---
_id: '3361'
abstract:
- lang: eng
text: In this paper, we investigate the computational complexity of quantitative
information flow (QIF) problems. Information-theoretic quantitative relaxations
of noninterference (based on Shannon entropy)have been introduced to enable more
fine-grained reasoning about programs in situations where limited information
flow is acceptable. The QIF bounding problem asks whether the information flow
in a given program is bounded by a constant $d$. Our first result is that the
QIF bounding problem is PSPACE-complete. The QIF memoryless synthesis problem
asks whether it is possible to resolve nondeterministic choices in a given partial
program in such a way that in the resulting deterministic program, the quantitative
information flow is bounded by a given constant $d$. Our second result is that
the QIF memoryless synthesis problem is also EXPTIME-complete. The QIF memoryless
synthesis problem generalizes to QIF general synthesis problem which does not
impose the memoryless requirement (that is, by allowing the synthesized program
to have more variables then the original partial program). Our third result is
that the QIF general synthesis problem is EXPTIME-hard.
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- 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
citation:
ama: 'Cerny P, Chatterjee K, Henzinger TA. The complexity of quantitative information
flow problems. In: IEEE; 2011:205-217. doi:10.1109/CSF.2011.21'
apa: 'Cerny, P., Chatterjee, K., & Henzinger, T. A. (2011). The complexity of
quantitative information flow problems (pp. 205–217). Presented at the CSF: Computer
Security Foundations, Cernay-la-Ville, France: IEEE. https://doi.org/10.1109/CSF.2011.21'
chicago: Cerny, Pavol, Krishnendu Chatterjee, and Thomas A Henzinger. “The Complexity
of Quantitative Information Flow Problems,” 205–17. IEEE, 2011. https://doi.org/10.1109/CSF.2011.21.
ieee: 'P. Cerny, K. Chatterjee, and T. A. Henzinger, “The complexity of quantitative
information flow problems,” presented at the CSF: Computer Security Foundations,
Cernay-la-Ville, France, 2011, pp. 205–217.'
ista: 'Cerny P, Chatterjee K, Henzinger TA. 2011. The complexity of quantitative
information flow problems. CSF: Computer Security Foundations, 205–217.'
mla: Cerny, Pavol, et al. The Complexity of Quantitative Information Flow Problems.
IEEE, 2011, pp. 205–17, doi:10.1109/CSF.2011.21.
short: P. Cerny, K. Chatterjee, T.A. Henzinger, in:, IEEE, 2011, pp. 205–217.
conference:
end_date: 2011-06-29
location: Cernay-la-Ville, France
name: 'CSF: Computer Security Foundations'
start_date: 2011-06-27
date_created: 2018-12-11T12:02:54Z
date_published: 2011-06-27T00:00:00Z
date_updated: 2021-01-12T07:42:56Z
day: '27'
ddc:
- '000'
- '005'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1109/CSF.2011.21
ec_funded: 1
file:
- access_level: open_access
checksum: 1a25be0c62459fc7640db88af08ff63a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:07Z
date_updated: 2020-07-14T12:46:10Z
file_id: '4792'
file_name: IST-2012-81-v1+1_The_complexity_of_quantitative_information_flow_problems.pdf
file_size: 299069
relation: main_file
file_date_updated: 2020-07-14T12:46:10Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 205 - 217
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: IEEE
publist_id: '3254'
pubrep_id: '81'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of quantitative information flow problems
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3358'
abstract:
- lang: eng
text: The static scheduling problem often arises as a fundamental problem in real-time
systems and grid computing. We consider the problem of statically scheduling a
large job expressed as a task graph on a large number of computing nodes, such
as a data center. This paper solves the large-scale static scheduling problem
using abstraction refinement, a technique commonly used in formal verification
to efficiently solve computationally hard problems. A scheduler based on abstraction
refinement first attempts to solve the scheduling problem with abstract representations
of the job and the computing resources. As abstract representations are generally
small, the scheduling can be done reasonably fast. If the obtained schedule does
not meet specified quality conditions (like data center utilization or schedule
makespan) then the scheduler refines the job and data center abstractions and,
again solves the scheduling problem. We develop different schedulers based on
abstraction refinement. We implemented these schedulers and used them to schedule
task graphs from various computing domains on simulated data centers with realistic
topologies. We compared the speed of scheduling and the quality of the produced
schedules with our abstraction refinement schedulers against a baseline scheduler
that does not use any abstraction. We conclude that abstraction refinement techniques
give a significant speed-up compared to traditional static scheduling heuristics,
at a reasonable cost in the quality of the produced schedules. We further used
our static schedulers in an actual system that we deployed on Amazon EC2 and compared
it against the Hadoop dynamic scheduler for large MapReduce jobs. Our experiments
indicate that there is great potential for static scheduling techniques.
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Vasu
full_name: Singh, Vasu
id: 4DAE2708-F248-11E8-B48F-1D18A9856A87
last_name: Singh
- first_name: Thomas
full_name: Wies, Thomas
id: 447BFB88-F248-11E8-B48F-1D18A9856A87
last_name: Wies
- first_name: Damien
full_name: Zufferey, Damien
id: 4397AC76-F248-11E8-B48F-1D18A9856A87
last_name: Zufferey
orcid: 0000-0002-3197-8736
citation:
ama: 'Henzinger TA, Singh V, Wies T, Zufferey D. Scheduling large jobs by abstraction
refinement. In: ACM; 2011:329-342. doi:10.1145/1966445.1966476'
apa: 'Henzinger, T. A., Singh, V., Wies, T., & Zufferey, D. (2011). Scheduling
large jobs by abstraction refinement (pp. 329–342). Presented at the EuroSys,
Salzburg, Austria: ACM. https://doi.org/10.1145/1966445.1966476'
chicago: Henzinger, Thomas A, Vasu Singh, Thomas Wies, and Damien Zufferey. “Scheduling
Large Jobs by Abstraction Refinement,” 329–42. ACM, 2011. https://doi.org/10.1145/1966445.1966476.
ieee: T. A. Henzinger, V. Singh, T. Wies, and D. Zufferey, “Scheduling large jobs
by abstraction refinement,” presented at the EuroSys, Salzburg, Austria, 2011,
pp. 329–342.
ista: Henzinger TA, Singh V, Wies T, Zufferey D. 2011. Scheduling large jobs by
abstraction refinement. EuroSys, 329–342.
mla: Henzinger, Thomas A., et al. Scheduling Large Jobs by Abstraction Refinement.
ACM, 2011, pp. 329–42, doi:10.1145/1966445.1966476.
short: T.A. Henzinger, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2011, pp. 329–342.
conference:
end_date: 2011-04-13
location: Salzburg, Austria
name: EuroSys
start_date: 2011-04-10
date_created: 2018-12-11T12:02:53Z
date_published: 2011-04-10T00:00:00Z
date_updated: 2021-01-12T07:42:55Z
day: '10'
department:
- _id: ToHe
doi: 10.1145/1966445.1966476
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://cs.nyu.edu/wies/publ/scheduling_large_jobs_by_abstraction_refinement.pdf
month: '04'
oa: 1
oa_version: Published Version
page: 329 - 342
publication_status: published
publisher: ACM
publist_id: '3257'
quality_controlled: '1'
scopus_import: 1
status: public
title: Scheduling large jobs by abstraction refinement
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3359'
abstract:
- lang: eng
text: "Motivated by improvements in constraint-solving technology and by the increase
of routinely available computational power, partial-program synthesis is emerging
as an effective approach for increasing programmer productivity. The goal of the
approach is to allow the programmer to specify a part of her intent imperatively
(that is, give a partial program) and a part of her intent declaratively, by specifying
which conditions need to be achieved or maintained. The task of the synthesizer
is to construct a program that satisfies the specification. As an example, consider
a partial program where threads access shared data without using any synchronization
mechanism, and a declarative specification that excludes data races and deadlocks.
The task of the synthesizer is then to place locks into the program code in order
for the program to meet the specification.\r\n\r\nIn this paper, we argue that
quantitative objectives are needed in partial-program synthesis in order to produce
higher-quality programs, while enabling simpler specifications. Returning to the
example, the synthesizer could construct a naive solution that uses one global
lock for shared data. This can be prevented either by constraining the solution
space further (which is error-prone and partly defeats the point of synthesis),
or by optimizing a quantitative objective that models performance. Other quantitative
notions useful in synthesis include fault tolerance, robustness, resource (memory,
power) consumption, and information flow."
acknowledgement: This work was partially supported by the ERC Advanced Grant QUAREM,
the FWF NFN Grant S11402-N23 (RiSE), and the EU NOE Grant ArtistDesign.
author:
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Cerny P, Henzinger TA. From boolean to quantitative synthesis. In: ACM; 2011:149-154.
doi:10.1145/2038642.2038666'
apa: 'Cerny, P., & Henzinger, T. A. (2011). From boolean to quantitative synthesis
(pp. 149–154). Presented at the EMSOFT: Embedded Software , Taipei; Taiwan: ACM.
https://doi.org/10.1145/2038642.2038666'
chicago: Cerny, Pavol, and Thomas A Henzinger. “From Boolean to Quantitative Synthesis,”
149–54. ACM, 2011. https://doi.org/10.1145/2038642.2038666.
ieee: 'P. Cerny and T. A. Henzinger, “From boolean to quantitative synthesis,” presented
at the EMSOFT: Embedded Software , Taipei; Taiwan, 2011, pp. 149–154.'
ista: 'Cerny P, Henzinger TA. 2011. From boolean to quantitative synthesis. EMSOFT:
Embedded Software , 149–154.'
mla: Cerny, Pavol, and Thomas A. Henzinger. From Boolean to Quantitative Synthesis.
ACM, 2011, pp. 149–54, doi:10.1145/2038642.2038666.
short: P. Cerny, T.A. Henzinger, in:, ACM, 2011, pp. 149–154.
conference:
end_date: 2011-10-14
location: Taipei; Taiwan
name: 'EMSOFT: Embedded Software '
start_date: 2011-10-09
date_created: 2018-12-11T12:02:53Z
date_published: 2011-10-09T00:00:00Z
date_updated: 2021-01-12T07:42:55Z
day: '09'
department:
- _id: ToHe
doi: 10.1145/2038642.2038666
ec_funded: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 149 - 154
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F1337C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '214373'
name: Design for Embedded Systems
publication_status: published
publisher: ACM
publist_id: '3256'
quality_controlled: '1'
status: public
title: From boolean to quantitative synthesis
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3357'
abstract:
- lang: eng
text: We consider two-player graph games whose objectives are request-response condition,
i.e conjunctions of conditions of the form "if a state with property Rq is visited,
then later a state with property Rp is visited". The winner of such games can
be decided in EXPTIME and the problem is known to be NP-hard. In this paper, we
close this gap by showing that this problem is, in fact, EXPTIME-complete. We
show that the problem becomes PSPACE-complete if we only consider games played
on DAGs, and NP-complete or PTIME-complete if there is only one player (depending
on whether he wants to enforce or spoil the request-response condition). We also
present near-optimal bounds on the memory needed to design winning strategies
for each player, in each case.
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Florian
full_name: Horn, Florian
id: 37327ACE-F248-11E8-B48F-1D18A9856A87
last_name: Horn
citation:
ama: 'Chatterjee K, Henzinger TA, Horn F. The complexity of request-response games.
In: Dediu A-H, Inenaga S, Martín-Vide C, eds. Vol 6638. Springer; 2011:227-237.
doi:10.1007/978-3-642-21254-3_17'
apa: 'Chatterjee, K., Henzinger, T. A., & Horn, F. (2011). The complexity of
request-response games. In A.-H. Dediu, S. Inenaga, & C. Martín-Vide (Eds.)
(Vol. 6638, pp. 227–237). Presented at the LATA: Language and Automata Theory
and Applications, Tarragona, Spain: Springer. https://doi.org/10.1007/978-3-642-21254-3_17'
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “The Complexity
of Request-Response Games.” edited by Adrian-Horia Dediu, Shunsuke Inenaga, and
Carlos Martín-Vide, 6638:227–37. Springer, 2011. https://doi.org/10.1007/978-3-642-21254-3_17.
ieee: 'K. Chatterjee, T. A. Henzinger, and F. Horn, “The complexity of request-response
games,” presented at the LATA: Language and Automata Theory and Applications,
Tarragona, Spain, 2011, vol. 6638, pp. 227–237.'
ista: 'Chatterjee K, Henzinger TA, Horn F. 2011. The complexity of request-response
games. LATA: Language and Automata Theory and Applications, LNCS, vol. 6638, 227–237.'
mla: Chatterjee, Krishnendu, et al. The Complexity of Request-Response Games.
Edited by Adrian-Horia Dediu et al., vol. 6638, Springer, 2011, pp. 227–37, doi:10.1007/978-3-642-21254-3_17.
short: K. Chatterjee, T.A. Henzinger, F. Horn, in:, A.-H. Dediu, S. Inenaga, C.
Martín-Vide (Eds.), Springer, 2011, pp. 227–237.
conference:
end_date: 2011-05-31
location: Tarragona, Spain
name: 'LATA: Language and Automata Theory and Applications'
start_date: 2011-05-26
date_created: 2018-12-11T12:02:52Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:54Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-642-21254-3_17
editor:
- first_name: Adrian-Horia
full_name: Dediu, Adrian-Horia
last_name: Dediu
- first_name: Shunsuke
full_name: Inenaga, Shunsuke
last_name: Inenaga
- first_name: Carlos
full_name: Martín-Vide, Carlos
last_name: Martín-Vide
intvolume: ' 6638'
language:
- iso: eng
month: '01'
oa_version: None
page: 227 - 237
publication_status: published
publisher: Springer
publist_id: '3258'
quality_controlled: '1'
scopus_import: 1
status: public
title: The complexity of request-response games
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6638
year: '2011'
...
---
_id: '336'
abstract:
- lang: eng
text: 'The growth kinetics of colloidal Bi2S3 nanorods was investigated. After nucleation,
the length distribution of the growing Bi 2S3 nanorods narrows with the reaction
time until a bimodal length distribution appears. From this critical reaction
time on, the smallest nanorods of the ensemble dissolve, feeding with monomer
the growth of the largest ones. A comprehensive characterization of the size-distribution
evolution of Bi2S3 nanorods is used here to illustrate the dependences of the
anisotropic growth rates of cylindrical nanoparticles on the nanoparticle dimensions
and the monomer concentration in solution. With this goal in mind, a diffusion-reaction
model is presented to explain the origin of the experimentally obtained length
distribution focusing mechanism. The model is able to reproduce the decrease of
the growth rate in the nanorod axial direction with both its thickness and length.
On the other hand, low lateral reaction rates prevent the nanorod thickness distribution
to be focused. In both crystallographic growth directions, a concentration-dependent
critical thickness exists, which discriminates between nanorods with positive
growth rates and those dissolving in the reaction solution. '
acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779,
MAT2008-03400-E/MAT, and ENE2008-03277-E/CON. Maria Ibáñez thanks the Ph.D. grant
from the Spanish MICINN.
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Ibáñez, Maria
id: 43C61214-F248-11E8-B48F-1D18A9856A87
last_name: Ibáñez
orcid: 0000-0001-5013-2843
- first_name: Pablo
full_name: Guardia, Pablo
last_name: Guardia
- first_name: Alexey
full_name: Shavel, Alexey
last_name: Shavel
- first_name: Doris
full_name: Cadavid, Doris
last_name: Cadavid
- first_name: Jordi
full_name: Arbiol, Jordi
last_name: Arbiol
- first_name: Joan
full_name: Morante, Joan
last_name: Morante
- first_name: Andreu
full_name: Cabot, Andreu
last_name: Cabot
citation:
ama: 'Ibáñez M, Guardia P, Shavel A, et al. Growth kinetics of asymmetric Bi2S3
nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry
C. 2011;115(16):7947-7955. doi:10.1021/jp2002904'
apa: 'Ibáñez, M., Guardia, P., Shavel, A., Cadavid, D., Arbiol, J., Morante, J.,
& Cabot, A. (2011). Growth kinetics of asymmetric Bi2S3 nanocrystals: Size
distribution focusing in nanorods. Journal of Physical Chemistry C. American
Chemical Society. https://doi.org/10.1021/jp2002904'
chicago: 'Ibáñez, Maria, Pablo Guardia, Alexey Shavel, Doris Cadavid, Jordi Arbiol,
Joan Morante, and Andreu Cabot. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals:
Size Distribution Focusing in Nanorods.” Journal of Physical Chemistry C.
American Chemical Society, 2011. https://doi.org/10.1021/jp2002904.'
ieee: 'M. Ibáñez et al., “Growth kinetics of asymmetric Bi2S3 nanocrystals:
Size distribution focusing in nanorods,” Journal of Physical Chemistry C,
vol. 115, no. 16. American Chemical Society, pp. 7947–7955, 2011.'
ista: 'Ibáñez M, Guardia P, Shavel A, Cadavid D, Arbiol J, Morante J, Cabot A. 2011.
Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in
nanorods. Journal of Physical Chemistry C. 115(16), 7947–7955.'
mla: 'Ibáñez, Maria, et al. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals: Size
Distribution Focusing in Nanorods.” Journal of Physical Chemistry C, vol.
115, no. 16, American Chemical Society, 2011, pp. 7947–55, doi:10.1021/jp2002904.'
short: M. Ibáñez, P. Guardia, A. Shavel, D. Cadavid, J. Arbiol, J. Morante, A. Cabot,
Journal of Physical Chemistry C 115 (2011) 7947–7955.
date_created: 2018-12-11T11:45:53Z
date_published: 2011-04-28T00:00:00Z
date_updated: 2021-01-12T07:42:56Z
day: '28'
doi: 10.1021/jp2002904
extern: '1'
intvolume: ' 115'
issue: '16'
language:
- iso: eng
month: '04'
oa_version: None
page: 7947 - 7955
publication: Journal of Physical Chemistry C
publication_status: published
publisher: American Chemical Society
publist_id: '7493'
quality_controlled: '1'
status: public
title: 'Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing
in nanorods'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2011'
...
---
_id: '3379'
abstract:
- lang: eng
text: The process of gastrulation is highly conserved across vertebrates on both
the genetic and morphological levels, despite great variety in embryonic shape
and speed of development. This mechanism spatially separates the germ layers and
establishes the organizational foundation for future development. Mesodermal identity
is specified in a superficial layer of cells, the epiblast, where cells maintain
an epithelioid morphology. These cells involute to join the deeper hypoblast layer
where they adopt a migratory, mesenchymal morphology. Expression of a cascade
of related transcription factors orchestrates the parallel genetic transition
from primitive to mature mesoderm. Although the early and late stages of this
process are increasingly well understood, the transition between them has remained
largely mysterious. We present here the first high resolution in vivo observations
of the blebby transitional morphology of involuting mesodermal cells in a vertebrate
embryo. We further demonstrate that the zebrafish spadetail mutation creates a
reversible block in the maturation program, stalling cells in the transition state.
This mutation creates an ideal system for dissecting the specific properties of
cells undergoing the morphological transition of maturing mesoderm, as we demonstrate
with a direct measurement of cell–cell adhesion.
article_type: original
author:
- first_name: Richard
full_name: Row, Richard
last_name: Row
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Benjamin
full_name: Martin, Benjamin
last_name: Martin
- first_name: Petra
full_name: Stockinger, Petra
id: 261CB030-E90D-11E9-B182-F697D44B663C
last_name: Stockinger
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: David
full_name: Kimelman, David
last_name: Kimelman
citation:
ama: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion
of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail.
Developmental Biology. 2011;354(1):102-110. doi:10.1016/j.ydbio.2011.03.025
apa: Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., &
Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in
zebrafish mesoderm requires Spadetail. Developmental Biology. Elsevier.
https://doi.org/10.1016/j.ydbio.2011.03.025
chicago: Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp
J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal
Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology.
Elsevier, 2011. https://doi.org/10.1016/j.ydbio.2011.03.025.
ieee: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D.
Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish
mesoderm requires Spadetail,” Developmental Biology, vol. 354, no. 1. Elsevier,
pp. 102–110, 2011.
ista: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011.
Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires
Spadetail. Developmental Biology. 354(1), 102–110.
mla: Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition
in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology, vol.
354, no. 1, Elsevier, 2011, pp. 102–10, doi:10.1016/j.ydbio.2011.03.025.
short: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman,
Developmental Biology 354 (2011) 102–110.
date_created: 2018-12-11T12:03:00Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T07:43:04Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ydbio.2011.03.025
external_id:
pmid:
- '1463614'
intvolume: ' 354'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/
month: '06'
oa: 1
oa_version: Submitted Version
page: 102 - 110
pmid: 1
publication: Developmental Biology
publication_status: published
publisher: Elsevier
publist_id: '3228'
quality_controlled: '1'
scopus_import: 1
status: public
title: Completion of the epithelial to mesenchymal transition in zebrafish mesoderm
requires Spadetail
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 354
year: '2011'
...
---
_id: '3376'
abstract:
- lang: eng
text: Regulatory conflicts occur when two signals that individually trigger opposite
cellular responses are present simultaneously. Here, we investigate regulatory
conflicts in the bacterial response to antibiotic combinations. We use an Escherichia
coli promoter-GFP library to study the transcriptional response of many promoters
to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution
of drug concentration. Surprisingly, we find that this data set can be characterized
as a linear sum of only two principal components. Component one, accounting for
over 70% of the response, represents the response to growth inhibition by the
drugs. Component two describes how regulatory conflicts are resolved. For the
additive drug pair, conflicts are resolved by linearly interpolating the single
drug responses, while for the antagonistic drug pair, the growth-limiting drug
dominates the response. Importantly, for a given drug pair, the same conflict
resolution strategy applies to almost all genes. These results provide a recipe
for predicting gene expression responses to antibiotic combinations.
acknowledgement: This work was supported by a Feodor Lynen Fellowship of the Alexander
von Humboldt Foundation (to T.B.).
author:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by
combinations of antibiotics. Molecular Cell. 2011;42(4):413-425. doi:10.1016/j.molcel.2011.04.016
apa: Bollenbach, M. T., & Kishony, R. (2011). Resolution of gene regulatory
conflicts caused by combinations of antibiotics. Molecular Cell. Cell Press.
https://doi.org/10.1016/j.molcel.2011.04.016
chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory
Conflicts Caused by Combinations of Antibiotics.” Molecular Cell. Cell
Press, 2011. https://doi.org/10.1016/j.molcel.2011.04.016.
ieee: M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts
caused by combinations of antibiotics,” Molecular Cell, vol. 42, no. 4.
Cell Press, pp. 413–425, 2011.
ista: Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused
by combinations of antibiotics. Molecular Cell. 42(4), 413–425.
mla: Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts
Caused by Combinations of Antibiotics.” Molecular Cell, vol. 42, no. 4,
Cell Press, 2011, pp. 413–25, doi:10.1016/j.molcel.2011.04.016.
short: M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.
date_created: 2018-12-11T12:02:59Z
date_published: 2011-05-20T00:00:00Z
date_updated: 2021-01-12T07:43:03Z
day: '20'
department:
- _id: ToBo
doi: 10.1016/j.molcel.2011.04.016
intvolume: ' 42'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/
month: '05'
oa: 1
oa_version: Submitted Version
page: 413 - 425
publication: Molecular Cell
publication_status: published
publisher: Cell Press
publist_id: '3231'
quality_controlled: '1'
scopus_import: 1
status: public
title: Resolution of gene regulatory conflicts caused by combinations of antibiotics
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2011'
...
---
_id: '3380'
abstract:
- lang: eng
text: Linkage between markers and genes that affect a phenotype of interest may
be determined by examining differences in marker allele frequency in the extreme
progeny of a cross between two inbred lines. This strategy is usually employed
when pooling is used to reduce genotyping costs. When the cross progeny are asexual,
the extreme progeny may be selected by multiple generations of asexual reproduction
and selection. We analyse this method of measuring phenotype in asexual progeny
and examine the changes in marker allele frequency due to selection over many
generations. Stochasticity in marker frequency in the selected population arises
due to the finite initial population size. We derive the distribution of marker
frequency as a result of selection at a single major locus, and show that in order
to avoid spurious changes in marker allele frequency in the selected population,
the initial population size should be in the low to mid hundreds.
article_processing_charge: No
article_type: original
author:
- first_name: Sayanthan
full_name: Logeswaran, Sayanthan
last_name: Logeswaran
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using
changes in marker allele frequency. Genetical Research. 2011;93(3):221-232.
doi:10.1017/S0016672311000115
apa: Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual
progeny using changes in marker allele frequency. Genetical Research. Cambridge
University Press. https://doi.org/10.1017/S0016672311000115
chicago: Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits
in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research.
Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115.
ieee: S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny
using changes in marker allele frequency,” Genetical Research, vol. 93,
no. 3. Cambridge University Press, pp. 221–232, 2011.
ista: Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny
using changes in marker allele frequency. Genetical Research. 93(3), 221–232.
mla: Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in
Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research,
vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115.
short: S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232.
date_created: 2018-12-11T12:03:00Z
date_published: 2011-05-18T00:00:00Z
date_updated: 2021-01-12T07:43:05Z
day: '18'
department:
- _id: NiBa
doi: 10.1017/S0016672311000115
intvolume: ' 93'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf
month: '05'
oa: 1
oa_version: Published Version
page: 221 - 232
publication: Genetical Research
publication_status: published
publisher: Cambridge University Press
publist_id: '3227'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mapping Mendelian traits in asexual progeny using changes in marker allele
frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2011'
...
---
_id: '3377'
abstract:
- lang: eng
text: By definition, transverse intersections are stable under in- finitesimal perturbations.
Using persistent homology, we ex- tend this notion to sizeable perturbations.
Specifically, we assign to each homology class of the intersection its robust-
ness, the magnitude of a perturbation necessary to kill it, and prove that robustness
is stable. Among the applications of this result is a stable notion of robustness
for fixed points of continuous mappings and a statement of stability for con-
tours of smooth mappings.
acknowledgement: This research is partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring
the robustness of intersections. Foundations of Computational Mathematics.
2011;11(3):345-361. doi:10.1007/s10208-011-9090-8
apa: Edelsbrunner, H., Morozov, D., & Patel, A. (2011). Quantifying transversality
by measuring the robustness of intersections. Foundations of Computational
Mathematics. Springer. https://doi.org/10.1007/s10208-011-9090-8
chicago: Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality
by Measuring the Robustness of Intersections.” Foundations of Computational
Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-011-9090-8.
ieee: H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by
measuring the robustness of intersections,” Foundations of Computational Mathematics,
vol. 11, no. 3. Springer, pp. 345–361, 2011.
ista: Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring
the robustness of intersections. Foundations of Computational Mathematics. 11(3),
345–361.
mla: Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the
Robustness of Intersections.” Foundations of Computational Mathematics,
vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:10.1007/s10208-011-9090-8.
short: H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics
11 (2011) 345–361.
date_created: 2018-12-11T12:02:59Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T07:43:04Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s10208-011-9090-8
intvolume: ' 11'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0911.2142
month: '06'
oa: 1
oa_version: Submitted Version
page: 345 - 361
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '3230'
quality_controlled: '1'
scopus_import: 1
status: public
title: Quantifying transversality by measuring the robustness of intersections
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2011'
...
---
_id: '3378'
abstract:
- lang: eng
text: The theory of intersection homology was developed to study the singularities
of a topologically stratified space. This paper in- corporates this theory into
the already developed framework of persistent homology. We demonstrate that persistent
intersec- tion homology gives useful information about the relationship between
an embedded stratified space and its singularities. We give, and prove the correctness
of, an algorithm for the computa- tion of the persistent intersection homology
groups of a filtered simplicial complex equipped with a stratification by subcom-
plexes. We also derive, from Poincare ́ Duality, some structural results about
persistent intersection homology.
acknowledgement: This research was partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grant HR0011-05-1-0007.
author:
- first_name: Paul
full_name: Bendich, Paul
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: John
full_name: Harer, John
last_name: Harer
citation:
ama: Bendich P, Harer J. Persistent intersection homology. Foundations of Computational
Mathematics. 2011;11(3):305-336. doi:10.1007/s10208-010-9081-1
apa: Bendich, P., & Harer, J. (2011). Persistent intersection homology. Foundations
of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-010-9081-1
chicago: Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations
of Computational Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-010-9081-1.
ieee: P. Bendich and J. Harer, “Persistent intersection homology,” Foundations
of Computational Mathematics, vol. 11, no. 3. Springer, pp. 305–336, 2011.
ista: Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of
Computational Mathematics. 11(3), 305–336.
mla: Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations
of Computational Mathematics, vol. 11, no. 3, Springer, 2011, pp. 305–36,
doi:10.1007/s10208-010-9081-1.
short: P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011)
305–336.
date_created: 2018-12-11T12:02:59Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2021-01-12T07:43:04Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/s10208-010-9081-1
intvolume: ' 11'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 305 - 336
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '3229'
quality_controlled: '1'
scopus_import: 1
status: public
title: Persistent intersection homology
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2011'
...