---
_id: '3772'
article_number: e1000987
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Understanding adaptation in large populations. PLoS Genetics.
2010;6(6). doi:10.1371/journal.pgen.1000987
apa: Barton, N. H. (2010). Understanding adaptation in large populations. PLoS
Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987
chicago: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987.
ieee: N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics,
vol. 6, no. 6. Public Library of Science, 2010.
ista: Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics.
6(6), e1000987.
mla: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS
Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987.
short: N.H. Barton, PLoS Genetics 6 (2010).
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2021-01-12T07:52:05Z
day: '17'
ddc:
- '570'
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pgen.1000987
file:
- access_level: open_access
checksum: 5c14de2680ab483cb835096c99ee734d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:24Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5075'
file_name: IST-2016-524-v1+1_journal.pgen.1000987.PDF
file_size: 349965
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '2454'
pubrep_id: '524'
quality_controlled: '1'
scopus_import: 1
status: public
title: Understanding adaptation in large populations
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2010'
...
---
_id: '3773'
abstract:
- lang: eng
text: If distinct biological species are to coexist in sympatry, they must be reproductively
isolated and must exploit different limiting resources. A two-niche Levene model
is analysed, in which habitat preference and survival depend on underlying additive
traits. The population genetics of preference and viability are equivalent. However,
there is a linear trade-off between the chances of settling in either niche, whereas
viabilities may be constrained arbitrarily. With a convex trade-off, a sexual
population evolves a single generalist genotype, whereas with a concave trade-off,
disruptive selection favours maximal variance. A pure habitat preference evolves
to global linkage equilibrium if mating occurs in a single pool, but remarkably,
evolves to pairwise linkage equilibrium within niches if mating is within those
niches--independent of the genetics. With a concave trade-off, the population
shifts sharply between a unimodal distribution with high gene flow and a bimodal
distribution with strong isolation, as the underlying genetic variance increases.
However, these alternative states are only simultaneously stable for a narrow
parameter range. A sharp threshold is only seen if survival in the 'wrong' niche
is low; otherwise, strong isolation is impossible. Gene flow from divergent demes
makes speciation much easier in parapatry than in sympatry.
acknowledgement: "The author thanks the Werner-Gren Foundation and the Royal Swedish
Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He
also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n"
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London Series B, Biological Sciences.
2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001
apa: Barton, N. H. (2010). What role does natural selection play in speciation?
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001
chicago: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001.
ieee: N. H. Barton, “What role does natural selection play in speciation?,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.
ista: Barton NH. 2010. What role does natural selection play in speciation? Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547),
1825–1840.
mla: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?”
Philosophical Transactions of the Royal Society of London. Series B, Biological
Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1825–1840.
date_created: 2018-12-11T12:05:05Z
date_published: 2010-06-12T00:00:00Z
date_updated: 2021-01-12T07:52:06Z
day: '12'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0001
external_id:
pmid:
- '20439284'
intvolume: ' 365'
issue: '1547'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20439284
month: '06'
oa: 1
oa_version: Submitted Version
page: 1825 - 1840
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2455'
quality_controlled: '1'
scopus_import: 1
status: public
title: What role does natural selection play in speciation?
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3776'
abstract:
- lang: eng
text: 'The prevalence of recombination in eukaryotes poses one of the most puzzling
questions in biology. The most compelling general explanation is that recombination
facilitates selection by breaking down the negative associations generated by
random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of
HRI owing to: deleterious mutation, balancing selection and selective sweeps on:
neutral diversity, rates of adaptation and the mutation load. These effects are
mediated primarily by the density of deleterious mutations and of selective sweeps.
Sequence polymorphism and divergence suggest that these rates may be high enough
to cause significant interference even in genomic regions of high recombination.
However, neither seems able to generate enough variance in fitness to select strongly
for high rates of recombination. It is plausible that spatial and temporal fluctuations
in selection generate much more fitness variance, and hence selection for recombination,
than can be explained by uniformly deleterious mutations or species-wide selective
sweeps.'
acknowledgement: "Royal Society and Wolfson Foundation for their support\r\nWe would
like to thank Brian Charlesworth and Sally Otto for their helpful comments."
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1552):2559-2569.
doi:10.1098/rstb.2010.0106
apa: Barton, N. H. (2010). Genetic linkage and natural selection. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2010.0106
chicago: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0106.
ieee: N. H. Barton, “Genetic linkage and natural selection,” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences, vol. 365, no.
1552. Royal Society, pp. 2559–2569, 2010.
ista: Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.
mla: Barton, Nicholas H. “Genetic Linkage and Natural Selection.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:10.1098/rstb.2010.0106.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 2559–2569.
date_created: 2018-12-11T12:05:06Z
date_published: 2010-08-27T00:00:00Z
date_updated: 2021-01-12T07:52:07Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1098/rstb.2010.0106
file:
- access_level: open_access
checksum: 4d8aade10db030124ab158b622e337e0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:40Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5093'
file_name: IST-2016-555-v1+1_RS2009_revised.pdf
file_size: 250255
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 365'
issue: '1552'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 2559 - 2569
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2450'
pubrep_id: '555'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genetic linkage and natural selection
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3777'
abstract:
- lang: eng
text: 'Under the classical view, selection depends more or less directly on mutation:
standing genetic variance is maintained by a balance between selection and mutation,
and adaptation is fuelled by new favourable mutations. Recombination is favoured
if it breaks negative associations among selected alleles, which interfere with
adaptation. Such associations may be generated by negative epistasis, or by random
drift (leading to the Hill-Robertson effect). Both deterministic and stochastic
explanations depend primarily on the genomic mutation rate, U. This may be large
enough to explain high recombination rates in some organisms, but seems unlikely
to be so in general. Random drift is a more general source of negative linkage
disequilibria, and can cause selection for recombination even in large populations,
through the chance loss of new favourable mutations. The rate of species-wide
substitutions is much too low to drive this mechanism, but local fluctuations
in selection, combined with gene flow, may suffice. These arguments are illustrated
by comparing the interaction between good and bad mutations at unlinked loci under
the infinitesimal model.'
acknowledgement: I would like to thank W. G. Hill and L. Loewe for organizing this
special issue, and the Royal Society and Wolfson Foundation for their support. Also,
A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Mutation and the evolution of recombination. Philosophical Transactions
of the Royal Society of London Series B, Biological Sciences. 2010;365(1544):1281-1294.
doi:10.1098/rstb.2009.0320
apa: Barton, N. H. (2010). Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society. https://doi.org/10.1098/rstb.2009.0320
chicago: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences.
Royal Society, 2010. https://doi.org/10.1098/rstb.2009.0320.
ieee: N. H. Barton, “Mutation and the evolution of recombination,” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.
ista: Barton NH. 2010. Mutation and the evolution of recombination. Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544),
1281–1294.
mla: Barton, Nicholas H. “Mutation and the Evolution of Recombination.” Philosophical
Transactions of the Royal Society of London. Series B, Biological Sciences,
vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:10.1098/rstb.2009.0320.
short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series
B, Biological Sciences 365 (2010) 1281–1294.
date_created: 2018-12-11T12:05:07Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2021-01-12T07:52:07Z
day: '27'
department:
- _id: NiBa
doi: 10.1098/rstb.2009.0320
external_id:
pmid:
- '20308104'
intvolume: ' 365'
issue: '1544'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pubmed/20308104
month: '04'
oa: 1
oa_version: Submitted Version
page: 1281 - 1294
pmid: 1
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society
publist_id: '2451'
quality_controlled: '1'
scopus_import: 1
status: public
title: Mutation and the evolution of recombination
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2010'
...
---
_id: '3779'
abstract:
- lang: eng
text: Crosses between closely related species give two contrasting results. One
result is that species hybrids may be inferior to their parents, for example,
being less fertile [1]. The other is that F1 hybrids may display superior performance
(heterosis), for example with increased vigour [2]. Although various hypotheses
have been proposed to account for these two aspects of hybridisation, their biological
basis is still poorly understood [3]. To gain further insights into this issue,
we analysed the role that variation in gene expression may play. We took a conserved
trait, flower asymmetry in Antirrhinum, and determined the extent to which the
underlying regulatory genes varied in expression among closely related species.
We show that expression of both genes analysed, CYC and RAD, varies significantly
between species because of cis-acting differences. By making a quantitative genotype-phenotype
map, using a range of mutant alleles, we demonstrate that the species lie on a
plateau in gene expression-morphology space, so that the variation has no detectable
phenotypic effect. However, phenotypic differences can be revealed by shifting
genotypes off the plateau through genetic crosses. Our results can be readily
explained if genomes are free to evolve within an effectively neutral zone in
gene expression space. The consequences of this drift will be negligible for individual
loci, but when multiple loci across the genome are considered, we show that the
variation may have significant effects on phenotype and fitness, causing a significant
drift load. By considering these consequences for various gene-expression-fitness
landscapes, we conclude that F1 hybrids might be expected to show increased performance
with regard to conserved traits, such as basic physiology, but reduced performance
with regard to others. Thus, our study provides a new way of explaining how various
aspects of hybrid performance may arise through natural variation in gene activity.
acknowledgement: "This was supported by a Marie Curie grant for early stage training
and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank
X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green,
A. Bangham and J. Pateman for advice and assistance on shape model procedures; F.
Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols
and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n"
article_number: e1000429
author:
- first_name: Ulises
full_name: Rosas, Ulises
last_name: Rosas
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Pierre
full_name: Barbier De Reuille, Pierre
last_name: Barbier De Reuille
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation
between species and the basis of hybrid performance. PLoS Biology. 2010;8(7).
doi:10.1371/journal.pbio.1000429
apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E.
(2010). Cryptic variation between species and the basis of hybrid performance.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429
chicago: Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille,
and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.”
PLoS Biology. Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000429.
ieee: U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic
variation between species and the basis of hybrid performance,” PLoS Biology,
vol. 8, no. 7. Public Library of Science, 2010.
ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic
variation between species and the basis of hybrid performance. PLoS Biology. 8(7),
e1000429.
mla: Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid
Performance.” PLoS Biology, vol. 8, no. 7, e1000429, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000429.
short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology
8 (2010).
date_created: 2018-12-11T12:05:07Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2023-02-23T14:07:34Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.1000429
file:
- access_level: open_access
checksum: ee1ce2fb283a6b4127544ae532d0b4a1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:11Z
date_updated: 2020-07-14T12:46:15Z
file_id: '5060'
file_name: IST-2015-366-v1+1_journal.pbio.1000429.pdf
file_size: 1089530
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2448'
pubrep_id: '366'
quality_controlled: '1'
related_material:
record:
- id: '9764'
relation: research_data
status: public
scopus_import: 1
status: public
title: Cryptic variation between species and the basis of hybrid performance
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '3787'
abstract:
- lang: eng
text: DNA samples were extracted from ethanol and formalin-fixed decapod crustacean
tissue using a new method based on Tetramethylsilane (TMS)-Chelex. It is shown
that neither an indigestible matrix of cross-linked protein nor soluble PCR inhibitors
impede PCR success when dealing with formalin-fixed material. Instead, amplification
success from formalin-fixed tissue appears to depend on the presence of unmodified
DNA in the extracted sample. A staining method that facilitates the targeting
of samples with a high content of unmodified DNA is provided.
acknowledgement: "The authors would like to thank two anonymous reviewers for their
remarks, which helped to improve the manuscript. This project was supported by the
Marine Biodiversity and Ecosystem Functioning Network of Excellence MarBEF (Contract
no. GOCE-CT-2003-505446) of the 6th European Framework Programme(FP6), the Zoology
Research Fund, Department of Zoology, NHM, London, a Research Grant from the Royal
Society to S.T., and a pre-doctoral fellowship awarded by the Autonomous Government
of Catalonia to F.P.(2006FIC-00082). This research received support from the SYNTHESYS
Project http://www.synthesys. info/ which is financed by European Community Research
Infrastructure Action under the FP6 “Structuring the European Research Area” Programme.
Many thanks are due to J. Fortuño for suggesting TMS as an alternative to critical
point drying, P.Crabb for helping with the UV-light photography setting and our
colleagues/friends in the Whale Basement Molecular Laboratories, Department of Zoology
NHM \r\n\r\n"
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Sally
full_name: Hall, Sally
last_name: Hall
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: David
full_name: Johnston, David
last_name: Johnston
- first_name: Jackie
full_name: Mackenzie Dodds, Jackie
last_name: Mackenzie Dodds
- first_name: Sven
full_name: Thatje, Sven
last_name: Thatje
citation:
ama: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. DNA extraction
from formalin-fixed tissue: new light from the deep sea. Scientia Marina.
2010;74(3):465-470. doi:10.3989/scimar.2010.74n3465'
apa: 'Palero, F., Hall, S., Clark, P., Johnston, D., Mackenzie Dodds, J., &
Thatje, S. (2010). DNA extraction from formalin-fixed tissue: new light from the
deep sea. Scientia Marina. Consejo Superior de Investigaciones Científicas.
https://doi.org/10.3989/scimar.2010.74n3465'
chicago: 'Palero, Ferran, Sally Hall, Paul Clark, David Johnston, Jackie Mackenzie
Dodds, and Sven Thatje. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina. Consejo Superior de Investigaciones
Científicas, 2010. https://doi.org/10.3989/scimar.2010.74n3465.'
ieee: 'F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, and S. Thatje,
“DNA extraction from formalin-fixed tissue: new light from the deep sea,” Scientia
Marina, vol. 74, no. 3. Consejo Superior de Investigaciones Científicas, pp.
465–470, 2010.'
ista: 'Palero F, Hall S, Clark P, Johnston D, Mackenzie Dodds J, Thatje S. 2010.
DNA extraction from formalin-fixed tissue: new light from the deep sea. Scientia
Marina. 74(3), 465–470.'
mla: 'Palero, Ferran, et al. “DNA Extraction from Formalin-Fixed Tissue: New Light
from the Deep Sea.” Scientia Marina, vol. 74, no. 3, Consejo Superior de
Investigaciones Científicas, 2010, pp. 465–70, doi:10.3989/scimar.2010.74n3465.'
short: F. Palero, S. Hall, P. Clark, D. Johnston, J. Mackenzie Dodds, S. Thatje,
Scientia Marina 74 (2010) 465–470.
date_created: 2018-12-11T12:05:10Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T07:52:11Z
day: '01'
department:
- _id: NiBa
doi: 10.3989/scimar.2010.74n3465
intvolume: ' 74'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprints.soton.ac.uk/68731/
month: '09'
oa: 1
oa_version: Submitted Version
page: 465 - 470
publication: Scientia Marina
publication_status: published
publisher: Consejo Superior de Investigaciones Científicas
publist_id: '2440'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'DNA extraction from formalin-fixed tissue: new light from the deep sea'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 74
year: '2010'
...
---
_id: '3790'
abstract:
- lang: eng
text: Cell shape and motility are primarily controlled by cellular mechanics. The
attachment of the plasma membrane to the underlying actomyosin cortex has been
proposed to be important for cellular processes involving membrane deformation.
However, little is known about the actual function of membrane-to-cortex attachment
(MCA) in cell protrusion formation and migration, in particular in the context
of the developing embryo. Here, we use a multidisciplinary approach to study MCA
in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells,
which migrate using a combination of different protrusion types, namely, lamellipodia,
filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity
of molecules linking the cortex to the membrane and measuring resulting changes
in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors
increases the proportion of cellular blebs and reduces the directionality of cell
migration. We propose that MCA is a key parameter controlling the relative proportions
of different cell protrusion types in mesendoderm progenitors, and thus is key
in controlling directed migration during gastrulation.
acknowledgement: "We would like to thank A. G. Clark, S. Grill, A. Oates, E. Raz,
L. Rohde, and M. Zerial for reading earlier versions of the manuscript. We are grateful
to W. Zachariae, Y. Arboleda-Estudillo, S. Schneider, P. Stockinger, D. Panhans,
M. Biro, J. C. Olaya, and the BIOTEC/MPI-CBG zebrafish and imaging facilities for
help and advice at various stages of this project and to J. Helenius for help with
programming. This work was supported by grants from the Boehringer Ingelheim Fonds
to MK, the Polish Ministry of Science and Higher Education to E. P., and the Deutsche
Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EP.\r\n"
article_number: e1000544
author:
- first_name: Alba
full_name: Diz Muñoz, Alba
last_name: Diz Muñoz
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Martin
full_name: Bergert, Martin
last_name: Bergert
- first_name: Itziar
full_name: Ibarlucea Benitez, Itziar
last_name: Ibarlucea Benitez
- first_name: Daniel
full_name: Müller, Daniel
last_name: Müller
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Diz Muñoz A, Krieg M, Bergert M, et al. Control of directed cell migration
in vivo by membrane-to-cortex attachment. PLoS Biology. 2010;8(11). doi:10.1371/journal.pbio.1000544
apa: Diz Muñoz, A., Krieg, M., Bergert, M., Ibarlucea Benitez, I., Müller, D., Paluch,
E., & Heisenberg, C.-P. J. (2010). Control of directed cell migration in vivo
by membrane-to-cortex attachment. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1000544
chicago: Diz Muñoz, Alba, Michael Krieg, Martin Bergert, Itziar Ibarlucea Benitez,
Daniel Müller, Ewa Paluch, and Carl-Philipp J Heisenberg. “Control of Directed
Cell Migration in Vivo by Membrane-to-Cortex Attachment.” PLoS Biology.
Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000544.
ieee: A. Diz Muñoz et al., “Control of directed cell migration in vivo by
membrane-to-cortex attachment,” PLoS Biology, vol. 8, no. 11. Public Library
of Science, 2010.
ista: Diz Muñoz A, Krieg M, Bergert M, Ibarlucea Benitez I, Müller D, Paluch E,
Heisenberg C-PJ. 2010. Control of directed cell migration in vivo by membrane-to-cortex
attachment. PLoS Biology. 8(11), e1000544.
mla: Diz Muñoz, Alba, et al. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex
Attachment.” PLoS Biology, vol. 8, no. 11, e1000544, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000544.
short: A. Diz Muñoz, M. Krieg, M. Bergert, I. Ibarlucea Benitez, D. Müller, E. Paluch,
C.-P.J. Heisenberg, PLoS Biology 8 (2010).
date_created: 2018-12-11T12:05:11Z
date_published: 2010-11-30T00:00:00Z
date_updated: 2021-01-12T07:52:13Z
day: '30'
ddc:
- '576'
department:
- _id: CaHe
doi: 10.1371/journal.pbio.1000544
file:
- access_level: open_access
checksum: 52d18c90ca6b02234cea5e8b399b7f46
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:24Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4685'
file_name: IST-2015-365-v1+1_journal.pbio.1000544.pdf
file_size: 799506
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2437'
pubrep_id: '365'
quality_controlled: '1'
scopus_import: 1
status: public
title: Control of directed cell migration in vivo by membrane-to-cortex attachment
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2010'
...
---
_id: '3793'
abstract:
- lang: eng
text: "Recent progress in per-pixel object class labeling of natural images can
be attributed to the use of multiple types of image features and sound statistical
learning approaches. Within the latter, Conditional Random Fields (CRF) are prominently
used for their ability to represent interactions between random variables. Despite
their popularity in computer vision, parameter learning for CRFs has remained
difficult, popular approaches being cross-validation and piecewise training.\r\nIn
this work, we propose a simple yet expressive tree-structured CRF based on a recent
hierarchical image segmentation method. Our model combines and weights multiple
image features within a hierarchical representation and allows simple and efficient
globally-optimal learning of ≈ 105 parameters. The tractability of our model allows
us to pose and answer some of the open questions regarding parameter learning
applying to CRF-based approaches. The key findings for learning CRF models are,
from the obvious to the surprising, i) multiple image features always help, ii)
the limiting dimension with respect to current models is the amount of training
data, iii) piecewise training is competitive, iv) current methods for max-margin
training fail for models with many parameters.\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Nowozin, Sebastian
last_name: Nowozin
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Nowozin S, Gehler P, Lampert C. On parameter learning in CRF-based approaches
to object class image segmentation. In: Vol 6316. Springer; 2010:98-111. doi:10.1007/978-3-642-15567-3_8'
apa: 'Nowozin, S., Gehler, P., & Lampert, C. (2010). On parameter learning in
CRF-based approaches to object class image segmentation (Vol. 6316, pp. 98–111).
Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete,
Greece: Springer. https://doi.org/10.1007/978-3-642-15567-3_8'
chicago: Nowozin, Sebastian, Peter Gehler, and Christoph Lampert. “On Parameter
Learning in CRF-Based Approaches to Object Class Image Segmentation,” 6316:98–111.
Springer, 2010. https://doi.org/10.1007/978-3-642-15567-3_8.
ieee: 'S. Nowozin, P. Gehler, and C. Lampert, “On parameter learning in CRF-based
approaches to object class image segmentation,” presented at the ECCV: European
Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6316, pp.
98–111.'
ista: 'Nowozin S, Gehler P, Lampert C. 2010. On parameter learning in CRF-based
approaches to object class image segmentation. ECCV: European Conference on Computer
Vision, LNCS, vol. 6316, 98–111.'
mla: Nowozin, Sebastian, et al. On Parameter Learning in CRF-Based Approaches
to Object Class Image Segmentation. Vol. 6316, Springer, 2010, pp. 98–111,
doi:10.1007/978-3-642-15567-3_8.
short: S. Nowozin, P. Gehler, C. Lampert, in:, Springer, 2010, pp. 98–111.
conference:
end_date: 2010-09-11
location: Heraklion, Crete, Greece
name: 'ECCV: European Conference on Computer Vision'
start_date: 2010-09-05
date_created: 2018-12-11T12:05:12Z
date_published: 2010-11-04T00:00:00Z
date_updated: 2021-01-12T07:52:14Z
day: '04'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/978-3-642-15567-3_8
file:
- access_level: open_access
checksum: 3716e10e161f7c714fd17ec193a223c3
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:27:34Z
date_updated: 2020-07-14T12:46:16Z
file_id: '7871'
file_name: 2010_ECCV_Nowozin.pdf
file_size: 4087332
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 6316'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 98 - 111
publication_status: published
publisher: Springer
publist_id: '2431'
quality_controlled: '1'
scopus_import: 1
status: public
title: On parameter learning in CRF-based approaches to object class image segmentation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6316
year: '2010'
...
---
_id: '3795'
abstract:
- lang: eng
text: 'The (apparent) contour of a smooth mapping from a 2-manifold to the plane,
f: M → R2 , is the set of critical values, that is, the image of the points at
which the gradients of the two component functions are linearly dependent. Assuming
M is compact and orientable and measuring difference with the erosion distance,
we prove that the contour is stable.'
acknowledgement: This research is partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.
alternative_title:
- Mathematics and Visualization
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Edelsbrunner H, Morozov D, Patel A. The stability of the apparent contour
of an orientable 2-manifold. In: Topological Data Analysis and Visualization:
Theory, Algorithms and Applications. Springer; 2010:27-42. doi:10.1007/978-3-642-15014-2_3'
apa: 'Edelsbrunner, H., Morozov, D., & Patel, A. (2010). The stability of the
apparent contour of an orientable 2-manifold. In Topological Data Analysis
and Visualization: Theory, Algorithms and Applications (pp. 27–42). Springer.
https://doi.org/10.1007/978-3-642-15014-2_3'
chicago: 'Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “The Stability
of the Apparent Contour of an Orientable 2-Manifold.” In Topological Data Analysis
and Visualization: Theory, Algorithms and Applications, 27–42. Springer, 2010.
https://doi.org/10.1007/978-3-642-15014-2_3.'
ieee: 'H. Edelsbrunner, D. Morozov, and A. Patel, “The stability of the apparent
contour of an orientable 2-manifold,” in Topological Data Analysis and Visualization:
Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.'
ista: 'Edelsbrunner H, Morozov D, Patel A. 2010.The stability of the apparent contour
of an orientable 2-manifold. In: Topological Data Analysis and Visualization:
Theory, Algorithms and Applications. Mathematics and Visualization, , 27–42.'
mla: 'Edelsbrunner, Herbert, et al. “The Stability of the Apparent Contour of an
Orientable 2-Manifold.” Topological Data Analysis and Visualization: Theory,
Algorithms and Applications, Springer, 2010, pp. 27–42, doi:10.1007/978-3-642-15014-2_3.'
short: 'H. Edelsbrunner, D. Morozov, A. Patel, in:, Topological Data Analysis and
Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.'
date_created: 2018-12-11T12:05:13Z
date_published: 2010-12-22T00:00:00Z
date_updated: 2021-01-12T07:52:15Z
day: '22'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-15014-2_3
file:
- access_level: open_access
checksum: f03a44c3d1c3e2d4fedb3b94404f3fd5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:40Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4896'
file_name: IST-2016-538-v1+1_2011-B-02-ApparentContour.pdf
file_size: 210710
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 27 - 42
publication: 'Topological Data Analysis and Visualization: Theory, Algorithms and
Applications'
publication_status: published
publisher: Springer
publist_id: '2428'
pubrep_id: '538'
quality_controlled: '1'
scopus_import: 1
status: public
title: The stability of the apparent contour of an orientable 2-manifold
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3831'
abstract:
- lang: eng
text: Fast-spiking, parvalbumin-expressing basket cells (BCs) play a key role in
feedforward and feedback inhibition in the hippocampus. However, the dendritic
mechanisms underlying rapid interneuron recruitment have remained unclear. To
quantitatively address this question, we developed detailed passive cable models
of BCs in the dentate gyrus based on dual somatic or somatodendritic recordings
and complete morphologic reconstructions. Both specific membrane capacitance and
axial resistivity were comparable to those of pyramidal neurons, but the average
somatodendritic specific membrane resistance (R(m)) was substantially lower in
BCs. Furthermore, R(m) was markedly nonuniform, being lowest in soma and proximal
dendrites, intermediate in distal dendrites, and highest in the axon. Thus, the
somatodendritic gradient of R(m) was the reverse of that in pyramidal neurons.
Further computational analysis revealed that these unique cable properties accelerate
the time course of synaptic potentials at the soma in response to fast inputs,
while boosting the efficacy of slow distal inputs. These properties will facilitate
both rapid phasic and efficient tonic activation of BCs in hippocampal microcircuits.
author:
- first_name: Anja
full_name: Norenberg, Anja
last_name: Norenberg
- first_name: Hua
full_name: Hua Hu
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. Distinct nonuniform cable properties
optimize rapid and efficient activation of fast-spiking GABAergic interneurons.
PNAS. 2010;107(2):894-899. doi:10.1073/pnas.0910716107
apa: Norenberg, A., Hu, H., Vida, I., Bartos, M., & Jonas, P. M. (2010). Distinct
nonuniform cable properties optimize rapid and efficient activation of fast-spiking
GABAergic interneurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0910716107
chicago: Norenberg, Anja, Hua Hu, Imre Vida, Marlene Bartos, and Peter M Jonas.
“Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation
of Fast-Spiking GABAergic Interneurons.” PNAS. National Academy of Sciences,
2010. https://doi.org/10.1073/pnas.0910716107.
ieee: A. Norenberg, H. Hu, I. Vida, M. Bartos, and P. M. Jonas, “Distinct nonuniform
cable properties optimize rapid and efficient activation of fast-spiking GABAergic
interneurons,” PNAS, vol. 107, no. 2. National Academy of Sciences, pp.
894–9, 2010.
ista: Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. 2010. Distinct nonuniform cable
properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons.
PNAS. 107(2), 894–9.
mla: Norenberg, Anja, et al. “Distinct Nonuniform Cable Properties Optimize Rapid
and Efficient Activation of Fast-Spiking GABAergic Interneurons.” PNAS,
vol. 107, no. 2, National Academy of Sciences, 2010, pp. 894–99, doi:10.1073/pnas.0910716107.
short: A. Norenberg, H. Hu, I. Vida, M. Bartos, P.M. Jonas, PNAS 107 (2010) 894–9.
date_created: 2018-12-11T12:05:24Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:31Z
day: '01'
doi: 10.1073/pnas.0910716107
extern: 1
intvolume: ' 107'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818894/#!po=4.16667
month: '01'
oa: 1
page: 894 - 9
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2379'
quality_controlled: 0
status: public
title: Distinct nonuniform cable properties optimize rapid and efficient activation
of fast-spiking GABAergic interneurons
type: journal_article
volume: 107
year: '2010'
...
---
_id: '3832'
abstract:
- lang: eng
text: A recent paper by von Engelhardt et al. identifies a novel auxiliary subunit
of native AMPARs, termedCKAMP44. Unlike other auxiliary subunits, CKAMP44 accelerates
desensitization and prolongs recovery from desensitization. CKAMP44 is highly
expressed in hippocampal dentate gyrus granule cells and decreases the paired-pulse
ratio at perforant path input synapses. Thus, both principal and auxiliary AMPAR
subunits control the time course of signaling at glutamatergic synapses.
article_processing_charge: No
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Guzmán J, Jonas PM. Beyond TARPs: The growing list of auxiliary AMPAR subunits.
Neuron. 2010;66(1):8-10. doi:10.1016/j.neuron.2010.04.003'
apa: 'Guzmán, J., & Jonas, P. M. (2010). Beyond TARPs: The growing list of auxiliary
AMPAR subunits. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2010.04.003'
chicago: 'Guzmán, José, and Peter M Jonas. “Beyond TARPs: The Growing List of Auxiliary
AMPAR Subunits.” Neuron. Elsevier, 2010. https://doi.org/10.1016/j.neuron.2010.04.003.'
ieee: 'J. Guzmán and P. M. Jonas, “Beyond TARPs: The growing list of auxiliary AMPAR
subunits,” Neuron, vol. 66, no. 1. Elsevier, pp. 8–10, 2010.'
ista: 'Guzmán J, Jonas PM. 2010. Beyond TARPs: The growing list of auxiliary AMPAR
subunits. Neuron. 66(1), 8–10.'
mla: 'Guzmán, José, and Peter M. Jonas. “Beyond TARPs: The Growing List of Auxiliary
AMPAR Subunits.” Neuron, vol. 66, no. 1, Elsevier, 2010, pp. 8–10, doi:10.1016/j.neuron.2010.04.003.'
short: J. Guzmán, P.M. Jonas, Neuron 66 (2010) 8–10.
date_created: 2018-12-11T12:05:25Z
date_published: 2010-04-15T00:00:00Z
date_updated: 2021-01-12T07:52:31Z
day: '15'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2010.04.003
external_id:
pmid:
- '20399724'
intvolume: ' 66'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/20399724
month: '04'
oa: 1
oa_version: Published Version
page: 8 - 10
pmid: 1
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2377'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Beyond TARPs: The growing list of auxiliary AMPAR subunits'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2010'
...
---
_id: '3834'
abstract:
- lang: eng
text: "Background\r\n\r\nThe chemical master equation (CME) is a system of ordinary
differential equations that describes the evolution of a network of chemical reactions
as a stochastic process. Its solution yields the probability density vector of
the system at each point in time. Solving the CME numerically is in many cases
computationally expensive or even infeasible as the number of reachable states
can be very large or infinite. We introduce the sliding window method, which computes
an approximate solution of the CME by performing a sequence of local analysis
steps. In each step, only a manageable subset of states is considered, representing
a "window" into the state space. In subsequent steps, the window follows
the direction in which the probability mass moves, until the time period of interest
has elapsed. We construct the window based on a deterministic approximation of
the future behavior of the system by estimating upper and lower bounds on the
populations of the chemical species.\r\nResults\r\n\r\nIn order to show the effectiveness
of our approach, we apply it to several examples previously described in the literature.
The experimental results show that the proposed method speeds up the analysis
considerably, compared to a global analysis, while still providing high accuracy.\r\n\r\n\r\nConclusions\r\n\r\nThe
sliding window method is a novel approach to address the performance problems
of numerical algorithms for the solution of the chemical master equation. The
method efficiently approximates the probability distributions at the time points
of interest for a variety of chemically reacting systems, including systems for
which no upper bound on the population sizes of the chemical species is known
a priori."
acknowledgement: This research has been partially funded by the Swiss National Science
Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal
Computing and Interaction at Saarland University.
author:
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
- first_name: Rushil
full_name: Goel, Rushil
last_name: Goel
- first_name: Maria
full_name: Mateescu, Maria
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
last_name: Mateescu
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Wolf V, Goel R, Mateescu M, Henzinger TA. Solving the chemical master equation
using sliding windows. BMC Systems Biology. 2010;4(42):1-19. doi:10.1186/1752-0509-4-42
apa: Wolf, V., Goel, R., Mateescu, M., & Henzinger, T. A. (2010). Solving the
chemical master equation using sliding windows. BMC Systems Biology. BioMed
Central. https://doi.org/10.1186/1752-0509-4-42
chicago: Wolf, Verena, Rushil Goel, Maria Mateescu, and Thomas A Henzinger. “Solving
the Chemical Master Equation Using Sliding Windows.” BMC Systems Biology.
BioMed Central, 2010. https://doi.org/10.1186/1752-0509-4-42.
ieee: V. Wolf, R. Goel, M. Mateescu, and T. A. Henzinger, “Solving the chemical
master equation using sliding windows,” BMC Systems Biology, vol. 4, no.
42. BioMed Central, pp. 1–19, 2010.
ista: Wolf V, Goel R, Mateescu M, Henzinger TA. 2010. Solving the chemical master
equation using sliding windows. BMC Systems Biology. 4(42), 1–19.
mla: Wolf, Verena, et al. “Solving the Chemical Master Equation Using Sliding Windows.”
BMC Systems Biology, vol. 4, no. 42, BioMed Central, 2010, pp. 1–19, doi:10.1186/1752-0509-4-42.
short: V. Wolf, R. Goel, M. Mateescu, T.A. Henzinger, BMC Systems Biology 4 (2010)
1–19.
date_created: 2018-12-11T12:05:25Z
date_published: 2010-04-08T00:00:00Z
date_updated: 2021-01-12T07:52:32Z
day: '08'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1186/1752-0509-4-42
file:
- access_level: open_access
checksum: 220239fae76f7b03c4d7f05d74ef426f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:29Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5217'
file_name: IST-2012-72-v1+1_Solving_the_chemical_master_equation_using_sliding_windows.pdf
file_size: 1919130
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '42'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1 - 19
publication: BMC Systems Biology
publication_status: published
publisher: BioMed Central
publist_id: '2374'
pubrep_id: '72'
quality_controlled: '1'
scopus_import: 1
status: public
title: Solving the chemical master equation using sliding windows
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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2010'
...
---
_id: '3838'
abstract:
- lang: eng
text: We present a numerical approximation technique for the analysis of continuous-time
Markov chains that describe net- works of biochemical reactions and play an important
role in the stochastic modeling of biological systems. Our approach is based on
the construction of a stochastic hybrid model in which certain discrete random
variables of the original Markov chain are approximated by continuous deterministic
variables. We compute the solution of the stochastic hybrid model using a numerical
algorithm that discretizes time and in each step performs a mutual update of the
transient prob- ability distribution of the discrete stochastic variables and
the values of the continuous deterministic variables. We im- plemented the algorithm
and we demonstrate its usefulness and efficiency on several case studies from
systems biology.
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
- first_name: Linar
full_name: Mikeev, Linar
last_name: Mikeev
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Henzinger TA, Mateescu M, Mikeev L, Wolf V. Hybrid numerical solution of the
chemical master equation. In: Springer; 2010:55-65. doi:10.1145/1839764.1839772'
apa: 'Henzinger, T. A., Mateescu, M., Mikeev, L., & Wolf, V. (2010). Hybrid
numerical solution of the chemical master equation (pp. 55–65). Presented at the
CMSB: Computational Methods in Systems Biology, Trento, Italy: Springer. https://doi.org/10.1145/1839764.1839772'
chicago: Henzinger, Thomas A, Maria Mateescu, Linar Mikeev, and Verena Wolf. “Hybrid
Numerical Solution of the Chemical Master Equation,” 55–65. Springer, 2010. https://doi.org/10.1145/1839764.1839772.
ieee: 'T. A. Henzinger, M. Mateescu, L. Mikeev, and V. Wolf, “Hybrid numerical solution
of the chemical master equation,” presented at the CMSB: Computational Methods
in Systems Biology, Trento, Italy, 2010, pp. 55–65.'
ista: 'Henzinger TA, Mateescu M, Mikeev L, Wolf V. 2010. Hybrid numerical solution
of the chemical master equation. CMSB: Computational Methods in Systems Biology,
55–65.'
mla: Henzinger, Thomas A., et al. Hybrid Numerical Solution of the Chemical Master
Equation. Springer, 2010, pp. 55–65, doi:10.1145/1839764.1839772.
short: T.A. Henzinger, M. Mateescu, L. Mikeev, V. Wolf, in:, Springer, 2010, pp.
55–65.
conference:
end_date: 2010-10-01
location: Trento, Italy
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2010-09-29
date_created: 2018-12-11T12:05:27Z
date_published: 2010-09-29T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '29'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1145/1839764.1839772
file:
- access_level: open_access
checksum: 81cb6f0babd97151b171d1ce86582831
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:55Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5179'
file_name: IST-2012-68-v1+1_Hybrid_Numerical_Solution_of_the_Chemical_Master_Equation.pdf
file_size: 671790
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 55 - 65
publication_status: published
publisher: Springer
publist_id: '2356'
pubrep_id: '68'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hybrid numerical solution of the chemical master equation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3839'
abstract:
- lang: eng
text: We present a loop property generation method for loops iterating over multi-dimensional
arrays. When used on matrices, our method is able to infer their shapes (also
called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties,
we first transform a nested loop iterating over a multi- dimensional array into
an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants
for each unnested loop using a generalization of a recurrence-based invariant
generation technique. These loop invariants give us conditions on matrices from
which we can derive matrix types automatically us- ing theorem provers. Invariant
generation is implemented in the software package Aligator and types are derived
by theorem provers and SMT solvers, including Vampire and Z3. When run on the
Java matrix package JAMA, our tool was able to infer automatically all matrix
types describing the matrix shapes guaranteed by JAMA’s API.
acknowledgement: The research was supported by the Swiss NSF.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L, Voronkov A. Invariant and type inference
for matrices. In: Vol 5944. Springer; 2010:163-179. doi:10.1007/978-3-642-11319-2_14'
apa: 'Henzinger, T. A., Hottelier, T., Kovács, L., & Voronkov, A. (2010). Invariant
and type inference for matrices (Vol. 5944, pp. 163–179). Presented at the VMCAI:
Verification, Model Checking and Abstract Interpretation, Madrid, Spain: Springer.
https://doi.org/10.1007/978-3-642-11319-2_14'
chicago: Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrei Voronkov.
“Invariant and Type Inference for Matrices,” 5944:163–79. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_14.
ieee: 'T. A. Henzinger, T. Hottelier, L. Kovács, and A. Voronkov, “Invariant and
type inference for matrices,” presented at the VMCAI: Verification, Model Checking
and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 163–179.'
ista: 'Henzinger TA, Hottelier T, Kovács L, Voronkov A. 2010. Invariant and type
inference for matrices. VMCAI: Verification, Model Checking and Abstract Interpretation,
LNCS, vol. 5944, 163–179.'
mla: Henzinger, Thomas A., et al. Invariant and Type Inference for Matrices.
Vol. 5944, Springer, 2010, pp. 163–79, doi:10.1007/978-3-642-11319-2_14.
short: T.A. Henzinger, T. Hottelier, L. Kovács, A. Voronkov, in:, Springer, 2010,
pp. 163–179.
conference:
end_date: 2010-01-19
location: Madrid, Spain
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2010-01-17
date_created: 2018-12-11T12:05:27Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-11319-2_14
file:
- access_level: open_access
checksum: da69b13a2d9a7a316c909e09c1090cef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:09Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4989'
file_name: IST-2012-69-v1+1_Invariant_and_type_inference_for_matrices.pdf
file_size: 251265
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 5944'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 163 - 179
publication_status: published
publisher: Springer
publist_id: '2357'
pubrep_id: '69'
quality_controlled: '1'
scopus_import: 1
status: public
title: Invariant and type inference for matrices
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5944
year: '2010'
...
---
_id: '3842'
abstract:
- lang: eng
text: Within systems biology there is an increasing interest in the stochastic behavior
of biochemical reaction networks. An appropriate stochastic description is provided
by the chemical master equation, which represents a continuous-time Markov chain
(CTMC). The uniformization technique is an efficient method to compute probability
distributions of a CTMC if the number of states is manageable. However, the size
of a CTMC that represents a biochemical reaction network is usually far beyond
what is feasible. In this paper we present an on-the-fly variant of uniformization,
where we improve the original algorithm at the cost of a small approximation error.
By means of several examples, we show that our approach is particularly well-suited
for biochemical reaction networks.
author:
- first_name: Frédéric
full_name: Didier, Frédéric
last_name: Didier
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of
the chemical master equation. IET Systems Biology. 2010;4(6):441-452. doi:10.1049/iet-syb.2010.0005
apa: Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). Fast adaptive
uniformization of the chemical master equation. IET Systems Biology. Institution
of Engineering and Technology. https://doi.org/10.1049/iet-syb.2010.0005
chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“Fast Adaptive Uniformization of the Chemical Master Equation.” IET Systems
Biology. Institution of Engineering and Technology, 2010. https://doi.org/10.1049/iet-syb.2010.0005.
ieee: F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization
of the chemical master equation,” IET Systems Biology, vol. 4, no. 6. Institution
of Engineering and Technology, pp. 441–452, 2010.
ista: Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. Fast adaptive uniformization
of the chemical master equation. IET Systems Biology. 4(6), 441–452.
mla: Didier, Frédéric, et al. “Fast Adaptive Uniformization of the Chemical Master
Equation.” IET Systems Biology, vol. 4, no. 6, Institution of Engineering
and Technology, 2010, pp. 441–52, doi:10.1049/iet-syb.2010.0005.
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, IET Systems Biology 4 (2010)
441–452.
date_created: 2018-12-11T12:05:28Z
date_published: 2010-11-15T00:00:00Z
date_updated: 2023-02-23T11:45:08Z
day: '15'
ddc:
- '570'
department:
- _id: ToHe
doi: 10.1049/iet-syb.2010.0005
file:
- access_level: open_access
checksum: 9a3bde48f43203991a0b3c6a277c2f5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:02Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5254'
file_name: IST-2012-66-v1+1_Fast_adaptive_uniformization_of_the_chemical_master_equation.pdf
file_size: 222890
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 441 - 452
publication: IET Systems Biology
publication_status: published
publisher: Institution of Engineering and Technology
publist_id: '2349'
pubrep_id: '66'
quality_controlled: '1'
related_material:
record:
- id: '3843'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Fast adaptive uniformization of the chemical master equation
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2010'
...
---
_id: '3845'
abstract:
- lang: eng
text: This paper presents Aligators, a tool for the generation of universally quantified
array invariants. Aligators leverages recurrence solving and algebraic techniques
to carry out inductive reasoning over array content. The Aligators’ loop extraction
module allows treatment of multi-path loops by exploiting their commutativity
and serializability properties. Our experience in applying Aligators on a collection
of loops from open source software projects indicates the applicability of recurrence
and algebraic solving techniques for reasoning about arrays.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. Aligators for arrays.
In: Vol 6397. Springer; 2010:348-356. doi:10.1007/978-3-642-16242-8_25'
apa: 'Henzinger, T. A., Hottelier, T., Kovács, L., & Rybalchenko, A. (2010).
Aligators for arrays (Vol. 6397, pp. 348–356). Presented at the LPAR: Logic for
Programming, Artificial Intelligence, and Reasoning, Yogyakarta, Indonesia: Springer.
https://doi.org/10.1007/978-3-642-16242-8_25'
chicago: Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrey Rybalchenko.
“Aligators for Arrays,” 6397:348–56. Springer, 2010. https://doi.org/10.1007/978-3-642-16242-8_25.
ieee: 'T. A. Henzinger, T. Hottelier, L. Kovács, and A. Rybalchenko, “Aligators
for arrays,” presented at the LPAR: Logic for Programming, Artificial Intelligence,
and Reasoning, Yogyakarta, Indonesia, 2010, vol. 6397, pp. 348–356.'
ista: 'Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. 2010. Aligators for arrays.
LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol.
6397, 348–356.'
mla: Henzinger, Thomas A., et al. Aligators for Arrays. Vol. 6397, Springer,
2010, pp. 348–56, doi:10.1007/978-3-642-16242-8_25.
short: T.A. Henzinger, T. Hottelier, L. Kovács, A. Rybalchenko, in:, Springer, 2010,
pp. 348–356.
conference:
end_date: 2010-10-15
location: Yogyakarta, Indonesia
name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
start_date: 2010-10-10
date_created: 2018-12-11T12:05:29Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2021-01-12T07:52:37Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-16242-8_25
file:
- access_level: open_access
checksum: 913af269da6710f2174f470b48ab7a82
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:05Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4790'
file_name: IST-2012-64-v1+1_Aligators_for_arrays.pdf
file_size: 186143
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 6397'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 348 - 356
publication_status: published
publisher: Springer
publist_id: '2342'
pubrep_id: '64'
quality_controlled: '1'
scopus_import: 1
status: public
title: Aligators for arrays
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6397
year: '2010'
...
---
_id: '3847'
abstract:
- lang: eng
text: The importance of stochasticity within biological systems has been shown repeatedly
during the last years and has raised the need for efficient stochastic tools.
We present SABRE, a tool for stochastic analysis of biochemical reaction networks.
SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation
algorithm for computing transient solutions of biochemical reaction networks.
Biochemical reactions networks represent biological systems studied at a molecular
level and these reactions can be modeled as transitions of a Markov chain. SABRE
accepts as input the formalism of guarded commands, which it interprets either
as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic
mode, SABRE may also perform a deterministic analysis by directly computing a
mean-field approximation of the system under study. We illustrate the different
functionalities of SABRE by means of biological case studies.
author:
- first_name: Frédéric
full_name: Didier, Frédéric
last_name: Didier
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Didier F, Henzinger TA, Mateescu M, Wolf V. SABRE: A tool for the stochastic
analysis of biochemical reaction networks. In: IEEE; 2010:193-194. doi:10.1109/QEST.2010.33'
apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). SABRE:
A tool for the stochastic analysis of biochemical reaction networks (pp. 193–194).
Presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA:
IEEE. https://doi.org/10.1109/QEST.2010.33'
chicago: 'Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,”
193–94. IEEE, 2010. https://doi.org/10.1109/QEST.2010.33.'
ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “SABRE: A tool for
the stochastic analysis of biochemical reaction networks,” presented at the QEST:
Quantitative Evaluation of Systems, Williamsburg, USA, 2010, pp. 193–194.'
ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. SABRE: A tool for the stochastic
analysis of biochemical reaction networks. QEST: Quantitative Evaluation of Systems,
193–194.'
mla: 'Didier, Frédéric, et al. SABRE: A Tool for the Stochastic Analysis of Biochemical
Reaction Networks. IEEE, 2010, pp. 193–94, doi:10.1109/QEST.2010.33.'
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.
conference:
end_date: 2010-09-18
location: Williamsburg, USA
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2010-09-15
date_created: 2018-12-11T12:05:29Z
date_published: 2010-10-14T00:00:00Z
date_updated: 2021-01-12T07:52:37Z
day: '14'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/QEST.2010.33
file:
- access_level: open_access
checksum: 38707b149d2174f01be406e794ffa849
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:03Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4726'
file_name: IST-2012-63-v1+1_SABRE-A_tool_for_the_stochastic_analysis_of_biochemical_reaction_networks.pdf
file_size: 433824
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 193 - 194
publication_status: published
publisher: IEEE
publist_id: '2339'
pubrep_id: '63'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'SABRE: A tool for the stochastic analysis of biochemical reaction networks'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3849'
abstract:
- lang: eng
text: Using ideas from persistent homology, the robustness of a level set of a real-valued
function is defined in terms of the magnitude of the perturbation necessary to
kill the classes. Prior work has shown that the homology and robustness information
can be read off the extended persistence diagram of the function. This paper extends
these results to a non-uniform error model in which perturbations vary in their
magnitude across the domain.
alternative_title:
- LNCS
author:
- first_name: Paul
full_name: Bendich, Paul
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Bendich P, Edelsbrunner H, Kerber M, Patel A. Persistent homology under non-uniform
error. In: Vol 6281. Springer; 2010:12-23. doi:10.1007/978-3-642-15155-2_2'
apa: 'Bendich, P., Edelsbrunner, H., Kerber, M., & Patel, A. (2010). Persistent
homology under non-uniform error (Vol. 6281, pp. 12–23). Presented at the MFCS:
Mathematical Foundations of Computer Science, Brno, Czech Republic: Springer.
https://doi.org/10.1007/978-3-642-15155-2_2'
chicago: Bendich, Paul, Herbert Edelsbrunner, Michael Kerber, and Amit Patel. “Persistent
Homology under Non-Uniform Error,” 6281:12–23. Springer, 2010. https://doi.org/10.1007/978-3-642-15155-2_2.
ieee: 'P. Bendich, H. Edelsbrunner, M. Kerber, and A. Patel, “Persistent homology
under non-uniform error,” presented at the MFCS: Mathematical Foundations of Computer
Science, Brno, Czech Republic, 2010, vol. 6281, pp. 12–23.'
ista: 'Bendich P, Edelsbrunner H, Kerber M, Patel A. 2010. Persistent homology under
non-uniform error. MFCS: Mathematical Foundations of Computer Science, LNCS, vol.
6281, 12–23.'
mla: Bendich, Paul, et al. Persistent Homology under Non-Uniform Error. Vol.
6281, Springer, 2010, pp. 12–23, doi:10.1007/978-3-642-15155-2_2.
short: P. Bendich, H. Edelsbrunner, M. Kerber, A. Patel, in:, Springer, 2010, pp.
12–23.
conference:
end_date: 2010-08-27
location: Brno, Czech Republic
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2010-08-23
date_created: 2018-12-11T12:05:30Z
date_published: 2010-08-10T00:00:00Z
date_updated: 2021-01-12T07:52:38Z
day: '10'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-15155-2_2
file:
- access_level: open_access
checksum: af61e1c2bb42f3d556179d4692caeb1b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:13Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4994'
file_name: IST-2016-537-v1+1_2010-P-05-NonuniformError.pdf
file_size: 142357
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 6281'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 12 - 23
publication_status: published
publisher: Springer
publist_id: '2333'
pubrep_id: '537'
quality_controlled: '1'
scopus_import: 1
status: public
title: Persistent homology under non-uniform error
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6281
year: '2010'
...
---
_id: '385'
abstract:
- lang: eng
text: 'Scanning tunneling spectroscopy studies on high-quality Bi2Te3 crystals exhibit
perfect correspondence to angle-resolved photoemission spectroscopy data, hence
enabling identification of different regimes measured in the local density of
states (LDOS). Oscillations of LDOS near a step are analyzed. Within the main
part of the surface band oscillations are strongly damped, supporting the hypothesis
of topological protection. At higher energies, as the surface band becomes concave,
oscillations appear, dispersing with a wave vector that may result from a hexagonal
warping term. '
author:
- first_name: Zhanybek
full_name: Alpichshev, Zhanybek
id: 45E67A2A-F248-11E8-B48F-1D18A9856A87
last_name: Alpichshev
orcid: 0000-0002-7183-5203
- first_name: James
full_name: Analytis, James
last_name: Analytis
- first_name: Jiunhaw
full_name: Chu, Jiunhaw
last_name: Chu
- first_name: Ian
full_name: Fisher, Ian
last_name: Fisher
- first_name: Yulin
full_name: Chen, Yulin
last_name: Chen
- first_name: Zhixun
full_name: Shen, Zhixun
last_name: Shen
- first_name: Aiping
full_name: Fang, Aiping
last_name: Fang
- first_name: Aharon
full_name: Kapitulnik, Aharon
last_name: Kapitulnik
citation:
ama: Alpichshev Z, Analytis J, Chu J, et al. STM imaging of electronic waves on
the surface of Bi2Te3 Topologically protected surface states and hexagonal warping
effects. Physical Review Letters. 2010;104(1). doi:10.1103/PhysRevLett.104.016401
apa: Alpichshev, Z., Analytis, J., Chu, J., Fisher, I., Chen, Y., Shen, Z., … Kapitulnik,
A. (2010). STM imaging of electronic waves on the surface of Bi2Te3 Topologically
protected surface states and hexagonal warping effects. Physical Review Letters.
American Physical Society. https://doi.org/10.1103/PhysRevLett.104.016401
chicago: Alpichshev, Zhanybek, James Analytis, Jiunhaw Chu, Ian Fisher, Yulin Chen,
Zhixun Shen, Aiping Fang, and Aharon Kapitulnik. “STM Imaging of Electronic Waves
on the Surface of Bi2Te3 Topologically Protected Surface States and Hexagonal
Warping Effects.” Physical Review Letters. American Physical Society, 2010.
https://doi.org/10.1103/PhysRevLett.104.016401.
ieee: Z. Alpichshev et al., “STM imaging of electronic waves on the surface
of Bi2Te3 Topologically protected surface states and hexagonal warping effects,”
Physical Review Letters, vol. 104, no. 1. American Physical Society, 2010.
ista: Alpichshev Z, Analytis J, Chu J, Fisher I, Chen Y, Shen Z, Fang A, Kapitulnik
A. 2010. STM imaging of electronic waves on the surface of Bi2Te3 Topologically
protected surface states and hexagonal warping effects. Physical Review Letters.
104(1).
mla: Alpichshev, Zhanybek, et al. “STM Imaging of Electronic Waves on the Surface
of Bi2Te3 Topologically Protected Surface States and Hexagonal Warping Effects.”
Physical Review Letters, vol. 104, no. 1, American Physical Society, 2010,
doi:10.1103/PhysRevLett.104.016401.
short: Z. Alpichshev, J. Analytis, J. Chu, I. Fisher, Y. Chen, Z. Shen, A. Fang,
A. Kapitulnik, Physical Review Letters 104 (2010).
date_created: 2018-12-11T11:46:10Z
date_published: 2010-01-04T00:00:00Z
date_updated: 2021-01-12T07:52:39Z
day: '04'
doi: 10.1103/PhysRevLett.104.016401
extern: '1'
intvolume: ' 104'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/pdf/0908.0371.pdf
month: '01'
oa: 1
oa_version: None
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '7444'
status: public
title: STM imaging of electronic waves on the surface of Bi2Te3 Topologically protected
surface states and hexagonal warping effects
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2010'
...
---
_id: '3851'
abstract:
- lang: eng
text: 'Energy parity games are infinite two-player turn-based games played on weighted
graphs. The objective of the game combines a (qualitative) parity condition with
the (quantitative) requirement that the sum of the weights (i.e., the level of
energy in the game) must remain positive. Beside their own interest in the design
and synthesis of resource-constrained omega-regular specifications, energy parity
games provide one of the simplest model of games with combined qualitative and
quantitative objective. Our main results are as follows: (a) exponential memory
is sufficient and may be necessary for winning strategies in energy parity games;
(b) the problem of deciding the winner in energy parity games can be solved in
NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to
energy games. We also show that the problem of deciding the winner in energy parity
games is polynomially equivalent to the problem of deciding the winner in mean-payoff
parity games, which can thus be solved in NP ∩ coNP. As a consequence we also
obtain a conceptually simple algorithm to solve mean-payoff parity games.'
alternative_title:
- LNCS
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
citation:
ama: 'Chatterjee K, Doyen L. Energy parity games. In: Vol 6199. Springer; 2010:599-610.
doi:10.1007/978-3-642-14162-1_50'
apa: 'Chatterjee, K., & Doyen, L. (2010). Energy parity games (Vol. 6199, pp.
599–610). Presented at the ICALP: Automata, Languages and Programming, 37th International
Colloquium, Bordeaux, France: Springer. https://doi.org/10.1007/978-3-642-14162-1_50'
chicago: Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games,” 6199:599–610.
Springer, 2010. https://doi.org/10.1007/978-3-642-14162-1_50.
ieee: 'K. Chatterjee and L. Doyen, “Energy parity games,” presented at the ICALP:
Automata, Languages and Programming, 37th International Colloquium, Bordeaux,
France, 2010, vol. 6199, pp. 599–610.'
ista: 'Chatterjee K, Doyen L. 2010. Energy parity games. ICALP: Automata, Languages
and Programming, 37th International Colloquium, LNCS, vol. 6199, 599–610.'
mla: Chatterjee, Krishnendu, and Laurent Doyen. Energy Parity Games. Vol.
6199, Springer, 2010, pp. 599–610, doi:10.1007/978-3-642-14162-1_50.
short: K. Chatterjee, L. Doyen, in:, Springer, 2010, pp. 599–610.
conference:
end_date: 2010-07-10
location: Bordeaux, France
name: ' ICALP: Automata, Languages and Programming, 37th International Colloquium'
start_date: 2010-07-06
date_created: 2018-12-11T12:05:31Z
date_published: 2010-09-10T00:00:00Z
date_updated: 2023-02-23T11:06:35Z
day: '10'
department:
- _id: KrCh
doi: 10.1007/978-3-642-14162-1_50
external_id:
arxiv:
- '1001.5183'
intvolume: ' 6199'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1001.5183
month: '09'
oa: 1
oa_version: Preprint
page: 599 - 610
publication_status: published
publisher: Springer
publist_id: '2330'
quality_controlled: '1'
related_material:
record:
- id: '2972'
relation: later_version
status: public
scopus_import: 1
status: public
title: Energy parity games
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6199
year: '2010'
...