---
_id: '9847'
abstract:
- lang: eng
text: information on culture conditions, phage mutagenesis, verification and lysate
preparation; Raw data
article_processing_charge: No
author:
- first_name: Maros
full_name: Pleska, Maros
id: 4569785E-F248-11E8-B48F-1D18A9856A87
last_name: Pleska
orcid: 0000-0001-7460-7479
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Pleska M, Guet CC. Supplementary materials and methods; Full data set from
effects of mutations in phage restriction sites during escape from restriction–modification.
2017. doi:10.6084/m9.figshare.5633917.v1
apa: Pleska, M., & Guet, C. C. (2017). Supplementary materials and methods;
Full data set from effects of mutations in phage restriction sites during escape
from restriction–modification. The Royal Society. https://doi.org/10.6084/m9.figshare.5633917.v1
chicago: Pleska, Maros, and Calin C Guet. “Supplementary Materials and Methods;
Full Data Set from Effects of Mutations in Phage Restriction Sites during Escape
from Restriction–Modification.” The Royal Society, 2017. https://doi.org/10.6084/m9.figshare.5633917.v1.
ieee: M. Pleska and C. C. Guet, “Supplementary materials and methods; Full data
set from effects of mutations in phage restriction sites during escape from restriction–modification.”
The Royal Society, 2017.
ista: Pleska M, Guet CC. 2017. Supplementary materials and methods; Full data set
from effects of mutations in phage restriction sites during escape from restriction–modification,
The Royal Society, 10.6084/m9.figshare.5633917.v1.
mla: Pleska, Maros, and Calin C. Guet. Supplementary Materials and Methods; Full
Data Set from Effects of Mutations in Phage Restriction Sites during Escape from
Restriction–Modification. The Royal Society, 2017, doi:10.6084/m9.figshare.5633917.v1.
short: M. Pleska, C.C. Guet, (2017).
date_created: 2021-08-09T13:54:38Z
date_published: 2017-11-27T00:00:00Z
date_updated: 2023-02-23T12:29:44Z
day: '27'
department:
- _id: CaGu
doi: 10.6084/m9.figshare.5633917.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.5633917.v1
month: '11'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '561'
relation: used_in_publication
status: public
status: public
title: Supplementary materials and methods; Full data set from effects of mutations
in phage restriction sites during escape from restriction–modification
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9845'
abstract:
- lang: eng
text: "Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of
heavy isotopes measured\tin single cells"
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public
Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017.
ieee: N. Nikolic et al., “Mathematical model.” Public Library of Science,
2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017.
mla: Nikolic, Nela, et al. Mathematical Model. Public Library of Science,
2017, doi:10.1371/journal.pgen.1007122.s017.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:31:51Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s017
month: '12'
oa_version: None
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Mathematical model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9849'
abstract:
- lang: eng
text: This text provides additional information about the model, a derivation of
the analytic results in Eq (4), and details about simulations of an additional
parameter set.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017.
doi:10.1371/journal.pcbi.1005609.s001
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation
details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and
Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.”
Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details,
Public Library of Science, 10.1371/journal.pcbi.1005609.s001.
mla: Lukacisinova, Marta, et al. Modelling and Simulation Details. Public
Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:02:34Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: NiBa
- _id: CaGu
doi: 10.1371/journal.pcbi.1005609.s001
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Modelling and simulation details
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9850'
abstract:
- lang: eng
text: In this text, we discuss how a cost of resistance and the possibility of lethal
mutations impact our model.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of
the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public
Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library
of Science, 10.1371/journal.pcbi.1005609.s002.
mla: Lukacisinova, Marta, et al. Extensions of the Model. Public Library
of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:05:24Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s002
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Extensions of the model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9846'
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Supplementary methods. 2017. doi:10.1371/journal.pgen.1007122.s016
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Supplementary methods. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1007122.s016
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.”
Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s016.
ieee: N. Nikolic et al., “Supplementary methods.” Public Library of Science,
2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Supplementary methods, Public Library of Science, 10.1371/journal.pgen.1007122.s016.
mla: Nikolic, Nela, et al. Supplementary Methods. Public Library of Science,
2017, doi:10.1371/journal.pgen.1007122.s016.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:35:17Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Supplementary methods
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '680'
abstract:
- lang: eng
text: In order to respond reliably to specific features of their environment, sensory
neurons need to integrate multiple incoming noisy signals. Crucially, they also
need to compete for the interpretation of those signals with other neurons representing
similar features. The form that this competition should take depends critically
on the noise corrupting these signals. In this study we show that for the type
of noise commonly observed in sensory systems, whose variance scales with the
mean signal, sensory neurons should selectively divide their input signals by
their predictions, suppressing ambiguous cues while amplifying others. Any change
in the stimulus context alters which inputs are suppressed, leading to a deep
dynamic reshaping of neural receptive fields going far beyond simple surround
suppression. Paradoxically, these highly variable receptive fields go alongside
and are in fact required for an invariant representation of external sensory features.
In addition to offering a normative account of context-dependent changes in sensory
responses, perceptual inference in the presence of signal-dependent noise accounts
for ubiquitous features of sensory neurons such as divisive normalization, gain
control and contrast dependent temporal dynamics.
article_number: e1005582
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Paul
full_name: Masset, Paul
last_name: Masset
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping
of receptive fields. PLoS Computational Biology. 2017;13(6). doi:10.1371/journal.pcbi.1005582
apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Sensory noise
predicts divisive reshaping of receptive fields. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582
chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory
Noise Predicts Divisive Reshaping of Receptive Fields.” PLoS Computational
Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.
ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts
divisive reshaping of receptive fields,” PLoS Computational Biology, vol.
13, no. 6. Public Library of Science, 2017.
ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive
reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582.
mla: Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive
Fields.” PLoS Computational Biology, vol. 13, no. 6, e1005582, Public Library
of Science, 2017, doi:10.1371/journal.pcbi.1005582.
short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13
(2017).
date_created: 2018-12-11T11:47:53Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T14:10:54Z
day: '01'
ddc:
- '571'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005582
file:
- access_level: open_access
checksum: 796a1026076af6f4405a47d985bc7b68
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:47Z
date_updated: 2020-07-14T12:47:40Z
file_id: '4645'
file_name: IST-2017-898-v1+1_journal.pcbi.1005582.pdf
file_size: 14555676
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '7035'
pubrep_id: '898'
quality_controlled: '1'
related_material:
record:
- id: '9855'
relation: research_data
status: public
scopus_import: 1
status: public
title: Sensory noise predicts divisive reshaping of receptive fields
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '9851'
abstract:
- lang: eng
text: Based on the intuitive derivation of the dynamics of SIM allele frequency
pM in the main text, we present a heuristic prediction for the long-term SIM allele
frequencies with χ > 1 stresses and compare it to numerical simulations.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses.
2017. doi:10.1371/journal.pcbi.1005609.s003
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction
for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction
for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple
stresses.” Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple
stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.
mla: Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses.
Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:08:14Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Heuristic prediction for multiple stresses
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9852'
abstract:
- lang: eng
text: We show how different combination strategies affect the fraction of individuals
that are multi-resistant.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination
strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies
for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies
for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different
combination strategies.” Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different
combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.
mla: Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination
Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:11:40Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s004
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Resistance frequencies for different combination strategies
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9855'
abstract:
- lang: eng
text: Includes derivation of optimal estimation algorithm, generalisation to non-poisson
noise statistics, correlated input noise, and implementation of in a multi-layer
neural network.
article_processing_charge: No
author:
- first_name: Matthew J
full_name: Chalk, Matthew J
id: 2BAAC544-F248-11E8-B48F-1D18A9856A87
last_name: Chalk
orcid: 0000-0001-7782-4436
- first_name: Paul
full_name: Masset, Paul
last_name: Masset
- first_name: Boris
full_name: Gutkin, Boris
last_name: Gutkin
- first_name: Sophie
full_name: Denève, Sophie
last_name: Denève
citation:
ama: Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:10.1371/journal.pcbi.1005582.s001
apa: Chalk, M. J., Masset, P., Gutkin, B., & Denève, S. (2017). Supplementary
appendix. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005582.s001
chicago: Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary
Appendix.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005582.s001.
ieee: M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.”
Public Library of Science, 2017.
ista: Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public
Library of Science, 10.1371/journal.pcbi.1005582.s001.
mla: Chalk, Matthew J., et al. Supplementary Appendix. Public Library of
Science, 2017, doi:10.1371/journal.pcbi.1005582.s001.
short: M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).
date_created: 2021-08-10T07:05:10Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T12:52:17Z
day: '01'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1005582.s001
month: '06'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '680'
relation: used_in_publication
status: public
status: public
title: Supplementary appendix
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '941'
abstract:
- lang: eng
text: 'Recently there has been a proliferation of automated program repair (APR)
techniques, targeting various programming languages. Such techniques can be generally
classified into two families: syntactic- and semantics-based. Semantics-based
APR, on which we focus, typically uses symbolic execution to infer semantic constraints
and then program synthesis to construct repairs conforming to them. While syntactic-based
APR techniques have been shown successful on bugs in real-world programs written
in both C and Java, semantics-based APR techniques mostly target C programs. This
leaves empirical comparisons of the APR families not fully explored, and developers
without a Java-based semantics APR technique. We present JFix, a semantics-based
APR framework that targets Java, and an associated Eclipse plugin. JFix is implemented
atop Symbolic PathFinder, a well-known symbolic execution engine for Java programs.
It extends one particular APR technique (Angelix), and is designed to be sufficiently
generic to support a variety of such techniques. We demonstrate that semantics-based
APR can indeed efficiently and effectively repair a variety of classes of bugs
in large real-world Java programs. This supports our claim that the framework
can both support developers seeking semantics-based repair of bugs in Java programs,
as well as enable larger scale empirical studies comparing syntactic- and semantics-based
APR targeting Java. The demonstration of our tool is available via the project
website at: https://xuanbachle.github.io/semanticsrepair/ '
author:
- first_name: Xuan
full_name: Le, Xuan
last_name: Le
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: David
full_name: Lo, David
last_name: Lo
- first_name: Claire
full_name: Le Goues, Claire
last_name: Le Goues
- first_name: Willem
full_name: Visser, Willem
last_name: Visser
citation:
ama: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. JFIX: Semantics-based repair of
Java programs via symbolic PathFinder. In: Proceedings of the 26th ACM SIGSOFT
International Symposium on Software Testing and Analysis. ACM; 2017:376-379.
doi:10.1145/3092703.3098225'
apa: 'Le, X., Chu, D. H., Lo, D., Le Goues, C., & Visser, W. (2017). JFIX: Semantics-based
repair of Java programs via symbolic PathFinder. In Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis (pp.
376–379). Santa Barbara, CA, United States: ACM. https://doi.org/10.1145/3092703.3098225'
chicago: 'Le, Xuan, Duc Hiep Chu, David Lo, Claire Le Goues, and Willem Visser.
“JFIX: Semantics-Based Repair of Java Programs via Symbolic PathFinder.” In Proceedings
of the 26th ACM SIGSOFT International Symposium on Software Testing and Analysis,
376–79. ACM, 2017. https://doi.org/10.1145/3092703.3098225.'
ieee: 'X. Le, D. H. Chu, D. Lo, C. Le Goues, and W. Visser, “JFIX: Semantics-based
repair of Java programs via symbolic PathFinder,” in Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis, Santa
Barbara, CA, United States, 2017, pp. 376–379.'
ista: 'Le X, Chu DH, Lo D, Le Goues C, Visser W. 2017. JFIX: Semantics-based repair
of Java programs via symbolic PathFinder. Proceedings of the 26th ACM SIGSOFT
International Symposium on Software Testing and Analysis. ISSTA: International
Symposium on Software Testing and Analysis, 376–379.'
mla: 'Le, Xuan, et al. “JFIX: Semantics-Based Repair of Java Programs via Symbolic
PathFinder.” Proceedings of the 26th ACM SIGSOFT International Symposium on
Software Testing and Analysis, ACM, 2017, pp. 376–79, doi:10.1145/3092703.3098225.'
short: X. Le, D.H. Chu, D. Lo, C. Le Goues, W. Visser, in:, Proceedings of the 26th
ACM SIGSOFT International Symposium on Software Testing and Analysis, ACM, 2017,
pp. 376–379.
conference:
end_date: 2017-07-14
location: Santa Barbara, CA, United States
name: 'ISSTA: International Symposium on Software Testing and Analysis'
start_date: 2017-07-10
date_created: 2018-12-11T11:49:19Z
date_published: 2017-07-10T00:00:00Z
date_updated: 2021-01-12T08:22:05Z
day: '10'
department:
- _id: ToHe
doi: 10.1145/3092703.3098225
language:
- iso: eng
month: '07'
oa_version: None
page: '376 - 379 '
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Proceedings of the 26th ACM SIGSOFT International Symposium on Software
Testing and Analysis
publication_status: published
publisher: ACM
publist_id: '6478'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'JFIX: Semantics-based repair of Java programs via symbolic PathFinder'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2017'
...