---
OA_place: repository
OA_type: green
_id: '20056'
abstract:
- lang: eng
text: Theoretical studies have shown that stochasticity can affect the dynamics
of ecosystems in counterintuitive ways. However, without knowing the equations
governing the dynamics of populations or ecosystems, it is difficult to ascertain
the role of stochasticity in real datasets. Therefore, the inverse problem of
inferring the governing stochastic equations from datasets is important. Here,
we present an equation discovery methodology that takes time series data of state
variables as input and outputs a stochastic differential equation. We achieve
this by combining traditional approaches from stochastic calculus with the equation
discovery techniques. We demonstrate the generality of the method via several
applications. First, we deliberately choose various stochastic models with fundamentally
different governing equations, yet they produce nearly identical steady-state
distributions. We show that we can recover the correct underlying equations, and
thus infer the structure of their stability, accurately from the analysis of time
series data alone. We demonstrate our method on two real-world datasets—fish schooling
and single-cell migration—that have vastly different spatiotemporal scales and
dynamics. We illustrate various limitations and potential pitfalls of the method
and how to overcome them via diagnostic measures. Finally, we provide our open-source
code via a package named PyDaDDy (Python Library for Data-Driven Dynamics).
acknowledgement: V.G. acknowledges support from the Science and Engi-neering Research
Board, Department of Biotechnology,and the Indo-French Centre for the Promotion
of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of
Science and Technology (DST) In-novation in Science Pursuit for Inspired Research
(IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral
fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B.
acknowledges support from the NOMIS Founda-tion and an European Molecular Biology
Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge
support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar,
Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments
on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada
translation of the title and abstract.Data-Driven Model Discovery E115
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Arshed
full_name: Nabeel, Arshed
last_name: Nabeel
- first_name: Ashwin
full_name: Karichannavar, Ashwin
last_name: Karichannavar
- first_name: Shuaib
full_name: Palathingal, Shuaib
last_name: Palathingal
- first_name: Jitesh
full_name: Jhawar, Jitesh
last_name: Jhawar
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Danny
full_name: Raj M, Danny
last_name: Raj M
- first_name: Vishwesha
full_name: Guttal, Vishwesha
last_name: Guttal
citation:
ama: Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical
equations from ecological time series data. The American Naturalist. 2025;205(4):E100-E117.
doi:10.1086/734083
apa: Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj
M, D., & Guttal, V. (2025). Discovering stochastic dynamical equations from
ecological time series data. The American Naturalist. University of Chicago
Press. https://doi.org/10.1086/734083
chicago: Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar,
David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical
Equations from Ecological Time Series Data.” The American Naturalist. University
of Chicago Press, 2025. https://doi.org/10.1086/734083.
ieee: A. Nabeel et al., “Discovering stochastic dynamical equations from
ecological time series data,” The American Naturalist, vol. 205, no. 4.
University of Chicago Press, pp. E100–E117, 2025.
ista: Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal
V. 2025. Discovering stochastic dynamical equations from ecological time series
data. The American Naturalist. 205(4), E100–E117.
mla: Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological
Time Series Data.” The American Naturalist, vol. 205, no. 4, University
of Chicago Press, 2025, pp. E100–17, doi:10.1086/734083.
short: A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj
M, V. Guttal, The American Naturalist 205 (2025) E100–E117.
date_created: 2025-07-21T08:37:27Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-09-30T14:14:43Z
day: '01'
department:
- _id: EdHa
doi: 10.1086/734083
external_id:
arxiv:
- '2205.02645'
isi:
- '001433250500001'
pmid:
- '40179429'
intvolume: ' 205'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2205.02645
month: '04'
oa: 1
oa_version: Preprint
page: E100-E117
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: The American Naturalist
publication_identifier:
eissn:
- 1537-5323
issn:
- 0003-0147
publication_status: published
publisher: University of Chicago Press
quality_controlled: '1'
related_material:
record:
- id: '20121'
relation: software
status: public
status: public
title: Discovering stochastic dynamical equations from ecological time series data
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 205
year: '2025'
...
---
OA_type: closed access
_id: '20259'
abstract:
- lang: eng
text: Cell migration in narrow microenvironments occurs in numerous physiological
processes. It involves successive cycles of confinement and release that drive
important morphological changes. However, it remains unclear whether migrating
cells can retain a memory of their past morphological states that could potentially
facilitate their navigation through confined spaces. We demonstrate that local
geometry governs a switch between two cell morphologies, thereby facilitating
cell passage through long and narrow gaps. We combined cell migration assays on
standardized microsystems with biophysical modelling and biochemical perturbations
to show that migrating cells have a long-term memory of past confinement events.
The morphological cell states correlate across transitions through actin cortex
remodelling. These findings indicate that mechanical memory in migrating cells
plays an active role in their migratory potential in confined environments.
acknowledgement: We are grateful to members of S.G.’s laboratory for feedback and
suggestions. We thank E. Hannezo, J. O. Rädler, M. Piel, O. du Roure and J. Heuvingh
for inspiring discussions. Y.K. and S.G. acknowledge J. B. Braquenier from Nikon
Instruments Belux and the Nikon BioImaging Lab in Leiden (the Netherlands) for their
support with the Nikon Spatial Array Confocal enhanced-resolution confocal microscopy.
We thank D. S. Herrador and M. Balland for their help in improving the microprinting
method. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an
EMBO Postdoctoral Fellowship (ALTF 343-2022). Y.K., M.L. and S.G. acknowledge funding
from the University of Mons (FEDER Prostem Research Project no. 1510614, Wallonia
DG06), the F.R.S.-FNRS (Epiforce Project no. T.0092.21, Cellsqueezer Project no.
J.0061.23 and Optopattern Project no. U.NO26.22) and the Interreg projects ANTIRESI
and MICROPLAITE, which are financially supported by Interreg France-Wallonie-Vlaanderen
(Fonds Européen de Développement Régional). Y.K. and M.L. are financially supported
by F.R.S.-FNRS as FRIA Grantee FNRS and Postdoctoral Fellow (Chargé de Recherches),
respectively. Y.K. and S.G. acknowledge le Fonds pour la Recherche Médicale dans
le Hainaut (FRMH). G.C. was supported by a grant from the Biotechnology and Biological
Sciences Research Council (grant no. BB/V007483/1).
article_processing_charge: No
article_type: original
author:
- first_name: Yohalie
full_name: Kalukula, Yohalie
last_name: Kalukula
- first_name: Marine
full_name: Luciano, Marine
last_name: Luciano
- first_name: Gleb
full_name: Simanov, Gleb
last_name: Simanov
- first_name: Guillaume
full_name: Charras, Guillaume
last_name: Charras
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Sylvain
full_name: Gabriele, Sylvain
last_name: Gabriele
citation:
ama: Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. The actin
cortex acts as a mechanical memory of morphology in confined migrating cells.
Nature Physics. 2025;21:1451-1461. doi:10.1038/s41567-025-02980-z
apa: Kalukula, Y., Luciano, M., Simanov, G., Charras, G., Brückner, D., & Gabriele,
S. (2025). The actin cortex acts as a mechanical memory of morphology in confined
migrating cells. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-02980-z
chicago: Kalukula, Yohalie, Marine Luciano, Gleb Simanov, Guillaume Charras, David
Brückner, and Sylvain Gabriele. “The Actin Cortex Acts as a Mechanical Memory
of Morphology in Confined Migrating Cells.” Nature Physics. Springer Nature,
2025. https://doi.org/10.1038/s41567-025-02980-z.
ieee: Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, and S. Gabriele,
“The actin cortex acts as a mechanical memory of morphology in confined migrating
cells,” Nature Physics, vol. 21. Springer Nature, pp. 1451–1461, 2025.
ista: Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. 2025.
The actin cortex acts as a mechanical memory of morphology in confined migrating
cells. Nature Physics. 21, 1451–1461.
mla: Kalukula, Yohalie, et al. “The Actin Cortex Acts as a Mechanical Memory of
Morphology in Confined Migrating Cells.” Nature Physics, vol. 21, Springer
Nature, 2025, pp. 1451–61, doi:10.1038/s41567-025-02980-z.
short: Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, S. Gabriele,
Nature Physics 21 (2025) 1451–1461.
corr_author: '1'
date_created: 2025-08-31T22:01:33Z
date_published: 2025-09-01T00:00:00Z
date_updated: 2025-12-30T09:34:11Z
day: '01'
department:
- _id: EdHa
doi: 10.1038/s41567-025-02980-z
external_id:
isi:
- '001556019400001'
intvolume: ' 21'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 1451-1461
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The actin cortex acts as a mechanical memory of morphology in confined migrating
cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20431'
abstract:
- lang: eng
text: Haptotaxis is the process of directed cell migration along gradients of extracellular
matrix density and is central to morphogenesis, immune responses and cancer invasion.
It is commonly assumed that cells respond to these gradients by migrating directionally
towards the regions of highest ligand density. In contrast with this view, here
we show that cells exposed to micropatterned fibronectin gradients exhibit a wide
range of complex trajectories, including directed haptotactic migration up the
gradient but also linear oscillations and circles with extended periods of migration
down the gradient. To explain this behaviour, we developed a biophysical model
of haptotactic cell migration based on a coarse-grained molecular clutch model
coupled to persistent stochastic polarity dynamics. Although initial haptotactic
migration is explained by the differential friction at the front and back of the
cell, the observed complex trajectories over longer timescales arise from the
interplay between differential friction, persistence and physical confinement.
Overall, our study reveals that confinement and persistence modulate the ability
of cells to sense and respond to haptotactic cues and provides a framework for
understanding how cells navigate complex environments.
acknowledgement: We thank all the members of our groups for discussions and support.
We thank A. Menéndez, S. Usieto, M. Purciolas and E. Coderch for technical assistance.
We thank G. Charras (London Centre for Nanotechnology, UK) and M. Sheetz (Columbia
University, USA) for sharing cells used in this work. We thank J. Ivaska (University
of Turku, Finland) for sharing integrin α5-GFP DNA plasmid. We thank P. Guillamat
for technical advice and A. Labernardie for providing the microfluidic channels.
We thank M. Gómez-González for sharing the 2D traction microscopy algorithm. Finally,
we thank P. Guillamat, J. Abenza, G. Ceada, L. Faure, E. Dalaka, M. Matejčić, A.
Beedle, I. Granero, O. Baguer, A. Albajar and N. Chahare for discussions. This paper
was funded by the Generalitat de Catalunya (Grant Nos. AGAUR SGR-2017-01602 to X.T.
and 2021 SGR 00523 to R.S. and the CERCA Programme and ICREA Academia awards to
P.R.-C.), the Spanish Ministry for Science and Innovation MICCINN/FEDER (Grant Nos.
PID2021-128635NB-I00, MCIN/AEI/10.13039/501100011033 and ERDF-EU A way of making
Europe to X.T., PID2021-128674OB-I00 and CNS2022-135533 to R.S. and PID2019-110298GB-I00
to P.R.-C.), the European Research Council (Grant Nos. 101097753 to P.R.-C. and
Adv-883739 to X.T.), Fundació la Marató de TV3 (Project Award 201903-30-31-32 to
X.T.), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957 to P.R.-C.
and X.T.) and La Caixa Foundation (Grant No. LCF/PR/HR20/52400004 to P.R.-C. and
X.T.). R.S. is a Serra-Hunter fellow. D.B.B. was supported by the NOMIS foundation
as a NOMIS fellow, by the European Molecular Biology Organization (Postdoctoral
Fellowship ALTF 343-2022) and by the Austrian Academy of Sciences through an APART-MINT
Fellowship. I.C.F. acknowledges support from the European Foundation for the Study
of Chronic Liver Failure. IBEC is recipient of a Severo Ochoa Award of Excellence
from MINECO.
article_processing_charge: No
article_type: original
author:
- first_name: Isabela Corina
full_name: Fortunato, Isabela Corina
last_name: Fortunato
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Steffen
full_name: Grosser, Steffen
last_name: Grosser
- first_name: Rohit
full_name: Nautiyal, Rohit
last_name: Nautiyal
- first_name: Leone
full_name: Rossetti, Leone
last_name: Rossetti
- first_name: Miquel
full_name: Bosch-Padrós, Miquel
last_name: Bosch-Padrós
- first_name: Jonel
full_name: Trebicka, Jonel
last_name: Trebicka
- first_name: Pere
full_name: Roca-Cusachs, Pere
last_name: Roca-Cusachs
- first_name: Raimon
full_name: Sunyer, Raimon
last_name: Sunyer
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
citation:
ama: Fortunato IC, Brückner D, Grosser S, et al. Single-cell migration along and
against confined haptotactic gradients. Nature Physics. 2025;21:1638-1647.
doi:10.1038/s41567-025-03015-3
apa: Fortunato, I. C., Brückner, D., Grosser, S., Nautiyal, R., Rossetti, L., Bosch-Padrós,
M., … Trepat, X. (2025). Single-cell migration along and against confined haptotactic
gradients. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-025-03015-3
chicago: Fortunato, Isabela Corina, David Brückner, Steffen Grosser, Rohit Nautiyal,
Leone Rossetti, Miquel Bosch-Padrós, Jonel Trebicka, et al. “Single-Cell Migration
along and against Confined Haptotactic Gradients.” Nature Physics. Springer
Nature, 2025. https://doi.org/10.1038/s41567-025-03015-3.
ieee: I. C. Fortunato et al., “Single-cell migration along and against confined
haptotactic gradients,” Nature Physics, vol. 21. Springer Nature, pp. 1638–1647,
2025.
ista: Fortunato IC, Brückner D, Grosser S, Nautiyal R, Rossetti L, Bosch-Padrós
M, Trebicka J, Roca-Cusachs P, Sunyer R, Hannezo EB, Trepat X. 2025. Single-cell
migration along and against confined haptotactic gradients. Nature Physics. 21,
1638–1647.
mla: Fortunato, Isabela Corina, et al. “Single-Cell Migration along and against
Confined Haptotactic Gradients.” Nature Physics, vol. 21, Springer Nature,
2025, pp. 1638–47, doi:10.1038/s41567-025-03015-3.
short: I.C. Fortunato, D. Brückner, S. Grosser, R. Nautiyal, L. Rossetti, M. Bosch-Padrós,
J. Trebicka, P. Roca-Cusachs, R. Sunyer, E.B. Hannezo, X. Trepat, Nature Physics
21 (2025) 1638–1647.
corr_author: '1'
date_created: 2025-10-05T22:01:36Z
date_published: 2025-10-01T00:00:00Z
date_updated: 2026-01-05T14:26:28Z
day: '01'
department:
- _id: EdHa
doi: 10.1038/s41567-025-03015-3
external_id:
isi:
- '001581659900001'
intvolume: ' 21'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.12.02.626413
month: '10'
oa: 1
oa_version: Preprint
page: 1638-1647
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-cell migration along and against confined haptotactic gradients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2025'
...
---
OA_type: closed access
_id: '18960'
abstract:
- lang: eng
text: The importance of physical forces in the morphogenesis, homeostatic function,
and pathological dysfunction of multicellular tissues is being increasingly characterized,
both theoretically and experimentally. Analogies between biological systems and
inert materials such as foams, gels, and liquid crystals have provided striking
insights into the core design principles underlying multicellular organization.
However, these connections can seem surprising given that a key feature of multicellular
systems is their ability to constantly consume energy, providing an active origin
for the forces that they produce. Key emerging questions are, therefore, to understand
whether and how this activity grants tissues novel properties that do not have
counterparts in classical materials, as well as their consequences for biological
function. Here, we review recent discoveries at the intersection of active matter
and tissue biology, with an emphasis on how modeling and experiments can be combined
to understand the dynamics of multicellular systems. These approaches suggest
that a number of key biological tissue-scale phenomena, such as morphogenetic
shape changes, collective migration, or fate decisions, share unifying design
principles that can be described by physical models of tissue active matter.
acknowledgement: We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg
for a critical reading of the manuscript and Claudia Flandoli for the artwork in
the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and
by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from
the European Research Council (ERC) under the European Union\u2019s Horizon 2020
Research and Innovation Programme Grant Agreement no. 851288.
article_number: a041653
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
citation:
ama: 'Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling
into dynamical models. Cold Spring Harbor Perspectives in Biology. 2025;17(4).
doi:10.1101/cshperspect.a041653'
apa: 'Brückner, D., & Hannezo, E. B. (2025). Tissue active matter: Integrating
mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/cshperspect.a041653'
chicago: 'Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating
Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives
in Biology. Cold Spring Harbor Laboratory Press, 2025. https://doi.org/10.1101/cshperspect.a041653.'
ieee: 'D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics
and signaling into dynamical models,” Cold Spring Harbor Perspectives in Biology,
vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.'
ista: 'Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics
and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology.
17(4), a041653.'
mla: 'Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating
Mechanics and Signaling into Dynamical Models.” Cold Spring Harbor Perspectives
in Biology, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press,
2025, doi:10.1101/cshperspect.a041653.'
short: D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17
(2025).
corr_author: '1'
date_created: 2025-01-29T13:33:47Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-12-30T07:08:34Z
day: '01'
department:
- _id: EdHa
doi: 10.1101/cshperspect.a041653
ec_funded: 1
external_id:
isi:
- '001456660400001'
pmid:
- '38951023'
intvolume: ' 17'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
publication: Cold Spring Harbor Perspectives in Biology
publication_identifier:
issn:
- 1943-0264
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Tissue active matter: Integrating mechanics and signaling into dynamical models'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19404'
abstract:
- lang: eng
text: Cell migration is a fundamental process during embryonic development. Most
studies in vivo have focused on the migration of cells using the extracellular
matrix (ECM) as their substrate for migration. In contrast, much less is known
about how cells migrate on other cells, as found in early embryos when the ECM
has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the
early zebrafish gastrula use the ectoderm as their substrate for migration. We
show that the lateral ectoderm is permissive for the animal-pole-directed migration
of LME cells, while the ectoderm at the animal pole halts it. These differences
in permissiveness depend on the lateral ectoderm being more cohesive than the
animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling
within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion
as one critical factor in regulating LME migration during zebrafish gastrulation.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
acknowledgement: 'We are grateful to the colleagues who contributed to this work with
discussions, technical advice, and feedback on the manuscript: Irene Steccari, David
Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian
Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the
Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing
Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter
Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was
supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral
Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship
(ALTF 1159-2018).'
article_number: '115387'
article_processing_charge: Yes
article_type: original
author:
- first_name: Ste
full_name: Tavano, Ste
id: 2F162F0C-F248-11E8-B48F-1D18A9856A87
last_name: Tavano
orcid: 0000-0001-9970-7804
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Saren
full_name: Tasciyan, Saren
id: 4323B49C-F248-11E8-B48F-1D18A9856A87
last_name: Tasciyan
orcid: 0000-0003-1671-393X
- first_name: Xin
full_name: Tong, Xin
id: 50F65CDC-AA30-11E9-A72B-8A12E6697425
last_name: Tong
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Alexandra
full_name: Schauer, Alexandra
id: 30A536BA-F248-11E8-B48F-1D18A9856A87
last_name: Schauer
orcid: 0000-0001-7659-9142
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm
tissue material properties modulates lateral mesendoderm cell migration during
early zebrafish gastrulation. Cell Reports. 2025;44(3). doi:10.1016/j.celrep.2025.115387
apa: Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A.,
… Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material
properties modulates lateral mesendoderm cell migration during early zebrafish
gastrulation. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2025.115387
chicago: Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra
Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning
of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration
during Early Zebrafish Gastrulation.” Cell Reports. Elsevier, 2025. https://doi.org/10.1016/j.celrep.2025.115387.
ieee: S. Tavano et al., “BMP-dependent patterning of ectoderm tissue material
properties modulates lateral mesendoderm cell migration during early zebrafish
gastrulation,” Cell Reports, vol. 44, no. 3. Elsevier, 2025.
ista: Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R,
Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties
modulates lateral mesendoderm cell migration during early zebrafish gastrulation.
Cell Reports. 44(3), 115387.
mla: Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties
Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.”
Cell Reports, vol. 44, no. 3, 115387, Elsevier, 2025, doi:10.1016/j.celrep.2025.115387.
short: S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild,
C.-P.J. Heisenberg, Cell Reports 44 (2025).
corr_author: '1'
date_created: 2025-03-16T23:01:24Z
date_published: 2025-03-25T00:00:00Z
date_updated: 2025-10-22T07:00:04Z
day: '25'
ddc:
- '570'
department:
- _id: CaHe
- _id: EdHa
- _id: MiSi
- _id: Bio
doi: 10.1016/j.celrep.2025.115387
external_id:
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creator: dernst
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month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
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grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
- _id: 269CD5C4-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1159-2018
name: 'Mechanosensation in cell migration: the role of friction forces in cell polarization
and directed migration'
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
issn:
- 2639-1856
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: BMP-dependent patterning of ectoderm tissue material properties modulates lateral
mesendoderm cell migration during early zebrafish gastrulation
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2025'
...
---
_id: '15315'
abstract:
- lang: eng
text: Single and collective cell migration are fundamental processes critical for
physiological phenomena ranging from embryonic development and immune response
to wound healing and cancer metastasis. To understand cell migration from a physical
perspective, a broad variety of models for the underlying physical mechanisms
that govern cell motility have been developed. A key challenge in the development
of such models is how to connect them to experimental observations, which often
exhibit complex stochastic behaviours. In this review, we discuss recent advances
in data-driven theoretical approaches that directly connect with experimental
data to infer dynamical models of stochastic cell migration. Leveraging advances
in nanofabrication, image analysis, and tracking technology, experimental studies
now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical
efforts have been directed towards integrating such datasets into physical models
from the single cell to the tissue scale with the aim of conceptualising the emergent
behaviour of cells. We first review how this inference problem has been addressed
in both freely migrating and confined cells. Next, we discuss why these dynamics
typically take the form of underdamped stochastic equations of motion, and how
such equations can be inferred from data. We then review applications of data-driven
inference and machine learning approaches to heterogeneity in cell behaviour,
subcellular degrees of freedom, and to the collective dynamics of multicellular
systems. Across these applications, we emphasise how data-driven methods can be
integrated with physical active matter models of migrating cells, and help reveal
how underlying molecular mechanisms control cell behaviour. Together, these data-driven
approaches are a promising avenue for building physical models of cell migration
directly from experimental data, and for providing conceptual links between different
length-scales of description.
acknowledgement: This work was supported by the Deutsche Forschungsgemeinschaft (German
Research Foundation)—Project-ID 201269156—SFB 1032 (Project B12). D B B was supported
by an NOMIS Fellowship and an EMBO Fellowship (ALTF 343-2022). We thank Joachim
Rädler, Alexandra Fink, Erwin Frey, Pierre Ronceray, Ricard Alert, Edouard Hannezo,
Henrik Flyvbjerg, Ulrich Schwarz, Joshua Shaevitz, Greg Stephens, Andrea Cavagna,
Grzegorz Gradziuk, Fridtjof Brauns, Nikolas Claussen, Tom Brandstätter, Johannes
Flommersfeld, Christoph Schreiber, Nicolas Arlt, Matthew Schmitt, Joris Messelink,
Federico Gnesotto, Federica Mura, Bram Hoogland, Manon Wigbers, Isabella Graf, Jessica
Lober, and many others for inspiring discussions. We also thank Claudia Flandoli
for the artwork in figures 1, 5, 8 and 9.
article_number: '056601'
article_processing_charge: Yes (in subscription journal)
article_type: review
arxiv: 1
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Chase P.
full_name: Broedersz, Chase P.
last_name: Broedersz
citation:
ama: 'Brückner D, Broedersz CP. Learning dynamical models of single and collective
cell migration: a review. Reports on Progress in Physics. 2024;87(5). doi:10.1088/1361-6633/ad36d2'
apa: 'Brückner, D., & Broedersz, C. P. (2024). Learning dynamical models of
single and collective cell migration: a review. Reports on Progress in Physics.
IOP Publishing. https://doi.org/10.1088/1361-6633/ad36d2'
chicago: 'Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of
Single and Collective Cell Migration: A Review.” Reports on Progress in Physics.
IOP Publishing, 2024. https://doi.org/10.1088/1361-6633/ad36d2.'
ieee: 'D. Brückner and C. P. Broedersz, “Learning dynamical models of single and
collective cell migration: a review,” Reports on Progress in Physics, vol.
87, no. 5. IOP Publishing, 2024.'
ista: 'Brückner D, Broedersz CP. 2024. Learning dynamical models of single and collective
cell migration: a review. Reports on Progress in Physics. 87(5), 056601.'
mla: 'Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single
and Collective Cell Migration: A Review.” Reports on Progress in Physics,
vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:10.1088/1361-6633/ad36d2.'
short: D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (2024).
corr_author: '1'
date_created: 2024-04-14T22:01:01Z
date_published: 2024-04-04T00:00:00Z
date_updated: 2025-09-04T13:39:07Z
day: '04'
ddc:
- '530'
department:
- _id: EdHa
doi: 10.1088/1361-6633/ad36d2
external_id:
arxiv:
- '2309.00545'
isi:
- '001196692400001'
pmid:
- '38518358'
file:
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checksum: c5910078230ade20f4dd83592e862a72
content_type: application/pdf
creator: dernst
date_created: 2024-08-20T11:00:03Z
date_updated: 2024-08-20T11:00:03Z
file_id: '17451'
file_name: 2024_ReportPhysics_Brueckner.pdf
file_size: 4376898
relation: main_file
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file_date_updated: 2024-08-20T11:00:03Z
has_accepted_license: '1'
intvolume: ' 87'
isi: 1
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Reports on Progress in Physics
publication_identifier:
eissn:
- 1361-6633
issn:
- 0034-4885
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Learning dynamical models of single and collective cell migration: a review'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 87
year: '2024'
...
---
APC_amount: 2570,79 EUR
OA_place: publisher
OA_type: hybrid
_id: '17123'
abstract:
- lang: eng
text: A key feature of many developmental systems is their ability to self-organize
spatial patterns of functionally distinct cell fates. To ensure proper biological
function, such patterns must be established reproducibly, by controlling and even
harnessing intrinsic and extrinsic fluctuations. While the relevant molecular
processes are increasingly well understood, we lack a principled framework to
quantify the performance of such stochastic self-organizing systems. To that end,
we introduce an information-theoretic measure for self-organized fate specification
during embryonic development. We show that the proposed measure assesses the total
information content of fate patterns and decomposes it into interpretable contributions
corresponding to the positional and correlational information. By optimizing the
proposed measure, our framework provides a normative theory for developmental
circuits, which we demonstrate on lateral inhibition, cell type proportioning,
and reaction–diffusion models of self-organization. This paves a way toward a
classification of developmental systems based on a common information-theoretic
language, thereby organizing the zoo of implicated chemical and mechanical signaling
processes.
acknowledgement: We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns,
Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo
for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS
Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship
(ALTF 343-2022). This research was performed in part at the Aspen Center for Physics,
which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical
Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon
and Betty Moore Foundation Grant No. 2919.02.
article_number: e2322326121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Brückner D, Tkačik G. Information content and optimization of self-organized
developmental systems. Proceedings of the National Academy of Sciences of the
United States of America. 2024;121(23). doi:10.1073/pnas.2322326121
apa: Brückner, D., & Tkačik, G. (2024). Information content and optimization
of self-organized developmental systems. Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences.
https://doi.org/10.1073/pnas.2322326121
chicago: Brückner, David, and Gašper Tkačik. “Information Content and Optimization
of Self-Organized Developmental Systems.” Proceedings of the National Academy
of Sciences of the United States of America. National Academy of Sciences,
2024. https://doi.org/10.1073/pnas.2322326121.
ieee: D. Brückner and G. Tkačik, “Information content and optimization of self-organized
developmental systems,” Proceedings of the National Academy of Sciences of
the United States of America, vol. 121, no. 23. National Academy of Sciences,
2024.
ista: Brückner D, Tkačik G. 2024. Information content and optimization of self-organized
developmental systems. Proceedings of the National Academy of Sciences of the
United States of America. 121(23), e2322326121.
mla: Brückner, David, and Gašper Tkačik. “Information Content and Optimization of
Self-Organized Developmental Systems.” Proceedings of the National Academy
of Sciences of the United States of America, vol. 121, no. 23, e2322326121,
National Academy of Sciences, 2024, doi:10.1073/pnas.2322326121.
short: D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of
the United States of America 121 (2024).
corr_author: '1'
date_created: 2024-06-09T22:01:02Z
date_published: 2024-06-04T00:00:00Z
date_updated: 2025-09-08T07:51:01Z
day: '04'
ddc:
- '570'
department:
- _id: EdHa
- _id: GaTk
doi: 10.1073/pnas.2322326121
external_id:
isi:
- '001244835000006'
pmid:
- '38819997'
file:
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checksum: 59797a75db7beb3721ed7a4d14c241f9
content_type: application/pdf
creator: dernst
date_created: 2024-06-10T10:27:37Z
date_updated: 2024-06-10T10:27:37Z
file_id: '17130'
file_name: 2024_PNAS_Brueckner.pdf
file_size: 12329234
relation: main_file
success: 1
file_date_updated: 2024-06-10T10:27:37Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '23'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/dbrueckner/SelforgInformation
- description: News on the ISTA website
relation: press_release
url: https://ista.ac.at/en/news/the-embryo-assembles-itself/
scopus_import: '1'
status: public
title: Information content and optimization of self-organized developmental systems
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...
---
OA_place: repository
OA_type: green
_id: '17269'
abstract:
- lang: eng
text: The directed migration of epithelial cell collectives through coordinated
movements plays a crucial role in various physiological processes and is increasingly
understood at the level of large confluent monolayers. However, numerous processes
rely on the migration of small groups of polarized epithelial clusters in complex
environments, and their responses to external geometries remain poorly understood.
To address this, we cultivate primary epithelial keratocyte tissues on adhesive
microstripes to create autonomous epithelial clusters with well-defined geometries.
We show that their migration efficiency is strongly influenced by the contact
geometry and the orientation of cell–cell contacts with respect to the direction
of migration. A combination of velocity and polarity alignment with contact regulation
of locomotion in an active matter model captures quantitatively the experimental
data. Furthermore, we predict that this combination of rules enables efficient
navigation in complex geometries, which we confirm experimentally. Altogether,
our findings provide a conceptual framework for extracting the interaction rules
of active systems from their interaction with physical boundaries, as well as
design principles for collective navigation in complex microenvironments.
acknowledgement: M.L., E.V. and S.G. acknowledge funding from the European Regional
Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the
Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS;
Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23),
the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE
project, which is financially supported by Interreg France-Wallonie-Vlaanderen,
ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow
(Aspirant FNRS) and Postdoctoral Researcher (Chargée de Recherches FNRS), respectively.
E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund
for Research Training in Industry and Agriculture (FRIA). This project was supported
by the European Research Council under the European Union’s Horizon 2020 Research
and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie Skłodowska-Curie
Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS
foundation as a NOMIS fellow and by the European Molecular Biology Organization
(Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen
Center for Physics, which is supported by the National Science Foundation (Grant
No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia
(Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for
Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research
Council (Grant No. Adv-883739), Fundació la Marató de TV3 (201903-30-31-32), the
European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation
and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the
Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient
of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade
and Business.
article_processing_charge: No
article_type: original
author:
- first_name: Eléonore
full_name: Vercruysse, Eléonore
last_name: Vercruysse
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Manuel
full_name: Gómez-González, Manuel
last_name: Gómez-González
- first_name: Alexandre
full_name: Remson, Alexandre
last_name: Remson
- first_name: Marine
full_name: Luciano, Marine
last_name: Luciano
- first_name: Yohalie
full_name: Kalukula, Yohalie
last_name: Kalukula
- first_name: Leone
full_name: Rossetti, Leone
last_name: Rossetti
- first_name: Xavier
full_name: Trepat, Xavier
last_name: Trepat
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Sylvain
full_name: Gabriele, Sylvain
last_name: Gabriele
citation:
ama: Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration
efficiency of autonomous epithelial cell clusters. Nature Physics. 2024;20:1492-1500.
doi:10.1038/s41567-024-02532-x
apa: Vercruysse, E., Brückner, D., Gómez-González, M., Remson, A., Luciano, M.,
Kalukula, Y., … Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous
epithelial cell clusters. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02532-x
chicago: Vercruysse, Eléonore, David Brückner, Manuel Gómez-González, Alexandre
Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard
B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous
Epithelial Cell Clusters.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02532-x.
ieee: E. Vercruysse et al., “Geometry-driven migration efficiency of autonomous
epithelial cell clusters,” Nature Physics, vol. 20. Springer Nature, pp.
1492–1500, 2024.
ista: Vercruysse E, Brückner D, Gómez-González M, Remson A, Luciano M, Kalukula
Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration
efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.
mla: Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous
Epithelial Cell Clusters.” Nature Physics, vol. 20, Springer Nature, 2024,
pp. 1492–500, doi:10.1038/s41567-024-02532-x.
short: E. Vercruysse, D. Brückner, M. Gómez-González, A. Remson, M. Luciano, Y.
Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20
(2024) 1492–1500.
corr_author: '1'
date_created: 2024-07-16T12:32:17Z
date_published: 2024-09-01T00:00:00Z
date_updated: 2025-09-08T08:28:31Z
day: '01'
department:
- _id: EdHa
doi: 10.1038/s41567-024-02532-x
ec_funded: 1
external_id:
isi:
- '001250246200004'
intvolume: ' 20'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2022.07.17.500364
month: '09'
oa: 1
oa_version: Preprint
page: 1492-1500
project:
- _id: 05943252-7A3F-11EA-A408-12923DDC885E
call_identifier: H2020
grant_number: '851288'
name: Design Principles of Branching Morphogenesis
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/a-railroad-of-cells/
scopus_import: '1'
status: public
title: Geometry-driven migration efficiency of autonomous epithelial cell clusters
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2024'
...
---
_id: '13261'
abstract:
- lang: eng
text: Chromosomes in the eukaryotic nucleus are highly compacted. However, for many
functional processes, including transcription initiation, the pairwise motion
of distal chromosomal elements such as enhancers and promoters is essential and
necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously
measure the positions of pairs of enhancers and promoters and their transcriptional
output while systematically varying the genomic separation between these two DNA
loci. Our analysis reveals the coexistence of a compact globular organization
and fast subdiffusive dynamics. These combined features cause an anomalous scaling
of polymer relaxation times with genomic separation leading to long-ranged correlations.
Thus, encounter times of DNA loci are much less dependent on genomic distance
than predicted by existing polymer models, with potential consequences for eukaryotic
gene expression.
acknowledgement: This work was supported in part by the U.S. National Science Foundation,
the Center for the Physics of Biological Function (grant PHY-1734030), and the National
Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B.
was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship
(ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.
article_processing_charge: No
article_type: original
author:
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
- first_name: Hongtao
full_name: Chen, Hongtao
last_name: Chen
- first_name: Lev
full_name: Barinov, Lev
last_name: Barinov
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
citation:
ama: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional
dynamics of pairs of distal DNA loci on a compacted chromosome. Science.
2023;380(6652):1357-1362. doi:10.1126/science.adf5568
apa: Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic
motion and transcriptional dynamics of pairs of distal DNA loci on a compacted
chromosome. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.adf5568
chicago: Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas
Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA
Loci on a Compacted Chromosome.” Science. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568.
ieee: D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion
and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,”
Science, vol. 380, no. 6652. American Association for the Advancement of
Science, pp. 1357–1362, 2023.
ista: Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion
and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.
Science. 380(6652), 1357–1362.
mla: Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of
Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380,
no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62,
doi:10.1126/science.adf5568.
short: D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023)
1357–1362.
date_created: 2023-07-23T22:01:12Z
date_published: 2023-06-29T00:00:00Z
date_updated: 2025-04-14T08:55:54Z
day: '29'
department:
- _id: EdHa
doi: 10.1126/science.adf5568
external_id:
isi:
- '001106405600028'
intvolume: ' 380'
isi: 1
issue: '6652'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.adf5568
month: '06'
oa: 1
oa_version: Preprint
page: 1357-1362
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Science
publication_identifier:
eissn:
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic motion and transcriptional dynamics of pairs of distal DNA loci
on a compacted chromosome
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 380
year: '2023'
...
---
_id: '14827'
abstract:
- lang: eng
text: Understanding complex living systems, which are fundamentally constrained
by physical phenomena, requires combining experimental data with theoretical physical
and mathematical models. To develop such models, collaborations between experimental
cell biologists and theoreticians are increasingly important but these two groups
often face challenges achieving mutual understanding. To help navigate these challenges,
this Perspective discusses different modelling approaches, including bottom-up
hypothesis-driven and top-down data-driven models, and highlights their strengths
and applications. Using cell mechanics as an example, we explore the integration
of specific physical models with experimental data from the molecular, cellular
and tissue level up to multiscale input. We also emphasize the importance of constraining
model complexity and outline strategies for crosstalk between experimental design
and model development. Furthermore, we highlight how physical models can provide
conceptual insights and produce unifying and generalizable frameworks for biological
phenomena. Overall, this Perspective aims to promote fruitful collaborations that
advance our understanding of complex biological systems.
acknowledgement: "We thank Prisca Liberali and Edouard Hannezo for many inspiring
discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical
reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3.
We would also like to thank The Company of Biologists for the opportunity to attend
the 2023 workshop on Collective Cell Migration, and all workshop participants for
discussions.\r\nC.S. was supported by a European Molecular Biology Organization
(EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program
(HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS
Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022)."
article_number: jcs.261515
article_processing_charge: No
article_type: original
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: David
full_name: Brückner, David
id: e1e86031-6537-11eb-953a-f7ab92be508d
last_name: Brückner
orcid: 0000-0001-7205-2975
citation:
ama: Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue
mechanics. Journal of Cell Science. 2023;136(24). doi:10.1242/jcs.261515
apa: Schwayer, C., & Brückner, D. (2023). Connecting theory and experiment in
cell and tissue mechanics. Journal of Cell Science. The Company of Biologists.
https://doi.org/10.1242/jcs.261515
chicago: Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment
in Cell and Tissue Mechanics.” Journal of Cell Science. The Company of
Biologists, 2023. https://doi.org/10.1242/jcs.261515.
ieee: C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and
tissue mechanics,” Journal of Cell Science, vol. 136, no. 24. The Company
of Biologists, 2023.
ista: Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and
tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.
mla: Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in
Cell and Tissue Mechanics.” Journal of Cell Science, vol. 136, no. 24,
jcs. 261515, The Company of Biologists, 2023, doi:10.1242/jcs.261515.
short: C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).
corr_author: '1'
date_created: 2024-01-17T12:46:55Z
date_published: 2023-12-27T00:00:00Z
date_updated: 2025-09-09T14:22:02Z
day: '27'
department:
- _id: EdHa
- _id: CaHe
doi: 10.1242/jcs.261515
external_id:
isi:
- '001165394900011'
pmid:
- '38149871'
intvolume: ' 136'
isi: 1
issue: '24'
keyword:
- Cell Biology
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
project:
- _id: 34e2a5b5-11ca-11ed-8bc3-b2265616ef0b
grant_number: ALTF 343-2022
name: A mechano-chemical theory for stem cell fate decisions in organoid development
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Connecting theory and experiment in cell and tissue mechanics
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 136
year: '2023'
...