---
_id: '956'
abstract:
- lang: eng
text: We study a class of ergodic quantum Markov semigroups on finite-dimensional
unital C⁎-algebras. These semigroups have a unique stationary state σ, and we
are concerned with those that satisfy a quantum detailed balance condition with
respect to σ. We show that the evolution on the set of states that is given by
such a quantum Markov semigroup is gradient flow for the relative entropy with
respect to σ in a particular Riemannian metric on the set of states. This metric
is a non-commutative analog of the 2-Wasserstein metric, and in several interesting
cases we are able to show, in analogy with work of Otto on gradient flows with
respect to the classical 2-Wasserstein metric, that the relative entropy is strictly
and uniformly convex with respect to the Riemannian metric introduced here. As
a consequence, we obtain a number of new inequalities for the decay of relative
entropy for ergodic quantum Markov semigroups with detailed balance.
article_processing_charge: No
author:
- first_name: Eric
full_name: Carlen, Eric
last_name: Carlen
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov
semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869.
doi:10.1016/j.jfa.2017.05.003
apa: Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for
quantum Markov semigroups with detailed balance. Journal of Functional Analysis.
Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003
chicago: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for
Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis.
Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003.
ieee: E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance,” Journal of Functional Analysis,
vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.
ista: Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5),
1810–1869.
mla: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum
Markov Semigroups with Detailed Balance.” Journal of Functional Analysis,
vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.
short: E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2023-09-22T10:00:18Z
day: '01'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2017.05.003
external_id:
isi:
- '000406082300005'
intvolume: ' 273'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.01254
month: '09'
oa: 1
oa_version: Submitted Version
page: 1810 - 1869
publication: Journal of Functional Analysis
publication_identifier:
issn:
- '00221236'
publication_status: published
publisher: Academic Press
publist_id: '6452'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradient flow and entropy inequalities for quantum Markov semigroups with detailed
balance
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 273
year: '2017'
...
---
_id: '957'
abstract:
- lang: eng
text: Small molecule biosensors based on Forster resonance energy transfer (FRET)
enable small molecule signaling to be monitored with high spatial and temporal
resolution in complex cellular environments. FRET sensors can be constructed by
fusing a pair of fluorescent proteins to a suitable recognition domain, such as
a member of the solute-binding protein (SBP) superfamily. However, naturally occurring
SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability,
which may preclude imaging under physiological conditions, or because the positions
of their N- and C-termini may be suboptimal for fusion of fluorescent proteins,
which may limit the dynamic range of the resulting sensors. Here, we show how
these problems can be overcome using ancestral protein reconstruction and circular
permutation. Ancestral protein reconstruction, used as a protein engineering strategy,
leverages phylogenetic information to improve the thermostability of proteins,
while circular permutation enables the termini of an SBP to be repositioned to
maximize the dynamic range of the resulting FRET sensor. We also provide a protocol
for cloning the engineered SBPs into FRET sensor constructs using Golden Gate
assembly and discuss considerations for in situ characterization of the FRET sensors.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction
and circular permutation for improving the stability and dynamic range of FRET
sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic
Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5'
apa: Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C.,
Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and
circular permutation for improving the stability and dynamic range of FRET sensors.
In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_5
chicago: Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde,
Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein
Reconstruction and Circular Permutation for Improving the Stability and Dynamic
Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor
Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.
ieee: B. Clifton et al., “Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors,” in Synthetic
Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.
ista: 'Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak
HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 71–87.'
mla: Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation
for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein
Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.
short: B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L.
Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer,
2017, pp. 71–87.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-03-15T00:00:00Z
date_updated: 2021-01-12T08:22:13Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_5
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
intvolume: ' 1596'
language:
- iso: eng
month: '03'
oa_version: None
page: 71 - 87
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors (HFSP Young Investigator)
publication: Synthetic Protein Switches
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6451'
quality_controlled: '1'
scopus_import: 1
series_title: Synthetic Protein Switches
status: public
title: Ancestral protein reconstruction and circular permutation for improving the
stability and dynamic range of FRET sensors
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '9574'
abstract:
- lang: eng
text: 'Consider the sum X(ξ)=∑ni=1aiξi, where a=(ai)ni=1 is a sequence of non-zero
reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that
is, Pr[ξi=1]=Pr[ξi=−1]=1/2). The classical Littlewood-Offord problem asks for
the best possible upper bound on the concentration probabilities Pr[X=x]. In this
paper we study a resilience version of the Littlewood-Offord problem: how many
of the ξi is an adversary typically allowed to change without being able to force
concentration on a particular value? We solve this problem asymptotically, and
present a few interesting open problems.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Afonso S.
full_name: Bandeira, Afonso S.
last_name: Bandeira
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
citation:
ama: Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood-Offord problem.
Electronic Notes in Discrete Mathematics. 2017;61:93-99. doi:10.1016/j.endm.2017.06.025
apa: Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood-Offord
problem. Electronic Notes in Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.endm.2017.06.025
chicago: Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for
the Littlewood-Offord Problem.” Electronic Notes in Discrete Mathematics.
Elsevier, 2017. https://doi.org/10.1016/j.endm.2017.06.025.
ieee: A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood-Offord
problem,” Electronic Notes in Discrete Mathematics, vol. 61. Elsevier,
pp. 93–99, 2017.
ista: Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood-Offord
problem. Electronic Notes in Discrete Mathematics. 61, 93–99.
mla: Bandeira, Afonso S., et al. “Resilience for the Littlewood-Offord Problem.”
Electronic Notes in Discrete Mathematics, vol. 61, Elsevier, 2017, pp.
93–99, doi:10.1016/j.endm.2017.06.025.
short: A.S. Bandeira, A. Ferber, M.A. Kwan, Electronic Notes in Discrete Mathematics
61 (2017) 93–99.
date_created: 2021-06-21T06:31:10Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2023-02-23T14:01:26Z
day: '01'
doi: 10.1016/j.endm.2017.06.025
extern: '1'
external_id:
arxiv:
- '1609.08136'
intvolume: ' 61'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.08136
month: '08'
oa: 1
oa_version: Preprint
page: 93-99
publication: Electronic Notes in Discrete Mathematics
publication_identifier:
issn:
- 1571-0653
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resilience for the Littlewood-Offord problem
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 61
year: '2017'
...
---
_id: '958'
abstract:
- lang: eng
text: Biosensors that exploit Forster resonance energy transfer (FRET) can be used
to visualize biological and physiological processes and are capable of providing
detailed information in both spatial and temporal dimensions. In a FRET-based
biosensor, substrate binding is associated with a change in the relative positions
of two fluorophores, leading to a change in FRET efficiency that may be observed
in the fluorescence spectrum. As a result, their design requires a ligand-binding
protein that exhibits a conformational change upon binding. However, not all ligand-binding
proteins produce responsive sensors upon conjugation to fluorescent proteins or
dyes, and identifying the optimum locations for the fluorophores often involves
labor-intensive iterative design or high-throughput screening. Combining the genetic
fusion of a fluorescent protein to the ligand-binding protein with site-specific
covalent attachment of a fluorescent dye can allow fine control over the positions
of the two fluorophores, allowing the construction of very sensitive sensors.
This relies upon the accurate prediction of the locations of the two fluorophores
in bound and unbound states. In this chapter, we describe a method for computational
identification of dye-attachment sites that allows the use of cysteine modification
to attach synthetic dyes that can be paired with a fluorescent protein for the
purposes of creating FRET sensors.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Megan
full_name: O'Mara, Megan
last_name: O'Mara
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors
using a synthetic dye fluorescent protein FRET pair and computational modeling
and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596.
Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6'
apa: Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara,
M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic
dye fluorescent protein FRET pair and computational modeling and assessment. In
V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_6
chicago: Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald
L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors
Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling
and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein,
1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.
ieee: J. Mitchell et al., “Method for developing optical sensors using a
synthetic dye fluorescent protein FRET pair and computational modeling and assessment,”
in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017,
pp. 89–99.
ista: 'Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson
C. 2017.Method for developing optical sensors using a synthetic dye fluorescent
protein FRET pair and computational modeling and assessment. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 89–99.'
mla: Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic
Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.”
Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer,
2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.
short: J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara,
C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp.
89–99.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-05-15T00:00:00Z
date_updated: 2021-01-12T08:22:13Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_6
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
intvolume: ' 1596'
language:
- iso: eng
month: '05'
oa_version: None
page: 89 - 99
publication: Synthetic Protein Switches
publication_identifier:
issn:
- '10643745'
publication_status: published
publisher: Springer
publist_id: '6450'
quality_controlled: '1'
scopus_import: 1
series_title: Synthetic Protein Switches
status: public
title: Method for developing optical sensors using a synthetic dye fluorescent protein
FRET pair and computational modeling and assessment
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '9588'
abstract:
- lang: eng
text: 'Consider the sum X(ξ)=∑ni=1aiξi , where a=(ai)ni=1 is a sequence of non-zero
reals and ξ=(ξi)ni=1 is a sequence of i.i.d. Rademacher random variables (that
is, Pr[ξi=1]=Pr[ξi=−1]=1/2 ). The classical Littlewood-Offord problem asks for
the best possible upper bound on the concentration probabilities Pr[X=x] . In
this paper we study a resilience version of the Littlewood-Offord problem: how
many of the ξi is an adversary typically allowed to change without being able
to force concentration on a particular value? We solve this problem asymptotically,
and present a few interesting open problems.'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Afonso S.
full_name: Bandeira, Afonso S.
last_name: Bandeira
- first_name: Asaf
full_name: Ferber, Asaf
last_name: Ferber
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
citation:
ama: Bandeira AS, Ferber A, Kwan MA. Resilience for the Littlewood–Offord problem.
Advances in Mathematics. 2017;319:292-312. doi:10.1016/j.aim.2017.08.031
apa: Bandeira, A. S., Ferber, A., & Kwan, M. A. (2017). Resilience for the Littlewood–Offord
problem. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2017.08.031
chicago: Bandeira, Afonso S., Asaf Ferber, and Matthew Alan Kwan. “Resilience for
the Littlewood–Offord Problem.” Advances in Mathematics. Elsevier, 2017.
https://doi.org/10.1016/j.aim.2017.08.031.
ieee: A. S. Bandeira, A. Ferber, and M. A. Kwan, “Resilience for the Littlewood–Offord
problem,” Advances in Mathematics, vol. 319. Elsevier, pp. 292–312, 2017.
ista: Bandeira AS, Ferber A, Kwan MA. 2017. Resilience for the Littlewood–Offord
problem. Advances in Mathematics. 319, 292–312.
mla: Bandeira, Afonso S., et al. “Resilience for the Littlewood–Offord Problem.”
Advances in Mathematics, vol. 319, Elsevier, 2017, pp. 292–312, doi:10.1016/j.aim.2017.08.031.
short: A.S. Bandeira, A. Ferber, M.A. Kwan, Advances in Mathematics 319 (2017) 292–312.
date_created: 2021-06-22T11:51:27Z
date_published: 2017-10-15T00:00:00Z
date_updated: 2023-02-23T14:01:57Z
day: '15'
doi: 10.1016/j.aim.2017.08.031
extern: '1'
external_id:
arxiv:
- '1609.08136'
intvolume: ' 319'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.08136
month: '10'
oa: 1
oa_version: Preprint
page: 292-312
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Resilience for the Littlewood–Offord problem
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 319
year: '2017'
...
---
_id: '9589'
abstract:
- lang: eng
text: We give an asymptotic expression for the expected number of spanning trees
in a random graph with a given degree sequence , provided that the number of edges
is at least , where is the maximum degree. A key part of our argument involves
establishing a concentration result for a certain family of functions over random
trees with given degrees, using Prüfer codes.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Catherine
full_name: Greenhill, Catherine
last_name: Greenhill
- first_name: Mikhail
full_name: Isaev, Mikhail
last_name: Isaev
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Brendan D.
full_name: McKay, Brendan D.
last_name: McKay
citation:
ama: Greenhill C, Isaev M, Kwan MA, McKay BD. The average number of spanning trees
in sparse graphs with given degrees. European Journal of Combinatorics.
2017;63:6-25. doi:10.1016/j.ejc.2017.02.003
apa: Greenhill, C., Isaev, M., Kwan, M. A., & McKay, B. D. (2017). The average
number of spanning trees in sparse graphs with given degrees. European Journal
of Combinatorics. Elsevier. https://doi.org/10.1016/j.ejc.2017.02.003
chicago: Greenhill, Catherine, Mikhail Isaev, Matthew Alan Kwan, and Brendan D.
McKay. “The Average Number of Spanning Trees in Sparse Graphs with given Degrees.”
European Journal of Combinatorics. Elsevier, 2017. https://doi.org/10.1016/j.ejc.2017.02.003.
ieee: C. Greenhill, M. Isaev, M. A. Kwan, and B. D. McKay, “The average number of
spanning trees in sparse graphs with given degrees,” European Journal of Combinatorics,
vol. 63. Elsevier, pp. 6–25, 2017.
ista: Greenhill C, Isaev M, Kwan MA, McKay BD. 2017. The average number of spanning
trees in sparse graphs with given degrees. European Journal of Combinatorics.
63, 6–25.
mla: Greenhill, Catherine, et al. “The Average Number of Spanning Trees in Sparse
Graphs with given Degrees.” European Journal of Combinatorics, vol. 63,
Elsevier, 2017, pp. 6–25, doi:10.1016/j.ejc.2017.02.003.
short: C. Greenhill, M. Isaev, M.A. Kwan, B.D. McKay, European Journal of Combinatorics
63 (2017) 6–25.
date_created: 2021-06-22T12:18:59Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T14:02:00Z
day: '01'
doi: 10.1016/j.ejc.2017.02.003
extern: '1'
external_id:
arxiv:
- '1606.01586'
intvolume: ' 63'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.ejc.2017.02.003
month: '06'
oa: 1
oa_version: Published Version
page: 6-25
publication: European Journal of Combinatorics
publication_identifier:
issn:
- 0195-6698
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The average number of spanning trees in sparse graphs with given degrees
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 63
year: '2017'
...
---
_id: '959'
abstract:
- lang: eng
text: In this work it is shown that scale-free tails in metabolic flux distributions
inferred in stationary models are an artifact due to reactions involved in thermodynamically
unfeasible cycles, unbounded by physical constraints and in principle able to
perform work without expenditure of free energy. After implementing thermodynamic
constraints by removing such loops, metabolic flux distributions scale meaningfully
with the physical limiting factors, acquiring in turn a richer multimodal structure
potentially leading to symmetry breaking while optimizing for objective functions.
article_processing_charge: No
author:
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
citation:
ama: De Martino D. Scales and multimodal flux distributions in stationary metabolic
network models via thermodynamics. Physical Review E Statistical Nonlinear
and Soft Matter Physics . 2017;95(6):062419. doi:10.1103/PhysRevE.95.062419
apa: De Martino, D. (2017). Scales and multimodal flux distributions in stationary
metabolic network models via thermodynamics. Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics. https://doi.org/10.1103/PhysRevE.95.062419
chicago: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary
Metabolic Network Models via Thermodynamics.” Physical Review E Statistical
Nonlinear and Soft Matter Physics . American Institute of Physics, 2017. https://doi.org/10.1103/PhysRevE.95.062419.
ieee: D. De Martino, “Scales and multimodal flux distributions in stationary metabolic
network models via thermodynamics,” Physical Review E Statistical Nonlinear
and Soft Matter Physics , vol. 95, no. 6. American Institute of Physics, p.
062419, 2017.
ista: De Martino D. 2017. Scales and multimodal flux distributions in stationary
metabolic network models via thermodynamics. Physical Review E Statistical Nonlinear
and Soft Matter Physics . 95(6), 062419.
mla: De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary
Metabolic Network Models via Thermodynamics.” Physical Review E Statistical
Nonlinear and Soft Matter Physics , vol. 95, no. 6, American Institute of
Physics, 2017, p. 062419, doi:10.1103/PhysRevE.95.062419.
short: D. De Martino, Physical Review E Statistical Nonlinear and Soft Matter Physics 95
(2017) 062419.
date_created: 2018-12-11T11:49:25Z
date_published: 2017-06-28T00:00:00Z
date_updated: 2023-09-22T09:59:01Z
day: '28'
department:
- _id: GaTk
doi: 10.1103/PhysRevE.95.062419
ec_funded: 1
external_id:
isi:
- '000404546400004'
intvolume: ' 95'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/1703.00853.pdf
month: '06'
oa: 1
oa_version: Submitted Version
page: '062419'
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Physical Review E Statistical Nonlinear and Soft Matter Physics '
publication_identifier:
issn:
- '24700045'
publication_status: published
publisher: American Institute of Physics
publist_id: '6446'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scales and multimodal flux distributions in stationary metabolic network models
via thermodynamics
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 95
year: '2017'
...
---
_id: '9590'
abstract:
- lang: eng
text: We show that for any fixed dense graph G and bounded-degree tree T on the
same number of vertices, a modest random perturbation of G will typically contain
a copy of T . This combines the viewpoints of the well-studied problems of embedding
trees into fixed dense graphs and into random graphs, and extends a sizeable body
of existing research on randomly perturbed graphs. Specifically, we show that
there is c=c(α,Δ) such that if G is an n-vertex graph with minimum degree at least
αn, and T is an n-vertex tree with maximum degree at most Δ , then if we add cn
uniformly random edges to G, the resulting graph will contain T asymptotically
almost surely (as n→∞ ). Our proof uses a lemma concerning the decomposition of
a dense graph into super-regular pairs of comparable sizes, which may be of independent
interest.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Krivelevich, Michael
last_name: Krivelevich
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Krivelevich M, Kwan MA, Sudakov B. Bounded-degree spanning trees in randomly
perturbed graphs. SIAM Journal on Discrete Mathematics. 2017;31(1):155-171.
doi:10.1137/15m1032910
apa: Krivelevich, M., Kwan, M. A., & Sudakov, B. (2017). Bounded-degree spanning
trees in randomly perturbed graphs. SIAM Journal on Discrete Mathematics.
Society for Industrial & Applied Mathematics. https://doi.org/10.1137/15m1032910
chicago: Krivelevich, Michael, Matthew Alan Kwan, and Benny Sudakov. “Bounded-Degree
Spanning Trees in Randomly Perturbed Graphs.” SIAM Journal on Discrete Mathematics.
Society for Industrial & Applied Mathematics, 2017. https://doi.org/10.1137/15m1032910.
ieee: M. Krivelevich, M. A. Kwan, and B. Sudakov, “Bounded-degree spanning trees
in randomly perturbed graphs,” SIAM Journal on Discrete Mathematics, vol.
31, no. 1. Society for Industrial & Applied Mathematics, pp. 155–171, 2017.
ista: Krivelevich M, Kwan MA, Sudakov B. 2017. Bounded-degree spanning trees in
randomly perturbed graphs. SIAM Journal on Discrete Mathematics. 31(1), 155–171.
mla: Krivelevich, Michael, et al. “Bounded-Degree Spanning Trees in Randomly Perturbed
Graphs.” SIAM Journal on Discrete Mathematics, vol. 31, no. 1, Society
for Industrial & Applied Mathematics, 2017, pp. 155–71, doi:10.1137/15m1032910.
short: M. Krivelevich, M.A. Kwan, B. Sudakov, SIAM Journal on Discrete Mathematics
31 (2017) 155–171.
date_created: 2021-06-22T12:26:25Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2023-02-23T14:02:05Z
day: '12'
doi: 10.1137/15m1032910
extern: '1'
external_id:
arxiv:
- '1507.07960'
intvolume: ' 31'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1507.07960
month: '01'
oa: 1
oa_version: Preprint
page: 155-171
publication: SIAM Journal on Discrete Mathematics
publication_identifier:
eissn:
- 1095-7146
issn:
- 0895-4801
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bounded-degree spanning trees in randomly perturbed graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 31
year: '2017'
...
---
_id: '960'
abstract:
- lang: eng
text: The human cerebral cortex is the seat of our cognitive abilities and composed
of an extraordinary number of neurons, organized in six distinct layers. The establishment
of specific morphological and physiological features in individual neurons needs
to be regulated with high precision. Impairments in the sequential developmental
programs instructing corticogenesis lead to alterations in the cortical cytoarchitecture
which is thought to represent the major underlying cause for several neurological
disorders including neurodevelopmental and psychiatric diseases. In this review
we discuss the role of cell polarity at sequential stages during cortex development.
We first provide an overview of morphological cell polarity features in cortical
neural stem cells and newly-born postmitotic neurons. We then synthesize a conceptual
molecular and biochemical framework how cell polarity is established at the cellular
level through a break in symmetry in nascent cortical projection neurons. Lastly
we provide a perspective how the molecular mechanisms applying to single cells
could be probed and integrated in an in vivo and tissue-wide context.
article_number: '176'
article_processing_charge: Yes
author:
- first_name: Andi H
full_name: Hansen, Andi H
id: 38853E16-F248-11E8-B48F-1D18A9856A87
last_name: Hansen
- first_name: Christian F
full_name: Düllberg, Christian F
id: 459064DC-F248-11E8-B48F-1D18A9856A87
last_name: Düllberg
orcid: 0000-0001-6335-9748
- first_name: Christine
full_name: Mieck, Christine
id: 34CAE85C-F248-11E8-B48F-1D18A9856A87
last_name: Mieck
orcid: 0000-0003-1919-7416
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. Cell polarity in cerebral
cortex development - cellular architecture shaped by biochemical networks. Frontiers
in Cellular Neuroscience. 2017;11. doi:10.3389/fncel.2017.00176
apa: Hansen, A. H., Düllberg, C. F., Mieck, C., Loose, M., & Hippenmeyer, S.
(2017). Cell polarity in cerebral cortex development - cellular architecture shaped
by biochemical networks. Frontiers in Cellular Neuroscience. Frontiers
Research Foundation. https://doi.org/10.3389/fncel.2017.00176
chicago: Hansen, Andi H, Christian F Düllberg, Christine Mieck, Martin Loose, and
Simon Hippenmeyer. “Cell Polarity in Cerebral Cortex Development - Cellular Architecture
Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience. Frontiers
Research Foundation, 2017. https://doi.org/10.3389/fncel.2017.00176.
ieee: A. H. Hansen, C. F. Düllberg, C. Mieck, M. Loose, and S. Hippenmeyer, “Cell
polarity in cerebral cortex development - cellular architecture shaped by biochemical
networks,” Frontiers in Cellular Neuroscience, vol. 11. Frontiers Research
Foundation, 2017.
ista: Hansen AH, Düllberg CF, Mieck C, Loose M, Hippenmeyer S. 2017. Cell polarity
in cerebral cortex development - cellular architecture shaped by biochemical networks.
Frontiers in Cellular Neuroscience. 11, 176.
mla: Hansen, Andi H., et al. “Cell Polarity in Cerebral Cortex Development - Cellular
Architecture Shaped by Biochemical Networks.” Frontiers in Cellular Neuroscience,
vol. 11, 176, Frontiers Research Foundation, 2017, doi:10.3389/fncel.2017.00176.
short: A.H. Hansen, C.F. Düllberg, C. Mieck, M. Loose, S. Hippenmeyer, Frontiers
in Cellular Neuroscience 11 (2017).
date_created: 2018-12-11T11:49:25Z
date_published: 2017-06-28T00:00:00Z
date_updated: 2024-03-25T23:30:23Z
day: '28'
ddc:
- '570'
department:
- _id: SiHi
- _id: MaLo
doi: 10.3389/fncel.2017.00176
ec_funded: 1
external_id:
isi:
- '000404486700001'
file:
- access_level: open_access
checksum: dc1f5a475b918d09a0f9f587400b1626
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:40Z
date_updated: 2020-07-14T12:48:16Z
file_id: '4764'
file_name: IST-2017-830-v1+1_2017_Hansen_CellPolarity.pdf
file_size: 2153858
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25985A36-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: T00817-B21
name: The biochemical basis of PAR polarization
publication: Frontiers in Cellular Neuroscience
publication_identifier:
issn:
- '16625102'
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '6445'
pubrep_id: '830'
quality_controlled: '1'
related_material:
record:
- id: '9962'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Cell polarity in cerebral cortex development - cellular architecture shaped
by biochemical networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11
year: '2017'
...
---
_id: '961'
abstract:
- lang: eng
text: Cell-cell contact formation constitutes the first step in the emergence of multicellularity in
evolution, thereby allowing the differentiation of specialized cell types. In metazoan
development, cell-cell contact formation is thought to influence cell fate specification,
and cell fate specification has been implicated in cell-cell contact
formation. However, remarkably little is yet known about whether and how the
interaction and feedback between cell-cell contact formation and cell fate specification
affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and
mesendoderm cell fate specification during zebrafish gastrulation. We show that long
lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor
cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further
show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an
effective positive feedback loop between ppl cell-cell contact duration and cell fate
specification. Finally, by using a combination of theoretical modeling and experimentation,
we show that this feedback loop determines whether anterior axial mesendoderm cells
become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal
that the gene regulatory networks leading to cell fate diversification within the developing
embryo are controlled by the interdependent activities of cell-cell signaling and contact
formation.
acknowledgement: "Many people accompanied me during this trip: I would not have reached
my destination nor \r\nenjoyed the travelling without them. First of all, thanks
to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting
and incredibly competent people and thanks for \r\nall the good science I witnessed
\ and participated in. It has been a \r\nblast, an incredibly \r\nexciting
\ one! Thanks to JLo, for teaching me how to master my pipettes and
\ showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching
me basically everything \r\nabout zebrafish and being always there to advice,
\ sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the
critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing
kicker matches, and Keisuke, for showing me the light, and to the three of them
\r\ntogether for all the good laughs we\r\nhad. My start in Vienna would
\ have been a lot more \r\ndifficult without you guys. Also it would not
\ have been possible without Elena and Inês: \r\nthanks for helping setting
\ up this lab and for the dinners in Gugging. Thanks to Martin, for
\r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp,
\ for the interest and \r\nadvice, and to Michael, for the Viennise take on things.
Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend
in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel
for the enthusiasm and the neverending energy and for all your \r\nhelp over the
years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat.
\ To Shayan, for being such a motivated student. To Matt, for helping
\ out\r\nwith coding \r\nand for finding punk solutions to data analysis problems.
Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla,
Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful
\ atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments
would have been much more difficult without your help. Special thanks to Katjia
\r\nfor setting up an amazing imaging facility and for building the best
\ team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith
all the late sortings and for helping with all \r\nthe technical problems. Thanks
to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald
Janovjak for being a present and helpful committee member over the years \r\nand
\ to Patrick Lemaire f\r\nor the helpful insight and extremely interesting
\ discussion we had \r\nabout the project. Also, this journey would not
\ have been the same without all the friends \r\nthat I met in Dresden and
then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne,
Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph,
\r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled
my days with \r\nfun and support. A special thank to my family, always close even
if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William,
\ e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri
di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe
crazy life of a scientist, the living apart for\r\nso long, never knowing when things
are going \r\nto happen. Thanks for being a great partner and my number one fan!"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
citation:
ama: 'Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish
gastrulation. 2017. doi:10.15479/AT:ISTA:th_825'
apa: 'Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop
during zebrafish gastrulation. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:th_825'
chicago: 'Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop
during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017.
https://doi.org/10.15479/AT:ISTA:th_825.'
ieee: 'V. Barone, “Cell adhesion and cell fate: An effective feedback loop during
zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.'
ista: 'Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during
zebrafish gastrulation. Institute of Science and Technology Austria.'
mla: 'Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop
during Zebrafish Gastrulation. Institute of Science and Technology Austria,
2017, doi:10.15479/AT:ISTA:th_825.'
short: 'V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during
Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.'
date_created: 2018-12-11T11:49:25Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-27T14:16:45Z
day: '01'
ddc:
- '570'
- '590'
degree_awarded: PhD
department:
- _id: CaHe
doi: 10.15479/AT:ISTA:th_825
file:
- access_level: closed
checksum: 242f88c87f2cf267bf05049fa26a687b
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:36:52Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6205'
file_name: 2017_Barone_thesis_final.docx
file_size: 14497822
relation: source_file
- access_level: open_access
checksum: ba5b0613ed8bade73a409acdd880fb8a
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:36:52Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6206'
file_name: 2017_Barone_thesis_.pdf
file_size: 14995941
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '109'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6444'
pubrep_id: '825'
related_material:
record:
- id: '1100'
relation: part_of_dissertation
status: public
- id: '1537'
relation: part_of_dissertation
status: public
- id: '1912'
relation: part_of_dissertation
status: public
- id: '2926'
relation: part_of_dissertation
status: public
- id: '3246'
relation: part_of_dissertation
status: public
- id: '676'
relation: part_of_dissertation
status: public
- id: '735'
relation: part_of_dissertation
status: public
status: public
supervisor:
- 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
title: 'Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation'
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: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '962'
abstract:
- lang: eng
text: 'We present a new algorithm for model counting of a class of string constraints.
In addition to the classic operation of concatenation, our class includes some
recursively defined operations such as Kleene closure, and replacement of substrings.
Additionally, our class also includes length constraints on the string expressions,
which means, by requiring reasoning about numbers, that we face a multi-sorted
logic. In the end, our string constraints are motivated by their use in programming
for web applications. Our algorithm comprises two novel features: the ability
to use a technique of (1) partial derivatives for constraints that are already
in a solved form, i.e. a form where its (string) satisfiability is clearly displayed,
and (2) non-progression, where cyclic reasoning in the reduction process may be
terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally
compare our model counter with two recent works on model counting of similar constraints,
SMC [18] and ABC [5], to demonstrate its superior performance.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Minh
full_name: Trinh, Minh
last_name: Trinh
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: Joxan
full_name: Jaffar, Joxan
last_name: Jaffar
citation:
ama: 'Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings.
In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21'
apa: 'Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined
strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented
at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21'
chicago: Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined
Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer,
2017. https://doi.org/10.1007/978-3-319-63390-9_21.
ieee: 'M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined
strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany,
2017, vol. 10427, pp. 399–418.'
ista: 'Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings.
CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.'
mla: Trinh, Minh, et al. Model Counting for Recursively-Defined Strings.
Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418,
doi:10.1007/978-3-319-63390-9_21.
short: M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer,
2017, pp. 399–418.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:49:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-22T09:58:02Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-63390-9_21
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
isi:
- '000431900900021'
intvolume: ' 10427'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 399 - 418
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication_identifier:
issn:
- '03029743'
publication_status: published
publisher: Springer
publist_id: '6443'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model counting for recursively-defined strings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10427
year: '2017'
...
---
_id: '963'
abstract:
- lang: eng
text: 'Network games are widely used as a model for selfish resource-allocation
problems. In the classical model, each player selects a path connecting her source
and target vertex. The cost of traversing an edge depends on the number of players
that traverse it. Thus, it abstracts the fact that different users may use a resource
at different times and for different durations, which plays an important role
in defining the costs of the users in reality. For example, when transmitting
packets in a communication network, routing traffic in a road network, or processing
a task in a production system, the traversal of the network involves an inherent
delay, and so sharing and congestion of resources crucially depends on time. We
study timed network games , which add a time component to network games. Each
vertex v in the network is associated with a cost function, mapping the load on
v to the price that a player pays for staying in v for one time unit with this
load. In addition, each edge has a guard, describing time intervals in which the
edge can be traversed, forcing the players to spend time on vertices. Unlike earlier
work that add a time component to network games, the time in our model is continuous
and cannot be discretized. In particular, players have uncountably many strategies,
and a game may have uncountably many pure Nash equilibria. We study properties
of timed network games with cost-sharing or congestion cost functions: their stability,
equilibrium inefficiency, and complexity. In particular, we show that the answer
to the question whether we can restrict attention to boundary strategies, namely
ones in which edges are traversed only at the boundaries of guards, is mixed. '
alternative_title:
- LIPIcs
article_number: '37'
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks
(Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science
(SG), Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science (SG), Aalborg, Denmark,
2017, vol. 83.'
ista: 'Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 83, 37.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science (SG)'
start_date: 2017-08-21
date_created: 2018-12-11T11:49:26Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-02-23T12:35:50Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.MFCS.2017.37
file:
- access_level: open_access
checksum: f55eaf7f3c36ea07801112acfedd17d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:10Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5059'
file_name: IST-2017-829-v1+1_mfcs-cr.pdf
file_size: 369730
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- '18688969'
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6438'
pubrep_id: '829'
quality_controlled: '1'
related_material:
record:
- id: '6005'
relation: later_version
status: public
scopus_import: 1
status: public
title: Timed network games with clocks
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2017'
...
---
_id: '9660'
abstract:
- lang: eng
text: In this paper we discuss how the information contained in atomistic simulations
of homogeneous nucleation should be used when fitting the parameters in macroscopic
nucleation models. We show how the number of solid and liquid atoms in such simulations
can be determined unambiguously by using a Gibbs dividing surface and how the
free energy as a function of the number of solid atoms in the nucleus can thus
be extracted. We then show that the parameters (the chemical potential, the interfacial
free energy, and a Tolman correction) of a model based on classical nucleation
theory can be fitted using the information contained in these free-energy profiles
but that the parameters in such models are highly correlated. This correlation
is unfortunate as it ensures that small errors in the computed free energy surface
can give rise to large errors in the extrapolated properties of the fitted model.
To resolve this problem we thus propose a method for fitting macroscopic nucleation
models that uses simulations of planar interfaces and simulations of three-dimensional
nuclei in tandem. We show that when the chemical potentials and the interface
energy are pinned to their planar-interface values, more precise estimates for
the Tolman length are obtained. Extrapolating the free energy profile obtained
from small simulation boxes to larger nuclei is thus more reliable.
article_number: '104707'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Cheng B, Tribello GA, Ceriotti M. The Gibbs free energy of homogeneous nucleation:
From atomistic nuclei to the planar limit. The Journal of Chemical Physics.
2017;147(10). doi:10.1063/1.4997180'
apa: 'Cheng, B., Tribello, G. A., & Ceriotti, M. (2017). The Gibbs free energy
of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/1.4997180'
chicago: 'Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs
Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.”
The Journal of Chemical Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4997180.'
ieee: 'B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous
nucleation: From atomistic nuclei to the planar limit,” The Journal of Chemical
Physics, vol. 147, no. 10. AIP Publishing, 2017.'
ista: 'Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous
nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical
Physics. 147(10), 104707.'
mla: 'Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation:
From Atomistic Nuclei to the Planar Limit.” The Journal of Chemical Physics,
vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:10.1063/1.4997180.'
short: B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147
(2017).
date_created: 2021-07-15T08:13:29Z
date_published: 2017-09-14T00:00:00Z
date_updated: 2023-02-23T14:04:02Z
day: '14'
doi: 10.1063/1.4997180
extern: '1'
external_id:
arxiv:
- '1703.06062'
pmid:
- '28915742'
intvolume: ' 147'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html
month: '09'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to
the planar limit'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 147
year: '2017'
...
---
_id: '9661'
abstract:
- lang: eng
text: Macroscopic theories of nucleation such as classical nucleation theory envision
that clusters of the bulk stable phase form inside the bulk metastable phase.
Molecular dynamics simulations are often used to elucidate nucleation mechanisms,
by capturing the microscopic configurations of all the atoms. In this paper, we
introduce a thermodynamic model that links macroscopic theories and atomic-scale
simulations and thus provide a simple and elegant framework for testing the limits
of classical nucleation theory.
article_number: '034106'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models
of homogeneous nucleation. The Journal of Chemical Physics. 2017;146(3).
doi:10.1063/1.4973883
apa: Cheng, B., & Ceriotti, M. (2017). Bridging the gap between atomistic and
macroscopic models of homogeneous nucleation. The Journal of Chemical Physics.
AIP Publishing. https://doi.org/10.1063/1.4973883
chicago: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic
and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical
Physics. AIP Publishing, 2017. https://doi.org/10.1063/1.4973883.
ieee: B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic
models of homogeneous nucleation,” The Journal of Chemical Physics, vol.
146, no. 3. AIP Publishing, 2017.
ista: Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic
models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106.
mla: Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic
and Macroscopic Models of Homogeneous Nucleation.” The Journal of Chemical
Physics, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:10.1063/1.4973883.
short: B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017).
date_created: 2021-07-15T08:27:31Z
date_published: 2017-01-21T00:00:00Z
date_updated: 2021-08-09T12:31:57Z
day: '21'
doi: 10.1063/1.4973883
extern: '1'
external_id:
arxiv:
- '1610.01322'
pmid:
- '28109231'
intvolume: ' 146'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1610.01322
month: '01'
oa: 1
oa_version: Preprint
pmid: 1
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bridging the gap between atomistic and macroscopic models of homogeneous nucleation
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 146
year: '2017'
...
---
_id: '9707'
abstract:
- lang: eng
text: Branching morphogenesis of the epithelial ureteric bud forms the renal collecting
duct system and is critical for normal nephron number, while low nephron number
is implicated in hypertension and renal disease. Ureteric bud growth and branching
requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric
bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling
up-regulates transcription factors Etv4 and Etv5, which are also critical for
branching. Despite extensive knowledge of the genetic control of these events,
it is not understood, at the cellular level, how renal branching morphogenesis
is achieved or how Ret signaling influences epithelial cell behaviors to promote
this process. Analysis of chimeric embryos previously suggested a role for Ret
signaling in promoting cell rearrangements in the nephric duct, but this method
was unsuited to study individual cell behaviors during ureteric bud branching.
Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture
and time-lapse imaging, to trace the movements and divisions of individual ureteric
bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type
clones in which the mutant and wild-type sister cells are differentially and heritably
marked by green and red fluorescent proteins. We find that, in normal kidneys,
most individual tip cells behave as self-renewing progenitors, some of whose progeny
remain at the tips while others populate the growing UB trunks. In Ret or Etv4
MADM clones, the wild-type cells generated at a UB tip are much more likely to
remain at, or move to, the new tips during branching and elongation, while their
Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks.
By tracking successive mitoses in a cell lineage, we find that Ret signaling has
little effect on proliferation, in contrast to its effects on cell movement. Our
results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric
bud tips, and suggest a model in which these cell movements mediate branching
morphogenesis.
article_processing_charge: No
author:
- first_name: Paul
full_name: Riccio, Paul
last_name: Riccio
- first_name: Christina
full_name: Cebrián, Christina
last_name: Cebrián
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Frank
full_name: Costantini, Frank
last_name: Costantini
citation:
ama: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and
Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.
2017. doi:10.5061/dryad.pk16b'
apa: 'Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017).
Data from: Ret and Etv4 promote directed movements of progenitor cells during
renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b'
chicago: 'Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank
Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor
Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b.'
ieee: 'P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data
from: Ret and Etv4 promote directed movements of progenitor cells during renal
branching morphogenesis.” Dryad, 2017.'
ista: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from:
Ret and Etv4 promote directed movements of progenitor cells during renal branching
morphogenesis, Dryad, 10.5061/dryad.pk16b.'
mla: 'Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements
of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.'
short: P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).
date_created: 2021-07-23T09:39:34Z
date_published: 2017-01-14T00:00:00Z
date_updated: 2022-08-25T13:34:55Z
day: '14'
department:
- _id: SiHi
doi: 10.5061/dryad.pk16b
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.pk16b
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9702'
relation: used_in_publication
status: deleted
status: public
title: 'Data from: Ret and Etv4 promote directed movements of progenitor cells during
renal branching morphogenesis'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9709'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
article_processing_charge: No
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust
modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc'
apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc'
chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.”
Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.'
ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data
from: Error-robust modes of the retinal population code.” Dryad, 2017.'
ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from:
Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.'
mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population
Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.'
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
date_created: 2021-07-23T11:34:34Z
date_published: 2017-10-18T00:00:00Z
date_updated: 2023-02-21T16:34:41Z
day: '18'
department:
- _id: GaTk
doi: 10.5061/dryad.1f1rc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.1f1rc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1197'
relation: used_in_publication
status: public
status: public
title: 'Data from: Error-robust modes of the retinal population code'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9842'
abstract:
- lang: eng
text: Mathematica notebooks used to generate figures.
article_processing_charge: No
author:
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic
adaptation. 2017. doi:10.17632/nw68fxzjpm.1'
apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new
habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1'
chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in
a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.'
ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat
by polygenic adaptation.” Mendeley Data, 2017.'
ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by
polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.'
mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a
New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.'
short: A. Etheridge, N.H. Barton, (2017).
date_created: 2021-08-09T13:18:55Z
date_published: 2017-12-29T00:00:00Z
date_updated: 2025-05-28T11:56:59Z
day: '29'
department:
- _id: NiBa
doi: 10.17632/nw68fxzjpm.1
main_file_link:
- open_access: '1'
url: https://doi.org/10.17632/nw68fxzjpm.1
month: '12'
oa: 1
oa_version: Published Version
publisher: Mendeley Data
related_material:
record:
- id: '564'
relation: used_in_publication
status: public
status: public
title: 'Data for: Establishment in a new habitat by polygenic adaptation'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9844'
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Source data for figures and tables.
2017. doi:10.1371/journal.pgen.1007122.s018
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Source data for figures and tables. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1007122.s018
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Source Data for Figures
and Tables.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s018.
ieee: N. Nikolic et al., “Source data for figures and tables.” Public Library
of Science, 2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Source data for figures and tables, Public Library of Science,
10.1371/journal.pgen.1007122.s018.
mla: Nikolic, Nela, et al. Source Data for Figures and Tables. Public Library
of Science, 2017, doi:10.1371/journal.pgen.1007122.s018.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:27:16Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s018
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Source data for figures and tables
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9845'
abstract:
- lang: eng
text: "Estimates of 13 C-arabinose and 2 H-glucose uptake from the fractions of
heavy isotopes measured\tin single cells"
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Mathematical model. 2017. doi:10.1371/journal.pgen.1007122.s017
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Mathematical model. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007122.s017
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Mathematical Model.” Public
Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s017.
ieee: N. Nikolic et al., “Mathematical model.” Public Library of Science,
2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Mathematical model, Public Library of Science, 10.1371/journal.pgen.1007122.s017.
mla: Nikolic, Nela, et al. Mathematical Model. Public Library of Science,
2017, doi:10.1371/journal.pgen.1007122.s017.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:31:51Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s017
month: '12'
oa_version: None
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Mathematical model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9846'
article_processing_charge: No
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
- first_name: Frank
full_name: Schreiber, Frank
last_name: Schreiber
- first_name: Alma
full_name: Dal Co, Alma
last_name: Dal Co
- first_name: Daniel
full_name: Kiviet, Daniel
last_name: Kiviet
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Sten
full_name: Littmann, Sten
last_name: Littmann
- first_name: Marcel
full_name: Kuypers, Marcel
last_name: Kuypers
- first_name: Martin
full_name: Ackermann, Martin
last_name: Ackermann
citation:
ama: Nikolic N, Schreiber F, Dal Co A, et al. Supplementary methods. 2017. doi:10.1371/journal.pgen.1007122.s016
apa: Nikolic, N., Schreiber, F., Dal Co, A., Kiviet, D., Bergmiller, T., Littmann,
S., … Ackermann, M. (2017). Supplementary methods. Public Library of Science.
https://doi.org/10.1371/journal.pgen.1007122.s016
chicago: Nikolic, Nela, Frank Schreiber, Alma Dal Co, Daniel Kiviet, Tobias Bergmiller,
Sten Littmann, Marcel Kuypers, and Martin Ackermann. “Supplementary Methods.”
Public Library of Science, 2017. https://doi.org/10.1371/journal.pgen.1007122.s016.
ieee: N. Nikolic et al., “Supplementary methods.” Public Library of Science,
2017.
ista: Nikolic N, Schreiber F, Dal Co A, Kiviet D, Bergmiller T, Littmann S, Kuypers
M, Ackermann M. 2017. Supplementary methods, Public Library of Science, 10.1371/journal.pgen.1007122.s016.
mla: Nikolic, Nela, et al. Supplementary Methods. Public Library of Science,
2017, doi:10.1371/journal.pgen.1007122.s016.
short: N. Nikolic, F. Schreiber, A. Dal Co, D. Kiviet, T. Bergmiller, S. Littmann,
M. Kuypers, M. Ackermann, (2017).
date_created: 2021-08-09T13:35:17Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-02-23T12:25:04Z
day: '18'
department:
- _id: CaGu
doi: 10.1371/journal.pgen.1007122.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '541'
relation: used_in_publication
status: public
status: public
title: Supplementary methods
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...