---
OA_place: publisher
_id: '22857'
abstract:
- lang: eng
text: "Artificial intelligence and machine learning have undergone an unprecedented
evolution in the past decade, motivating a research effort toward a theory able
to capture the qualitative behavior of large-scale neural systems. A central puzzle
has been the clear benefit of scaling architecture size and overfitting the training
set in supervised learning tasks. This evidence, in apparent contradiction with
classical statistical learning theory, pushed researchers to develop a new theory
capturing the interplay between the algorithmic and architectural bias of training
and the specific target function, differently from previous methods rooted in
uniform stability.\r\nThis approach has enabled a grounded understanding of novel
learning regimes, typically through formal limits where the number of training
samples $n$, data dimensions $d$, and model parameters $p$ grow to infinity at
different rates. \\\\\r\nIn this thesis, we follow this approach, focusing on
the trustworthiness of high-dimensional models: properties that are difficult
to control during training or deployment and often emerge under unpredictable
or adversarial conditions. In such settings, it is crucial to formally ensure
a priori the reliability of machine learning systems.\r\nFirst, we study data
memorization, both as label fitting and as the storage of private information
about training samples in trained parameters. We prove that $p = \\Omega(n)$ parameters
are sufficient for a deep neural network to memorize a generic set of labels,
and for a model to memorize spurious features across training data. We then give
evidence that $p = \\Omega(dn)$ parameters are instead necessary for an adversary
to reconstruct the full training set from the trained parameters.\r\nSecond, we
study robustness, both to adversarial perturbations and to distribution shift.
We first prove that $p = \\Omega(dn)$ parameters can be sufficient for a class
of neural networks to overfit the training data while guaranteeing robustness
to adversarial perturbations. Then, we focus on spurious correlations learning
in high-dimensional regression, studying the effect of the ridge regularization
parameter in the proportional regime $n = \\Theta(d)$, and connecting it via an
equivalence argument to the role of over-parameterization $p = \\Omega(n)$ in
neural networks. We also investigate the architectural bias of attention-based
networks, showing that they are sensitive to the replacement of individual words
in an embedded sentence, allowing them to generalize on sentences where the contextual
meaning depends on one or few words.\r\nFinally, we study differentially private
optimization in high-dimensional regimes. We prove that standard private gradient
methods do not suffer in the over-parameterized regime $p = \\Omega(n)$, challenging
the current wisdom based on stability-derived generalization bounds. We then consider
linear regression in the proportional regime $n = \\Theta(d)$, showing that standard
private gradient descent can achieve optimal rates under appropriate hyper-parameter
scaling, such as sufficiently small gradient clipping constants, whose role is
still debated in practice."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This project was partially supported by the 2019 Lopez-Loreta prize,\r\nthe
European Union (ERC, INF2\r\n, project number 101161364), the Austrian Science Fund\r\n(FWF)
10.55776/COE12, and a Google PhD fellowship in machine intelligence. Furthermore,\r\nthe
candidate acknowledges the support from the Scientific Service Units of the Institute
of\r\nScience and Technology Austria through resources provided by Scientific Computing."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Simone
full_name: Bombari, Simone
id: ca726dda-de17-11ea-bc14-f9da834f63aa
last_name: Bombari
citation:
ama: Bombari S. Trustworthy machine learning in high dimensions. 2026. doi:10.15479/AT-ISTA-22857
apa: Bombari, S. (2026). Trustworthy machine learning in high dimensions.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22857
chicago: Bombari, Simone. “Trustworthy Machine Learning in High Dimensions.” Institute
of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22857.
ieee: S. Bombari, “Trustworthy machine learning in high dimensions,” Institute of
Science and Technology Austria, 2026.
ista: Bombari S. 2026. Trustworthy machine learning in high dimensions. Institute
of Science and Technology Austria.
mla: Bombari, Simone. Trustworthy Machine Learning in High Dimensions. Institute
of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22857.
short: S. Bombari, Trustworthy Machine Learning in High Dimensions, Institute of
Science and Technology Austria, 2026.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-09-08T13:40:08Z
date_published: 2026-09-08T00:00:00Z
date_updated: 2026-10-16T10:42:36Z
day: '08'
ddc:
- '519'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaMo
doi: 10.15479/AT-ISTA-22857
doi_confirm: '1'
file:
- access_level: closed
checksum: 8eab99d6dc6e4476826bdfc7c00fdebb
content_type: application/zip
creator: sbombari
date_created: 2026-09-08T13:28:38Z
date_updated: 2026-09-08T13:28:38Z
file_id: '22859'
file_name: Thesis copy.zip
file_size: 99154325
relation: source_file
- access_level: open_access
checksum: 007033bafe4622ff4c2e758301354df1
content_type: application/pdf
creator: sbombari
date_created: 2026-09-10T10:03:48Z
date_updated: 2026-09-10T10:03:48Z
file_id: '22898'
file_name: 2026_Bombari_Simone_Thesis.pdf
file_size: 12856211
relation: main_file
success: 1
file_date_updated: 2026-09-10T10:03:48Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22857
has_accepted_license: '1'
keyword:
- machine learning
- high-dimensional statistics
- deep learning theory
- privacy
- memorization
- robustness
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '446'
project:
- _id: 92099302-16d5-11f0-9cad-f9a785f54fbd
name: 'Trustworthy Deep Learning Theory: Private Over-Parameterized Models and Robust
LLMs'
- _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf
grant_number: '101161364'
name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits'
- _id: 74caaef7-b034-11f1-8f2d-e0e993bb422e
grant_number: COE12
name: Bilateral Artificial Intelligence (Mondelli)
publication_identifier:
isbn:
- 978-3-99078-091-6
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12537'
relation: part_of_dissertation
status: public
- id: '21324'
relation: part_of_dissertation
status: public
- id: '22894'
relation: part_of_dissertation
status: public
- id: '19627'
relation: part_of_dissertation
status: public
- id: '12859'
relation: part_of_dissertation
status: public
- id: '18973'
relation: part_of_dissertation
status: public
- id: '18972'
relation: part_of_dissertation
status: public
researchdata_availability: no
status: public
supervisor:
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
supplementarymaterial: no
title: Trustworthy machine learning in high dimensions
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '23156'
abstract:
- lang: eng
text: "Extracting the current-phase relationship (CPR) of a single superconducting
junction is challenging in practice and traditionally involves embedding the junction
in a larger superconducting circuit containing SQUIDs and/or resonators. Applying
ac driving to the junction has proven to be a viable and less invasive way to
extract information about the few lowest harmonics of the CPR, by locating the
integer and fractional Shapiro steps in the \U0001D43C\U0001D449-curve of the
driven junction. Here, we present an alternative driving-based method that allows
to extract the full harmonic content of a CPR in a relatively noninvasive way,
by fitting the measured critical currents of the driven junction as a function
of driving power. We test our method, both using numerical simulations and in
experiments, and we show that it works accurately."
acknowledgement: 'The authors thank Afonso Oliveira, Stefano Calcaterra, Daniel Chrastina,
and Giovanni Isella for providing the Ge/SiGe heterostructure. This work was supported
by the Research Council of Norway through its Centers of Excellence funding scheme,
Project No. 262633, “QuSpin,” the FWF Project with DOI:10.55776/PAT7682124, OeAD
“ISTA Austria: ISTernship Summer Programme, Non-EU countries” (Ref. No.: MPC-2025-00945),
the Spanish Comunidad de Madrid (CM) “Talento Program” (Project No. 2022-T1/IND-24070),
and the Spanish Ministry of Science, Innovation, and Universities through Grants
No. CEX2024-001445-S (Severo Ochoa Centres of Excellence program) and No. PID2022-140552NA-I00,
funded by MCIN/AEI/10.13039/501100011033.'
article_number: '044017'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Maxim
full_name: Tjøtta, Maxim
last_name: Tjøtta
- first_name: Devashish C
full_name: Shah, Devashish C
id: de191434-4e7e-11ef-bf4b-9a056fc19fc3
last_name: Shah
orcid: 0009-0007-5829-7707
- first_name: Kanishk
full_name: Modi, Kanishk
id: f05345fd-900f-11f1-bfd8-8c0b6eadcc7f
last_name: Modi
- first_name: Marco
full_name: Valentini, Marco
id: C0BB2FAC-D767-11E9-B658-BC13E6697425
last_name: Valentini
- first_name: Rubén
full_name: Seoane Souto, Rubén
last_name: Seoane Souto
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
- first_name: Jeroen
full_name: Danon, Jeroen
last_name: Danon
citation:
ama: Tjøtta M, Shah DC, Modi K, et al. Fast-driving spectroscopy of current-phase
relationships of individual Josephson elements. Physical Review Applied.
2026;26(4). doi:10.1103/d3gl-qntm
apa: Tjøtta, M., Shah, D. C., Modi, K., Valentini, M., Seoane Souto, R., Katsaros,
G., & Danon, J. (2026). Fast-driving spectroscopy of current-phase relationships
of individual Josephson elements. Physical Review Applied. American Physical
Society. https://doi.org/10.1103/d3gl-qntm
chicago: Tjøtta, Maxim, Devashish C Shah, Kanishk Modi, Marco Valentini, Rubén Seoane
Souto, Georgios Katsaros, and Jeroen Danon. “Fast-Driving Spectroscopy of Current-Phase
Relationships of Individual Josephson Elements.” Physical Review Applied.
American Physical Society, 2026. https://doi.org/10.1103/d3gl-qntm.
ieee: M. Tjøtta et al., “Fast-driving spectroscopy of current-phase relationships
of individual Josephson elements,” Physical Review Applied, vol. 26, no.
4. American Physical Society, 2026.
ista: Tjøtta M, Shah DC, Modi K, Valentini M, Seoane Souto R, Katsaros G, Danon
J. 2026. Fast-driving spectroscopy of current-phase relationships of individual
Josephson elements. Physical Review Applied. 26(4), 044017.
mla: Tjøtta, Maxim, et al. “Fast-Driving Spectroscopy of Current-Phase Relationships
of Individual Josephson Elements.” Physical Review Applied, vol. 26, no.
4, 044017, American Physical Society, 2026, doi:10.1103/d3gl-qntm.
short: M. Tjøtta, D.C. Shah, K. Modi, M. Valentini, R. Seoane Souto, G. Katsaros,
J. Danon, Physical Review Applied 26 (2026).
das_tickbox: '1'
dataavailabilitystatement: The data that support the findings of this article are
openly available at [10.5281/zenodo.22646275].
date_created: 2026-10-18T22:01:52Z
date_published: 2026-10-01T00:00:00Z
date_updated: 2026-10-19T07:25:01Z
day: '01'
department:
- _id: GeKa
- _id: GradSch
doi: 10.1103/d3gl-qntm
external_id:
arxiv:
- '2511.14313'
fulldoi: https://doi.org/10.1103/d3gl-qntm
intvolume: ' 26'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2511.14313
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 5b9e579c-ab3d-11f0-914f-88754c5b5a3f
grant_number: PAT 7682124
name: Superconducting spin qubits in planar Ge
publication: Physical Review Applied
publication_identifier:
eissn:
- 2331-7019
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Fast-driving spectroscopy of current-phase relationships of individual Josephson
elements
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '23159'
abstract:
- lang: eng
text: The Vera C. Rubin Observatory has now seen first light, and over a 10 year
duration, Legacy Survey of Space and Time (LSST) is projected to catalog tens
of millions of quasars, many of which are expected to be associated with subparsec
supermassive black hole binaries (SMBHBs). Out of these SMBHBs, up to thousands
of relatively massive binary-quasars are expected to exhibit gravitational self-lensing
flares (SLFs) that last for at least 20–30 days. We assess the effectiveness of
the Lomb-Scargle (LS) periodogram and matched filters (MFs) as methods for systematic
searches for these binaries, using toy-models of hydrodynamical, Doppler, and
self-lensing variability from equal-mass, eccentric SMBHBs. We inject SLFs into
random realizations of damped random walk (DRW) lightcurves, representing stochastic
quasar variability, and compute the LS periodogram with and without the SLF. We
find that periodograms of SLF+DRW light-curves do not have maximum peak heights
that could not arise from DRW-only periodograms. On the other hand, the matched
filter signal-to-noise ratio (SNR) can distinguish SLFs from noise even with LSST-like
cadences and DRW noise. Furthermore, we develop a three-step procedure with matched
filters, which can also recover injected binary parameters from these light-curves.
We expect this method to be computationally efficient enough to be applicable
to millions of quasar light-curves in LSST.
acknowledgement: We acknowledge support by NASA Grants No. 80NSSC22K0822 and No. 80NSSC24K0440
(Z. H). V. A. V. acknowledges support through the David and Lucile Packard Foundation,
National Science Foundation under No. PHY-2019786 (The NSF AI Institute for Artificial
Intelligence and Fundamental Interactions, [63]), No. AST-2433718, No. AST-2407922
and No. AST-2406110, as well as an Aramont Fellowship for Emerging Science Research.
J. D. acknowledges support by a joint Columbia/Flatiron Postdoctoral Fellowship.
Research at the Flatiron Institute is supported by the Simons Foundation. This research
was supported in part by the National Science Foundation under Grant No. NSF PHY-1748958
to the Kavli Institute for Theoretical Physics (KITP). This research has made use
of NASA’s Astrophysics Data System. The authors acknowledge the Texas Advanced Computing
Center (TACC) at The University of Texas at Austin for providing computational resources.
V. A. V. acknowledges support through the David and Lucile Packard Foundation, National
Science Foundation under No. AST-2433718, No. AST-2407922 and No. AST-2406110, as
well as an Aramont Fellowship for Emerging Science Research. This work is supported
by the National Science Foundation under Cooperative Agreement No. PHY-2019786 (The
NSF AI Institute for Artificial Intelligence and Fundamental Interactions, [63]).
article_number: '043055'
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Kevin S
full_name: Park, Kevin S
id: c0a7603b-66e5-11f0-aaf9-b02edf8b2969
last_name: Park
- first_name: Zoltán
full_name: Haiman, Zoltán
id: 7c006e8c-cc0d-11ee-8322-cb904ef76f36
last_name: Haiman
orcid: 0000-0003-3633-5403
- first_name: Chengcheng
full_name: Xin, Chengcheng
last_name: Xin
- first_name: Tzuken
full_name: Shen, Tzuken
last_name: Shen
- first_name: Ashley
full_name: Villar, Ashley
last_name: Villar
- first_name: Jordy
full_name: Davelaar, Jordy
last_name: Davelaar
citation:
ama: Park KS, Haiman Z, Xin C, Shen T, Villar A, Davelaar J. Self-lensing flares
from black hole binaries. V. Systematic searches in LSST. Physical Review D.
2026;113(4). doi:10.1103/p328-62sl
apa: Park, K. S., Haiman, Z., Xin, C., Shen, T., Villar, A., & Davelaar, J.
(2026). Self-lensing flares from black hole binaries. V. Systematic searches in
LSST. Physical Review D. American Physical Society. https://doi.org/10.1103/p328-62sl
chicago: Park, Kevin S, Zoltán Haiman, Chengcheng Xin, Tzuken Shen, Ashley Villar,
and Jordy Davelaar. “Self-Lensing Flares from Black Hole Binaries. V. Systematic
Searches in LSST.” Physical Review D. American Physical Society, 2026.
https://doi.org/10.1103/p328-62sl.
ieee: K. S. Park, Z. Haiman, C. Xin, T. Shen, A. Villar, and J. Davelaar, “Self-lensing
flares from black hole binaries. V. Systematic searches in LSST,” Physical
Review D, vol. 113, no. 4. American Physical Society, 2026.
ista: Park KS, Haiman Z, Xin C, Shen T, Villar A, Davelaar J. 2026. Self-lensing
flares from black hole binaries. V. Systematic searches in LSST. Physical Review
D. 113(4), 043055.
mla: Park, Kevin S., et al. “Self-Lensing Flares from Black Hole Binaries. V. Systematic
Searches in LSST.” Physical Review D, vol. 113, no. 4, 043055, American
Physical Society, 2026, doi:10.1103/p328-62sl.
short: K.S. Park, Z. Haiman, C. Xin, T. Shen, A. Villar, J. Davelaar, Physical Review
D 113 (2026).
das_tickbox: '1'
dataavailabilitystatement: The data are not publicly available. The data are available
from the authors upon reasonable request.
date_created: 2026-10-18T22:01:53Z
date_published: 2026-02-25T00:00:00Z
date_updated: 2026-10-19T08:08:21Z
day: '25'
ddc:
- '520'
department:
- _id: GradSch
- _id: ZoHa
doi: 10.1103/p328-62sl
external_id:
arxiv:
- '2512.08427'
file:
- access_level: open_access
checksum: 764bd6512975216dd63655da64ceeb95
content_type: application/pdf
creator: dernst
date_created: 2026-10-19T08:06:17Z
date_updated: 2026-10-19T08:06:17Z
file_id: '23167'
file_name: 2026_PhysicalReviewD_Park.pdf
file_size: 3535182
relation: main_file
success: 1
file_date_updated: 2026-10-19T08:06:17Z
fulldoi: https://doi.org/10.1103/p328-62sl
has_accepted_license: '1'
intvolume: ' 113'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Physical Review D
publication_identifier:
eissn:
- 2470-0029
issn:
- 2470-0010
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Self-lensing flares from black hole binaries. V. Systematic searches in LSST
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: 113
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '23155'
abstract:
- lang: eng
text: "In this work we establish several monotonicity and decomposition results
in the framework of random regular graphs. Among other results, we\r\nshow that,
for a wide range of parameters d1 ≤ d2, there exists a coupling of\r\nG(n,d1)
and G(n,d2) satisfying that G(n,d1) ⊆ G(n,d2) with high probability, confirming
a conjecture of Gao, Isaev and McKay in a new regime.\r\nOur contributions include
new tools for analysing contiguity and total variation distance between random
regular graph models, a novel procedure for\r\ngenerating unions of random edge-disjoint
perfect matchings, and refined estimates of Gao’s bounds on the number of perfect
matchings in random regular graphs. In addition, we make progress towards another
conjecture of Isaev,\r\nMcKay, Southwell and Zhukovskii."
acknowledgement: "We are grateful to Béla Bollobás, to Matthew Kwan and to Fabio\r\nToninelli
for their helpful comments and suggestions, and to Nicholas Wormald for useful\r\nremarks
on a preliminary version of this work and pointing us towards the reference [29].\r\nThe
authors would also like to thank several anonymous referees for many useful suggestions,\r\nincluding
pointing out that Lemma 2.10 already appeared in [11].\r\nPart of this research
was done during a visit of the fourth author to IST Austria. We thank\r\nIST Austria
for its hospitality.\r\nFor open access purposes, the authors have applied a CC
BY public copyright license to\r\nany author accepted manuscript version arising
from this submission. L. Hollom was supported by the Internal Graduate Studentship
of Trinity College, Cambridge.\r\nL. Lichev was supported by the Austrian Science
Fund (FWF) grant No. 10.55776/ESP624.\r\nA. Mond was supported by UK Research and
Innovation grant MR/W007320/2. Wang was\r\nsupported by the ERC Starting Grant “RANDSTRUCT”
No. 101076777."
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Lawrence
full_name: Hollom, Lawrence
last_name: Hollom
- first_name: Lyuben
full_name: Lichev, Lyuben
id: 9aa8388e-d003-11ee-8458-c4c1d7447977
last_name: Lichev
- first_name: Adva
full_name: Mond, Adva
last_name: Mond
- first_name: Julien
full_name: Portier, Julien
last_name: Portier
- first_name: Yiting
full_name: Wang, Yiting
id: 1917d194-076e-11ed-97cd-837255f88785
last_name: Wang
citation:
ama: Hollom L, Lichev L, Mond A, Portier J, Wang Y. Monotonicity and decompositions
of random regular graphs. Annals of Applied Probability. 2026;36(5):4716-4738.
doi:10.1214/26-AAP2345
apa: Hollom, L., Lichev, L., Mond, A., Portier, J., & Wang, Y. (2026). Monotonicity
and decompositions of random regular graphs. Annals of Applied Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/26-AAP2345
chicago: Hollom, Lawrence, Lyuben Lichev, Adva Mond, Julien Portier, and Yiting
Wang. “Monotonicity and Decompositions of Random Regular Graphs.” Annals of
Applied Probability. Institute of Mathematical Statistics, 2026. https://doi.org/10.1214/26-AAP2345.
ieee: L. Hollom, L. Lichev, A. Mond, J. Portier, and Y. Wang, “Monotonicity and
decompositions of random regular graphs,” Annals of Applied Probability,
vol. 36, no. 5. Institute of Mathematical Statistics, pp. 4716–4738, 2026.
ista: Hollom L, Lichev L, Mond A, Portier J, Wang Y. 2026. Monotonicity and decompositions
of random regular graphs. Annals of Applied Probability. 36(5), 4716–4738.
mla: Hollom, Lawrence, et al. “Monotonicity and Decompositions of Random Regular
Graphs.” Annals of Applied Probability, vol. 36, no. 5, Institute of Mathematical
Statistics, 2026, pp. 4716–38, doi:10.1214/26-AAP2345.
short: L. Hollom, L. Lichev, A. Mond, J. Portier, Y. Wang, Annals of Applied Probability
36 (2026) 4716–4738.
das_tickbox: '0'
date_created: 2026-10-18T22:01:52Z
date_published: 2026-10-01T00:00:00Z
date_updated: 2026-10-19T07:39:17Z
day: '01'
ddc:
- '500'
department:
- _id: MaKw
- _id: GradSch
doi: 10.1214/26-AAP2345
external_id:
arxiv:
- '2505.22875'
file:
- access_level: open_access
checksum: 46101e61d29cf40f0a204801d15a848f
content_type: application/pdf
creator: dernst
date_created: 2026-10-19T07:33:58Z
date_updated: 2026-10-19T07:33:58Z
file_id: '23165'
file_name: 2026_AnnalsAppliedProbability_Hollom.pdf
file_size: 320593
relation: main_file
success: 1
file_date_updated: 2026-10-19T07:33:58Z
fulldoi: https://doi.org/10.1214/26-AAP2345
has_accepted_license: '1'
intvolume: ' 36'
issue: '5'
keyword:
- Random regular graphs
- coupling
- contiguity
- total variation distance
- decomposition
language:
- iso: eng
mathsc:
- 05C80
month: '10'
oa: 1
oa_version: Published Version
page: 4716-4738
project:
- _id: bd95085b-d553-11ed-ba76-e55d3349be45
grant_number: '101076777'
name: Randomness and structure in combinatorics
- _id: e19fef4c-1f3d-11f0-ac04-b8b1af6886d8
grant_number: E624
name: THRESHOLDS IN SEMI-RANDOM PROCESSES AND GRAPH EMBEDDINGS
publication: Annals of Applied Probability
publication_identifier:
eissn:
- 2168-8737
issn:
- 1050-5164
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Monotonicity and decompositions of random regular graphs
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: 36
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '23173'
abstract:
- lang: eng
text: The prevalence of proline residues in intrinsically disordered proteins, functional
hinges of enzymes, and protein interaction sites highlights the importance of
studying their local dynamics and interactions at atomic resolution. While nuclear
magnetic resonance (NMR) spectroscopy is, in principle, ideally suited for such
investigations, the absence of an amide proton precludes the use of conventional
1H–15N amide-detected experiments. 1H–13C-based approaches, though possible, remain
challenging in large proteins. In this work, we present a selective labeling strategy
that introduces an isolated 1H2δ–13Cδ–15N spin system in proline residues in otherwise
deuterated proteins. Our method leverages the enzymatic conversion of ornithine,
synthesized from cost-effective isotopic precursors. We demonstrate the utility
of this approach by applying it to a 134 kDa enzyme using magic-angle spinning
NMR, highlighting its potential to efficiently probe functionally relevant sites
in proteins.
acknowledged_ssus:
- _id: NMR
- _id: LifeSc
acknowledgement: We thank Undina Guillerm, Rajkumar Singh and Anna Kapitonova for
help with protein production. We are grateful to Dominique Madern for discussions
and for providing the plasmid of IiMDH. We acknowledge the Scientific Service Units
(SSU) of the Institute of Science and Technology Austria (ISTA) through resources
provided by the NMR Facility and the Lab Support Facility, as well as the NMR centre
and MS centre of the University of Vienna. This work was supported by the Austrian
Science Fund (FWF; project number I5812-B) through a French-Austrian binational
research project, as well as by the L’Oréal-UNESCO For Women in Science Fellowship,
awarded in cooperation with the Austrian Academy of Sciences (ÖAW) and the Austrian
Commission for UNESCO.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Darja
full_name: Rohden, Darja
id: 81dc668a-19fa-11f0-bf31-d56534059ef3
last_name: Rohden
- first_name: Federico
full_name: Napoli, Federico
id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b
last_name: Napoli
orcid: 0000-0002-9043-136X
- first_name: Roman J.
full_name: Lichtenecker, Roman J.
last_name: Lichtenecker
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Rohden D, Napoli F, Lichtenecker RJ, Schanda P. Chemoenzymatic proline isotope
labeling for solution and magic-angle spinning protein nuclear magnetic resonance.
ACS Chemical Biology. 2026. doi:10.1021/acschembio.6c00587
apa: Rohden, D., Napoli, F., Lichtenecker, R. J., & Schanda, P. (2026). Chemoenzymatic
proline isotope labeling for solution and magic-angle spinning protein nuclear
magnetic resonance. ACS Chemical Biology. American Chemical Society. https://doi.org/10.1021/acschembio.6c00587
chicago: Rohden, Darja, Federico Napoli, Roman J. Lichtenecker, and Paul Schanda.
“Chemoenzymatic Proline Isotope Labeling for Solution and Magic-Angle Spinning
Protein Nuclear Magnetic Resonance.” ACS Chemical Biology. American Chemical
Society, 2026. https://doi.org/10.1021/acschembio.6c00587.
ieee: D. Rohden, F. Napoli, R. J. Lichtenecker, and P. Schanda, “Chemoenzymatic
proline isotope labeling for solution and magic-angle spinning protein nuclear
magnetic resonance,” ACS Chemical Biology. American Chemical Society, 2026.
ista: Rohden D, Napoli F, Lichtenecker RJ, Schanda P. 2026. Chemoenzymatic proline
isotope labeling for solution and magic-angle spinning protein nuclear magnetic
resonance. ACS Chemical Biology.
mla: Rohden, Darja, et al. “Chemoenzymatic Proline Isotope Labeling for Solution
and Magic-Angle Spinning Protein Nuclear Magnetic Resonance.” ACS Chemical
Biology, American Chemical Society, 2026, doi:10.1021/acschembio.6c00587.
short: D. Rohden, F. Napoli, R.J. Lichtenecker, P. Schanda, ACS Chemical Biology
(2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "Supporting Information is available free of charge at
https://pubs.acs.org/10.1021/acschembio.6c00587.\r\n\r\nDetailed description of
experimental methods; spectra supporting the residue assignment for IiMDH; relaxation
analysis of IiMDH proline-Cδ sites; NMR spectra of isolated [13Cδ,15N,2Hβγ4]-Pro
(PDF)"
date_created: 2026-10-19T11:12:28Z
date_published: 2026-10-13T00:00:00Z
date_updated: 2026-10-19T11:20:33Z
day: '13'
ddc:
- '540'
department:
- _id: PaSc
- _id: GradSch
doi: 10.1021/acschembio.6c00587
external_id:
pmid:
- '42863127'
fulldoi: https://doi.org/10.1021/acschembio.6c00587
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acschembio.6c00587
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf
grant_number: I05812
name: AlloSpace. The emergence and mechanisms of allostery
publication: ACS Chemical Biology
publication_identifier:
eissn:
- 1554-8937
issn:
- 1554-8929
publication_status: epub_ahead
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chemoenzymatic proline isotope labeling for solution and magic-angle spinning
protein nuclear magnetic resonance
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
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21707'
abstract:
- lang: eng
text: Structural and functional differences between brain hemispheres are a common
feature of animal nervous systems with reduced bilateral asymmetry often linked
to impaired cognitive performance. How neuronal left-right asymmetry is initiated
and integrated into a bilaterally symmetrical ground pattern is poorly understood.
Here, we show that the directional asymmetry of a Drosophila central brain circuit
originates from axonal interactions of two types of bilateral pioneer neurons.
Subsequent recruitment of neighboring neurons into the asymmetric neuropil primordium
results in hemisphere-specific microcircuits. Circuit lateralization requires
dynamic expression of the cell adhesion molecule Fasciclin 2 to maintain structural
plasticity in axonal remodeling. Reduced circuit asymmetry following cell type–specific
Fasciclin 2 manipulation affects adult brain function. These results reveal an
unexpected degree of developmental plasticity of late-born Drosophila neurons
in the formation of a circuit node via the lateralized recruitment of symmetric
circuit components.
acknowledgement: "We thank I. Salecker (Flybow), B. Altenhein (Fas2-Gal4Mz507), A.
Nose (UAS-intra- and extra-Fas2::YFP), and C. S. Goodman (UAS-Fas2PEST+/−), as well
as the Bloomington Stock Center for providing materials and fly stocks. We thank
S. Waddell and the lab, especially B. Senapati, for providing the opportunity to
conduct memory experiments at the CNCB, University of Oxford, and for supervision
and discussions during this period. We also thank W. Kallina, S. Ilgerl, D. Bartel,
A. Grimm, and A. Litin for technical support and the Hummel Lab for stimulating
discussions and critical comments on the manuscript. We acknowledge the early exploratory
work of A. Mattia, S. Trkulja, C. Schönherr, S. Bogner, B. Simpson, L. Tomasek,
H. Roth, H. Vokač, R. Gredler, F. Kapelari, T. Kolarova, C. Ignitsch, Á. Bautista-Soldevila,
and M. Kassem.\r\nThis research was funded by the University of Vienna, the Vienna
Doctoral School Cognition, Behaviour and Neuroscience (uni:docs fellowship) (to
J.W.M.) and by the Austrian Science Fund (FWF) (Cluster of Excellence Neuronal Circuits
in Health and Disease, grant DOI 10.55776/COE16; https://www.fwf.ac.at/en/research-radar/10.55776/COE16)
(to T.H.). For open access purposes, the author has applied a CC BY public copyright
license to any author-accepted manuscript version arising from this submission."
article_number: eaea6020
article_processing_charge: Yes
article_type: original
author:
- first_name: Johann W.
full_name: Markovitsch, Johann W.
last_name: Markovitsch
- first_name: Daniel
full_name: Mitić, Daniel
last_name: Mitić
- first_name: Alisa
full_name: Del Pilar Jiménez García, Alisa
last_name: Del Pilar Jiménez García
- first_name: Alsberga
full_name: Zane, Alsberga
id: 60f7509a-f652-11ea-9d86-b963d6490d7c
last_name: Zane
orcid: 0009-0003-0415-7603
- first_name: Sarah
full_name: Kainz, Sarah
last_name: Kainz
- first_name: Rashmit
full_name: Kaur, Rashmit
last_name: Kaur
- first_name: Thomas
full_name: Hummel, Thomas
last_name: Hummel
citation:
ama: Markovitsch JW, Mitić D, Del Pilar Jiménez García A, et al. Sequential formation
of Drosophila circuit asymmetry via prolonged structural plasticity. Science
Advances. 2026;12(13). doi:10.1126/sciadv.aea6020
apa: Markovitsch, J. W., Mitić, D., Del Pilar Jiménez García, A., Zane, A., Kainz,
S., Kaur, R., & Hummel, T. (2026). Sequential formation of Drosophila circuit
asymmetry via prolonged structural plasticity. Science Advances. AAAS.
https://doi.org/10.1126/sciadv.aea6020
chicago: Markovitsch, Johann W., Daniel Mitić, Alisa Del Pilar Jiménez García, Alsberga
Zane, Sarah Kainz, Rashmit Kaur, and Thomas Hummel. “Sequential Formation of Drosophila
Circuit Asymmetry via Prolonged Structural Plasticity.” Science Advances.
AAAS, 2026. https://doi.org/10.1126/sciadv.aea6020.
ieee: J. W. Markovitsch et al., “Sequential formation of Drosophila circuit
asymmetry via prolonged structural plasticity,” Science Advances, vol.
12, no. 13. AAAS, 2026.
ista: Markovitsch JW, Mitić D, Del Pilar Jiménez García A, Zane A, Kainz S, Kaur
R, Hummel T. 2026. Sequential formation of Drosophila circuit asymmetry via prolonged
structural plasticity. Science Advances. 12(13), eaea6020.
mla: Markovitsch, Johann W., et al. “Sequential Formation of Drosophila Circuit
Asymmetry via Prolonged Structural Plasticity.” Science Advances, vol.
12, no. 13, eaea6020, AAAS, 2026, doi:10.1126/sciadv.aea6020.
short: J.W. Markovitsch, D. Mitić, A. Del Pilar Jiménez García, A. Zane, S. Kainz,
R. Kaur, T. Hummel, Science Advances 12 (2026).
date_created: 2026-04-12T22:01:48Z
date_published: 2026-03-27T00:00:00Z
date_updated: 2026-10-20T08:11:29Z
day: '27'
ddc:
- '570'
department:
- _id: MiSi
- _id: GradSch
doi: 10.1126/sciadv.aea6020
file:
- access_level: open_access
checksum: 3eed470fe73e53d2a8d55d6fba6934e3
content_type: application/pdf
creator: dernst
date_created: 2026-05-04T09:16:36Z
date_updated: 2026-05-04T09:16:36Z
file_id: '21786'
file_name: 2026_ScienceAdv_Markovitsch.pdf
file_size: 11101140
relation: main_file
success: 1
file_date_updated: 2026-05-04T09:16:36Z
fulldoi: https://doi.org/10.1126/sciadv.aea6020
has_accepted_license: '1'
intvolume: ' 12'
issue: '13'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sequential formation of Drosophila circuit asymmetry via prolonged structural
plasticity
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: 12
year: '2026'
...
---
OA_embargo: '12'
OA_place: publisher
_id: '22744'
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: ScienComp
- _id: LifeSc
acknowledgement: "This work was supported by the ERC StG grant ActinID (PRA01221F1049A)
awarded to Florian\r\nSchur, the ERC-SyG grant Pushing from within (P01071793) awarded
to Michael Sixt, and by ISTA.\r\nI would like to thank the Scientific Service Units
at ISTA for their essential support throughout\r\nthis work. In particular, I am
grateful to the Electron Microscopy Facility, Imaging and Optics\r\nFacility, Zebrafish
Facility, Scientific Computing Facility, and Lab Support Facility for their services,\r\nand
technical support, all of which were important for the successful completion of
this project."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Manjunath
full_name: Javoor, Manjunath
id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2
last_name: Javoor
orcid: 0000-0003-2311-2112
citation:
ama: Javoor M. Large-scale imaging of cellular actin networks at single filament
resolution using montage cryo-electron tomography. 2026. doi:10.15479/AT-ISTA-22744
apa: Javoor, M. (2026). Large-scale imaging of cellular actin networks at single
filament resolution using montage cryo-electron tomography. Institute of Science
and Technology Austria . https://doi.org/10.15479/AT-ISTA-22744
chicago: Javoor, Manjunath. “Large-Scale Imaging of Cellular Actin Networks at Single
Filament Resolution Using Montage Cryo-Electron Tomography.” Institute of Science
and Technology Austria , 2026. https://doi.org/10.15479/AT-ISTA-22744.
ieee: M. Javoor, “Large-scale imaging of cellular actin networks at single filament
resolution using montage cryo-electron tomography,” Institute of Science and Technology
Austria , 2026.
ista: Javoor M. 2026. Large-scale imaging of cellular actin networks at single filament
resolution using montage cryo-electron tomography. Institute of Science and Technology
Austria .
mla: Javoor, Manjunath. Large-Scale Imaging of Cellular Actin Networks at Single
Filament Resolution Using Montage Cryo-Electron Tomography. Institute of Science
and Technology Austria , 2026, doi:10.15479/AT-ISTA-22744.
short: M. Javoor, Large-Scale Imaging of Cellular Actin Networks at Single Filament
Resolution Using Montage Cryo-Electron Tomography, Institute of Science and Technology
Austria , 2026.
corr_author: '1'
date_created: 2026-08-21T09:11:04Z
date_published: 2026-08-21T00:00:00Z
date_updated: 2026-10-20T08:55:33Z
day: '21'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: FlSc
- _id: MiSi
doi: 10.15479/AT-ISTA-22744
doi_confirm: '1'
file:
- access_level: closed
checksum: f9c2847df9f1ac5a3d60c06b3b81a450
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: mjavoor
date_created: 2026-08-26T12:02:47Z
date_updated: 2026-08-27T12:48:42Z
file_id: '22767'
file_name: 2026_Javoor_Manjunath_Thesis.docx
file_size: 27430796
relation: source_file
- access_level: closed
checksum: 8e9b4c0fcafbccf5c3796eacc9134a08
content_type: application/pdf
creator: mjavoor
date_created: 2026-08-26T12:02:46Z
date_updated: 2026-08-26T12:02:46Z
embargo: 2027-08-21
embargo_to: open_access
file_id: '22768'
file_name: 2026_Javoor_Manjunath_Thesis.pdf
file_size: 19489230
relation: main_file
file_date_updated: 2026-08-27T12:48:42Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22744
has_accepted_license: '1'
keyword:
- Actin cytoskeleton
- Cell migration
- cryo-electron tomography
language:
- iso: eng
month: '08'
oa_version: None
page: '121'
project:
- _id: bd980d18-d553-11ed-ba76-ceaa645c97eb
grant_number: '101076260'
name: A molecular atlas of Actin filament IDentities in the cell motility machinery
- _id: bd91e723-d553-11ed-ba76-fe7eeb2185fd
grant_number: '101071793'
name: 'Pushing from within: Control of cell shape, integrity and motility by cytoskeletal
pushing forces'
publication_identifier:
isbn:
- '978-3-99078-090-9 '
issn:
- 2663-337X
publication_status: published
publisher: 'Institute of Science and Technology Austria '
related_material:
record:
- id: '12334'
relation: part_of_dissertation
status: public
- id: '21762'
relation: part_of_dissertation
status: public
- id: '12421'
relation: part_of_dissertation
status: public
- id: '19795'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: Large-scale imaging of cellular actin networks at single filament resolution
using montage cryo-electron tomography
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20986'
abstract:
- lang: eng
text: During complex vocal interactions, different features of acoustic stimuli
are integrated to produce appropriate vocal responses,1 such as copying sounds
during vocal matching behavior in some animals.2,3,4,5,6,7,8,9,10,11,12 However,
little is known about the interplay and possible trade-offs between the different
temporal and spectral acoustic features during these vocal exchanges.2,13,14 Nightingales
can flexibly match the pitch of their tonal “whistle songs” in real time during
counter-singing duels.15,16 Here, we show that the syllable duration of whistle
playbacks could alter the song responses of wild nightingales, causing their whistle
duration distribution to shift toward the presented stimulus duration. When exposed
to whistle playbacks featuring unnatural combinations of pitch and duration, nightingales
demonstrate a flexible trade-off between pitch matching and temporal imitation,
yet they are constrained by their vocal repertoire. They selectively adapted their
vocal responses to approximate these novel stimuli, aligning them with their natural
whistle repertoire. We developed a computational model of nightingale whistle-matching
behavior that revealed a hierarchical organization of acoustic feature production.
During whistle matching, the feature integration process is constrained by the
duration of syllables, and pitch matching follows within this temporal framework,
forcing a trade-off between the two features. Our findings reveal a complex interplay
between the spectral and temporal domains that shapes song-matching behavior.
acknowledgement: 'We would like to thank J. Benichov and N. Hein for their help with
fieldwork; M. Ramadas for helping with the segmentation analysis; T. Eliav, C. Chintaluri,
G. Tkacik, and A. Navas for providing helpful comments to the project and manuscript;
and A. Costalunga for the drawings of nightingales. Funding sources: The Joachim
Herz Stiftung Add-on Fellowships for Interdisciplinary Life Science, awarded to
G.C.; the ERC Consolidator Grant 819603 SYNAPSEEK, awarded to T.P.V.; and DFG Research
Unit 5768–532521431, DFG Research Grant-547921981, DFG SFB 1315–327654276, and the
ERC Starting Grant 757459 MIDNIGHT, awarded to D.V.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Juan Sebastian
full_name: Calderon Garcia, Juan Sebastian
id: 1271b54b-dbcd-11ea-9d1d-d92da838fe2c
last_name: Calderon Garcia
- first_name: Giacomo
full_name: Costalunga, Giacomo
last_name: Costalunga
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Daniela
full_name: Vallentin, Daniela
last_name: Vallentin
citation:
ama: Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. Interplay between
syllable duration and pitch during whistle matching in wild nightingales. Current
Biology. 2026;36(3):791-798.e6. doi:10.1016/j.cub.2025.12.025
apa: Calderon Garcia, J. S., Costalunga, G., Vogels, T. P., & Vallentin, D.
(2026). Interplay between syllable duration and pitch during whistle matching
in wild nightingales. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2025.12.025
chicago: Calderon Garcia, Juan Sebastian, Giacomo Costalunga, Tim P Vogels, and
Daniela Vallentin. “Interplay between Syllable Duration and Pitch during Whistle
Matching in Wild Nightingales.” Current Biology. Cell Press, 2026. https://doi.org/10.1016/j.cub.2025.12.025.
ieee: J. S. Calderon Garcia, G. Costalunga, T. P. Vogels, and D. Vallentin, “Interplay
between syllable duration and pitch during whistle matching in wild nightingales,”
Current Biology, vol. 36, no. 3. Cell Press, p. 791–798.e6, 2026.
ista: Calderon Garcia JS, Costalunga G, Vogels TP, Vallentin D. 2026. Interplay
between syllable duration and pitch during whistle matching in wild nightingales.
Current Biology. 36(3), 791–798.e6.
mla: Calderon Garcia, Juan Sebastian, et al. “Interplay between Syllable Duration
and Pitch during Whistle Matching in Wild Nightingales.” Current Biology,
vol. 36, no. 3, Cell Press, 2026, p. 791–798.e6, doi:10.1016/j.cub.2025.12.025.
short: J.S. Calderon Garcia, G. Costalunga, T.P. Vogels, D. Vallentin, Current Biology
36 (2026) 791–798.e6.
das_tickbox: '1'
dataavailabilitystatement: "All data have been deposited at https://github.com/vallentinlab/NG-whistle-durations
and are publicly available as of the date of publication.\r\nAll original code has
been deposited at https://github.com/vallentinlab/NG-whistle-durations and is publicly
available as of the date of publication.\r\nAny additional information required
to reanalyze the data reported in this paper is available from the lead contact
upon request."
date_created: 2026-01-14T12:00:29Z
date_published: 2026-02-02T00:00:00Z
date_updated: 2026-10-20T09:02:18Z
day: '02'
ddc:
- '570'
- '577'
department:
- _id: GradSch
- _id: TiVo
doi: 10.1016/j.cub.2025.12.025
ec_funded: 1
external_id:
pmid:
- '41529680'
file:
- access_level: open_access
checksum: e17c3537193d5ab4886596d1a04f9b0e
content_type: application/pdf
creator: dernst
date_created: 2026-07-27T10:47:55Z
date_updated: 2026-07-27T10:47:55Z
file_id: '22416'
file_name: 2026_CurrentBiology_CalderonGarcia.pdf
file_size: 7120959
relation: main_file
success: 1
file_date_updated: 2026-07-27T10:47:55Z
fulldoi: https://doi.org/10.1016/j.cub.2025.12.025
has_accepted_license: '1'
intvolume: ' 36'
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 791-798.e6
pmid: 1
project:
- _id: 0aacfa84-070f-11eb-9043-d7eb2c709234
call_identifier: H2020
grant_number: '819603'
name: Learning the shape of synaptic plasticity rules for neuronal architectures
and function through machine learning.
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Interplay between syllable duration and pitch during whistle matching in wild
nightingales
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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: 36
year: '2026'
...
---
OA_type: closed access
_id: '22286'
abstract:
- lang: eng
text: Plants are remarkable organisms. Unlike animals, they cannot flee and, rooted
in one place, they must cope with whatever challenges arise — nutrient scarcity,
drought, shade, wind or obstacles in the soil. Their extraordinary ability to
survive in such unstable environmental conditions lies in their capacity to adapt.
In response to environmental signals, plants can rapidly adjust the rate of organ
growth, change the direction of growth, bend toward resources, or remodel their
body architecture by promoting or suppressing the formation of new organs such
as lateral roots, branches, leaves, or flowers. This unique developmental plasticity
depends on chemical signals, plant hormones that serve as regulators and coordinators
of endogenous molecular and cellular processes. Chief among these signals is auxin,
a plant hormone central to nearly every aspect of plant life.
article_processing_charge: No
article_type: original
author:
- first_name: Valentin
full_name: Leitner, Valentin
id: 4c665ce3-0016-11ec-bea0-e44de7a4fa3d
last_name: Leitner
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Leitner V, Benková E. Auxin and the control of plant growth and development.
Current Biology. 2026;36(13):R739-R744. doi:10.1016/j.cub.2026.04.047
apa: Leitner, V., & Benková, E. (2026). Auxin and the control of plant growth
and development. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2026.04.047
chicago: Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth
and Development.” Current Biology. Cell Press, 2026. https://doi.org/10.1016/j.cub.2026.04.047.
ieee: V. Leitner and E. Benková, “Auxin and the control of plant growth and development,”
Current Biology, vol. 36, no. 13. Cell Press, pp. R739–R744, 2026.
ista: Leitner V, Benková E. 2026. Auxin and the control of plant growth and development.
Current Biology. 36(13), R739–R744.
mla: Leitner, Valentin, and Eva Benková. “Auxin and the Control of Plant Growth
and Development.” Current Biology, vol. 36, no. 13, Cell Press, 2026, pp.
R739–44, doi:10.1016/j.cub.2026.04.047.
short: V. Leitner, E. Benková, Current Biology 36 (2026) R739–R744.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-07-13T09:39:40Z
date_published: 2026-07-06T00:00:00Z
date_updated: 2026-10-20T09:00:35Z
day: '06'
department:
- _id: EvBe
- _id: GradSch
doi: 10.1016/j.cub.2026.04.047
external_id:
pmid:
- '42407441'
fulldoi: https://doi.org/10.1016/j.cub.2026.04.047
intvolume: ' 36'
issue: '13'
language:
- iso: eng
month: '07'
oa_version: None
page: R739-R744
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Auxin and the control of plant growth and development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21746'
abstract:
- lang: eng
text: As vertebrates transitioned from water to land, locomotion shifted from undulatory
swimming to limb-based movement. How spinal circuits and their cell types evolved
to support this transition remains unclear. We leverage frog metamorphosis, which
recapitulates this transition within a single organism, to define how spinal circuits
generate aquatic versus terrestrial motor patterns. At swim stages, spinal architecture
is uniform, with a transcriptionally and anatomically homogeneous motor and interneurons.
As limbs develop and their movement complexifies, spinal circuits expand in neuron
number and subtype diversity. This expansion is most pronounced for V1 inhibitory
neurons, which increase ∼70-fold and diversify into transcriptionally distinct
subtypes. Disrupting transcription factors defining emerging motor and V1 populations
reveals molecular segregation between swim and limb circuits, highlighting the
role of subtype diversity in motor coordination. A multifold increase in inhibitory
neuron diversity thus underlies the tail-to-limb locomotor transition, providing
a framework for spinal circuit adaptation during vertebrate evolution.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: 'We would like to thank the members of the Sweeney Lab, Mario de
Bono, Michael Forsthofer, Katharina Lust, and Meital Oren, for comments on the manuscript.
We are also grateful to Tom Jessell and Chris Kintner for their scientific insight
and mentorship during the conception of this project. It would also have not been
possible without the technical support of the Aquatics and Imaging and Optics Facility
support teams (ISTA). We thank Martin Estermann for preparing the initial draft
of the graphical abstract and Niki Barolini for the final version. In addition,
we thank our funding sources for providing the resources to do these experiments:
GFF NÖ FTI Strategy Lower Austria dissertation grant FT121-D-046 (to D.V.), Horizon
Europe ERC starting grant 101041551 (to Y.I., L.B.S., F.A.T., and D.V.), Special
Research Program (SFB) of the Austrian Science Fund (FWF) project F7814-B (to L.B.S.),
Austrian Science Fund (FWF) 10.55776/COE16 (to Y.I. and L.B.S.), NINDS 5R35NS116858
(to J.S.D.), CZI grant DAF2020-225401 (DOI) 10.37921/120055ratwvi (to R.H.), NIH
grant R01NS123116 (to J.B.B.), American Lebanese Syrian Associated Charities (ALSAC)
(to J.B.B.), German Academic Exchange Service (DAAD) IFI grant 57515251-91853472
(to Z.H.), and Project A.L.S. (to S.B.-M.).'
article_number: '117227'
article_processing_charge: Yes
article_type: original
author:
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
orcid: 0000-0002-5494-0941
- first_name: 'Florina Alexandra '
full_name: 'Toma, Florina Alexandra '
id: 2f73f876-f128-11eb-9611-b96b5a30cb0e
last_name: Toma
- first_name: Y
full_name: Ignatyev, Y
last_name: Ignatyev
- first_name: Zoe P
full_name: Harrington, Zoe P
id: a8144562-32c9-11ee-b5ce-d9800628bda2
last_name: Harrington
orcid: 0009-0008-0158-4032
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Matthijs Geert
full_name: Smits, Matthijs Geert
id: 7a231d52-e216-11ee-a0bb-8acd55f8f1f0
last_name: Smits
- first_name: Marco
full_name: Dalla Vecchia, Marco
id: 02a7a869-ff06-11ed-a87f-86649d6077e5
last_name: Dalla Vecchia
- first_name: Alexandra J.
full_name: Trevisan, Alexandra J.
last_name: Trevisan
- first_name: Phillip
full_name: Chapman, Phillip
last_name: Chapman
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
last_name: Julseth
- first_name: Susan
full_name: Brenner-Morton, Susan
last_name: Brenner-Morton
- first_name: Mariano I.
full_name: Gabitto, Mariano I.
last_name: Gabitto
- first_name: Jeremy S.
full_name: Dasen, Jeremy S.
last_name: Dasen
- first_name: Jay B.
full_name: Bikoff, Jay B.
last_name: Bikoff
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Vijatovic D, Toma FA, Ignatyev Y, et al. Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. 2026;45(4). doi:10.1016/j.celrep.2026.117227
apa: Vijatovic, D., Toma, F. A., Ignatyev, Y., Harrington, Z. P., Sommer, C. M.,
Hauschild, R., … Sweeney, L. B. (2026). Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2026.117227
chicago: Vijatovic, David, Florina Alexandra Toma, Y Ignatyev, Zoe P Harrington,
Christoph M Sommer, Robert Hauschild, Matthijs Geert Smits, et al. “Multifold
Increase in Spinal Inhibitory Cell Types with Emergence of Limb Movement.” Cell
Reports. Cell Press, 2026. https://doi.org/10.1016/j.celrep.2026.117227.
ieee: D. Vijatovic et al., “Multifold increase in spinal inhibitory cell
types with emergence of limb movement,” Cell Reports, vol. 45, no. 4. Cell
Press, 2026.
ista: Vijatovic D, Toma FA, Ignatyev Y, Harrington ZP, Sommer CM, Hauschild R, Smits
MG, Dalla Vecchia M, Trevisan AJ, Chapman P, Julseth M, Brenner-Morton S, Gabitto
MI, Dasen JS, Bikoff JB, Sweeney LB. 2026. Multifold increase in spinal inhibitory
cell types with emergence of limb movement. Cell Reports. 45(4), 117227.
mla: Vijatovic, David, et al. “Multifold Increase in Spinal Inhibitory Cell Types
with Emergence of Limb Movement.” Cell Reports, vol. 45, no. 4, 117227,
Cell Press, 2026, doi:10.1016/j.celrep.2026.117227.
short: D. Vijatovic, F.A. Toma, Y. Ignatyev, Z.P. Harrington, C.M. Sommer, R. Hauschild,
M.G. Smits, M. Dalla Vecchia, A.J. Trevisan, P. Chapman, M. Julseth, S. Brenner-Morton,
M.I. Gabitto, J.S. Dasen, J.B. Bikoff, L.B. Sweeney, Cell Reports 45 (2026).
corr_author: '1'
date_created: 2026-04-19T22:07:43Z
date_published: 2026-04-28T00:00:00Z
date_updated: 2026-10-20T09:04:23Z
day: '28'
ddc:
- '570'
department:
- _id: LoSw
- _id: GradSch
- _id: TiVo
- _id: Bio
- _id: NiBa
doi: 10.1016/j.celrep.2026.117227
external_id:
pmid:
- '41964955 '
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month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
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grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: 8da85f50-16d5-11f0-9cad-eab8b0ff6c9e
grant_number: F7814
name: 'Stem Cell Modulation in Neural Development and Regeneration/ P14-Swim-to-limb
transition: cell type to connection diversity'
- _id: c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473
grant_number: CZI01
name: Tools for automation and feedback microscopy
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
- _id: cf428362-b037-11f1-b015-8277a8a2f63d
grant_number: COE16
name: Neuronal circuits in health and disease (Sweeney)
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
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relation: dissertation_contains
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scopus_import: '1'
status: public
title: Multifold increase in spinal inhibitory cell types with emergence of limb movement
tmp:
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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: 45
year: '2026'
...
---
OA_place: publisher
_id: '22258'
abstract:
- lang: eng
text: "Uncovering the genetic architecture of complex traits and pinpointing causal
molecular drivers require the ability to distinguish true signals from noise within
massive, high-dimensional omics datasets. To extract meaningful biological insights
from these datasets, such as identifying causal genetic variants and proteins,
scalable and accurate inference methods are essential. To this end, this thesis
develops novel Bayesian inference frameworks based on Vector Approximate Message
Passing and demonstrates their effectiveness in the modeling of disease onset
times and quantitative physical and clinical measures.\r\n\r\nFirst, we introduce
gVAMP, a Bayesian framework tailored for Genome-Wide Association Studies that
enables the joint modeling of quantitative complex traits across millions of genetic
variants. gVAMP demonstrates superior accuracy in variable selection and out-of-sample
polygenic risk prediction compared to state-of-the-art approaches. We model human
height using 17 million whole-genome sequence variants from the UK Biobank, incorporating
a vast number of rare variants and revealing novel associations. gVAMP achieves
a prediction accuracy of approximately 46% for human height, representing the
highest reported performance for this trait to date. \r\n\r\nSecond, we present
vampW, a Bayesian framework for survival analysis applied to proteomic data. By
effectively handling right-censoring and complex protein dependencies within the
UK Biobank Pharma Proteomics Project dataset, vampW identifies 219 protein associations
across 24 disease outcomes, the majority of which are not among the top marginal
discoveries. We further adjust protein levels for exponential age effects, yielding
1,308 associations and highlighting the sensitivity of the analysis to the chosen
age-correction methodology. Finally, vampW improves upon the variable selection
capabilities of the commonly used (penalized) variants of the Cox proportional
hazards model and delivers state-of-the-art out-of-sample prediction of disease
onset times.\r\n\r\nCollectively, these methods provide powerful tools for dissecting
the genetic architecture of complex traits and the proteomic drivers of disease
onset. Furthermore, by delivering accurate polygenic risk scores and precise predictions
of onset times, this work advances the capabilities of personalized medicine and
clinical risk stratification."
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported in part by the Swiss National Science Foundation
through the\r\nEccellenza Grant \"Improving estimation and prediction of common
complex disease risk\"\r\n(grant number PCEGP3_181181); the European Research Council
through the grant\r\n\"Inference in High Dimensions: Light-speed Algorithms and
Information Limits\" (grant\r\nnumber 101161364); and the Fondation Jean-Jacques
et Felicia Lopez-Loreta through the\r\nPrix Lopez-Loretta 2019.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Al
full_name: Depope, Al
id: 0b77531d-dbcd-11ea-9d1d-a8eee0bf3830
last_name: Depope
citation:
ama: 'Depope A. From sparse selection to risk prediction: Approximate message passing
for proteomic survival models and large-scale genomics. 2026. doi:10.15479/AT-ISTA-22258'
apa: 'Depope, A. (2026). From sparse selection to risk prediction: Approximate
message passing for proteomic survival models and large-scale genomics. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22258'
chicago: 'Depope, Al. “From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics.” Institute of
Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22258.'
ieee: 'A. Depope, “From sparse selection to risk prediction: Approximate message
passing for proteomic survival models and large-scale genomics,” Institute of
Science and Technology Austria, 2026.'
ista: 'Depope A. 2026. From sparse selection to risk prediction: Approximate message
passing for proteomic survival models and large-scale genomics. Institute of Science
and Technology Austria.'
mla: 'Depope, Al. From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics. Institute
of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22258.'
short: 'A. Depope, From Sparse Selection to Risk Prediction: Approximate Message
Passing for Proteomic Survival Models and Large-Scale Genomics, Institute of Science
and Technology Austria, 2026.'
corr_author: '1'
das_tickbox: '1'
date_created: 2026-07-10T13:27:20Z
date_published: 2026-07-11T00:00:00Z
date_updated: 2026-10-20T09:03:21Z
day: '11'
ddc:
- '576'
- '610'
- '006'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MaRo
- _id: MaMo
doi: 10.15479/AT-ISTA-22258
doi_confirm: '1'
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file_date_updated: 2026-07-13T14:56:41Z
fulldoi: https://doi.org/10.15479/AT-ISTA-22258
has_accepted_license: '1'
keyword:
- Approximate Message Passing
- GWAS
- Genomics
- Proteomics
- Survival modeling
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '169'
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
- _id: 911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf
grant_number: '101161364'
name: 'Inference in High Dimensions: Light-speed Algorithms and Information Limits'
- _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A
grant_number: PCEGP3_181181
name: Improving estimation and prediction of common complex disease risk
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21488'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
title: 'From sparse selection to risk prediction: Approximate message passing for
proteomic survival models and large-scale genomics'
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
_id: '22667'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "I am also grateful for the financial support that made this work
possible, including the\r\nEuropean Research Council (ERC Starting Grant 101041551),
the Austrian Science\r\nFund (FWF, Cluster of Excellence 10.55776/COE16), the GFF
Lower Austria FTI\r\nStrategy Dissertation Fellowship (FTI21-D-046), and the FENS/IBRO-PERC\r\nExchange
Fellowship. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: David
full_name: Vijatovic, David
id: cf391e77-ec3c-11ea-a124-d69323410b58
last_name: Vijatovic
orcid: 0000-0002-5494-0941
citation:
ama: Vijatovic D. Dissecting the molecular and functional basis of motor control
in the frog Xenopus laevis. 2026. doi:10.15479/AT-ISTA-22667
apa: Vijatovic, D. (2026). Dissecting the molecular and functional basis of motor
control in the frog Xenopus laevis. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-22667
chicago: Vijatovic, David. “Dissecting the Molecular and Functional Basis of Motor
Control in the Frog Xenopus Laevis.” Institute of Science and Technology Austria,
2026. https://doi.org/10.15479/AT-ISTA-22667.
ieee: D. Vijatovic, “Dissecting the molecular and functional basis of motor control
in the frog Xenopus laevis,” Institute of Science and Technology Austria, 2026.
ista: Vijatovic D. 2026. Dissecting the molecular and functional basis of motor
control in the frog Xenopus laevis. Institute of Science and Technology Austria.
mla: Vijatovic, David. Dissecting the Molecular and Functional Basis of Motor
Control in the Frog Xenopus Laevis. Institute of Science and Technology Austria,
2026, doi:10.15479/AT-ISTA-22667.
short: D. Vijatovic, Dissecting the Molecular and Functional Basis of Motor Control
in the Frog Xenopus Laevis, Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-08-10T13:44:30Z
date_published: 2026-08-10T00:00:00Z
date_updated: 2026-10-20T09:04:22Z
day: '10'
ddc:
- '573'
degree_awarded: PhD
department:
- _id: GradSch
- _id: LoSw
doi: 10.15479/AT-ISTA-22667
doi_confirm: '1'
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has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa_version: Published Version
page: '172'
project:
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: bd73af52-d553-11ed-ba76-912049f0ac7a
grant_number: FTI21-D-046
name: Development of V1 interneuron diversity during swim-to-walk transition of
Xenopus metamorphosis
- _id: 34a02c70-11ca-11ed-8bc3-fbfd2c86c88f
grant_number: 3(GG016346-01)
name: Development of Viral Vectors for Amphibian Gene Delivery and Manipulation
publication_identifier:
isbn:
- 978-3-99078-082-4
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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status: public
- id: '21746'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
title: Dissecting the molecular and functional basis of motor control in the frog
Xenopus laevis
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
_id: '22399'
alternative_title:
- ISTA Master’s Thesis
article_processing_charge: No
author:
- first_name: Aleksa
full_name: Spasić, Aleksa
id: ecee9d38-4040-11ef-8843-b941efb445d6
last_name: Spasić
citation:
ama: Spasić A. Studying the evolutionary systems biology of the lac operon. 2026.
doi:10.15479/AT-ISTA-22399
apa: Spasić, A. (2026). Studying the evolutionary systems biology of the lac
operon. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22399
chicago: Spasić, Aleksa. “Studying the Evolutionary Systems Biology of the Lac Operon.”
Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22399.
ieee: A. Spasić, “Studying the evolutionary systems biology of the lac operon,”
Institute of Science and Technology Austria, 2026.
ista: Spasić A. 2026. Studying the evolutionary systems biology of the lac operon.
Institute of Science and Technology Austria.
mla: Spasić, Aleksa. Studying the Evolutionary Systems Biology of the Lac Operon.
Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22399.
short: A. Spasić, Studying the Evolutionary Systems Biology of the Lac Operon, Institute
of Science and Technology Austria, 2026.
corr_author: '1'
das_tickbox: '0'
date_created: 2026-07-25T13:08:32Z
date_published: 2026-07-27T00:00:00Z
date_updated: 2026-10-21T07:47:08Z
day: '27'
ddc:
- '576'
degree_awarded: MS
department:
- _id: GradSch
- _id: GaTk
- _id: CaGu
doi: 10.15479/AT-ISTA-22399
doi_confirm: '1'
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language:
- iso: eng
month: '07'
oa_version: Published Version
page: '32'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
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
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Studying the evolutionary systems biology of the lac operon
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
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...
---
OA_place: publisher
_id: '22281'
abstract:
- lang: eng
text: "In this thesis, we took a look at networks, and more specifically, at networks
that change over time, whether those are networks in the distributed algorithms
sense of the word, or the graph algorithm sense. \r\n\r\nIn distributed algorithms,
we looked at two main problems. First, the broadcast problem: given n agents,
each agent is tasked to forward a (unique) message to every other agent. Agents
collaborate and can copy and forward all messages they have received up until
that point. Broadcast is achieved when one agent has successfully broadcast its
message to everyone else. We studied the case where the communication network
is controlled by an adversary, under the condition that the graph is rooted in
every round of communication. We show that the adversary can delay broadcast for
at most l\r\n(1 + √\r\n2)n\r\nm\r\n rounds, improving on the $O(n\\log\\log n)$
previous upper bound~\\cite{fugger2020radius}, and asymptotically matching the
$\\sim 1.5n$ lower bound~\\cite{schwarz2017linear}.\r\n\r\nWe then looked at the
stochastic version of the problem: here, the adversary -- parametrized by $k$
where $k=0$ signifies that the adversary has no control, and $k=n$ that the adversary
has full control -- can choose parts of the graph, and the graph is then completed
stochastically. Here, we are able to look at a stronger version of broadcast:
instead of having $n$ messages trying to be broadcast in parallel, we can assume
that only one message needs to be broadcasted. We show the bound $\\Theta(k+\\log
n)$.\r\n\r\nThen, we looked at undecided states dynamics in population protocols:
given a population of $n$ agents, where each initially holds an opinion among
$k$ different ones. In each round, two agents are chosen uniformly at random,
and can interact. If they have different opinions, they forget their opinions
and become undecided. If one of them is undecided while the other has an opinion,
they undecided agent copies they opinion of the decided one. The question is then,
how many interactions does it take for the whole population to share the same
opinion? We show a $\\Omega(kn\\log \\frac {\\sqrt n} {k \\log n})$ lower bound
\ for any $k = o\\left(\\frac {\\sqrt n}{\\log n}\\right)$.\r\nThis is tight for
any $ k \\le n^{\\frac 1 2 - \\epsilon}$, where $\\epsilon >0$ can be any small
constant, matching the known $O(kn\\log n)$ upper bound for $k = O\\left(\\frac
{\\sqrt n} {\\log ^2 n}\\right)$~\\cite{DBLP:conf/podc/AmirABBHKL23}.\r\n\r\nFinally,
in dynamic algorithms, we study the minimum cut problem: we are given a graph,
whose vertex set we want to partition into two subsets such that the number of
edges crossing from one subset to the other is minimized. Then, the graph can
be updated via edge insertions or deletions, and we must update the solution without
recomputing everything from scratch. We present an exact fully-dynamic minimum
cut algorithm that runs in $n^{o(1)}$ deterministic update time when the minimum
cut size is at most $2^{\\Theta(\\log^{3/4-c}n)}$ for any $c>0$, improving on
the previous algorithm~\\cite{DBLP:conf/soda/JinST24} whose minimum cut size limit
is $(\\log n)^{o(1)}$. Using sparsification and randomization techniques, we are
able to extend this to all values of the minimum cut in weighted graphs, at the
cost of a $(1+o(1))$-approximation ratio."
acknowledgement: "This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(MoDynStruct, No. 101019564)\r\n\"The Design and Evaluation of Modern Fully Dynamic
Data Structures\" , from the\r\nAustrian Science Fund (FWF) grant DOI 10.55776/I5982
\"Static and Dynamic Hierarchical\r\nGraph Decompositions\", and from the Austrian
Science Fund (FWF) and netIDEE SCIENCE\r\nproject P 33775-N, \"Fast Algorithms for
a Reactive Network Layer\".\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Antoine
full_name: El-Hayek, Antoine
id: 888a098e-fcac-11ee-aff7-d347be57b725
last_name: El-Hayek
orcid: 0000-0003-4268-7368
citation:
ama: 'El-Hayek A. Handling updates and failures: Dynamic graph algorithms and distributed
computing on dynamic networks. 2026. doi:10.15479/AT-ISTA-22281'
apa: 'El-Hayek, A. (2026). Handling updates and failures: Dynamic graph algorithms
and distributed computing on dynamic networks. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT-ISTA-22281'
chicago: 'El-Hayek, Antoine. “Handling Updates and Failures: Dynamic Graph Algorithms
and Distributed Computing on Dynamic Networks.” Institute of Science and Technology
Austria, 2026. https://doi.org/10.15479/AT-ISTA-22281.'
ieee: 'A. El-Hayek, “Handling updates and failures: Dynamic graph algorithms and
distributed computing on dynamic networks,” Institute of Science and Technology
Austria, 2026.'
ista: 'El-Hayek A. 2026. Handling updates and failures: Dynamic graph algorithms
and distributed computing on dynamic networks. Institute of Science and Technology
Austria.'
mla: 'El-Hayek, Antoine. Handling Updates and Failures: Dynamic Graph Algorithms
and Distributed Computing on Dynamic Networks. Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-22281.'
short: 'A. El-Hayek, Handling Updates and Failures: Dynamic Graph Algorithms and
Distributed Computing on Dynamic Networks, Institute of Science and Technology
Austria, 2026.'
corr_author: '1'
date_created: 2026-07-13T09:39:59Z
date_published: 2026-07-13T00:00:00Z
date_updated: 2026-10-21T08:05:35Z
day: '13'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: GradSch
- _id: MoHe
doi: 10.15479/AT-ISTA-22281
doi_confirm: '1'
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month: '07'
oa: 1
oa_version: Published Version
page: '244'
project:
- _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62
call_identifier: H2020
grant_number: '101019564'
name: The design and evaluation of modern fully dynamic data structures
- _id: bda196b2-d553-11ed-ba76-8e8ee6c21103
grant_number: I05982
name: Static and Dynamic Hierarchical Graph Decompositions
- _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe
grant_number: P33775
name: Fast Algorithms for a Reactive Network Layer
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publisher_comment: Sections 2.4 and 7.1 and chapter 6 are not CC-BY 4.0, they are
All Rights Reserved.
related_material:
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- id: '21720'
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- id: '22374'
relation: part_of_dissertation
status: public
- id: '22373'
relation: part_of_dissertation
status: public
- id: '18557'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Monika H
full_name: Henzinger, Monika H
id: 540c9bbd-f2de-11ec-812d-d04a5be85630
last_name: Henzinger
orcid: 0000-0002-5008-6530
title: 'Handling updates and failures: Dynamic graph algorithms and distributed computing
on dynamic networks'
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image: /images/cc_by.png
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type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: publisher
_id: '20991'
abstract:
- lang: eng
text: "Rapid local adaptation to new environments is critical for species persistence,
especially in introduced populations. The evolutionary success of these populations
is fundamentally dictated by the organization of genetic variation—the genomic
architecture—in the face of severe demographic constraints, such as the founder
effects and genetic bottlenecks that frequently accompany colonization. A central
question in evolutionary biology is whether rapid adaptation relies on major-effect
loci, such as chromosomal inversions, or on many small-effect loci dispersed across
the genome. Furthermore, the genomic architecture strongly influences the extent
to which evolutionary outcomes are predictable. Using introduced populations of
the marine snail, Littorina saxatilis, as a model, this thesis investigates how
genetic variation and genomic structure drive adaptation following introduction.
We employed a population genomics approach on experimentally and accidentally
introduced populations to dissect the specific genomic features that underpin
divergence in newly colonized environments.\r\n\r\nIn Chapter 2, we tested the
predictability of local adaptation through an uncommon 30-year transplant experiment
in nature. By distinguishing allele and chromosomal inversion frequency changes
from neutral expectations, we found that evolutionary change was highly predictable
at the macro-scale (phenotypes and chromosomal inversions), but less robust at
the level of individual collinear loci. This result demonstrates that evolution
can be predictable when a population possesses sufficient standing genetic variation
(SGV), with chromosomal inversions acting as key integrated units that facilitate
a rapid response to selection. Building on this, Chapter 3 applied whole-genome
sequencing to three accidentally introduced populations (Venice, San Francisco,
and Redwood City) to investigate their likely source and genomic patterns of divergence.
We identified genomic regions of remarkable divergence potentially associated
with local adaptation, and likely fuelled by SGV, while explicitly acknowledging
the difficulty in disentangling selection signals from the genome-wide effects
of demographic processes. Furthermore, we found that the divergence patterns relied
extensively on the collinear genome in these introduced populations, and less
clearly on the chromosomal inversions. This observation contrasts with local adaptation
observed in the experimental system that relied on both collinear loci and highly
selected chromosomal inversions, highlighting how demographic history and genomic
architecture influence the detectable signature of local adaptation.\r\n\r\nA
major limitation to conducting large-scale comparative evolutionary studies is
the lack of data standardization, which prevents the integration of community
knowledge and high-resolution environmental and genetic data. Chapter 4 addresses
this by developing a community database for the Littorina system. This platform
implements standardized protocols for the integration of diverse phenotypic and
environmental data from multiple Littorina species. Likewise, the platform also
centralizes the availability of associated genomic data through links to external
repositories. This database represents a crucial tool to test complex, large-scale
evolutionary hypotheses.\r\n\r\nCollectively, this thesis strongly reinforces
the fundamental importance of SGV as the raw material for successful local adaptation,
a conclusion supported by evidence in both experimental and accidental introductions.
Furthermore, this work highlights the critical role of the genomic architecture—specifically
chromosomal inversions—in driving the predictability and effectiveness of adaptive
responses. Our findings underscore how the interplay between SGV and genomic architecture
dictates the trajectory and detectability of evolution in colonizing populations,
while simultaneously providing a necessary tool to advance comparative evolutionary
genomics in emerging model organisms."
acknowledgement: "I acknowledge the funding agencies 1Norwegian Research Council RCN
project 315287.\r\n2The FIASCO project \"Illuminating range shifts through evolutionary
FIASCO: contrasting\r\nFaIling And Successful ColOnizations in replicated wild populations\",
funded by the\r\nEuropean Union - Next Generation EU (Piano Nazionale di Ripresa
e Resilienza - MUR\r\ncode: P202229JBC, CUP: C53D23007100001). 3Ecotypic formation
in Littorina saxatilis\r\nin the Western Atlantic and comparisons across the North
Atlantic. University of\r\nGothenburg Research Travel Grant, Tjarno Marine Laboratory,
Sweden. $3023 (2018).\r\n4JIN project (Young Researchers, Spanish Ministry of Science,
RTI2018-101274-J-I00)"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Diego Fernando
full_name: Garcia Castillo, Diego Fernando
id: ae681a14-dc74-11ea-a0a7-c6ef18161701
last_name: Garcia Castillo
citation:
ama: Garcia Castillo DF. The genomic architecture of local adaptation in introduced
populations. 2026. doi:10.15479/AT-ISTA-20991
apa: Garcia Castillo, D. F. (2026). The genomic architecture of local adaptation
in introduced populations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20991
chicago: Garcia Castillo, Diego Fernando. “The Genomic Architecture of Local Adaptation
in Introduced Populations.” Institute of Science and Technology Austria, 2026.
https://doi.org/10.15479/AT-ISTA-20991.
ieee: D. F. Garcia Castillo, “The genomic architecture of local adaptation in introduced
populations,” Institute of Science and Technology Austria, 2026.
ista: Garcia Castillo DF. 2026. The genomic architecture of local adaptation in
introduced populations. Institute of Science and Technology Austria.
mla: Garcia Castillo, Diego Fernando. The Genomic Architecture of Local Adaptation
in Introduced Populations. Institute of Science and Technology Austria, 2026,
doi:10.15479/AT-ISTA-20991.
short: D.F. Garcia Castillo, The Genomic Architecture of Local Adaptation in Introduced
Populations, Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-01-16T09:47:59Z
date_published: 2026-01-16T00:00:00Z
date_updated: 2026-10-21T08:18:21Z
day: '16'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT-ISTA-20991
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date_updated: 2026-01-16T13:08:14Z
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LittorinaDB web application developed as a product of the 4th chapter of the thesis.
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has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
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page: '199'
publication_identifier:
isbn:
- 978-3-99078-077-0
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
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status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
title: The genomic architecture of local adaptation in introduced populations
tmp:
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short: CC BY-NC-SA (4.0)
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2026'
...
---
OA_place: publisher
_id: '22684'
abstract:
- lang: eng
text: "Contact electrification (CE) is a simple yet elusive phenomenon that occurs
when two materials come into contact and separate, leaving behind net electrical
charge. Despite its ubiquity, the microscopic origin of CE remains unclear. In
this thesis, we investigate CE from three complementary perspectives: developing
a quantitative method to measure charge at the nanoscale, exploring the dynamic
behavior of charge on insulating surfaces, and uncovering the role of mechanical
history in forming a triboelectric series.\r\n\r\nIn the first part, we establish
a rigorous framework for converting qualitative Kelvin probe force microscopy
(KPFM) voltage maps into quantitative charge density distributions. Using finite
element method (FEM) simulations, we determine the point-spread function of the
KPFM tip–sample geometry and demonstrate that the true surface charge can be reconstructed
by numerical deconvolution. This procedure enables the recovery of both the magnitude
and sign of charge density with high fidelity, resolving nanoscale features that
are otherwise obscured. Applying the method to contact-charged SiO$_2$ surfaces,
we show that existing analytical approximations, such as parallel plate or spherical
models, can miscalculate charge magnitude by orders of magnitude. Our hybrid FEM/KPFM
approach therefore provides a fast and general method to convert qualitative KPFM
signals into quantitative charge data, enabling nanoscale charge mapping under
realistic experimental conditions.\r\n\r\nIn the second part, we study the temporal
stability of CE-induced charges and identify the key material factors that determine
whether KPFM can capture meaningful charge patterns. Through time-resolved experiments
combining a custom-built transfer system with both microscopic and macroscopic
measurements, we demonstrate that only the best insulators, such as SiO$_2$, preserve
CE charge long enough for stationary imaging. For less conductive polymers, such
as PDMS, charge decays within the duration of a single KPFM scan due to bulk conduction.
Using a simple capacitor-based model, we reproduce the observed decay dynamics
and confirm that the transferred charge decays characteristic to the sample's
bulk conductivity. Further, we always observe homogeneous charge transfer.\r\n\r\nIn
the third part, we address the question: can we form a triboelectric series with
identical materials? Using controlled repetitive contact experiments, we show
that nominally identical materials can progressively order themselves into a triboelectric
series, where surfaces with more contact history charge negatively relative to
fresher ones. By constructing a minimal model based on this ``contact bias'',
we replicate the evolution from random to ordered charging observed in experiments.
Supporting surface analyses, including atomic force microscopy, reveal that repeated
contact induces nanoscale morphological changes, suggesting a mechanism tightly
coupled to mechanical strain. These results highlight the crucial role of surface
history and nanoscale mechanics in dictating charge transfer, motivating further
exploration of mechanisms such as mechanochemical bond cleavage and flexoelectric
polarization."
acknowledged_ssus:
- _id: NanoFab
- _id: ScienComp
- _id: LifeSc
- _id: M-Shop
- _id: EM-Fac
acknowledgement: "This project has received financing from the European Research Council
grant agreement\r\nno. 949120 under the European Union’s Horizon 2020 research and
innovation programme.\r\nThis research was supported by the Scientific Service Units
of The Institute of Science\r\nand Technology Austria (ISTA) through resources provided
by the Miba Machine Shop, the\r\nNanofabrication Facility, the Lab Support Facility,
the Scientific Computing Facility and the\r\nElectron Microscopy Facility. We thank
Florian Stumpf from Park Systems for useful discussions\r\nand support with scanning
probe microscopy. We thank Joaquin Garcia-Suarez and Guillaume\r\nAnciaux for the
suggestion to look into the roughness power spectral density. We thank\r\nIrina-Malina
Strugaru for help with testing the device for Young’s modulus measurements.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Felix
full_name: Pertl, Felix
id: 6313aec0-15b2-11ec-abd3-ed67d16139af
last_name: Pertl
orcid: 0000-0003-0463-5794
citation:
ama: Pertl F. Experimental probing of nanoscale charge features and surface morphology
changes during tribocharging. 2026. doi:10.15479/AT-ISTA-22684
apa: Pertl, F. (2026). Experimental probing of nanoscale charge features and
surface morphology changes during tribocharging. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT-ISTA-22684
chicago: Pertl, Felix. “Experimental Probing of Nanoscale Charge Features and Surface
Morphology Changes during Tribocharging.” Institute of Science and Technology
Austria, 2026. https://doi.org/10.15479/AT-ISTA-22684.
ieee: F. Pertl, “Experimental probing of nanoscale charge features and surface morphology
changes during tribocharging,” Institute of Science and Technology Austria, 2026.
ista: Pertl F. 2026. Experimental probing of nanoscale charge features and surface
morphology changes during tribocharging. Institute of Science and Technology Austria.
mla: Pertl, Felix. Experimental Probing of Nanoscale Charge Features and Surface
Morphology Changes during Tribocharging. Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-22684.
short: F. Pertl, Experimental Probing of Nanoscale Charge Features and Surface Morphology
Changes during Tribocharging, Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-08-12T09:44:40Z
date_published: 2026-08-12T00:00:00Z
date_updated: 2026-10-21T08:39:24Z
day: '12'
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degree_awarded: PhD
department:
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doi: 10.15479/AT-ISTA-22684
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call_identifier: H2020
grant_number: '949120'
name: 'Tribocharge: a multi-scale approach to an enduring problem in physics'
publication_identifier:
isbn:
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issn:
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publisher: Institute of Science and Technology Austria
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status: public
status: public
supervisor:
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
title: Experimental probing of nanoscale charge features and surface morphology changes
during tribocharging
tmp:
image: /images/cc_by.png
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name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_place: repository
OA_type: green
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abstract:
- lang: eng
text: Reactive oxygen species (ROS) have been implicated in multiple signaling processes
in plants, but the underlying mechanisms and roles remain enigmatic. In this study,
we developed a method of live imaging of apoplastic ROS at the root surface. Distinct
signals, including auxin, extracellular adenosine triphosphate, and rapid alkalinization
factor 1 peptide, induce cytosolic calcium transients and apoplastic ROS bursts.
Genetic and optogenetic manipulations of Arabidopsis identified calcium transients
as necessary and sufficient for ROS bursts through activation of reduced nicotinamide
adenine dinucleotide phosphate (NADPH) oxidases RBOHC and RBOHF. Apoplastic ROS
bursts are not required, but they do limit gravity-induced root bending. Root
bending is sensed by the stretch-activated calcium channel MCA1, leading to NADPH
oxidase activation. The resulting ROS production stiffens cell walls to facilitate
soil penetration. Apoplastic ROS thus provides a means to balance tissue flexibility
and stiffness to navigate soil.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We gratefully acknowledge the Lab Support Facility (LSF) and the
Imaging and Optics Facility (IOF) (both of ISTA) and the Hounsfield CT Facility
(University of Nottingham) for support with imaging and the Growth Facility (IPMB)
for plant cultivation. We thank M. Fendrych and his team for help with the microfluidics
upgrades and J. Atkinson at the University of Nottingham MakerSpace for 3D printing
of Arabidopsis mini-soil columns.\r\nThis project received funding from the European
Research Council (ERC; 101142681 CYNIPS) and the Austrian Science Fund (FWF; P 37051-B).
I.K. was cofunded by the European Union, Horizon Europe, project MOLIPEC, ID 101087030
and CSF project 25-16449S. L.V. and B.K.P. acknowledge funding from UK Research
and Innovation (UKRI) Frontiers Research (EP/Y036697/1). M.J.B. acknowledges funding
from ERC SYNERGY (grant 101118769 HYDROSENSING). The study was partially supported
by the Université Paris Cité, Idex ANR-18-IDEX-0001, funded by the French Government
through its “Investments for the Future” program and also by the projects “Mecha-Nuc”
ANR-20-CE13-0025-03 and “scEm-bryoMech” ANR-21-CE13-0046. P.D. acknowledges support
by Human Frontier Science Program Organization grant 2022-RG107. P.V. acknowledges
support provided by “Programme blanc” of the Graduate School BIOSPHERA, Université
Paris-Saclay. Phytohormonal analysis was performed using the service laboratory
funded by Toward Next GENeration Crops, reg. no. CZ.02.01.01/00/22_008/0004581 of
the European Regional Development Fund (ERDF) program Johannes Amos Comenius. This
research was funded in whole or in part by the Austrian Science Fund (P 37051-B)
and UK Research and Innovation (EP/Y036697/1), cOAlition S organizations, and by
the European Research Council (101142681 CYNIPS, 101118769 HYDROSENSING); as required,
the author will make the Author Accepted Manuscript (AAM) version available under
a CC BY public copyright license."
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Kulich, Ivan
id: 57a1567c-8314-11eb-9063-c9ddc3451a54
last_name: Kulich
- first_name: Dmitrii
full_name: Vladimirtsev, Dmitrii
id: 60466724-5355-11ee-ae5a-fa55e8f99c3d
last_name: Vladimirtsev
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
- first_name: Shiqiang
full_name: Gao, Shiqiang
last_name: Gao
- first_name: Matteo
full_name: Citterico, Matteo
last_name: Citterico
- first_name: Kai R.
full_name: Konrad, Kai R.
last_name: Konrad
- first_name: Georg
full_name: Nagel, Georg
last_name: Nagel
- first_name: Michael
full_name: Wrzaczek, Michael
last_name: Wrzaczek
- first_name: Léa
full_name: Cascaro, Léa
last_name: Cascaro
- first_name: Pauline
full_name: Vinet, Pauline
last_name: Vinet
- first_name: Pauline
full_name: Durand, Pauline
last_name: Durand
- first_name: Atef
full_name: Asnacios, Atef
last_name: Asnacios
- first_name: Lokesh
full_name: Verma, Lokesh
last_name: Verma
- first_name: Malcolm J.
full_name: Bennett, Malcolm J.
last_name: Bennett
- first_name: Bipin K.
full_name: Pandey, Bipin K.
last_name: Pandey
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kulich I, Vladimirtsev D, Randuch M, et al. Calcium-triggered apoplastic ROS
bursts balance gravity and mechanical signals for soil navigation. Science.
2026;392(6795):296-300. doi:10.1126/science.adu8197
apa: Kulich, I., Vladimirtsev, D., Randuch, M., Gao, S., Citterico, M., Konrad,
K. R., … Friml, J. (2026). Calcium-triggered apoplastic ROS bursts balance gravity
and mechanical signals for soil navigation. Science. AAAS. https://doi.org/10.1126/science.adu8197
chicago: Kulich, Ivan, Dmitrii Vladimirtsev, Marek Randuch, Shiqiang Gao, Matteo
Citterico, Kai R. Konrad, Georg Nagel, et al. “Calcium-Triggered Apoplastic ROS
Bursts Balance Gravity and Mechanical Signals for Soil Navigation.” Science.
AAAS, 2026. https://doi.org/10.1126/science.adu8197.
ieee: I. Kulich et al., “Calcium-triggered apoplastic ROS bursts balance
gravity and mechanical signals for soil navigation,” Science, vol. 392,
no. 6795. AAAS, pp. 296–300, 2026.
ista: Kulich I, Vladimirtsev D, Randuch M, Gao S, Citterico M, Konrad KR, Nagel
G, Wrzaczek M, Cascaro L, Vinet P, Durand P, Asnacios A, Verma L, Bennett MJ,
Pandey BK, Friml J. 2026. Calcium-triggered apoplastic ROS bursts balance gravity
and mechanical signals for soil navigation. Science. 392(6795), 296–300.
mla: Kulich, Ivan, et al. “Calcium-Triggered Apoplastic ROS Bursts Balance Gravity
and Mechanical Signals for Soil Navigation.” Science, vol. 392, no. 6795,
AAAS, 2026, pp. 296–300, doi:10.1126/science.adu8197.
short: I. Kulich, D. Vladimirtsev, M. Randuch, S. Gao, M. Citterico, K.R. Konrad,
G. Nagel, M. Wrzaczek, L. Cascaro, P. Vinet, P. Durand, A. Asnacios, L. Verma,
M.J. Bennett, B.K. Pandey, J. Friml, Science 392 (2026) 296–300.
corr_author: '1'
date_created: 2026-04-26T22:01:47Z
date_published: 2026-04-16T00:00:00Z
date_updated: 2026-10-22T09:15:44Z
day: '16'
ddc:
- '580'
department:
- _id: JiFr
- _id: GradSch
doi: 10.1126/science.adu8197
external_id:
pmid:
- '41990180'
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oa_version: Accepted Version
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grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
- _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6
grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
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publication_identifier:
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- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: AAAS
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related_material:
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Calcium-triggered apoplastic ROS bursts balance gravity and mechanical signals
for soil navigation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 392
year: '2026'
...
---
OA_place: publisher
_id: '23145'
acknowledged_ssus:
- _id: LifeSc
- _id: M-Shop
- _id: CampIT
- _id: Bio
acknowledgement: "European Research Council (101142681 CYNIPS), Cyclic nucleotides
as second messengers \r\nin plants, DOI: https://doi.org/10.3030/101142681 \r\nAustrian
Science Fund (P 37051-B), Guanylate cyclase activity of TIR1/AFBs auxin receptors,
\r\nDOI: https://doi.org/10.55776/P37051 "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marek
full_name: Randuch, Marek
id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae
last_name: Randuch
citation:
ama: 'Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic
. 2026. doi:10.15479/AT-ISTA-23145'
apa: 'Randuch, M. (2026). Fast growth responses in plants: Growth regulation
and phospho-proteomic . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-23145'
chicago: 'Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and
Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-23145.'
ieee: 'M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic
,” Institute of Science and Technology Austria, 2026.'
ista: 'Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic
. Institute of Science and Technology Austria.'
mla: 'Randuch, Marek. Fast Growth Responses in Plants: Growth Regulation and
Phospho-Proteomic . Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-23145.'
short: 'M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic
, Institute of Science and Technology Austria, 2026.'
corr_author: '1'
date_created: 2026-10-16T17:14:40Z
date_published: 2026-10-18T00:00:00Z
date_updated: 2026-10-22T09:15:44Z
day: '18'
ddc:
- '580'
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license: https://creativecommons.org/licenses/by-sa/4.0/
month: '10'
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page: '289'
project:
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grant_number: P37051
name: Guanylate cyclase activity of TIR1/AFBs auxin receptors
- _id: 8f347782-16d5-11f0-9cad-8c19706ee739
grant_number: '101142681'
name: Cyclic nucleotides as second messengers in plants
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
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relation: part_of_dissertation
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- id: '21763'
relation: part_of_dissertation
status: public
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relation: part_of_dissertation
status: public
- id: '23174'
relation: part_of_dissertation
status: public
- id: '20656'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: 'Fast growth responses in plants: Growth regulation and phospho-proteomic '
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '18706'
abstract:
- lang: eng
text: "We prove discrete-to-continuum convergence for dynamical optimal transport
on Zd\r\n -periodic graphs with cost functional having linear growth at infinity.
This result provides an answer to a problem left open by Gladbach, Kopfer, Maas,
and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the
convergence behaviour of discrete boundary-value dynamical transport problems
is proved under the stronger assumption of superlinear growth. Our result extends
the known literature to some important classes of examples, such as scaling limits
of 1 -Wasserstein transport problems. Similarly to what happens in the quadratic
case, the geometry of the graph plays a crucial role in the structure of the limit
cost function, as we discuss in the final part of this work, which includes some
visual representations."
acknowledgement: L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft
(DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1,
Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science
Fund (FWF) project 10.55776/F65.
article_processing_charge: Yes
article_type: original
author:
- first_name: Lorenzo
full_name: Portinale, Lorenzo
id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
last_name: Portinale
- first_name: Filippo
full_name: Quattrocchi, Filippo
id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308
last_name: Quattrocchi
orcid: 0009-0000-9773-1931
citation:
ama: Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport
with linear growth on periodic graphs. European Journal of Applied Mathematics.
2026;37(3):614-642. doi:10.1017/s0956792524000810
apa: Portinale, L., & Quattrocchi, F. (2026). Discrete-to-continuum limits of
optimal transport with linear growth on periodic graphs. European Journal of
Applied Mathematics. Cambridge University Press. https://doi.org/10.1017/s0956792524000810
chicago: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits
of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal
of Applied Mathematics. Cambridge University Press, 2026. https://doi.org/10.1017/s0956792524000810.
ieee: L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal
transport with linear growth on periodic graphs,” European Journal of Applied
Mathematics, vol. 37, no. 3. Cambridge University Press, pp. 614–642, 2026.
ista: Portinale L, Quattrocchi F. 2026. Discrete-to-continuum limits of optimal
transport with linear growth on periodic graphs. European Journal of Applied Mathematics.
37(3), 614–642.
mla: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits
of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal
of Applied Mathematics, vol. 37, no. 3, Cambridge University Press, 2026,
pp. 614–42, doi:10.1017/s0956792524000810.
short: L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics 37
(2026) 614–642.
das_tickbox: '0'
date_created: 2024-12-23T11:03:59Z
date_published: 2026-06-01T00:00:00Z
date_updated: 2026-10-26T23:31:03Z
day: '01'
ddc:
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date_created: 2026-07-23T05:55:03Z
date_updated: 2026-07-23T05:55:03Z
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success: 1
file_date_updated: 2026-07-23T05:55:03Z
fulldoi: https://doi.org/10.1017/s0956792524000810
has_accepted_license: '1'
intvolume: ' 37'
isi: 1
issue: '3'
keyword:
- optimal transport
- discrete-to-continuum
- homogenisation
- linear growth
- gamma-convergence
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 614-642
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
publication: European Journal of Applied Mathematics
publication_identifier:
eissn:
- 1469-4425
issn:
- 0956-7925
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
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researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: Discrete-to-continuum limits of optimal transport with linear growth on periodic
graphs
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 37
year: '2026'
...
---
OA_place: repository
_id: '21423'
abstract:
- lang: eng
text: "Biological systems, such as cytoskeletal filaments and multicellular collectives,
exhibit rich \r\nself-organization driven by their intrinsic activity and physical
constraints. Across scales, \r\ngeometry plays a central role: the shape of active
units and the structure of their environment \r\nstrongly influence how order
emerges in these far-from-equilibrium systems. In this thesis, \r\nwe combine
minimal active-matter models with bottom-up in vitro experiments to identify \r\nthe
principles by which geometry and activity shape collective behavior in biological
matter. \r\nAt the subcellular scale, we investigate how the physical properties
of chiral FtsZ filaments \r\ngovern their large-scale organization. Using a mesoscopic
model validated by reconstituted \r\nfilament assays, we show that filament shape,
intrinsic curvature, and flexibility, together with \r\nactivity-driven straightening,
determine whether filaments form chiral rings, polar bands, or \r\nnematic-like
states. Our model shows that small changes in filament mechanics produce large
\r\nshifts in collective structures, revealing how the geometry of individual
filaments amplifies \r\nthrough activity to control patterns relevant for bacterial
cytokinesis. \r\nAt the cellular scale, we examine how geometry of the external
environment influences \r\ncollective cancer cell migration. Experiments in controlled
microfabricated obstacle \r\nenvironments demonstrate that geometric disorder
alone can induce a transition from \r\ncollective to single-cell invasion. A minimal
model of active particles in disordered geometries \r\nreproduces these effects,
demonstrating that cell dissemination results both from local \r\ngeometrical
constraints and a global integration of spatial disorder over time. Surprisingly,
\r\nthis transition is accompanied by a change in the universality class of interface
dynamics, \r\nrevealing that cell-environment interactions can shift the collective
behavior of an invasive \r\nfront purely through mechanics. \r\nIn the last system,
we study how cell-intrinsic geometry and chirality affect collective motion \r\nin
confined and unconfined settings. Using a minimal model inspired by in vitro experiments,
\r\nwe analyze motile cells that exhibit persistent rotation due to intrinsic
left-right asymmetry. \r\nIn circular confinement, this simplified chiral model
reproduces several experimentally \r\nobserved features within specific parameter
regimes. At high densities in unconfined \r\nenvironments, however, intrinsic
chirality becomes masked even before the onset of the \r\njamming transition.
These results show that single-cell geometric asymmetry does not \r\nnecessarily
translate into large-scale chiral flows, offering new insight into how forces
and \r\nsymmetries shape collective motion in dense cellular systems. \r\nOverall,
this work uncovers how geometric constraints – embedded in the intrinsic \r\narchitecture
of an active filament or encoded in the complexity of a microenvironment \r\ncouple
to active forces to generate different classes of complex behaviors. "
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Finally, I gratefully acknowledge funding from the DOC Fellowship
of the Austrian Academy\r\nof Sciences (OeAW): grant agreement 26360."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Zuzana
full_name: Dunajova, Zuzana
id: 4B39F286-F248-11E8-B48F-1D18A9856A87
last_name: Dunajova
citation:
ama: Dunajova Z. Geometry-driven self-organization of migrating cells and chiral
filaments. 2026. doi:10.15479/AT-ISTA-21423
apa: Dunajova, Z. (2026). Geometry-driven self-organization of migrating cells
and chiral filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21423
chicago: Dunajova, Zuzana. “Geometry-Driven Self-Organization of Migrating Cells
and Chiral Filaments.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21423.
ieee: Z. Dunajova, “Geometry-driven self-organization of migrating cells and chiral
filaments,” Institute of Science and Technology Austria, 2026.
ista: Dunajova Z. 2026. Geometry-driven self-organization of migrating cells and
chiral filaments. Institute of Science and Technology Austria.
mla: Dunajova, Zuzana. Geometry-Driven Self-Organization of Migrating Cells and
Chiral Filaments. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-21423.
short: Z. Dunajova, Geometry-Driven Self-Organization of Migrating Cells and Chiral
Filaments, Institute of Science and Technology Austria, 2026.
corr_author: '1'
date_created: 2026-03-11T08:30:49Z
date_published: 2026-03-11T00:00:00Z
date_updated: 2026-10-16T08:12:11Z
day: '11'
ddc:
- '539'
- '570'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EdHa
doi: 10.15479/AT-ISTA-21423
doi_confirm: '1'
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month: '03'
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grant_number: '26360'
name: Motile active matter models of migrating cells and chiral filaments
publication_identifier:
isbn:
- 978-3-99078-076-3
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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supervisor:
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
title: Geometry-driven self-organization of migrating cells and chiral filaments
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