---
_id: '2856'
abstract:
- lang: eng
text: 'G protein–coupled receptors (GPCRs), the largest family of membrane signaling
proteins, respond to neurotransmitters, hormones and small environmental molecules.
The neuronal function of many GPCRs has been difficult to resolve because of an
inability to gate them with subtype specificity, spatial precision, speed and
reversibility. To address this, we developed an approach for opto-chemical engineering
of native GPCRs. We applied this to the metabotropic glutamate receptors (mGluRs)
to generate light-agonized and light-antagonized mGluRs (LimGluRs). The light-agonized
LimGluR2, on which we focused, was fast, bistable and supported multiple rounds
of on/off switching. Light gated two of the primary neuronal functions of mGluR2:
suppression of excitability and inhibition of neurotransmitter release. We found
that the light-antagonized tool LimGluR2-block was able to manipulate negative
feedback of synaptically released glutamate on transmitter release. We generalized
the optical control to two additional family members: mGluR3 and mGluR6. This
system worked in rodent brain slices and in zebrafish in vivo, where we found
that mGluR2 modulated the threshold for escape behavior. These light-gated mGluRs
pave the way for determining the roles of mGluRs in synaptic plasticity, memory
and disease.'
acknowledgement: National Science Foundation grants CHE-0233882 and CHE-0840505 (to
the College of Chemistry at the University of California, Berkeley), a postdoctoral
fellowship of the European Molecular Biology Organization (H.J.)
article_processing_charge: No
author:
- first_name: Joshua
full_name: Levitz, Joshua
last_name: Levitz
- first_name: Carlos
full_name: Pantoja, Carlos
last_name: Pantoja
- first_name: Benjamin
full_name: Gaub, Benjamin
last_name: Gaub
- 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: Andreas
full_name: Reiner, Andreas
last_name: Reiner
- first_name: Adam
full_name: Hoagland, Adam
last_name: Hoagland
- first_name: David
full_name: Schoppik, David
last_name: Schoppik
- first_name: Brian
full_name: Kane, Brian
last_name: Kane
- first_name: Philipp
full_name: Stawski, Philipp
last_name: Stawski
- first_name: Alexander
full_name: Schier, Alexander
last_name: Schier
- first_name: Dirk
full_name: Trauner, Dirk
last_name: Trauner
- first_name: Ehud
full_name: Isacoff, Ehud
last_name: Isacoff
citation:
ama: Levitz J, Pantoja C, Gaub B, et al. Optical control of metabotropic glutamate
receptors. Nature Neuroscience. 2013;16:507-516. doi:10.1038/nn.3346
apa: Levitz, J., Pantoja, C., Gaub, B., Janovjak, H. L., Reiner, A., Hoagland, A.,
… Isacoff, E. (2013). Optical control of metabotropic glutamate receptors. Nature
Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3346
chicago: Levitz, Joshua, Carlos Pantoja, Benjamin Gaub, Harald L Janovjak, Andreas
Reiner, Adam Hoagland, David Schoppik, et al. “Optical Control of Metabotropic
Glutamate Receptors.” Nature Neuroscience. Nature Publishing Group, 2013.
https://doi.org/10.1038/nn.3346.
ieee: J. Levitz et al., “Optical control of metabotropic glutamate receptors,”
Nature Neuroscience, vol. 16. Nature Publishing Group, pp. 507–516, 2013.
ista: Levitz J, Pantoja C, Gaub B, Janovjak HL, Reiner A, Hoagland A, Schoppik D,
Kane B, Stawski P, Schier A, Trauner D, Isacoff E. 2013. Optical control of metabotropic
glutamate receptors. Nature Neuroscience. 16, 507–516.
mla: Levitz, Joshua, et al. “Optical Control of Metabotropic Glutamate Receptors.”
Nature Neuroscience, vol. 16, Nature Publishing Group, 2013, pp. 507–16,
doi:10.1038/nn.3346.
short: J. Levitz, C. Pantoja, B. Gaub, H.L. Janovjak, A. Reiner, A. Hoagland, D.
Schoppik, B. Kane, P. Stawski, A. Schier, D. Trauner, E. Isacoff, Nature Neuroscience
16 (2013) 507–516.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-03-03T00:00:00Z
date_updated: 2025-09-29T13:39:33Z
day: '03'
department:
- _id: HaJa
doi: 10.1038/nn.3346
external_id:
isi:
- '000316723700023'
pmid:
- '23455609'
intvolume: ' 16'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681425/
month: '03'
oa: 1
oa_version: Submitted Version
page: 507 - 516
pmid: 1
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '3936'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Optical control of metabotropic glutamate receptors
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 16
year: '2013'
...
---
_id: '2857'
abstract:
- lang: eng
text: In the vibrant field of optogenetics, optics and genetic targeting are combined
to commandeer cellular functions, such as the neuronal action potential, by optically
stimulating light-sensitive ion channels expressed in the cell membrane. One broadly
applicable manifestation of this approach are covalently attached photochromic
tethered ligands (PTLs) that allow activating ligand-gated ion channels with outstanding
spatial and temporal resolution. Here, we describe all steps towards the successful
development and application of PTL-gated ion channels in cell lines and primary
cells. The basis for these experiments forms a combination of molecular modeling,
genetic engineering, cell culture, and electrophysiology. The light-gated glutamate
receptor (LiGluR), which consists of the PTL-functionalized GluK2 receptor, serves
as a model.
alternative_title:
- MIMB
author:
- first_name: Stephanie
full_name: Szobota, Stephanie
last_name: Szobota
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
citation:
ama: Szobota S, Mckenzie C, Janovjak HL. Optical control of ligand-gated ion channels.
Methods in Molecular Biology. 2013;998:417-435. doi:10.1007/978-1-62703-351-0_32
apa: Szobota, S., Mckenzie, C., & Janovjak, H. L. (2013). Optical control of
ligand-gated ion channels. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-62703-351-0_32
chicago: Szobota, Stephanie, Catherine Mckenzie, and Harald L Janovjak. “Optical
Control of Ligand-Gated Ion Channels.” Methods in Molecular Biology. Springer,
2013. https://doi.org/10.1007/978-1-62703-351-0_32.
ieee: S. Szobota, C. Mckenzie, and H. L. Janovjak, “Optical control of ligand-gated
ion channels,” Methods in Molecular Biology, vol. 998. Springer, pp. 417–435,
2013.
ista: Szobota S, Mckenzie C, Janovjak HL. 2013. Optical control of ligand-gated
ion channels. Methods in Molecular Biology. 998, 417–435.
mla: Szobota, Stephanie, et al. “Optical Control of Ligand-Gated Ion Channels.”
Methods in Molecular Biology, vol. 998, Springer, 2013, pp. 417–35, doi:10.1007/978-1-62703-351-0_32.
short: S. Szobota, C. Mckenzie, H.L. Janovjak, Methods in Molecular Biology 998
(2013) 417–435.
date_created: 2018-12-11T11:59:57Z
date_published: 2013-02-22T00:00:00Z
date_updated: 2025-04-15T06:43:12Z
day: '22'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.1007/978-1-62703-351-0_32
ec_funded: 1
file:
- access_level: open_access
checksum: 1701f0d989f27ddac471b19a894ec0d1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:34Z
date_updated: 2020-07-14T12:45:51Z
file_id: '4952'
file_name: IST-2017-834-v1+1_szobota.pdf
file_size: 336734
relation: main_file
file_date_updated: 2020-07-14T12:45:51Z
has_accepted_license: '1'
intvolume: ' 998'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Submitted Version
page: 417 - 435
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors
- _id: 25548C20-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303564'
name: Microbial Ion Channels for Synthetic Neurobiology
publication: Methods in Molecular Biology
publication_status: published
publisher: Springer
publist_id: '3932'
pubrep_id: '834'
quality_controlled: '1'
scopus_import: 1
status: public
title: Optical control of ligand-gated ion channels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 998
year: '2013'
...
---
_id: '2860'
abstract:
- lang: eng
text: 'In the hippocampus, cell assemblies forming mnemonic representations of space
are thought to arise as a result of changes in functional connections of pyramidal
cells. We have found that CA1 interneuron circuits are also reconfigured during
goal-oriented spatial learning through modification of inputs from pyramidal cells.
As learning progressed, new pyramidal assemblies expressed in theta cycles alternated
with previously established ones, and eventually overtook them. The firing patterns
of interneurons developed a relationship to new, learning-related assemblies:
some interneurons associated their activity with new pyramidal assemblies while
some others dissociated from them. These firing associations were explained by
changes in the weight of monosynaptic inputs received by interneurons from new
pyramidal assemblies, as these predicted the associational changes. Spatial learning
thus engages circuit modifications in the hippocampus that incorporate a redistribution
of inhibitory activity that might assist in the segregation of competing pyramidal
cell assembly patterns in space and time.'
acknowledgement: D.D. and J.C. were supported by a MRC Intramural Programme Grant
U138197111
article_processing_charge: No
author:
- first_name: David
full_name: Dupret, David
last_name: Dupret
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Dupret D, O’Neill J, Csicsvari JL. Dynamic reconfiguration of hippocampal interneuron
circuits during spatial learning. Neuron. 2013;78(1):166-180. doi:10.1016/j.neuron.2013.01.033
apa: Dupret, D., O’Neill, J., & Csicsvari, J. L. (2013). Dynamic reconfiguration
of hippocampal interneuron circuits during spatial learning. Neuron. Elsevier.
https://doi.org/10.1016/j.neuron.2013.01.033
chicago: Dupret, David, Joseph O’Neill, and Jozsef L Csicsvari. “Dynamic Reconfiguration
of Hippocampal Interneuron Circuits during Spatial Learning.” Neuron. Elsevier,
2013. https://doi.org/10.1016/j.neuron.2013.01.033.
ieee: D. Dupret, J. O’Neill, and J. L. Csicsvari, “Dynamic reconfiguration of hippocampal
interneuron circuits during spatial learning,” Neuron, vol. 78, no. 1.
Elsevier, pp. 166–180, 2013.
ista: Dupret D, O’Neill J, Csicsvari JL. 2013. Dynamic reconfiguration of hippocampal
interneuron circuits during spatial learning. Neuron. 78(1), 166–180.
mla: Dupret, David, et al. “Dynamic Reconfiguration of Hippocampal Interneuron Circuits
during Spatial Learning.” Neuron, vol. 78, no. 1, Elsevier, 2013, pp. 166–80,
doi:10.1016/j.neuron.2013.01.033.
short: D. Dupret, J. O’Neill, J.L. Csicsvari, Neuron 78 (2013) 166–180.
corr_author: '1'
date_created: 2018-12-11T11:59:59Z
date_published: 2013-03-21T00:00:00Z
date_updated: 2025-09-29T13:37:37Z
day: '21'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1016/j.neuron.2013.01.033
ec_funded: 1
external_id:
isi:
- '000317556000015'
file:
- access_level: open_access
checksum: 0e18cb8561153ddb50bb5af16e7c9e97
content_type: application/pdf
creator: dernst
date_created: 2019-01-23T08:08:07Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5877'
file_name: 2013_Neuron_Dupret.pdf
file_size: 2637837
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 166 - 180
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3929'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic reconfiguration of hippocampal interneuron circuits during spatial
learning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 78
year: '2013'
...
---
_id: '2861'
abstract:
- lang: eng
text: We consider a two-parameter family of piecewise linear maps in which the moduli
of the two slopes take different values. We provide numerical evidence of the
existence of some parameter regions in which the Lyapunov exponent and the topological
entropy remain constant. Analytical proof of this phenomenon is also given for
certain cases. Surprisingly however, the systems with that property are not conjugate
as we prove by using kneading theory.
article_number: '125101'
article_processing_charge: No
author:
- first_name: Vicente
full_name: Botella Soler, Vicente
id: 421234E8-F248-11E8-B48F-1D18A9856A87
last_name: Botella Soler
orcid: 0000-0002-8790-1914
- first_name: José
full_name: Oteo, José
last_name: Oteo
- first_name: Javier
full_name: Ros, Javier
last_name: Ros
- first_name: Paul
full_name: Glendinning, Paul
last_name: Glendinning
citation:
ama: 'Botella Soler V, Oteo J, Ros J, Glendinning P. Lyapunov exponent and topological
entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical
and Theoretical. 2013;46(12). doi:10.1088/1751-8113/46/12/125101'
apa: 'Botella Soler, V., Oteo, J., Ros, J., & Glendinning, P. (2013). Lyapunov
exponent and topological entropy plateaus in piecewise linear maps. Journal
of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8113/46/12/125101'
chicago: 'Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov
Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.” Journal
of Physics A: Mathematical and Theoretical. IOP Publishing, 2013. https://doi.org/10.1088/1751-8113/46/12/125101.'
ieee: 'V. Botella Soler, J. Oteo, J. Ros, and P. Glendinning, “Lyapunov exponent
and topological entropy plateaus in piecewise linear maps,” Journal of Physics
A: Mathematical and Theoretical, vol. 46, no. 12. IOP Publishing, 2013.'
ista: 'Botella Soler V, Oteo J, Ros J, Glendinning P. 2013. Lyapunov exponent and
topological entropy plateaus in piecewise linear maps. Journal of Physics A: Mathematical
and Theoretical. 46(12), 125101.'
mla: 'Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy
Plateaus in Piecewise Linear Maps.” Journal of Physics A: Mathematical and
Theoretical, vol. 46, no. 12, 125101, IOP Publishing, 2013, doi:10.1088/1751-8113/46/12/125101.'
short: 'V. Botella Soler, J. Oteo, J. Ros, P. Glendinning, Journal of Physics A:
Mathematical and Theoretical 46 (2013).'
corr_author: '1'
date_created: 2018-12-11T11:59:59Z
date_published: 2013-03-29T00:00:00Z
date_updated: 2025-09-29T13:36:56Z
day: '29'
department:
- _id: GaTk
doi: 10.1088/1751-8113/46/12/125101
external_id:
isi:
- '000316058200010'
intvolume: ' 46'
isi: 1
issue: '12'
language:
- iso: eng
month: '03'
oa_version: None
publication: 'Journal of Physics A: Mathematical and Theoretical'
publication_status: published
publisher: IOP Publishing
publist_id: '3928'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lyapunov exponent and topological entropy plateaus in piecewise linear maps
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 46
year: '2013'
...
---
_id: '2862'
abstract:
- lang: eng
text: Motile cilia perform crucial functions during embryonic development and throughout
adult life. Development of organs containing motile cilia involves regulation
of cilia formation (ciliogenesis) and formation of a luminal space (lumenogenesis)
in which cilia generate fluid flows. Control of ciliogenesis and lumenogenesis
is not yet fully understood, and it remains unclear whether these processes are
coupled. In the zebrafish embryo, lethal giant larvae 2 (lgl2) is expressed prominently
in ciliated organs. Lgl proteins are involved in establishing cell polarity and
have been implicated in vesicle trafficking. Here, we identified a role for Lgl2
in development of ciliated epithelia in Kupffer's vesicle, which directs left-right
asymmetry of the embryo; the otic vesicles, which give rise to the inner ear;
and the pronephric ducts of the kidney. Using Kupffer's vesicle as a model ciliated
organ, we found that depletion of Lgl2 disrupted lumen formation and reduced cilia
number and length. Immunofluorescence and time-lapse imaging of Kupffer's vesicle
morphogenesis in Lgl2-deficient embryos suggested cell adhesion defects and revealed
loss of the adherens junction component E-cadherin at lateral membranes. Genetic
interaction experiments indicate that Lgl2 interacts with Rab11a to regulate E-cadherin
and mediate lumen formation that is uncoupled from cilia formation. These results
uncover new roles and interactions for Lgl2 that are crucial for both lumenogenesis
and ciliogenesis and indicate that these processes are genetically separable in
zebrafish.
acknowledgement: Deposited in PMC for release after 12 months. We thank members of
the Amack lab for helpful discussions and Mahendra Sonawane for donating reagents.
article_processing_charge: No
author:
- first_name: Hwee
full_name: Tay, Hwee
last_name: Tay
- first_name: Sabrina
full_name: Schulze, Sabrina
last_name: Schulze
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Fiona
full_name: Foley, Fiona
last_name: Foley
- 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
- first_name: H Joseph
full_name: Yost, H Joseph
last_name: Yost
- first_name: Salim
full_name: Abdelilah Seyfried, Salim
last_name: Abdelilah Seyfried
- first_name: Jeffrey
full_name: Amack, Jeffrey
last_name: Amack
citation:
ama: Tay H, Schulze S, Compagnon J, et al. Lethal giant larvae 2 regulates development
of the ciliated organ Kupffer’s vesicle. Development. 2013;140(7):1550-1559.
doi:10.1242/dev.087130
apa: Tay, H., Schulze, S., Compagnon, J., Foley, F., Heisenberg, C.-P. J., Yost,
H. J., … Amack, J. (2013). Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle. Development. Company of Biologists. https://doi.org/10.1242/dev.087130
chicago: Tay, Hwee, Sabrina Schulze, Julien Compagnon, Fiona Foley, Carl-Philipp
J Heisenberg, H Joseph Yost, Salim Abdelilah Seyfried, and Jeffrey Amack. “Lethal
Giant Larvae 2 Regulates Development of the Ciliated Organ Kupffer’s Vesicle.”
Development. Company of Biologists, 2013. https://doi.org/10.1242/dev.087130.
ieee: H. Tay et al., “Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle,” Development, vol. 140, no. 7. Company
of Biologists, pp. 1550–1559, 2013.
ista: Tay H, Schulze S, Compagnon J, Foley F, Heisenberg C-PJ, Yost HJ, Abdelilah
Seyfried S, Amack J. 2013. Lethal giant larvae 2 regulates development of the
ciliated organ Kupffer’s vesicle. Development. 140(7), 1550–1559.
mla: Tay, Hwee, et al. “Lethal Giant Larvae 2 Regulates Development of the Ciliated
Organ Kupffer’s Vesicle.” Development, vol. 140, no. 7, Company of Biologists,
2013, pp. 1550–59, doi:10.1242/dev.087130.
short: H. Tay, S. Schulze, J. Compagnon, F. Foley, C.-P.J. Heisenberg, H.J. Yost,
S. Abdelilah Seyfried, J. Amack, Development 140 (2013) 1550–1559.
date_created: 2018-12-11T11:59:59Z
date_published: 2013-04-01T00:00:00Z
date_updated: 2025-09-29T13:36:20Z
day: '01'
department:
- _id: CaHe
doi: 10.1242/dev.087130
external_id:
isi:
- '000316096400018'
pmid:
- '23482490'
intvolume: ' 140'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3596994/
month: '04'
oa: 1
oa_version: Submitted Version
page: 1550 - 1559
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3927'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lethal giant larvae 2 regulates development of the ciliated organ Kupffer’s
vesicle
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 140
year: '2013'
...
---
_id: '2863'
abstract:
- lang: eng
text: Neural populations encode information about their stimulus in a collective
fashion, by joint activity patterns of spiking and silence. A full account of
this mapping from stimulus to neural activity is given by the conditional probability
distribution over neural codewords given the sensory input. For large populations,
direct sampling of these distributions is impossible, and so we must rely on constructing
appropriate models. We show here that in a population of 100 retinal ganglion
cells in the salamander retina responding to temporal white-noise stimuli, dependencies
between cells play an important encoding role. We introduce the stimulus-dependent
maximum entropy (SDME) model—a minimal extension of the canonical linear-nonlinear
model of a single neuron, to a pairwise-coupled neural population. We find that
the SDME model gives a more accurate account of single cell responses and in particular
significantly outperforms uncoupled models in reproducing the distributions of
population codewords emitted in response to a stimulus. We show how the SDME model,
in conjunction with static maximum entropy models of population vocabulary, can
be used to estimate information-theoretic quantities like average surprise and
information transmission in a neural population.
article_number: e1002922
article_processing_charge: No
author:
- first_name: Einat
full_name: Granot Atedgi, Einat
last_name: Granot Atedgi
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Ronen
full_name: Segev, Ronen
last_name: Segev
- first_name: Elad
full_name: Schneidman, Elad
last_name: Schneidman
citation:
ama: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. Stimulus-dependent maximum
entropy models of neural population codes. PLoS Computational Biology.
2013;9(3). doi:10.1371/journal.pcbi.1002922
apa: Granot Atedgi, E., Tkačik, G., Segev, R., & Schneidman, E. (2013). Stimulus-dependent
maximum entropy models of neural population codes. PLoS Computational Biology.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1002922
chicago: Granot Atedgi, Einat, Gašper Tkačik, Ronen Segev, and Elad Schneidman.
“Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS
Computational Biology. Public Library of Science, 2013. https://doi.org/10.1371/journal.pcbi.1002922.
ieee: E. Granot Atedgi, G. Tkačik, R. Segev, and E. Schneidman, “Stimulus-dependent
maximum entropy models of neural population codes,” PLoS Computational Biology,
vol. 9, no. 3. Public Library of Science, 2013.
ista: Granot Atedgi E, Tkačik G, Segev R, Schneidman E. 2013. Stimulus-dependent
maximum entropy models of neural population codes. PLoS Computational Biology.
9(3), e1002922.
mla: Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of
Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922,
Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.
short: E. Granot Atedgi, G. Tkačik, R. Segev, E. Schneidman, PLoS Computational
Biology 9 (2013).
corr_author: '1'
date_created: 2018-12-11T12:00:00Z
date_published: 2013-03-01T00:00:00Z
date_updated: 2025-09-29T13:35:44Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1002922
external_id:
isi:
- '000316864200003'
file:
- access_level: open_access
checksum: 5a30876c193209fa05b26db71845dd16
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:45Z
date_updated: 2020-07-14T12:45:52Z
file_id: '5099'
file_name: IST-2013-120-v1+1_journal.pcbi.1002922.pdf
file_size: 1548120
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '3926'
pubrep_id: '120'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stimulus-dependent maximum entropy models of neural population codes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 9
year: '2013'
...
---
_id: '2877'
abstract:
- lang: eng
text: 'Premise of the study: To reach favorable conditions for photosynthesis, seedlings
grow upward when deprived of light upon underground germination. To direct their
growth, they use their negative gravitropic capacity. Negative gravitropism is
under tight control of multiple hormones. • Methods: By counting the number of
standing plants in a population or by real time monitoring of the reorientation
of gravistimulated seedlings of Arabidopsis thaliana, we evaluated the negative
gravitropism of ethylene or brassinosteroid (BR) treated plants. Meta-analysis
of transcriptomic data on AUX / IAA genes was gathered, and subsequent mutant
analysis was performed. • Key results: Ethylene and BR have opposite effects in
regulating shoot gravitropism. Lack of BR enhances gravitropic reorientation in
2-d-old seedlings, whereas ethylene does not. Lack of ethylene signaling results
in enhanced BR sensitivity. Ethylene and BRs regulate overlapping sets of AUX
/ IAA genes. BRs regulate a wider range of auxin signaling components than ethylene.
• Conclusions: Upward growth in seedlings depends strongly on the internal hormonal
balance. Endogenous ethylene stimulates, whereas BRs reduce negative gravitropism
in a manner that depends on the function of different, yet overlapping sets of
auxin signaling components.'
author:
- first_name: Filip
full_name: Vandenbussche, Filip
last_name: Vandenbussche
- first_name: Pieter
full_name: Callebert, Pieter
last_name: Callebert
- first_name: Petra
full_name: Žádníková, Petra
last_name: Žádníková
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Dominique
full_name: Van Der Straeten, Dominique
last_name: Van Der Straeten
citation:
ama: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D. Brassinosteroid
control of shoot gravitropism interacts with ethylene and depends on auxin signaling
components. American Journal of Botany. 2013;100(1):215-225. doi:10.3732/ajb.1200264
apa: Vandenbussche, F., Callebert, P., Žádníková, P., Benková, E., & Van Der
Straeten, D. (2013). Brassinosteroid control of shoot gravitropism interacts with
ethylene and depends on auxin signaling components. American Journal of Botany.
Botanical Society of America. https://doi.org/10.3732/ajb.1200264
chicago: Vandenbussche, Filip, Pieter Callebert, Petra Žádníková, Eva Benková, and
Dominique Van Der Straeten. “Brassinosteroid Control of Shoot Gravitropism Interacts
with Ethylene and Depends on Auxin Signaling Components.” American Journal
of Botany. Botanical Society of America, 2013. https://doi.org/10.3732/ajb.1200264.
ieee: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, and D. Van Der Straeten,
“Brassinosteroid control of shoot gravitropism interacts with ethylene and depends
on auxin signaling components,” American Journal of Botany, vol. 100, no.
1. Botanical Society of America, pp. 215–225, 2013.
ista: Vandenbussche F, Callebert P, Žádníková P, Benková E, Van Der Straeten D.
2013. Brassinosteroid control of shoot gravitropism interacts with ethylene and
depends on auxin signaling components. American Journal of Botany. 100(1), 215–225.
mla: Vandenbussche, Filip, et al. “Brassinosteroid Control of Shoot Gravitropism
Interacts with Ethylene and Depends on Auxin Signaling Components.” American
Journal of Botany, vol. 100, no. 1, Botanical Society of America, 2013, pp.
215–25, doi:10.3732/ajb.1200264.
short: F. Vandenbussche, P. Callebert, P. Žádníková, E. Benková, D. Van Der Straeten,
American Journal of Botany 100 (2013) 215–225.
date_created: 2018-12-11T12:00:06Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:25Z
day: '01'
doi: 10.3732/ajb.1200264
extern: 1
intvolume: ' 100'
issue: '1'
month: '01'
page: 215 - 225
publication: American Journal of Botany
publication_status: published
publisher: Botanical Society of America
publist_id: '3883'
quality_controlled: 0
status: public
title: Brassinosteroid control of shoot gravitropism interacts with ethylene and depends
on auxin signaling components
type: journal_article
volume: 100
year: '2013'
...
---
_id: '2880'
abstract:
- lang: eng
text: Lateral root (LR) formation is initiated when pericycle cells accumulate auxin,
thereby acquiring founder cell (FC) status and triggering asymmetric cell divisions,
giving rise to a new primordium. How this auxin maximum in pericycle cells builds
up and remains focused is not understood. We report that the endodermis plays
an active role in the regulation of auxin accumulation and is instructive for
FCs to progress during the LR initiation (LRI) phase. We describe the functional
importance of a PIN3 (PIN-formed) auxin efflux carrier-dependent hormone reflux
pathway between overlaying endodermal and pericycle FCs. Disrupting this reflux
pathway causes dramatic defects in the progress of FCs towards the next initiation
phase. Our data identify an unexpected regulatory function for the endodermis
in LRI as part of the fine-tuning mechanism that appears to act as a check point
in LR organogenesis after FCs are specified.
article_processing_charge: No
author:
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Bert
full_name: De Rybel, Bert
last_name: De Rybel
- first_name: Ding
full_name: Zhaojun, Ding
last_name: Zhaojun
- first_name: Malcolm
full_name: Bennett, Malcolm
last_name: Bennett
- first_name: Tom
full_name: Beeckman, Tom
last_name: Beeckman
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Marhavý P, Vanstraelen M, De Rybel B, et al. Auxin reflux between the endodermis
and pericycle promotes lateral root initiation. EMBO Journal. 2013;32(1):149-158.
doi:10.1038/emboj.2012.303
apa: Marhavý, P., Vanstraelen, M., De Rybel, B., Zhaojun, D., Bennett, M., Beeckman,
T., & Benková, E. (2013). Auxin reflux between the endodermis and pericycle
promotes lateral root initiation. EMBO Journal. Wiley-Blackwell. https://doi.org/10.1038/emboj.2012.303
chicago: Marhavý, Peter, Marleen Vanstraelen, Bert De Rybel, Ding Zhaojun, Malcolm
Bennett, Tom Beeckman, and Eva Benková. “Auxin Reflux between the Endodermis and
Pericycle Promotes Lateral Root Initiation.” EMBO Journal. Wiley-Blackwell,
2013. https://doi.org/10.1038/emboj.2012.303.
ieee: P. Marhavý et al., “Auxin reflux between the endodermis and pericycle
promotes lateral root initiation,” EMBO Journal, vol. 32, no. 1. Wiley-Blackwell,
pp. 149–158, 2013.
ista: Marhavý P, Vanstraelen M, De Rybel B, Zhaojun D, Bennett M, Beeckman T, Benková
E. 2013. Auxin reflux between the endodermis and pericycle promotes lateral root
initiation. EMBO Journal. 32(1), 149–158.
mla: Marhavý, Peter, et al. “Auxin Reflux between the Endodermis and Pericycle Promotes
Lateral Root Initiation.” EMBO Journal, vol. 32, no. 1, Wiley-Blackwell,
2013, pp. 149–58, doi:10.1038/emboj.2012.303.
short: P. Marhavý, M. Vanstraelen, B. De Rybel, D. Zhaojun, M. Bennett, T. Beeckman,
E. Benková, EMBO Journal 32 (2013) 149–158.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2025-09-29T13:35:12Z
day: '09'
department:
- _id: EvBe
doi: 10.1038/emboj.2012.303
ec_funded: 1
external_id:
isi:
- '000314141900014'
pmid:
- '23178590'
intvolume: ' 32'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545298/
month: '01'
oa: 1
oa_version: Submitted Version
page: 149 - 158
pmid: 1
project:
- _id: 253FCA6A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '207362'
name: Hormonal cross-talk in plant organogenesis
publication: EMBO Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3882'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Auxin reflux between the endodermis and pericycle promotes lateral root initiation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 32
year: '2013'
...
---
_id: '2881'
abstract:
- lang: eng
text: The puzzle piece-shaped Arabidopsis leaf pavement cells (PCs) with interdigitated
lobes and indents is a good model system to investigate the mechanisms that coordinate
cell polarity and shape formation within a tissue. Auxin has been shown to coordinate
the interdigitation by activating ROP GTPase-dependent signaling pathways. To
identify additional components or mechanisms, we screened for mutants with abnormal
PC morphogenesis and found that cytokinin signaling regulates the PC interdigitation
pattern. Reduction in cytokinin accumulation and defects in cytokinin signaling
(such as in ARR7-over-expressing lines, the ahk3cre1 cytokinin receptor mutant,
and the ahp12345 cytokinin signaling mutant) enhanced PC interdigitation, whereas
over-production of cytokinin and over-activation of cytokinin signaling in an
ARR20 over-expression line delayed or abolished PC interdigitation throughout
the cotyledon. Genetic and biochemical analyses suggest that cytokinin signaling
acts upstream of ROPs to suppress the formation of interdigitated pattern. Our
results provide novel mechanistic understanding of the pathways controlling PC
shape and uncover a new role for cytokinin signaling in cell morphogenesis.
acknowledgement: is work was supported by grants from the US National Institute of
General Medical Sciences (GM081451 and GM081451-03S2) to ZY. We thank National Science
Foundation grant (IOS-1147250) to GVR and MX. HL and DL were partially supported
by the Chinese Scholarship Council.
author:
- first_name: Hongjiang
full_name: Hongjiang Li
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Deshu
full_name: Lin, Deshu
last_name: Lin
- first_name: Mingzhang
full_name: Wen, Mingzhang
last_name: Wen
- first_name: Mingtang
full_name: Xie, Mingtang
last_name: Xie
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Jungmook
full_name: Kim, Jungmook
last_name: Kim
- first_name: G Venugopala
full_name: Reddy, G Venugopala
last_name: Reddy
- first_name: Jianru
full_name: Zuo, Jianru
last_name: Zuo
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hongwei
full_name: Guo, Hongwei
last_name: Guo
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Li H, Xu T, Lin D, et al. Cytokinin signaling regulates pavement cell morphogenesis
in Arabidopsis. Cell Research. 2013;23(2):290-299. doi:10.1038/cr.2012.146
apa: Li, H., Xu, T., Lin, D., Wen, M., Xie, M., Duclercq, J., … Yang, Z. (2013).
Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis. Cell
Research. Nature Publishing Group. https://doi.org/10.1038/cr.2012.146
chicago: Li, Hongjiang, Tongda Xu, Deshu Lin, Mingzhang Wen, Mingtang Xie, Jérôme
Duclercq, Agnieszka Bielach, et al. “Cytokinin Signaling Regulates Pavement Cell
Morphogenesis in Arabidopsis.” Cell Research. Nature Publishing Group,
2013. https://doi.org/10.1038/cr.2012.146.
ieee: H. Li et al., “Cytokinin signaling regulates pavement cell morphogenesis
in Arabidopsis,” Cell Research, vol. 23, no. 2. Nature Publishing Group,
pp. 290–299, 2013.
ista: Li H, Xu T, Lin D, Wen M, Xie M, Duclercq J, Bielach A, Kim J, Reddy GV, Zuo
J, Benková E, Friml J, Guo H, Yang Z. 2013. Cytokinin signaling regulates pavement
cell morphogenesis in Arabidopsis. Cell Research. 23(2), 290–299.
mla: Li, Hongjiang, et al. “Cytokinin Signaling Regulates Pavement Cell Morphogenesis
in Arabidopsis.” Cell Research, vol. 23, no. 2, Nature Publishing Group,
2013, pp. 290–99, doi:10.1038/cr.2012.146.
short: H. Li, T. Xu, D. Lin, M. Wen, M. Xie, J. Duclercq, A. Bielach, J. Kim, G.V.
Reddy, J. Zuo, E. Benková, J. Friml, H. Guo, Z. Yang, Cell Research 23 (2013)
290–299.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T07:00:27Z
day: '01'
doi: 10.1038/cr.2012.146
extern: 1
intvolume: ' 23'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3567823/
month: '02'
oa: 1
page: 290 - 299
publication: Cell Research
publication_status: published
publisher: Nature Publishing Group
publist_id: '3881'
quality_controlled: 0
status: public
title: Cytokinin signaling regulates pavement cell morphogenesis in Arabidopsis
type: journal_article
volume: 23
year: '2013'
...
---
_id: '2882'
abstract:
- lang: eng
text: Gravitropic bending of plant organs is mediated by an asymmetric signaling
of the plant hormone auxin between the upper and lower side of the respective
organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows
asymmetric action during gravitropic responses. Immunodetection using an antibody
against GA and monitoring GA signaling output by downstream degradation of DELLA
proteins revealed an asymmetric GA distribution and response with the maximum
at the lower side of gravistimulated roots. Genetic or pharmacological manipulation
of GA levels or response affects gravity-mediated auxin redistribution and root
bending response. The higher GA levels at the lower side of the root correlate
with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane.
The observed increase in PIN2 stability is caused by a specific GA effect on trafficking
of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin
A-sensitive endosomes. Our results suggest that asymmetric auxin distribution
instructive for gravity-induced differential growth is consolidated by the asymmetric
action of GA that stabilizes the PIN-dependent auxin stream along the lower side
of gravistimulated roots.
article_processing_charge: No
author:
- first_name: Christian
full_name: Löfke, Christian
last_name: Löfke
- first_name: Marta
full_name: Zwiewka, Marta
last_name: Zwiewka
- first_name: Ingo
full_name: Heilmann, Ingo
last_name: Heilmann
- first_name: Marc
full_name: Van Montagu, Marc
last_name: Van Montagu
- first_name: Thomas
full_name: Teichmann, Thomas
last_name: Teichmann
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. Asymmetric
gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters
during root gravitropism. PNAS. 2013;110(9):3627-3632. doi:10.1073/pnas.1300107110
apa: Löfke, C., Zwiewka, M., Heilmann, I., Van Montagu, M., Teichmann, T., &
Friml, J. (2013). Asymmetric gibberellin signaling regulates vacuolar trafficking
of PIN auxin transporters during root gravitropism. PNAS. National Academy
of Sciences. https://doi.org/10.1073/pnas.1300107110
chicago: Löfke, Christian, Marta Zwiewka, Ingo Heilmann, Marc Van Montagu, Thomas
Teichmann, and Jiří Friml. “Asymmetric Gibberellin Signaling Regulates Vacuolar
Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS.
National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1300107110.
ieee: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, and J. Friml,
“Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin
transporters during root gravitropism,” PNAS, vol. 110, no. 9. National
Academy of Sciences, pp. 3627–3632, 2013.
ista: Löfke C, Zwiewka M, Heilmann I, Van Montagu M, Teichmann T, Friml J. 2013.
Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters
during root gravitropism. PNAS. 110(9), 3627–3632.
mla: Löfke, Christian, et al. “Asymmetric Gibberellin Signaling Regulates Vacuolar
Trafficking of PIN Auxin Transporters during Root Gravitropism.” PNAS,
vol. 110, no. 9, National Academy of Sciences, 2013, pp. 3627–32, doi:10.1073/pnas.1300107110.
short: C. Löfke, M. Zwiewka, I. Heilmann, M. Van Montagu, T. Teichmann, J. Friml,
PNAS 110 (2013) 3627–3632.
date_created: 2018-12-11T12:00:07Z
date_published: 2013-02-26T00:00:00Z
date_updated: 2025-09-29T13:34:38Z
day: '26'
department:
- _id: JiFr
doi: 10.1073/pnas.1300107110
external_id:
isi:
- '000315841900083'
pmid:
- '23391733'
intvolume: ' 110'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587205/
month: '02'
oa: 1
oa_version: Submitted Version
page: 3627 - 3632
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3879'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin
transporters during root gravitropism
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 110
year: '2013'
...
---
_id: '2883'
abstract:
- lang: eng
text: Plant architecture is influenced by the polar, cell-to-cell transport of auxin
that is primarily provided and regulated by plasma membrane efflux catalysts of
the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were
shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1
(TWD1), although underlying mechanisms are unclear. By genetic manipulation of
TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and,
thus, downstream developmental traits, such as epidermal twisting and gravitropism
of the root. Using immunological assays, we demonstrate a predominant lateral,
mainly outward-facing, plasma membrane location for TWD1 in the root epidermis
characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3.
At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1.
In planta bioluminescence resonance energy transfer analysis was used to verify
specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model
in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein
interaction at the plasma membrane, minimizing reflux from the root apoplast into
the cytoplasm.
acknowledgement: We would thank Vincent Vincenzetti and Laurence Charrier for excellent
technical assistance, A. von Arnim for the donation of BRET vectors, E. Spalding
for TWD1-CFP, TWD1-CFP/29-1-GFP/ER-YFP, and ABCB4-GFP lines, M. Palmgren for discussion
and support, and E. Martinoia for TT12 cDNA, support, and mentorship. Imaging data
were partially collected at the Center for Advanced Bioimaging, University of Copenhagen,
Denmark. This work was supported by grants from the Novartis Foundation (to M.G.),
from the Danish Research School for Biotechnology (to M.G. and A.S.), from the Forschungskredit
of the University of Zurich (to A.B.), from the Pool de Recherche of the University
of Fribourg (to M.G.), and from the Swiss National Funds (to M.G.). M.G. dedicates
this work to his father, who passed away during the resubmission process.
article_processing_charge: No
author:
- first_name: Bangjun
full_name: Wang, Bangjun
last_name: Wang
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Marta
full_name: Zwiewk, Marta
last_name: Zwiewk
- first_name: Sina
full_name: Henrichs, Sina
last_name: Henrichs
- first_name: Elisa
full_name: Azzarello, Elisa
last_name: Azzarello
- first_name: Stefano
full_name: Mancuso, Stefano
last_name: Mancuso
- first_name: Masayoshi
full_name: Maeshima, Masayoshi
last_name: Maeshima
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Alexander
full_name: Schulz, Alexander
last_name: Schulz
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
citation:
ama: Wang B, Bailly A, Zwiewk M, et al. Arabidopsis TWISTED DWARF1 functionally
interacts with auxin exporter ABCB1 on the root plasma membrane. Plant Cell.
2013;25(1):202-214. doi:10.1105/tpc.112.105999
apa: Wang, B., Bailly, A., Zwiewk, M., Henrichs, S., Azzarello, E., Mancuso, S.,
… Geisler, M. (2013). Arabidopsis TWISTED DWARF1 functionally interacts with auxin
exporter ABCB1 on the root plasma membrane. Plant Cell. American Society
of Plant Biologists. https://doi.org/10.1105/tpc.112.105999
chicago: Wang, Bangjun, Aurélien Bailly, Marta Zwiewk, Sina Henrichs, Elisa Azzarello,
Stefano Mancuso, Masayoshi Maeshima, Jiří Friml, Alexander Schulz, and Markus
Geisler. “Arabidopsis TWISTED DWARF1 Functionally Interacts with Auxin Exporter
ABCB1 on the Root Plasma Membrane.” Plant Cell. American Society of Plant
Biologists, 2013. https://doi.org/10.1105/tpc.112.105999.
ieee: B. Wang et al., “Arabidopsis TWISTED DWARF1 functionally interacts
with auxin exporter ABCB1 on the root plasma membrane,” Plant Cell, vol.
25, no. 1. American Society of Plant Biologists, pp. 202–214, 2013.
ista: Wang B, Bailly A, Zwiewk M, Henrichs S, Azzarello E, Mancuso S, Maeshima M,
Friml J, Schulz A, Geisler M. 2013. Arabidopsis TWISTED DWARF1 functionally interacts
with auxin exporter ABCB1 on the root plasma membrane. Plant Cell. 25(1), 202–214.
mla: Wang, Bangjun, et al. “Arabidopsis TWISTED DWARF1 Functionally Interacts with
Auxin Exporter ABCB1 on the Root Plasma Membrane.” Plant Cell, vol. 25,
no. 1, American Society of Plant Biologists, 2013, pp. 202–14, doi:10.1105/tpc.112.105999.
short: B. Wang, A. Bailly, M. Zwiewk, S. Henrichs, E. Azzarello, S. Mancuso, M.
Maeshima, J. Friml, A. Schulz, M. Geisler, Plant Cell 25 (2013) 202–214.
date_created: 2018-12-11T12:00:08Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2025-09-29T13:34:07Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.112.105999
external_id:
isi:
- '000315572400017'
pmid:
- '23321285'
intvolume: ' 25'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584535/
month: '01'
oa: 1
oa_version: Submitted Version
page: 202 - 214
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3878'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1
on the root plasma membrane
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 25
year: '2013'
...
---
_id: '2884'
article_processing_charge: No
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Hélène
full_name: Berthoumieux, Hélène
last_name: Berthoumieux
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Guillaume
full_name: Salbreux, Guillaume
last_name: Salbreux
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish
gastrulation. Medecine Sciences. 2013;29(2):147-150. doi:10.1051/medsci/2013292011
apa: Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch,
E., & Heisenberg, C.-P. J. (2013). Cell adhesion mechanics of zebrafish gastrulation.
Medecine Sciences. Éditions Médicales et Scientifiques. https://doi.org/10.1051/medsci/2013292011
chicago: Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux,
Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Cell Adhesion Mechanics
of Zebrafish Gastrulation.” Medecine Sciences. Éditions Médicales et Scientifiques,
2013. https://doi.org/10.1051/medsci/2013292011.
ieee: J.-L. Maître et al., “Cell adhesion mechanics of zebrafish gastrulation,”
Medecine Sciences, vol. 29, no. 2. Éditions Médicales et Scientifiques,
pp. 147–150, 2013.
ista: Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg
C-PJ. 2013. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences.
29(2), 147–150.
mla: Maître, Jean-Léon, et al. “Cell Adhesion Mechanics of Zebrafish Gastrulation.”
Medecine Sciences, vol. 29, no. 2, Éditions Médicales et Scientifiques,
2013, pp. 147–50, doi:10.1051/medsci/2013292011.
short: J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch,
C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150.
date_created: 2018-12-11T12:00:08Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2025-09-29T13:33:31Z
day: '01'
department:
- _id: CaHe
doi: 10.1051/medsci/2013292011
external_id:
isi:
- '000315749700011'
intvolume: ' 29'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 147 - 150
project:
- _id: 252064B8-B435-11E9-9278-68D0E5697425
grant_number: HE_3231/6-1
name: Analysis of the Formation and Function of Different Cell Protusion Types During
Cell Migration in Vivo
- _id: 2527D5CC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I812-B12
name: Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation
publication: Medecine Sciences
publication_status: published
publisher: Éditions Médicales et Scientifiques
publist_id: '3877'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell adhesion mechanics of zebrafish gastrulation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 29
year: '2013'
...
---
_id: '2885'
abstract:
- lang: eng
text: 'This volume contains the post-proceedings of the 8th Doctoral Workshop on
Mathematical and Engineering Methods in Computer Science, MEMICS 2012, held in
Znojmo, Czech Republic, in October, 2012. The 13 thoroughly revised papers were
carefully selected out of 31 submissions and are presented together with 6 invited
papers. The topics covered by the papers include: computer-aided analysis and
verification, applications of game theory in computer science, networks and security,
modern trends of graph theory in computer science, electronic systems design and
testing, and quantum information processing.'
acknowledgement: Red Hat Czech Republic, Y Soft
alternative_title:
- LNCS
citation:
ama: Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D, eds. Mathematical
and Engineering Methods in Computer Science. Vol 7721. Springer; 2013:1-228.
doi:10.1007/978-3-642-36046-6
apa: 'Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., & Antos, D. (Eds.).
(2013). Mathematical and Engineering Methods in Computer Science (Vol.
7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods
in computer science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6'
chicago: Kucera, Antonin, Thomas A Henzinger, Jaroslav Nesetril, Tomas Vojnar, and
David Antos, eds. Mathematical and Engineering Methods in Computer Science.
Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6.
ieee: A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., Mathematical
and Engineering Methods in Computer Science, vol. 7721. Springer, 2013, pp.
1–228.
ista: Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical
and Engineering Methods in Computer Science, Springer,p.
mla: Kucera, Antonin, et al., editors. Mathematical and Engineering Methods in
Computer Science. Vol. 7721, Springer, 2013, pp. 1–228, doi:10.1007/978-3-642-36046-6.
short: A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical
and Engineering Methods in Computer Science, Springer, 2013.
conference:
end_date: 2012-10-28
location: Znojmo, Czech Republic
name: 'MEMICS: Mathematical and Engineering methods in computer science'
start_date: 2012-10-25
date_created: 2018-12-11T12:00:08Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2019-08-02T12:37:55Z
day: '09'
department:
- _id: ToHe
doi: 10.1007/978-3-642-36046-6
editor:
- first_name: Antonin
full_name: Kucera, Antonin
last_name: Kucera
- 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: Jaroslav
full_name: Nesetril, Jaroslav
last_name: Nesetril
- first_name: Tomas
full_name: Vojnar, Tomas
last_name: Vojnar
- first_name: David
full_name: Antos, David
last_name: Antos
intvolume: ' 7721'
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 228
publication_status: published
publisher: Springer
publist_id: '3874'
quality_controlled: '1'
series_title: Lecture Notes in Computer Science
status: public
title: Mathematical and Engineering Methods in Computer Science
type: conference_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7721
year: '2013'
...
---
_id: '2886'
abstract:
- lang: eng
text: We focus on the realizability problem of Message Sequence Graphs (MSG), i.e.
the problem whether a given MSG specification is correctly distributable among
parallel components communicating via messages. This fundamental problem of MSG
is known to be undecidable. We introduce a well motivated restricted class of
MSG, so called controllable-choice MSG, and show that all its models are realizable
and moreover it is decidable whether a given MSG model is a member of this class.
In more detail, this class of MSG specifications admits a deadlock-free realization
by overloading existing messages with additional bounded control data. We also
show that the presented class is the largest known subclass of MSG that allows
for deadlock-free realization.
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Vojtěch
full_name: Řehák, Vojtěch
last_name: Řehák
citation:
ama: Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130.
doi:10.1007/978-3-642-36046-6_12
apa: 'Chmelik, M., & Řehák, V. (2013). Controllable-choice message sequence
graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer
Science, Znojmo, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-36046-6_12'
chicago: Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence
Graphs.” Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36046-6_12.
ieee: M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol.
7721. Springer, pp. 118–130, 2013.
ista: Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721,
118–130.
mla: Chmelik, Martin, and Vojtěch Řehák. Controllable-Choice Message Sequence
Graphs. Vol. 7721, Springer, 2013, pp. 118–30, doi:10.1007/978-3-642-36046-6_12.
short: M. Chmelik, V. Řehák, 7721 (2013) 118–130.
conference:
end_date: 2012-10-28
location: Znojmo, Czech Republic
name: 'MEMICS: Mathematical and Engineering Methods in Computer Science'
start_date: 2012-10-25
corr_author: '1'
date_created: 2018-12-11T12:00:09Z
date_published: 2013-01-09T00:00:00Z
date_updated: 2025-06-11T08:05:09Z
day: '09'
department:
- _id: KrCh
doi: 10.1007/978-3-642-36046-6_12
ec_funded: 1
external_id:
arxiv:
- '1209.4499'
intvolume: ' 7721'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1209.4499
month: '01'
oa: 1
oa_version: Submitted Version
page: 118 - 130
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '3873'
quality_controlled: '1'
scopus_import: '1'
series_title: Lecture Notes in Computer Science
status: public
title: Controllable-choice message sequence graphs
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7721
year: '2013'
...
---
_id: '2887'
abstract:
- lang: eng
text: 'Root system growth and development is highly plastic and is influenced by
the surrounding environment. Roots frequently grow in heterogeneous environments
that include interactions from neighboring plants and physical impediments in
the rhizosphere. To investigate how planting density and physical objects affect
root system growth, we grew rice in a transparent gel system in close proximity
with another plant or a physical object. Root systems were imaged and reconstructed
in three dimensions. Root-root interaction strength was calculated using quantitative
metrics that characterize the extent towhich the reconstructed root systems overlap
each other. Surprisingly, we found the overlap of root systems of the same genotype
was significantly higher than that of root systems of different genotypes. Root
systems of the same genotype tended to grow toward each other but those of different
genotypes appeared to avoid each other. Shoot separation experiments excluded
the possibility of aerial interactions, suggesting root communication. Staggered
plantings indicated that interactions likely occur at root tips in close proximity.
Recognition of obstacles also occurred through root tips, but through physical
contact in a size-dependent manner. These results indicate that root systems use
two different forms of communication to recognize objects and alter root architecture:
root-root recognition, possibly mediated through root exudates, and root-object
recognition mediated by physical contact at the root tips. This finding suggests
that root tips act as local sensors that integrate rhizosphere information into
global root architectural changes.'
article_processing_charge: No
article_type: original
author:
- first_name: Suqin
full_name: Fang, Suqin
last_name: Fang
- first_name: Randy
full_name: Clark, Randy
last_name: Clark
- first_name: Ying
full_name: Zheng, Ying
last_name: Zheng
- first_name: Anjali
full_name: Iyer Pascuzzi, Anjali
last_name: Iyer Pascuzzi
- first_name: Joshua
full_name: Weitz, Joshua
last_name: Weitz
- first_name: Leon
full_name: Kochian, Leon
last_name: Kochian
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Hong
full_name: Liao, Hong
last_name: Liao
- first_name: Philip
full_name: Benfey, Philip
last_name: Benfey
citation:
ama: Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses
by rice roots. PNAS. 2013;110(7):2670-2675. doi:10.1073/pnas.1222821110
apa: Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L.,
… Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots.
PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1222821110
chicago: Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz,
Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition
and Spatial Responses by Rice Roots.” PNAS. National Academy of Sciences,
2013. https://doi.org/10.1073/pnas.1222821110.
ieee: S. Fang et al., “Genotypic recognition and spatial responses by rice
roots,” PNAS, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675,
2013.
ista: Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner
H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice
roots. PNAS. 110(7), 2670–2675.
mla: Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.”
PNAS, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75,
doi:10.1073/pnas.1222821110.
short: S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner,
H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675.
date_created: 2018-12-11T12:00:09Z
date_published: 2013-02-12T00:00:00Z
date_updated: 2026-06-18T18:36:41Z
day: '12'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1073/pnas.1222821110
external_id:
isi:
- '000315812800060'
pmid:
- '23362379'
intvolume: ' 110'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/
month: '02'
oa: 1
oa_version: Published Version
page: 2670 - 2675
pmid: 1
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3872'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genotypic recognition and spatial responses by rice roots
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 110
year: '2013'
...
---
_id: '2900'
author:
- first_name: Ricardo
full_name: Azevedo, Ricardo B
last_name: Azevedo
- first_name: Rolf
full_name: Lohaus, Rolf
last_name: Lohaus
- first_name: Tiago
full_name: Tiago Paixao
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Azevedo R, Lohaus R, Paixao T. Networking networks. Evolution & Development.
2013;10(5):514-515.
apa: Azevedo, R., Lohaus, R., & Paixao, T. (2013). Networking networks. Evolution
& Development. Wiley-Blackwell.
chicago: Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.”
Evolution & Development. Wiley-Blackwell, 2013.
ieee: R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” Evolution
& Development, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013.
ista: Azevedo R, Lohaus R, Paixao T. 2013. Networking networks. Evolution &
Development. 10(5), 514–515.
mla: Azevedo, Ricardo, et al. “Networking Networks.” Evolution & Development,
vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15.
short: R. Azevedo, R. Lohaus, T. Paixao, Evolution & Development 10 (2013) 514–515.
date_created: 2018-12-11T12:00:14Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:00:34Z
day: '01'
extern: 1
intvolume: ' 10'
issue: '5'
main_file_link:
- open_access: '0'
url: http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract
month: '01'
page: 514 - 515
publication: Evolution & Development
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3858'
quality_controlled: 0
status: public
title: Networking networks
type: journal_article
volume: 10
year: '2013'
...
---
_id: '2906'
abstract:
- lang: eng
text: "Motivated by an application in cell biology, we describe an extension of
the kinetic data structures framework from Delaunay triangulations to fixed-radius
alpha complexes. Our algorithm is implemented\r\nusing CGAL, following the exact
geometric computation paradigm. We report on several\r\ntechniques to accelerate
the computation that turn our implementation applicable to the underlying biological\r\nproblem."
alternative_title:
- ALENEX
article_processing_charge: No
author:
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation.
In: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments.
Society for Industrial and Applied Mathematics; 2013:70-77. doi:10.1137/1.9781611972931.6'
apa: 'Kerber, M., & Edelsbrunner, H. (2013). 3D kinetic alpha complexes and
their implementation. In 2013 Proceedings of the 15th Workshop on Algorithm
Engineering and Experiments (pp. 70–77). New Orleans, LA, United States: Society
for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611972931.6'
chicago: Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes
and Their Implementation.” In 2013 Proceedings of the 15th Workshop on Algorithm
Engineering and Experiments, 70–77. Society for Industrial and Applied Mathematics,
2013. https://doi.org/10.1137/1.9781611972931.6.
ieee: M. Kerber and H. Edelsbrunner, “3D kinetic alpha complexes and their implementation,”
in 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments,
New Orleans, LA, United States, 2013, pp. 70–77.
ista: 'Kerber M, Edelsbrunner H. 2013. 3D kinetic alpha complexes and their implementation.
2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments.
ALENEX: Algorithm Engineering and Experiments, ALENEX, , 70–77.'
mla: Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and
Their Implementation.” 2013 Proceedings of the 15th Workshop on Algorithm Engineering
and Experiments, Society for Industrial and Applied Mathematics, 2013, pp.
70–77, doi:10.1137/1.9781611972931.6.
short: M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on
Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics,
2013, pp. 70–77.
conference:
end_date: 2013-01-07
location: New Orleans, LA, United States
name: 'ALENEX: Algorithm Engineering and Experiments'
start_date: 2013-01-07
corr_author: '1'
date_created: 2018-12-11T12:00:16Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2025-06-03T11:47:11Z
day: '01'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1137/1.9781611972931.6
file:
- access_level: open_access
checksum: a15a3ba22df9445731507f3e06c9fcee
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:57Z
date_updated: 2020-07-14T12:45:52Z
file_id: '4720'
file_name: IST-2016-547-v1+1_2013-P-08-MedusaII.pdf
file_size: 403013
relation: main_file
file_date_updated: 2020-07-14T12:45:52Z
has_accepted_license: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 70 - 77
publication: 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments
publication_status: published
publisher: Society for Industrial and Applied Mathematics
publist_id: '3841'
pubrep_id: '547'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 3D kinetic alpha complexes and their implementation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2907'
abstract:
- lang: eng
text: 'Sex and recombination are among the most striking features of the living
world, and they play a crucial role in allowing the evolution of complex adaptation.
The sharing of genomes through the sexual union of different individuals requires
elaborate behavioral and physiological adaptations. At the molecular level, the
alignment of two DNA double helices, followed by their precise cutting and rejoining,
is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary
consequences: distinct sexes, elaborate mating displays, selfish genetic elements,
and so on.'
author:
- 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: 'Barton NH. Recombination and sex. In: The Princeton Guide to Evolution.
Princeton University Press; 2013:328-333.'
apa: Barton, N. H. (2013). Recombination and sex. In The Princeton Guide to Evolution
(pp. 328–333). Princeton University Press.
chicago: Barton, Nicholas H. “Recombination and Sex.” In The Princeton Guide
to Evolution, 328–33. Princeton University Press, 2013.
ieee: N. H. Barton, “Recombination and sex,” in The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–333.
ista: 'Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution.
, 328–333.'
mla: Barton, Nicholas H. “Recombination and Sex.” The Princeton Guide to Evolution,
Princeton University Press, 2013, pp. 328–33.
short: N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University
Press, 2013, pp. 328–333.
corr_author: '1'
date_created: 2018-12-11T12:00:16Z
date_published: 2013-11-04T00:00:00Z
date_updated: 2024-10-09T20:55:04Z
day: '04'
ddc:
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department:
- _id: NiBa
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language:
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month: '11'
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oa_version: Submitted Version
page: 328 - 333
publication: The Princeton Guide to Evolution
publication_identifier:
isbn:
- '9780691149776'
publication_status: published
publisher: Princeton University Press
publist_id: '3839'
pubrep_id: '119'
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title: Recombination and sex
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2013'
...
---
_id: '2908'
abstract:
- lang: eng
text: 'Hybridization is an almost inevitable component of speciation, and its study
can tell us much about that process. However, hybridization itself may have a
negligible influence on the origin of species: on the one hand, universally favoured
alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous
selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional
hybridisation may hardly affect the process of divergence.'
article_processing_charge: No
author:
- 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: Barton NH. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 2013;26(2):267-269. doi:10.1111/jeb.12015
apa: Barton, N. H. (2013). Does hybridisation influence speciation? . Journal
of Evolutionary Biology. Wiley-Blackwell. https://doi.org/10.1111/jeb.12015
chicago: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology. Wiley-Blackwell, 2013. https://doi.org/10.1111/jeb.12015.
ieee: N. H. Barton, “Does hybridisation influence speciation? ,” Journal of
Evolutionary Biology, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013.
ista: Barton NH. 2013. Does hybridisation influence speciation? . Journal of Evolutionary
Biology. 26(2), 267–269.
mla: Barton, Nicholas H. “Does Hybridisation Influence Speciation? .” Journal
of Evolutionary Biology, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69,
doi:10.1111/jeb.12015.
short: N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.
corr_author: '1'
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-17T00:00:00Z
date_updated: 2025-09-29T13:31:43Z
day: '17'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/jeb.12015
external_id:
isi:
- '000313747600007'
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date_updated: 2020-07-14T12:45:52Z
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has_accepted_license: '1'
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isi: 1
issue: '2'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 267 - 269
publication: Journal of Evolutionary Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3835'
pubrep_id: '111'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Does hybridisation influence speciation? '
type: journal_article
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volume: 26
year: '2013'
...
---
_id: '2909'
abstract:
- lang: eng
text: "We survey a class of models for spatially structured populations\r\nwhich
we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework
for modelling in which the key innovation is that random genetic drift\r\nis driven
by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes
some of the obstructions to modelling populations which evolve in two-\r\n(and
higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved
in data and how it fits with classical models. Finally we outline some\r\ndirections
for future research."
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013;2013(1). doi:10.1088/1742-5468/2013/01/P01002
apa: Barton, N. H., Etheridge, A., & Véber, A. (2013). Modelling evolution in
a spatial continuum. Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing. https://doi.org/10.1088/1742-5468/2013/01/P01002
chicago: Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution
in a Spatial Continuum.” Journal of Statistical Mechanics Theory and Experiment.
IOP Publishing, 2013. https://doi.org/10.1088/1742-5468/2013/01/P01002.
ieee: N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial
continuum,” Journal of Statistical Mechanics Theory and Experiment, vol.
2013, no. 1. IOP Publishing, 2013.
ista: Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum.
Journal of Statistical Mechanics Theory and Experiment. 2013(1).
mla: Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” Journal
of Statistical Mechanics Theory and Experiment, vol. 2013, no. 1, IOP Publishing,
2013, doi:10.1088/1742-5468/2013/01/P01002.
short: N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory
and Experiment 2013 (2013).
corr_author: '1'
date_created: 2018-12-11T12:00:17Z
date_published: 2013-01-16T00:00:00Z
date_updated: 2025-09-29T13:31:08Z
day: '16'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1088/1742-5468/2013/01/P01002
ec_funded: 1
external_id:
isi:
- '000315410500003'
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date_created: 2018-12-12T10:16:52Z
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issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Journal of Statistical Mechanics Theory and Experiment
publication_status: published
publisher: IOP Publishing
publist_id: '3834'
pubrep_id: '557'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modelling evolution in a spatial continuum
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 2013
year: '2013'
...