---
_id: '7105'
abstract:
- lang: eng
text: Cell migration is hypothesized to involve a cycle of behaviours beginning
with leading edge extension. However, recent evidence suggests that the leading
edge may be dispensable for migration, raising the question of what actually controls
cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages
to bridge the different temporal scales of the behaviours controlling motility.
This approach reveals that edge fluctuations during random motility are not persistent
and are weakly correlated with motion. In contrast, flow of the actin network
behind the leading edge is highly persistent. Quantification of actin flow structure
during migration reveals a stable organization and asymmetry in the cell-wide
flowfield that strongly correlates with cell directionality. This organization
is regulated by a gradient of actin network compression and destruction, which
is controlled by myosin contraction and cofilin-mediated disassembly. It is this
stable actin-flow polarity, which integrates rapid fluctuations of the leading
edge, that controls inherent cellular persistence.
article_processing_charge: No
article_type: original
author:
- first_name: Lawrence
full_name: Yolland, Lawrence
last_name: Yolland
- first_name: Mubarik
full_name: Burki, Mubarik
last_name: Burki
- first_name: Stefania
full_name: Marcotti, Stefania
last_name: Marcotti
- first_name: Andrei
full_name: Luchici, Andrei
last_name: Luchici
- first_name: Fiona N.
full_name: Kenny, Fiona N.
last_name: Kenny
- first_name: John Robert
full_name: Davis, John Robert
last_name: Davis
- first_name: Eduardo
full_name: Serna-Morales, Eduardo
last_name: Serna-Morales
- first_name: Jan
full_name: Müller, Jan
id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
last_name: Müller
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Andrew
full_name: Davidson, Andrew
last_name: Davidson
- first_name: Will
full_name: Wood, Will
last_name: Wood
- first_name: Linus J.
full_name: Schumacher, Linus J.
last_name: Schumacher
- first_name: Robert G.
full_name: Endres, Robert G.
last_name: Endres
- first_name: Mark
full_name: Miodownik, Mark
last_name: Miodownik
- first_name: Brian M.
full_name: Stramer, Brian M.
last_name: Stramer
citation:
ama: Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin
flow is essential for directionality during cell migration. Nature Cell Biology.
2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5
apa: Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J.
R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential
for directionality during cell migration. Nature Cell Biology. Springer
Nature. https://doi.org/10.1038/s41556-019-0411-5
chicago: Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona
N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized
Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature
Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5.
ieee: L. Yolland et al., “Persistent and polarized global actin flow is essential
for directionality during cell migration,” Nature Cell Biology, vol. 21,
no. 11. Springer Nature, pp. 1370–1381, 2019.
ista: Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales
E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik
M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for
directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.
mla: Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential
for Directionality during Cell Migration.” Nature Cell Biology, vol. 21,
no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5.
short: L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E.
Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G.
Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.
date_created: 2019-11-25T08:55:00Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-09-06T11:08:52Z
day: '01'
department:
- _id: MiSi
doi: 10.1038/s41556-019-0411-5
external_id:
isi:
- '000495888300009'
pmid:
- '31685997'
intvolume: ' 21'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891
month: '11'
oa: 1
oa_version: Submitted Version
page: 1370-1381
pmid: 1
publication: Nature Cell Biology
publication_identifier:
eissn:
- 1476-4679
issn:
- 1465-7392
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Persistent and polarized global actin flow is essential for directionality
during cell migration
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 21
year: '2019'
...
---
_id: '7109'
abstract:
- lang: eng
text: We show how to construct temporal testers for the logic MITL, a prominent
linear-time logic for real-time systems. A temporal tester is a transducer that
inputs a signal holding the Boolean value of atomic propositions and outputs the
truth value of a formula along time. Here we consider testers over continuous-time
Boolean signals that use clock variables to enforce duration constraints, as in
timed automata. We first rewrite the MITL formula into a “simple” formula using
a limited set of temporal modalities. We then build testers for these specific
modalities and show how to compose testers for simple formulae into complex ones.
Temporal testers can be turned into acceptors, yielding a compositional translation
from MITL to timed automata. This construction is much simpler than previously
known and remains asymptotically optimal. It supports both past and future operators
and can easily be extended.
article_number: '19'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Ničković, Dejan
last_name: Ničković
- first_name: Amir
full_name: Pnueli, Amir
last_name: Pnueli
citation:
ama: Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata.
Journal of the ACM. 2019;66(3). doi:10.1145/3286976
apa: Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time
logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976
chicago: Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time
Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976.
ieee: T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to
timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.
ista: Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed
automata. Journal of the ACM. 66(3), 19.
mla: Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal
of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976.
short: T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019).
date_created: 2019-11-26T10:22:32Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-09-06T11:11:56Z
day: '01'
department:
- _id: ToHe
doi: 10.1145/3286976
external_id:
isi:
- '000495406300005'
intvolume: ' 66'
isi: 1
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: From real-time logic to timed automata
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2019'
...
---
_id: '7108'
abstract:
- lang: eng
text: We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial
complex is shellable is NP-hard, hence NP-complete. This resolves a question raised,
e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d
≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable
is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible
pure d-dimensional complexes. Another simple corollary of our result is that it
is NP-hard to decide whether a given poset is CL-shellable.
article_number: '21'
article_processing_charge: No
article_type: original
author:
- first_name: Xavier
full_name: Goaoc, Xavier
last_name: Goaoc
- first_name: Pavel
full_name: Patak, Pavel
id: B593B804-1035-11EA-B4F1-947645A5BB83
last_name: Patak
- first_name: Zuzana
full_name: Patakova, Zuzana
id: 48B57058-F248-11E8-B48F-1D18A9856A87
last_name: Patakova
orcid: 0000-0002-3975-1683
- first_name: Martin
full_name: Tancer, Martin
last_name: Tancer
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete.
Journal of the ACM. 2019;66(3). doi:10.1145/3314024
apa: Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability
is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024
chicago: Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner.
“Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024.
ieee: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is
NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019.
ista: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete.
Journal of the ACM. 66(3), 21.
mla: Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM,
vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024.
short: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM
66 (2019).
date_created: 2019-11-26T10:13:59Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-09-06T11:10:58Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3314024
external_id:
arxiv:
- '1711.08436'
isi:
- '000495406300007'
intvolume: ' 66'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/1711.08436.pdf
month: '06'
oa: 1
oa_version: Preprint
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '184'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Shellability is NP-complete
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 66
year: '2019'
...
---
_id: '7147'
abstract:
- lang: eng
text: "The expression of a gene is characterised by its transcription factors and
the function processing them. If the transcription factors are not affected by
gene products, the regulating function is often represented as a combinational
logic circuit, where the outputs (product) are determined by current input values
(transcription factors) only, and are hence independent on their relative arrival
times. However, the simultaneous arrival of transcription factors (TFs) in genetic
circuits is a strong assumption, given that the processes of transcription and
translation of a gene into a protein introduce intrinsic time delays and that
there is no global synchronisation among the arrival times of different molecular
species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally
implementable genetic circuit with two inputs and a single output, such that,
in presence of small delays in input arrival, the circuit exhibits qualitatively
distinct observable phenotypes. In particular, these phenotypes are long lived
transients: they all converge to a single value, but so slowly, that they seem
stable for an extended time period, longer than typical experiment duration. We
used rule-based language to prototype our circuit, and we implemented a search
for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe
behaviour of our prototype circuit has wide implications. First, it suggests that
GRNs can exploit event timing to create phenotypes. Second, it opens the possibility
that GRNs are using event timing to react to stimuli and memorise events, without
explicit feedback in regulation. From the modelling perspective, our prototype
circuit demonstrates the critical importance of analysing the transient dynamics
at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
- first_name: Ali
full_name: Sezgin, Ali
id: 4C7638DA-F248-11E8-B48F-1D18A9856A87
last_name: Sezgin
citation:
ama: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene
regulation. In: 17th International Conference on Computational Methods in Systems
Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9'
apa: 'Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019).
Transient memory in gene regulation. In 17th International Conference on Computational
Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer
Nature. https://doi.org/10.1007/978-3-030-31304-3_9'
chicago: Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali
Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference
on Computational Methods in Systems Biology, 11773:155–87. Springer Nature,
2019. https://doi.org/10.1007/978-3-030-31304-3_9.
ieee: C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient
memory in gene regulation,” in 17th International Conference on Computational
Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187.
ista: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory
in gene regulation. 17th International Conference on Computational Methods in
Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773,
155–187.'
mla: Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International
Conference on Computational Methods in Systems Biology, vol. 11773, Springer
Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9.
short: C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International
Conference on Computational Methods in Systems Biology, Springer Nature, 2019,
pp. 155–187.
conference:
end_date: 2019-09-20
location: Trieste, Italy
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2019-09-18
date_created: 2019-12-04T16:07:50Z
date_published: 2019-09-17T00:00:00Z
date_updated: 2023-09-06T11:18:08Z
day: '17'
department:
- _id: CaGu
- _id: ToHe
doi: 10.1007/978-3-030-31304-3_9
external_id:
isi:
- '000557875100009'
intvolume: ' 11773'
isi: 1
language:
- iso: eng
month: '09'
oa_version: None
page: 155-187
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture
publication: 17th International Conference on Computational Methods in Systems Biology
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030313036'
- '9783030313043'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transient memory in gene regulation
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11773
year: '2019'
...
---
_id: '7136'
abstract:
- lang: eng
text: "It is well established that the notion of min-entropy fails to satisfy the
\\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy.
Such a property would help to analyze how min-entropy is split among smaller blocks.
Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe
show that any sequence of variables exhibits a very strong strong block-source
structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil
few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination
properties} hold. In particular, we have many nice properties that min-entropy
doesn't obey in general, for example strong chain rules, \"information can't hurt\"
inequalities, equivalences of average and worst-case conditional entropy definitions
and others. Quantitatively, for any sequence X1,…,Xt of random variables over
an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt)
bits of auxiliary information, all conditional distributions of the form Xi|X2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240'
apa: 'Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled.
In 2019 IEEE International Symposium on Information Theory. Paris, France:
IEEE. https://doi.org/10.1109/isit.2019.8849240'
chicago: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.”
In 2019 IEEE International Symposium on Information Theory. IEEE, 2019.
https://doi.org/10.1109/isit.2019.8849240.
ieee: M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in
2019 IEEE International Symposium on Information Theory, Paris, France,
2019.
ista: 'Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled.
2019 IEEE International Symposium on Information Theory. ISIT: International Symposium
on Information Theory, 8849240.'
mla: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.”
2019 IEEE International Symposium on Information Theory, 8849240, IEEE,
2019, doi:10.1109/isit.2019.8849240.
short: M. Skórski, in:, 2019 IEEE International Symposium on Information Theory,
IEEE, 2019.
conference:
end_date: 2019-07-12
location: Paris, France
name: 'ISIT: International Symposium on Information Theory'
start_date: 2019-07-07
date_created: 2019-11-28T10:19:21Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-09-06T11:15:41Z
day: '01'
department:
- _id: KrPi
doi: 10.1109/isit.2019.8849240
external_id:
arxiv:
- '1702.08476'
isi:
- '000489100301043'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1702.08476
month: '07'
oa: 1
oa_version: Preprint
publication: 2019 IEEE International Symposium on Information Theory
publication_identifier:
isbn:
- '9781538692912'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strong chain rules for min-entropy under few bits spoiled
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...