main contributions are parametric and non-parametric models and algorithms
to solve these frameworks. In the parametric approach, we explore an autoencoder
model combined with the large margin nearest neighbor principle for mid-level
feature learning, and linear support vector machines for learning with privileged
information. In the non-parametric approach, we propose a supervised Indian Buffet
Process for automatic augmentation of semantic attributes, and explore the Gaussian
Processes classification framework for learning with privileged information. A
thorough experimental analysis shows the effectiveness of the proposed models
in both parametric and non-parametric views.'
acknowledgement: "I would like to thank my supervisor, Christoph Lampert, for guidance
throughout my studies and for patience in transforming me into a scientist, and
my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice.
\r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative
needs and was always nice and friendly to me, and the campus team for making the
IST Austria campus my second home. \r\nI was honored to collaborate with brilliant
researchers and to learn from their experience. Undoubtedly, I learned most of all
from Novi Quadrianto: brainstorming our projects and getting exciting results was
the most enjoyable part of my work – thank you! I am also grateful to David Knowles,
Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina
for the fantastic projects we worked on together, and to Kristen Grauman and Adriana
Kovashka for the exceptional experience working with user studies. I would like
to thank my colleagues at IST Austria and my office mates who shared their happy
moods, scientific breakthroughs and thought-provoking conversations with me: Chao,
Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina,
Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael,
Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games
of table soccer we played together and the tournaments we teamed up for: we will
definitely win next time:) A very warm hug to Asya for always being so inspiring
and supportive to me, and for helping me to increase the proportion of female computer
scientists in our group. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
citation:
ama: 'Sharmanska V. Learning with attributes for object recognition: Parametric
and non-parametrics views. 2015. doi:10.15479/at:ista:1401'
apa: 'Sharmanska, V. (2015). Learning with attributes for object recognition:
Parametric and non-parametrics views. Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:1401'
chicago: 'Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition:
Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria,
2015. https://doi.org/10.15479/at:ista:1401.'
ieee: 'V. Sharmanska, “Learning with attributes for object recognition: Parametric
and non-parametrics views,” Institute of Science and Technology Austria, 2015.'
ista: 'Sharmanska V. 2015. Learning with attributes for object recognition: Parametric
and non-parametrics views. Institute of Science and Technology Austria.'
mla: 'Sharmanska, Viktoriia. Learning with Attributes for Object Recognition:
Parametric and Non-Parametrics Views. Institute of Science and Technology
Austria, 2015, doi:10.15479/at:ista:1401.'
short: 'V. Sharmanska, Learning with Attributes for Object Recognition: Parametric
and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.'
date_created: 2018-12-11T11:51:48Z
date_published: 2015-04-01T00:00:00Z
date_updated: 2023-09-07T11:40:11Z
day: '01'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: ChLa
- _id: GradSch
doi: 10.15479/at:ista:1401
file:
- access_level: open_access
checksum: 3605b402bb6934e09ae4cf672c84baf7
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:33:17Z
date_updated: 2021-02-22T11:33:17Z
file_id: '9177'
file_name: 2015_Thesis_Sharmanska.pdf
file_size: 7964342
relation: main_file
success: 1
- access_level: closed
checksum: e37593b3ee75bf3180629df2d6ca8f4e
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-16T14:40:45Z
date_updated: 2021-11-17T13:47:24Z
file_id: '10297'
file_name: 2015_Thesis_Sharmanska_pdfa.pdf
file_size: 7372241
relation: main_file
file_date_updated: 2021-11-17T13:47:24Z
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- url: http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf
month: '04'
oa: 1
oa_version: Published Version
page: '144'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '5806'
status: public
supervisor:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
title: 'Learning with attributes for object recognition: Parametric and non-parametrics
views'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2015'
...
---
_id: '1424'
abstract:
- lang: eng
text: We consider the problem of statistical computations with persistence diagrams,
a summary representation of topological features in data. These diagrams encode
persistent homology, a widely used invariant in topological data analysis. While
several avenues towards a statistical treatment of the diagrams have been explored
recently, we follow an alternative route that is motivated by the success of methods
based on the embedding of probability measures into reproducing kernel Hilbert
spaces. In fact, a positive definite kernel on persistence diagrams has recently
been proposed, connecting persistent homology to popular kernel-based learning
techniques such as support vector machines. However, important properties of that
kernel enabling a principled use in the context of probability measure embeddings
remain to be explored. Our contribution is to close this gap by proving universality
of a variant of the original kernel, and to demonstrate its effective use in twosample
hypothesis testing on synthetic as well as real-world data.
acknowledgement: This work was partially supported by the Austrian Science FUnd, project
no. KLI 00012.
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Roland
full_name: Kwitt, Roland
last_name: Kwitt
- first_name: Stefan
full_name: Huber, Stefan
id: 4700A070-F248-11E8-B48F-1D18A9856A87
last_name: Huber
orcid: 0000-0002-8871-5814
- first_name: Marc
full_name: Niethammer, Marc
last_name: Niethammer
- first_name: Weili
full_name: Lin, Weili
last_name: Lin
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
citation:
ama: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. Statistical topological data
analysis-A kernel perspective. In: Vol 28. Neural Information Processing Systems;
2015:3070-3078.'
apa: 'Kwitt, R., Huber, S., Niethammer, M., Lin, W., & Bauer, U. (2015). Statistical
topological data analysis-A kernel perspective (Vol. 28, pp. 3070–3078). Presented
at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information
Processing Systems.'
chicago: Kwitt, Roland, Stefan Huber, Marc Niethammer, Weili Lin, and Ulrich Bauer.
“Statistical Topological Data Analysis-A Kernel Perspective,” 28:3070–78. Neural
Information Processing Systems, 2015.
ieee: 'R. Kwitt, S. Huber, M. Niethammer, W. Lin, and U. Bauer, “Statistical topological
data analysis-A kernel perspective,” presented at the NIPS: Neural Information
Processing Systems, Montreal, Canada, 2015, vol. 28, pp. 3070–3078.'
ista: 'Kwitt R, Huber S, Niethammer M, Lin W, Bauer U. 2015. Statistical topological
data analysis-A kernel perspective. NIPS: Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 28, 3070–3078.'
mla: Kwitt, Roland, et al. Statistical Topological Data Analysis-A Kernel Perspective.
Vol. 28, Neural Information Processing Systems, 2015, pp. 3070–78.
short: R. Kwitt, S. Huber, M. Niethammer, W. Lin, U. Bauer, in:, Neural Information
Processing Systems, 2015, pp. 3070–3078.
conference:
end_date: 2015-12-12
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2015-12-07
date_created: 2018-12-11T11:51:56Z
date_published: 2015-12-01T00:00:00Z
date_updated: 2021-01-12T06:50:38Z
day: '01'
department:
- _id: HeEd
intvolume: ' 28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/5887-statistical-topological-data-analysis-a-kernel-perspective
month: '12'
oa: 1
oa_version: Submitted Version
page: 3070 - 3078
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5782'
quality_controlled: '1'
status: public
title: Statistical topological data analysis-A kernel perspective
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2015'
...
---
_id: '1425'
abstract:
- lang: eng
text: 'In this work we aim at extending the theoretical foundations of lifelong
learning. Previous work analyzing this scenario is based on the assumption that
learning tasks are sampled i.i.d. from a task environment or limited to strongly
constrained data distributions. Instead, we study two scenarios when lifelong
learning is possible, even though the observed tasks do not form an i.i.d. sample:
first, when they are sampled from the same environment, but possibly with dependencies,
and second, when the task environment is allowed to change over time in a consistent
way. In the first case we prove a PAC-Bayesian theorem that can be seen as a direct
generalization of the analogous previous result for the i.i.d. case. For the second
scenario we propose to learn an inductive bias in form of a transfer procedure.
We present a generalization bound and show on a toy example how it can be used
to identify a beneficial transfer algorithm.'
alternative_title:
- Advances in Neural Information Processing Systems
author:
- first_name: Anastasia
full_name: Pentina, Anastasia
id: 42E87FC6-F248-11E8-B48F-1D18A9856A87
last_name: Pentina
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Pentina A, Lampert C. Lifelong learning with non-i.i.d. tasks. In: Vol 2015.
Neural Information Processing Systems; 2015:1540-1548.'
apa: 'Pentina, A., & Lampert, C. (2015). Lifelong learning with non-i.i.d. tasks
(Vol. 2015, pp. 1540–1548). Presented at the NIPS: Neural Information Processing
Systems, Montreal, Canada: Neural Information Processing Systems.'
chicago: Pentina, Anastasia, and Christoph Lampert. “Lifelong Learning with Non-i.i.d.
Tasks,” 2015:1540–48. Neural Information Processing Systems, 2015.
ieee: 'A. Pentina and C. Lampert, “Lifelong learning with non-i.i.d. tasks,” presented
at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2015, vol.
2015, pp. 1540–1548.'
ista: 'Pentina A, Lampert C. 2015. Lifelong learning with non-i.i.d. tasks. NIPS:
Neural Information Processing Systems, Advances in Neural Information Processing
Systems, vol. 2015, 1540–1548.'
mla: Pentina, Anastasia, and Christoph Lampert. Lifelong Learning with Non-i.i.d.
Tasks. Vol. 2015, Neural Information Processing Systems, 2015, pp. 1540–48.
short: A. Pentina, C. Lampert, in:, Neural Information Processing Systems, 2015,
pp. 1540–1548.
conference:
end_date: 2015-12-12
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2015-12-07
date_created: 2018-12-11T11:51:57Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T06:50:39Z
day: '01'
department:
- _id: ChLa
ec_funded: 1
intvolume: ' 2015'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://papers.nips.cc/paper/6007-lifelong-learning-with-non-iid-tasks
month: '01'
oa: 1
oa_version: None
page: 1540 - 1548
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5781'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lifelong learning with non-i.i.d. tasks
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2015
year: '2015'
...
---
_id: '1430'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse their runtime on many illustrative
problems. Here we apply this theory to a simple model of natural evolution. In
the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between
occurrence of new mutations is much longer than the time it takes for a new beneficial
mutation to take over the population. In this situation, the population only contains
copies of one genotype and evolution can be modelled as a (1+1)-type process where
the probability of accepting a new genotype (improvements or worsenings) depends
on the change in fitness. We present an initial runtime analysis of SSWM, quantifying
its performance for various parameters and investigating differences to the (1+1)
EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing
fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking
advantage of information on the fitness gradient.
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime
comparison of natural and artificial evolution. In: Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462.
doi:10.1145/2739480.2754758'
apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps
towards a runtime comparison of natural and artificial evolution. In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp.
1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758'
chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First
Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62.
ACM, 2015. https://doi.org/10.1145/2739480.2754758.
ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards
a runtime comparison of natural and artificial evolution,” in Proceedings of
the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid,
Spain, 2015, pp. 1455–1462.
ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a
runtime comparison of natural and artificial evolution. Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and
evolutionary computation conference, 1455–1462.'
mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural
and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic
and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.
short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the
2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp.
1455–1462.
conference:
end_date: 2015-07-15
location: Madrid, Spain
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2015-07-11
date_created: 2018-12-11T11:51:58Z
date_published: 2015-07-11T00:00:00Z
date_updated: 2021-01-12T06:50:41Z
day: '11'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2739480.2754758
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.06260
month: '07'
oa: 1
oa_version: Preprint
page: 1455 - 1462
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary
Computation
publication_status: published
publisher: ACM
publist_id: '5768'
quality_controlled: '1'
scopus_import: 1
status: public
title: First steps towards a runtime comparison of natural and artificial evolution
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '9532'
abstract:
- lang: eng
text: Genomic imprinting, an inherently epigenetic phenomenon defined by parent
of origin-dependent gene expression, is observed in mammals and flowering plants.
Genome-scale surveys of imprinted expression and the underlying differential epigenetic
marks have led to the discovery of hundreds of imprinted plant genes and confirmed
DNA and histone methylation as key regulators of plant imprinting. However, the
biological roles of the vast majority of imprinted plant genes are unknown, and
the evolutionary forces shaping plant imprinting remain rather opaque. Here, we
review the mechanisms of plant genomic imprinting and discuss theories of imprinting
evolution and biological significance in light of recent findings.
article_processing_charge: No
article_type: review
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Zilberman D. Evolution and function of genomic imprinting in
plants. Genes and Development. 2015;29(24):2517–2531. doi:10.1101/gad.269902.115
apa: Rodrigues, J. A., & Zilberman, D. (2015). Evolution and function of genomic
imprinting in plants. Genes and Development. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gad.269902.115
chicago: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of
Genomic Imprinting in Plants.” Genes and Development. Cold Spring Harbor
Laboratory Press, 2015. https://doi.org/10.1101/gad.269902.115.
ieee: J. A. Rodrigues and D. Zilberman, “Evolution and function of genomic imprinting
in plants,” Genes and Development, vol. 29, no. 24. Cold Spring Harbor
Laboratory Press, pp. 2517–2531, 2015.
ista: Rodrigues JA, Zilberman D. 2015. Evolution and function of genomic imprinting
in plants. Genes and Development. 29(24), 2517–2531.
mla: Rodrigues, Jessica A., and Daniel Zilberman. “Evolution and Function of Genomic
Imprinting in Plants.” Genes and Development, vol. 29, no. 24, Cold Spring
Harbor Laboratory Press, 2015, pp. 2517–2531, doi:10.1101/gad.269902.115.
short: J.A. Rodrigues, D. Zilberman, Genes and Development 29 (2015) 2517–2531.
date_created: 2021-06-08T09:56:24Z
date_published: 2015-12-15T00:00:00Z
date_updated: 2021-12-14T07:58:15Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1101/gad.269902.115
extern: '1'
external_id:
pmid:
- '26680300'
file:
- access_level: open_access
checksum: 086a88cfca4677646da26ed960cb02e9
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:55:10Z
date_updated: 2021-06-08T09:55:10Z
file_id: '9533'
file_name: 2015_GenesAndDevelopment_Rodrigues.pdf
file_size: 1116846
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:55:10Z
has_accepted_license: '1'
intvolume: ' 29'
issue: '24'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 2517–2531
pmid: 1
publication: Genes and Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution and function of genomic imprinting in plants
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 29
year: '2015'
...
---
_id: '12196'
abstract:
- lang: eng
text: SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular
Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in
the induction of defense responses. However, the molecular mechanisms underlying
NLR activation and the subsequent provocation of immune responses are only partially
characterized. To identify negative regulators of NLR-mediated immunity, a forward
genetic screen was undertaken to search for enhancers of the dwarf, autoimmune
gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism,
the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display
wild-type-like morphology and resistance. M2 progeny were screened for mutant,
snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes.
The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated
expression of the pPR2-GUS defense marker reporter gene and enhanced resistance
to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning
and Illumina sequencing, it was determined that the muse9 mutation is in the gene
encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10.
The syd-10 single mutant has no observable alteration from wild-type-like resistance,
although the syd-4 T-DNA insertion allele displays enhanced resistance to the
bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of
SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays
a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated
immunity. SYD may work with other proteins at the chromatin level to repress SNC1
transcription; such regulation is important for fine-tuning the expression of
NLR-encoding genes to prevent unpropitious autoimmunity.
acknowledgement: "This work was supported by the National Sciences and Engineering
Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery
Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the
Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang
and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles
Copeland for critical reading of the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Kaeli C.M.
full_name: Johnson, Kaeli C.M.
last_name: Johnson
- first_name: Shitou
full_name: Xia, Shitou
last_name: Xia
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xin
full_name: Li, Xin
last_name: Li
citation:
ama: Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively
regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623.
doi:10.1093/pcp/pcv087
apa: Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler
SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology.
Oxford University Press. https://doi.org/10.1093/pcp/pcv087
chicago: Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin
Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell
Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087.
ieee: K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED
negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology,
vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.
ista: Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively
regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.
mla: Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates
SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford
University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087.
short: K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015)
1616–1623.
date_created: 2023-01-16T09:20:22Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2023-05-08T11:03:23Z
department:
- _id: XiFe
doi: 10.1093/pcp/pcv087
extern: '1'
external_id:
pmid:
- '26063389'
intvolume: ' 56'
issue: '8'
keyword:
- Cell Biology
- Plant Science
- Physiology
- General Medicine
language:
- iso: eng
month: '08'
oa_version: None
page: 1616-1623
pmid: 1
publication: Plant and Cell Physiology
publication_identifier:
issn:
- 0032-0781
- 1471-9053
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2015'
...
---
_id: '12881'
acknowledgement: This work was supported by the DFG (SPP 1527) and the EU (FP7, REA
grant no 291734).
article_processing_charge: No
author:
- first_name: Georg S
full_name: Martius, Georg S
id: 3A276B68-F248-11E8-B48F-1D18A9856A87
last_name: Martius
- first_name: Eckehard
full_name: Olbrich, Eckehard
last_name: Olbrich
citation:
ama: 'Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous
robots. In: Proceedings of the 13th European Conference on Artificial Life.
MIT Press; 2015:78. doi:10.7551/978-0-262-33027-5-ch018'
apa: 'Martius, G. S., & Olbrich, E. (2015). Quantifying self-organizing behavior
of autonomous robots. In Proceedings of the 13th European Conference on Artificial
Life (p. 78). York, United Kingdom: MIT Press. https://doi.org/10.7551/978-0-262-33027-5-ch018'
chicago: Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior
of Autonomous Robots.” In Proceedings of the 13th European Conference on Artificial
Life, 78. MIT Press, 2015. https://doi.org/10.7551/978-0-262-33027-5-ch018.
ieee: G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous
robots,” in Proceedings of the 13th European Conference on Artificial Life,
York, United Kingdom, 2015, p. 78.
ista: 'Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous
robots. Proceedings of the 13th European Conference on Artificial Life. ECAL:
European Conference on Artificial Life, 78.'
mla: Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior
of Autonomous Robots.” Proceedings of the 13th European Conference on Artificial
Life, MIT Press, 2015, p. 78, doi:10.7551/978-0-262-33027-5-ch018.
short: G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference
on Artificial Life, MIT Press, 2015, p. 78.
conference:
end_date: 2015-07-24
location: York, United Kingdom
name: 'ECAL: European Conference on Artificial Life'
start_date: 2015-07-20
date_created: 2023-04-30T22:01:07Z
date_published: 2015-07-01T00:00:00Z
date_updated: 2023-05-02T07:06:21Z
day: '01'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.7551/978-0-262-33027-5-ch018
ec_funded: 1
file:
- access_level: open_access
checksum: 880eabe59c9df12f06a882aa1bc4e600
content_type: application/pdf
creator: dernst
date_created: 2023-05-02T07:02:59Z
date_updated: 2023-05-02T07:02:59Z
file_id: '12882'
file_name: 2015_ECAL_Martius.pdf
file_size: 1674241
relation: main_file
success: 1
file_date_updated: 2023-05-02T07:02:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '78'
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Proceedings of the 13th European Conference on Artificial Life
publication_identifier:
isbn:
- '9780262330275'
publication_status: published
publisher: MIT Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantifying self-organizing behavior of autonomous robots
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2015'
...
---
_id: '9711'
article_processing_charge: No
author:
- first_name: Guillaume
full_name: Chevereau, Guillaume
id: 424D78A0-F248-11E8-B48F-1D18A9856A87
last_name: Chevereau
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Tugce
full_name: Batur, Tugce
last_name: Batur
- first_name: Aysegul
full_name: Guvenek, Aysegul
last_name: Guvenek
- first_name: Dilay Hazal
full_name: Ayhan, Dilay Hazal
last_name: Ayhan
- first_name: Erdal
full_name: Toprak, Erdal
last_name: Toprak
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Chevereau G, Lukacisinova M, Batur T, et al. Excel file containing the raw
data for all figures. 2015. doi:10.1371/journal.pbio.1002299.s001
apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D. H., Toprak,
E., & Bollenbach, M. T. (2015). Excel file containing the raw data for all
figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299.s001
chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek,
Dilay Hazal Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Excel File Containing
the Raw Data for All Figures.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299.s001.
ieee: G. Chevereau et al., “Excel file containing the raw data for all figures.”
Public Library of Science, 2015.
ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan DH, Toprak E, Bollenbach
MT. 2015. Excel file containing the raw data for all figures, Public Library of
Science, 10.1371/journal.pbio.1002299.s001.
mla: Chevereau, Guillaume, et al. Excel File Containing the Raw Data for All
Figures. Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299.s001.
short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D.H. Ayhan, E. Toprak,
M.T. Bollenbach, (2015).
date_created: 2021-07-23T11:53:50Z
date_published: 2015-11-18T00:00:00Z
date_updated: 2023-02-23T10:07:02Z
day: '18'
department:
- _id: ToBo
doi: 10.1371/journal.pbio.1002299.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1619'
relation: used_in_publication
status: public
status: public
title: Excel file containing the raw data for all figures
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '9712'
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- 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: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison
& for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness
models for comparison & for interacting TFBSs. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1005639.s001
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other
Fitness Models for Comparison & for Interacting TFBSs.” Public Library of
Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for
comparison & for interacting TFBSs.” Public Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison
& for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001.
mla: Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting
TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015).
date_created: 2021-07-23T12:00:37Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2025-05-28T11:57:04Z
day: '06'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639.s001
month: '11'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1666'
relation: used_in_publication
status: public
status: public
title: Other fitness models for comparison & for interacting TFBSs
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...