---
_id: '9900'
abstract:
- lang: eng
text: Pan-genome statistics by species. (CSV 3 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808886.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808886.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1.
ieee: O. M. Sigalova et al., “Additional file 5 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808886.v1.
mla: Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T08:44:49Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808886.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808886.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 5 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9901'
abstract:
- lang: eng
text: Clusters of Orthologous Genes (COGs) and corresponding functional categories
assigned to OGs. (CSV 117 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808907.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808907.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808907.v1.
ieee: O. M. Sigalova et al., “Additional file 9 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808907.v1.
mla: Sigalova, Olga M., et al. Additional File 9 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808907.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T10:54:03Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808907.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808907.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 9 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '405'
abstract:
- lang: eng
text: We investigate the quantum Jensen divergences from the viewpoint of joint
convexity. It turns out that the set of the functions which generate jointly convex
quantum Jensen divergences on positive matrices coincides with the Matrix Entropy
Class which has been introduced by Chen and Tropp quite recently.
acknowledgement: The author was supported by the ISTFELLOW program of the Institute
of Science and Technology Austria (project code IC1027FELL01) and partially supported
by the Hungarian National Research, Development and Innovation Office – NKFIH (grant
no. K124152)
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. Jointly convex quantum Jensen divergences. Linear Algebra and
Its Applications. 2019;576:67-78. doi:10.1016/j.laa.2018.03.002
apa: Virosztek, D. (2019). Jointly convex quantum Jensen divergences. Linear
Algebra and Its Applications. Elsevier. https://doi.org/10.1016/j.laa.2018.03.002
chicago: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear
Algebra and Its Applications. Elsevier, 2019. https://doi.org/10.1016/j.laa.2018.03.002.
ieee: D. Virosztek, “Jointly convex quantum Jensen divergences,” Linear Algebra
and Its Applications, vol. 576. Elsevier, pp. 67–78, 2019.
ista: Virosztek D. 2019. Jointly convex quantum Jensen divergences. Linear Algebra
and Its Applications. 576, 67–78.
mla: Virosztek, Daniel. “Jointly Convex Quantum Jensen Divergences.” Linear Algebra
and Its Applications, vol. 576, Elsevier, 2019, pp. 67–78, doi:10.1016/j.laa.2018.03.002.
short: D. Virosztek, Linear Algebra and Its Applications 576 (2019) 67–78.
date_created: 2018-12-11T11:46:17Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-24T14:31:47Z
day: '01'
department:
- _id: LaEr
doi: 10.1016/j.laa.2018.03.002
ec_funded: 1
external_id:
arxiv:
- '1712.05324'
isi:
- '000470955300005'
intvolume: ' 576'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1712.05324
month: '09'
oa: 1
oa_version: Preprint
page: 67-78
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Linear Algebra and Its Applications
publication_status: published
publisher: Elsevier
publist_id: '7424'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Jointly convex quantum Jensen divergences
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 576
year: '2019'
...
---
_id: '429'
abstract:
- lang: eng
text: We consider real symmetric or complex hermitian random matrices with correlated
entries. We prove local laws for the resolvent and universality of the local eigenvalue
statistics in the bulk of the spectrum. The correlations have fast decay but are
otherwise of general form. The key novelty is the detailed stability analysis
of the corresponding matrix valued Dyson equation whose solution is the deterministic
limit of the resolvent.
acknowledgement: "Open access funding provided by Institute of Science and Technology
(IST Austria).\r\n"
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Oskari H
full_name: Ajanki, Oskari H
id: 36F2FB7E-F248-11E8-B48F-1D18A9856A87
last_name: Ajanki
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Torben H
full_name: Krüger, Torben H
id: 3020C786-F248-11E8-B48F-1D18A9856A87
last_name: Krüger
orcid: 0000-0002-4821-3297
citation:
ama: Ajanki OH, Erdös L, Krüger TH. Stability of the matrix Dyson equation and random
matrices with correlations. Probability Theory and Related Fields. 2019;173(1-2):293–373.
doi:10.1007/s00440-018-0835-z
apa: Ajanki, O. H., Erdös, L., & Krüger, T. H. (2019). Stability of the matrix
Dyson equation and random matrices with correlations. Probability Theory and
Related Fields. Springer. https://doi.org/10.1007/s00440-018-0835-z
chicago: Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Stability of the
Matrix Dyson Equation and Random Matrices with Correlations.” Probability Theory
and Related Fields. Springer, 2019. https://doi.org/10.1007/s00440-018-0835-z.
ieee: O. H. Ajanki, L. Erdös, and T. H. Krüger, “Stability of the matrix Dyson equation
and random matrices with correlations,” Probability Theory and Related Fields,
vol. 173, no. 1–2. Springer, pp. 293–373, 2019.
ista: Ajanki OH, Erdös L, Krüger TH. 2019. Stability of the matrix Dyson equation
and random matrices with correlations. Probability Theory and Related Fields.
173(1–2), 293–373.
mla: Ajanki, Oskari H., et al. “Stability of the Matrix Dyson Equation and Random
Matrices with Correlations.” Probability Theory and Related Fields, vol.
173, no. 1–2, Springer, 2019, pp. 293–373, doi:10.1007/s00440-018-0835-z.
short: O.H. Ajanki, L. Erdös, T.H. Krüger, Probability Theory and Related Fields
173 (2019) 293–373.
date_created: 2018-12-11T11:46:25Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-08-24T14:39:00Z
day: '01'
ddc:
- '510'
department:
- _id: LaEr
doi: 10.1007/s00440-018-0835-z
ec_funded: 1
external_id:
isi:
- '000459396500007'
file:
- access_level: open_access
checksum: f9354fa5c71f9edd17132588f0dc7d01
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T16:12:08Z
date_updated: 2020-07-14T12:46:26Z
file_id: '5720'
file_name: 2018_ProbTheory_Ajanki.pdf
file_size: 1201840
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 173'
isi: 1
issue: 1-2
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: 293–373
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: B67AFEDC-15C9-11EA-A837-991A96BB2854
name: IST Austria Open Access Fund
publication: Probability Theory and Related Fields
publication_identifier:
eissn:
- '14322064'
issn:
- '01788051'
publication_status: published
publisher: Springer
publist_id: '7394'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stability of the matrix Dyson equation and random matrices with correlations
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 173
year: '2019'
...
---
_id: '439'
abstract:
- lang: eng
text: "We count points over a finite field on wild character varieties,of Riemann
surfaces for singularities with regular semisimple leading term. The new feature
in our counting formulas is the appearance of characters of Yokonuma–Hecke algebras.
Our result leads to the conjecture that the mixed Hodge polynomials of these character
varieties agree with previously conjectured perverse Hodge polynomials of certain
twisted parabolic Higgs moduli spaces, indicating the\r\npossibility of a P =
W conjecture for a suitable wild Hitchin system."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Tamas
full_name: Hausel, Tamas
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Martin
full_name: Mereb, Martin
id: 43D735EE-F248-11E8-B48F-1D18A9856A87
last_name: Mereb
- first_name: Michael
full_name: Wong, Michael
last_name: Wong
citation:
ama: Hausel T, Mereb M, Wong M. Arithmetic and representation theory of wild character
varieties. Journal of the European Mathematical Society. 2019;21(10):2995-3052.
doi:10.4171/JEMS/896
apa: Hausel, T., Mereb, M., & Wong, M. (2019). Arithmetic and representation
theory of wild character varieties. Journal of the European Mathematical Society.
European Mathematical Society. https://doi.org/10.4171/JEMS/896
chicago: Hausel, Tamás, Martin Mereb, and Michael Wong. “Arithmetic and Representation
Theory of Wild Character Varieties.” Journal of the European Mathematical Society.
European Mathematical Society, 2019. https://doi.org/10.4171/JEMS/896.
ieee: T. Hausel, M. Mereb, and M. Wong, “Arithmetic and representation theory of
wild character varieties,” Journal of the European Mathematical Society,
vol. 21, no. 10. European Mathematical Society, pp. 2995–3052, 2019.
ista: Hausel T, Mereb M, Wong M. 2019. Arithmetic and representation theory of wild
character varieties. Journal of the European Mathematical Society. 21(10), 2995–3052.
mla: Hausel, Tamás, et al. “Arithmetic and Representation Theory of Wild Character
Varieties.” Journal of the European Mathematical Society, vol. 21, no.
10, European Mathematical Society, 2019, pp. 2995–3052, doi:10.4171/JEMS/896.
short: T. Hausel, M. Mereb, M. Wong, Journal of the European Mathematical Society
21 (2019) 2995–3052.
date_created: 2018-12-11T11:46:29Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-08-24T14:24:49Z
day: '01'
department:
- _id: TaHa
doi: 10.4171/JEMS/896
ec_funded: 1
external_id:
arxiv:
- '1604.03382'
isi:
- '000480413600002'
intvolume: ' 21'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.03382
month: '10'
oa: 1
oa_version: Preprint
page: 2995-3052
project:
- _id: 25E549F4-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '320593'
name: Arithmetic and physics of Higgs moduli spaces
publication: Journal of the European Mathematical Society
publication_identifier:
eissn:
- 1435-9855
publication_status: published
publisher: European Mathematical Society
publist_id: '7384'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arithmetic and representation theory of wild character varieties
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 21
year: '2019'
...
---
_id: '441'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nikita
full_name: Kalinin, Nikita
last_name: Kalinin
- first_name: Mikhail
full_name: Shkolnikov, Mikhail
id: 35084A62-F248-11E8-B48F-1D18A9856A87
last_name: Shkolnikov
orcid: 0000-0002-4310-178X
citation:
ama: Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z).
European Journal of Mathematics. 2019;5(3):909–928. doi:10.1007/s40879-018-0218-0
apa: Kalinin, N., & Shkolnikov, M. (2019). Tropical formulae for summation over
a part of SL(2,Z). European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-018-0218-0
chicago: Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation
over a Part of SL(2,Z).” European Journal of Mathematics. Springer Nature,
2019. https://doi.org/10.1007/s40879-018-0218-0.
ieee: N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part
of SL(2,Z),” European Journal of Mathematics, vol. 5, no. 3. Springer Nature,
pp. 909–928, 2019.
ista: Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part
of SL(2,Z). European Journal of Mathematics. 5(3), 909–928.
mla: Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over
a Part of SL(2,Z).” European Journal of Mathematics, vol. 5, no. 3, Springer
Nature, 2019, pp. 909–928, doi:10.1007/s40879-018-0218-0.
short: N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928.
date_created: 2018-12-11T11:46:29Z
date_published: 2019-09-15T00:00:00Z
date_updated: 2021-01-12T07:56:46Z
day: '15'
department:
- _id: TaHa
doi: 10.1007/s40879-018-0218-0
ec_funded: 1
external_id:
arxiv:
- '1711.02089'
intvolume: ' 5'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.02089
month: '09'
oa: 1
oa_version: Preprint
page: 909–928
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: European Journal of Mathematics
publication_identifier:
eissn:
- 2199-6768
issn:
- 2199-675X
publication_status: published
publisher: Springer Nature
publist_id: '7382'
quality_controlled: '1'
scopus_import: 1
status: public
title: Tropical formulae for summation over a part of SL(2,Z)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 5
year: '2019'
...
---
_id: '25'
abstract:
- lang: eng
text: 'Partially observable Markov decision processes (POMDPs) are the standard
models for planning under uncertainty with both finite and infinite horizon. Besides
the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs)
is another classical objective for POMDPs. In this case, given a set of target
states and a positive cost for each transition, the optimization objective is
to minimize the expected total cost until a target state is reached. In the literature,
RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving
Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees,
and HSVI may even fail to terminate its trials. We give the following contributions:
(1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they
prevent the original HSVI from converging. (2) We present a novel algorithm inspired
by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees.
(3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples.'
acknowledgement: '∗This work has been supported by Vienna Science and Technology Fund
(WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE),
and ERC Starting grant (279307: Graph Games). This research was sponsored by the
Army Research Laboratory and was accomplished under Cooperative Agreement Number
W911NF-13-2-0045 (ARL Cyber Security CRA). '
article_processing_charge: No
author:
- first_name: Karel
full_name: Horák, Karel
last_name: Horák
- first_name: Branislav
full_name: Bošanský, Branislav
last_name: Bošanský
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration
for goal-POMDPs. In: Proceedings of the Twenty-Seventh International Joint
Conference on Artificial Intelligence. Vol 2018-July. IJCAI; 2018:4764-4770.
doi:10.24963/ijcai.2018/662'
apa: 'Horák, K., Bošanský, B., & Chatterjee, K. (2018). Goal-HSVI: Heuristic
search value iteration for goal-POMDPs. In Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence (Vol. 2018–July,
pp. 4764–4770). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/662'
chicago: 'Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI:
Heuristic Search Value Iteration for Goal-POMDPs.” In Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence, 2018–July:4764–70.
IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/662.'
ieee: 'K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value
iteration for goal-POMDPs,” in Proceedings of the Twenty-Seventh International
Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol.
2018–July, pp. 4764–4770.'
ista: 'Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value
iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint
Conference on Artificial Intelligence. IJCAI: International Joint Conference on
Artificial Intelligence vol. 2018–July, 4764–4770.'
mla: 'Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.”
Proceedings of the Twenty-Seventh International Joint Conference on Artificial
Intelligence, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:10.24963/ijcai.2018/662.'
short: K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh
International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770.
conference:
end_date: 2018-07-19
location: Stockholm, Sweden
name: 'IJCAI: International Joint Conference on Artificial Intelligence'
start_date: 2018-07-13
date_created: 2018-12-11T11:44:13Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2025-06-02T08:53:40Z
day: '01'
department:
- _id: KrCh
doi: 10.24963/ijcai.2018/662
ec_funded: 1
external_id:
isi:
- '000764175404127'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.24963/ijcai.2018/662
month: '07'
oa: 1
oa_version: Published Version
page: 4764 - 4770
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided 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 Twenty-Seventh International Joint Conference on Artificial
Intelligence
publication_status: published
publisher: IJCAI
publist_id: '8030'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Goal-HSVI: Heuristic search value iteration for goal-POMDPs'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2018-July
year: '2018'
...
---
_id: '26'
abstract:
- lang: eng
text: Expression of genes is a fundamental molecular phenotype that is subject to
evolution by different types of mutations. Both the rate and the effect of mutations
may depend on the DNA sequence context of a particular gene or a particular promoter
sequence. In this thesis I investigate the nature of this dependence using simple
genetic systems in Escherichia coli. With these systems I explore the evolution
of constitutive gene expression from random starting sequences at different loci
on the chromosome and at different locations in sequence space. First, I dissect
chromosomal neighborhood effects that underlie locus-dependent differences in
the potential of a gene under selection to become more highly expressed. Next,
I find that the effects of point mutations in promoter sequences are dependent
on sequence context, and that an existing energy matrix model performs poorly
in predicting relative expression of unrelated sequences. Finally, I show that
a substantial fraction of random sequences contain functional promoters and I
present an extended thermodynamic model that predicts promoter strength in full
sequence space. Taken together, these results provide new insights and guides
on how to integrate information on sequence context to improve our qualitative
and quantitative understanding of bacterial gene expression, with implications
for rapid evolution of drug resistance, de novo evolution of genes, and horizontal
gene transfer.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Magdalena
full_name: Steinrück, Magdalena
id: 2C023F40-F248-11E8-B48F-1D18A9856A87
last_name: Steinrück
orcid: 0000-0003-1229-9719
citation:
ama: Steinrück M. The influence of sequence context on the evolution of bacterial
gene expression. 2018. doi:10.15479/AT:ISTA:th1059
apa: Steinrück, M. (2018). The influence of sequence context on the evolution
of bacterial gene expression. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:th1059
chicago: Steinrück, Magdalena. “The Influence of Sequence Context on the Evolution
of Bacterial Gene Expression.” Institute of Science and Technology Austria, 2018.
https://doi.org/10.15479/AT:ISTA:th1059.
ieee: M. Steinrück, “The influence of sequence context on the evolution of bacterial
gene expression,” Institute of Science and Technology Austria, 2018.
ista: Steinrück M. 2018. The influence of sequence context on the evolution of bacterial
gene expression. Institute of Science and Technology Austria.
mla: Steinrück, Magdalena. The Influence of Sequence Context on the Evolution
of Bacterial Gene Expression. Institute of Science and Technology Austria,
2018, doi:10.15479/AT:ISTA:th1059.
short: M. Steinrück, The Influence of Sequence Context on the Evolution of Bacterial
Gene Expression, Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:44:14Z
date_published: 2018-10-30T00:00:00Z
date_updated: 2023-09-07T12:48:43Z
day: '30'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:th1059
file:
- access_level: closed
checksum: 413cbce1cd1debeae3abe2a25dbc70d1
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-02-08T10:51:22Z
date_updated: 2020-07-14T12:45:43Z
embargo_to: open_access
file_id: '5941'
file_name: Thesis_Steinrueck_final.docx
file_size: 9190845
relation: source_file
- access_level: open_access
checksum: 3def8b7854c8b42d643597ce0215efac
content_type: application/pdf
creator: dernst
date_created: 2019-02-08T10:51:22Z
date_updated: 2021-02-11T11:17:14Z
embargo: 2019-11-02
file_id: '5942'
file_name: Thesis_Steinrueck_final.pdf
file_size: 7521973
relation: main_file
file_date_updated: 2021-02-11T11:17:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '109'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '8029'
pubrep_id: '1059'
related_material:
record:
- id: '704'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: The influence of sequence context on the evolution of bacterial gene expression
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '273'
abstract:
- lang: eng
text: The accuracy of information retrieval systems is often measured using complex
loss functions such as the average precision (AP) or the normalized discounted
cumulative gain (NDCG). Given a set of positive and negative samples, the parameters
of a retrieval system can be estimated by minimizing these loss functions. However,
the non-differentiability and non-decomposability of these loss functions does
not allow for simple gradient based optimization algorithms. This issue is generally
circumvented by either optimizing a structured hinge-loss upper bound to the loss
function or by using asymptotic methods like the direct-loss minimization framework.
Yet, the high computational complexity of loss-augmented inference, which is necessary
for both the frameworks, prohibits its use in large training data sets. To alleviate
this deficiency, we present a novel quicksort flavored algorithm for a large class
of non-decomposable loss functions. We provide a complete characterization of
the loss functions that are amenable to our algorithm, and show that it includes
both AP and NDCG based loss functions. Furthermore, we prove that no comparison
based algorithm can improve upon the computational complexity of our approach
asymptotically. We demonstrate the effectiveness of our approach in the context
of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning
models for a variety of vision tasks. We show that our approach provides significantly
better results than simpler decomposable loss functions, while requiring a comparable
training time.
article_processing_charge: No
arxiv: 1
author:
- first_name: Pritish
full_name: Mohapatra, Pritish
last_name: Mohapatra
- first_name: Michal
full_name: Rolinek, Michal
id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87
last_name: Rolinek
- first_name: C V
full_name: Jawahar, C V
last_name: Jawahar
- first_name: Vladimir
full_name: Kolmogorov, Vladimir
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: M Pawan
full_name: Kumar, M Pawan
last_name: Kumar
citation:
ama: 'Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization
for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision
and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389'
apa: 'Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M.
P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF
Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt
Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389'
chicago: Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and
M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018
IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701.
IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389.
ieee: P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient
optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on
Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp.
3693–3701.
ista: 'Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient
optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer
Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern
Recognition, 3693–3701.'
mla: Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.”
2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE,
2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389.
short: P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018
IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp.
3693–3701.
conference:
end_date: 2018-06-22
location: Salt Lake City, UT, USA
name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
start_date: 2018-06-18
date_created: 2018-12-11T11:45:33Z
date_published: 2018-06-28T00:00:00Z
date_updated: 2023-09-11T13:24:43Z
day: '28'
department:
- _id: VlKo
doi: 10.1109/cvpr.2018.00389
ec_funded: 1
external_id:
arxiv:
- '1604.08269'
isi:
- '000457843603087'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1604.08269
month: '06'
oa: 1
oa_version: Preprint
page: 3693-3701
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '616160'
name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition
publication_identifier:
isbn:
- '9781538664209'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient optimization for rank-based loss functions
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '275'
abstract:
- lang: eng
text: Lymphatic endothelial cells (LECs) release extracellular chemokines to guide
the migration of dendritic cells. In this study, we report that LECs also release
basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater
numbers in the presence of inflammatory cytokines and accumulate in the perivascular
stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic
analyses of EEV fractions identified > 1,700 cargo proteins and revealed a
dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions
augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion
and enhanced the directional migratory response of human dendritic cells along
guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory
behavior and thus promote directional migration of CX3CR1-expressing cells in
complex tissue environments.
acknowledgement: M. Brown was supported by the Cell Communication in Health and Disease
Graduate Study Program of the Austrian Science Fund and Medizinische Universität
Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science
Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson
and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical
Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer
Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European
Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland
postdoctoral research grant (287853). This project has received funding from the
European Union’s Horizon 2020 research and innovation program under grant agreement
No. 668036 (RELENT).
article_processing_charge: No
author:
- first_name: Markus
full_name: Brown, Markus
id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87
last_name: Brown
- first_name: Louise
full_name: Johnson, Louise
last_name: Johnson
- first_name: Dario
full_name: Leone, Dario
last_name: Leone
- first_name: Peter
full_name: Májek, Peter
last_name: Májek
- first_name: Kari
full_name: Vaahtomeri, Kari
id: 368EE576-F248-11E8-B48F-1D18A9856A87
last_name: Vaahtomeri
orcid: 0000-0001-7829-3518
- first_name: Daniel
full_name: Senfter, Daniel
last_name: Senfter
- first_name: Nora
full_name: Bukosza, Nora
last_name: Bukosza
- first_name: Helga
full_name: Schachner, Helga
last_name: Schachner
- first_name: Gabriele
full_name: Asfour, Gabriele
last_name: Asfour
- first_name: Brigitte
full_name: Langer, Brigitte
last_name: Langer
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Katja
full_name: Parapatics, Katja
last_name: Parapatics
- first_name: Young
full_name: Hong, Young
last_name: Hong
- first_name: Keiryn
full_name: Bennett, Keiryn
last_name: Bennett
- first_name: Renate
full_name: Kain, Renate
last_name: Kain
- first_name: Michael
full_name: Detmar, Michael
last_name: Detmar
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: David
full_name: Jackson, David
last_name: Jackson
- first_name: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
citation:
ama: Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell
migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221.
doi:10.1083/jcb.201612051
apa: Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D.,
… Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along
guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051
chicago: Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri,
Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell
Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University
Press, 2018. https://doi.org/10.1083/jcb.201612051.
ieee: M. Brown et al., “Lymphatic exosomes promote dendritic cell migration
along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller
University Press, pp. 2205–2221, 2018.
ista: Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N,
Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K,
Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote
dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6),
2205–2221.
mla: Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration
along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller
University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051.
short: M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza,
H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett,
R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology
217 (2018) 2205–2221.
date_created: 2018-12-11T11:45:33Z
date_published: 2018-04-12T00:00:00Z
date_updated: 2023-09-13T08:51:29Z
day: '12'
ddc:
- '570'
department:
- _id: MiSi
- _id: Bio
doi: 10.1083/jcb.201612051
ec_funded: 1
external_id:
isi:
- '000438077800026'
pmid:
- '29650776'
file:
- access_level: open_access
checksum: 9c7eba51a35c62da8c13f98120b64df4
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T12:50:07Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5704'
file_name: 2018_JournalCellBiology_Brown.pdf
file_size: 2252043
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 217'
isi: 1
issue: '6'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 2205 - 2221
pmid: 1
project:
- _id: 25A8E5EA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 564-B12
name: Cytoskeletal force generation and transduction of leukocytes (FWF)
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
(EU)
publication: Journal of Cell Biology
publication_status: published
publisher: Rockefeller University Press
publist_id: '7627'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lymphatic exosomes promote dendritic cell migration along guidance cues
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: 217
year: '2018'
...
---
_id: '276'
abstract:
- lang: eng
text: Directed migration of cells relies on their ability to sense directional guidance
cues and to interact with pericellular structures in order to transduce contractile
cytoskeletal- into mechanical forces. These biomechanical processes depend highly
on microenvironmental factors such as exposure to 2D surfaces or 3D matrices.
In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell
migration are mostly derived from intravital microscopy or collagen-based in vitro
assays. Both approaches offer only limited controlla-bility of experimental conditions.
Here, we developed an automated microfluidic system that allows positioning of
cells in 3D microenvironments containing highly controlled diffusion-based chemokine
gradients. Tracking migration in such gradients was feasible in real time at the
single cell level. Moreover, the setup allowed on-chip immunocytochemistry and
thus linking of functional with phenotypical properties in individual cells. Spatially
defined retrieval of cells from the device allows down-stream off-chip analysis.
Using dendritic cells as a model, our setup specifically allowed us for the first
time to quantitate key migration characteristics of cells exposed to identical
gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration
properties between 2D and 3D migration were distinct. Morphological features of
cells migrating in an in vitro 3D environment were similar to those of cells migrating
in animal tissues, but different from cells migrating on a surface. Our system
thus offers a highly controllable in vitro-mimic of a 3D environment that cells
traffic in vivo.
acknowledgement: This work was supported by the Swiss National Science Foundation
(MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863
to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.),
a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship
(ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409)
to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders
had no role in study design, data collection and analysis, decision to publish,
or preparation of the manuscript.
article_number: e0198330
article_processing_charge: No
article_type: original
author:
- first_name: Corina
full_name: Frick, Corina
last_name: Frick
- first_name: Philip
full_name: Dettinger, Philip
last_name: Dettinger
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Annaïse
full_name: Jauch, Annaïse
last_name: Jauch
- first_name: Christoph
full_name: Berger, Christoph
last_name: Berger
- first_name: Mike
full_name: Recher, Mike
last_name: Recher
- first_name: Timm
full_name: Schroeder, Timm
last_name: Schroeder
- first_name: Matthias
full_name: Mehling, Matthias
last_name: Mehling
citation:
ama: Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study
3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330
apa: Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M.,
… Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single
cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330
chicago: Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph
Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics
to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library
of Science, 2018. https://doi.org/10.1371/journal.pone.0198330.
ieee: C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at
the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science,
2018.
ista: Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder
T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single
cell level. PLoS One. 13(6), e0198330.
mla: Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the
Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library
of Science, 2018, doi:10.1371/journal.pone.0198330.
short: C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T.
Schroeder, M. Mehling, PLoS One 13 (2018).
date_created: 2018-12-11T11:45:34Z
date_published: 2018-06-07T00:00:00Z
date_updated: 2023-09-13T09:00:15Z
day: '07'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.1371/journal.pone.0198330
external_id:
isi:
- '000434384900031'
file:
- access_level: open_access
checksum: 95fc5dc3938b3ad3b7697d10c83cc143
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:10:32Z
date_updated: 2020-07-14T12:45:45Z
file_id: '5709'
file_name: 2018_Plos_Frick.pdf
file_size: 7682167
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 13'
isi: 1
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '7626'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nano-scale microfluidics to study 3D chemotaxis at the single cell level
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: 13
year: '2018'
...
---
_id: '277'
abstract:
- lang: eng
text: 'Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA
levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant
suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2.
Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions.
We previously identified interaction of the C-terminal domain of Arabidopsis telomerase
reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing
protein. Here we explore protein–protein interactions of the ARM protein, AtTERT
domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling
protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid
(Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both
the N- and C-terminal domains of AtTERT in different cellular compartments. ARM
interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly
or through interaction with POT1a. The putative human ARM homolog co-precipitates
telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis
arm mutants shows no obvious changes in telomere length or telomerase activity,
suggesting that ARM is not essential for telomere maintenance. The observed interactions
with telomerase and Myb-like domain proteins (TRF-like family I) may therefore
reflect possible non-telomeric functions. Transcript levels of several DNA repair
and ribosomal genes are affected in arm mutants, and ARM, likely in association
with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs
in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric
functions of telomerase, and can also perform its own telomerase-independent functions.'
article_processing_charge: No
article_type: original
author:
- first_name: Ladislav
full_name: Dokládal, Ladislav
last_name: Dokládal
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: David
full_name: Honys, David
last_name: Honys
- first_name: Nikoleta
full_name: Dupláková, Nikoleta
last_name: Dupláková
- first_name: Lan
full_name: Lee, Lan
last_name: Lee
- first_name: Stanton
full_name: Gelvin, Stanton
last_name: Gelvin
- first_name: Eva
full_name: Sýkorová, Eva
last_name: Sýkorová
citation:
ama: Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates
in a telomerase interaction network. Plant Molecular Biology. 2018;97(5):407-420.
doi:10.1007/s11103-018-0747-4
apa: Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., &
Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase
interaction network. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-018-0747-4
chicago: Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee,
Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in
a Telomerase Interaction Network.” Plant Molecular Biology. Springer, 2018.
https://doi.org/10.1007/s11103-018-0747-4.
ieee: L. Dokládal et al., “An armadillo-domain protein participates in a
telomerase interaction network,” Plant Molecular Biology, vol. 97, no.
5. Springer, pp. 407–420, 2018.
ista: Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E.
2018. An armadillo-domain protein participates in a telomerase interaction network.
Plant Molecular Biology. 97(5), 407–420.
mla: Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase
Interaction Network.” Plant Molecular Biology, vol. 97, no. 5, Springer,
2018, pp. 407–20, doi:10.1007/s11103-018-0747-4.
short: L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová,
Plant Molecular Biology 97 (2018) 407–420.
date_created: 2018-12-11T11:45:34Z
date_published: 2018-06-12T00:00:00Z
date_updated: 2023-09-08T13:21:05Z
day: '12'
ddc:
- '580'
department:
- _id: EvBe
doi: 10.1007/s11103-018-0747-4
external_id:
isi:
- '000438981700009'
file:
- access_level: open_access
checksum: 451ae47616e6af2533099f596b2a47fb
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T12:23:08Z
date_updated: 2020-07-14T12:45:45Z
file_id: '7834'
file_name: 2018_PlantMolecBio_Dokladal.pdf
file_size: 1150679
relation: main_file
file_date_updated: 2020-07-14T12:45:45Z
has_accepted_license: '1'
intvolume: ' 97'
isi: 1
issue: '5'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 407 - 420
publication: Plant Molecular Biology
publication_status: published
publisher: Springer
publist_id: '7625'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An armadillo-domain protein participates in a telomerase interaction network
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 97
year: '2018'
...
---
_id: '278'
abstract:
- lang: eng
text: 'Consortial subscription contracts regulate the digital access to publications
between publishers and scientific libraries. However, since a couple of years
the tendency towards a freely accessible publishing (Open Access) intensifies.
As a consequence of this trend the contractual relationship between licensor and
licensee is gradually changing as well: More and more contracts exercise influence
on open access publishing. The present study attempts to compare Austrian examples
of consortial licence contracts, which include components of open access. It describes
the difference between pure subscription contracts and differing innovative deals
including open access components. Thereby it becomes obvious that for the evaluation
of this licence contracts new methods are needed. An essential new element of
such analyses is the evaluation of the open access publication numbers. So this
study tries to carry out such publication analyses for Austrian open access deals
focusing on quantitative questions: How does the number of publications evolve?
How does the open access share change? Publications reports of the publishers
and database queries from Scopus form the data basis. The analysis of the data
points out that differing approaches of contracts result in highly divergent results:
Particular deals can prioritize a saving in costs or else the increase of the
open access rate. It is to be assumed that within the following years further
numerous open access deals will be negotiated. The finding of this study shall
provide guidance.'
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. Lizenzverträge mit Open-Access-Komponenten an österreichischen
Bibliotheken. 2018.
apa: Villányi, M. (2018). Lizenzverträge mit Open-Access-Komponenten an österreichischen
Bibliotheken. Universität Wien.
chicago: Villányi, Márton. “Lizenzverträge mit Open-Access-Komponenten an österreichischen
Bibliotheken.” Universität Wien, 2018.
ieee: M. Villányi, “Lizenzverträge mit Open-Access-Komponenten an österreichischen
Bibliotheken,” Universität Wien, 2018.
ista: Villányi M. 2018. Lizenzverträge mit Open-Access-Komponenten an österreichischen
Bibliotheken. Universität Wien.
mla: Villányi, Márton. Lizenzverträge mit Open-Access-Komponenten an österreichischen
Bibliotheken. Universität Wien, 2018.
short: M. Villányi, Lizenzverträge mit Open-Access-Komponenten an österreichischen
Bibliotheken, Universität Wien, 2018.
date_created: 2018-12-11T11:45:34Z
date_published: 2018-04-06T00:00:00Z
date_updated: 2024-02-21T13:44:07Z
day: '06'
department:
- _id: E-Lib
language:
- iso: ger
main_file_link:
- open_access: '1'
url: http://othes.univie.ac.at/51113/
month: '04'
oa: 1
oa_version: Published Version
page: '94'
publication_status: published
publisher: Universität Wien
publist_id: '7624'
related_material:
record:
- id: '5577'
relation: dissertation_contains
status: public
- id: '5574'
relation: dissertation_contains
status: public
- id: '5578'
relation: dissertation_contains
status: public
- id: '5579'
relation: dissertation_contains
status: public
- id: '5576'
relation: dissertation_contains
status: public
- id: '5575'
relation: dissertation_contains
status: public
- id: '5582'
relation: dissertation_contains
status: public
- id: '5581'
relation: dissertation_contains
status: public
- id: '5580'
relation: dissertation_contains
status: public
status: public
supervisor:
- first_name: Brigitte
full_name: Kromp, Brigitte
last_name: Kromp
title: Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '279'
abstract:
- lang: eng
text: 'Background: Natural selection shapes cancer genomes. Previous studies used
signatures of positive selection to identify genes driving malignant transformation.
However, the contribution of negative selection against somatic mutations that
affect essential tumor functions or specific domains remains a controversial topic.
Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA
data to explore the portion of the cancer exome under negative selection. Although
we find most of the genes neutrally evolving in a pan-cancer framework, we identify
essential cancer genes and immune-exposed protein regions under significant negative
selection. Moreover, our simulations suggest that the amount of negative selection
is underestimated. We therefore choose an empirical approach to identify genes,
functions, and protein regions under negative selection. We find that expression
and mutation status of negatively selected genes is indicative of patient survival.
Processes that are most strongly conserved are those that play fundamental cellular
roles such as protein synthesis, glucose metabolism, and molecular transport.
Intriguingly, we observe strong signals of selection in the immunopeptidome and
proteins controlling peptide exposition, highlighting the importance of immune
surveillance evasion. Additionally, tumor type-specific immune activity correlates
with the strength of negative selection on human epitopes. Conclusions: In summary,
our results show that negative selection is a hallmark of cell essentiality and
immune response in cancer. The functional domains identified could be exploited
therapeutically, ultimately allowing for the development of novel cancer treatments.'
article_number: '67'
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative
selection in tumor genome evolution acts on essential cellular functions and the
immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0
apa: Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0
chicago: Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential
Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central,
2018. https://doi.org/10.1186/s13059-018-1434-0.
ieee: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Negative selection in tumor genome evolution acts on essential cellular functions
and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.
ista: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative
selection in tumor genome evolution acts on essential cellular functions and the
immunopeptidome. Genome Biology. 19, 67.
mla: Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on
Essential Cellular Functions and the Immunopeptidome.” Genome Biology,
vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
Genome Biology 19 (2018).
date_created: 2018-12-11T11:45:35Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:32Z
day: '31'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s13059-018-1434-0
ec_funded: 1
external_id:
isi:
- '000433986200001'
file:
- access_level: open_access
checksum: f3e4922486bd9bf1483271bdbed394a7
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:05:01Z
date_updated: 2020-07-14T12:45:47Z
file_id: '5708'
file_name: 2018_GenomeBiology_Zapata.pdf
file_size: 1414722
relation: main_file
file_date_updated: 2020-07-14T12:45:47Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '7620'
quality_controlled: '1'
related_material:
record:
- id: '9811'
relation: research_data
status: public
- id: '9812'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Negative selection in tumor genome evolution acts on essential cellular functions
and the immunopeptidome
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: 19
year: '2018'
...
---
_id: '28'
abstract:
- lang: eng
text: 'This scientific commentary refers to ‘NEGR1 and FGFR2 cooperatively regulate
cortical development and core behaviours related to autism disorders in mice’
by Szczurkowska et al. '
article_processing_charge: No
author:
- first_name: Ximena
full_name: Contreras, Ximena
id: 475990FE-F248-11E8-B48F-1D18A9856A87
last_name: Contreras
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Contreras X, Hippenmeyer S. Incorrect trafficking route leads to autism. Brain
a journal of neurology. 2018;141(9):2542-2544. doi:10.1093/brain/awy218
apa: Contreras, X., & Hippenmeyer, S. (2018). Incorrect trafficking route leads
to autism. Brain a Journal of Neurology. Oxford University Press. https://doi.org/10.1093/brain/awy218
chicago: Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route
Leads to Autism.” Brain a Journal of Neurology. Oxford University Press,
2018. https://doi.org/10.1093/brain/awy218.
ieee: X. Contreras and S. Hippenmeyer, “Incorrect trafficking route leads to autism,”
Brain a journal of neurology, vol. 141, no. 9. Oxford University Press,
pp. 2542–2544, 2018.
ista: Contreras X, Hippenmeyer S. 2018. Incorrect trafficking route leads to autism.
Brain a journal of neurology. 141(9), 2542–2544.
mla: Contreras, Ximena, and Simon Hippenmeyer. “Incorrect Trafficking Route Leads
to Autism.” Brain a Journal of Neurology, vol. 141, no. 9, Oxford University
Press, 2018, pp. 2542–44, doi:10.1093/brain/awy218.
short: X. Contreras, S. Hippenmeyer, Brain a Journal of Neurology 141 (2018) 2542–2544.
date_created: 2018-12-11T11:44:14Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-03-25T23:30:23Z
day: '01'
department:
- _id: SiHi
doi: 10.1093/brain/awy218
external_id:
isi:
- '000446548100012'
intvolume: ' 141'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 2542 - 2544
publication: Brain a journal of neurology
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '7902'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Incorrect trafficking route leads to autism
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 141
year: '2018'
...
---
_id: '280'
abstract:
- lang: eng
text: Flowers have a species-specific functional life span that determines the time
window in which pollination, fertilization and seed set can occur. The stigma
tissue plays a key role in flower receptivity by intercepting pollen and initiating
pollen tube growth toward the ovary. In this article, we show that a developmentally
controlled cell death programme terminates the functional life span of stigma
cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also
known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074)
as partially redundant transcription factors that modulate stigma longevity by
controlling the expression of programmed cell death-associated genes. KIRA1 expression
is sufficient to induce cell death and terminate floral receptivity, whereas lack
of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly,
the extension of stigma longevity is accompanied by only a moderate extension
of flower receptivity, suggesting that additional processes participate in the
control of the flower's receptive life span.
acknowledgement: We gratefully acknowledge funding from the Chinese Scholarship Council
(CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek
(FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the
Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation
by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.),
the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH
(project number 639234 to M.K.N.).
article_processing_charge: No
author:
- first_name: Zhen
full_name: Gao, Zhen
last_name: Gao
- first_name: Anna
full_name: Daneva, Anna
last_name: Daneva
- first_name: Yuliya
full_name: Salanenka, Yuliya
id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87
last_name: Salanenka
- first_name: Matthias
full_name: Van Durme, Matthias
last_name: Van Durme
- first_name: Marlies
full_name: Huysmans, Marlies
last_name: Huysmans
- first_name: Zongcheng
full_name: Lin, Zongcheng
last_name: Lin
- first_name: Freya
full_name: De Winter, Freya
last_name: De Winter
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Mansour
full_name: Karimi, Mansour
last_name: Karimi
- first_name: Jan
full_name: Van De Velde, Jan
last_name: Van De Velde
- first_name: Klaas
full_name: Vandepoele, Klaas
last_name: Vandepoele
- first_name: Davy
full_name: Van De Walle, Davy
last_name: Van De Walle
- first_name: Koen
full_name: Dewettinck, Koen
last_name: Dewettinck
- first_name: Bart
full_name: Lambrecht, Bart
last_name: Lambrecht
- first_name: Moritz
full_name: Nowack, Moritz
last_name: Nowack
citation:
ama: Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity
by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375.
doi:10.1038/s41477-018-0160-7
apa: Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., …
Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting
cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing
Group. https://doi.org/10.1038/s41477-018-0160-7
chicago: Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans,
Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity
by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature
Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7.
ieee: Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by
promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol.
4, no. 6. Nature Publishing Group, pp. 365–375, 2018.
ista: Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F,
Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck
K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity
by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.
mla: Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting
Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6,
Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7.
short: Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De
Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle,
K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.
date_created: 2018-12-11T11:45:35Z
date_published: 2018-05-28T00:00:00Z
date_updated: 2023-09-13T08:24:17Z
day: '28'
department:
- _id: JiFr
doi: 10.1038/s41477-018-0160-7
external_id:
isi:
- '000435571000017'
intvolume: ' 4'
isi: 1
issue: '6'
language:
- iso: eng
month: '05'
oa_version: None
page: 365 - 375
publication: Nature Plants
publication_status: published
publisher: Nature Publishing Group
publist_id: '7619'
quality_controlled: '1'
scopus_import: '1'
status: public
title: KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in
the stigma of Arabidopsis
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 4
year: '2018'
...
---
_id: '281'
abstract:
- lang: eng
text: 'Although cells respond specifically to environments, how environmental identity
is encoded intracellularly is not understood. Here, we study this organization
of information in budding yeast by estimating the mutual information between environmental
transitions and the dynamics of nuclear translocation for 10 transcription factors.
Our method of estimation is general, scalable, and based on decoding from single
cells. The dynamics of the transcription factors are necessary to encode the highest
amounts of extracellular information, and we show that information is transduced
through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can
encode the nature of multiple stresses, but only if stress is high; specialists
(Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly
and for a wider range of magnitudes. In particular, Dot6 encodes almost as much
information as Msn2, the master regulator of the environmental stress response.
Each transcription factor reports differently, and it is only their collective
behavior that distinguishes between multiple environmental states. Changes in
the dynamics of the localization of transcription factors thus constitute a precise,
distributed internal representation of extracellular change. We predict that such
multidimensional representations are common in cellular decision-making.'
acknowledgement: This work was supported by the Biotechnology and Biological Sciences
Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences
Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to
G.T.).
article_processing_charge: No
article_type: original
author:
- first_name: Alejandro
full_name: Granados, Alejandro
last_name: Granados
- first_name: Julian
full_name: Pietsch, Julian
last_name: Pietsch
- first_name: Sarah A
full_name: Cepeda Humerez, Sarah A
id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87
last_name: Cepeda Humerez
- first_name: Isebail
full_name: Farquhar, Isebail
last_name: Farquhar
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Peter
full_name: Swain, Peter
last_name: Swain
citation:
ama: Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed
and dynamic intracellular organization of extracellular information. PNAS.
2018;115(23):6088-6093. doi:10.1073/pnas.1716659115
apa: Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G.,
& Swain, P. (2018). Distributed and dynamic intracellular organization of
extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115
chicago: Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar,
Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization
of Extracellular Information.” PNAS. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1716659115.
ieee: A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and
P. Swain, “Distributed and dynamic intracellular organization of extracellular
information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp.
6088–6093, 2018.
ista: Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018.
Distributed and dynamic intracellular organization of extracellular information.
PNAS. 115(23), 6088–6093.
mla: Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization
of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy
of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.
short: A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P.
Swain, PNAS 115 (2018) 6088–6093.
date_created: 2018-12-11T11:45:35Z
date_published: 2018-06-05T00:00:00Z
date_updated: 2023-09-11T12:58:24Z
day: '05'
department:
- _id: GaTk
doi: 10.1073/pnas.1716659115
external_id:
isi:
- '000434114900071'
pmid:
- '29784812'
intvolume: ' 115'
isi: 1
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/early/2017/09/21/192039
month: '06'
oa: 1
oa_version: Preprint
page: 6088 - 6093
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '7618'
quality_controlled: '1'
related_material:
record:
- id: '6473'
relation: part_of_dissertation
status: public
scopus_import: '1'
status: public
title: Distributed and dynamic intracellular organization of extracellular information
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '282'
abstract:
- lang: eng
text: Adaptive introgression is common in nature and can be driven by selection
acting on multiple, linked genes. We explore the effects of polygenic selection
on introgression under the infinitesimal model with linkage. This model assumes
that the introgressing block has an effectively infinite number of genes, each
with an infinitesimal effect on the trait under selection. The block is assumed
to introgress under directional selection within a native population that is genetically
homogeneous. We use individual-based simulations and a branching process approximation
to compute various statistics of the introgressing block, and explore how these
depend on parameters such as the map length and initial trait value associated
with the introgressing block, the genetic variability along the block, and the
strength of selection. Our results show that the introgression dynamics of a block
under infinitesimal selection is qualitatively different from the dynamics of
neutral introgression. We also find that in the long run, surviving descendant
blocks are likely to have intermediate lengths, and clarify how the length is
shaped by the interplay between linkage and infinitesimal selection. Our results
suggest that it may be difficult to distinguish introgression of single loci from
that of genomic blocks with multiple, tightly linked and weakly selected loci.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- 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: Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal
selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018
apa: Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome
under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018
chicago: Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301018.
ieee: H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal
selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp.
1279–1303, 2018.
ista: Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal
selection. Genetics. 209(4), 1279–1303.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society
of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.
short: H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.
date_created: 2018-12-11T11:45:36Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T08:22:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301018
external_id:
isi:
- '000440014100020'
intvolume: ' 209'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/early/2017/11/30/227082
month: '08'
oa: 1
oa_version: Submitted Version
page: 1279 - 1303
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7617'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introgression of a block of genome under infinitesimal selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '283'
abstract:
- lang: eng
text: Light represents the principal signal driving circadian clock entrainment.
However, how light influences the evolution of the clock remains poorly understood.
The cavefish Phreatichthys andruzzii represents a fascinating model to explore
how evolution under extreme aphotic conditions shapes the circadian clock, since
in this species the clock is unresponsive to light. We have previously demonstrated
that loss-of-function mutations targeting non-visual opsins contribute in part
to this blind clock phenotype. Here, we have compared orthologs of two core clock
genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish
and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii
per2 transcript. The most abundant transcript encodes a truncated protein lacking
the C-terminal Cry binding domain and incorporating an intronic, transposon-derived
coding sequence. We demonstrate that the transposon insertion leads to a predominantly
cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish
ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems
that during evolution in complete darkness, the photic entrainment pathway of
the circadian clock has been subject to mutation at multiple levels, extending
from opsin photoreceptors to nuclear effectors.
article_number: '8754'
article_processing_charge: No
author:
- first_name: Rosa Maria
full_name: Ceinos, Rosa Maria
last_name: Ceinos
- first_name: Elena
full_name: Frigato, Elena
last_name: Frigato
- first_name: Cristina
full_name: Pagano, Cristina
last_name: Pagano
- first_name: Nadine
full_name: Frohlich, Nadine
last_name: Frohlich
- first_name: Pietro
full_name: Negrini, Pietro
last_name: Negrini
- first_name: Nicola
full_name: Cavallari, Nicola
id: 457160E6-F248-11E8-B48F-1D18A9856A87
last_name: Cavallari
- first_name: Daniela
full_name: Vallone, Daniela
last_name: Vallone
- first_name: Silvia
full_name: Fuselli, Silvia
last_name: Fuselli
- first_name: Cristiano
full_name: Bertolucci, Cristiano
last_name: Bertolucci
- first_name: Nicholas S
full_name: Foulkes, Nicholas S
last_name: Foulkes
citation:
ama: Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the
light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1).
doi:10.1038/s41598-018-27080-2
apa: Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari,
N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated
circadian clock gene period 2. Scientific Reports. Nature Publishing Group.
https://doi.org/10.1038/s41598-018-27080-2
chicago: Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro
Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci,
and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated
Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group,
2018. https://doi.org/10.1038/s41598-018-27080-2.
ieee: R. M. Ceinos et al., “Mutations in blind cavefish target the light
regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no.
1. Nature Publishing Group, 2018.
ista: Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone
D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target
the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754.
mla: Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated
Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754,
Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2.
short: R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari,
D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018).
date_created: 2018-12-11T11:45:36Z
date_published: 2018-06-08T00:00:00Z
date_updated: 2023-09-13T08:59:27Z
day: '08'
ddc:
- '570'
department:
- _id: EvBe
doi: 10.1038/s41598-018-27080-2
external_id:
isi:
- '000434640800008'
file:
- access_level: open_access
checksum: 9c3942d772f84f3df032ffde0ed9a8ea
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T13:04:46Z
date_updated: 2020-07-14T12:45:49Z
file_id: '5707'
file_name: 2018_ScientificReports_Ceinos.pdf
file_size: 1855324
relation: main_file
file_date_updated: 2020-07-14T12:45:49Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '7616'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutations in blind cavefish target the light regulated circadian clock gene
period 2
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: 8
year: '2018'
...
---
_id: '284'
abstract:
- lang: eng
text: "Borel probability measures living on metric spaces are fundamental\r\nmathematical
objects. There are several meaningful distance functions that make the collection
of the probability measures living on a certain space a metric space. We are interested
in the description of the structure of the isometries of such metric spaces. We
overview some of the recent results of the topic and we also provide some new
ones concerning the Wasserstein distance. More specifically, we consider the space
of all Borel probability measures on the unit sphere of a Euclidean space endowed
with the Wasserstein metric W_p for arbitrary p >= 1, and we show that the
action of a Wasserstein isometry on the set of Dirac measures is induced by an
isometry of the underlying unit sphere."
acknowledgement: The author was supported by the ISTFELLOW program of the Institute
of Science and Technol- ogy Austria (project code IC1027FELL01) and partially supported
by the Hungarian National Research, Development and Innovation Office, NKFIH (grant
no. K124152).
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daniel
full_name: Virosztek, Daniel
id: 48DB45DA-F248-11E8-B48F-1D18A9856A87
last_name: Virosztek
orcid: 0000-0003-1109-5511
citation:
ama: Virosztek D. Maps on probability measures preserving certain distances - a
survey and some new results. Acta Scientiarum Mathematicarum. 2018;84(1-2):65-80.
doi:10.14232/actasm-018-753-y
apa: Virosztek, D. (2018). Maps on probability measures preserving certain distances
- a survey and some new results. Acta Scientiarum Mathematicarum. Springer
Nature. https://doi.org/10.14232/actasm-018-753-y
chicago: Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances
- a Survey and Some New Results.” Acta Scientiarum Mathematicarum. Springer
Nature, 2018. https://doi.org/10.14232/actasm-018-753-y.
ieee: D. Virosztek, “Maps on probability measures preserving certain distances -
a survey and some new results,” Acta Scientiarum Mathematicarum, vol. 84,
no. 1–2. Springer Nature, pp. 65–80, 2018.
ista: Virosztek D. 2018. Maps on probability measures preserving certain distances
- a survey and some new results. Acta Scientiarum Mathematicarum. 84(1–2), 65–80.
mla: Virosztek, Daniel. “Maps on Probability Measures Preserving Certain Distances
- a Survey and Some New Results.” Acta Scientiarum Mathematicarum, vol.
84, no. 1–2, Springer Nature, 2018, pp. 65–80, doi:10.14232/actasm-018-753-y.
short: D. Virosztek, Acta Scientiarum Mathematicarum 84 (2018) 65–80.
date_created: 2018-12-11T11:45:36Z
date_published: 2018-06-04T00:00:00Z
date_updated: 2023-10-16T10:29:22Z
day: '04'
department:
- _id: LaEr
doi: 10.14232/actasm-018-753-y
ec_funded: 1
external_id:
arxiv:
- '1802.03305'
intvolume: ' 84'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.03305
month: '06'
oa: 1
oa_version: Preprint
page: 65 - 80
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Acta Scientiarum Mathematicarum
publication_identifier:
eissn:
- 2064-8316
issn:
- 0001-6969
publication_status: published
publisher: Springer Nature
publist_id: '7615'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Maps on probability measures preserving certain distances - a survey and some
new results
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2018'
...