---
_id: '2932'
abstract:
- lang: eng
text: |+
We describe a new implementation of the Edmonds’s algorithm for computing a perfect matching of minimum cost, to which we refer as Blossom V. A key feature of our implementation is a combination of two ideas that were shown to be effective for this problem: the “variable dual updates” approach of Cook and Rohe (INFORMS J Comput 11(2):138–148, 1999) and the use of priority queues. We achieve this by maintaining an auxiliary graph whose nodes correspond to alternating trees in the Edmonds’s algorithm. While our use of priority queues does not improve the worst-case complexity, it appears to lead to an efficient technique. In the majority of our tests Blossom V outperformed previous implementations of Cook and Rohe (INFORMS J Comput 11(2):138–148, 1999) and Mehlhorn and Schäfer (J Algorithmics Exp (JEA) 7:4, 2002), sometimes by an order of magnitude. We also show that for large VLSI instances it is beneficial to update duals by solving a linear program, contrary to a conjecture by Cook and Rohe.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
citation:
ama: 'Kolmogorov V. Blossom V: A new implementation of a minimum cost perfect matching
algorithm. Mathematical Programming Computation. 2009;1(1):43-67. doi:10.1007/s12532-009-0002-8'
apa: 'Kolmogorov, V. (2009). Blossom V: A new implementation of a minimum cost perfect
matching algorithm. Mathematical Programming Computation. Springer. https://doi.org/10.1007/s12532-009-0002-8'
chicago: 'Kolmogorov, Vladimir. “Blossom V: A New Implementation of a Minimum Cost
Perfect Matching Algorithm.” Mathematical Programming Computation. Springer,
2009. https://doi.org/10.1007/s12532-009-0002-8.'
ieee: 'V. Kolmogorov, “Blossom V: A new implementation of a minimum cost perfect
matching algorithm,” Mathematical Programming Computation, vol. 1, no.
1. Springer, pp. 43–67, 2009.'
ista: 'Kolmogorov V. 2009. Blossom V: A new implementation of a minimum cost perfect
matching algorithm. Mathematical Programming Computation. 1(1), 43–67.'
mla: 'Kolmogorov, Vladimir. “Blossom V: A New Implementation of a Minimum Cost Perfect
Matching Algorithm.” Mathematical Programming Computation, vol. 1, no.
1, Springer, 2009, pp. 43–67, doi:10.1007/s12532-009-0002-8.'
short: V. Kolmogorov, Mathematical Programming Computation 1 (2009) 43–67.
date_created: 2018-12-11T12:00:25Z
date_published: 2009-07-01T00:00:00Z
date_updated: 2021-01-12T07:00:47Z
day: '01'
doi: 10.1007/s12532-009-0002-8
extern: 1
intvolume: ' 1'
issue: '1'
month: '07'
page: 43 - 67
publication: Mathematical Programming Computation
publication_status: published
publisher: Springer
publist_id: '3804'
quality_controlled: 0
status: public
title: 'Blossom V: A new implementation of a minimum cost perfect matching algorithm'
type: journal_article
volume: 1
year: '2009'
...
...
---
_id: '3046'
abstract:
- lang: eng
text: Plant-parasitic nematodes are destructive plant pathogens that cause significant
yield losses. They induce highly specialized feeding sites (NFS) in infected plant
roots from which they withdraw nutrients. In order to establish these NFS, it
is thought that the nematodes manipulate the molecular and physiological pathways
of their hosts. Evidence is accumulating that the plant signalling molecule auxin
is involved in the initiation and development of the feeding sites of sedentary
plant-parasitic nematodes. Intercellular transport of auxin is essential for various
aspects of plant growth and development. Here, we analysed the spatial and temporal
expression of PIN auxin transporters during the early events of NFS establishment
using promoter-GUS/GFP fusion lines. Additionally, single and double pin mutants
were used in infection studies to analyse the role of the different PIN proteins
during cyst nematode infection. Based on our results, we postulate a model in
which PIN1-mediated auxin transport is needed to deliver auxin to the initial
syncytial cell, whereas PIN3 and PIN4 distribute the accumulated auxin laterally
and are involved in the radial expansion of the NFS. Our data demonstrate that
cyst nematodes are able to hijack the auxin distribution network in order to facilitate
the infection process. © 2009 Grunewald et al
author:
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Bernard
full_name: Cannoot, Bernard
last_name: Cannoot
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Godelieve
full_name: Gheysen, Godelieve
last_name: Gheysen
citation:
ama: Grunewald W, Cannoot B, Friml J, Gheysen G. Parasitic nematodes modulate PIN
mediated auxin transport to facilitate infection. PLoS Pathogens. 2009;5(1).
doi: 10.1371/journal.ppat.1000266
apa: Grunewald, W., Cannoot, B., Friml, J., & Gheysen, G. (2009). Parasitic
nematodes modulate PIN mediated auxin transport to facilitate infection. PLoS
Pathogens. Public Library of Science. https://doi.org/
10.1371/journal.ppat.1000266
chicago: Grunewald, Wim, Bernard Cannoot, Jiří Friml, and Godelieve Gheysen. “Parasitic
Nematodes Modulate PIN Mediated Auxin Transport to Facilitate Infection.” PLoS
Pathogens. Public Library of Science, 2009. https://doi.org/
10.1371/journal.ppat.1000266.
ieee: W. Grunewald, B. Cannoot, J. Friml, and G. Gheysen, “Parasitic nematodes modulate
PIN mediated auxin transport to facilitate infection,” PLoS Pathogens,
vol. 5, no. 1. Public Library of Science, 2009.
ista: Grunewald W, Cannoot B, Friml J, Gheysen G. 2009. Parasitic nematodes modulate
PIN mediated auxin transport to facilitate infection. PLoS Pathogens. 5(1).
mla: Grunewald, Wim, et al. “Parasitic Nematodes Modulate PIN Mediated Auxin Transport
to Facilitate Infection.” PLoS Pathogens, vol. 5, no. 1, Public Library
of Science, 2009, doi:
10.1371/journal.ppat.1000266.
short: W. Grunewald, B. Cannoot, J. Friml, G. Gheysen, PLoS Pathogens 5 (2009).
date_created: 2018-12-11T12:01:03Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:40Z
day: '01'
doi: ' 10.1371/journal.ppat.1000266'
extern: 1
intvolume: ' 5'
issue: '1'
month: '01'
publication: PLoS Pathogens
publication_status: published
publisher: Public Library of Science
publist_id: '3656'
quality_controlled: 0
status: public
title: Parasitic nematodes modulate PIN mediated auxin transport to facilitate infection
type: journal_article
volume: 5
year: '2009'
...
---
_id: '3047'
abstract:
- lang: eng
text: "\n\nAuxin transport is mediated at the cellular level by three independent
mechanisms that are characterised by the PIN-formed (PIN), P-glycoprotein (ABCB/PGP)
and AUX/LAX transport proteins. The PIN and ABCB transport proteins, best represented
by PIN1 and ABCB19 (PGP19), have been shown to coordinately regulate auxin efflux.
When PIN1 and ABCB19 coincide on the plasma membrane, their interaction enhances
the rate and specificity of auxin efflux and the dynamic cycling of PIN1 is reduced.
However, ABCB19 function is not regulated by the dynamic cellular trafficking
mechanisms that regulate PIN1 in apical tissues, as localisation of ABCB19 on
the plasma membrane was not inhibited by short-term treatments with latrunculin
B, oryzalin, brefeldin A (BFA) or wortmannin - all of which have been shown to
alter PIN1 and/or PIN2 plasma membrane localisation. When taken up by endocytosis,
the styryl dye FM4-64 labels diffuse rather than punctuate intracellular bodies
in abcb19 (pgp19), and some aggregations of PIN1 induced by short-term BFA treatment
did not disperse after BFA washout in abcb19. Although the subcellular localisations
of ABCB19 and PIN1 in the reciprocal mutant backgrounds were like those in wild
type, PIN1 plasma membrane localisation in abcb19 roots was more easily perturbed
by the detergent Triton X-100, but not other non-ionic detergents. ABCB19 is stably
associated with sterol/sphingolipid-enriched membrane fractions containing BIG/TIR3
and partitions into Triton X-100 detergent-resistant membrane (DRM) fractions.
In the wild type, PIN1 was also present in DRMs, but was less abundant in abcb19
DRMs. These observations suggested a rationale for the observed lack of auxin
transport activity when PIN1 is expressed in a non-plant heterologous system.
PIN1 was therefore expressed in Schizosaccharomyces pombe, which has plant-like
sterol-enriched microdomains, and catalysed auxin transport in these cells. These
data suggest that ABCB19 stabilises PIN1 localisation at the plasma membrane in
discrete cellular subdomains where PIN1 and ABCB19 expression overlaps. "
author:
- first_name: Boosaree
full_name: Titapiwatanakun, Boosaree
last_name: Titapiwatanakun
- first_name: Joshua
full_name: Blakeslee, Joshua
last_name: Blakeslee
- first_name: Anindita
full_name: Bandyopadhyay, Anindita
last_name: Bandyopadhyay
- first_name: Haibing
full_name: Yang, Haibing
last_name: Yang
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Yan
full_name: Cheng, Yan
last_name: Cheng
- first_name: Jiří
full_name: Adamec, Jiří
last_name: Adamec
- first_name: Akitomo
full_name: Nagashima, Akitomo
last_name: Nagashima
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Tatsuya
full_name: Sakai, Tatsuya
last_name: Sakai
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Wendy
full_name: Peer, Wendy A
last_name: Peer
- first_name: Angus
full_name: Murphy, Angus S
last_name: Murphy
citation:
ama: Titapiwatanakun B, Blakeslee J, Bandyopadhyay A, et al. ABCB19 PGP19 stabilises
PIN1 in membrane microdomains in Arabidopsis. Plant Journal. 2009;57(1):27-44.
doi:10.1111/j.1365-313X.2008.03668.x
apa: Titapiwatanakun, B., Blakeslee, J., Bandyopadhyay, A., Yang, H., Mravec, J.,
Sauer, M., … Murphy, A. (2009). ABCB19 PGP19 stabilises PIN1 in membrane microdomains
in Arabidopsis. Plant Journal. Wiley-Blackwell. https://doi.org/10.1111/j.1365-313X.2008.03668.x
chicago: Titapiwatanakun, Boosaree, Joshua Blakeslee, Anindita Bandyopadhyay, Haibing
Yang, Jozef Mravec, Michael Sauer, Yan Cheng, et al. “ABCB19 PGP19 Stabilises
PIN1 in Membrane Microdomains in Arabidopsis.” Plant Journal. Wiley-Blackwell,
2009. https://doi.org/10.1111/j.1365-313X.2008.03668.x.
ieee: B. Titapiwatanakun et al., “ABCB19 PGP19 stabilises PIN1 in membrane
microdomains in Arabidopsis,” Plant Journal, vol. 57, no. 1. Wiley-Blackwell,
pp. 27–44, 2009.
ista: Titapiwatanakun B, Blakeslee J, Bandyopadhyay A, Yang H, Mravec J, Sauer M,
Cheng Y, Adamec J, Nagashima A, Geisler M, Sakai T, Friml J, Peer W, Murphy A.
2009. ABCB19 PGP19 stabilises PIN1 in membrane microdomains in Arabidopsis. Plant
Journal. 57(1), 27–44.
mla: Titapiwatanakun, Boosaree, et al. “ABCB19 PGP19 Stabilises PIN1 in Membrane
Microdomains in Arabidopsis.” Plant Journal, vol. 57, no. 1, Wiley-Blackwell,
2009, pp. 27–44, doi:10.1111/j.1365-313X.2008.03668.x.
short: B. Titapiwatanakun, J. Blakeslee, A. Bandyopadhyay, H. Yang, J. Mravec, M.
Sauer, Y. Cheng, J. Adamec, A. Nagashima, M. Geisler, T. Sakai, J. Friml, W. Peer,
A. Murphy, Plant Journal 57 (2009) 27–44.
date_created: 2018-12-11T12:01:03Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:40:40Z
day: '01'
doi: 10.1111/j.1365-313X.2008.03668.x
extern: 1
intvolume: ' 57'
issue: '1'
month: '01'
page: 27 - 44
publication: Plant Journal
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3655'
quality_controlled: 0
status: public
title: ABCB19 PGP19 stabilises PIN1 in membrane microdomains in Arabidopsis
type: journal_article
volume: 57
year: '2009'
...
---
_id: '3048'
abstract:
- lang: eng
text: Endocytic vesicle trafficking is crucial for regulating activity and localization
of plasma membrane components, but the process is still poorly genetically defined
in plants. Membrane proteins of the PIN-FORMED (PIN) family exhibit polar localization
in plant cells and facilitate cellular efflux of the plant hormone auxin, thereby
regulating multiple developmental processes [1, 2]. PIN proteins undergo constitutive
endocytosis and GNOM ARF GEF-dependent recycling [3-5], and their localization
is under extensive regulation by developmental and environmental cues [6-9]. We
designed a fluorescence imaging-based screen to identify Arabidopsis thaliana
mutants defective in internalization of proteins including PINs from the plasma
membrane. We identified three mutant loci, BFA-visualized endocytic trafficking
defective1 (ben1) through ben3 that do not efficiently accumulate PIN1-GFP in
intracellular compartments after inhibition of recycling and secretion by fungal
toxin brefeldin A (BFA). Fine mapping revealed that BEN1 encodes an ARF GEF vesicle
trafficking regulator from the functionally uncharacterized BIG class. ben1 mutant
has been previously implicated in pathogen response [10] and shows cell polarity,
BFA sensitivity, and growth defects. BEN1 is involved in endocytosis of plasma
membrane proteins and localizes to early endocytic compartments distinct from
GNOM-positive endosomes. Our results identify BEN1 as the ARF GEF mediating early
endosomal traffic.
author:
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Riet
full_name: De Rycke, Riet M
last_name: De Rycke
- first_name: Ruth
full_name: De Groodt, Ruth
last_name: De Groodt
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Tanaka H, Kitakura S, De Rycke R, De Groodt R, Friml J. Fluorescence imaging
based screen identifies ARF GEF component of early endosomal trafficking. Current
Biology. 2009;19(5):391-397. doi:10.1016/j.cub.2009.01.057
apa: Tanaka, H., Kitakura, S., De Rycke, R., De Groodt, R., & Friml, J. (2009).
Fluorescence imaging based screen identifies ARF GEF component of early endosomal
trafficking. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2009.01.057
chicago: Tanaka, Hirokazu, Saeko Kitakura, Riet De Rycke, Ruth De Groodt, and Jiří
Friml. “Fluorescence Imaging Based Screen Identifies ARF GEF Component of Early
Endosomal Trafficking.” Current Biology. Cell Press, 2009. https://doi.org/10.1016/j.cub.2009.01.057.
ieee: H. Tanaka, S. Kitakura, R. De Rycke, R. De Groodt, and J. Friml, “Fluorescence
imaging based screen identifies ARF GEF component of early endosomal trafficking,”
Current Biology, vol. 19, no. 5. Cell Press, pp. 391–397, 2009.
ista: Tanaka H, Kitakura S, De Rycke R, De Groodt R, Friml J. 2009. Fluorescence
imaging based screen identifies ARF GEF component of early endosomal trafficking.
Current Biology. 19(5), 391–397.
mla: Tanaka, Hirokazu, et al. “Fluorescence Imaging Based Screen Identifies ARF
GEF Component of Early Endosomal Trafficking.” Current Biology, vol. 19,
no. 5, Cell Press, 2009, pp. 391–97, doi:10.1016/j.cub.2009.01.057.
short: H. Tanaka, S. Kitakura, R. De Rycke, R. De Groodt, J. Friml, Current Biology
19 (2009) 391–397.
date_created: 2018-12-11T12:01:03Z
date_published: 2009-03-10T00:00:00Z
date_updated: 2021-01-12T07:40:41Z
day: '10'
doi: 10.1016/j.cub.2009.01.057
extern: 1
intvolume: ' 19'
issue: '5'
month: '03'
page: 391 - 397
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '3653'
quality_controlled: 0
status: public
title: Fluorescence imaging based screen identifies ARF GEF component of early endosomal
trafficking
type: journal_article
volume: 19
year: '2009'
...
---
_id: '3049'
abstract:
- lang: eng
text: Postembryonic de novo organogenesis represents an important competence evolved
in plants that allows their physiological and developmental adaptation to changing
environmental conditions. The phytohormones auxin and cytokinin (CK) are important
regulators of the developmental fate of pluripotent plant cells. However, the
molecular nature of their interaction(s) in control of plant organogenesis is
largely unknown. Here, we show that CK modulates auxin-induced organogenesis (AIO)
via regulation of the efflux-dependent intercellular auxin distribution. We used
the hypocotyl explants-based in vitro system to study the mechanism underlying
de novo organogenesis. We show that auxin, but not CK, is capable of triggering
organogenesis in hypocotyl explants. The AIO is accompanied by endogenous CK production
and tissue-specific activation of CK signaling. CK affects differential auxin
distribution, and the CK-mediated modulation of organogenesis is simulated by
inhibition of polar auxin transport. CK reduces auxin efflux from cultured tobacco
cells and regulates expression of auxin efflux carriers from the PIN family in
hypocotyl explants. Moreover, endogenous CK levels influence PIN transcription
and are necessary to maintain intercellular auxin distribution in planta. Based
on these findings, we propose a model in which auxin acts as a trigger of the
organogenic processes, whose output is modulated by the endogenously produced
CKs. We propose that an important mechanism of this CK action is its effect on
auxin distribution via regulation of expression of auxin efflux carriers.
author:
- first_name: Markéta
full_name: Pernisová, Markéta
last_name: Pernisová
- first_name: Petr
full_name: Klíma, Petr
last_name: Klíma
- first_name: Jakub
full_name: Horák, Jakub
last_name: Horák
- first_name: Martina
full_name: Válková, Martina
last_name: Válková
- first_name: Jiří
full_name: Malbeck, Jiří
last_name: Malbeck
- first_name: Přemysl
full_name: Souček, Přemysl
last_name: Souček
- first_name: Pavel
full_name: Reichman, Pavel
last_name: Reichman
- first_name: Klára
full_name: Hoyerová, Klára
last_name: Hoyerová
- first_name: Jaroslava
full_name: Dubová, Jaroslava
last_name: Dubová
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Jan
full_name: Hejátko, Jan
last_name: Hejátko
citation:
ama: Pernisová M, Klíma P, Horák J, et al. Cytokinins modulate auxin induced organogenesis
in plants via regulation of the auxin efflux. PNAS. 2009;106(9):3609-3614.
doi:10.1073/pnas.0811539106
apa: Pernisová, M., Klíma, P., Horák, J., Válková, M., Malbeck, J., Souček, P.,
… Hejátko, J. (2009). Cytokinins modulate auxin induced organogenesis in plants
via regulation of the auxin efflux. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.0811539106
chicago: Pernisová, Markéta, Petr Klíma, Jakub Horák, Martina Válková, Jiří Malbeck,
Přemysl Souček, Pavel Reichman, et al. “Cytokinins Modulate Auxin Induced Organogenesis
in Plants via Regulation of the Auxin Efflux.” PNAS. National Academy of
Sciences, 2009. https://doi.org/10.1073/pnas.0811539106.
ieee: M. Pernisová et al., “Cytokinins modulate auxin induced organogenesis
in plants via regulation of the auxin efflux,” PNAS, vol. 106, no. 9. National
Academy of Sciences, pp. 3609–3614, 2009.
ista: Pernisová M, Klíma P, Horák J, Válková M, Malbeck J, Souček P, Reichman P,
Hoyerová K, Dubová J, Friml J, Zažímalová E, Hejátko J. 2009. Cytokinins modulate
auxin induced organogenesis in plants via regulation of the auxin efflux. PNAS.
106(9), 3609–3614.
mla: Pernisová, Markéta, et al. “Cytokinins Modulate Auxin Induced Organogenesis
in Plants via Regulation of the Auxin Efflux.” PNAS, vol. 106, no. 9, National
Academy of Sciences, 2009, pp. 3609–14, doi:10.1073/pnas.0811539106.
short: M. Pernisová, P. Klíma, J. Horák, M. Válková, J. Malbeck, P. Souček, P. Reichman,
K. Hoyerová, J. Dubová, J. Friml, E. Zažímalová, J. Hejátko, PNAS 106 (2009) 3609–3614.
date_created: 2018-12-11T12:01:04Z
date_published: 2009-03-03T00:00:00Z
date_updated: 2021-01-12T07:40:41Z
day: '03'
doi: 10.1073/pnas.0811539106
extern: 1
intvolume: ' 106'
issue: '9'
month: '03'
page: 3609 - 3614
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3654'
quality_controlled: 0
status: public
title: Cytokinins modulate auxin induced organogenesis in plants via regulation of
the auxin efflux
type: journal_article
volume: 106
year: '2009'
...
---
_id: '3050'
abstract:
- lang: eng
text: 'Plant development is governed by signaling molecules called phytohormones.
Typically, in certain developmental processes more than 1 hormone is implicated
and, thus, coordination of their overlapping activities is crucial for correct
plant development. However, molecular mechanisms underlying the hormonal crosstalk
are only poorly understood. Multiple hormones including cytokinin and auxin have
been implicated in the regulation of root development. Here we dissect the roles
of cytokinin in modulating growth of the primary root. We show that cytokinin
effect on root elongation occurs through ethylene signaling whereas cytokinin
effect on the root meristem size involves ethylene-independent modulation of transport-dependent
asymmetric auxin distribution. Exogenous or endogenous modification of cytokinin
levels and cytokinin signaling lead to specific changes in transcription of several
auxin efflux carrier genes from the PIN family having a direct impact on auxin
efflux from cultured cells and on auxin distribution in the root apex. We propose
a novel model for cytokinin action in regulating root growth: Cytokinin influences
cell-to-cell auxin transport by modification of expression of several auxin transport
components and thus modulates auxin distribution important for regulation of activity
and size of the root meristem.'
author:
- first_name: Kamil
full_name: Růžička, Kamil
last_name: Růžička
- first_name: Mária
full_name: Šimášková, Mária
last_name: Šimášková
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Sibu
full_name: Sibu Simon
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Marc
full_name: Van Montagu, Marc C
last_name: Van Montagu
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Růžička K, Šimášková M, Duclercq J, et al. Cytokinin regulates root meristem
activity via modulation of the polar auxin transport. PNAS. 2009;106(11):4284-4289.
doi:10.1073/pnas.0900060106
apa: Růžička, K., Šimášková, M., Duclercq, J., Petrášek, J., Zažímalová, E., Simon,
S., … Benková, E. (2009). Cytokinin regulates root meristem activity via modulation
of the polar auxin transport. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0900060106
chicago: Růžička, Kamil, Mária Šimášková, Jérôme Duclercq, Jan Petrášek, Eva Zažímalová,
Sibu Simon, Jiří Friml, Marc Van Montagu, and Eva Benková. “Cytokinin Regulates
Root Meristem Activity via Modulation of the Polar Auxin Transport.” PNAS.
National Academy of Sciences, 2009. https://doi.org/10.1073/pnas.0900060106.
ieee: K. Růžička et al., “Cytokinin regulates root meristem activity via
modulation of the polar auxin transport,” PNAS, vol. 106, no. 11. National
Academy of Sciences, pp. 4284–4289, 2009.
ista: Růžička K, Šimášková M, Duclercq J, Petrášek J, Zažímalová E, Simon S, Friml
J, Van Montagu M, Benková E. 2009. Cytokinin regulates root meristem activity
via modulation of the polar auxin transport. PNAS. 106(11), 4284–4289.
mla: Růžička, Kamil, et al. “Cytokinin Regulates Root Meristem Activity via Modulation
of the Polar Auxin Transport.” PNAS, vol. 106, no. 11, National Academy
of Sciences, 2009, pp. 4284–89, doi:10.1073/pnas.0900060106.
short: K. Růžička, M. Šimášková, J. Duclercq, J. Petrášek, E. Zažímalová, S. Simon,
J. Friml, M. Van Montagu, E. Benková, PNAS 106 (2009) 4284–4289.
date_created: 2018-12-11T12:01:04Z
date_published: 2009-03-17T00:00:00Z
date_updated: 2021-01-12T07:40:42Z
day: '17'
doi: 10.1073/pnas.0900060106
extern: 1
intvolume: ' 106'
issue: '11'
month: '03'
page: 4284 - 4289
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '3652'
quality_controlled: 0
status: public
title: Cytokinin regulates root meristem activity via modulation of the polar auxin
transport
type: journal_article
volume: 106
year: '2009'
...
---
_id: '3051'
article_type: original
author:
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Weijers D, Friml J. SnapShot: Auxin signaling and transport. Cell.
2009;136(6):1172-1172. doi:10.1016/j.cell.2009.03.009'
apa: 'Weijers, D., & Friml, J. (2009). SnapShot: Auxin signaling and transport.
Cell. Cell Press. https://doi.org/10.1016/j.cell.2009.03.009'
chicago: 'Weijers, Dolf, and Jiří Friml. “SnapShot: Auxin Signaling and Transport.”
Cell. Cell Press, 2009. https://doi.org/10.1016/j.cell.2009.03.009.'
ieee: 'D. Weijers and J. Friml, “SnapShot: Auxin signaling and transport,” Cell,
vol. 136, no. 6. Cell Press, pp. 1172–1172, 2009.'
ista: 'Weijers D, Friml J. 2009. SnapShot: Auxin signaling and transport. Cell.
136(6), 1172–1172.'
mla: 'Weijers, Dolf, and Jiří Friml. “SnapShot: Auxin Signaling and Transport.”
Cell, vol. 136, no. 6, Cell Press, 2009, pp. 1172–1172, doi:10.1016/j.cell.2009.03.009.'
short: D. Weijers, J. Friml, Cell 136 (2009) 1172–1172.
date_created: 2018-12-11T12:01:05Z
date_published: 2009-03-20T00:00:00Z
date_updated: 2021-01-12T07:40:42Z
day: '20'
doi: 10.1016/j.cell.2009.03.009
extern: '1'
external_id:
pmid:
- ' 19303857'
intvolume: ' 136'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/19303857
month: '03'
oa: 1
oa_version: Published Version
page: 1172 - 1172
pmid: 1
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3650'
quality_controlled: '1'
status: public
title: 'SnapShot: Auxin signaling and transport'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2009'
...
---
_id: '3052'
abstract:
- lang: eng
text: The dynamic, differential distribution of the hormone auxin within plant tissues
controls an impressive variety of developmental processes, which tailor plant
growth and morphology to environmental conditions. Various environmental and endogenous
signals can be integrated into changes in auxin distribution through their effects
on local auxin biosynthesis and intercellular auxin transport. Individual cells
interpret auxin largely by a nuclear signaling pathway that involves the F box
protein TIR1 acting as an auxin receptor. Auxin-dependent TIR1 activity leads
to ubiquitination-based degradation of transcriptional repressors and complex
transcriptional reprogramming. Thus, auxin appears to be a versatile trigger of
preprogrammed developmental changes in plant cells.
author:
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Vanneste S, Friml J. Auxin: A trigger for change in plant development. Cell.
2009;136(6):1005-1016. doi:10.1016/j.cell.2009.03.001'
apa: 'Vanneste, S., & Friml, J. (2009). Auxin: A trigger for change in plant
development. Cell. Cell Press. https://doi.org/10.1016/j.cell.2009.03.001'
chicago: 'Vanneste, Steffen, and Jiří Friml. “Auxin: A Trigger for Change in Plant
Development.” Cell. Cell Press, 2009. https://doi.org/10.1016/j.cell.2009.03.001.'
ieee: 'S. Vanneste and J. Friml, “Auxin: A trigger for change in plant development,”
Cell, vol. 136, no. 6. Cell Press, pp. 1005–1016, 2009.'
ista: 'Vanneste S, Friml J. 2009. Auxin: A trigger for change in plant development.
Cell. 136(6), 1005–1016.'
mla: 'Vanneste, Steffen, and Jiří Friml. “Auxin: A Trigger for Change in Plant Development.”
Cell, vol. 136, no. 6, Cell Press, 2009, pp. 1005–16, doi:10.1016/j.cell.2009.03.001.'
short: S. Vanneste, J. Friml, Cell 136 (2009) 1005–1016.
date_created: 2018-12-11T12:01:05Z
date_published: 2009-03-20T00:00:00Z
date_updated: 2021-01-12T07:40:43Z
day: '20'
doi: 10.1016/j.cell.2009.03.001
extern: '1'
external_id:
pmid:
- ' 19303845'
intvolume: ' 136'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/19303845
month: '03'
oa: 1
oa_version: Published Version
page: 1005 - 1016
pmid: 1
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '3651'
quality_controlled: '1'
status: public
title: 'Auxin: A trigger for change in plant development'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2009'
...
---
_id: '3053'
author:
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Maria
full_name: Ivanchenko, Maria
last_name: Ivanchenko
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Svetlana
full_name: Shishkova, Svetlana
last_name: Shishkova
- first_name: Joseph
full_name: Dubrovsky, Joseph
last_name: Dubrovsky
citation:
ama: 'Benková E, Ivanchenko M, Friml J, Shishkova S, Dubrovsky J. A morphogenetic
trigger: Is there an emerging concept in plant developmental biology? Trends
in Plant Science. 2009;14(4):189-193. doi:10.1016/j.tplants.2009.01.006'
apa: 'Benková, E., Ivanchenko, M., Friml, J., Shishkova, S., & Dubrovsky, J.
(2009). A morphogenetic trigger: Is there an emerging concept in plant developmental
biology? Trends in Plant Science. Cell Press. https://doi.org/10.1016/j.tplants.2009.01.006'
chicago: 'Benková, Eva, Maria Ivanchenko, Jiří Friml, Svetlana Shishkova, and Joseph
Dubrovsky. “A Morphogenetic Trigger: Is There an Emerging Concept in Plant Developmental
Biology?” Trends in Plant Science. Cell Press, 2009. https://doi.org/10.1016/j.tplants.2009.01.006.'
ieee: 'E. Benková, M. Ivanchenko, J. Friml, S. Shishkova, and J. Dubrovsky, “A morphogenetic
trigger: Is there an emerging concept in plant developmental biology?,” Trends
in Plant Science, vol. 14, no. 4. Cell Press, pp. 189–193, 2009.'
ista: 'Benková E, Ivanchenko M, Friml J, Shishkova S, Dubrovsky J. 2009. A morphogenetic
trigger: Is there an emerging concept in plant developmental biology? Trends in
Plant Science. 14(4), 189–193.'
mla: 'Benková, Eva, et al. “A Morphogenetic Trigger: Is There an Emerging Concept
in Plant Developmental Biology?” Trends in Plant Science, vol. 14, no.
4, Cell Press, 2009, pp. 189–93, doi:10.1016/j.tplants.2009.01.006.'
short: E. Benková, M. Ivanchenko, J. Friml, S. Shishkova, J. Dubrovsky, Trends in
Plant Science 14 (2009) 189–193.
date_created: 2018-12-11T12:01:05Z
date_published: 2009-04-01T00:00:00Z
date_updated: 2021-01-12T07:40:43Z
day: '01'
doi: 10.1016/j.tplants.2009.01.006
extern: '1'
intvolume: ' 14'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 189 - 193
publication: Trends in Plant Science
publication_status: published
publisher: Cell Press
publist_id: '3649'
status: public
title: 'A morphogenetic trigger: Is there an emerging concept in plant developmental
biology?'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2009'
...
---
_id: '3054'
abstract:
- lang: eng
text: As multicellular organisms, plants, like animals, use endogenous signaling
molecules to coordinate their own physiology and development. To compensate for
the absence of a cardiovascular system, plants have evolved specialized transport
pathways to distribute signals and nutrients. The main transport streams include
the xylem flow of the nutrients from the root to the shoot and the phloem flow
of materials from the photosynthetic active tissues. These long-distance transport
processes are complemented by several intercellular transport mechanisms (apoplastic,
symplastic and transcellular transport). A prominent example of transcellular
flow is transport of the phytohormone auxin within tissues. The process is mediated
by influx and efflux carriers, whose polar localization in the plasma membrane
determines the directionality of the flow. This polar auxin transport generates
auxin maxima and gradients within tissues that are instrumental in the diverse
regulation of various plant developmental processes, including embryogenesis,
organogenesis, vascular tissue formation and tropisms.
author:
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Robert H, Friml J. Auxin and other signals on the move in plants. Nature
Chemical Biology. 2009;5(5):325-332. doi:10.1038/nchembio.170
apa: Robert, H., & Friml, J. (2009). Auxin and other signals on the move in
plants. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.170
chicago: Robert, Hélène, and Jiří Friml. “Auxin and Other Signals on the Move in
Plants.” Nature Chemical Biology. Nature Publishing Group, 2009. https://doi.org/10.1038/nchembio.170.
ieee: H. Robert and J. Friml, “Auxin and other signals on the move in plants,” Nature
Chemical Biology, vol. 5, no. 5. Nature Publishing Group, pp. 325–332, 2009.
ista: Robert H, Friml J. 2009. Auxin and other signals on the move in plants. Nature
Chemical Biology. 5(5), 325–332.
mla: Robert, Hélène, and Jiří Friml. “Auxin and Other Signals on the Move in Plants.”
Nature Chemical Biology, vol. 5, no. 5, Nature Publishing Group, 2009,
pp. 325–32, doi:10.1038/nchembio.170.
short: H. Robert, J. Friml, Nature Chemical Biology 5 (2009) 325–332.
date_created: 2018-12-11T12:01:06Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:40:43Z
day: '01'
doi: 10.1038/nchembio.170
extern: '1'
external_id:
pmid:
- ' 19377459'
intvolume: ' 5'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 325 - 332
pmid: 1
publication: Nature Chemical Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '3648'
quality_controlled: '1'
status: public
title: Auxin and other signals on the move in plants
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2009'
...
---
_id: '3055'
abstract:
- lang: eng
text: 'ACAP-type ARF GTPase activating proteins (ARF-GAPs) regulate multiple cellular
processes, including endocytosis, secretion, phagocytosis, cell adhesion and cell
migration. However, the regulation of ACAP functions by other cellular proteins
is poorly understood. We have reported previously that a plant ACAP, VAN3, plays
a pivotal role in plant venation continuity. Here, we report on newly identified
VAN3 regulators: the CVP2 (cotyledon vascular pattern 2) 5 PTase, which is considered
to degrade IP3 and also to produce PtdIns(4)P from PtdIns(4,5)P2; and a PH domain-containing
protein, VAB (VAN3 binding protein). Combinational mutations of both CVP2 and
its closest homologue CVL1 (CVP2 like 1) phenocopied the strong allele of van3
mutants, showing severe vascular continuity. The phenotype of double mutants between
van3, cvp2 and vab suggested that VAN3, CVP2 and VAB function in vascular pattern
formation in the same pathway. Localization analysis revealed that both CVP2 and
VAB colocalize with VAN3 in the trans- Golgi network (TGN), supporting their functions
in the same pathway. The subcellular localization of VAN3 was dependent on its
PH domain, and mislocalization of VAN3 was induced in cvp2 or vab mutants. These
results suggest that CVP2 and VAB cooperatively regulate the subcellular localization
of VAN3 through the interaction between its PH domain and phosphoinositides and/or
inositol phosphates. In addition, PtdIns(4)P, to which VAN3 binds preferentially,
enhanced the ARF-GAP activity of VAN3, whereas IP3 inhibited it. These results
suggest the existence of PtdIns(4)P and/or IP3-dependent subcellular targeting
and regulation of VAN3 ACAP activity that governs plant vascular tissue continuity.'
author:
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Shinichiro
full_name: Sawa, Shinichiro
last_name: Sawa
- first_name: Koji
full_name: Koizumi, Koji
last_name: Koizumi
- first_name: Tomohiro
full_name: Uemura, Tomohiro
last_name: Uemura
- first_name: Takashi
full_name: Ueda, Takashi
last_name: Ueda
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Akihiko
full_name: Nakano, Akihiko
last_name: Nakano
- first_name: Hiroo
full_name: Fukuda, Hiroo
last_name: Fukuda
citation:
ama: Naramoto S, Sawa S, Koizumi K, et al. Phosphoinositide-dependent regulation
of VAN3 ARF-GAP localization and activity essential for vascular tissue continuity
in plants. Development. 2009;136(9):1529-1538. doi:10.1242/dev.030098
apa: Naramoto, S., Sawa, S., Koizumi, K., Uemura, T., Ueda, T., Friml, J., … Fukuda,
H. (2009). Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization
and activity essential for vascular tissue continuity in plants. Development.
Company of Biologists. https://doi.org/10.1242/dev.030098
chicago: Naramoto, Satoshi, Shinichiro Sawa, Koji Koizumi, Tomohiro Uemura, Takashi
Ueda, Jiří Friml, Akihiko Nakano, and Hiroo Fukuda. “Phosphoinositide-Dependent
Regulation of VAN3 ARF-GAP Localization and Activity Essential for Vascular Tissue
Continuity in Plants.” Development. Company of Biologists, 2009. https://doi.org/10.1242/dev.030098.
ieee: S. Naramoto et al., “Phosphoinositide-dependent regulation of VAN3
ARF-GAP localization and activity essential for vascular tissue continuity in
plants,” Development, vol. 136, no. 9. Company of Biologists, pp. 1529–1538,
2009.
ista: Naramoto S, Sawa S, Koizumi K, Uemura T, Ueda T, Friml J, Nakano A, Fukuda
H. 2009. Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and
activity essential for vascular tissue continuity in plants. Development. 136(9),
1529–1538.
mla: Naramoto, Satoshi, et al. “Phosphoinositide-Dependent Regulation of VAN3 ARF-GAP
Localization and Activity Essential for Vascular Tissue Continuity in Plants.”
Development, vol. 136, no. 9, Company of Biologists, 2009, pp. 1529–38,
doi:10.1242/dev.030098.
short: S. Naramoto, S. Sawa, K. Koizumi, T. Uemura, T. Ueda, J. Friml, A. Nakano,
H. Fukuda, Development 136 (2009) 1529–1538.
date_created: 2018-12-11T12:01:06Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:40:44Z
day: '01'
doi: 10.1242/dev.030098
extern: 1
intvolume: ' 136'
issue: '9'
month: '05'
page: 1529 - 1538
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3647'
quality_controlled: 0
status: public
title: Phosphoinositide-dependent regulation of VAN3 ARF-GAP localization and activity
essential for vascular tissue continuity in plants
type: journal_article
volume: 136
year: '2009'
...
---
_id: '3056'
abstract:
- lang: eng
text: Local hormone maxima are essential for the development of multicellular structures
and organs. For example, steroid hormones accumulate in specific cell types of
the animal fetus to induce sexual differentiation and concentration peaks of the
plant hormone auxin direct organ initiation and mediate tissue patterning. Here
we provide an example of a regulated local hormone minimum required during organogenesis.
Our results demonstrate that formation of a local auxin minimum is necessary for
specification of the valve margin separation layer where Arabidopsis fruit opening
takes place. Consequently, ectopic production of auxin, specifically in valve
margin cells, leads to a complete loss of proper cell fate determination. The
valve margin identity factor INDEHISCENT (IND) is responsible for forming the
auxin minimum by coordinating auxin efflux in separation-layer cells. We propose
that the simplicity of formation and maintenance make local hormone minima particularly
well suited to specify a small number of cells such as the stripes at the valve
margins.
author:
- first_name: Karim
full_name: Sorefan, Karim
last_name: Sorefan
- first_name: Thomas
full_name: Girin, Thomas
last_name: Girin
- first_name: Sarah
full_name: Liljegren, Sarah J
last_name: Liljegren
- first_name: Karin
full_name: Ljung, Karin
last_name: Ljung
- first_name: Pedro
full_name: Robles, Pedro
last_name: Robles
- first_name: Carlos
full_name: Galván-Ampudia, Carlos S
last_name: Galván Ampudia
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Martin
full_name: Yanofsky, Martin F
last_name: Yanofsky
- first_name: Lars
full_name: Østergaard, Lars
last_name: Østergaard
citation:
ama: Sorefan K, Girin T, Liljegren S, et al. A regulated auxin minimum is required
for seed dispersal in Arabidopsis. Nature. 2009;459(7246):583-586. doi:10.1038/nature07875
apa: Sorefan, K., Girin, T., Liljegren, S., Ljung, K., Robles, P., Galván Ampudia,
C., … Østergaard, L. (2009). A regulated auxin minimum is required for seed dispersal
in Arabidopsis. Nature. Nature Publishing Group. https://doi.org/10.1038/nature07875
chicago: Sorefan, Karim, Thomas Girin, Sarah Liljegren, Karin Ljung, Pedro Robles,
Carlos Galván Ampudia, Remko Offringa, Jiří Friml, Martin Yanofsky, and Lars Østergaard.
“A Regulated Auxin Minimum Is Required for Seed Dispersal in Arabidopsis.” Nature.
Nature Publishing Group, 2009. https://doi.org/10.1038/nature07875.
ieee: K. Sorefan et al., “A regulated auxin minimum is required for seed
dispersal in Arabidopsis,” Nature, vol. 459, no. 7246. Nature Publishing
Group, pp. 583–586, 2009.
ista: Sorefan K, Girin T, Liljegren S, Ljung K, Robles P, Galván Ampudia C, Offringa
R, Friml J, Yanofsky M, Østergaard L. 2009. A regulated auxin minimum is required
for seed dispersal in Arabidopsis. Nature. 459(7246), 583–586.
mla: Sorefan, Karim, et al. “A Regulated Auxin Minimum Is Required for Seed Dispersal
in Arabidopsis.” Nature, vol. 459, no. 7246, Nature Publishing Group, 2009,
pp. 583–86, doi:10.1038/nature07875.
short: K. Sorefan, T. Girin, S. Liljegren, K. Ljung, P. Robles, C. Galván Ampudia,
R. Offringa, J. Friml, M. Yanofsky, L. Østergaard, Nature 459 (2009) 583–586.
date_created: 2018-12-11T12:01:06Z
date_published: 2009-05-28T00:00:00Z
date_updated: 2021-01-12T07:40:44Z
day: '28'
doi: 10.1038/nature07875
extern: 1
intvolume: ' 459'
issue: '7246'
month: '05'
page: 583 - 586
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3646'
quality_controlled: 0
status: public
title: A regulated auxin minimum is required for seed dispersal in Arabidopsis
type: journal_article
volume: 459
year: '2009'
...
---
_id: '3057'
abstract:
- lang: eng
text: The differential distribution of the plant signaling molecule auxin is required
for many aspects of plant development. Local auxin maxima and gradients arise
as a result of local auxin metabolism and, predominantly, from directional cell-to-cell
transport. In this primer, we discuss how the coordinated activity of several
auxin influx and efflux systems, which transport auxin across the plasma membrane,
mediates directional auxin flow. This activity crucially contributes to the correct
setting of developmental cues in embryogenesis, organogenesis, vascular tissue
formation and directional growth in response to environmental stimuli.
author:
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Petrášek J, Friml J. Auxin transport routes in plant development. Development.
2009;136(16):2675-2688. doi:10.1242/dev.030353
apa: Petrášek, J., & Friml, J. (2009). Auxin transport routes in plant development.
Development. Company of Biologists. https://doi.org/10.1242/dev.030353
chicago: Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.”
Development. Company of Biologists, 2009. https://doi.org/10.1242/dev.030353.
ieee: J. Petrášek and J. Friml, “Auxin transport routes in plant development,” Development,
vol. 136, no. 16. Company of Biologists, pp. 2675–2688, 2009.
ista: Petrášek J, Friml J. 2009. Auxin transport routes in plant development. Development.
136(16), 2675–2688.
mla: Petrášek, Jan, and Jiří Friml. “Auxin Transport Routes in Plant Development.”
Development, vol. 136, no. 16, Company of Biologists, 2009, pp. 2675–88,
doi:10.1242/dev.030353.
short: J. Petrášek, J. Friml, Development 136 (2009) 2675–2688.
date_created: 2018-12-11T12:01:07Z
date_published: 2009-08-15T00:00:00Z
date_updated: 2021-01-12T07:40:45Z
day: '15'
doi: 10.1242/dev.030353
extern: '1'
external_id:
pmid:
- ' 19633168'
intvolume: ' 136'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/19633168
month: '08'
oa: 1
oa_version: Published Version
page: 2675 - 2688
pmid: 1
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3644'
quality_controlled: '1'
status: public
title: Auxin transport routes in plant development
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2009'
...
---
_id: '3058'
abstract:
- lang: eng
text: The plant signalling molecule auxin provides positional informa-tion in a
variety of developmental processes by means of its differential distribution (gradients)
within plant tissues. Thus, cellular auxin levels often determine the developmental
output of auxin signalling. Conceptually, transmembrane transport and metabolic
processes regulate the steady-state levels of auxin in any given cell2,3. In particular,
PIN auxin-efflux-carrier-mediated, directional transport between cells is crucial
for generating auxin gradients2,4,5. Here we show that Arabidopsis thaliana PIN5,
an atypical member of the PIN gene family, encodes a functional auxin transporter
that is required for auxin-mediated develop-ment. PIN5 does not have a direct
role in cell-to-cell transport but regulates intracellular auxin homeostasis and
metabolism. PIN5 localizes, unlike other characterized plasma membrane PIN proteins,
to endoplasmic reticulum (ER), presumably medi-ating auxin flow from the cytosol
to the lumen of the ER. The ER localization of other PIN5-like transporters (including
the moss PIN) indicates that the diversification of PIN protein functions in mediating
auxin homeostasis at the ER, and cell-to-cell auxin transport at the plasma membrane,
represent an ancient event during the evolution of land plants.
author:
- first_name: Jozef
full_name: Mravec, Jozef
last_name: Mravec
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Aurélien
full_name: Bailly, Aurélien
last_name: Bailly
- first_name: Klára
full_name: Hoyerová, Klára
last_name: Hoyerová
- first_name: Pavel
full_name: Křeček, Pavel
last_name: Křeček
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
- first_name: Vassilena
full_name: Gaykova, Vassilena
last_name: Gaykova
- first_name: York
full_name: Stierhof, York-Dieter
last_name: Stierhof
- first_name: Petre
full_name: Dobrev, Petre I
last_name: Dobrev
- first_name: Kateřina
full_name: Schwarzerová, Kateřina
last_name: Schwarzerová
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Daniela
full_name: Seifertová, Daniela
last_name: Seifertová
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Jirí
full_name: Jirí Friml
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Mravec J, Skůpa P, Bailly A, et al. Subcellular homeostasis of phytohormone
auxin is mediated by the ER localized PIN5 transporter. Nature. 2009;459(7250):1136-1140.
doi:10.1038/nature08066
apa: Mravec, J., Skůpa, P., Bailly, A., Hoyerová, K., Křeček, P., Bielach, A., …
Friml, J. (2009). Subcellular homeostasis of phytohormone auxin is mediated by
the ER localized PIN5 transporter. Nature. Nature Publishing Group. https://doi.org/10.1038/nature08066
chicago: Mravec, Jozef, Petr Skůpa, Aurélien Bailly, Klára Hoyerová, Pavel Křeček,
Agnieszka Bielach, Jan Petrášek, et al. “Subcellular Homeostasis of Phytohormone
Auxin Is Mediated by the ER Localized PIN5 Transporter.” Nature. Nature
Publishing Group, 2009. https://doi.org/10.1038/nature08066.
ieee: J. Mravec et al., “Subcellular homeostasis of phytohormone auxin is
mediated by the ER localized PIN5 transporter,” Nature, vol. 459, no. 7250.
Nature Publishing Group, pp. 1136–1140, 2009.
ista: Mravec J, Skůpa P, Bailly A, Hoyerová K, Křeček P, Bielach A, Petrášek J,
Zhang J, Gaykova V, Stierhof Y, Dobrev P, Schwarzerová K, Rolčík J, Seifertová
D, Luschnig C, Benková E, Zažímalová E, Geisler M, Friml J. 2009. Subcellular
homeostasis of phytohormone auxin is mediated by the ER localized PIN5 transporter.
Nature. 459(7250), 1136–1140.
mla: Mravec, Jozef, et al. “Subcellular Homeostasis of Phytohormone Auxin Is Mediated
by the ER Localized PIN5 Transporter.” Nature, vol. 459, no. 7250, Nature
Publishing Group, 2009, pp. 1136–40, doi:10.1038/nature08066.
short: J. Mravec, P. Skůpa, A. Bailly, K. Hoyerová, P. Křeček, A. Bielach, J. Petrášek,
J. Zhang, V. Gaykova, Y. Stierhof, P. Dobrev, K. Schwarzerová, J. Rolčík, D. Seifertová,
C. Luschnig, E. Benková, E. Zažímalová, M. Geisler, J. Friml, Nature 459 (2009)
1136–1140.
date_created: 2018-12-11T12:01:07Z
date_published: 2009-06-25T00:00:00Z
date_updated: 2021-01-12T07:40:45Z
day: '25'
doi: 10.1038/nature08066
extern: 1
intvolume: ' 459'
issue: '7250'
month: '06'
page: 1136 - 1140
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '3645'
quality_controlled: 0
status: public
title: Subcellular homeostasis of phytohormone auxin is mediated by the ER localized
PIN5 transporter
type: journal_article
volume: 459
year: '2009'
...
---
_id: '3059'
abstract:
- lang: eng
text: The phytohormone auxin plays a major role in embryonic and postembryonic plant
development. The temporal and spatial distribution of auxin largely depends on
the subcellular polar localization of members of the PIN-FORMED (PIN) auxin efflux
carrier family. The Ser/Thr protein kinase PINOID (PID) catalyzes PIN phosphorylation
and crucially contributes to the regulation of apical-basal PIN polarity. The
GTP exchange factor on ADP-ribosylation factors (ARF-GEF), GNOM preferentially
mediates PIN recycling at the basal side of the cell. Interference with GNOM activity
leads to dynamic PIN transcytosis between different sides of the cell. Our genetic,
pharmacological, and cell biological approaches illustrate that PID and GNOM influence
PIN polarity and plant development in an antagonistic manner and that the PID-dependent
PIN phosphorylation results in GNOM-independent polar PIN targeting. The data
suggest that PID and the protein phosphatase 2A not only regulate the static PIN
polarity, but also act antagonistically on the rate of GNOM-dependent polar PIN
transcytosis. We propose a model that includes PID-dependent PIN phosphorylation
at the plasma membrane and the subsequent sorting of PIN proteins to a GNOM-independent
pathway for polarity alterations during developmental processes, such as lateral
root formation and leaf vasculature development.
author:
- first_name: Jürgen
full_name: Kleine-Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Fang
full_name: Huang, Fang
last_name: Huang
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Jing
full_name: Zhang, Jing
last_name: Zhang
- first_name: Marta
full_name: Michniewicz, Marta
last_name: Michniewicz
- first_name: Remko
full_name: Offringa, Remko
last_name: Offringa
- 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, Huang F, Naramoto S, et al. PIN auxin efflux carrier polarity
is regulated by PINOID kinase mediated recruitment into GNOM independent trafficking
in arabidopsis. Plant Cell. 2009;21(12):3839-3849. doi:10.1105/tpc.109.071639
apa: Kleine Vehn, J., Huang, F., Naramoto, S., Zhang, J., Michniewicz, M., Offringa,
R., & Friml, J. (2009). PIN auxin efflux carrier polarity is regulated by
PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis.
Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.109.071639
chicago: Kleine Vehn, Jürgen, Fang Huang, Satoshi Naramoto, Jing Zhang, Marta Michniewicz,
Remko Offringa, and Jiří Friml. “PIN Auxin Efflux Carrier Polarity Is Regulated
by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.”
Plant Cell. American Society of Plant Biologists, 2009. https://doi.org/10.1105/tpc.109.071639.
ieee: J. Kleine Vehn et al., “PIN auxin efflux carrier polarity is regulated
by PINOID kinase mediated recruitment into GNOM independent trafficking in arabidopsis,”
Plant Cell, vol. 21, no. 12. American Society of Plant Biologists, pp.
3839–3849, 2009.
ista: Kleine Vehn J, Huang F, Naramoto S, Zhang J, Michniewicz M, Offringa R, Friml
J. 2009. PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated
recruitment into GNOM independent trafficking in arabidopsis. Plant Cell. 21(12),
3839–3849.
mla: Kleine Vehn, Jürgen, et al. “PIN Auxin Efflux Carrier Polarity Is Regulated
by PINOID Kinase Mediated Recruitment into GNOM Independent Trafficking in Arabidopsis.”
Plant Cell, vol. 21, no. 12, American Society of Plant Biologists, 2009,
pp. 3839–49, doi:10.1105/tpc.109.071639.
short: J. Kleine Vehn, F. Huang, S. Naramoto, J. Zhang, M. Michniewicz, R. Offringa,
J. Friml, Plant Cell 21 (2009) 3839–3849.
date_created: 2018-12-11T12:01:07Z
date_published: 2009-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:45Z
day: '01'
doi: 10.1105/tpc.109.071639
extern: 1
intvolume: ' 21'
issue: '12'
month: '12'
page: 3839 - 3849
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '3643'
quality_controlled: 0
status: public
title: PIN auxin efflux carrier polarity is regulated by PINOID kinase mediated recruitment
into GNOM independent trafficking in arabidopsis
type: journal_article
volume: 21
year: '2009'
...
---
_id: '3060'
article_type: letter_note
author:
- first_name: Karin
full_name: Schumacher, Karin
last_name: Schumacher
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Schumacher K, Friml J. Cell biology. Current Opinion in Plant Biology.
2009;12(6):651-652. doi:10.1016/j.pbi.2009.10.009
apa: Schumacher, K., & Friml, J. (2009). Cell biology. Current Opinion in
Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2009.10.009
chicago: Schumacher, Karin, and Jiří Friml. “Cell Biology.” Current Opinion in
Plant Biology. Elsevier, 2009. https://doi.org/10.1016/j.pbi.2009.10.009.
ieee: K. Schumacher and J. Friml, “Cell biology,” Current Opinion in Plant Biology,
vol. 12, no. 6. Elsevier, pp. 651–652, 2009.
ista: Schumacher K, Friml J. 2009. Cell biology. Current Opinion in Plant Biology.
12(6), 651–652.
mla: Schumacher, Karin, and Jiří Friml. “Cell Biology.” Current Opinion in Plant
Biology, vol. 12, no. 6, Elsevier, 2009, pp. 651–52, doi:10.1016/j.pbi.2009.10.009.
short: K. Schumacher, J. Friml, Current Opinion in Plant Biology 12 (2009) 651–652.
date_created: 2018-12-11T12:01:08Z
date_published: 2009-12-01T00:00:00Z
date_updated: 2021-01-12T07:40:46Z
day: '01'
doi: 10.1016/j.pbi.2009.10.009
extern: '1'
intvolume: ' 12'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 651 - 652
publication: Current Opinion in Plant Biology
publication_status: published
publisher: Elsevier
publist_id: '3641'
quality_controlled: '1'
status: public
title: Cell biology
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2009'
...
---
_id: '3061'
abstract:
- lang: eng
text: The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux
of the plant signal molecule auxin from cells. They are asymmetrically localized
within cells and their polarity determines the directionality of intercellular
auxin flow. PIN genes are found exclusively in the genomes of multicellular plants
and play an important role in regulating asymmetric auxin distribution in multiple
developmental processes, including embryogenesis, organogenesis, tissue differentiation
and tropic responses. All PIN proteins have a similar structure with amino- and
carboxy-terminal hydrophobic, membrane-spanning domains separated by a central
hydrophilic domain. The structure of the hydrophobic domains is well conserved.
The hydrophilic domain is more divergent and it determines eight groups within
the protein family. The activity of PIN proteins is regulated at multiple levels,
including transcription, protein stability, subcellular localization and transport
activity. Different endogenous and environmental signals can modulate PIN activity
and thus modulate auxin-distribution-dependent development. A large group of PIN
proteins, including the most ancient members known from mosses, localize to the
endoplasmic reticulum and they regulate the subcellular compartmentalization of
auxin and thus auxin metabolism. Further work is needed to establish the physiological
importance of this unexpected mode of auxin homeostasis regulation. Furthermore,
the evolution of PIN-based transport, PIN protein structure and more detailed
biochemical characterization of the transport function are important topics for
further studies.
author:
- first_name: Pavel
full_name: Křeček, Pavel
last_name: Křeček
- first_name: Petr
full_name: Skůpa, Petr
last_name: Skůpa
- first_name: Jiří
full_name: Libus, Jiří
last_name: Libus
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Ricardo
full_name: Tejos, Ricardo
last_name: Tejos
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: Křeček P, Skůpa P, Libus J, et al. The PIN-FORMED (PIN) protein family of auxin
transporters. Genome Biology. 2009;10(12). doi:10.1186/gb-2009-10-12-249
apa: Křeček, P., Skůpa, P., Libus, J., Naramoto, S., Tejos, R., Friml, J., &
Zažímalová, E. (2009). The PIN-FORMED (PIN) protein family of auxin transporters.
Genome Biology. BioMed Central. https://doi.org/10.1186/gb-2009-10-12-249
chicago: Křeček, Pavel, Petr Skůpa, Jiří Libus, Satoshi Naramoto, Ricardo Tejos,
Jiří Friml, and Eva Zažímalová. “The PIN-FORMED (PIN) Protein Family of Auxin
Transporters.” Genome Biology. BioMed Central, 2009. https://doi.org/10.1186/gb-2009-10-12-249.
ieee: P. Křeček et al., “The PIN-FORMED (PIN) protein family of auxin transporters,”
Genome Biology, vol. 10, no. 12. BioMed Central, 2009.
ista: Křeček P, Skůpa P, Libus J, Naramoto S, Tejos R, Friml J, Zažímalová E. 2009.
The PIN-FORMED (PIN) protein family of auxin transporters. Genome Biology. 10(12).
mla: Křeček, Pavel, et al. “The PIN-FORMED (PIN) Protein Family of Auxin Transporters.”
Genome Biology, vol. 10, no. 12, BioMed Central, 2009, doi:10.1186/gb-2009-10-12-249.
short: P. Křeček, P. Skůpa, J. Libus, S. Naramoto, R. Tejos, J. Friml, E. Zažímalová,
Genome Biology 10 (2009).
date_created: 2018-12-11T12:01:08Z
date_published: 2009-12-29T00:00:00Z
date_updated: 2021-01-12T07:40:46Z
day: '29'
doi: 10.1186/gb-2009-10-12-249
extern: '1'
external_id:
pmid:
- '20053306'
intvolume: ' 10'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812941/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '3640'
quality_controlled: '1'
status: public
title: The PIN-FORMED (PIN) protein family of auxin transporters
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2009'
...
---
_id: '3197'
abstract:
- lang: eng
text: |-
The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.
We show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches.
author:
- first_name: M Pawan
full_name: Kumar, M Pawan
last_name: Kumar
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Philip
full_name: Torr, Philip H
last_name: Torr
citation:
ama: Kumar MP, Kolmogorov V, Torr P. An analysis of convex relaxations for MAP estimation
of discrete MRFs. Journal of Machine Learning Research. 2009;10:71-106.
apa: Kumar, M. P., Kolmogorov, V., & Torr, P. (2009). An analysis of convex
relaxations for MAP estimation of discrete MRFs. Journal of Machine Learning
Research. Microtome Publishing.
chicago: Kumar, M Pawan, Vladimir Kolmogorov, and Philip Torr. “An Analysis of Convex
Relaxations for MAP Estimation of Discrete MRFs.” Journal of Machine Learning
Research. Microtome Publishing, 2009.
ieee: M. P. Kumar, V. Kolmogorov, and P. Torr, “An analysis of convex relaxations
for MAP estimation of discrete MRFs,” Journal of Machine Learning Research,
vol. 10. Microtome Publishing, pp. 71–106, 2009.
ista: Kumar MP, Kolmogorov V, Torr P. 2009. An analysis of convex relaxations for
MAP estimation of discrete MRFs. Journal of Machine Learning Research. 10, 71–106.
mla: Kumar, M. Pawan, et al. “An Analysis of Convex Relaxations for MAP Estimation
of Discrete MRFs.” Journal of Machine Learning Research, vol. 10, Microtome
Publishing, 2009, pp. 71–106.
short: M.P. Kumar, V. Kolmogorov, P. Torr, Journal of Machine Learning Research
10 (2009) 71–106.
date_created: 2018-12-11T12:01:57Z
date_published: 2009-01-01T00:00:00Z
date_updated: 2021-01-12T07:41:44Z
day: '01'
extern: 1
intvolume: ' 10'
main_file_link:
- open_access: '1'
url: https://hal.inria.fr/hal-00773608
month: '01'
oa: 1
page: 71 - 106
publication: Journal of Machine Learning Research
publication_status: published
publisher: Microtome Publishing
publist_id: '3484'
quality_controlled: 0
status: public
title: An analysis of convex relaxations for MAP estimation of discrete MRFs
type: journal_article
volume: 10
year: '2009'
...
---
_id: '3199'
abstract:
- lang: eng
text: Many interactive image segmentation approaches use an objective function which
includes appearance models as an unknown variable. Since the resulting optimization
problem is NP-hard the segmentation and appearance are typically optimized separately,
in an EM-style fashion. One contribution of this paper is to express the objective
function purely in terms of the unknown segmentation, using higher-order cliques.
This formulation reveals an interesting bias of the model towards balanced segmentations.
Furthermore, it enables us to develop a new dual decomposition optimization procedure,
which provides additionally a lower bound. Hence, we are able to improve on existing
optimizers, and verify that for a considerable number of real world examples we
even achieve global optimality. This is important since we are able, for the first
time, to analyze the deficiencies of the model. Another contribution is to establish
a property of a particular dual decomposition approach which involves convex functions
depending on foreground area. As a consequence, we show that the optimal decomposition
for our problem can be computed efficiently via a parametric maxflow algorithm.
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. Joint optimization of segmentation and
appearance models. In: IEEE; 2009:755-762. doi:10.1109/ICCV.2009.5459287'
apa: 'Vicente, S., Kolmogorov, V., & Rother, C. (2009). Joint optimization of
segmentation and appearance models (pp. 755–762). Presented at the ICCV: International
Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2009.5459287'
chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Joint Optimization
of Segmentation and Appearance Models,” 755–62. IEEE, 2009. https://doi.org/10.1109/ICCV.2009.5459287.
ieee: 'S. Vicente, V. Kolmogorov, and C. Rother, “Joint optimization of segmentation
and appearance models,” presented at the ICCV: International Conference on Computer
Vision, 2009, pp. 755–762.'
ista: 'Vicente S, Kolmogorov V, Rother C. 2009. Joint optimization of segmentation
and appearance models. ICCV: International Conference on Computer Vision, 755–762.'
mla: Vicente, Sara, et al. Joint Optimization of Segmentation and Appearance
Models. IEEE, 2009, pp. 755–62, doi:10.1109/ICCV.2009.5459287.
short: S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2009, pp. 755–762.
conference:
name: 'ICCV: International Conference on Computer Vision'
date_created: 2018-12-11T12:01:58Z
date_published: 2009-05-01T00:00:00Z
date_updated: 2021-01-12T07:41:44Z
day: '01'
doi: 10.1109/ICCV.2009.5459287
extern: 1
main_file_link:
- open_access: '0'
url: http://www.robots.ox.ac.uk/~vgg/rg/papers/segmentationappearance.pdf
month: '05'
page: 755 - 762
publication_status: published
publisher: IEEE
publist_id: '3482'
quality_controlled: 0
status: public
title: Joint optimization of segmentation and appearance models
type: conference
year: '2009'
...
---
_id: '3200'
abstract:
- lang: eng
text: Motivated by various applications to computer vision, we consider the convex
cost tension problem, which is the dual of the convex cost flow problem. In this
paper, we first propose a primal algorithm for computing an optimal solution of
the problem. Our primal algorithm iteratively updates primal variables by solving
associated minimum cut problems. We show that the time complexity of the primal
algorithm is O (K {dot operator} T (n, m)), where K is the range of primal variables
and T (n, m) is the time needed to compute a minimum cut in a graph with n nodes
and m edges. We then develop an improved version of the primal algorithm, called
the primal-dual algorithm, by making good use of dual variables in addition to
primal variables. Although its time complexity is the same as that of the primal
algorithm, we can expect a better performance in practice. We finally consider
an application to a computer vision problem called the panoramic image stitching.
author:
- first_name: Vladimir
full_name: Vladimir Kolmogorov
id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
last_name: Kolmogorov
- first_name: Akiyoshi
full_name: Shioura, Akiyoshi
last_name: Shioura
citation:
ama: Kolmogorov V, Shioura A. New algorithms for convex cost tension problem with
application to computer vision. Discrete Optimization. 2009;6(4):378-393.
doi:10.1016/j.disopt.2009.04.006
apa: Kolmogorov, V., & Shioura, A. (2009). New algorithms for convex cost tension
problem with application to computer vision. Discrete Optimization. Elsevier.
https://doi.org/10.1016/j.disopt.2009.04.006
chicago: Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex
Cost Tension Problem with Application to Computer Vision.” Discrete Optimization.
Elsevier, 2009. https://doi.org/10.1016/j.disopt.2009.04.006.
ieee: V. Kolmogorov and A. Shioura, “New algorithms for convex cost tension problem
with application to computer vision,” Discrete Optimization, vol. 6, no.
4. Elsevier, pp. 378–393, 2009.
ista: Kolmogorov V, Shioura A. 2009. New algorithms for convex cost tension problem
with application to computer vision. Discrete Optimization. 6(4), 378–393.
mla: Kolmogorov, Vladimir, and Akiyoshi Shioura. “New Algorithms for Convex Cost
Tension Problem with Application to Computer Vision.” Discrete Optimization,
vol. 6, no. 4, Elsevier, 2009, pp. 378–93, doi:10.1016/j.disopt.2009.04.006.
short: V. Kolmogorov, A. Shioura, Discrete Optimization 6 (2009) 378–393.
date_created: 2018-12-11T12:01:58Z
date_published: 2009-11-01T00:00:00Z
date_updated: 2021-01-12T07:41:45Z
day: '01'
doi: 10.1016/j.disopt.2009.04.006
extern: 1
intvolume: ' 6'
issue: '4'
month: '11'
page: 378 - 393
publication: Discrete Optimization
publication_status: published
publisher: Elsevier
publist_id: '3483'
quality_controlled: 0
status: public
title: New algorithms for convex cost tension problem with application to computer
vision
type: journal_article
volume: 6
year: '2009'
...