---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21115'
abstract:
- lang: eng
text: Quantifying cell morphology is central to understanding cellular regulation,
fate, and heterogeneity, yet conventional image-based analyses often struggle
with diverse or irregular shapes. We present a computational framework that uses
topological data analysis to characterise and compare single-cell morphologies
from fluorescence microscopy. Each cell is represented by its contour together
with the position of its nucleus, from which we construct a filtration based on
a radial distance function and derive a persistence diagram encoding the shape’s
topological evolution. The similarity between two cells is quantified using the
2-Wasserstein distance between their diagrams, yielding a shape distance we call
the PH distance. We apply this method to two representative experimental systems—primary
human mesenchymal stem cells (hMSCs) and HeLa cells—and show that PH distances
enable the detection of outliers in those systems, the identification of sub-populations,
and the quantification of shape heterogeneity. We benchmark PH against three established
contour-based distances (aspect ratio, Fourier descriptors, and elastic shape
analysis) and show that PH offers better separation between cell types and greater
robustness when clustering heterogeneous populations. Together, these results
demonstrate that persistent-homology-based signatures provide a principled and
sensitive approach for analysing cell morphology in settings where traditional
geometric or image-based descriptors are insufficient.
acknowledgement: We thank Stephan Huckemann, Katharine Turner, Benjamin Eltzner, Stephan
Tillmann, Fariza Rashid, Vanessa Robins, and Lamiae Azizi for many useful discussions
at various stages of this project. FR and PY gratefully acknowledge Matthias Weiss
(Experimental Physics I, University of Bayreuth, Germany) for granting access to
cell culture and laboratories, as well as funding consumables and the fruitful discussion
that contributed to this work. 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: e1013890
article_processing_charge: Yes
article_type: original
author:
- first_name: Yossi
full_name: Bleile, Yossi
id: 920a7385-7995-11ef-9bfd-8c434cd8f3c2
last_name: Bleile
orcid: 0000-0002-4861-9174
- first_name: Pooja
full_name: Yadav, Pooja
last_name: Yadav
- first_name: Patrice
full_name: Koehl, Patrice
last_name: Koehl
- first_name: Florian
full_name: Rehfeldt, Florian
last_name: Rehfeldt
citation:
ama: 'Bokor Bleile Y, Yadav P, Koehl P, Rehfeldt F. Persistence diagrams as morphological
signatures of cells: A method to measure and compare cells within a population.
PLoS Computational Biology. 2026;22. doi:10.1371/journal.pcbi.1013890'
apa: 'Bokor Bleile, Y., Yadav, P., Koehl, P., & Rehfeldt, F. (2026). Persistence
diagrams as morphological signatures of cells: A method to measure and compare
cells within a population. PLoS Computational Biology. Public Library of
Science. https://doi.org/10.1371/journal.pcbi.1013890'
chicago: 'Bokor Bleile, Yossi, Pooja Yadav, Patrice Koehl, and Florian Rehfeldt.
“Persistence Diagrams as Morphological Signatures of Cells: A Method to Measure
and Compare Cells within a Population.” PLoS Computational Biology. Public
Library of Science, 2026. https://doi.org/10.1371/journal.pcbi.1013890.'
ieee: 'Y. Bokor Bleile, P. Yadav, P. Koehl, and F. Rehfeldt, “Persistence diagrams
as morphological signatures of cells: A method to measure and compare cells within
a population,” PLoS Computational Biology, vol. 22. Public Library of Science,
2026.'
ista: 'Bokor Bleile Y, Yadav P, Koehl P, Rehfeldt F. 2026. Persistence diagrams
as morphological signatures of cells: A method to measure and compare cells within
a population. PLoS Computational Biology. 22, e1013890.'
mla: 'Bokor Bleile, Yossi, et al. “Persistence Diagrams as Morphological Signatures
of Cells: A Method to Measure and Compare Cells within a Population.” PLoS
Computational Biology, vol. 22, e1013890, Public Library of Science, 2026,
doi:10.1371/journal.pcbi.1013890.'
short: Y. Bokor Bleile, P. Yadav, P. Koehl, F. Rehfeldt, PLoS Computational Biology
22 (2026).
corr_author: '1'
date_created: 2026-01-30T10:36:32Z
date_published: 2026-01-28T00:00:00Z
date_updated: 2026-06-11T11:51:13Z
day: '28'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1371/journal.pcbi.1013890
external_id:
pmid:
- '41604421'
file:
- access_level: open_access
checksum: 3899d929ee9be0453c95524e49992d72
content_type: application/pdf
creator: dernst
date_created: 2026-02-10T07:13:06Z
date_updated: 2026-02-10T07:13:06Z
file_id: '21204'
file_name: 2026_PloSCompBio_Bleile.pdf
file_size: 8908746
relation: main_file
success: 1
file_date_updated: 2026-02-10T07:13:06Z
has_accepted_license: '1'
intvolume: ' 22'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/yossibokorbleile/correa
scopus_import: '1'
status: public
title: 'Persistence diagrams as morphological signatures of cells: A method to measure
and compare cells within a population'
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: 22
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '15258'
abstract:
- lang: eng
text: Inclusion at academic events is facing increased scrutiny as the communities
these events serve raise their expectations for who can practically attend. Active
efforts in recent years to bring more diversity to academic events have brought
progress and created momentum. However, we must reflect on these efforts and determine
which underrepresented groups are being disadvantaged. Inclusion at academic events
is important to ensure diversity of discourse and opinion, to help build networks,
and to avoid academic siloing. All of these contribute to the development of a
robust and resilient academic field. We have developed these Ten Simple Rules
both to amplify the voices that have been speaking out and to celebrate the progress
of many Equity, Diversity, and Inclusivity practices that continue to drive the
organisation of academic events. The Rules aim to raise awareness as well as provide
actionable suggestions and tools to support these initiatives further. This aims
to support academic organisations such as the Deep Learning Indaba, Neuromatch
Academy, the IBRO-Simons Computational Neuroscience Imbizo, Biodiversity Information
Standards (TDWG), Arabs in Neuroscience, FAIRPoints, and OLS (formerly Open Life
Science). This article is a call to action for organisers to reevaluate the impact
and reach of their inclusive practices.
acknowledgement: "We would like to recognise the feedback and ideas shared with us
by all attendees during the\r\nfocus groups that contributed to the development
of this paper. Acknowledgements are given\r\nto Elisee Jafsia, Umar Farouk Ahmad,
Zohra Slim, Mizanur Rahman, Rev. Katie Tupling,\r\nChristopher Emmanuel, Abdalrhman
Mostafa, Pradeep Eranti, Toby Hodges, Avishkar\r\nBhoopchand, and Carolyn Dickson.
We would like to thank our community members and\r\nacknowledge their bravery for
sharing their stories that shaped the narrative of these Ten Simple\r\nRules. The
stories shared with us formed the case studies, and while they are anonymous\r\nfor
privacy and protection reasons, it is these stories that were on our mind during
the entire\r\nprocess and kept us going. We acknowledge the efforts of the organisers
that contribute to the\r\nhighly successful events that are the inspiration for
the ideas presented here: the Deep\r\nLearning Indaba, Neuromatch Academy, the IBRO
Simons Computational Neuroscience\r\nImbizo, and OLS. OLS also supported this project
through their mentorship programme,\r\nOpen Seeds."
article_number: e1011797
article_processing_charge: Yes
article_type: original
author:
- first_name: Siobhan Mackenzie
full_name: Hall, Siobhan Mackenzie
last_name: Hall
- first_name: Daniel
full_name: Kochin, Daniel
last_name: Kochin
- first_name: Carmel
full_name: Carne, Carmel
last_name: Carne
- first_name: Patricia
full_name: Herterich, Patricia
last_name: Herterich
- first_name: Kristen Lenay
full_name: Lewers, Kristen Lenay
last_name: Lewers
- first_name: Mohamed
full_name: Abdelhack, Mohamed
last_name: Abdelhack
- first_name: Arun
full_name: Ramasubramanian, Arun
last_name: Ramasubramanian
- first_name: Juno Felecia
full_name: Michael Alphonse, Juno Felecia
last_name: Michael Alphonse
- first_name: Visotheary
full_name: Ung, Visotheary
last_name: Ung
- first_name: Sara
full_name: El-Gebali, Sara
last_name: El-Gebali
- first_name: Christopher
full_name: Currin, Christopher
id: e8321fc5-3091-11eb-8a53-83f309a11ac9
last_name: Currin
orcid: 0000-0002-4809-5059
- first_name: Esther
full_name: Plomp, Esther
last_name: Plomp
- first_name: Rachel
full_name: Thompson, Rachel
last_name: Thompson
- first_name: Malvika
full_name: Sharan, Malvika
last_name: Sharan
citation:
ama: Hall SM, Kochin D, Carne C, et al. Ten simple rules for pushing boundaries
of inclusion at academic events. PLOS Computational Biology. 2024;20(3).
doi:10.1371/journal.pcbi.1011797
apa: Hall, S. M., Kochin, D., Carne, C., Herterich, P., Lewers, K. L., Abdelhack,
M., … Sharan, M. (2024). Ten simple rules for pushing boundaries of inclusion
at academic events. PLOS Computational Biology. Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1011797
chicago: Hall, Siobhan Mackenzie, Daniel Kochin, Carmel Carne, Patricia Herterich,
Kristen Lenay Lewers, Mohamed Abdelhack, Arun Ramasubramanian, et al. “Ten Simple
Rules for Pushing Boundaries of Inclusion at Academic Events.” PLOS Computational
Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011797.
ieee: S. M. Hall et al., “Ten simple rules for pushing boundaries of inclusion
at academic events,” PLOS Computational Biology, vol. 20, no. 3. Public
Library of Science, 2024.
ista: Hall SM, Kochin D, Carne C, Herterich P, Lewers KL, Abdelhack M, Ramasubramanian
A, Michael Alphonse JF, Ung V, El-Gebali S, Currin C, Plomp E, Thompson R, Sharan
M. 2024. Ten simple rules for pushing boundaries of inclusion at academic events.
PLOS Computational Biology. 20(3), e1011797.
mla: Hall, Siobhan Mackenzie, et al. “Ten Simple Rules for Pushing Boundaries of
Inclusion at Academic Events.” PLOS Computational Biology, vol. 20, no.
3, e1011797, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011797.
short: S.M. Hall, D. Kochin, C. Carne, P. Herterich, K.L. Lewers, M. Abdelhack,
A. Ramasubramanian, J.F. Michael Alphonse, V. Ung, S. El-Gebali, C. Currin, E.
Plomp, R. Thompson, M. Sharan, PLOS Computational Biology 20 (2024).
date_created: 2024-04-02T11:37:32Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2025-09-04T13:24:19Z
day: '01'
ddc:
- '000'
department:
- _id: TiVo
doi: 10.1371/journal.pcbi.1011797
external_id:
isi:
- '001181690200005'
pmid:
- '38427633'
file:
- access_level: open_access
checksum: 1f0f837c5b4341f54f6347370ed8c1b7
content_type: application/pdf
creator: dernst
date_created: 2024-04-03T13:29:36Z
date_updated: 2024-04-03T13:29:36Z
file_id: '15289'
file_name: 2024_PloS_Hall.pdf
file_size: 858521
relation: main_file
success: 1
file_date_updated: 2024-04-03T13:29:36Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ten simple rules for pushing boundaries of inclusion at academic events
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: 20
year: '2024'
...
---
_id: '12152'
abstract:
- lang: eng
text: ESCRT-III filaments are composite cytoskeletal polymers that can constrict
and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III
filaments undergo a series of dramatic composition and geometry changes in the
presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the
membrane morphology. We set out to understand the physical mechanisms involved
in translating the changes in ESCRT-III polymer composition into membrane deformation.
We have built a coarse-grained model in which ESCRT-III polymers of different
geometries and mechanical properties are allowed to copolymerise and bind to a
deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific
polymers, we identify mechanical regimes in which changes in filament composition
trigger the associated membrane transition from a flat to a buckled state, and
then to a tubule state that eventually undergoes scission to release a small cargo-loaded
vesicle. We then characterise how the location and kinetics of polymer loss affects
the extent of membrane deformation and the efficiency of membrane neck scission.
Our results identify the near-minimal mechanical conditions for the operation
of shape-shifting composite polymers that sever membrane necks.
acknowledgement: "A.S . received an award from European Research Council (https://erc.europa.eu,
“NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org,
UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences
Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award
from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open,
Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an
award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation,
Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc,
MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research
(https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and
an award from the European Research Council\r\nConsolidator (https://erc.europa.eu,
311536). The funders had no role in study design, data collection and analysis,
decision to publish, or preparation of the manuscript."
article_number: e1010586
article_processing_charge: No
article_type: original
author:
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Anna-Katharina
full_name: Pfitzner, Anna-Katharina
last_name: Pfitzner
- first_name: Elene
full_name: Lominadze, Elene
last_name: Lominadze
- first_name: Aurélien
full_name: Roux, Aurélien
last_name: Roux
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane
reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational
Biology. 2022;18(10). doi:10.1371/journal.pcbi.1010586
apa: Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K.,
Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged
polymerization of ESCRT-III filaments. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1010586
chicago: Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos,
Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela
Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.”
PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010586.
ieee: X. Jiang et al., “Modelling membrane reshaping by staged polymerization
of ESCRT-III filaments,” PLOS Computational Biology, vol. 18, no. 10. Public
Library of Science, 2022.
ista: Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze
E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization
of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.
mla: Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization
of ESCRT-III Filaments.” PLOS Computational Biology, vol. 18, no. 10, e1010586,
Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010586.
short: X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E.
Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022).
corr_author: '1'
date_created: 2023-01-12T12:08:10Z
date_published: 2022-10-17T00:00:00Z
date_updated: 2025-06-12T06:19:28Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1371/journal.pcbi.1010586
ec_funded: 1
external_id:
isi:
- '000924885500005'
pmid:
- '36251703'
file:
- access_level: open_access
checksum: bada6a7865e470cf42bbdfa67dd471d2
content_type: application/pdf
creator: dernst
date_created: 2023-01-24T10:45:01Z
date_updated: 2023-01-24T10:45:01Z
file_id: '12359'
file_name: 2022_PLoSCompBio_Jiang.pdf
file_size: 2641067
relation: main_file
success: 1
file_date_updated: 2023-01-24T10:45:01Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '10'
keyword:
- Computational Theory and Mathematics
- Cellular and Molecular Neuroscience
- Genetics
- Molecular Biology
- Ecology
- Modeling and Simulation
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: eba0f67c-77a9-11ec-83b8-cc8501b3e222
grant_number: '96752'
name: 'The evolution of trafficking: from archaea to eukaryotes'
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/sharonJXY/3-filament-model
scopus_import: '1'
status: public
title: Modelling membrane reshaping by staged polymerization of ESCRT-III filaments
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: 18
year: '2022'
...
---
_id: '8997'
abstract:
- lang: eng
text: Phenomenological relations such as Ohm’s or Fourier’s law have a venerable
history in physics but are still scarce in biology. This situation restrains predictive
theory. Here, we build on bacterial “growth laws,” which capture physiological
feedback between translation and cell growth, to construct a minimal biophysical
model for the combined action of ribosome-targeting antibiotics. Our model predicts
drug interactions like antagonism or synergy solely from responses to individual
drugs. We provide analytical results for limiting cases, which agree well with
numerical results. We systematically refine the model by including direct physical
interactions of different antibiotics on the ribosome. In a limiting case, our
model provides a mechanistic underpinning for recent predictions of higher-order
interactions that were derived using entropy maximization. We further refine the
model to include the effects of antibiotics that mimic starvation and the presence
of resistance genes. We describe the impact of a starvation-mimicking antibiotic
on drug interactions analytically and verify it experimentally. Our extended model
suggests a change in the type of drug interaction that depends on the strength
of resistance, which challenges established rescaling paradigms. We experimentally
show that the presence of unregulated resistance genes can lead to altered drug
interaction, which agrees with the prediction of the model. While minimal, the
model is readily adaptable and opens the door to predicting interactions of second
and higher-order in a broad range of biological systems.
acknowledgement: 'This work was supported in part by Tum stipend of Knafelj foundation
(to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and
P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation
(DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG)
Collaborative Research Centre (SFB) 1310 (to T.B.). '
article_number: e1008529
article_processing_charge: Yes
article_type: original
author:
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Tobias
full_name: Bollenbach, Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic
action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529
apa: Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical
model of combined antibiotic action. PLOS Computational Biology. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1008529
chicago: Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical
Model of Combined Antibiotic Action.” PLOS Computational Biology. Public
Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.
ieee: B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of
combined antibiotic action,” PLOS Computational Biology, vol. 17. Public
Library of Science, 2021.
ista: Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined
antibiotic action. PLOS Computational Biology. 17, e1008529.
mla: Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.”
PLOS Computational Biology, vol. 17, e1008529, Public Library of Science,
2021, doi:10.1371/journal.pcbi.1008529.
short: B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021).
date_created: 2021-01-08T07:16:18Z
date_published: 2021-01-07T00:00:00Z
date_updated: 2025-06-12T06:33:18Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1008529
external_id:
isi:
- '000608045000010'
pmid:
- '33411759'
file:
- access_level: open_access
checksum: e29f2b42651bef8e034781de8781ffac
content_type: application/pdf
creator: dernst
date_created: 2021-02-04T12:30:48Z
date_updated: 2021-02-04T12:30:48Z
file_id: '9092'
file_name: 2021_PlosComBio_Kavcic.pdf
file_size: 3690053
relation: main_file
success: 1
file_date_updated: 2021-02-04T12:30:48Z
has_accepted_license: '1'
intvolume: ' 17'
isi: 1
keyword:
- Modelling and Simulation
- Genetics
- Molecular Biology
- Antibiotics
- Drug interactions
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '8930'
relation: research_data
status: public
- id: '7673'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Minimal biophysical model of combined antibiotic action
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: 17
year: '2021'
...
---
_id: '17132'
abstract:
- lang: eng
text: Extracellular recording is an accessible technique used in animals
and humans to study the brain physiology and pathology. As the number of recording
channels and their density grows it is natural to ask how much improvement the
additional channels bring in and how we can optimally use the new capabilities
for monitoring the brain. Here we show that for any given distribution of electrodes
we can establish exactly what information about current sources in the brain can
be recovered and what information is strictly unobservable. We demonstrate this
in the general setting of previously proposed kernel Current Source Density method
and illustrate it with simplified examples as well as using evoked potentials
from the barrel cortex obtained with a Neuropixels probe and with compatible model
data. We show that with conceptual separation of the estimation space from experimental
setup one can recover sources not accessible to standard methods.
article_number: e1008615
article_processing_charge: No
article_type: original
author:
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: Marta
full_name: Bejtka, Marta
last_name: Bejtka
- first_name: Władysław
full_name: Średniawa, Władysław
last_name: Średniawa
- first_name: Michał
full_name: Czerwiński, Michał
last_name: Czerwiński
- first_name: Jakub M.
full_name: Dzik, Jakub M.
last_name: Dzik
- first_name: Joanna
full_name: Jędrzejewska-Szmek, Joanna
last_name: Jędrzejewska-Szmek
- first_name: Kacper
full_name: Kondrakiewicz, Kacper
last_name: Kondrakiewicz
- first_name: Ewa
full_name: Kublik, Ewa
last_name: Kublik
- first_name: Daniel K.
full_name: Wójcik, Daniel K.
last_name: Wójcik
citation:
ama: Chintaluri C, Bejtka M, Średniawa W, et al. What we can and what we cannot
see with extracellular multielectrodes. PLOS Computational Biology. 2021;17(5).
doi:10.1371/journal.pcbi.1008615
apa: Chintaluri, C., Bejtka, M., Średniawa, W., Czerwiński, M., Dzik, J. M., Jędrzejewska-Szmek,
J., … Wójcik, D. K. (2021). What we can and what we cannot see with extracellular
multielectrodes. PLOS Computational Biology. Public Library of Science.
https://doi.org/10.1371/journal.pcbi.1008615
chicago: Chintaluri, Chaitanya, Marta Bejtka, Władysław Średniawa, Michał Czerwiński,
Jakub M. Dzik, Joanna Jędrzejewska-Szmek, Kacper Kondrakiewicz, Ewa Kublik, and
Daniel K. Wójcik. “What We Can and What We Cannot See with Extracellular Multielectrodes.”
PLOS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008615.
ieee: C. Chintaluri et al., “What we can and what we cannot see with extracellular
multielectrodes,” PLOS Computational Biology, vol. 17, no. 5. Public Library
of Science, 2021.
ista: Chintaluri C, Bejtka M, Średniawa W, Czerwiński M, Dzik JM, Jędrzejewska-Szmek
J, Kondrakiewicz K, Kublik E, Wójcik DK. 2021. What we can and what we cannot
see with extracellular multielectrodes. PLOS Computational Biology. 17(5), e1008615.
mla: Chintaluri, Chaitanya, et al. “What We Can and What We Cannot See with Extracellular
Multielectrodes.” PLOS Computational Biology, vol. 17, no. 5, e1008615,
Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008615.
short: C. Chintaluri, M. Bejtka, W. Średniawa, M. Czerwiński, J.M. Dzik, J. Jędrzejewska-Szmek,
K. Kondrakiewicz, E. Kublik, D.K. Wójcik, PLOS Computational Biology 17 (2021).
date_created: 2024-06-11T14:43:37Z
date_published: 2021-05-14T00:00:00Z
date_updated: 2024-06-17T10:48:15Z
day: '14'
doi: 10.1371/journal.pcbi.1008615
extern: '1'
has_accepted_license: '1'
intvolume: ' 17'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pcbi.1008615
month: '05'
oa: 1
oa_version: Published Version
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: What we can and what we cannot see with extracellular multielectrodes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2021'
...
---
_id: '7569'
abstract:
- lang: eng
text: 'Genes differ in the frequency at which they are expressed and in the form
of regulation used to control their activity. In particular, positive or negative
regulation can lead to activation of a gene in response to an external signal.
Previous works proposed that the form of regulation of a gene correlates with
its frequency of usage: positive regulation when the gene is frequently expressed
and negative regulation when infrequently expressed. Such network design means
that, in the absence of their regulators, the genes are found in their least required
activity state, hence regulatory intervention is often necessary. Due to the multitude
of genes and regulators, spurious binding and unbinding events, called “crosstalk”,
could occur. To determine how the form of regulation affects the global crosstalk
in the network, we used a mathematical model that includes multiple regulators
and multiple target genes. We found that crosstalk depends non-monotonically on
the availability of regulators. Our analysis showed that excess use of regulation
entailed by the formerly suggested network design caused high crosstalk levels
in a large part of the parameter space. We therefore considered the opposite ‘idle’
design, where the default unregulated state of genes is their frequently required
activity state. We found, that ‘idle’ design minimized the use of regulation and
thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae
using transcription factors binding data. We demonstrated that even partial network
data could suffice to estimate its global crosstalk, suggesting its applicability
to additional organisms. We found that S. cerevisiae estimated crosstalk is lower
than that of a random network, suggesting that natural selection reduces crosstalk.
In summary, our study highlights a new type of protein production cost which is
typically overlooked: that of regulatory interference caused by the presence of
excess regulators in the cell. It demonstrates the importance of whole-network
descriptions, which could show effects missed by single-gene models.'
article_number: e1007642
article_processing_charge: No
article_type: original
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. The relation between crosstalk and gene regulation form
revisited. PLOS Computational Biology. 2020;16(2). doi:10.1371/journal.pcbi.1007642
apa: Grah, R., & Friedlander, T. (2020). The relation between crosstalk and
gene regulation form revisited. PLOS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642
chicago: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene
Regulation Form Revisited.” PLOS Computational Biology. Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.
ieee: R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation
form revisited,” PLOS Computational Biology, vol. 16, no. 2. Public Library
of Science, 2020.
ista: Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation
form revisited. PLOS Computational Biology. 16(2), e1007642.
mla: Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene
Regulation Form Revisited.” PLOS Computational Biology, vol. 16, no. 2,
e1007642, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.
short: R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).
date_created: 2020-03-06T07:39:38Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2026-04-08T07:25:08Z
day: '25'
ddc:
- '000'
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642
external_id:
isi:
- '000526725200019'
pmid:
- '32097416'
file:
- access_level: open_access
checksum: 5239dd134dc6e1c71fe7b3ce2953da37
content_type: application/pdf
creator: dernst
date_created: 2020-03-09T15:12:21Z
date_updated: 2020-07-14T12:48:00Z
file_id: '7579'
file_name: 2020_PlosCompBio_Grah.pdf
file_size: 2209325
relation: main_file
file_date_updated: 2020-07-14T12:48:00Z
has_accepted_license: '1'
intvolume: ' 16'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
record:
- id: '9716'
relation: research_data
status: deleted
- id: '9776'
relation: research_data
status: public
- id: '9779'
relation: research_data
status: public
- id: '9777'
relation: research_data
status: public
- id: '8155'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The relation between crosstalk and gene regulation form revisited
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: 16
year: '2020'
...
---
_id: '8013'
article_number: e1007049
article_processing_charge: No
article_type: original
author:
- first_name: Christopher B.
full_name: Currin, Christopher B.
last_name: Currin
- first_name: Phumlani N.
full_name: Khoza, Phumlani N.
last_name: Khoza
- first_name: Alexander D.
full_name: Antrobus, Alexander D.
last_name: Antrobus
- first_name: Peter E.
full_name: Latham, Peter E.
last_name: Latham
- 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: Joseph V.
full_name: Raimondo, Joseph V.
last_name: Raimondo
citation:
ama: 'Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think:
Theory for Africa. PLOS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007049'
apa: 'Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P.,
& Raimondo, J. V. (2019). Think: Theory for Africa. PLOS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007049'
chicago: 'Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter
E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” PLOS
Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007049.'
ieee: 'C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and
J. V. Raimondo, “Think: Theory for Africa,” PLOS Computational Biology,
vol. 15, no. 7. Public Library of Science, 2019.'
ista: 'Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019.
Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049.'
mla: 'Currin, Christopher B., et al. “Think: Theory for Africa.” PLOS Computational
Biology, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007049.'
short: C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo,
PLOS Computational Biology 15 (2019).
date_created: 2020-06-25T12:50:39Z
date_published: 2019-07-11T00:00:00Z
date_updated: 2021-01-12T08:16:31Z
day: '11'
ddc:
- '570'
doi: 10.1371/journal.pcbi.1007049
extern: '1'
external_id:
pmid:
- '31295253'
file:
- access_level: open_access
checksum: 723bdfb6ee5c747cbbb32baf01d17fad
content_type: application/pdf
creator: cziletti
date_created: 2020-07-02T12:22:57Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8079'
file_name: 2019_PlosCompBio_Currin.pdf
file_size: 773969
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: 'Think: Theory for Africa'
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 15
year: '2019'
...
---
_id: '7103'
abstract:
- lang: eng
text: Origin and functions of intermittent transitions among sleep stages, including
short awakenings and arousals, constitute a challenge to the current homeostatic
framework for sleep regulation, focusing on factors modulating sleep over large
time scales. Here we propose that the complex micro-architecture characterizing
the sleep-wake cycle results from an underlying non-equilibrium critical dynamics,
bridging collective behaviors across spatio-temporal scales. We investigate θ
and δ wave dynamics in control rats and in rats with lesions of sleep-promoting
neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and
δ rhythms exhibit a complex temporal organization, with long-range power-law correlations
and a robust duality of power law (θ-bursts, active phase) and exponential-like
(δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium
systems self-organizing at criticality. Crucially, such temporal organization
relates to anti-correlated coupling between θ- and δ-bursts, and is independent
of the dominant physiologic state and lesions, a solid indication of a basic principle
in sleep dynamics.
article_number: e1007268
article_processing_charge: No
article_type: original
author:
- first_name: Jilin W. J. L.
full_name: Wang, Jilin W. J. L.
last_name: Wang
- first_name: Fabrizio
full_name: Lombardi, Fabrizio
id: A057D288-3E88-11E9-986D-0CF4E5697425
last_name: Lombardi
orcid: 0000-0003-2623-5249
- first_name: Xiyun
full_name: Zhang, Xiyun
last_name: Zhang
- first_name: Christelle
full_name: Anaclet, Christelle
last_name: Anaclet
- first_name: Plamen Ch.
full_name: Ivanov, Plamen Ch.
last_name: Ivanov
citation:
ama: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical
dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and
wake micro-architecture. PLoS Computational Biology. 2019;15(11). doi:10.1371/journal.pcbi.1007268
apa: Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., & Ivanov, P. C.
(2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental
characteristic of sleep and wake micro-architecture. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007268
chicago: Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet,
and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ
Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” PLoS
Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007268.
ieee: J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium
critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of
sleep and wake micro-architecture,” PLoS Computational Biology, vol. 15,
no. 11. Public Library of Science, 2019.
ista: Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium
critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of
sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268.
mla: Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in
θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.”
PLoS Computational Biology, vol. 15, no. 11, e1007268, Public Library of
Science, 2019, doi:10.1371/journal.pcbi.1007268.
short: J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational
Biology 15 (2019).
date_created: 2019-11-25T08:20:47Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2025-04-14T07:44:06Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007268
ec_funded: 1
external_id:
isi:
- '000500976100014'
pmid:
- '31725712'
file:
- access_level: open_access
checksum: 2a096a9c6dcc6eaa94077b2603bc6c12
content_type: application/pdf
creator: dernst
date_created: 2019-11-25T08:24:01Z
date_updated: 2020-07-14T12:47:49Z
file_id: '7104'
file_name: 2019_PLOSComBio_Wang.pdf
file_size: 3982516
relation: main_file
file_date_updated: 2020-07-14T12:47:49Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553-7358
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental
characteristic of sleep and wake micro-architecture
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: 15
year: '2019'
...