---
_id: '1024'
abstract:
- lang: eng
text: The history of auxin and cytokinin biology including the initial discoveries
by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt
(1919) is a beautiful demonstration of unceasing continuity of research. Novel
findings are integrated into existing hypotheses and models and deepen our understanding
of biological principles. At the same time new questions are triggered and hand
to hand with this new methodologies are developed to address these new challenges.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Andrej
full_name: Hurny, Andrej
id: 4DC4AF46-F248-11E8-B48F-1D18A9856A87
last_name: Hurny
orcid: 0000-0003-3638-1426
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Hurny A, Benková E. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1
apa: Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin
biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1
chicago: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.
ieee: A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,”
Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29,
2017.
ista: Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology.
Auxins and Cytokinins in Plant Biology. 1569, 1–29.
mla: Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin
Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer,
2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.
short: A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017)
1–29.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2024-03-25T23:30:09Z
day: '17'
ddc:
- '575'
department:
- _id: EvBe
doi: 10.1007/978-1-4939-6831-2_1
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:18Z
date_updated: 2019-10-15T07:47:05Z
file_id: '5068'
file_name: IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf
file_size: 840646
relation: main_file
file_date_updated: 2019-10-15T07:47:05Z
has_accepted_license: '1'
intvolume: ' 1569'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 29
project:
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
publication: Auxins and Cytokinins in Plant Biology
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6369'
pubrep_id: '1019'
quality_controlled: '1'
related_material:
record:
- id: '539'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Methodological advances in auxin and cytokinin biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1569
year: '2017'
...
---
_id: '1025'
abstract:
- lang: eng
text: Many organ surfaces are covered by a protective epithelial-cell layer. It
emerges that such layers are maintained by cell stretching that triggers cell
division mediated by the force-sensitive ion-channel protein Piezo1. See Letter
p.118
article_processing_charge: No
author:
- 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
citation:
ama: 'Heisenberg C-PJ. Cell biology: Stretched divisions. Nature. 2017;543(7643):43-44.
doi:10.1038/nature21502'
apa: 'Heisenberg, C.-P. J. (2017). Cell biology: Stretched divisions. Nature.
Nature Publishing Group. https://doi.org/10.1038/nature21502'
chicago: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature.
Nature Publishing Group, 2017. https://doi.org/10.1038/nature21502.'
ieee: 'C.-P. J. Heisenberg, “Cell biology: Stretched divisions,” Nature,
vol. 543, no. 7643. Nature Publishing Group, pp. 43–44, 2017.'
ista: 'Heisenberg C-PJ. 2017. Cell biology: Stretched divisions. Nature. 543(7643),
43–44.'
mla: 'Heisenberg, Carl-Philipp J. “Cell Biology: Stretched Divisions.” Nature,
vol. 543, no. 7643, Nature Publishing Group, 2017, pp. 43–44, doi:10.1038/nature21502.'
short: C.-P.J. Heisenberg, Nature 543 (2017) 43–44.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-03-02T00:00:00Z
date_updated: 2023-09-22T09:26:59Z
day: '02'
department:
- _id: CaHe
doi: 10.1038/nature21502
external_id:
isi:
- '000395671500025'
intvolume: ' 543'
isi: 1
issue: '7643'
language:
- iso: eng
month: '03'
oa_version: None
page: 43 - 44
publication: Nature
publication_identifier:
issn:
- '00280836'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6367'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Cell biology: Stretched divisions'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 543
year: '2017'
...
---
_id: '1026'
abstract:
- lang: eng
text: The optogenetic revolution enabled spatially-precise and temporally-precise
control over protein function, signaling pathway activation, and animal behavior
with tremendous success in the dissection of signaling networks and neural circuits.
Very recently, optogenetic methods have been paired with optical reporters in
novel drug screening platforms. In these all-optical platforms, light remotely
activated ion channels and kinases thereby obviating the use of electrophysiology
or reagents. Consequences were remarkable operational simplicity, throughput,
and cost-effectiveness that culminated in the identification of new drug candidates.
These blueprints for all-optical assays also revealed potential pitfalls and inspire
all-optical variants of other screens, such as those that aim at better understanding
dynamic drug action or orphan protein function.
acknowledgement: This work was supported by grants of the European Union Seventh Framework
Programme (CIG-303564), the Human Frontier Science Program (RGY0084_2012), and the
Austrian Science Fund FWF (W1232 MolecularDrugTargets).
article_processing_charge: No
article_type: original
author:
- first_name: Viviana
full_name: Agus, Viviana
last_name: Agus
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: 'Agus V, Janovjak HL. Optogenetic methods in drug screening: Technologies and
applications. Current Opinion in Biotechnology. 2017;48:8-14. doi:10.1016/j.copbio.2017.02.006'
apa: 'Agus, V., & Janovjak, H. L. (2017). Optogenetic methods in drug screening:
Technologies and applications. Current Opinion in Biotechnology. Elsevier.
https://doi.org/10.1016/j.copbio.2017.02.006'
chicago: 'Agus, Viviana, and Harald L Janovjak. “Optogenetic Methods in Drug Screening:
Technologies and Applications.” Current Opinion in Biotechnology. Elsevier,
2017. https://doi.org/10.1016/j.copbio.2017.02.006.'
ieee: 'V. Agus and H. L. Janovjak, “Optogenetic methods in drug screening: Technologies
and applications,” Current Opinion in Biotechnology, vol. 48. Elsevier,
pp. 8–14, 2017.'
ista: 'Agus V, Janovjak HL. 2017. Optogenetic methods in drug screening: Technologies
and applications. Current Opinion in Biotechnology. 48, 8–14.'
mla: 'Agus, Viviana, and Harald L. Janovjak. “Optogenetic Methods in Drug Screening:
Technologies and Applications.” Current Opinion in Biotechnology, vol.
48, Elsevier, 2017, pp. 8–14, doi:10.1016/j.copbio.2017.02.006.'
short: V. Agus, H.L. Janovjak, Current Opinion in Biotechnology 48 (2017) 8–14.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-22T09:26:06Z
day: '01'
department:
- _id: HaJa
doi: 10.1016/j.copbio.2017.02.006
ec_funded: 1
external_id:
isi:
- '000418313200003'
intvolume: ' 48'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 8 - 14
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)
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 255A6082-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets
publication: Current Opinion in Biotechnology
publication_identifier:
issn:
- '09581669'
publication_status: published
publisher: Elsevier
publist_id: '6365'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Optogenetic methods in drug screening: Technologies and applications'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 48
year: '2017'
...
---
_id: '1027'
abstract:
- lang: eng
text: The rising prevalence of antibiotic resistant bacteria is an increasingly
serious public health challenge. To address this problem, recent work ranging
from clinical studies to theoretical modeling has provided valuable insights into
the mechanisms of resistance, its emergence and spread, and ways to counteract
it. A deeper understanding of the underlying dynamics of resistance evolution
will require a combination of experimental and theoretical expertise from different
disciplines and new technology for studying evolution in the laboratory. Here,
we review recent advances in the quantitative understanding of the mechanisms
and evolution of antibiotic resistance. We focus on key theoretical concepts and
new technology that enables well-controlled experiments. We further highlight
key challenges that can be met in the near future to ultimately develop effective
strategies for combating resistance.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- 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: Lukacisinova M, Bollenbach MT. Toward a quantitative understanding of antibiotic
resistance evolution. Current Opinion in Biotechnology. 2017;46:90-97.
doi:10.1016/j.copbio.2017.02.013
apa: Lukacisinova, M., & Bollenbach, M. T. (2017). Toward a quantitative understanding
of antibiotic resistance evolution. Current Opinion in Biotechnology. Elsevier.
https://doi.org/10.1016/j.copbio.2017.02.013
chicago: Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative
Understanding of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology.
Elsevier, 2017. https://doi.org/10.1016/j.copbio.2017.02.013.
ieee: M. Lukacisinova and M. T. Bollenbach, “Toward a quantitative understanding
of antibiotic resistance evolution,” Current Opinion in Biotechnology,
vol. 46. Elsevier, pp. 90–97, 2017.
ista: Lukacisinova M, Bollenbach MT. 2017. Toward a quantitative understanding of
antibiotic resistance evolution. Current Opinion in Biotechnology. 46, 90–97.
mla: Lukacisinova, Marta, and Mark Tobias Bollenbach. “Toward a Quantitative Understanding
of Antibiotic Resistance Evolution.” Current Opinion in Biotechnology,
vol. 46, Elsevier, 2017, pp. 90–97, doi:10.1016/j.copbio.2017.02.013.
short: M. Lukacisinova, M.T. Bollenbach, Current Opinion in Biotechnology 46 (2017)
90–97.
date_created: 2018-12-11T11:49:45Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2024-03-25T23:30:15Z
day: '01'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1016/j.copbio.2017.02.013
ec_funded: 1
external_id:
isi:
- '000408077400015'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:57:57Z
date_updated: 2019-01-18T09:57:57Z
file_id: '5846'
file_name: 2017_CurrentOpinion_Lukaciinova.pdf
file_size: 858338
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:57:57Z
has_accepted_license: '1'
intvolume: ' 46'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 90 - 97
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25EB3A80-B435-11E9-9278-68D0E5697425
grant_number: RGP0042/2013
name: Revealing the fundamental limits of cell growth
publication: Current Opinion in Biotechnology
publication_status: published
publisher: Elsevier
publist_id: '6364'
pubrep_id: '801'
quality_controlled: '1'
related_material:
record:
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Toward a quantitative understanding of antibiotic resistance evolution
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 46
year: '2017'
...
---
_id: '1028'
abstract:
- lang: eng
text: Optogenetics and photopharmacology provide spatiotemporally precise control
over protein interactions and protein function in cells and animals. Optogenetic
methods that are sensitive to green light and can be used to break protein complexes
are not broadly available but would enable multichromatic experiments with previously
inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12)
binding domains of bacterial CarH transcription factors for green-light-induced
receptor dissociation. In cultured cells, we observed oligomerization-induced
cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding
domains in the dark that was rapidly eliminated upon illumination. In zebrafish
embryos expressing fusion receptors, green light endowed control over aberrant
fibroblast growth factor signaling during development. Green-light-induced domain
dissociation and light-inactivated receptors will critically expand the optogenetic
toolbox for control of biological processes.
acknowledgement: "This work was supported by a grant from the European Union\U0010FC1Ds
Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program
MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship
(Austrian Research Promotion Agency, 3580812)"
article_processing_charge: No
author:
- first_name: Stephanie
full_name: Kainrath, Stephanie
id: 32CFBA64-F248-11E8-B48F-1D18A9856A87
last_name: Kainrath
- first_name: Manuela
full_name: Stadler, Manuela
last_name: Stadler
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Martin
full_name: Distel, Martin
last_name: Distel
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced
inactivation of receptor signaling using cobalamin-binding domains. Angewandte
Chemie - International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998
apa: Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak,
H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.201611998
chicago: Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel,
and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling
Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition.
Wiley-Blackwell, 2017. https://doi.org/10.1002/anie.201611998.
ieee: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak,
“Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains,” Angewandte Chemie - International Edition, vol. 56, no. 16. Wiley-Blackwell,
pp. 4608–4611, 2017.
ista: Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017.
Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains. Angewandte Chemie - International Edition. 56(16), 4608–4611.
mla: Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling
Using Cobalamin-Binding Domains.” Angewandte Chemie - International Edition,
vol. 56, no. 16, Wiley-Blackwell, 2017, pp. 4608–11, doi:10.1002/anie.201611998.
short: S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak,
Angewandte Chemie - International Edition 56 (2017) 4608–4611.
date_created: 2018-12-11T11:49:46Z
date_published: 2017-03-20T00:00:00Z
date_updated: 2024-03-25T23:30:08Z
day: '20'
ddc:
- '540'
department:
- _id: CaGu
- _id: HaJa
doi: 10.1002/anie.201611998
ec_funded: 1
external_id:
isi:
- '000398154000038'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:39:55Z
date_updated: 2019-01-18T09:39:55Z
file_id: '5845'
file_name: 2017_communications_Kainrath.pdf
file_size: 2614942
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:39:55Z
has_accepted_license: '1'
intvolume: ' 56'
isi: 1
issue: '16'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 4608-4611
project:
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
- _id: 26AA4EF2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232-B24
name: Molecular Drug Targets [do not use to be deleted]
publication: Angewandte Chemie - International Edition
publication_identifier:
issn:
- '14337851'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6362'
quality_controlled: '1'
related_material:
record:
- id: '418'
relation: dissertation_contains
status: public
- id: '7680'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Green-light-induced inactivation of receptor signaling using cobalamin-binding
domains
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 56
year: '2017'
...
---
_id: '1029'
abstract:
- lang: eng
text: RNA Polymerase II pauses and backtracks during transcription, with many consequences
for gene expression and cellular physiology. Here, we show that the energy required
to melt double-stranded nucleic acids in the transcription bubble predicts pausing
in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do.
In addition, the same energy difference also determines when the RNA polymerase
backtracks instead of continuing to move forward. This data-driven model corroborates—in
a genome wide and quantitative manner—previous evidence that sequence-dependent
thermodynamic features of nucleic acids influence both transcriptional pausing
and backtracking.
article_number: e0174066
article_processing_charge: Yes
author:
- first_name: Martin
full_name: Lukacisin, Martin
id: 298FFE8C-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisin
orcid: 0000-0001-6549-4177
- first_name: Matthieu
full_name: Landon, Matthieu
last_name: Landon
- first_name: Rishi
full_name: Jajoo, Rishi
last_name: Jajoo
citation:
ama: Lukacisin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast.
PLoS One. 2017;12(3). doi:10.1371/journal.pone.0174066
apa: Lukacisin, M., Landon, M., & Jajoo, R. (2017). Sequence-specific thermodynamic
properties of nucleic acids influence both transcriptional pausing and backtracking
in yeast. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0174066
chicago: Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “Sequence-Specific
Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing
and Backtracking in Yeast.” PLoS One. Public Library of Science, 2017.
https://doi.org/10.1371/journal.pone.0174066.
ieee: M. Lukacisin, M. Landon, and R. Jajoo, “Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast,”
PLoS One, vol. 12, no. 3. Public Library of Science, 2017.
ista: Lukacisin M, Landon M, Jajoo R. 2017. Sequence-specific thermodynamic properties
of nucleic acids influence both transcriptional pausing and backtracking in yeast.
PLoS One. 12(3), e0174066.
mla: Lukacisin, Martin, et al. “Sequence-Specific Thermodynamic Properties of Nucleic
Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” PLoS
One, vol. 12, no. 3, e0174066, Public Library of Science, 2017, doi:10.1371/journal.pone.0174066.
short: M. Lukacisin, M. Landon, R. Jajoo, PLoS One 12 (2017).
date_created: 2018-12-11T11:49:46Z
date_published: 2017-03-16T00:00:00Z
date_updated: 2024-03-25T23:30:03Z
day: '16'
ddc:
- '570'
department:
- _id: ToBo
doi: 10.1371/journal.pone.0174066
external_id:
isi:
- '000396318300121'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:47Z
date_updated: 2018-12-12T10:09:47Z
file_id: '4772'
file_name: IST-2017-800-v1+1_journal.pone.0174066.pdf
file_size: 3429381
relation: main_file
file_date_updated: 2018-12-12T10:09:47Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_identifier:
issn:
- '19326203'
publication_status: published
publisher: Public Library of Science
publist_id: '6361'
pubrep_id: '800'
quality_controlled: '1'
related_material:
record:
- id: '5556'
relation: popular_science
status: public
- id: '6392'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Sequence-specific thermodynamic properties of nucleic acids influence both
transcriptional pausing and backtracking in yeast
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 12
year: '2017'
...
---
_id: '1030'
abstract:
- lang: ger
text: Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung
IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt
wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche
Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte
Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die
Bibliothek auf eine erfolgreiche Implementierung zurückblicken.
- lang: eng
text: "IST Austria was looking for a new library system until 2014 when the research
institute decided\r\nto implement Koha. The library first activated basic functions
of the open-source product and\r\nthen brought additional tools into operation.
The high flexibility of the system allows customized\r\nsolutions for different
institutions. Although the library faced some challenges, it can now look\r\nback
on a successful implementation."
article_processing_charge: No
article_type: original
author:
- first_name: Márton
full_name: Villányi, Márton
id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
last_name: Villányi
orcid: 0000-0001-8126-0426
citation:
ama: Villányi M. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. 2017;3(1).
doi:10.11588/ip.2017.1.35227
apa: Villányi, M. (2017). Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. Verein
Informationspraxis . https://doi.org/10.11588/ip.2017.1.35227
chicago: Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken
– Werkstattbericht Der IST Austria Library.” Informationspraxis. Verein
Informationspraxis , 2017. https://doi.org/10.11588/ip.2017.1.35227.
ieee: M. Villányi, “Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library,” Informationspraxis, vol. 3,
no. 1. Verein Informationspraxis , 2017.
ista: Villányi M. 2017. Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken
– Werkstattbericht der IST Austria Library. Informationspraxis. 3(1).
mla: Villányi, Márton. “Ein Freies Bibliothekssystem Für Wissenschaftliche Bibliotheken
– Werkstattbericht Der IST Austria Library.” Informationspraxis, vol. 3,
no. 1, Verein Informationspraxis , 2017, doi:10.11588/ip.2017.1.35227.
short: M. Villányi, Informationspraxis 3 (2017).
date_created: 2018-12-11T11:49:46Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-10-18T07:49:29Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.11588/ip.2017.1.35227
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:20Z
date_updated: 2018-12-12T10:08:20Z
file_id: '4680'
file_name: IST-2017-799-v1+1_35227-112025-1-PB.pdf
file_size: 201163
relation: main_file
file_date_updated: 2018-12-12T10:08:20Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
popular_science: '1'
publication: Informationspraxis
publication_identifier:
issn:
- 2297-3249
publication_status: published
publisher: 'Verein Informationspraxis '
publist_id: '6360'
pubrep_id: '799'
status: public
title: Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht
der IST Austria Library
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: 3
year: '2017'
...
---
_id: '10416'
abstract:
- lang: eng
text: 'A fundamental algorithmic problem at the heart of static analysis is Dyck
reachability. The input is a graph where the edges are labeled with different
types of opening and closing parentheses, and the reachability information is
computed via paths whose parentheses are properly matched. We present new results
for Dyck reachability problems with applications to alias analysis and data-dependence
analysis. Our main contributions, that include improved upper bounds as well as
lower bounds that establish optimality guarantees, are as follows: First, we consider
Dyck reachability on bidirected graphs, which is the standard way of performing
field-sensitive points-to analysis. Given a bidirected graph with n nodes and
m edges, we present: (i) an algorithm with worst-case running time O(m + n · α(n)),
where α(n) is the inverse Ackermann function, improving the previously known O(n2)
time bound; (ii) a matching lower bound that shows that our algorithm is optimal
wrt to worst-case complexity; and (iii) an optimal average-case upper bound of
O(m) time, improving the previously known O(m · logn) bound. Second, we consider
the problem of context-sensitive data-dependence analysis, where the task is to
obtain analysis summaries of library code in the presence of callbacks. Our algorithm
preprocesses libraries in almost linear time, after which the contribution of
the library in the complexity of the client analysis is only linear, and only
wrt the number of call sites. Third, we prove that combinatorial algorithms for
Dyck reachability on general graphs with truly sub-cubic bounds cannot be obtained
without obtaining sub-cubic combinatorial algorithms for Boolean Matrix Multiplication,
which is a long-standing open problem. Thus we establish that the existing combinatorial
algorithms for Dyck reachability are (conditionally) optimal for general graphs.
We also show that the same hardness holds for graphs of constant treewidth. Finally,
we provide a prototype implementation of our algorithms for both alias analysis
and data-dependence analysis. Our experimental evaluation demonstrates that the
new algorithms significantly outperform all existing methods on the two problems,
over real-world benchmarks.'
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Start grant
(279307: Graph Games).\r\n"
article_number: '30'
article_processing_charge: No
article_type: original
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: Bhavya
full_name: Choudhary, Bhavya
last_name: Choudhary
- 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, Choudhary B, Pavlogiannis A. Optimal Dyck reachability for data-dependence
and Alias analysis. Proceedings of the ACM on Programming Languages. 2017;2(POPL).
doi:10.1145/3158118
apa: 'Chatterjee, K., Choudhary, B., & Pavlogiannis, A. (2017). Optimal Dyck
reachability for data-dependence and Alias analysis. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158118'
chicago: Chatterjee, Krishnendu, Bhavya Choudhary, and Andreas Pavlogiannis. “Optimal
Dyck Reachability for Data-Dependence and Alias Analysis.” Proceedings of the
ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158118.
ieee: K. Chatterjee, B. Choudhary, and A. Pavlogiannis, “Optimal Dyck reachability
for data-dependence and Alias analysis,” Proceedings of the ACM on Programming
Languages, vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chatterjee K, Choudhary B, Pavlogiannis A. 2017. Optimal Dyck reachability
for data-dependence and Alias analysis. Proceedings of the ACM on Programming
Languages. 2(POPL), 30.
mla: Chatterjee, Krishnendu, et al. “Optimal Dyck Reachability for Data-Dependence
and Alias Analysis.” Proceedings of the ACM on Programming Languages, vol.
2, no. POPL, 30, Association for Computing Machinery, 2017, doi:10.1145/3158118.
short: K. Chatterjee, B. Choudhary, A. Pavlogiannis, Proceedings of the ACM on Programming
Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:48Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:13Z
day: '27'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3158118
ec_funded: 1
external_id:
arxiv:
- '1910.00241'
file:
- access_level: open_access
checksum: faa3f7b3fe8aab84b50ed805c26a0ee5
content_type: application/pdf
creator: cchlebak
date_created: 2021-12-07T08:06:28Z
date_updated: 2021-12-07T08:06:28Z
file_id: '10421'
file_name: 2017_ACMProgLang_Chatterjee.pdf
file_size: 460188
relation: main_file
success: 1
file_date_updated: 2021-12-07T08:06:28Z
has_accepted_license: '1'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _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
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5455'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Optimal Dyck reachability for data-dependence and Alias analysis
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '10417'
abstract:
- lang: eng
text: "We present a new dynamic partial-order reduction method for stateless model
checking of concurrent programs. A common approach for exploring program behaviors
relies on enumerating the traces of the program, without storing the visited states
(aka stateless exploration). As the number of distinct traces grows exponentially,
dynamic partial-order reduction (DPOR) techniques have been successfully used
to partition the space of traces into equivalence classes (Mazurkiewicz partitioning),
with the goal of exploring only few representative traces from each class.\r\n\r\nWe
introduce a new equivalence on traces under sequential consistency semantics,
which we call the observation equivalence. Two traces are observationally equivalent
if every read event observes the same write event in both traces. While the traditional
Mazurkiewicz equivalence is control-centric, our new definition is data-centric.
We show that our observation equivalence is coarser than the Mazurkiewicz equivalence,
and in many cases even exponentially coarser. We devise a DPOR exploration of
the trace space, called data-centric DPOR, based on the observation equivalence."
acknowledgement: "The research was partly supported by Austrian Science Fund (FWF)
Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant
(279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061."
article_number: '31'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marek
full_name: Chalupa, Marek
last_name: Chalupa
- 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: Nishant
full_name: Sinha, Nishant
last_name: Sinha
- first_name: Kapil
full_name: Vaidya, Kapil
last_name: Vaidya
citation:
ama: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic
partial order reduction. Proceedings of the ACM on Programming Languages.
2017;2(POPL). doi:10.1145/3158119
apa: 'Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K.
(2017). Data-centric dynamic partial order reduction. Proceedings of the ACM
on Programming Languages. Los Angeles, CA, United States: Association for
Computing Machinery. https://doi.org/10.1145/3158119'
chicago: Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha,
and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages. Association for Computing Machinery,
2017. https://doi.org/10.1145/3158119.
ieee: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric
dynamic partial order reduction,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2017. Data-centric
dynamic partial order reduction. Proceedings of the ACM on Programming Languages.
2(POPL), 31.
mla: Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for
Computing Machinery, 2017, doi:10.1145/3158119.
short: M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings
of the ACM on Programming Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2017-12-27T00:00:00Z
date_updated: 2023-02-23T12:27:16Z
day: '27'
department:
- _id: KrCh
doi: 10.1145/3158119
ec_funded: 1
external_id:
arxiv:
- '1610.01188'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3158119
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '5448'
relation: earlier_version
status: public
- id: '5456'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Data-centric dynamic partial order reduction
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '10418'
abstract:
- lang: eng
text: We present a new proof rule for proving almost-sure termination of probabilistic
programs, including those that contain demonic non-determinism. An important question
for a probabilistic program is whether the probability mass of all its diverging
runs is zero, that is that it terminates "almost surely". Proving that can be
hard, and this paper presents a new method for doing so. It applies directly to
the program's source code, even if the program contains demonic choice. Like others,
we use variant functions (a.k.a. "super-martingales") that are real-valued and
decrease randomly on each loop iteration; but our key innovation is that the amount
as well as the probability of the decrease are parametric. We prove the soundness
of the new rule, indicate where its applicability goes beyond existing rules,
and explain its connection to classical results on denumerable (non-demonic) Markov
chains.
acknowledgement: "McIver and Morgan are grateful to David Basin and the Information
Security Group at ETH Zürich for hosting a six-month stay in Switzerland, during
part of which this work began. And thanks particularly to Andreas Lochbihler, who
shared with us the probabilistic termination problem that led to it. They acknowledge
the support of ARC grant DP140101119. Part of this work was carried out during the
Workshop on Probabilistic Programming Semantics\r\nat McGill University’s Bellairs
Research Institute on Barbados organised by Alexandra Silva and\r\nPrakash Panangaden.
Kaminski and Katoen are grateful to Sebastian Junges for spotting a flaw in §5.4."
article_number: '33'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Annabelle
full_name: Mciver, Annabelle
last_name: Mciver
- first_name: Carroll
full_name: Morgan, Carroll
last_name: Morgan
- first_name: Benjamin Lucien
full_name: Kaminski, Benjamin Lucien
last_name: Kaminski
- first_name: Joost P
full_name: Katoen, Joost P
id: 4524F760-F248-11E8-B48F-1D18A9856A87
last_name: Katoen
citation:
ama: Mciver A, Morgan C, Kaminski BL, Katoen JP. A new proof rule for almost-sure
termination. Proceedings of the ACM on Programming Languages. 2017;2(POPL).
doi:10.1145/3158121
apa: 'Mciver, A., Morgan, C., Kaminski, B. L., & Katoen, J. P. (2017). A new
proof rule for almost-sure termination. Proceedings of the ACM on Programming
Languages. Los Angeles, CA, United States: Association for Computing Machinery.
https://doi.org/10.1145/3158121'
chicago: Mciver, Annabelle, Carroll Morgan, Benjamin Lucien Kaminski, and Joost
P Katoen. “A New Proof Rule for Almost-Sure Termination.” Proceedings of the
ACM on Programming Languages. Association for Computing Machinery, 2017. https://doi.org/10.1145/3158121.
ieee: A. Mciver, C. Morgan, B. L. Kaminski, and J. P. Katoen, “A new proof rule
for almost-sure termination,” Proceedings of the ACM on Programming Languages,
vol. 2, no. POPL. Association for Computing Machinery, 2017.
ista: Mciver A, Morgan C, Kaminski BL, Katoen JP. 2017. A new proof rule for almost-sure
termination. Proceedings of the ACM on Programming Languages. 2(POPL), 33.
mla: Mciver, Annabelle, et al. “A New Proof Rule for Almost-Sure Termination.” Proceedings
of the ACM on Programming Languages, vol. 2, no. POPL, 33, Association for
Computing Machinery, 2017, doi:10.1145/3158121.
short: A. Mciver, C. Morgan, B.L. Kaminski, J.P. Katoen, Proceedings of the ACM
on Programming Languages 2 (2017).
conference:
end_date: 2018-01-13
location: Los Angeles, CA, United States
name: 'POPL: Programming Languages'
start_date: 2018-01-07
date_created: 2021-12-05T23:01:49Z
date_published: 2017-12-07T00:00:00Z
date_updated: 2021-12-07T08:04:14Z
day: '07'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1145/3158121
external_id:
arxiv:
- '1711.03588'
intvolume: ' 2'
issue: POPL
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://dl.acm.org/doi/10.1145/3158121
month: '12'
oa: 1
oa_version: Published Version
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
eissn:
- 2475-1421
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new proof rule for almost-sure termination
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2017'
...
---
_id: '1063'
abstract:
- lang: eng
text: Severe environmental change can drive a population extinct unless the population
adapts in time to the new conditions (“evolutionary rescue”). How does biparental
sexual reproduction influence the chances of population persistence compared to
clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele
model for adaptation in diploid species, where rescue is contingent on the establishment
of the mutant homozygote. Reproduction can occur by random mating, selfing, or
clonally. Random mating generates and destroys the rescue mutant; selfing is efficient
at generating it but at the same time depletes the heterozygote, which can lead
to a low mutant frequency in the standing genetic variation. Due to these (and
other) antagonistic effects, we find a nontrivial dependence of population survival
on the rate of sex/selfing, which is strongly influenced by the dominance coefficient
of the mutation before and after the environmental change. Importantly, since
mating with the wild‐type breaks the mutant homozygote up, a slow decay of the
wild‐type population size can impede rescue in randomly mating populations.
article_processing_charge: No
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
citation:
ama: Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations.
Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191
apa: Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191
chicago: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and
Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.
ieee: H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,”
Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.
ista: Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. 71(4), 845–858.
mla: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal
Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58,
doi:10.1111/evo.13191.
short: H. Uecker, Evolution 71 (2017) 845–858.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2025-05-28T11:42:51Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.13191
ec_funded: 1
external_id:
isi:
- '000398545200003'
intvolume: ' 71'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2016/10/14/081042
month: '04'
oa: 1
oa_version: Submitted Version
page: 845 - 858
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6327'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary rescue in randomly mating, selfing, and clonal populations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '1065'
abstract:
- lang: eng
text: 'We consider the problem of reachability in pushdown graphs. We study the
problem for pushdown graphs with constant treewidth. Even for pushdown graphs
with treewidth 1, for the reachability problem we establish the following: (i)
the problem is PTIME-complete, and (ii) any subcubic algorithm for the problem
would contradict the k-clique conjecture and imply faster combinatorial algorithms
for cliques in graphs.'
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: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
citation:
ama: Chatterjee K, Osang GF. Pushdown reachability with constant treewidth. Information
Processing Letters. 2017;122:25-29. doi:10.1016/j.ipl.2017.02.003
apa: Chatterjee, K., & Osang, G. F. (2017). Pushdown reachability with constant
treewidth. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2017.02.003
chicago: Chatterjee, Krishnendu, and Georg F Osang. “Pushdown Reachability with
Constant Treewidth.” Information Processing Letters. Elsevier, 2017. https://doi.org/10.1016/j.ipl.2017.02.003.
ieee: K. Chatterjee and G. F. Osang, “Pushdown reachability with constant treewidth,”
Information Processing Letters, vol. 122. Elsevier, pp. 25–29, 2017.
ista: Chatterjee K, Osang GF. 2017. Pushdown reachability with constant treewidth.
Information Processing Letters. 122, 25–29.
mla: Chatterjee, Krishnendu, and Georg F. Osang. “Pushdown Reachability with Constant
Treewidth.” Information Processing Letters, vol. 122, Elsevier, 2017, pp.
25–29, doi:10.1016/j.ipl.2017.02.003.
short: K. Chatterjee, G.F. Osang, Information Processing Letters 122 (2017) 25–29.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:08:18Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
- _id: HeEd
doi: 10.1016/j.ipl.2017.02.003
ec_funded: 1
external_id:
isi:
- '000399506600005'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:17Z
date_updated: 2019-10-15T07:44:51Z
file_id: '4998'
file_name: IST-2018-991-v1+2_2018_Chatterjee_Pushdown_PREPRINT.pdf
file_size: 247657
relation: main_file
file_date_updated: 2019-10-15T07:44:51Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 25 - 29
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: Information Processing Letters
publication_identifier:
issn:
- '00200190'
publication_status: published
publisher: Elsevier
publist_id: '6323'
pubrep_id: '991'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Pushdown reachability with constant treewidth
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 122
year: '2017'
...
---
_id: '1066'
abstract:
- lang: eng
text: "Simulation is an attractive alternative to language inclusion for automata
as it is an under-approximation of language inclusion, but usually has much lower
complexity. Simulation has also been extended in two orthogonal directions, namely,
(1) fair simulation, for simulation over specified set of infinite runs; and (2)
quantitative simulation, for simulation between weighted automata. While fair
trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial
time. For weighted automata, the (quantitative) language inclusion problem is
undecidable in general, whereas the (quantitative) simulation reduces to quantitative
games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we
study (quantitative) simulation for weighted automata with Büchi acceptance conditions,
i.e., we generalize fair simulation from non-weighted automata to weighted automata.
We show that imposing Büchi acceptance conditions on weighted automata changes
many fundamental properties of the simulation games, yet they still admit pseudo-polynomial
time algorithms."
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: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jan
full_name: Otop, Jan
id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87
last_name: Otop
- first_name: Yaron
full_name: Velner, Yaron
last_name: Velner
citation:
ama: Chatterjee K, Henzinger TA, Otop J, Velner Y. Quantitative fair simulation
games. Information and Computation. 2017;254(2):143-166. doi:10.1016/j.ic.2016.10.006
apa: Chatterjee, K., Henzinger, T. A., Otop, J., & Velner, Y. (2017). Quantitative
fair simulation games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2016.10.006
chicago: Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner.
“Quantitative Fair Simulation Games.” Information and Computation. Elsevier,
2017. https://doi.org/10.1016/j.ic.2016.10.006.
ieee: K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, “Quantitative fair
simulation games,” Information and Computation, vol. 254, no. 2. Elsevier,
pp. 143–166, 2017.
ista: Chatterjee K, Henzinger TA, Otop J, Velner Y. 2017. Quantitative fair simulation
games. Information and Computation. 254(2), 143–166.
mla: Chatterjee, Krishnendu, et al. “Quantitative Fair Simulation Games.” Information
and Computation, vol. 254, no. 2, Elsevier, 2017, pp. 143–66, doi:10.1016/j.ic.2016.10.006.
short: K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Information and Computation
254 (2017) 143–166.
date_created: 2018-12-11T11:49:58Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:07:48Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1016/j.ic.2016.10.006
ec_funded: 1
external_id:
isi:
- '000402025600002'
intvolume: ' 254'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa_version: None
page: 143 - 166
project:
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _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: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: Information and Computation
publication_status: published
publisher: Elsevier
publist_id: '6322'
quality_controlled: '1'
related_material:
record:
- id: '5428'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Quantitative fair simulation games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 254
year: '2017'
...
---
_id: '1067'
abstract:
- lang: eng
text: Embryo morphogenesis relies on highly coordinated movements of different tissues.
However, remarkably little is known about how tissues coordinate their movements
to shape the embryo. In zebrafish embryogenesis, coordinated tissue movements
first become apparent during “doming,” when the blastoderm begins to spread over
the yolk sac, a process involving coordinated epithelial surface cell layer expansion
and mesenchymal deep cell intercalations. Here, we find that active surface cell
expansion represents the key process coordinating tissue movements during doming.
By using a combination of theory and experiments, we show that epithelial surface
cells not only trigger blastoderm expansion by reducing tissue surface tension,
but also drive blastoderm thinning by inducing tissue contraction through radial
deep cell intercalations. Thus, coordinated tissue expansion and thinning during
doming relies on surface cells simultaneously controlling tissue surface tension
and radial tissue contraction.
acknowledged_ssus:
- _id: PreCl
article_processing_charge: No
author:
- first_name: Hitoshi
full_name: Morita, Hitoshi
id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87
last_name: Morita
- first_name: Silvia
full_name: Grigolon, Silvia
last_name: Grigolon
- first_name: Martin
full_name: Bock, Martin
last_name: Bock
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- 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
citation:
ama: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. The physical
basis of coordinated tissue spreading in zebrafish gastrulation. Developmental
Cell. 2017;40(4):354-366. doi:10.1016/j.devcel.2017.01.010
apa: Morita, H., Grigolon, S., Bock, M., Krens, G., Salbreux, G., & Heisenberg,
C.-P. J. (2017). The physical basis of coordinated tissue spreading in zebrafish
gastrulation. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2017.01.010
chicago: Morita, Hitoshi, Silvia Grigolon, Martin Bock, Gabriel Krens, Guillaume
Salbreux, and Carl-Philipp J Heisenberg. “The Physical Basis of Coordinated Tissue
Spreading in Zebrafish Gastrulation.” Developmental Cell. Cell Press, 2017.
https://doi.org/10.1016/j.devcel.2017.01.010.
ieee: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, and C.-P. J. Heisenberg,
“The physical basis of coordinated tissue spreading in zebrafish gastrulation,”
Developmental Cell, vol. 40, no. 4. Cell Press, pp. 354–366, 2017.
ista: Morita H, Grigolon S, Bock M, Krens G, Salbreux G, Heisenberg C-PJ. 2017.
The physical basis of coordinated tissue spreading in zebrafish gastrulation.
Developmental Cell. 40(4), 354–366.
mla: Morita, Hitoshi, et al. “The Physical Basis of Coordinated Tissue Spreading
in Zebrafish Gastrulation.” Developmental Cell, vol. 40, no. 4, Cell Press,
2017, pp. 354–66, doi:10.1016/j.devcel.2017.01.010.
short: H. Morita, S. Grigolon, M. Bock, G. Krens, G. Salbreux, C.-P.J. Heisenberg,
Developmental Cell 40 (2017) 354–366.
date_created: 2018-12-11T11:49:58Z
date_published: 2017-02-27T00:00:00Z
date_updated: 2023-09-20T12:06:27Z
day: '27'
ddc:
- '572'
- '597'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2017.01.010
ec_funded: 1
external_id:
isi:
- '000395368300007'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:57Z
date_updated: 2018-12-12T10:10:57Z
file_id: '4849'
file_name: IST-2017-869-v1+1_1-s2.0-S1534580717300370-main.pdf
file_size: 6866187
relation: main_file
file_date_updated: 2018-12-12T10:10:57Z
has_accepted_license: '1'
intvolume: ' 40'
isi: 1
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 354 - 366
project:
- _id: 2524F500-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '201439'
name: Developing High-Throughput Bioassays for Human Cancers in Zebrafish
publication: Developmental Cell
publication_identifier:
issn:
- '15345807'
publication_status: published
publisher: Cell Press
publist_id: '6320'
pubrep_id: '869'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The physical basis of coordinated tissue spreading in zebrafish gastrulation
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 40
year: '2017'
...
---
_id: '1072'
abstract:
- lang: eng
text: Given a finite set of points in Rn and a radius parameter, we study the Čech,
Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized
discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel
sets of generalized discrete Morse functions, we prove that the four complexes
are simple-homotopy equivalent by a sequence of simplicial collapses, which are
explicitly described by a single discrete gradient field.
acknowledgement: This research has been supported by the EU project Toposys(FP7-ICT-318493-STREP),
by ESF under the ACAT Research Network Programme, by the Russian Government under
mega project 11.G34.31.0053, and by the DFG Collaborative Research Center SFB/TRR
109 “Discretization in Geometry and Dynamics”.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
id: 2ADD483A-F248-11E8-B48F-1D18A9856A87
last_name: Bauer
orcid: 0000-0002-9683-0724
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Bauer U, Edelsbrunner H. The Morse theory of Čech and delaunay complexes. Transactions
of the American Mathematical Society. 2017;369(5):3741-3762. doi:10.1090/tran/6991
apa: Bauer, U., & Edelsbrunner, H. (2017). The Morse theory of Čech and delaunay
complexes. Transactions of the American Mathematical Society. American
Mathematical Society. https://doi.org/10.1090/tran/6991
chicago: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and
Delaunay Complexes.” Transactions of the American Mathematical Society.
American Mathematical Society, 2017. https://doi.org/10.1090/tran/6991.
ieee: U. Bauer and H. Edelsbrunner, “The Morse theory of Čech and delaunay complexes,”
Transactions of the American Mathematical Society, vol. 369, no. 5. American
Mathematical Society, pp. 3741–3762, 2017.
ista: Bauer U, Edelsbrunner H. 2017. The Morse theory of Čech and delaunay complexes.
Transactions of the American Mathematical Society. 369(5), 3741–3762.
mla: Bauer, Ulrich, and Herbert Edelsbrunner. “The Morse Theory of Čech and Delaunay
Complexes.” Transactions of the American Mathematical Society, vol. 369,
no. 5, American Mathematical Society, 2017, pp. 3741–62, doi:10.1090/tran/6991.
short: U. Bauer, H. Edelsbrunner, Transactions of the American Mathematical Society
369 (2017) 3741–3762.
date_created: 2018-12-11T11:49:59Z
date_published: 2017-05-01T00:00:00Z
date_updated: 2023-09-20T12:05:56Z
day: '01'
department:
- _id: HeEd
doi: 10.1090/tran/6991
ec_funded: 1
external_id:
arxiv:
- '1312.1231'
isi:
- '000398030400024'
intvolume: ' 369'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.1231
month: '05'
oa: 1
oa_version: Preprint
page: 3741 - 3762
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Transactions of the American Mathematical Society
publication_status: published
publisher: American Mathematical Society
publist_id: '6311'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Morse theory of Čech and delaunay complexes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 369
year: '2017'
...
---
_id: '1073'
abstract:
- lang: eng
text: Let X and Y be finite simplicial sets (e.g. finite simplicial complexes),
both equipped with a free simplicial action of a finite group G. Assuming that
Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes
the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|;
the existence of such a map can be decided even for dimX≤2d+1. This yields the
first algorithm for deciding topological embeddability of a k-dimensional finite
simplicial complex into Rn under the condition k≤23n−1. More generally, we present
an algorithm that, given a lifting-extension problem satisfying an appropriate
stability assumption, computes the set of all homotopy classes of solutions. This
result is new even in the non-equivariant situation.
article_processing_charge: No
author:
- first_name: Martin
full_name: Čadek, Martin
last_name: Čadek
- first_name: Marek
full_name: Krcál, Marek
id: 33E21118-F248-11E8-B48F-1D18A9856A87
last_name: Krcál
- first_name: Lukáš
full_name: Vokřínek, Lukáš
last_name: Vokřínek
citation:
ama: Čadek M, Krcál M, Vokřínek L. Algorithmic solvability of the lifting extension
problem. Discrete & Computational Geometry. 2017;54(4):915-965. doi:10.1007/s00454-016-9855-6
apa: Čadek, M., Krcál, M., & Vokřínek, L. (2017). Algorithmic solvability of
the lifting extension problem. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-016-9855-6
chicago: Čadek, Martin, Marek Krcál, and Lukáš Vokřínek. “Algorithmic Solvability
of the Lifting Extension Problem.” Discrete & Computational Geometry.
Springer, 2017. https://doi.org/10.1007/s00454-016-9855-6.
ieee: M. Čadek, M. Krcál, and L. Vokřínek, “Algorithmic solvability of the lifting
extension problem,” Discrete & Computational Geometry, vol. 54, no.
4. Springer, pp. 915–965, 2017.
ista: Čadek M, Krcál M, Vokřínek L. 2017. Algorithmic solvability of the lifting
extension problem. Discrete & Computational Geometry. 54(4), 915–965.
mla: Čadek, Martin, et al. “Algorithmic Solvability of the Lifting Extension Problem.”
Discrete & Computational Geometry, vol. 54, no. 4, Springer, 2017,
pp. 915–65, doi:10.1007/s00454-016-9855-6.
short: M. Čadek, M. Krcál, L. Vokřínek, Discrete & Computational Geometry 54
(2017) 915–965.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T12:01:28Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s00454-016-9855-6
external_id:
isi:
- '000400072700008'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1307.6444
month: '06'
oa: 1
oa_version: Submitted Version
page: 915 - 965
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- '01795376'
publication_status: published
publisher: Springer
publist_id: '6309'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Algorithmic solvability of the lifting extension problem
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '1074'
abstract:
- lang: eng
text: Recently it has become feasible to detect long blocks of nearly identical
sequence shared between pairs of genomes. These IBD blocks are direct traces of
recent coalescence events and, as such, contain ample signal to infer recent demography.
Here, we examine sharing of such blocks in two-dimensional populations with local
migration. Using a diffusion approximation to trace genetic ancestry, we derive
analytical formulae for patterns of isolation by distance of IBD blocks, which
can also incorporate recent population density changes. We introduce an inference
scheme that uses a composite likelihood approach to fit these formulae. We then
extensively evaluate our theory and inference method on a range of scenarios using
simulated data. We first validate the diffusion approximation by showing that
the theoretical results closely match the simulated block sharing patterns. We
then demonstrate that our inference scheme can accurately and robustly infer dispersal
rate and effective density, as well as bounds on recent dynamics of population
density. To demonstrate an application, we use our estimation scheme to explore
the fit of a diffusion model to Eastern European samples in the POPRES data set.
We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last
centuries, combined with accelerating population growth, can explain the observed
exponential decay of block sharing with increasing pairwise sample distance.
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Graham
full_name: Coop, Graham
last_name: Coop
- 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: Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351.
doi:10.1534/genetics.116.196220
apa: Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography
from isolation by distance of long shared sequence blocks. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.116.196220
chicago: Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent
Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics.
Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.
ieee: H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from
isolation by distance of long shared sequence blocks,” Genetics, vol. 205,
no. 3. Genetics Society of America, pp. 1335–1351, 2017.
ista: Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.
mla: Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance
of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society
of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.
short: H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2025-05-28T11:42:51Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.196220
ec_funded: 1
external_id:
isi:
- '000395807200023'
intvolume: ' 205'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biorxiv.org/content/early/2016/09/23/076810
month: '03'
oa: 1
oa_version: Preprint
page: 1335 - 1351
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6307'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Inferring recent demography from isolation by distance of long shared sequence
blocks
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1076'
abstract:
- lang: eng
text: Signatures of the Coulomb corrections in the photoelectron momentum distribution
during laser-induced ionization of atoms or ions in tunneling and multiphoton
regimes are investigated analytically in the case of a one-dimensional problem.
A high-order Coulomb-corrected strong-field approximation is applied, where the
exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov
state including the second-order corrections to the eikonal. Although without
high-order corrections our theory coincides with the known analytical R-matrix
(ARM) theory, we propose a simplified procedure for the matrix element derivation.
Rather than matching the eikonal Coulomb-Volkov wave function with the bound state
as in the ARM theory to remove the Coulomb singularity, we calculate the matrix
element via the saddle-point integration method by time as well as by coordinate,
and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron
momentum distribution with respect to the ARM theory due to high-order corrections
is analyzed for tunneling and multiphoton regimes. The relation of the quantum
corrections to the tunneling delay time is discussed.
article_number: '023403'
article_processing_charge: No
author:
- first_name: Michael
full_name: Klaiber, Michael
last_name: Klaiber
- first_name: Jiří
full_name: Daněk, Jiří
last_name: Daněk
- first_name: Enderalp
full_name: Yakaboylu, Enderalp
id: 38CB71F6-F248-11E8-B48F-1D18A9856A87
last_name: Yakaboylu
orcid: 0000-0001-5973-0874
- first_name: Karen
full_name: Hatsagortsyan, Karen
last_name: Hatsagortsyan
- first_name: Christoph
full_name: Keitel, Christoph
last_name: Keitel
citation:
ama: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. Strong-field ionization
via a high-order Coulomb-corrected strong-field approximation. Physical Review
A - Atomic, Molecular, and Optical Physics. 2017;95(2). doi:10.1103/PhysRevA.95.023403
apa: Klaiber, M., Daněk, J., Yakaboylu, E., Hatsagortsyan, K., & Keitel, C.
(2017). Strong-field ionization via a high-order Coulomb-corrected strong-field
approximation. Physical Review A - Atomic, Molecular, and Optical Physics.
American Physical Society. https://doi.org/10.1103/PhysRevA.95.023403
chicago: Klaiber, Michael, Jiří Daněk, Enderalp Yakaboylu, Karen Hatsagortsyan,
and Christoph Keitel. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics. American Physical Society, 2017. https://doi.org/10.1103/PhysRevA.95.023403.
ieee: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, and C. Keitel, “Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation,”
Physical Review A - Atomic, Molecular, and Optical Physics, vol. 95, no. 2.
American Physical Society, 2017.
ista: Klaiber M, Daněk J, Yakaboylu E, Hatsagortsyan K, Keitel C. 2017. Strong-field
ionization via a high-order Coulomb-corrected strong-field approximation. Physical
Review A - Atomic, Molecular, and Optical Physics. 95(2), 023403.
mla: Klaiber, Michael, et al. “Strong-Field Ionization via a High-Order Coulomb-Corrected
Strong-Field Approximation.” Physical Review A - Atomic, Molecular, and Optical
Physics, vol. 95, no. 2, 023403, American Physical Society, 2017, doi:10.1103/PhysRevA.95.023403.
short: M. Klaiber, J. Daněk, E. Yakaboylu, K. Hatsagortsyan, C. Keitel, Physical
Review A - Atomic, Molecular, and Optical Physics 95 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:57:23Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.95.023403
ec_funded: 1
external_id:
isi:
- '000400571700011'
intvolume: ' 95'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.07018
month: '02'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review A - Atomic, Molecular, and Optical Physics'
publication_identifier:
issn:
- '24699926'
publication_status: published
publisher: American Physical Society
publist_id: '6305'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong-field ionization via a high-order Coulomb-corrected strong-field approximation
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '1077'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the fX174 phage family by first reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_number: '20160139'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay
between structure, energy and epistasis in the coat protein of the ϕX174 phage
family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2017). Evolutionary interplay between structure, energy and epistasis in the
coat protein of the ϕX174 phage family. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in
the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface.
Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family,” Journal of the Royal Society Interface, vol. 14, no. 126.
Royal Society of London, 2017.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. Journal of the Royal Society Interface. 14(126), 20160139.
mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure,
Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal
of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society
of London, 2017, doi:10.1098/rsif.2016.0139.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal
of the Royal Society Interface 14 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-04T00:00:00Z
date_updated: 2025-05-28T11:42:51Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
- _id: JoBo
doi: 10.1098/rsif.2016.0139
ec_funded: 1
external_id:
isi:
- '000393380400001'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:14:02Z
date_updated: 2019-01-18T09:14:02Z
file_id: '5843'
file_name: 2017_JRSI_Redondo.pdf
file_size: 1092015
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:14:02Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '126'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society of London
publist_id: '6303'
quality_controlled: '1'
related_material:
record:
- id: '9864'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2017'
...
---
_id: '1078'
abstract:
- lang: eng
text: 'One of the key questions in understanding plant development is how single
cells behave in a larger context of the tissue. Therefore, it requires the observation
of the whole organ with a high spatial- as well as temporal resolution over prolonged
periods of time, which may cause photo-toxic effects. This protocol shows a plant
sample preparation method for light-sheet microscopy, which is characterized by
mounting the plant vertically on the surface of a gel. The plant is mounted in
such a way that the roots are submerged in a liquid medium while the leaves remain
in the air. In order to ensure photosynthetic activity of the plant, a custom-made
lighting system illuminates the leaves. To keep the roots in darkness the water
surface is covered with sheets of black plastic foil. This method allows long-term
imaging of plant organ development in standardized conditions. '
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
article_number: e55044
article_processing_charge: No
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: von Wangenheim D, Hauschild R, Friml J. Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel. Journal of visualized experiments
JoVE. 2017;2017(119). doi:10.3791/55044
apa: von Wangenheim, D., Hauschild, R., & Friml, J. (2017). Light sheet fluorescence
microscopy of plant roots growing on the surface of a gel. Journal of Visualized
Experiments JoVE. Journal of Visualized Experiments. https://doi.org/10.3791/55044
chicago: Wangenheim, Daniel von, Robert Hauschild, and Jiří Friml. “Light Sheet
Fluorescence Microscopy of Plant Roots Growing on the Surface of a Gel.” Journal
of Visualized Experiments JoVE. Journal of Visualized Experiments, 2017. https://doi.org/10.3791/55044.
ieee: D. von Wangenheim, R. Hauschild, and J. Friml, “Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel,” Journal of visualized experiments
JoVE, vol. 2017, no. 119. Journal of Visualized Experiments, 2017.
ista: von Wangenheim D, Hauschild R, Friml J. 2017. Light sheet fluorescence microscopy
of plant roots growing on the surface of a gel. Journal of visualized experiments
JoVE. 2017(119), e55044.
mla: von Wangenheim, Daniel, et al. “Light Sheet Fluorescence Microscopy of Plant
Roots Growing on the Surface of a Gel.” Journal of Visualized Experiments JoVE,
vol. 2017, no. 119, e55044, Journal of Visualized Experiments, 2017, doi:10.3791/55044.
short: D. von Wangenheim, R. Hauschild, J. Friml, Journal of Visualized Experiments
JoVE 2017 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-18T00:00:00Z
date_updated: 2025-05-07T11:12:33Z
day: '18'
ddc:
- '580'
department:
- _id: JiFr
- _id: Bio
doi: 10.3791/55044
ec_funded: 1
external_id:
isi:
- '000397847200041'
file:
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:31Z
date_updated: 2018-12-12T10:16:31Z
file_id: '5219'
file_name: IST-2017-808-v1+1_2017_VWangenheim_list.pdf
file_size: 57678
relation: main_file
- access_level: open_access
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:32Z
date_updated: 2018-12-12T10:16:32Z
file_id: '5220'
file_name: IST-2017-808-v1+2_2017_VWangenheim_article.pdf
file_size: 1317820
relation: main_file
file_date_updated: 2018-12-12T10:16:32Z
has_accepted_license: '1'
intvolume: ' 2017'
isi: 1
issue: '119'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Journal of visualized experiments JoVE
publication_status: published
publisher: Journal of Visualized Experiments
publist_id: '6302'
pubrep_id: '808'
related_material:
record:
- id: '5565'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Light sheet fluorescence microscopy of plant roots growing on the surface of
a gel
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...