---
_id: '3074'
abstract:
- lang: eng
text: Auxin is an essential phytohormone that regulates many aspects of plant development.
To identify new genes that function in auxin signaling, we performed a genetic
screen for Arabidopsis thaliana mutants with an alteration in the expression of
the auxin-responsive reporter DR5rev:GFP (for green fluorescent protein). One
of the mutants recovered in this screen, called weak auxin response1 (wxr1), has
a defect in auxin response and exhibits a variety of auxin-related growth defects
in the root. Polar auxin transport is reduced in wxr1 seedlings, resulting in
auxin accumulation in the hypocotyl and cotyledons and a reduction in auxin levels
in the root apex. In addition, the levels of the PIN auxin transport proteins
are reduced in the wxr1 root. We also show that WXR1 is ROOT UV-B SENSITIVE2 (RUS2),
a member of the broadly conserved DUF647 domain protein family found in diverse
eukaryotic organisms. Our data indicate that RUS2/WXR1 is required for auxin transport
and to maintain the normal levels of PIN proteins in the root.
author:
- first_name: Lei
full_name: Ge, Lei
last_name: Ge
- first_name: Wendy
full_name: Peer, Wendy A
last_name: Peer
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Ranjan
full_name: Swarup, Ranjan
last_name: Swarup
- first_name: Songqing
full_name: Ye, Songqing
last_name: Ye
- first_name: Michael
full_name: Prigge, Michael J
last_name: Prigge
- first_name: Jerry
full_name: Cohen, Jerry D
last_name: Cohen
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
- first_name: Ding
full_name: Tang, Ding
last_name: Tang
- first_name: Mark
full_name: Estelle, Mark A
last_name: Estelle
citation:
ama: Ge L, Peer W, Robert S, et al. Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1
is required for polar auxin transport. Plant Cell. 2010;22(6):1749-1761.
doi:10.1105/tpc.110.074195
apa: Ge, L., Peer, W., Robert, S., Swarup, R., Ye, S., Prigge, M., … Estelle, M.
(2010). Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar
auxin transport. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.110.074195
chicago: Ge, Lei, Wendy Peer, Stéphanie Robert, Ranjan Swarup, Songqing Ye, Michael
Prigge, Jerry Cohen, et al. “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1
Is Required for Polar Auxin Transport.” Plant Cell. American Society of
Plant Biologists, 2010. https://doi.org/10.1105/tpc.110.074195.
ieee: L. Ge et al., “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1
is required for polar auxin transport,” Plant Cell, vol. 22, no. 6. American
Society of Plant Biologists, pp. 1749–1761, 2010.
ista: Ge L, Peer W, Robert S, Swarup R, Ye S, Prigge M, Cohen J, Friml J, Murphy
A, Tang D, Estelle M. 2010. Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1
is required for polar auxin transport. Plant Cell. 22(6), 1749–1761.
mla: Ge, Lei, et al. “Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 Is Required
for Polar Auxin Transport.” Plant Cell, vol. 22, no. 6, American Society
of Plant Biologists, 2010, pp. 1749–61, doi:10.1105/tpc.110.074195.
short: L. Ge, W. Peer, S. Robert, R. Swarup, S. Ye, M. Prigge, J. Cohen, J. Friml,
A. Murphy, D. Tang, M. Estelle, Plant Cell 22 (2010) 1749–1761.
date_created: 2018-12-11T12:01:13Z
date_published: 2010-06-01T00:00:00Z
date_updated: 2021-01-12T07:40:52Z
day: '01'
doi: 10.1105/tpc.110.074195
extern: 1
intvolume: ' 22'
issue: '6'
month: '06'
page: 1749 - 1761
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3628'
quality_controlled: 0
status: public
title: Arabidopsis ROOT UVB SENSITIVE2 WEAK AUXIN RESPONSE1 is required for polar
auxin transport
type: journal_article
volume: 22
year: '2010'
...
---
_id: '3075'
abstract:
- lang: eng
text: |2-
Spatial distribution of the plant hormone auxin regulates multiple aspects of plant development. These self-regulating auxin gradients are established by the action of PIN auxin transporters, whose activity is regulated by their constitutive cycling between the plasma membrane and endosomes. Here, we show that auxin signaling by the auxin receptor AUXIN-BINDING PROTEIN 1 (ABP1) inhibits the clathrin-mediated internalization of PIN proteins. ABP1 acts as a positive factor in clathrin recruitment to the plasma membrane, thereby promoting endocytosis. Auxin binding to ABP1 interferes with this action and leads to the inhibition of clathrin-mediated endocytosis. Our study demonstrates that ABP1 mediates a nontranscriptional auxin signaling that regulates the evolutionarily conserved process of clathrin-mediated endocytosis and suggests that this signaling may be essential for the developmentally important feedback of auxin on its own transport.
author:
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Elke
full_name: Barbez, Elke
last_name: Barbez
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Tomasz
full_name: Paciorek, Tomasz
last_name: Paciorek
- first_name: Pawel
full_name: Pawel Baster
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
- first_name: Sibu
full_name: Sibu Simon
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Milada
full_name: Čovanová, Milada
last_name: Čovanová
- first_name: Kenichiro
full_name: Hayashi, Kenichiro
last_name: Hayashi
- first_name: Pankaj
full_name: Dhonukshe, Pankaj
last_name: Dhonukshe
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
- first_name: Sebastian
full_name: Bednarek, Sebastian Y
last_name: Bednarek
- first_name: Alan
full_name: Jones, Alan M
last_name: Jones
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Fernando
full_name: Aniento, Fernando
last_name: Aniento
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Robert S, Kleine Vehn J, Barbez E, et al. ABP1 mediates auxin inhibition of
clathrin-dependent endocytosis in Arabidopsis. Cell. 2010;143(1):111-121.
doi:10.1016/j.cell.2010.09.027
apa: Robert, S., Kleine Vehn, J., Barbez, E., Sauer, M., Paciorek, T., Baster, P.,
… Friml, J. (2010). ABP1 mediates auxin inhibition of clathrin-dependent endocytosis
in Arabidopsis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2010.09.027
chicago: Robert, Stéphanie, Jürgen Kleine Vehn, Elke Barbez, Michael Sauer, Tomasz
Paciorek, Pawel Baster, Steffen Vanneste, et al. “ABP1 Mediates Auxin Inhibition
of Clathrin-Dependent Endocytosis in Arabidopsis.” Cell. Cell Press, 2010.
https://doi.org/10.1016/j.cell.2010.09.027.
ieee: S. Robert et al., “ABP1 mediates auxin inhibition of clathrin-dependent
endocytosis in Arabidopsis,” Cell, vol. 143, no. 1. Cell Press, pp. 111–121,
2010.
ista: Robert S, Kleine Vehn J, Barbez E, Sauer M, Paciorek T, Baster P, Vanneste
S, Zhang J, Simon S, Čovanová M, Hayashi K, Dhonukshe P, Yang Z, Bednarek S, Jones
A, Luschnig C, Aniento F, Zažímalová E, Friml J. 2010. ABP1 mediates auxin inhibition
of clathrin-dependent endocytosis in Arabidopsis. Cell. 143(1), 111–121.
mla: Robert, Stéphanie, et al. “ABP1 Mediates Auxin Inhibition of Clathrin-Dependent
Endocytosis in Arabidopsis.” Cell, vol. 143, no. 1, Cell Press, 2010, pp.
111–21, doi:10.1016/j.cell.2010.09.027.
short: S. Robert, J. Kleine Vehn, E. Barbez, M. Sauer, T. Paciorek, P. Baster, S.
Vanneste, J. Zhang, S. Simon, M. Čovanová, K. Hayashi, P. Dhonukshe, Z. Yang,
S. Bednarek, A. Jones, C. Luschnig, F. Aniento, E. Zažímalová, J. Friml, Cell
143 (2010) 111–121.
date_created: 2018-12-11T12:01:13Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2021-01-12T07:40:52Z
day: '01'
doi: 10.1016/j.cell.2010.09.027
extern: 1
intvolume: ' 143'
issue: '1'
month: '10'
page: 111 - 121
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3626'
quality_controlled: 0
status: public
title: ABP1 mediates auxin inhibition of clathrin-dependent endocytosis in Arabidopsis
type: journal_article
volume: 143
year: '2010'
...
---
_id: '3076'
abstract:
- lang: eng
text: Auxin is a multifunctional hormone essential for plant development and pattern
formation. A nuclear auxin-signaling system controlling auxin-induced gene expression
is well established, but cytoplasmic auxin signaling, as in its coordination of
cell polarization, is unexplored. We found a cytoplasmic auxin-signaling mechanism
that modulates the interdigitated growth of Arabidopsis leaf epidermal pavement
cells (PCs), which develop interdigitated lobes and indentations to form a puzzle-piece
shape in a two-dimensional plane. PC interdigitation is compromised in leaves
deficient in either auxin biosynthesis or its export mediated by PINFORMED 1 localized
at the lobe tip. Auxin coordinately activates two Rho GTPases, ROP2 and ROP6,
which promote the formation of complementary lobes and indentations, respectively.
Activation of these ROPs by auxin occurs within 30 s and depends on AUXIN-BINDING
PROTEIN 1. These findings reveal Rho GTPase-based auxin-signaling mechanisms,
which modulate the spatial coordination of cell expansion across a field of cells.
author:
- first_name: Tongda
full_name: Xu, Tongda
last_name: Xu
- first_name: Mingzhang
full_name: Wen, Mingzhang
last_name: Wen
- first_name: Shingo
full_name: Nagawa, Shingo
last_name: Nagawa
- first_name: Ying
full_name: Fu, Ying
last_name: Fu
- first_name: Jin
full_name: Chen, Jin-Gui
last_name: Chen
- first_name: Ming
full_name: Wu, Ming-Jing
last_name: Wu
- first_name: Catherine
full_name: Perrot-Rechenmann, Catherine
last_name: Perrot Rechenmann
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Alan
full_name: Jones, Alan M
last_name: Jones
- first_name: Zhenbiao
full_name: Yang, Zhenbiao
last_name: Yang
citation:
ama: Xu T, Wen M, Nagawa S, et al. Cell surface- and Rho GTPase-based auxin signaling
controls cellular interdigitation in Arabidopsis. Cell. 2010;143(1):99-110.
doi:10.1016/j.cell.2010.09.003
apa: Xu, T., Wen, M., Nagawa, S., Fu, Y., Chen, J., Wu, M., … Yang, Z. (2010). Cell
surface- and Rho GTPase-based auxin signaling controls cellular interdigitation
in Arabidopsis. Cell. Cell Press. https://doi.org/10.1016/j.cell.2010.09.003
chicago: Xu, Tongda, Mingzhang Wen, Shingo Nagawa, Ying Fu, Jin Chen, Ming Wu, Catherine
Perrot Rechenmann, Jiří Friml, Alan Jones, and Zhenbiao Yang. “Cell Surface- and
Rho GTPase-Based Auxin Signaling Controls Cellular Interdigitation in Arabidopsis.”
Cell. Cell Press, 2010. https://doi.org/10.1016/j.cell.2010.09.003.
ieee: T. Xu et al., “Cell surface- and Rho GTPase-based auxin signaling controls
cellular interdigitation in Arabidopsis,” Cell, vol. 143, no. 1. Cell Press,
pp. 99–110, 2010.
ista: Xu T, Wen M, Nagawa S, Fu Y, Chen J, Wu M, Perrot Rechenmann C, Friml J, Jones
A, Yang Z. 2010. Cell surface- and Rho GTPase-based auxin signaling controls cellular
interdigitation in Arabidopsis. Cell. 143(1), 99–110.
mla: Xu, Tongda, et al. “Cell Surface- and Rho GTPase-Based Auxin Signaling Controls
Cellular Interdigitation in Arabidopsis.” Cell, vol. 143, no. 1, Cell Press,
2010, pp. 99–110, doi:10.1016/j.cell.2010.09.003.
short: T. Xu, M. Wen, S. Nagawa, Y. Fu, J. Chen, M. Wu, C. Perrot Rechenmann, J.
Friml, A. Jones, Z. Yang, Cell 143 (2010) 99–110.
date_created: 2018-12-11T12:01:14Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2021-01-12T07:40:53Z
day: '01'
doi: 10.1016/j.cell.2010.09.003
extern: 1
intvolume: ' 143'
issue: '1'
month: '10'
page: 99 - 110
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3625'
quality_controlled: 0
status: public
title: Cell surface- and Rho GTPase-based auxin signaling controls cellular interdigitation
in Arabidopsis
type: journal_article
volume: 143
year: '2010'
...
---
_id: '3077'
author:
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Angharad
full_name: Jones, Angharad
last_name: Jones
citation:
ama: 'Friml J, Jones A. Endoplasmic reticulum: The rising compartment in auxin biology.
Plant Physiology. 2010;154(2):458-462. doi:10.1104/pp.110.161380'
apa: 'Friml, J., & Jones, A. (2010). Endoplasmic reticulum: The rising compartment
in auxin biology. Plant Physiology. American Society of Plant Biologists.
https://doi.org/10.1104/pp.110.161380'
chicago: 'Friml, Jiří, and Angharad Jones. “Endoplasmic Reticulum: The Rising Compartment
in Auxin Biology.” Plant Physiology. American Society of Plant Biologists,
2010. https://doi.org/10.1104/pp.110.161380.'
ieee: 'J. Friml and A. Jones, “Endoplasmic reticulum: The rising compartment in
auxin biology,” Plant Physiology, vol. 154, no. 2. American Society of
Plant Biologists, pp. 458–462, 2010.'
ista: 'Friml J, Jones A. 2010. Endoplasmic reticulum: The rising compartment in
auxin biology. Plant Physiology. 154(2), 458–462.'
mla: 'Friml, Jiří, and Angharad Jones. “Endoplasmic Reticulum: The Rising Compartment
in Auxin Biology.” Plant Physiology, vol. 154, no. 2, American Society
of Plant Biologists, 2010, pp. 458–62, doi:10.1104/pp.110.161380.'
short: J. Friml, A. Jones, Plant Physiology 154 (2010) 458–462.
date_created: 2018-12-11T12:01:14Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2021-01-12T07:40:53Z
day: '01'
doi: 10.1104/pp.110.161380
extern: '1'
external_id:
pmid:
- '20921163'
intvolume: ' 154'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/20921163
month: '10'
oa: 1
oa_version: Published Version
page: 458 - 462
pmid: 1
publication: Plant Physiology
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3624'
status: public
title: 'Endoplasmic reticulum: The rising compartment in auxin biology'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 154
year: '2010'
...
---
_id: '3078'
abstract:
- lang: eng
text: Rapid advances in the field of plant biology, especially in plant cell biology,
have created the need for methods that allow the localization of proteins in situ
at subcellular resolution. Although in many cases recombinant proteins with fluorescent
proteins can fulfill this task, antibody-based immunological detection of proteins
is a complementary technique, which avoids the risk of inducing side effects by
a fusion protein, such as misexpression, mistargeting, altered stability, or toxicity.
Moreover, recombinant protein techniques are applicable only to a rather limited
set of model plants. The immunolocalization protocols presented here can be used
to display protein localization patterns in different tissues of various plant
species. This chapter describes a whole mount immunolocalization protocol, which
has been extensively used in Arabidopsis roots and some above-ground tissues,
and that also works in other species. Additionally, for bulky or hard tissue types,
a variation of this protocol for paraffin-embedded sections is given.
alternative_title:
- Methods in Molecular Biology
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Sauer M, Friml J. Immunolocalization of proteins in plants . In: Hennig L,
Köhler C, eds. Plant Developmental Biology. Vol 655. Humana Press; 2010:253-263.
doi:10.1007/978-1-60761-765-5_17'
apa: Sauer, M., & Friml, J. (2010). Immunolocalization of proteins in plants
. In L. Hennig & C. Köhler (Eds.), Plant Developmental Biology (Vol.
655, pp. 253–263). Humana Press. https://doi.org/10.1007/978-1-60761-765-5_17
chicago: Sauer, Michael, and Jiří Friml. “Immunolocalization of Proteins in Plants
.” In Plant Developmental Biology, edited by Lars Hennig and Claudia Köhler,
655:253–63. Humana Press, 2010. https://doi.org/10.1007/978-1-60761-765-5_17.
ieee: M. Sauer and J. Friml, “Immunolocalization of proteins in plants ,” in Plant
Developmental Biology, vol. 655, L. Hennig and C. Köhler, Eds. Humana Press,
2010, pp. 253–263.
ista: 'Sauer M, Friml J. 2010.Immunolocalization of proteins in plants . In: Plant
Developmental Biology. Methods in Molecular Biology, vol. 655, 253–263.'
mla: Sauer, Michael, and Jiří Friml. “Immunolocalization of Proteins in Plants .”
Plant Developmental Biology, edited by Lars Hennig and Claudia Köhler,
vol. 655, Humana Press, 2010, pp. 253–63, doi:10.1007/978-1-60761-765-5_17.
short: M. Sauer, J. Friml, in:, L. Hennig, C. Köhler (Eds.), Plant Developmental
Biology, Humana Press, 2010, pp. 253–263.
date_created: 2018-12-11T12:01:14Z
date_published: 2010-08-12T00:00:00Z
date_updated: 2021-01-12T07:40:53Z
day: '12'
doi: 10.1007/978-1-60761-765-5_17
editor:
- first_name: Lars
full_name: Hennig, Lars
last_name: Hennig
- first_name: Claudia
full_name: Köhler, Claudia
last_name: Köhler
extern: 1
intvolume: ' 655'
month: '08'
page: 253 - 263
publication: Plant Developmental Biology
publication_status: published
publisher: Humana Press
publist_id: '3623'
quality_controlled: 0
status: public
title: 'Immunolocalization of proteins in plants '
type: book_chapter
volume: 655
year: '2010'
...
---
_id: '3079'
abstract:
- lang: eng
text: Plant development is exceptionally flexible as manifested by its potential
for organogenesis and regeneration, which are processes involving rearrangements
of tissue polarities. Fundamental questions concern how individual cells can polarize
in a coordinated manner to integrate into the multicellular context. In canalization
models, the signaling molecule auxin acts as a polarizing cue, and feedback on
the intercellular auxin flow is key for synchronized polarity rearrangements.
We provide a novel mechanistic framework for canalization, based on up-to-date
experimental data and minimal, biologically plausible assumptions. Our model combines
the intracellular auxin signaling for expression of PINFORMED (PIN) auxin transporters
and the theoretical postulation of extracellular auxin signaling for modulation
of PIN subcellular dynamics. Computer simulations faithfully and robustly recapitulated
the experimentally observed patterns of tissue polarity and asymmetric auxin distribution
during formation and regeneration of vascular systems and during the competitive
regulation of shoot branching by apical dominance. Additionally, our model generated
new predictions that could be experimentally validated, highlighting a mechanistically
conceivable explanation for the PIN polarization and canalization of the auxin
flow in plants.
author:
- first_name: Krzysztof T
full_name: Krzysztof Wabnik
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Jozef
full_name: Balla, Jozef
last_name: Balla
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Vilém
full_name: Reinöhl, Vilém
last_name: Reinöhl
- first_name: Roeland
full_name: Merks, Roeland M
last_name: Merks
- first_name: Willy
full_name: Govaerts, Willy J
last_name: Govaerts
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Wabnik KT, Kleine Vehn J, Balla J, et al. Emergence of tissue polarization
from synergy of intracellular and extracellular auxin signaling. Molecular
Systems Biology. 2010;6. doi:10.1038/msb.2010.103
apa: Wabnik, K. T., Kleine Vehn, J., Balla, J., Sauer, M., Naramoto, S., Reinöhl,
V., … Friml, J. (2010). Emergence of tissue polarization from synergy of intracellular
and extracellular auxin signaling. Molecular Systems Biology. Nature Publishing
Group. https://doi.org/10.1038/msb.2010.103
chicago: Wabnik, Krzysztof T, Jürgen Kleine Vehn, Jozef Balla, Michael Sauer, Satoshi
Naramoto, Vilém Reinöhl, Roeland Merks, Willy Govaerts, and Jiří Friml. “Emergence
of Tissue Polarization from Synergy of Intracellular and Extracellular Auxin Signaling.”
Molecular Systems Biology. Nature Publishing Group, 2010. https://doi.org/10.1038/msb.2010.103.
ieee: K. T. Wabnik et al., “Emergence of tissue polarization from synergy
of intracellular and extracellular auxin signaling,” Molecular Systems Biology,
vol. 6. Nature Publishing Group, 2010.
ista: Wabnik KT, Kleine Vehn J, Balla J, Sauer M, Naramoto S, Reinöhl V, Merks R,
Govaerts W, Friml J. 2010. Emergence of tissue polarization from synergy of intracellular
and extracellular auxin signaling. Molecular Systems Biology. 6.
mla: Wabnik, Krzysztof T., et al. “Emergence of Tissue Polarization from Synergy
of Intracellular and Extracellular Auxin Signaling.” Molecular Systems Biology,
vol. 6, Nature Publishing Group, 2010, doi:10.1038/msb.2010.103.
short: K.T. Wabnik, J. Kleine Vehn, J. Balla, M. Sauer, S. Naramoto, V. Reinöhl,
R. Merks, W. Govaerts, J. Friml, Molecular Systems Biology 6 (2010).
date_created: 2018-12-11T12:01:15Z
date_published: 2010-12-21T00:00:00Z
date_updated: 2021-01-12T07:40:54Z
day: '21'
doi: 10.1038/msb.2010.103
extern: 1
intvolume: ' 6'
month: '12'
publication: Molecular Systems Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3622'
quality_controlled: 0
status: public
title: Emergence of tissue polarization from synergy of intracellular and extracellular
auxin signaling
type: journal_article
volume: 6
year: '2010'
...
---
_id: '3080'
abstract:
- lang: eng
text: Auxin is an essential plant-specific regulator of patterning processes that
also controls directional growth of roots and shoots. In response to gravity stimulation,
the PIN3 auxin transporter polarizes to the bottomside of gravity-sensing root
cells, presumably redirecting the auxin flux toward the lower side of the root
and triggering gravitropic bending. By combining live-cell imaging techniques
with pharmacological and genetic approaches, we demonstrate that PIN3 polarization
does not require secretion of de novo synthesized proteins or protein degradation,
but instead involves rapid, transient stimulation of PIN endocytosis, presumably
via a clathrin-dependent pathway. Moreover, gravity-induced PIN3 polarization
requires the activity of the guanine nucleotide exchange factors for ARF GTPases
(ARF-GEF) GNOM-dependent polar-targeting path-ways and might involve endosome-based
PIN3 translocation from one cell side to another. Our data suggest that gravity
perception acts at several instances of PIN3 trafficking, ultimately leading to
the polarization of PIN3, which presumably aligns auxin fluxes with gravity vector
and mediates downstream root gravitropic response.
author:
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
- first_name: Angharad
full_name: Jones, Angharad R
last_name: Jones
- first_name: Masao
full_name: Tasaka, Masao
last_name: Tasaka
- first_name: Miyo
full_name: Morita, Miyo T
last_name: Morita
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Kleine Vehn J, Ding Z, Jones A, Tasaka M, Morita M, Friml J. Gravity induced
PIN transcytosis for polarization of auxin fluxes in gravity sensing root cells.
PNAS. 2010;107(51):22344-22349. doi:10.1073/pnas.1013145107
apa: Kleine Vehn, J., Ding, Z., Jones, A., Tasaka, M., Morita, M., & Friml,
J. (2010). Gravity induced PIN transcytosis for polarization of auxin fluxes in
gravity sensing root cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1013145107
chicago: Kleine Vehn, Jürgen, Zhaojun Ding, Angharad Jones, Masao Tasaka, Miyo Morita,
and Jiří Friml. “Gravity Induced PIN Transcytosis for Polarization of Auxin Fluxes
in Gravity Sensing Root Cells.” PNAS. National Academy of Sciences, 2010.
https://doi.org/10.1073/pnas.1013145107.
ieee: J. Kleine Vehn, Z. Ding, A. Jones, M. Tasaka, M. Morita, and J. Friml, “Gravity
induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root
cells,” PNAS, vol. 107, no. 51. National Academy of Sciences, pp. 22344–22349,
2010.
ista: Kleine Vehn J, Ding Z, Jones A, Tasaka M, Morita M, Friml J. 2010. Gravity
induced PIN transcytosis for polarization of auxin fluxes in gravity sensing root
cells. PNAS. 107(51), 22344–22349.
mla: Kleine Vehn, Jürgen, et al. “Gravity Induced PIN Transcytosis for Polarization
of Auxin Fluxes in Gravity Sensing Root Cells.” PNAS, vol. 107, no. 51,
National Academy of Sciences, 2010, pp. 22344–49, doi:10.1073/pnas.1013145107.
short: J. Kleine Vehn, Z. Ding, A. Jones, M. Tasaka, M. Morita, J. Friml, PNAS 107
(2010) 22344–22349.
date_created: 2018-12-11T12:01:15Z
date_published: 2010-12-21T00:00:00Z
date_updated: 2021-01-12T07:40:55Z
day: '21'
doi: 10.1073/pnas.1013145107
extern: 1
intvolume: ' 107'
issue: '51'
month: '12'
page: 22344 - 22349
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3620'
quality_controlled: 0
status: public
title: Gravity induced PIN transcytosis for polarization of auxin fluxes in gravity
sensing root cells
type: journal_article
volume: 107
year: '2010'
...
---
_id: '3081'
abstract:
- lang: eng
text: Endocytosis is crucial for various cellular functions and development of multicellular
organisms. In mammals and yeast, ADP-ribosylation factor (ARF) GTPases, key components
of vesicle formation, and their regulators ARF-guanine nucleotide exchange factors
(GEFs) and ARF-GTPase-activating protein (GAPs) mediate endocytosis. A similar
role has not been established in plants,mainly because of the lack of the canonical
ARF and ARF-GEF components that are involved in endocytosis in other eukaryotes.
In this study, we revealed a regulatory mechanism of endocytosis in plants based
on ARF GTPase activity.Weidentified that ARF-GEFGNOMand ARF-GAP VASCULAR NETWORK
DEFECTIVE 3 (VAN3), both of which are involved in polar auxin transport-dependent
morphogenesis, localize at the plasma membranes as well as in intracellular structures.
Variable angle epifluorescence microscopy revealed that GNOM and VAN3 localize
to partially overlapping discrete foci at the plasmamembranes that are regularly
associated with the endocytic vesicle coat clathrin. Genetic studies revealed
that GNOM and VAN3 activities are required for endocytosis and internalization
of plasma membrane proteins, including PIN-FORMED auxin transporters. These findings
identified ARF GTPase-based regulatory mechanisms for endocytosis in plants. GNOMand
VAN3 previously were proposed to function solely at the recycling endosomes and
trans-Golgi networks, respectively. Therefore our findings uncovered an additional
cellular function of these prominent developmental regulators.
author:
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Masaru
full_name: Fujimoto, Masaru
last_name: Fujimoto
- first_name: Tomoko
full_name: Dainobu, Tomoko
last_name: Dainobu
- first_name: Tomasz
full_name: Paciorek, Tomasz
last_name: Paciorek
- first_name: Takashi
full_name: Ueda, Takashi
last_name: Ueda
- first_name: Akihiko
full_name: Nakano, Akihiko
last_name: Nakano
- first_name: Marc
full_name: Van Montagu, Marc C
last_name: Van Montagu
- first_name: Hiroo
full_name: Fukuda, Hiroo
last_name: Fukuda
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Naramoto S, Kleine Vehn J, Robert S, et al. ADP ribosylation factor machinery
mediates endocytosis in plant cells. PNAS. 2010;107(50):21890-21895. doi:10.1073/pnas.1016260107
apa: Naramoto, S., Kleine Vehn, J., Robert, S., Fujimoto, M., Dainobu, T., Paciorek,
T., … Friml, J. (2010). ADP ribosylation factor machinery mediates endocytosis
in plant cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1016260107
chicago: Naramoto, Satoshi, Jürgen Kleine Vehn, Stéphanie Robert, Masaru Fujimoto,
Tomoko Dainobu, Tomasz Paciorek, Takashi Ueda, et al. “ADP Ribosylation Factor
Machinery Mediates Endocytosis in Plant Cells.” PNAS. National Academy
of Sciences, 2010. https://doi.org/10.1073/pnas.1016260107.
ieee: S. Naramoto et al., “ADP ribosylation factor machinery mediates endocytosis
in plant cells,” PNAS, vol. 107, no. 50. National Academy of Sciences,
pp. 21890–21895, 2010.
ista: Naramoto S, Kleine Vehn J, Robert S, Fujimoto M, Dainobu T, Paciorek T, Ueda
T, Nakano A, Van Montagu M, Fukuda H, Friml J. 2010. ADP ribosylation factor machinery
mediates endocytosis in plant cells. PNAS. 107(50), 21890–21895.
mla: Naramoto, Satoshi, et al. “ADP Ribosylation Factor Machinery Mediates Endocytosis
in Plant Cells.” PNAS, vol. 107, no. 50, National Academy of Sciences,
2010, pp. 21890–95, doi:10.1073/pnas.1016260107.
short: S. Naramoto, J. Kleine Vehn, S. Robert, M. Fujimoto, T. Dainobu, T. Paciorek,
T. Ueda, A. Nakano, M. Van Montagu, H. Fukuda, J. Friml, PNAS 107 (2010) 21890–21895.
date_created: 2018-12-11T12:01:15Z
date_published: 2010-12-14T00:00:00Z
date_updated: 2021-01-12T07:40:55Z
day: '14'
doi: 10.1073/pnas.1016260107
extern: 1
intvolume: ' 107'
issue: '50'
month: '12'
page: 21890 - 21895
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3621'
quality_controlled: 0
status: public
title: ADP ribosylation factor machinery mediates endocytosis in plant cells
type: journal_article
volume: 107
year: '2010'
...
---
_id: '3146'
abstract:
- lang: eng
text: 'Coordinated migration of newly born neurons to their prospective target laminae
is a prerequisite for neural circuit assembly in the developing brain. The evolutionarily
conserved LIS1/NDEL1 complex is essential for neuronal migration in the mammalian
cerebral cortex. The cytoplasmic nature of LIS1 and NDEL1 proteins suggest that
they regulate neuronal migration cell autonomously. Here, we extend mosaic analysis
with double markers (MADM) to mouse chromosome 11 where Lis1, Ndel1, and 14-3-3e{open}
(encoding a LIS1/NDEL1 signaling partner) are located. Analyses of sparse and
uniquely labeled mutant cells in mosaic animals reveal distinct cell-autonomous
functions for these three genes. Lis1 regulates neuronal migration efficiency
in a dose-dependent manner, while Ndel1 is essential for a specific, previously
uncharacterized, late step of neuronal migration: entry into the target lamina.
Comparisons with previous genetic perturbations of Lis1 and Ndel1 also suggest
a surprising degree of cell-nonautonomous function for these proteins in regulating
neuronal migration.'
author:
- first_name: Simon
full_name: Simon Hippenmeyer
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Yong
full_name: Youn, Yong H
last_name: Youn
- first_name: Hyang
full_name: Moon, Hyang M
last_name: Moon
- first_name: Kazunari
full_name: Miyamichi, Kazunari
last_name: Miyamichi
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
- first_name: Anthony
full_name: Wynshaw-Boris, Anthony
last_name: Wynshaw Boris
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: Hippenmeyer S, Youn Y, Moon H, et al. Genetic mosaic dissection of Lis1 and
Ndel1 in neuronal migration. Neuron. 2010;68(4):695-709. doi:10.1016/j.neuron.2010.09.027
apa: Hippenmeyer, S., Youn, Y., Moon, H., Miyamichi, K., Zong, H., Wynshaw Boris,
A., & Luo, L. (2010). Genetic mosaic dissection of Lis1 and Ndel1 in neuronal
migration. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2010.09.027
chicago: Hippenmeyer, Simon, Yong Youn, Hyang Moon, Kazunari Miyamichi, Hui Zong,
Anthony Wynshaw Boris, and Liqun Luo. “Genetic Mosaic Dissection of Lis1 and Ndel1
in Neuronal Migration.” Neuron. Elsevier, 2010. https://doi.org/10.1016/j.neuron.2010.09.027.
ieee: S. Hippenmeyer et al., “Genetic mosaic dissection of Lis1 and Ndel1
in neuronal migration,” Neuron, vol. 68, no. 4. Elsevier, pp. 695–709,
2010.
ista: Hippenmeyer S, Youn Y, Moon H, Miyamichi K, Zong H, Wynshaw Boris A, Luo L.
2010. Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration. Neuron.
68(4), 695–709.
mla: Hippenmeyer, Simon, et al. “Genetic Mosaic Dissection of Lis1 and Ndel1 in
Neuronal Migration.” Neuron, vol. 68, no. 4, Elsevier, 2010, pp. 695–709,
doi:10.1016/j.neuron.2010.09.027.
short: S. Hippenmeyer, Y. Youn, H. Moon, K. Miyamichi, H. Zong, A. Wynshaw Boris,
L. Luo, Neuron 68 (2010) 695–709.
date_created: 2018-12-11T12:01:39Z
date_published: 2010-11-18T00:00:00Z
date_updated: 2021-01-12T07:41:22Z
day: '18'
doi: 10.1016/j.neuron.2010.09.027
extern: 1
intvolume: ' 68'
issue: '4'
month: '11'
page: 695 - 709
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '3550'
quality_controlled: 0
status: public
title: Genetic mosaic dissection of Lis1 and Ndel1 in neuronal migration
type: journal_article
volume: 68
year: '2010'
...
---
_id: '3153'
abstract:
- lang: eng
text: Human immune cells have to penetrate an endothelial barrier during their beneficial
pursuit of infection and their destructive infiltration of tissues in autoimmune
diseases. This transmigration requires Rap1 GTPase to activate integrin affinity.
We define a new model system for this process by demonstrating, with live imaging
and genetics, that during embryonic development Drosophila melanogaster immune
cells penetrate an epithelial, Drosophila E-cadherin (DE-cadherin)-based tissue
barrier. A mutant in RhoL, a GTPase homologue that is specifically expressed in
haemocytes, blocks this invasive step but not other aspects of guided migration.
RhoL mediates integrin adhesion caused by Drosophila Rap1 overexpression and moves
Rap1 away from a concentration in the cytoplasm to the leading edge during invasive
migration. These findings indicate that a programmed migratory step during Drosophila
development bears striking molecular similarities to vertebrate immune cell transmigration
during inflammation, and identify RhoL as a new regulator of invasion, adhesion
and Rap1 localization. Our work establishes the utility of Drosophila for identifying
novel components of immune cell transmigration and for understanding the in vivo
interplay of immune cells with the barriers they penetrate.
author:
- first_name: Daria E
full_name: Daria Siekhaus
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Martin
full_name: Haesemeyer, Martin
last_name: Haesemeyer
- first_name: Olivia
full_name: Moffitt, Olivia
last_name: Moffitt
- first_name: Ruth
full_name: Lehmann, Ruth
last_name: Lehmann
citation:
ama: Siekhaus DE, Haesemeyer M, Moffitt O, Lehmann R. RhoL controls invasion and
Rap1 localization during immune cell transmigration in Drosophila. Nature Cell
Biology. 2010;12(6):605-610.
apa: Siekhaus, D. E., Haesemeyer, M., Moffitt, O., & Lehmann, R. (2010). RhoL
controls invasion and Rap1 localization during immune cell transmigration in Drosophila.
Nature Cell Biology. Nature Publishing Group.
chicago: Siekhaus, Daria E, Martin Haesemeyer, Olivia Moffitt, and Ruth Lehmann.
“RhoL Controls Invasion and Rap1 Localization during Immune Cell Transmigration
in Drosophila.” Nature Cell Biology. Nature Publishing Group, 2010.
ieee: D. E. Siekhaus, M. Haesemeyer, O. Moffitt, and R. Lehmann, “RhoL controls
invasion and Rap1 localization during immune cell transmigration in Drosophila,”
Nature Cell Biology, vol. 12, no. 6. Nature Publishing Group, pp. 605–610,
2010.
ista: Siekhaus DE, Haesemeyer M, Moffitt O, Lehmann R. 2010. RhoL controls invasion
and Rap1 localization during immune cell transmigration in Drosophila. Nature
Cell Biology. 12(6), 605–610.
mla: Siekhaus, Daria E., et al. “RhoL Controls Invasion and Rap1 Localization during
Immune Cell Transmigration in Drosophila.” Nature Cell Biology, vol. 12,
no. 6, Nature Publishing Group, 2010, pp. 605–10.
short: D.E. Siekhaus, M. Haesemeyer, O. Moffitt, R. Lehmann, Nature Cell Biology
12 (2010) 605–610.
date_created: 2018-12-11T12:01:42Z
date_published: 2010-06-01T00:00:00Z
date_updated: 2021-01-12T07:41:25Z
day: '01'
extern: 1
intvolume: ' 12'
issue: '6'
main_file_link:
- open_access: '0'
url: 10.1038/ncb2063 PubMed
month: '06'
page: 605 - 610
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3542'
quality_controlled: 0
status: public
title: RhoL controls invasion and Rap1 localization during immune cell transmigration
in Drosophila
type: journal_article
volume: 12
year: '2010'
...
---
_id: '3201'
abstract:
- lang: eng
text: 'The problem of cosegmentation consists of segmenting the same object (or
objects of the same class) in two or more distinct images. Recently a number of
different models have been proposed for this problem. However, no comparison of
such models and corresponding optimization techniques has been done so far. We
analyze three existing models: the L1 norm model of Rother et al. [1], the L2
norm model of Mukherjee et al. [2] and the "reward" model of Hochbaum
and Singh [3]. We also study a new model, which is a straightforward extension
of the Boykov-Jolly model for single image segmentation [4]. In terms of optimization,
we use a Dual Decomposition (DD) technique in addition to optimization methods
in [1,2]. Experiments show a significant improvement of DD over published methods.
Our main conclusion, however, is that the new model is the best overall because
it: (i) has fewest parameters; (ii) is most robust in practice, and (iii) can
be optimized well with an efficient EM-style procedure.'
alternative_title:
- LNCS
author:
- first_name: Sara
full_name: Vicente, Sara
last_name: Vicente
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Carsten
full_name: Rother, Carsten
last_name: Rother
citation:
ama: 'Vicente S, Kolmogorov V, Rother C. Cosegmentation revisited: Models and optimization.
In: Vol 6312. Springer; 2010:465-479. doi:10.1007/978-3-642-15552-9_34'
apa: 'Vicente, S., Kolmogorov, V., & Rother, C. (2010). Cosegmentation revisited:
Models and optimization (Vol. 6312, pp. 465–479). Presented at the ECCV: European
Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-642-15552-9_34'
chicago: 'Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Cosegmentation
Revisited: Models and Optimization,” 6312:465–79. Springer, 2010. https://doi.org/10.1007/978-3-642-15552-9_34.'
ieee: 'S. Vicente, V. Kolmogorov, and C. Rother, “Cosegmentation revisited: Models
and optimization,” presented at the ECCV: European Conference on Computer Vision,
2010, vol. 6312, pp. 465–479.'
ista: 'Vicente S, Kolmogorov V, Rother C. 2010. Cosegmentation revisited: Models
and optimization. ECCV: European Conference on Computer Vision, LNCS, vol. 6312,
465–479.'
mla: 'Vicente, Sara, et al. Cosegmentation Revisited: Models and Optimization.
Vol. 6312, Springer, 2010, pp. 465–79, doi:10.1007/978-3-642-15552-9_34.'
short: S. Vicente, V. Kolmogorov, C. Rother, in:, Springer, 2010, pp. 465–479.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:01:59Z
date_published: 2010-08-30T00:00:00Z
date_updated: 2021-01-12T07:41:46Z
day: '30'
doi: 10.1007/978-3-642-15552-9_34
extern: 1
intvolume: ' 6312'
main_file_link:
- open_access: '0'
url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.330.6803df
month: '08'
page: 465 - 479
publication_status: published
publisher: Springer
publist_id: '3479'
quality_controlled: 0
status: public
title: 'Cosegmentation revisited: Models and optimization'
type: conference
volume: 6312
year: '2010'
...
---
_id: '3202'
abstract:
- lang: eng
text: 'We consider the following problem: given an undirected weighted graph G =
(V,E,c) with nonnegative weights, minimize function c(δ(Π))- λ|Π| for all values
of parameter λ. Here Π is a partition of the set of nodes, the first term is the
cost of edges whose endpoints belong to different components of the partition,
and |Π| is the number of components. The current best known algorithm for this
problem has complexity O(|V| 2) maximum flow computations. We improve it to |V|
parametric maximum flow computations. We observe that the complexity can be improved
further for families of graphs which admit a good separator, e.g. for planar graphs.'
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: Kolmogorov V. A faster algorithm for computing the principal sequence of partitions
of a graph. Algorithmica. 2010;56(4):394-412. doi:10.1007/s00453-008-9177-z
apa: Kolmogorov, V. (2010). A faster algorithm for computing the principal sequence
of partitions of a graph. Algorithmica. Springer. https://doi.org/10.1007/s00453-008-9177-z
chicago: Kolmogorov, Vladimir. “A Faster Algorithm for Computing the Principal Sequence
of Partitions of a Graph.” Algorithmica. Springer, 2010. https://doi.org/10.1007/s00453-008-9177-z.
ieee: V. Kolmogorov, “A faster algorithm for computing the principal sequence of
partitions of a graph,” Algorithmica, vol. 56, no. 4. Springer, pp. 394–412,
2010.
ista: Kolmogorov V. 2010. A faster algorithm for computing the principal sequence
of partitions of a graph. Algorithmica. 56(4), 394–412.
mla: Kolmogorov, Vladimir. “A Faster Algorithm for Computing the Principal Sequence
of Partitions of a Graph.” Algorithmica, vol. 56, no. 4, Springer, 2010,
pp. 394–412, doi:10.1007/s00453-008-9177-z.
short: V. Kolmogorov, Algorithmica 56 (2010) 394–412.
date_created: 2018-12-11T12:01:59Z
date_published: 2010-04-01T00:00:00Z
date_updated: 2021-01-12T07:41:46Z
day: '01'
doi: 10.1007/s00453-008-9177-z
extern: 1
intvolume: ' 56'
issue: '4'
month: '04'
page: 394 - 412
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '3480'
quality_controlled: 0
status: public
title: A faster algorithm for computing the principal sequence of partitions of a
graph
type: journal_article
volume: 56
year: '2010'
...
---
_id: '3233'
abstract:
- lang: eng
text: We present a general parallel-repetition theorem with an efficient reduction.
As a corollary of this theorem we establish that parallel repetition reduces the
soundness error at an exponential rate in any public-coin argument, and more generally,
any argument where the verifier's messages, but not necessarily its decision to
accept or reject, can be efficiently simulated with noticeable probability.
alternative_title:
- LNCS
author:
- first_name: Johan
full_name: Håstad, Johan
last_name: Håstad
- first_name: Rafael
full_name: Pass, Rafael
last_name: Pass
- first_name: Douglas
full_name: Wikström, Douglas
last_name: Wikström
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Håstad J, Pass R, Wikström D, Pietrzak KZ. An efficient parallel repetition
theorem. In: Vol 5978. Springer; 2010:1-18. doi:10.1007/978-3-642-11799-2_1'
apa: 'Håstad, J., Pass, R., Wikström, D., & Pietrzak, K. Z. (2010). An efficient
parallel repetition theorem (Vol. 5978, pp. 1–18). Presented at the TCC: Theory
of Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-11799-2_1'
chicago: Håstad, Johan, Rafael Pass, Douglas Wikström, and Krzysztof Z Pietrzak.
“An Efficient Parallel Repetition Theorem,” 5978:1–18. Springer, 2010. https://doi.org/10.1007/978-3-642-11799-2_1.
ieee: 'J. Håstad, R. Pass, D. Wikström, and K. Z. Pietrzak, “An efficient parallel
repetition theorem,” presented at the TCC: Theory of Cryptography Conference,
2010, vol. 5978, pp. 1–18.'
ista: 'Håstad J, Pass R, Wikström D, Pietrzak KZ. 2010. An efficient parallel repetition
theorem. TCC: Theory of Cryptography Conference, LNCS, vol. 5978, 1–18.'
mla: Håstad, Johan, et al. An Efficient Parallel Repetition Theorem. Vol.
5978, Springer, 2010, pp. 1–18, doi:10.1007/978-3-642-11799-2_1.
short: J. Håstad, R. Pass, D. Wikström, K.Z. Pietrzak, in:, Springer, 2010, pp.
1–18.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:10Z
date_published: 2010-03-26T00:00:00Z
date_updated: 2021-01-12T07:41:59Z
day: '26'
doi: 10.1007/978-3-642-11799-2_1
extern: 1
intvolume: ' 5978'
month: '03'
page: 1 - 18
publication_status: published
publisher: Springer
publist_id: '3446'
quality_controlled: 0
status: public
title: An efficient parallel repetition theorem
type: conference
volume: 5978
year: '2010'
...
---
_id: '3234'
abstract:
- lang: eng
text: 'The strongest standard security notion for digital signature schemes is unforgeability
under chosen message attacks. In practice, however, this notion can be insufficient
due to "side-channel attacks" which exploit leakage of information about
the secret internal state. In this work we put forward the notion of "leakage-resilient
signatures," which strengthens the standard security notion by giving the
adversary the additional power to learn a bounded amount of arbitrary information
about the secret state that was accessed during every signature generation. This
notion naturally implies security against all side-channel attacks as long as
the amount of information leaked on each invocation is bounded and "only
computation leaks information." The main result of this paper is a construction
which gives a (tree-based, stateful) leakage-resilient signature scheme based
on any 3-time signature scheme. The amount of information that our scheme can
safely leak per signature generation is 1/3 of the information the underlying
3-time signature scheme can leak in total. Signature schemes that remain secure
even if a bounded total amount of information is leaked were recently constructed,
hence instantiating our construction with these schemes gives the first constructions
of provably secure leakage-resilient signature schemes. The above construction
assumes that the signing algorithm can sample truly random bits, and thus an implementation
would need some special hardware (randomness gates). Simply generating this randomness
using a leakage-resilient stream-cipher will in general not work. Our second contribution
is a sound general principle to replace uniform random bits in any leakage-resilient
construction with pseudorandom ones: run two leakage-resilient stream-ciphers
(with independent keys) in parallel and then apply a two-source extractor to their
outputs. '
alternative_title:
- LNCS
author:
- first_name: Sebastian
full_name: Faust, Sebastian
last_name: Faust
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
- first_name: Guy
full_name: Rothblum, Guy N
last_name: Rothblum
citation:
ama: 'Faust S, Kiltz E, Pietrzak KZ, Rothblum G. Leakage resilient signatures. In:
Vol 5978. Springer; 2010:343-360. doi:10.1007/978-3-642-11799-2_21'
apa: 'Faust, S., Kiltz, E., Pietrzak, K. Z., & Rothblum, G. (2010). Leakage
resilient signatures (Vol. 5978, pp. 343–360). Presented at the TCC: Theory of
Cryptography Conference, Springer. https://doi.org/10.1007/978-3-642-11799-2_21'
chicago: Faust, Sebastian, Eike Kiltz, Krzysztof Z Pietrzak, and Guy Rothblum. “Leakage
Resilient Signatures,” 5978:343–60. Springer, 2010. https://doi.org/10.1007/978-3-642-11799-2_21.
ieee: 'S. Faust, E. Kiltz, K. Z. Pietrzak, and G. Rothblum, “Leakage resilient signatures,”
presented at the TCC: Theory of Cryptography Conference, 2010, vol. 5978, pp.
343–360.'
ista: 'Faust S, Kiltz E, Pietrzak KZ, Rothblum G. 2010. Leakage resilient signatures.
TCC: Theory of Cryptography Conference, LNCS, vol. 5978, 343–360.'
mla: Faust, Sebastian, et al. Leakage Resilient Signatures. Vol. 5978, Springer,
2010, pp. 343–60, doi:10.1007/978-3-642-11799-2_21.
short: S. Faust, E. Kiltz, K.Z. Pietrzak, G. Rothblum, in:, Springer, 2010, pp.
343–360.
conference:
name: 'TCC: Theory of Cryptography Conference'
date_created: 2018-12-11T12:02:10Z
date_published: 2010-03-26T00:00:00Z
date_updated: 2021-01-12T07:41:59Z
day: '26'
doi: 10.1007/978-3-642-11799-2_21
extern: 1
intvolume: ' 5978'
month: '03'
page: 343 - 360
publication_status: published
publisher: Springer
publist_id: '3447'
quality_controlled: 0
status: public
title: Leakage resilient signatures
type: conference
volume: 5978
year: '2010'
...
---
_id: '3235'
abstract:
- lang: eng
text: 'A cryptographic primitive is leakage-resilient, if it remains secure even
if an adversary can learn a bounded amount of arbitrary information about the
computation with every invocation. As a consequence, the physical implementation
of a leakage-resilient primitive is secure against every side-channel as long
as the amount of information leaked per invocation is bounded. In this paper we
prove positive and negative results about the feasibility of constructing leakage-resilient
pseudorandom functions and permutations (i.e. block-ciphers). Our results are
three fold: 1. We construct (from any standard PRF) a PRF which satisfies a relaxed
notion of leakage-resilience where (1) the leakage function is fixed (and not
adaptively chosen with each query.) and (2) the computation is split into several
steps which leak individually (a "step" will be the invocation of the
underlying PRF.) 2. We prove that a Feistel network with a super-logarithmic number
of rounds, each instantiated with a leakage-resilient PRF, is a leakage resilient
PRP. This reduction also holds for the non-adaptive notion just discussed, we
thus get a block-cipher which is leakage-resilient (against non-adaptive leakage).
3. We propose generic side-channel attacks against Feistel networks. The attacks
are generic in the sense that they work for any round functions (e.g. uniformly
random functions) and only require some simple leakage from the inputs to the
round functions. For example we show how to invert an r round Feistel network
over 2n bits making 4•(n+1) r-2 forward queries, if with each query we are also
given as leakage the Hamming weight of the inputs to the r round functions. This
complements the result from the previous item showing that a super-constant number
of rounds is necessary.'
alternative_title:
- LNCS
author:
- first_name: Yevgeniy
full_name: Dodis, Yevgeniy
last_name: Dodis
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Dodis Y, Pietrzak KZ. Leakage resilient pseudorandom functions and side channel
attacks on feistel networks. In: Vol 6223. Springer; 2010:21-40. doi:10.1007/978-3-642-14623-7_2'
apa: 'Dodis, Y., & Pietrzak, K. Z. (2010). Leakage resilient pseudorandom functions
and side channel attacks on feistel networks (Vol. 6223, pp. 21–40). Presented
at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/10.1007/978-3-642-14623-7_2'
chicago: Dodis, Yevgeniy, and Krzysztof Z Pietrzak. “Leakage Resilient Pseudorandom
Functions and Side Channel Attacks on Feistel Networks,” 6223:21–40. Springer,
2010. https://doi.org/10.1007/978-3-642-14623-7_2.
ieee: 'Y. Dodis and K. Z. Pietrzak, “Leakage resilient pseudorandom functions and
side channel attacks on feistel networks,” presented at the CRYPTO: International
Cryptology Conference, 2010, vol. 6223, pp. 21–40.'
ista: 'Dodis Y, Pietrzak KZ. 2010. Leakage resilient pseudorandom functions and
side channel attacks on feistel networks. CRYPTO: International Cryptology Conference,
LNCS, vol. 6223, 21–40.'
mla: Dodis, Yevgeniy, and Krzysztof Z. Pietrzak. Leakage Resilient Pseudorandom
Functions and Side Channel Attacks on Feistel Networks. Vol. 6223, Springer,
2010, pp. 21–40, doi:10.1007/978-3-642-14623-7_2.
short: Y. Dodis, K.Z. Pietrzak, in:, Springer, 2010, pp. 21–40.
conference:
name: 'CRYPTO: International Cryptology Conference'
date_created: 2018-12-11T12:02:10Z
date_published: 2010-09-30T00:00:00Z
date_updated: 2021-01-12T07:42:00Z
day: '30'
doi: 10.1007/978-3-642-14623-7_2
extern: 1
intvolume: ' 6223'
month: '09'
page: 21 - 40
publication_status: published
publisher: Springer
publist_id: '3445'
quality_controlled: 0
status: public
title: Leakage resilient pseudorandom functions and side channel attacks on feistel
networks
type: conference
volume: 6223
year: '2010'
...
---
_id: '3237'
abstract:
- lang: eng
text: 'Blinding is a popular and well-known countermeasure to protect public-key
cryptosystems against side-channel attacks. The high level idea is to randomize
an exponentiation in order to prevent multiple measurements of the same operation
on different data, as such measurements might allow the adversary to learn the
secret exponent. Several variants of blinding have been proposed in the literature,
using additive or multiplicative secret-sharing to blind either the base or the
exponent. These countermeasures usually aim at preventing particular side-channel
attacks (mostly power analysis) and come without any formal security guarantee.
In this work we investigate to which extend blinding can provide provable security
against a general class of side-channel attacks. Surprisingly, it turns out that
in the context of public-key encryption some blinding techniques are more suited
than others. In particular, we consider a multiplicatively blinded version of
ElGamal public-key encryption where - we prove that the scheme, instantiated over
bilinear groups of prime order p (where p - 1 is not smooth) is leakage resilient
in the generic-group model. Here we consider the model of chosen-ciphertext security
in the presence of continuous leakage, i.e., the scheme remains chosen-ciphertext
secure even if with every decryption query the adversary can learn a bounded amount
(roughly log(p)/2 bits) of arbitrary, adversarially chosen information about the
computation. - we conjecture that the scheme, instantiated over arbitrary groups
of prime order p (where p - 1 is not smooth) is leakage resilient. Previous to
this work no encryption scheme secure against continuous leakage was known. Constructing
a scheme that can be proven secure in the standard model remains an interesting
open problem. '
alternative_title:
- LNCS
author:
- first_name: Eike
full_name: Kiltz, Eike
last_name: Kiltz
- first_name: Krzysztof Z
full_name: Krzysztof Pietrzak
id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87
last_name: Pietrzak
orcid: 0000-0002-9139-1654
citation:
ama: 'Kiltz E, Pietrzak KZ. Leakage resilient ElGamal encryption. In: Vol 6477.
Springer; 2010:595-612. doi:10.1007/978-3-642-17373-8_34'
apa: 'Kiltz, E., & Pietrzak, K. Z. (2010). Leakage resilient ElGamal encryption
(Vol. 6477, pp. 595–612). Presented at the ASIACRYPT: Theory and Application of
Cryptology and Information Security, Springer. https://doi.org/10.1007/978-3-642-17373-8_34'
chicago: Kiltz, Eike, and Krzysztof Z Pietrzak. “Leakage Resilient ElGamal Encryption,”
6477:595–612. Springer, 2010. https://doi.org/10.1007/978-3-642-17373-8_34.
ieee: 'E. Kiltz and K. Z. Pietrzak, “Leakage resilient ElGamal encryption,” presented
at the ASIACRYPT: Theory and Application of Cryptology and Information Security,
2010, vol. 6477, pp. 595–612.'
ista: 'Kiltz E, Pietrzak KZ. 2010. Leakage resilient ElGamal encryption. ASIACRYPT:
Theory and Application of Cryptology and Information Security, LNCS, vol. 6477,
595–612.'
mla: Kiltz, Eike, and Krzysztof Z. Pietrzak. Leakage Resilient ElGamal Encryption.
Vol. 6477, Springer, 2010, pp. 595–612, doi:10.1007/978-3-642-17373-8_34.
short: E. Kiltz, K.Z. Pietrzak, in:, Springer, 2010, pp. 595–612.
conference:
name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security'
date_created: 2018-12-11T12:02:11Z
date_published: 2010-01-14T00:00:00Z
date_updated: 2021-01-12T07:42:01Z
day: '14'
doi: 10.1007/978-3-642-17373-8_34
extern: 1
intvolume: ' 6477'
month: '01'
page: 595 - 612
publication_status: published
publisher: Springer
publist_id: '3444'
quality_controlled: 0
status: public
title: Leakage resilient ElGamal encryption
type: conference
volume: 6477
year: '2010'
...
---
_id: '3294'
abstract:
- lang: eng
text: 'Olfactory responses of Drosophila undergo pronounced changes after eclosion.
The flies develop attraction to odors to which they are exposed and aversion to
other odors. Behavioral adaptation is correlated with changes in the firing pattern
of olfactory receptor neurons (ORNs). In this article, we present an information-theoretic
analysis of the firing pattern of ORNs. Flies reared in a synthetic odorless medium
were transferred after eclosion to three different media: (i) a synthetic medium
relatively devoid of odor cues, (ii) synthetic medium infused with a single odorant,
and (iii) complex cornmeal medium rich in odors. Recordings were made from an
identified sensillum (type II), and the Jensen-Shannon divergence (D(JS)) was
used to assess quantitatively the differences between ensemble spike responses
to different odors. Analysis shows that prolonged exposure to ethyl acetate and
several related esters increases sensitivity to these esters but does not improve
the ability of the fly to distinguish between them. Flies exposed to cornmeal
display varied sensitivity to these odorants and at the same time develop greater
capacity to distinguish between odors. Deprivation of odor experience on an odorless
synthetic medium leads to a loss of both sensitivity and acuity. Rich olfactory
experience thus helps to shape the ORNs response and enhances its discriminative
power. The experiments presented here demonstrate an experience-dependent adaptation
at the level of the receptor neuron.'
author:
- first_name: Atulya
full_name: Iyengar, Atulya
last_name: Iyengar
- first_name: Subhra
full_name: Chakraborty Tuhin, Subhra
last_name: Chakraborty Tuhin
- first_name: Sarit
full_name: Sarit Goswami
id: 3A578F32-F248-11E8-B48F-1D18A9856A87
last_name: Goswami
- first_name: Chun
full_name: Wu, Chun Fang
last_name: Wu
- first_name: Obaid
full_name: Siddiqi, Obaid
last_name: Siddiqi
citation:
ama: Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. Post eclosion odor
experience modifies olfactory receptor neuron coding in Drosophila. PNAS.
2010;107(21):9855-9860. doi:10.1073/pnas.1003856107
apa: Iyengar, A., Chakraborty Tuhin, S., Goswami, S., Wu, C., & Siddiqi, O.
(2010). Post eclosion odor experience modifies olfactory receptor neuron coding
in Drosophila. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1003856107
chicago: Iyengar, Atulya, Subhra Chakraborty Tuhin, Sarit Goswami, Chun Wu, and
Obaid Siddiqi. “Post Eclosion Odor Experience Modifies Olfactory Receptor Neuron
Coding in Drosophila.” PNAS. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1003856107.
ieee: A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, and O. Siddiqi, “Post
eclosion odor experience modifies olfactory receptor neuron coding in Drosophila,”
PNAS, vol. 107, no. 21. National Academy of Sciences, pp. 9855–60, 2010.
ista: Iyengar A, Chakraborty Tuhin S, Goswami S, Wu C, Siddiqi O. 2010. Post eclosion
odor experience modifies olfactory receptor neuron coding in Drosophila. PNAS.
107(21), 9855–60.
mla: Iyengar, Atulya, et al. “Post Eclosion Odor Experience Modifies Olfactory Receptor
Neuron Coding in Drosophila.” PNAS, vol. 107, no. 21, National Academy
of Sciences, 2010, pp. 9855–60, doi:10.1073/pnas.1003856107.
short: A. Iyengar, S. Chakraborty Tuhin, S. Goswami, C. Wu, O. Siddiqi, PNAS 107
(2010) 9855–60.
date_created: 2018-12-11T12:02:31Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:27Z
day: '01'
doi: 10.1073/pnas.1003856107
extern: 1
intvolume: ' 107'
issue: '21'
month: '01'
page: 9855 - 60
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3347'
quality_controlled: 0
status: public
title: Post eclosion odor experience modifies olfactory receptor neuron coding in
Drosophila
type: journal_article
volume: 107
year: '2010'
...
---
_id: '3296'
abstract:
- lang: eng
text: "Accurate computational representations of highly deformable surfaces are
indispensable in the fields of computer animation, medical simulation, computer
vision, digital modeling, and computational physics. The focus of this dissertation
is on the animation of physics-based phenomena with highly detailed deformable
surfaces represented by triangle meshes.\r\n \r\nWe first present results from
an algorithm that generates continuum mechanics animations with intricate surface
features. This method combines a finite element method with a tetrahedral mesh
generator and a high resolution surface mesh, and it is orders of magnitude more
efficient than previous approaches. Next, we present an efficient solution for
the challenging problem of computing topological changes in detailed dynamic surface
meshes. We then introduce a new physics-inspired surface tracking algorithm that
is capable of preserving arbitrarily thin features and reproducing realistic fine-scale
topological changes like Rayleigh-Plateau instabilities. This physics-inspired
surface tracking technique also opens the door for a unique coupling between surficial
finite element methods and volumetric finite difference methods, in order to simulate
liquid surface tension phenomena more efficiently than any previous method. Due
to its dramatic increase in computational resolution and efficiency, this method
yielded the first computer simulations of a fully developed crown splash with
droplet pinch off."
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
citation:
ama: Wojtan C. Animating physical phenomena with embedded surface meshes. 2010:1-175.
apa: Wojtan, C. (2010). Animating physical phenomena with embedded surface meshes.
Georgia Institute of Technology.
chicago: Wojtan, Chris. “Animating Physical Phenomena with Embedded Surface Meshes.”
Georgia Institute of Technology, 2010.
ieee: C. Wojtan, “Animating physical phenomena with embedded surface meshes,” Georgia
Institute of Technology, 2010.
ista: Wojtan C. 2010. Animating physical phenomena with embedded surface meshes.
Georgia Institute of Technology.
mla: Wojtan, Chris. Animating Physical Phenomena with Embedded Surface Meshes.
Georgia Institute of Technology, 2010, pp. 1–175.
short: C. Wojtan, Animating Physical Phenomena with Embedded Surface Meshes, Georgia
Institute of Technology, 2010.
date_created: 2018-12-11T12:02:31Z
date_published: 2010-11-17T00:00:00Z
date_updated: 2023-02-23T11:21:00Z
day: '17'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://hdl.handle.net/1853/37256
month: '11'
oa_version: None
page: 1 - 175
publication_status: published
publisher: Georgia Institute of Technology
publist_id: '3345'
status: public
supervisor:
- first_name: Irfan
full_name: Essa, Irfan
last_name: Essa
- first_name: Karen
full_name: Liu, Karen
last_name: Liu
- first_name: Peter
full_name: Mucha, Peter
last_name: Mucha
- first_name: Jarek
full_name: Rossignac, Jarek
last_name: Rossignac
title: Animating physical phenomena with embedded surface meshes
type: dissertation
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3303'
abstract:
- lang: eng
text: 'Biological traits result in part from interactions between different genetic
loci. This can lead to sign epistasis, in which a beneficial adaptation involves
a combination of individually deleterious or neutral mutations; in this case,
a population must cross a “fitness valley” to adapt. Recombination can assist
this process by combining mutations from different individuals or retard it by
breaking up the adaptive combination. Here, we analyze the simplest fitness valley,
in which an adaptation requires one mutation at each of two loci to provide a
fitness benefit. We present a theoretical analysis of the effect of recombination
on the valley-crossing process across the full spectrum of possible parameter
regimes. We find that low recombination rates can speed up valley crossing relative
to the asexual case, while higher recombination rates slow down valley crossing,
with the transition between the two regimes occurring when the recombination rate
between the loci is approximately equal to the selective advantage provided by
the adaptation. In large populations, if the recombination rate is high and selection
against single mutants is substantial, the time to cross the valley grows exponentially
with population size, effectively meaning that the population cannot acquire the
adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing
time by up to several orders of magnitude relative to that in an asexual population. '
acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate
Fellowship and European Research Council grant 250152 (to D.B.W.) and by National
Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many
ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer
for their helpful suggestions. "
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus
last_name: Feldman
- first_name: Daniel
full_name: Fisher, Daniel
last_name: Fisher
citation:
ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual
populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240
apa: Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley
crossing in sexual populations. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.110.123240
chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley
Crossing in Sexual Populations.” Genetics. Genetics Society of America,
2010. https://doi.org/10.1534/genetics.110.123240.
ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing
in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of
America, pp. 1389–1410, 2010.
ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing
in sexual populations. Genetics. 186(4), 1389–1410.
mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.”
Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410,
doi:10.1534/genetics.110.123240.
short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.
date_created: 2018-12-11T12:02:33Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.110.123240
ec_funded: 1
intvolume: ' 186'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1389 - 1410
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3337'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rate of fitness-valley crossing in sexual populations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 186
year: '2010'
...
---
_id: '3306'
abstract:
- lang: eng
text: We use methods from combinatorics and algebraic statistics to study analogues
of birth-and-death processes that have as their state space a finite subset of
the m-dimensional lattice and for which the m matrices that record the transition
probabilities in each of the lattice directions commute pairwise. One reason such
processes are of interest is that the transition matrix is straightforward to
diagonalize, and hence it is easy to compute n step transition probabilities.
The set of commuting birth-and-death processes decomposes as a union of toric
varieties, with the main component being the closure of all processes whose nearest
neighbor transition probabilities are positive. We exhibit an explicit monomial
parametrization for this main component, and we explore the boundary components
using primary decomposition.
acknowledgement: Steven N. Evans was supported in part by NSF Grants DMS-04-05778
and DMS-09-07630. Bernd Sturmfels was supported in part by NSF Grants DMS-04-56960
and DMS-07-57236. Caroline Uhler was supported by an International Fulbright Science
and Technology Fellowship.
author:
- first_name: Steven
full_name: Evans, Steven N
last_name: Evans
- first_name: Bernd
full_name: Sturmfels, Bernd
last_name: Sturmfels
- first_name: Caroline
full_name: Caroline Uhler
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Evans S, Sturmfels B, Uhler C. Commuting birth and death processes. The
Annals of Applied Probability. 2010;20:238-266. doi:10.1214/09-AAP615
apa: Evans, S., Sturmfels, B., & Uhler, C. (2010). Commuting birth and death
processes. The Annals of Applied Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/09-AAP615
chicago: Evans, Steven, Bernd Sturmfels, and Caroline Uhler. “Commuting Birth and
Death Processes.” The Annals of Applied Probability. Institute of Mathematical
Statistics, 2010. https://doi.org/10.1214/09-AAP615.
ieee: S. Evans, B. Sturmfels, and C. Uhler, “Commuting birth and death processes,”
The Annals of Applied Probability, vol. 20. Institute of Mathematical Statistics,
pp. 238–266, 2010.
ista: Evans S, Sturmfels B, Uhler C. 2010. Commuting birth and death processes.
The Annals of Applied Probability. 20, 238–266.
mla: Evans, Steven, et al. “Commuting Birth and Death Processes.” The Annals
of Applied Probability, vol. 20, Institute of Mathematical Statistics, 2010,
pp. 238–66, doi:10.1214/09-AAP615.
short: S. Evans, B. Sturmfels, C. Uhler, The Annals of Applied Probability 20 (2010)
238–266.
date_created: 2018-12-11T12:02:35Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:32Z
day: '01'
doi: 10.1214/09-AAP615
extern: 1
intvolume: ' 20'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/0812.2724
month: '01'
oa: 1
page: 238 - 266
publication: The Annals of Applied Probability
publication_status: published
publisher: Institute of Mathematical Statistics
publist_id: '3334'
quality_controlled: 0
status: public
title: Commuting birth and death processes
type: journal_article
volume: 20
year: '2010'
...