---
_id: '9499'
abstract:
- lang: eng
text: EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative
development. Loss of function mutants in the EMF1 gene mimic the phenotype caused
by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors
that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb
Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of
lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination.
Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with
known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the
EMF1 functions and its mechanism of action, we performed genome-wide mapping of
EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1
binding pattern is similar to that of H3K27me3 modification on the chromosomal
and genic level. ChIPOTLe peak finding and clustering analyses both show that
the highly trimethylated genes also have high enrichment levels of EMF1 binding,
termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced
to allow vegetative growth, and with genes specifying cell fates during growth
and differentiation. H3K27me3 marks not only these genes but also some genes that
are involved in endosperm development and maternal effects. Transcriptome analysis,
coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants
showed that EMF1 represses gene activities via diverse mechanisms and plays a
novel role in the PcG mechanism.
article_number: e1002512
article_processing_charge: No
article_type: original
author:
- first_name: Sang Yeol
full_name: Kim, Sang Yeol
last_name: Kim
- first_name: Jungeun
full_name: Lee, Jungeun
last_name: Lee
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Z. Renee
full_name: Sung, Z. Renee
last_name: Sung
citation:
ama: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate
to repress key regulators of Arabidopsis development. PLoS Genetics. 2012;8(3).
doi:10.1371/journal.pgen.1002512
apa: Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., & Sung, Z. R. (2012).
EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development.
PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002512
chicago: Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and
Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis
Development.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002512.
ieee: S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1
and PRC2 cooperate to repress key regulators of Arabidopsis development,” PLoS
Genetics, vol. 8, no. 3. Public Library of Science, 2012.
ista: Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2
cooperate to repress key regulators of Arabidopsis development. PLoS Genetics.
8(3), e1002512.
mla: Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of
Arabidopsis Development.” PLoS Genetics, vol. 8, no. 3, e1002512, Public
Library of Science, 2012, doi:10.1371/journal.pgen.1002512.
short: S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics
8 (2012).
date_created: 2021-06-07T11:07:56Z
date_published: 2012-03-22T00:00:00Z
date_updated: 2021-12-14T08:31:14Z
day: '22'
department:
- _id: DaZi
doi: 10.1371/journal.pgen.1002512
extern: '1'
external_id:
pmid:
- '22457632'
intvolume: ' 8'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pgen.1002512
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS Genetics
publication_identifier:
eissn:
- 1553-7404
issn:
- 1553-7390
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 8
year: '2012'
...
---
_id: '9528'
abstract:
- lang: eng
text: Accumulating evidence points toward diverse functions for plant chromatin.
Remarkable progress has been made over the last few years in elucidating the mechanisms
for a number of these functions. Activity of the histone demethylase IBM1 accurately
targets DNA methylation to silent repeats and transposable elements, not to genes.
A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes
in sensing precise differences in ambient temperature and consequent gene regulation.
Precise maintenance of chromosome number is assured by a histone modification
that suppresses inappropriate DNA replication and by centromeric histone H3 regulation
of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS
C, the expression of which quantitatively measures the duration of cold exposure,
functioning as memory of winter. These findings are a testament to the power of
using plants to research chromatin organization, and demonstrate examples of how
chromatin functions to achieve biological accuracy, precision, and memory.
article_processing_charge: No
article_type: review
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory
by plant chromatin organization. Current Opinion in Genetics and Development.
2012;22(2):132-138. doi:10.1016/j.gde.2012.01.007
apa: Huff, J. T., & Zilberman, D. (2012). Regulation of biological accuracy,
precision, and memory by plant chromatin organization. Current Opinion in Genetics
and Development. Elsevier. https://doi.org/10.1016/j.gde.2012.01.007
chicago: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy,
Precision, and Memory by Plant Chromatin Organization.” Current Opinion in
Genetics and Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.01.007.
ieee: J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision,
and memory by plant chromatin organization,” Current Opinion in Genetics and
Development, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.
ista: Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision,
and memory by plant chromatin organization. Current Opinion in Genetics and Development.
22(2), 132–138.
mla: Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision,
and Memory by Plant Chromatin Organization.” Current Opinion in Genetics and
Development, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:10.1016/j.gde.2012.01.007.
short: J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012)
132–138.
date_created: 2021-06-08T08:58:52Z
date_published: 2012-04-01T00:00:00Z
date_updated: 2021-12-14T08:32:38Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2012.01.007
extern: '1'
external_id:
pmid:
- '22336527'
intvolume: ' 22'
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
page: 132-138
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Regulation of biological accuracy, precision, and memory by plant chromatin
organization
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 22
year: '2012'
...
---
_id: '9535'
abstract:
- lang: eng
text: The most well-studied function of DNA methylation in eukaryotic cells is the
transcriptional silencing of genes and transposons. More recent results showed
that many eukaryotes methylate the bodies of genes as well and that this methylation
correlates with transcriptional activity rather than repression. The purpose of
gene body methylation remains mysterious, but is potentially related to the histone
variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions
of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and
other investigators have shown that this relationship is likely to be the result
of an ancient but unknown mechanism by which DNA methylation prevents the incorporation
of H2A.Z. Recently, we discovered strong correlations between the presence of
H2A.Z within gene bodies, the degree to which a gene's expression varies across
tissue types or environmental conditions, and transcriptional misregulation in
an h2a.z mutant. We propose that one basal function of gene body methylation is
the establishment of constitutive expression patterns within housekeeping genes
by excluding H2A.Z from their bodies.
article_processing_charge: No
article_type: review
author:
- first_name: D.
full_name: Coleman-Derr, D.
last_name: Coleman-Derr
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of
constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology.
2012;77:147-154. doi:10.1101/sqb.2012.77.014944
apa: Coleman-Derr, D., & Zilberman, D. (2012). DNA methylation, H2A.Z, and the
regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative
Biology. Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/sqb.2012.77.014944
chicago: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the
Regulation of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative
Biology. Cold Spring Harbor Laboratory Press, 2012. https://doi.org/10.1101/sqb.2012.77.014944.
ieee: D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation
of constitutive expression,” Cold Spring Harbor Symposia on Quantitative Biology,
vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.
ista: Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation
of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology.
77, 147–154.
mla: Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation
of Constitutive Expression.” Cold Spring Harbor Symposia on Quantitative Biology,
vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:10.1101/sqb.2012.77.014944.
short: D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative
Biology 77 (2012) 147–154.
date_created: 2021-06-08T13:01:23Z
date_published: 2012-12-18T00:00:00Z
date_updated: 2021-12-14T08:33:09Z
day: '18'
department:
- _id: DaZi
doi: 10.1101/sqb.2012.77.014944
extern: '1'
external_id:
pmid:
- '23250988'
intvolume: ' 77'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/sqb.2012.77.014944
month: '12'
oa: 1
oa_version: Published Version
page: 147-154
pmid: 1
publication: Cold Spring Harbor Symposia on Quantitative Biology
publication_identifier:
eissn:
- 1943-4456
issn:
- 0091-7451
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation, H2A.Z, and the regulation of constitutive expression
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 77
year: '2012'
...
---
_id: '9755'
abstract:
- lang: eng
text: Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated
disease defences at the individual and colony level. An intriguing yet little
understood phenomenon is that social contact to pathogen-exposed individuals reduces
susceptibility of previously naive nestmates to this pathogen. We tested whether
such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium
anisopliae is based on active upregulation of the immune system of nestmates following
contact to an infectious individual or passive protection via transfer of immune
effectors among group members—that is, active versus passive immunisation. We
found no evidence for involvement of passive immunisation via transfer of antimicrobials
among colony members. Instead, intensive allogrooming behaviour between naive
and pathogen-exposed ants before fungal conidia firmly attached to their cuticle
suggested passage of the pathogen from the exposed individuals to their nestmates.
By tracing fluorescence-labelled conidia we indeed detected frequent pathogen
transfer to the nestmates, where they caused low-level infections as revealed
by growth of small numbers of fungal colony forming units from their dissected
body content. These infections rarely led to death, but instead promoted an enhanced
ability to inhibit fungal growth and an active upregulation of immune genes involved
in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there
was no upregulation of the gene cathepsin L, which is associated with antibacterial
and antiviral defences, and we found no increased antibacterial activity of nestmates
of fungus-exposed ants. This indicates that social immunisation after fungal exposure
is specific, similar to recent findings for individual-level immune priming in
invertebrates. Epidemiological modeling further suggests that active social immunisation
is adaptive, as it leads to faster elimination of the disease and lower death
rates than passive immunisation. Interestingly, humans have also utilised the
protective effect of low-level infections to fight smallpox by intentional transfer
of low pathogen doses (“variolation” or “inoculation”).
article_processing_charge: No
author:
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Meghan
full_name: Vyleta, Meghan
id: 418901AA-F248-11E8-B48F-1D18A9856A87
last_name: Vyleta
- first_name: Fabian
full_name: Theis, Fabian
last_name: Theis
- first_name: Miriam
full_name: Stock, Miriam
id: 42462816-F248-11E8-B48F-1D18A9856A87
last_name: Stock
- first_name: Martina
full_name: Klatt, Martina
id: E60F29C6-E9AE-11E9-AF6E-D190C7302F38
last_name: Klatt
- first_name: Verena
full_name: Drescher, Verena
last_name: Drescher
- first_name: Carsten
full_name: Marr, Carsten
last_name: Marr
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic
fungus promotes active immunisation in ant colonies. 2012. doi:10.5061/dryad.sv37s'
apa: 'Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer,
S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation
in ant colonies. Dryad. https://doi.org/10.5061/dryad.sv37s'
chicago: 'Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt,
Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from:
Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.”
Dryad, 2012. https://doi.org/10.5061/dryad.sv37s.'
ieee: 'M. Konrad et al., “Data from: Social transfer of pathogenic fungus
promotes active immunisation in ant colonies.” Dryad, 2012.'
ista: 'Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig
LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active
immunisation in ant colonies, Dryad, 10.5061/dryad.sv37s.'
mla: 'Konrad, Matthias, et al. Data from: Social Transfer of Pathogenic Fungus
Promotes Active Immunisation in Ant Colonies. Dryad, 2012, doi:10.5061/dryad.sv37s.'
short: M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr,
L.V. Ugelvig, S. Cremer, (2012).
date_created: 2021-07-30T08:39:13Z
date_published: 2012-09-27T00:00:00Z
date_updated: 2023-02-23T11:18:41Z
day: '27'
department:
- _id: SyCr
doi: 10.5061/dryad.sv37s
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.sv37s
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '3242'
relation: used_in_publication
status: public
status: public
title: 'Data from: Social transfer of pathogenic fungus promotes active immunisation
in ant colonies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '9757'
abstract:
- lang: eng
text: To fight infectious diseases, host immune defences are employed at multiple
levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a
first line of defence to prevent infection [1] before activation of the physiological
immune system. Insect societies have evolved a wide range of collective hygiene
measures and intensive health care towards pathogen-exposed group members [2].
One of the most common behaviours is allogrooming, in which nestmates remove infectious
particles from the body surfaces of exposed individuals [3]. Here we show that,
in invasive garden ants, grooming of fungus-exposed brood is effective beyond
the sheer mechanical removal of fungal conidiospores as it also includes chemical
disinfection through the application of poison produced by the ants themselves.
Formic acid is the main active component of the poison. It inhibits fungal growth
of conidiospores remaining on the brood surface after grooming and also those
collected in the mouth of the grooming ant. This dual function is achieved by
uptake of the poison droplet into the mouth through acidopore self-grooming and
subsequent application onto the infectious brood via brood grooming. This extraordinary
behaviour extends current understanding of grooming and the establishment of social
immunity in insect societies.
article_processing_charge: No
author:
- first_name: Simon
full_name: Tragust, Simon
id: 35A7A418-F248-11E8-B48F-1D18A9856A87
last_name: Tragust
- first_name: Barbara
full_name: Mitteregger, Barbara
id: 479DDAAC-E9CD-11E9-9B5F-82450873F7A1
last_name: Mitteregger
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Matthias
full_name: Konrad, Matthias
id: 46528076-F248-11E8-B48F-1D18A9856A87
last_name: Konrad
- first_name: Line V
full_name: Ugelvig, Line V
id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87
last_name: Ugelvig
orcid: 0000-0003-1832-8883
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
citation:
ama: 'Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from:
Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.
2012. doi:10.5061/dryad.61649'
apa: 'Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &
Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake
and spread of their poison. Dryad. https://doi.org/10.5061/dryad.61649'
chicago: 'Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad,
Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood
by Oral Uptake and Spread of Their Poison.” Dryad, 2012. https://doi.org/10.5061/dryad.61649.'
ieee: 'S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer,
“Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their
poison.” Dryad, 2012.'
ista: 'Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012.
Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their
poison, Dryad, 10.5061/dryad.61649.'
mla: 'Tragust, Simon, et al. Data from: Ants Disinfect Fungus-Exposed Brood by
Oral Uptake and Spread of Their Poison. Dryad, 2012, doi:10.5061/dryad.61649.'
short: S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer,
(2012).
date_created: 2021-07-30T12:31:31Z
date_published: 2012-12-14T00:00:00Z
date_updated: 2023-02-23T11:04:28Z
day: '14'
department:
- _id: SyCr
doi: 10.5061/dryad.61649
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.61649
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2926'
relation: used_in_publication
status: public
status: public
title: 'Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of
their poison'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '9758'
abstract:
- lang: eng
text: 'We propose a two-step procedure for estimating multiple migration rates in
an approximate Bayesian computation (ABC) framework, accounting for global nuisance
parameters. The approach is not limited to migration, but generally of interest
for inference problems with multiple parameters and a modular structure (e.g.
independent sets of demes or loci). We condition on a known, but complex demographic
model of a spatially subdivided population, motivated by the reintroduction of
Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters
ancestral mutation rate and male mating skew have been estimated for the whole
population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step,
we estimate in this study the migration rates independently for clusters of demes
putatively connected by migration. For large clusters (many migration rates),
ABC faces the problem of too many summary statistics. We therefore assess by simulation
if estimation per pair of demes is a valid alternative. We find that the trade-off
between reduced dimensionality for the pairwise estimation on the one hand and
lower accuracy due to the assumption of pairwise independence on the other depends
on the number of migration rates to be inferred: the accuracy of the pairwise
approach increases with the number of parameters, relative to the joint estimation
approach. To distinguish between low and zero migration, we perform ABC-type model
comparison between a model with migration and one without. Applying the approach
to microsatellite data from Alpine ibex, we find no evidence for substantial gene
flow via migration, except for one pair of demes in one direction.'
article_processing_charge: No
author:
- first_name: Simon
full_name: Aeschbacher, Simon
id: 2D35326E-F248-11E8-B48F-1D18A9856A87
last_name: Aeschbacher
- first_name: Andreas
full_name: Futschik, Andreas
last_name: Futschik
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
citation:
ama: 'Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation
for modular inference problems with many parameters: the example of migration
rates. 2012. doi:10.5061/dryad.274b1'
apa: 'Aeschbacher, S., Futschik, A., & Beaumont, M. (2012). Data from: Approximate
Bayesian computation for modular inference problems with many parameters: the
example of migration rates. Dryad. https://doi.org/10.5061/dryad.274b1'
chicago: 'Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate
Bayesian Computation for Modular Inference Problems with Many Parameters: The
Example of Migration Rates.” Dryad, 2012. https://doi.org/10.5061/dryad.274b1.'
ieee: 'S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates.” Dryad, 2012.'
ista: 'Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian
computation for modular inference problems with many parameters: the example of
migration rates, Dryad, 10.5061/dryad.274b1.'
mla: 'Aeschbacher, Simon, et al. Data from: Approximate Bayesian Computation
for Modular Inference Problems with Many Parameters: The Example of Migration
Rates. Dryad, 2012, doi:10.5061/dryad.274b1.'
short: S. Aeschbacher, A. Futschik, M. Beaumont, (2012).
date_created: 2021-07-30T12:36:39Z
date_published: 2012-11-14T00:00:00Z
date_updated: 2023-02-23T11:05:19Z
day: '14'
department:
- _id: NiBa
doi: 10.5061/dryad.274b1
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.274b1
month: '11'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2944'
relation: used_in_publication
status: public
status: public
title: 'Data from: Approximate Bayesian computation for modular inference problems
with many parameters: the example of migration rates'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2012'
...
---
_id: '10907'
abstract:
- lang: eng
text: This paper presents a method to create a model of an articulated object using
the planar motion in an initialization video. The model consists of rigid parts
connected by points of articulation. The rigid parts are described by the positions
of salient feature-points tracked throughout the video. Following a filtering
step that identifies points that belong to different objects, rigid parts are
found by a grouping process in a graph pyramid. Valid articulation points are
selected by verifying multiple hypotheses for each pair of parts.
acknowledgement: This work has been partially supported by the Austrian Science Fund
under grants S9103-N13 and P18716-N13.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Nicole M.
full_name: Artner, Nicole M.
last_name: Artner
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
- first_name: Walter G.
full_name: Kropatsch, Walter G.
last_name: Kropatsch
citation:
ama: 'Artner NM, Ion A, Kropatsch WG. Spatio-temporal extraction of articulated
models in a graph pyramid. In: Jiang X, Ferrer M, Torsello A, eds. Graph-Based
Representations in Pattern Recognition. Vol 6658. LNIP. Berlin, Heidelberg:
Springer; 2011:215-224. doi:10.1007/978-3-642-20844-7_22'
apa: 'Artner, N. M., Ion, A., & Kropatsch, W. G. (2011). Spatio-temporal extraction
of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, & A. Torsello
(Eds.), Graph-Based Representations in Pattern Recognition (Vol. 6658,
pp. 215–224). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-20844-7_22'
chicago: 'Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal
Extraction of Articulated Models in a Graph Pyramid.” In Graph-Based Representations
in Pattern Recognition, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea
Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. https://doi.org/10.1007/978-3-642-20844-7_22.'
ieee: N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of
articulated models in a graph pyramid,” in Graph-Based Representations in Pattern
Recognition, Münster, Germany, 2011, vol. 6658, pp. 215–224.
ista: 'Artner NM, Ion A, Kropatsch WG. 2011. Spatio-temporal extraction of articulated
models in a graph pyramid. Graph-Based Representations in Pattern Recognition.
GbRPR: Graph-based Representations in Pattern RecognitionLNIP, LNCS, vol. 6658,
215–224.'
mla: Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models
in a Graph Pyramid.” Graph-Based Representations in Pattern Recognition,
edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:10.1007/978-3-642-20844-7_22.
short: N.M. Artner, A. Ion, W.G. Kropatsch, in:, X. Jiang, M. Ferrer, A. Torsello
(Eds.), Graph-Based Representations in Pattern Recognition, Springer, Berlin,
Heidelberg, 2011, pp. 215–224.
conference:
end_date: 2011-05-20
location: Münster, Germany
name: 'GbRPR: Graph-based Representations in Pattern Recognition'
start_date: 2011-05-18
date_created: 2022-03-21T08:08:35Z
date_published: 2011-06-01T00:00:00Z
date_updated: 2023-09-05T14:10:15Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-20844-7_22
editor:
- first_name: Xiaoyi
full_name: Jiang, Xiaoyi
last_name: Jiang
- first_name: Miquel
full_name: Ferrer, Miquel
last_name: Ferrer
- first_name: Andrea
full_name: Torsello, Andrea
last_name: Torsello
intvolume: ' 6658'
language:
- iso: eng
month: '06'
oa_version: None
page: 215-224
place: Berlin, Heidelberg
publication: Graph-Based Representations in Pattern Recognition
publication_identifier:
eisbn:
- '9783642208447'
eissn:
- 1611-3349
isbn:
- '9783642208430'
issn:
- 0302-9743
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
series_title: LNIP
status: public
title: Spatio-temporal extraction of articulated models in a graph pyramid
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6658
year: '2011'
...
---
_id: '3163'
abstract:
- lang: eng
text: We study multi-label prediction for structured output sets, a problem that
occurs, for example, in object detection in images, secondary structure prediction
in computational biology, and graph matching with symmetries. Conventional multilabel
classification techniques are typically not applicable in this situation, because
they require explicit enumeration of the label set, which is infeasible in case
of structured outputs. Relying on techniques originally designed for single-label
structured prediction, in particular structured support vector machines, results
in reduced prediction accuracy, or leads to infeasible optimization problems.
In this work we derive a maximum-margin training formulation for multi-label structured
prediction that remains computationally tractable while achieving high prediction
accuracy. It also shares most beneficial properties with single-label maximum-margin
approaches, in particular formulation as a convex optimization problem, efficient
working set training, and PAC-Bayesian generalization bounds.
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Maximum margin multi-label structured prediction. In: Neural Information
Processing Systems; 2011.'
apa: 'Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented
at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information
Processing Systems.'
chicago: Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.”
Neural Information Processing Systems, 2011.
ieee: 'C. Lampert, “Maximum margin multi-label structured prediction,” presented
at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.'
ista: 'Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS:
Neural Information Processing Systems.'
mla: Lampert, Christoph. Maximum Margin Multi-Label Structured Prediction.
Neural Information Processing Systems, 2011.
short: C. Lampert, in:, Neural Information Processing Systems, 2011.
conference:
end_date: 2011-12-14
location: Granada, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2011-12-12
date_created: 2018-12-11T12:01:45Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2023-10-17T11:47:35Z
day: '01'
department:
- _id: ChLa
language:
- iso: eng
month: '12'
oa_version: None
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '3522'
quality_controlled: '1'
related_material:
record:
- id: '3322'
relation: later_version
status: public
scopus_import: 1
status: public
title: Maximum margin multi-label structured prediction
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3264'
abstract:
- lang: eng
text: Verification of programs with procedures, multi-threaded programs, and higher-order
functional programs can be effectively au- tomated using abstraction and refinement
schemes that rely on spurious counterexamples for abstraction discovery. The analysis
of counterexam- ples can be automated by a series of interpolation queries, or,
alterna- tively, as a constraint solving query expressed by a set of recursion
free Horn clauses. (A set of interpolation queries can be formulated as a single
constraint over Horn clauses with linear dependency structure between the unknown
relations.) In this paper we present an algorithm for solving recursion free Horn
clauses over a combined theory of linear real/rational arithmetic and uninterpreted
functions. Our algorithm performs resolu- tion to deal with the clausal structure
and relies on partial solutions to deal with (non-local) instances of functionality
axioms.
alternative_title:
- LNCS
author:
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Corneliu
full_name: Popeea, Corneliu
last_name: Popeea
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over
LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:10.1007/978-3-642-25318-8_16'
apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2011). Solving recursion-free
Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented
at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan:
Springer. https://doi.org/10.1007/978-3-642-25318-8_16'
chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free
Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011.
https://doi.org/10.1007/978-3-642-25318-8_16.
ieee: 'A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses
over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages
and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.'
ista: 'Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses
over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS,
vol. 7078, 188–203.'
mla: Gupta, Ashutosh, et al. Solving Recursion-Free Horn Clauses over LI+UIF.
Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:10.1007/978-3-642-25318-8_16.
short: A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011,
pp. 188–203.
conference:
end_date: 2011-12-07
location: Kenting, Taiwan
name: 'APLAS: Asian Symposium on Programming Languages and Systems'
start_date: 2011-12-05
date_created: 2018-12-11T12:02:20Z
date_published: 2011-12-05T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '05'
department:
- _id: ToHe
doi: 10.1007/978-3-642-25318-8_16
ec_funded: 1
editor:
- first_name: Hongseok
full_name: Yang, Hongseok
last_name: Yang
intvolume: ' 7078'
language:
- iso: eng
month: '12'
oa_version: None
page: 188 - 203
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
publication_status: published
publisher: Springer
publist_id: '3383'
quality_controlled: '1'
status: public
title: Solving recursion-free Horn clauses over LI+UIF
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 7078
year: '2011'
...
---
_id: '3266'
abstract:
- lang: eng
text: We present a joint image segmentation and labeling model (JSL) which, given
a bag of figure-ground segment hypotheses extracted at multiple image locations
and scales, constructs a joint probability distribution over both the compatible
image interpretations (tilings or image segmentations) composed from those segments,
and over their labeling into categories. The process of drawing samples from the
joint distribution can be interpreted as first sampling tilings, modeled as maximal
cliques, from a graph connecting spatially non-overlapping segments in the bag
[1], followed by sampling labels for those segments, conditioned on the choice
of a particular tiling. We learn the segmentation and labeling parameters jointly,
based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure.
The partition function over tilings and labelings is increasingly more accurately
approximated by including incorrect configurations that a not-yet-competent model
rates probable during learning. We show that the proposed methodologymatches the
current state of the art in the Stanford dataset [2], as well as in VOC2010, where
41.7% accuracy on the test set is achieved.
author:
- first_name: Adrian
full_name: Ion, Adrian
id: 29F89302-F248-11E8-B48F-1D18A9856A87
last_name: Ion
- first_name: Joao
full_name: Carreira, Joao
last_name: Carreira
- first_name: Cristian
full_name: Sminchisescu, Cristian
last_name: Sminchisescu
citation:
ama: 'Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation
and labeling. In: NIPS Proceedings. Vol 24. Neural Information Processing
Systems Foundation; 2011:1827-1835.'
apa: 'Ion, A., Carreira, J., & Sminchisescu, C. (2011). Probabilistic joint
image segmentation and labeling. In NIPS Proceedings (Vol. 24, pp. 1827–1835).
Granada, Spain: Neural Information Processing Systems Foundation.'
chicago: Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint
Image Segmentation and Labeling.” In NIPS Proceedings, 24:1827–35. Neural
Information Processing Systems Foundation, 2011.
ieee: A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation
and labeling,” in NIPS Proceedings, Granada, Spain, 2011, vol. 24, pp.
1827–1835.
ista: 'Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation
and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol.
24, 1827–1835.'
mla: Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.”
NIPS Proceedings, vol. 24, Neural Information Processing Systems Foundation,
2011, pp. 1827–35.
short: A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information
Processing Systems Foundation, 2011, pp. 1827–1835.
conference:
end_date: 2011-12-14
location: Granada, Spain
name: 'NIPS: Neural Information Processing Systems'
start_date: 2011-12-12
date_created: 2018-12-11T12:02:21Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:15Z
day: '01'
department:
- _id: HeEd
intvolume: ' 24'
language:
- iso: eng
month: '12'
oa_version: None
page: 1827 - 1835
publication: NIPS Proceedings
publication_status: published
publisher: Neural Information Processing Systems Foundation
publist_id: '3381'
quality_controlled: '1'
scopus_import: 1
status: public
title: Probabilistic joint image segmentation and labeling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2011'
...
---
_id: '3267'
abstract:
- lang: eng
text: 'We address the problem of localizing homology classes, namely, finding the
cycle representing a given class with the most concise geometric measure. We study
the problem with different measures: volume, diameter and radius. For volume,
that is, the 1-norm of a cycle, two main results are presented. First, we prove
that the problem is NP-hard to approximate within any constant factor. Second,
we prove that for homology of dimension two or higher, the problem is NP-hard
to approximate even when the Betti number is O(1). The latter result leads to
the inapproximability of the problem of computing the nonbounding cycle with the
smallest volume and computing cycles representing a homology basis with the minimal
total volume. As for the other two measures defined by pairwise geodesic distance,
diameter and radius, we show that the localization problem is NP-hard for diameter
but is polynomial for radius. Our work is restricted to homology over the ℤ2 field.'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Daniel
full_name: Freedman, Daniel
last_name: Freedman
citation:
ama: Chen C, Freedman D. Hardness results for homology localization. Discrete
& Computational Geometry. 2011;45(3):425-448. doi:10.1007/s00454-010-9322-8
apa: Chen, C., & Freedman, D. (2011). Hardness results for homology localization.
Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-010-9322-8
chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Discrete & Computational Geometry. Springer, 2011. https://doi.org/10.1007/s00454-010-9322-8.
ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” Discrete
& Computational Geometry, vol. 45, no. 3. Springer, pp. 425–448, 2011.
ista: Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete
& Computational Geometry. 45(3), 425–448.
mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Discrete & Computational Geometry, vol. 45, no. 3, Springer, 2011,
pp. 425–48, doi:10.1007/s00454-010-9322-8.
short: C. Chen, D. Freedman, Discrete & Computational Geometry 45 (2011) 425–448.
date_created: 2018-12-11T12:02:21Z
date_published: 2011-01-14T00:00:00Z
date_updated: 2023-02-21T16:07:10Z
day: '14'
department:
- _id: HeEd
doi: 10.1007/s00454-010-9322-8
intvolume: ' 45'
issue: '3'
language:
- iso: eng
month: '01'
oa_version: None
page: 425 - 448
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '3379'
quality_controlled: '1'
related_material:
record:
- id: '10909'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Hardness results for homology localization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 45
year: '2011'
...
---
_id: '3269'
abstract:
- lang: eng
text: The unintentional scattering of light between neighboring surfaces in complex
projection environments increases the brightness and decreases the contrast, disrupting
the appearance of the desired imagery. To achieve satisfactory projection results,
the inverse problem of global illumination must be solved to cancel this secondary
scattering. In this paper, we propose a global illumination cancellation method
that minimizes the perceptual difference between the desired imagery and the actual
total illumination in the resulting physical environment. Using Gauss-Newton and
active set methods, we design a fast solver for the bound constrained nonlinear
least squares problem raised by the perceptual error metrics. Our solver is further
accelerated with a CUDA implementation and multi-resolution method to achieve
1–2 fps for problems with approximately 3000 variables. We demonstrate the global
illumination cancellation algorithm with our multi-projector system. Results show
that our method preserves the color fidelity of the desired imagery significantly
better than previous methods.
article_processing_charge: No
article_type: original
author:
- first_name: Yu
full_name: Sheng, Yu
last_name: Sheng
- first_name: Barbara
full_name: Cutler, Barbara
last_name: Cutler
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Joshua
full_name: Nasman, Joshua
last_name: Nasman
citation:
ama: Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation
in complex projection environments. Computer Graphics Forum. 2011;30(4):1261-1268.
doi:10.1111/j.1467-8659.2011.01985.x
apa: Sheng, Y., Cutler, B., Chen, C., & Nasman, J. (2011). Perceptual global
illumination cancellation in complex projection environments. Computer Graphics
Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2011.01985.x
chicago: Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global
Illumination Cancellation in Complex Projection Environments.” Computer Graphics
Forum. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1467-8659.2011.01985.x.
ieee: Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination
cancellation in complex projection environments,” Computer Graphics Forum,
vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011.
ista: Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination
cancellation in complex projection environments. Computer Graphics Forum. 30(4),
1261–1268.
mla: Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection
Environments.” Computer Graphics Forum, vol. 30, no. 4, Wiley-Blackwell,
2011, pp. 1261–68, doi:10.1111/j.1467-8659.2011.01985.x.
short: Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011)
1261–1268.
date_created: 2018-12-11T12:02:22Z
date_published: 2011-07-19T00:00:00Z
date_updated: 2021-01-12T07:42:16Z
day: '19'
department:
- _id: HeEd
doi: 10.1111/j.1467-8659.2011.01985.x
intvolume: ' 30'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf
month: '07'
oa: 1
oa_version: Published Version
page: 1261 - 1268
publication: Computer Graphics Forum
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3377'
quality_controlled: '1'
scopus_import: 1
status: public
title: Perceptual global illumination cancellation in complex projection environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2011'
...
---
_id: '3270'
abstract:
- lang: eng
text: 'The persistence diagram of a filtered simplicial com- plex is usually computed
by reducing the boundary matrix of the complex. We introduce a simple op- timization
technique: by processing the simplices of the complex in decreasing dimension,
we can “kill” columns (i.e., set them to zero) without reducing them. This technique
completely avoids reduction on roughly half of the columns. We demonstrate that
this idea significantly improves the running time of the reduction algorithm in
practice. We also give an output-sensitive complexity analysis for the new al-
gorithm which yields to sub-cubic asymptotic bounds under certain assumptions.'
author:
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
citation:
ama: 'Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund;
2011:197-200.'
apa: 'Chen, C., & Kerber, M. (2011). Persistent homology computation with a
twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational
Geometry, Morschach, Switzerland: TU Dortmund.'
chicago: Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a
Twist,” 197–200. TU Dortmund, 2011.
ieee: 'C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented
at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland,
2011, pp. 197–200.'
ista: 'Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG:
European Workshop on Computational Geometry, 197–200.'
mla: Chen, Chao, and Michael Kerber. Persistent Homology Computation with a Twist.
TU Dortmund, 2011, pp. 197–200.
short: C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200.
conference:
end_date: 2011-03-30
location: Morschach, Switzerland
name: 'EuroCG: European Workshop on Computational Geometry'
start_date: 2011-03-28
date_created: 2018-12-11T12:02:22Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:17Z
day: '01'
department:
- _id: HeEd
language:
- iso: eng
month: '01'
oa_version: None
page: 197 - 200
publication_status: published
publisher: TU Dortmund
publist_id: '3376'
quality_controlled: '1'
status: public
title: Persistent homology computation with a twist
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3271'
abstract:
- lang: eng
text: In this paper we present an efficient framework for computation of persis-
tent homology of cubical data in arbitrary dimensions. An existing algorithm using
simplicial complexes is adapted to the setting of cubical complexes. The proposed
approach enables efficient application of persistent homology in domains where
the data is naturally given in a cubical form. By avoiding triangulation of the
data, we significantly reduce the size of the complex. We also present a data-structure
de- signed to compactly store and quickly manipulate cubical complexes. By means
of numerical experiments, we show high speed and memory efficiency of our ap-
proach. We compare our framework to other available implementations, showing its
superiority. Finally, we report performance on selected 3D and 4D data-sets.
alternative_title:
- Theory, Algorithms, and Applications
author:
- first_name: Hubert
full_name: Wagner, Hubert
last_name: Wagner
- first_name: Chao
full_name: Chen, Chao
id: 3E92416E-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Erald
full_name: Vuçini, Erald
last_name: Vuçini
citation:
ama: 'Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for
cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. Topological Methods
in Data Analysis and Visualization II. Springer; 2011:91-106. doi:10.1007/978-3-642-23175-9_7'
apa: Wagner, H., Chen, C., & Vuçini, E. (2011). Efficient computation of persistent
homology for cubical data. In R. Peikert, H. Hauser, H. Carr, & R. Fuchs (Eds.),
Topological Methods in Data Analysis and Visualization II (pp. 91–106).
Springer. https://doi.org/10.1007/978-3-642-23175-9_7
chicago: Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of
Persistent Homology for Cubical Data.” In Topological Methods in Data Analysis
and Visualization II, edited by Ronald Peikert, Helwig Hauser, Hamish Carr,
and Raphael Fuchs, 91–106. Springer, 2011. https://doi.org/10.1007/978-3-642-23175-9_7.
ieee: H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology
for cubical data,” in Topological Methods in Data Analysis and Visualization
II, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp.
91–106.
ista: 'Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology
for cubical data. In: Topological Methods in Data Analysis and Visualization II.
Theory, Algorithms, and Applications, , 91–106.'
mla: Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical
Data.” Topological Methods in Data Analysis and Visualization II, edited
by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:10.1007/978-3-642-23175-9_7.
short: H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs
(Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011,
pp. 91–106.
date_created: 2018-12-11T12:02:23Z
date_published: 2011-11-14T00:00:00Z
date_updated: 2021-01-12T07:42:18Z
day: '14'
department:
- _id: HeEd
doi: 10.1007/978-3-642-23175-9_7
editor:
- first_name: Ronald
full_name: Peikert, Ronald
last_name: Peikert
- first_name: Helwig
full_name: Hauser, Helwig
last_name: Hauser
- first_name: Hamish
full_name: Carr, Hamish
last_name: Carr
- first_name: Raphael
full_name: Fuchs, Raphael
last_name: Fuchs
language:
- iso: eng
month: '11'
oa_version: None
page: 91 - 106
publication: Topological Methods in Data Analysis and Visualization II
publication_status: published
publisher: Springer
publist_id: '3375'
quality_controlled: '1'
scopus_import: 1
status: public
title: Efficient computation of persistent homology for cubical data
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2011'
...
---
_id: '3273'
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
citation:
ama: Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors.
2011.
apa: Maître, J.-L. (2011). Mechanics of adhesion and de‐adhesion in zebrafish
germ layer progenitors. Institute of Science and Technology Austria.
chicago: Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish
Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.
ieee: J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer
progenitors,” Institute of Science and Technology Austria, 2011.
ista: Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ
layer progenitors. Institute of Science and Technology Austria.
mla: Maître, Jean-Léon. Mechanics of Adhesion and De‐adhesion in Zebrafish Germ
Layer Progenitors. Institute of Science and Technology Austria, 2011.
short: J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer
Progenitors, Institute of Science and Technology Austria, 2011.
date_created: 2018-12-11T12:02:23Z
date_published: 2011-12-12T00:00:00Z
date_updated: 2023-09-07T11:30:16Z
day: '12'
degree_awarded: PhD
department:
- _id: CaHe
language:
- iso: eng
month: '12'
oa_version: None
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '3373'
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2011'
...
---
_id: '3275'
abstract:
- lang: eng
text: 'Chemokines organize immune cell trafficking by inducing either directed (tactic)
or random (kinetic) migration and by activating integrins in order to support
surface adhesion (haptic). Beyond that the same chemokines can establish clearly
defined functional areas in secondary lymphoid organs. Until now it is unclear
how chemokines can fulfill such diverse functions. One decisive prerequisite to
explain these capacities is to know how chemokines are presented in tissue. In
theory chemokines could occur either soluble or immobilized, and could be distributed
either homogenously or as a concentration gradient. To dissect if and how the
presenting mode of chemokines influences immune cells, I tested the response of
dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen
presenting cells that reside in the periphery and migrate into draining lymph
nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs
are guided to and within the LN by the chemokine receptor CCR7, which has two
ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic
reticular cells in the LN, but differ in their ability to bind to heparan sulfate
residues. CCL21 has a highly charged C-terminal extension, which mediates binding
to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes
as a soluble molecule. This study shows that surface-bound CCL21 causes random,
haptokinetic DC motility, which is confined to the chemokine coated area by insideout
activation of β2 integrins that mediate cell binding to the surface. CCL19 on
the other hand forms concentration gradients which trigger directional, chemotactic
movement, but no surface adhesion. In addition DCs can actively manipulate this
system by recruiting and activating serine proteases on their surfaces, which
create - by proteolytically removing the adhesive C-terminus - a solubilized variant
of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration
gradient DCs establish a positive feedback loop to recruit further DCs from the
periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients
as well as immobilized haptokinetic fields at the same time and integrate these
signals. The result is chemotactically biased haptokinesis - directional migration
confined to a chemokine coated track or area - which could explain the dynamic
but spatially tightly controlled swarming leukocyte locomotion patterns that have
been observed in lymphatic organs by intravital microscopists. The finding that
DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces
coated with immobilized cues raises the question how these cells transmit intracellular
forces to the environment, especially in the non-adherent migration mode. In order
to migrate, cells have to generate and transmit force to the extracellular substrate.
Force transmission is the prerequisite to procure an expansion of the leading
edge and a forward motion of the whole cell body. In the current conceptions actin
polymerization at the leading edge is coupled to extracellular ligands via the
integrin family of transmembrane receptors, which allows the transmission of intracellular
force. Against the paradigm of force transmission during migration, leukocytes,
like DCs, are able to migrate in threedimensional environments without using integrin
transmembrane receptors (Lämmermann et al., 2008). This reflects the biological
function of leukocytes, as they can invade almost all tissues, whereby their migration
has to be independent from the extracellular environment. How the cells can achieve
this is unclear. For this study I examined DC migration in a defined threedimensional
environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result
was that chemotactic DCs can switch between integrin-dependent and integrin- independent
locomotion and can thereby adapt to the adhesive properties of their environment.
If the cells are able to couple their actin cytoskeleton to the substrate, actin
polymerization is entirely converted into protrusion. Without coupling the actin
cortex undergoes slippage and retrograde actin flow can be observed. But retrograde
actin flow can be completely compensated by higher actin polymerization rate keeping
the migration velocity and the shape of the cells unaltered. Mesenchymal cells
like fibroblast cannot balance the loss of adhesive interaction, cannot protrude
into open space and, therefore, strictly depend on integrinmediated force coupling.
This leukocyte specific phenomenon of “adaptive force transmission” endows these
cells with the unique ability to transit and invade almost every type of tissue. '
acknowledgement: "I would like to express my sincere gratitude to the following people
who made with their continuous support and encouragement this thesis possible: First,
I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring,
especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and
the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant
support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf.
Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my
thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz,
the Recombinant Protein Production core facility and the animal care takers for
providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler,
Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy
labmates for their help, a lot of discussions and to make the Sixt lab to a convenient
place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele
Weber and Alexander Eichner All members of the Department of Molecular Medicine
for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael
Ruppert for their friendship, nice chats and their uncensored point of view. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Kathrin
full_name: Schumann, Kathrin
id: F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F
last_name: Schumann
citation:
ama: Schumann K. The role of chemotactic gradients in dendritic cell migration.
2011.
apa: Schumann, K. (2011). The role of chemotactic gradients in dendritic cell
migration. Institute of Science and Technology Austria.
chicago: Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell
Migration.” Institute of Science and Technology Austria, 2011.
ieee: K. Schumann, “The role of chemotactic gradients in dendritic cell migration,”
Institute of Science and Technology Austria, 2011.
ista: Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration.
Institute of Science and Technology Austria.
mla: Schumann, Kathrin. The Role of Chemotactic Gradients in Dendritic Cell Migration.
Institute of Science and Technology Austria, 2011.
short: K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration,
Institute of Science and Technology Austria, 2011.
date_created: 2018-12-11T12:02:24Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2023-09-07T11:31:48Z
day: '01'
ddc:
- '570'
- '579'
degree_awarded: PhD
department:
- _id: MiSi
file:
- access_level: closed
checksum: e69eee6252660f0b694a2ea8923ddc72
content_type: application/pdf
creator: dernst
date_created: 2019-03-26T08:12:21Z
date_updated: 2020-07-14T12:46:06Z
file_id: '6177'
file_name: 2011_Thesis_Kathrin_Schumann.pdf
file_size: 4487708
relation: main_file
- access_level: open_access
checksum: 71727d63f424b5b446f68f4b87ecadc0
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T11:24:30Z
date_updated: 2021-02-22T11:24:30Z
file_id: '9175'
file_name: 2011_Thesis_Schumann_noS.pdf
file_size: 4313127
relation: main_file
success: 1
file_date_updated: 2021-02-22T11:24:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '141'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '3371'
pubrep_id: '11'
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: The role of chemotactic gradients in dendritic cell migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2011'
...
---
_id: '3287'
abstract:
- lang: eng
text: 'Diffusing membrane constituents are constantly exposed to a variety of forces
that influence their stochastic path. Single molecule experiments allow for resolving
trajectories at extremely high spatial and temporal accuracy, thereby offering
insights into en route interactions of the tracer. In this review we discuss approaches
to derive information about the underlying processes, based on single molecule
tracking experiments. In particular, we focus on a new versatile way to analyze
single molecule diffusion in the absence of a full analytical treatment. The method
is based on comprehensive comparison of an experimental data set against the hypothetical
outcome of multiple experiments performed on the computer. Since Monte Carlo simulations
can be easily and rapidly performed even on state-of-the-art PCs, our method provides
a simple way for testing various - even complicated - diffusion models. We describe
the new method in detail, and show the applicability on two specific examples:
firstly, kinetic rate constants can be derived for the transient interaction of
mobile membrane proteins; secondly, residence time and corral size can be extracted
for confined diffusion.'
author:
- first_name: Verena
full_name: Ruprecht, Verena
id: 4D71A03A-F248-11E8-B48F-1D18A9856A87
last_name: Ruprecht
orcid: 0000-0003-4088-8633
- first_name: Markus
full_name: Axmann, Markus
last_name: Axmann
- first_name: Stefan
full_name: Wieser, Stefan
id: 355AA5A0-F248-11E8-B48F-1D18A9856A87
last_name: Wieser
orcid: 0000-0002-2670-2217
- first_name: Gerhard
full_name: Schuetz, Gerhard
last_name: Schuetz
citation:
ama: Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule
trajectories? Current Protein & Peptide Science. 2011;12(8):714-724.
doi:10.2174/138920311798841753
apa: Ruprecht, V., Axmann, M., Wieser, S., & Schuetz, G. (2011). What can we
learn from single molecule trajectories? Current Protein & Peptide Science.
Bentham Science Publishers. https://doi.org/10.2174/138920311798841753
chicago: Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What
Can We Learn from Single Molecule Trajectories?” Current Protein & Peptide
Science. Bentham Science Publishers, 2011. https://doi.org/10.2174/138920311798841753.
ieee: V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from
single molecule trajectories?,” Current Protein & Peptide Science,
vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.
ista: Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single
molecule trajectories? Current Protein & Peptide Science. 12(8), 714–724.
mla: Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?”
Current Protein & Peptide Science, vol. 12, no. 8, Bentham Science
Publishers, 2011, pp. 714–24, doi:10.2174/138920311798841753.
short: V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein & Peptide
Science 12 (2011) 714–724.
date_created: 2018-12-11T12:02:28Z
date_published: 2011-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:24Z
day: '01'
department:
- _id: CaHe
- _id: MiSi
doi: 10.2174/138920311798841753
intvolume: ' 12'
issue: '8'
language:
- iso: eng
month: '12'
oa_version: None
page: 714 - 724
publication: Current Protein & Peptide Science
publication_status: published
publisher: Bentham Science Publishers
publist_id: '3358'
quality_controlled: '1'
scopus_import: 1
status: public
title: What can we learn from single molecule trajectories?
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2011'
...
---
_id: '3288'
abstract:
- lang: eng
text: 'The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion
where cellular forces are exerted and resisted. Increasing evidence indicates
that E-cadherin adhesion molecules at the ZA serve to sense force applied on the
junctions and coordinate cytoskeletal responses to those forces. Efforts to understand
the role that cadherins play in mechanotransduction have been limited by the lack
of assays to measure the impact of forces on the ZA. In this study we used 4D
imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions
in confluent epithelial monolayers displayed prominent movements oriented orthogonal
(perpendicular) to the ZA itself. Two components were identified in these movements:
a relatively slow unidirectional (translational) component that could be readily
fitted by least-squares regression analysis, upon which were superimposed more
rapid oscillatory movements. Myosin IIB was a dominant factor responsible for
driving the unilateral translational movements. In contrast, frequency spectrum
analysis revealed that depletion of Myosin IIA increased the power of the oscillatory
movements. This implies that Myosin IIA may serve to dampen oscillatory movements
of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate
that Myosin IIA and Myosin IIB make distinct contributions to junctional movement
at the ZA.'
acknowledgement: his work was funded by the National Health and Medical Research Council
(NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the
Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research
Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship.
A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the
Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the
Institute for Molecular Bioscience, established with the generous support of the
ACRF.
author:
- first_name: Michael
full_name: Smutny, Michael
id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87
last_name: Smutny
orcid: 0000-0002-5920-9090
- first_name: Selwin
full_name: Wu, Selwin
last_name: Wu
- first_name: Guillermo
full_name: Gomez, Guillermo
last_name: Gomez
- first_name: Sabine
full_name: Mangold, Sabine
last_name: Mangold
- first_name: Alpha
full_name: Yap, Alpha
last_name: Yap
- first_name: Nicholas
full_name: Hamilton, Nicholas
last_name: Hamilton
citation:
ama: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis
of junctional movements regulated by Myosin II isoforms at the epithelial zonula
adherens. PLoS One. 2011;6(7). doi:10.1371/journal.pone.0022458
apa: Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., & Hamilton, N. (2011).
Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0022458
chicago: Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap,
and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One. Public
Library of Science, 2011. https://doi.org/10.1371/journal.pone.0022458.
ieee: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens,” PLoS One, vol. 6, no. 7. Public Library of Science, 2011.
ista: Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent
analysis of junctional movements regulated by Myosin II isoforms at the epithelial
zonula adherens. PLoS One. 6(7).
mla: Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated
by Myosin II Isoforms at the Epithelial Zonula Adherens.” PLoS One, vol.
6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0022458.
short: M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).
date_created: 2018-12-11T12:02:28Z
date_published: 2011-07-22T00:00:00Z
date_updated: 2021-01-12T07:42:25Z
day: '22'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pone.0022458
file:
- access_level: open_access
checksum: 57a5eb11dd05241c48c44f492b3ec3ac
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T10:51:43Z
date_updated: 2020-07-14T12:46:06Z
file_id: '6399'
file_name: 2011_PLOS_Smutny.PDF
file_size: 1984567
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3357'
quality_controlled: '1'
status: public
title: Multicomponent analysis of junctional movements regulated by Myosin II isoforms
at the epithelial zonula adherens
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2011'
...
---
_id: '3290'
abstract:
- lang: eng
text: 'Analysis of genomic data requires an efficient way to calculate likelihoods
across very large numbers of loci. We describe a general method for finding the
distribution of genealogies: we allow migration between demes, splitting of demes
[as in the isolation-with-migration (IM) model], and recombination between linked
loci. These processes are described by a set of linear recursions for the generating
function of branch lengths. Under the infinite-sites model, the probability of
any configuration of mutations can be found by differentiating this generating
function. Such calculations are feasible for small numbers of sampled genomes:
as an example, we show how the generating function can be derived explicitly for
three genes under the two-deme IM model. This derivation is done automatically,
using Mathematica. Given data from a large number of unlinked and nonrecombining
blocks of sequence, these results can be used to find maximum-likelihood estimates
of model parameters by tabulating the probabilities of all relevant mutational
configurations and then multiplying across loci. The feasibility of the method
is demonstrated by applying it to simulated data and to a data set previously
analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila
simulans and D. melanogaster. Our results suggest that such likelihood calculations
are scalable to genomic data as long as the numbers of sampled individuals and
mutations per sequence block are small.'
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Richard
full_name: Harrison, Richard
last_name: Harrison
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods
under the coalescent process. Genetics. 2011;189(3):977-987. doi:10.1534/genetics.111.129569
apa: Lohse, K., Harrison, R., & Barton, N. H. (2011). A general method for calculating
likelihoods under the coalescent process. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.111.129569
chicago: Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method
for Calculating Likelihoods under the Coalescent Process.” Genetics. Genetics
Society of America, 2011. https://doi.org/10.1534/genetics.111.129569.
ieee: K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating
likelihoods under the coalescent process,” Genetics, vol. 189, no. 3. Genetics
Society of America, pp. 977–987, 2011.
ista: Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods
under the coalescent process. Genetics. 189(3), 977–987.
mla: Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the
Coalescent Process.” Genetics, vol. 189, no. 3, Genetics Society of America,
2011, pp. 977–87, doi:10.1534/genetics.111.129569.
short: K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.
date_created: 2018-12-11T12:02:29Z
date_published: 2011-11-01T00:00:00Z
date_updated: 2021-01-12T07:42:26Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.111.129569
ec_funded: 1
intvolume: ' 189'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/
month: '11'
oa: 1
oa_version: Submitted Version
page: 977 - 987
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: '3355'
quality_controlled: '1'
scopus_import: 1
status: public
title: A general method for calculating likelihoods under the coalescent process
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 189
year: '2011'
...
---
_id: '3297'
abstract:
- lang: eng
text: "Animating detailed liquid surfaces has always been a challenge for computer
graphics researchers and visual effects artists. Over the past few years, researchers
in this field have focused on mesh-based surface tracking to synthesize extremely
detailed liquid surfaces as efficiently as possible. This course provides a solid
understanding of the steps required to create a fluid simulator with a mesh-based
liquid surface.\r\n\r\nThe course begins with an overview of several existing
liquid-surface-tracking techniques and the pros and cons of each method. Then
it explains how to embed a triangle mesh into a finite-difference-based fluid
simulator and describes several methods for allowing the liquid surface to merge
together or break apart. The final section showcases the benefits and further
applications of a mesh-based liquid surface, highlighting state-of-the-art methods
for tracking colors and textures, maintaining liquid volume, preserving small
surface features, and simulating realistic surface-tension waves."
article_number: '8'
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Matthias
full_name: Müller Fischer, Matthias
last_name: Müller Fischer
- first_name: Tyson
full_name: Brochu, Tyson
last_name: Brochu
citation:
ama: 'Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface
tracking. In: ACM; 2011. doi:10.1145/2037636.2037644'
apa: 'Wojtan, C., Müller Fischer, M., & Brochu, T. (2011). Liquid simulation
with mesh-based surface tracking. Presented at the SIGGRAPH: Special Interest
Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada:
ACM. https://doi.org/10.1145/2037636.2037644'
chicago: Wojtan, Chris, Matthias Müller Fischer, and Tyson Brochu. “Liquid Simulation
with Mesh-Based Surface Tracking.” ACM, 2011. https://doi.org/10.1145/2037636.2037644.
ieee: 'C. Wojtan, M. Müller Fischer, and T. Brochu, “Liquid simulation with mesh-based
surface tracking,” presented at the SIGGRAPH: Special Interest Group on Computer
Graphics and Interactive Techniques, Vancouver, BC, Canada, 2011.'
ista: 'Wojtan C, Müller Fischer M, Brochu T. 2011. Liquid simulation with mesh-based
surface tracking. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive
Techniques, 8.'
mla: Wojtan, Chris, et al. Liquid Simulation with Mesh-Based Surface Tracking.
8, ACM, 2011, doi:10.1145/2037636.2037644.
short: C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011.
conference:
end_date: 2011-08-11
location: Vancouver, BC, Canada
name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques'
start_date: 2011-08-07
date_created: 2018-12-11T12:02:31Z
date_published: 2011-08-07T00:00:00Z
date_updated: 2023-02-23T11:21:02Z
day: '07'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1145/2037636.2037644
file:
- access_level: open_access
checksum: 8d508ad7c82f50978acbaa4170ee0a75
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:34Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5018'
file_name: IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf
file_size: 34672096
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
publication_status: published
publisher: ACM
publist_id: '3344'
pubrep_id: '599'
quality_controlled: '1'
scopus_import: 1
status: public
title: Liquid simulation with mesh-based surface tracking
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2011'
...