---
_id: '3395'
abstract:
- lang: eng
text: Defining population structure and genetic diversity levels is of the utmost
importance for developing efficient conservation strategies. Overfishing has caused
mean annual catches of the European spiny lobster (Palinurus elephas) to decrease
alarmingly along its distribution area. In this context, there is a need for comprehensive
studies aiming to evaluate the genetic health of the exploited populations. The
present study is based on a set of ten nuclear markers amplified in 331 individuals
from ten different localities covering most of P. elephas distribution area. Samples
from Atlantic and Mediterranean basins showed small but significant differences,
indicating that P. elephas populations do not behave as a single panmictic unit
but form two partially-overlapping groups. Despite intense overfishing, our dataset
did not recover a recent bottleneck signal, and instead showed a large and stable
historical effective size. This result could be accounted for by specific life-history
traits (reproduction and longevity) and the limitations of molecular markers in
covering recent timescales for nontemporal samples. The findings of the present
study emphasize the need to integrate information on effective population sizes
and life-history parameters when evaluating population connectivity levels from
genetic data.
acknowledgement: This work was supported by a pre-doctoral fellowship awarded by the
Autonomous Government of Catalonia to F.P. (2006FIC-00082). Research was funded
by projects FBBVA-BIOCON 08-187/09, CGL2006-13423, and CTM2007-66635. The authors
are part of the research group 2009SGR-636, 2009SGR-655, and 2009SGR-1364 of the
Generalitat de Catalunya. F.P. acknowledges EU-Synthesys grant (GB-TAF-4474).
article_processing_charge: No
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
- first_name: Enrique
full_name: Macpherson, Enrique
last_name: Macpherson
- first_name: Mark
full_name: Beaumont, Mark
last_name: Beaumont
- first_name: Marta
full_name: Pascual, Marta
last_name: Pascual
citation:
ama: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 2011;104(2):407-418.
doi:10.1111/j.1095-8312.2011.01728.x
apa: Palero, F., Abello, P., Macpherson, E., Beaumont, M., & Pascual, M. (2011).
Effect of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas. Biological Journal of the
Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2011.01728.x
chicago: Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta
Pascual. “Effect of Oceanographic Barriers and Overfishing on the Population Genetic
Structure of the European Spiny Lobster Palinurus Elephas.” Biological Journal
of the Linnean Society. Wiley-Blackwell, 2011. https://doi.org/10.1111/j.1095-8312.2011.01728.x.
ieee: F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Effect
of oceanographic barriers and overfishing on the population genetic structure
of the European spiny lobster Palinurus elephas,” Biological Journal of the
Linnean Society, vol. 104, no. 2. Wiley-Blackwell, pp. 407–418, 2011.
ista: Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Effect of oceanographic
barriers and overfishing on the population genetic structure of the European spiny
lobster Palinurus elephas. Biological Journal of the Linnean Society. 104(2),
407–418.
mla: Palero, Ferran, et al. “Effect of Oceanographic Barriers and Overfishing on
the Population Genetic Structure of the European Spiny Lobster Palinurus Elephas.”
Biological Journal of the Linnean Society, vol. 104, no. 2, Wiley-Blackwell,
2011, pp. 407–18, doi:10.1111/j.1095-8312.2011.01728.x.
short: F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, Biological
Journal of the Linnean Society 104 (2011) 407–418.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-14T00:00:00Z
date_updated: 2023-02-23T14:07:31Z
day: '14'
department:
- _id: NiBa
doi: 10.1111/j.1095-8312.2011.01728.x
intvolume: ' 104'
issue: '2'
language:
- iso: eng
month: '09'
oa_version: None
page: 407 - 418
publication: Biological Journal of the Linnean Society
publication_status: published
publisher: Wiley-Blackwell
publist_id: '3212'
quality_controlled: '1'
related_material:
record:
- id: '9762'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Effect of oceanographic barriers and overfishing on the population genetic
structure of the European spiny lobster Palinurus elephas
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 104
year: '2011'
...
---
_id: '3396'
abstract:
- lang: eng
text: Facial branchiomotor neurons (FBMNs) in zebrafish and mouse embryonic hindbrain
undergo a characteristic tangential migration from rhombomere (r) 4, where they
are born, to r6/7. Cohesion among neuroepithelial cells (NCs) has been suggested
to function in FBMN migration by inhibiting FBMNs positioned in the basal neuroepithelium
such that they move apically between NCs towards the midline of the neuroepithelium
instead of tangentially along the basal side of the neuroepithelium towards r6/7.
However, direct experimental evaluation of this hypothesis is still lacking. Here,
we have used a combination of biophysical cell adhesion measurements and high-resolution
time-lapse microscopy to determine the role of NC cohesion in FBMN migration.
We show that reducing NC cohesion by interfering with Cadherin 2 (Cdh2) activity
results in FBMNs positioned at the basal side of the neuroepithelium moving apically
towards the neural tube midline instead of tangentially towards r6/7. In embryos
with strongly reduced NC cohesion, ectopic apical FBMN movement frequently results
in fusion of the bilateral FBMN clusters over the apical midline of the neural
tube. By contrast, reducing cohesion among FBMNs by interfering with Contactin
2 (Cntn2) expression in these cells has little effect on apical FBMN movement,
but reduces the fusion of the bilateral FBMN clusters in embryos with strongly
diminished NC cohesion. These data provide direct experimental evidence that NC
cohesion functions in tangential FBMN migration by restricting their apical movement.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
article_type: original
author:
- first_name: Petra
full_name: Stockinger, Petra
id: 261CB030-E90D-11E9-B182-F697D44B663C
last_name: Stockinger
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
citation:
ama: Stockinger P, Heisenberg C-PJ, Maître J-L. Defective neuroepithelial cell cohesion
affects tangential branchiomotor neuron migration in the zebrafish neural tube.
Development. 2011;138(21):4673-4683. doi:10.1242/dev.071233
apa: Stockinger, P., Heisenberg, C.-P. J., & Maître, J.-L. (2011). Defective
neuroepithelial cell cohesion affects tangential branchiomotor neuron migration
in the zebrafish neural tube. Development. Company of Biologists. https://doi.org/10.1242/dev.071233
chicago: Stockinger, Petra, Carl-Philipp J Heisenberg, and Jean-Léon Maître. “Defective
Neuroepithelial Cell Cohesion Affects Tangential Branchiomotor Neuron Migration
in the Zebrafish Neural Tube.” Development. Company of Biologists, 2011.
https://doi.org/10.1242/dev.071233.
ieee: P. Stockinger, C.-P. J. Heisenberg, and J.-L. Maître, “Defective neuroepithelial
cell cohesion affects tangential branchiomotor neuron migration in the zebrafish
neural tube,” Development, vol. 138, no. 21. Company of Biologists, pp.
4673–4683, 2011.
ista: Stockinger P, Heisenberg C-PJ, Maître J-L. 2011. Defective neuroepithelial
cell cohesion affects tangential branchiomotor neuron migration in the zebrafish
neural tube. Development. 138(21), 4673–4683.
mla: Stockinger, Petra, et al. “Defective Neuroepithelial Cell Cohesion Affects
Tangential Branchiomotor Neuron Migration in the Zebrafish Neural Tube.” Development,
vol. 138, no. 21, Company of Biologists, 2011, pp. 4673–83, doi:10.1242/dev.071233.
short: P. Stockinger, C.-P.J. Heisenberg, J.-L. Maître, Development 138 (2011) 4673–4683.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-09-28T00:00:00Z
date_updated: 2021-01-12T07:43:11Z
day: '28'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1242/dev.071233
file:
- access_level: open_access
checksum: ca12b79e01ef36c1ef1aea31cf7e7139
content_type: application/pdf
creator: dernst
date_created: 2019-10-07T14:19:42Z
date_updated: 2020-07-14T12:46:12Z
file_id: '6930'
file_name: 2011_Development_Stockinger.pdf
file_size: 4672439
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 138'
issue: '21'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 4673 - 4683
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '3210'
quality_controlled: '1'
scopus_import: 1
status: public
title: Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron
migration in the zebrafish neural tube
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 138
year: '2011'
...
---
_id: '3397'
abstract:
- lang: eng
text: Recent advances in microscopy techniques and biophysical measurements have
provided novel insight into the molecular, cellular and biophysical basis of cell
adhesion. However, comparably little is known about a core element of cell–cell
adhesion—the energy of adhesion at the cell–cell contact. In this review, we discuss
approaches to understand the nature and regulation of adhesion energy, and propose
strategies to determine adhesion energy between cells in vitro and in vivo.
author:
- first_name: Jean-Léon
full_name: Maître, Jean-Léon
id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87
last_name: Maître
orcid: 0000-0002-3688-1474
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Maître J-L, Heisenberg C-PJ. The role of adhesion energy in controlling cell-cell
contacts. Current Opinion in Cell Biology. 2011;23(5):508-514. doi:10.1016/j.ceb.2011.07.004
apa: Maître, J.-L., & Heisenberg, C.-P. J. (2011). The role of adhesion energy
in controlling cell-cell contacts. Current Opinion in Cell Biology. Elsevier.
https://doi.org/10.1016/j.ceb.2011.07.004
chicago: Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “The Role of Adhesion
Energy in Controlling Cell-Cell Contacts.” Current Opinion in Cell Biology.
Elsevier, 2011. https://doi.org/10.1016/j.ceb.2011.07.004.
ieee: J.-L. Maître and C.-P. J. Heisenberg, “The role of adhesion energy in controlling
cell-cell contacts,” Current Opinion in Cell Biology, vol. 23, no. 5. Elsevier,
pp. 508–514, 2011.
ista: Maître J-L, Heisenberg C-PJ. 2011. The role of adhesion energy in controlling
cell-cell contacts. Current Opinion in Cell Biology. 23(5), 508–514.
mla: Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “The Role of Adhesion Energy
in Controlling Cell-Cell Contacts.” Current Opinion in Cell Biology, vol.
23, no. 5, Elsevier, 2011, pp. 508–14, doi:10.1016/j.ceb.2011.07.004.
short: J.-L. Maître, C.-P.J. Heisenberg, Current Opinion in Cell Biology 23 (2011)
508–514.
date_created: 2018-12-11T12:03:06Z
date_published: 2011-10-01T00:00:00Z
date_updated: 2021-01-12T07:43:12Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/j.ceb.2011.07.004
intvolume: ' 23'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188705/
month: '10'
oa: 1
oa_version: Submitted Version
page: 508 - 514
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '3211'
quality_controlled: '1'
scopus_import: 1
status: public
title: The role of adhesion energy in controlling cell-cell contacts
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2011'
...
---
_id: '3399'
abstract:
- lang: eng
text: Context-dependent adjustment of mating tactics can drastically increase the
mating success of behaviourally flexible animals. We used the ant Cardiocondyla
obscurior as a model system to study adaptive adjustment of male mating tactics.
This species shows a male diphenism of wingless fighter males and peaceful winged
males. Whereas the wingless males stay and exclusively mate in the maternal colony,
the mating behaviour of winged males is plastic. They copulate with female sexuals
in their natal nests early in life but later disperse in search for sexuals outside.
In this study, we observed the nest-leaving behaviour of winged males under different
conditions and found that they adaptively adjust the timing of their dispersal
to the availability of mating partners, as well as the presence, and even the
type of competitors in their natal nests. In colonies with virgin female queens
winged males stayed longest when they were the only male in the nest. They left
earlier when mating partners were not available or when other males were present.
In the presence of wingless, locally mating fighter males, winged males dispersed
earlier than in the presence of docile, winged competitors. This suggests that
C. obscurior males are capable of estimating their local breeding chances and
adaptively adjust their dispersal behaviour in both an opportunistic and a risk-sensitive
way, thus showing hitherto unknown behavioural plasticity in social insect males.
acknowledgement: This work was supported by the German Science Foundation (www.dfg.de,
He 1623/23).
article_number: e17323
author:
- first_name: Sylvia
full_name: Cremer, Sylvia
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
- first_name: Alexandra
full_name: Schrempf, Alexandra
last_name: Schrempf
- first_name: Jürgen
full_name: Heinze, Jürgen
last_name: Heinze
citation:
ama: Cremer S, Schrempf A, Heinze J. Competition and opportunity shape the reproductive
tactics of males in the ant Cardiocondyla obscurior. PLoS One. 2011;6(3).
doi:10.1371/journal.pone.0017323
apa: Cremer, S., Schrempf, A., & Heinze, J. (2011). Competition and opportunity
shape the reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS
One. Public Library of Science. https://doi.org/10.1371/journal.pone.0017323
chicago: Cremer, Sylvia, Alexandra Schrempf, and Jürgen Heinze. “Competition and
Opportunity Shape the Reproductive Tactics of Males in the Ant Cardiocondyla Obscurior.”
PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0017323.
ieee: S. Cremer, A. Schrempf, and J. Heinze, “Competition and opportunity shape
the reproductive tactics of males in the ant Cardiocondyla obscurior,” PLoS
One, vol. 6, no. 3. Public Library of Science, 2011.
ista: Cremer S, Schrempf A, Heinze J. 2011. Competition and opportunity shape the
reproductive tactics of males in the ant Cardiocondyla obscurior. PLoS One. 6(3),
e17323.
mla: Cremer, Sylvia, et al. “Competition and Opportunity Shape the Reproductive
Tactics of Males in the Ant Cardiocondyla Obscurior.” PLoS One, vol. 6,
no. 3, e17323, Public Library of Science, 2011, doi:10.1371/journal.pone.0017323.
short: S. Cremer, A. Schrempf, J. Heinze, PLoS One 6 (2011).
date_created: 2018-12-11T12:03:07Z
date_published: 2011-03-29T00:00:00Z
date_updated: 2021-01-12T07:43:12Z
day: '29'
ddc:
- '576'
department:
- _id: SyCr
doi: 10.1371/journal.pone.0017323
file:
- access_level: open_access
checksum: 46f8cbde61f06fcacf8fa297cacfa0e5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:40Z
date_updated: 2020-07-14T12:46:12Z
file_id: '5162'
file_name: IST-2015-377-v1+1_journal.pone.0017323.pdf
file_size: 147367
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '3059'
pubrep_id: '377'
quality_controlled: '1'
scopus_import: 1
status: public
title: Competition and opportunity shape the reproductive tactics of males in the
ant Cardiocondyla obscurior
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: '3405'
abstract:
- lang: eng
text: Glutamate is the major excitatory neurotransmitter in the mammalian central
nervous system and gates non-selective cation channels. The origins of glutamate
receptors are not well understood as they differ structurally and functionally
from simple bacterial ligand-gated ion channels. Here we report the discovery
of an ionotropic glutamate receptor that combines the typical eukaryotic domain
architecture with the 'TXVGYG' signature sequence of the selectivity filter found
in K+ channels. This receptor exhibits functional properties intermediate between
bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the
evolution of ionotropic glutamate receptors.
author:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Guillaume
full_name: Sandoz, Guillaume
last_name: Sandoz
- first_name: Ehud
full_name: Isacoff, Ehud
last_name: Isacoff
citation:
ama: Janovjak HL, Sandoz G, Isacoff E. Modern ionotropic glutamate receptor with
a K+ selectivity signature sequence. Nature Communications. 2011;2(232):1-6.
doi:10.1038/ncomms1231
apa: Janovjak, H. L., Sandoz, G., & Isacoff, E. (2011). Modern ionotropic glutamate
receptor with a K+ selectivity signature sequence. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms1231
chicago: Janovjak, Harald L, Guillaume Sandoz, and Ehud Isacoff. “Modern Ionotropic
Glutamate Receptor with a K+ Selectivity Signature Sequence.” Nature Communications.
Nature Publishing Group, 2011. https://doi.org/10.1038/ncomms1231.
ieee: H. L. Janovjak, G. Sandoz, and E. Isacoff, “Modern ionotropic glutamate receptor
with a K+ selectivity signature sequence,” Nature Communications, vol.
2, no. 232. Nature Publishing Group, pp. 1–6, 2011.
ista: Janovjak HL, Sandoz G, Isacoff E. 2011. Modern ionotropic glutamate receptor
with a K+ selectivity signature sequence. Nature Communications. 2(232), 1–6.
mla: Janovjak, Harald L., et al. “Modern Ionotropic Glutamate Receptor with a K+
Selectivity Signature Sequence.” Nature Communications, vol. 2, no. 232,
Nature Publishing Group, 2011, pp. 1–6, doi:10.1038/ncomms1231.
short: H.L. Janovjak, G. Sandoz, E. Isacoff, Nature Communications 2 (2011) 1–6.
date_created: 2018-12-11T12:03:09Z
date_published: 2011-03-08T00:00:00Z
date_updated: 2021-01-12T07:43:15Z
day: '08'
ddc:
- '570'
- '571'
department:
- _id: HaJa
doi: 10.1038/ncomms1231
file:
- access_level: open_access
checksum: 6b68d65aadd97c18d663eb117a0a9d35
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:36Z
date_updated: 2020-07-14T12:46:12Z
file_id: '4891'
file_name: IST-2017-832-v1+1_janovjak.pdf
file_size: 387654
relation: main_file
file_date_updated: 2020-07-14T12:46:12Z
has_accepted_license: '1'
intvolume: ' 2'
issue: '232'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1 - 6
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '2997'
pubrep_id: '832'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modern ionotropic glutamate receptor with a K+ selectivity signature sequence
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2011'
...
---
_id: '3429'
abstract:
- lang: eng
text: Transcription factors are central to sustaining pluripotency, yet little is
known about transcription factor dynamics in defining pluripotency in the early
mammalian embryo. Here, we establish a fluorescence decay after photoactivation
(FDAP) assay to quantitatively study the kinetic behaviour of Oct4, a key transcription
factor controlling pre-implantation development in the mouse embryo. FDAP measurements
reveal that each cell in a developing embryo shows one of two distinct Oct4 kinetics,
before there are any morphologically distinguishable differences or outward signs
of lineage patterning. The differences revealed by FDAP are due to differences
in the accessibility of Oct4 to its DNA binding sites in the nucleus. Lineage
tracing of the cells in the two distinct sub-populations demonstrates that the
Oct4 kinetics predict lineages of the early embryo. Cells with slower Oct4 kinetics
are more likely to give rise to the pluripotent cell lineage that contributes
to the inner cell mass. Those with faster Oct4 kinetics contribute mostly to the
extra-embryonic lineage. Our findings identify Oct4 kinetics, rather than differences
in total transcription factor expression levels, as a predictive measure of developmental
cell lineage patterning in the early mouse embryo.
acknowledgement: This work was supported by the Beckman Institute and Biological Imaging
Center at the California Institute of Technology and by the NHGRI Center of Excellence
in Genomic Science grant P50HG004071.
author:
- first_name: Nicolas
full_name: Plachta, Nicolas
last_name: Plachta
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
- first_name: Shirley
full_name: Pease, Shirley
last_name: Pease
- first_name: Scott
full_name: Fraser, Scott
last_name: Fraser
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
citation:
ama: Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. Oct4 kinetics predict
cell lineage patterning in the early mammalian embryo. Nature Cell Biology.
2011;13(2):117-123. doi:10.1038/ncb2154
apa: Plachta, N., Bollenbach, M. T., Pease, S., Fraser, S., & Pantazis, P. (2011).
Oct4 kinetics predict cell lineage patterning in the early mammalian embryo. Nature
Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2154
chicago: Plachta, Nicolas, Mark Tobias Bollenbach, Shirley Pease, Scott Fraser,
and Periklis Pantazis. “Oct4 Kinetics Predict Cell Lineage Patterning in the Early
Mammalian Embryo.” Nature Cell Biology. Nature Publishing Group, 2011.
https://doi.org/10.1038/ncb2154.
ieee: N. Plachta, M. T. Bollenbach, S. Pease, S. Fraser, and P. Pantazis, “Oct4
kinetics predict cell lineage patterning in the early mammalian embryo,” Nature
Cell Biology, vol. 13, no. 2. Nature Publishing Group, pp. 117–123, 2011.
ista: Plachta N, Bollenbach MT, Pease S, Fraser S, Pantazis P. 2011. Oct4 kinetics
predict cell lineage patterning in the early mammalian embryo. Nature Cell Biology.
13(2), 117–123.
mla: Plachta, Nicolas, et al. “Oct4 Kinetics Predict Cell Lineage Patterning in
the Early Mammalian Embryo.” Nature Cell Biology, vol. 13, no. 2, Nature
Publishing Group, 2011, pp. 117–23, doi:10.1038/ncb2154.
short: N. Plachta, M.T. Bollenbach, S. Pease, S. Fraser, P. Pantazis, Nature Cell
Biology 13 (2011) 117–123.
date_created: 2018-12-11T12:03:17Z
date_published: 2011-01-23T00:00:00Z
date_updated: 2021-01-12T07:43:24Z
day: '23'
department:
- _id: ToBo
doi: 10.1038/ncb2154
intvolume: ' 13'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 117 - 123
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '2971'
scopus_import: 1
status: public
title: Oct4 kinetics predict cell lineage patterning in the early mammalian embryo
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2011'
...
---
_id: '3505'
abstract:
- lang: eng
text: Cell migration on two-dimensional (2D) substrates follows entirely different
rules than cell migration in three-dimensional (3D) environments. This is especially
relevant for leukocytes that are able to migrate in the absence of adhesion receptors
within the confined geometry of artificial 3D extracellular matrix scaffolds and
within the interstitial space in vivo. Here, we describe in detail a simple and
economical protocol to visualize dendritic cell migration in 3D collagen scaffolds
along chemotactic gradients. This method can be adapted to other cell types and
may serve as a physiologically relevant paradigm for the directed locomotion of
most amoeboid cells.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
article_type: original
author:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
citation:
ama: Sixt MK, Lämmermann T. In vitro analysis of chemotactic leukocyte migration
in 3D environments. Cell Migration. 2011;769:149-165. doi:10.1007/978-1-61779-207-6_11
apa: Sixt, M. K., & Lämmermann, T. (2011). In vitro analysis of chemotactic
leukocyte migration in 3D environments. Cell Migration. Springer. https://doi.org/10.1007/978-1-61779-207-6_11
chicago: Sixt, Michael K, and Tim Lämmermann. “In Vitro Analysis of Chemotactic
Leukocyte Migration in 3D Environments.” Cell Migration. Springer, 2011.
https://doi.org/10.1007/978-1-61779-207-6_11.
ieee: M. K. Sixt and T. Lämmermann, “In vitro analysis of chemotactic leukocyte
migration in 3D environments,” Cell Migration, vol. 769. Springer, pp.
149–165, 2011.
ista: Sixt MK, Lämmermann T. 2011. In vitro analysis of chemotactic leukocyte migration
in 3D environments. Cell Migration. 769, 149–165.
mla: Sixt, Michael K., and Tim Lämmermann. “In Vitro Analysis of Chemotactic Leukocyte
Migration in 3D Environments.” Cell Migration, vol. 769, Springer, 2011,
pp. 149–65, doi:10.1007/978-1-61779-207-6_11.
short: M.K. Sixt, T. Lämmermann, Cell Migration 769 (2011) 149–165.
date_created: 2018-12-11T12:03:41Z
date_published: 2011-05-17T00:00:00Z
date_updated: 2021-01-12T07:43:55Z
day: '17'
department:
- _id: MiSi
doi: 10.1007/978-1-61779-207-6_11
intvolume: ' 769'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pure.mpg.de/pubman/item/item_3219628_1/component/file_3219630/Sixt%20et%20al..pdf
month: '05'
oa: 1
oa_version: Published Version
page: 149 - 165
publication: Cell Migration
publication_status: published
publisher: Springer
publist_id: '2882'
quality_controlled: '1'
status: public
title: In vitro analysis of chemotactic leukocyte migration in 3D environments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 769
year: '2011'
...
---
_id: '3771'
abstract:
- lang: eng
text: The small-sized frugivorous bat Carollia perspicillata is an understory specialist
and occurs in a wide range of lowland habitats, tending to be more common in tropical
dry or moist forests of South and Central America. Its sister species, Carollia
brevicauda, occurs almost exclusively in the Amazon rainforest. A recent phylogeographic
study proposed a hypothesis of origin and subsequent diversification for C. perspicillata
along the Atlantic coastal forest of Brazil. Additionally, it also found two allopatric
clades for C. brevicauda separated by the Amazon Basin. We used cytochrome b gene
sequences and a more extensive sampling to test hypotheses related to the origin
and diversification of C. perspicillata plus C. brevicauda clade in South America.
The results obtained indicate that there are two sympatric evolutionary lineages
within each species. In C. perspicillata, one lineage is limited to the Southern
Atlantic Forest, whereas the other is widely distributed. Coalescent analysis
points to a simultaneous origin for C. perspicillata and C. brevicauda, although
no place for the diversification of each species can be firmly suggested. The
phylogeographic pattern shown by C. perspicillata is also congruent with the Pleistocene
refugia hypothesis as a likely vicariant phenomenon shaping the present distribution
of its intraspecific lineages.
author:
- first_name: Ana
full_name: Pavan, Ana
last_name: Pavan
- first_name: Felipe
full_name: Martins, Felipe
last_name: Martins
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
- first_name: Albert
full_name: Ditchfield, Albert
last_name: Ditchfield
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
citation:
ama: 'Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. Patterns
of diversification in two species of short-tailed bats (Carollia Gray, 1838):
the effects of historical fragmentation of Brazilian rainforests. Biological
Journal of the Linnean Society. 2011;102(3):527-539. doi:10.1111/j.1095-8312.2010.01601.x'
apa: 'Pavan, A., Martins, F., Santos, F., Ditchfield, A., & Fernandes Redondo,
R. A. (2011). Patterns of diversification in two species of short-tailed bats
(Carollia Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.
Biological Journal of the Linnean Society. Wiley-Blackwell. https://doi.org/10.1111/j.1095-8312.2010.01601.x'
chicago: 'Pavan, Ana, Felipe Martins, Fabrício Santos, Albert Ditchfield, and Rodrigo
A Fernandes Redondo. “Patterns of Diversification in Two Species of Short-Tailed
Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian
Rainforests.” Biological Journal of the Linnean Society. Wiley-Blackwell,
2011. https://doi.org/10.1111/j.1095-8312.2010.01601.x.'
ieee: 'A. Pavan, F. Martins, F. Santos, A. Ditchfield, and R. A. Fernandes Redondo,
“Patterns of diversification in two species of short-tailed bats (Carollia Gray,
1838): the effects of historical fragmentation of Brazilian rainforests.,” Biological
Journal of the Linnean Society, vol. 102, no. 3. Wiley-Blackwell, pp. 527–539,
2011.'
ista: 'Pavan A, Martins F, Santos F, Ditchfield A, Fernandes Redondo RA. 2011. Patterns
of diversification in two species of short-tailed bats (Carollia Gray, 1838):
the effects of historical fragmentation of Brazilian rainforests. Biological Journal
of the Linnean Society. 102(3), 527–539.'
mla: 'Pavan, Ana, et al. “Patterns of Diversification in Two Species of Short-Tailed
Bats (Carollia Gray, 1838): The Effects of Historical Fragmentation of Brazilian
Rainforests.” Biological Journal of the Linnean Society, vol. 102, no.
3, Wiley-Blackwell, 2011, pp. 527–39, doi:10.1111/j.1095-8312.2010.01601.x.'
short: A. Pavan, F. Martins, F. Santos, A. Ditchfield, R.A. Fernandes Redondo, Biological
Journal of the Linnean Society 102 (2011) 527–539.
date_created: 2018-12-11T12:05:05Z
date_published: 2011-02-10T00:00:00Z
date_updated: 2021-01-12T07:52:05Z
day: '10'
department:
- _id: FyKo
doi: 10.1111/j.1095-8312.2010.01601.x
intvolume: ' 102'
issue: '3'
language:
- iso: eng
month: '02'
oa_version: None
page: 527 - 539
publication: Biological Journal of the Linnean Society
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2456'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Patterns of diversification in two species of short-tailed bats (Carollia
Gray, 1838): the effects of historical fragmentation of Brazilian rainforests.'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 102
year: '2011'
...
---
_id: '3778'
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. Estimating linkage disequilibria. Heredity. 2011;106(2):205-206.
doi:10.1038/hdy.2010.67
apa: Barton, N. H. (2011). Estimating linkage disequilibria. Heredity. Nature
Publishing Group. https://doi.org/10.1038/hdy.2010.67
chicago: Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity.
Nature Publishing Group, 2011. https://doi.org/10.1038/hdy.2010.67.
ieee: N. H. Barton, “Estimating linkage disequilibria,” Heredity, vol. 106,
no. 2. Nature Publishing Group, pp. 205–206, 2011.
ista: Barton NH. 2011. Estimating linkage disequilibria. Heredity. 106(2), 205–206.
mla: Barton, Nicholas H. “Estimating Linkage Disequilibria.” Heredity, vol.
106, no. 2, Nature Publishing Group, 2011, pp. 205–06, doi:10.1038/hdy.2010.67.
short: N.H. Barton, Heredity 106 (2011) 205–206.
date_created: 2018-12-11T12:05:07Z
date_published: 2011-02-01T00:00:00Z
date_updated: 2021-01-12T07:52:08Z
day: '01'
department:
- _id: NiBa
doi: 10.1038/hdy.2010.67
external_id:
pmid:
- '20502479'
intvolume: ' 106'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183869/
month: '02'
oa: 1
oa_version: Submitted Version
page: 205 - 206
pmid: 1
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '2449'
scopus_import: 1
status: public
title: Estimating linkage disequilibria
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 106
year: '2011'
...
---
_id: '3781'
abstract:
- lang: eng
text: We bound the difference in length of two curves in terms of their total curvatures
and the Fréchet distance. The bound is independent of the dimension of the ambient
Euclidean space, it improves upon a bound by Cohen-Steiner and Edelsbrunner, and
it generalizes a result by Fáry and Chakerian.
acknowledgement: Funded by Graduate Aid in Areas of National Need (GAANN) Fellowship.
author:
- first_name: Brittany Terese
full_name: Fasy, Brittany Terese
id: F65D502E-E68D-11E9-9252-C644099818F6
last_name: Fasy
citation:
ama: Fasy BT. The difference in length of curves in R^n. Acta Sci Math (Szeged).
2011;77(1-2):359-367.
apa: Fasy, B. T. (2011). The difference in length of curves in R^n. Acta Sci.
Math. (Szeged). Szegedi Tudományegyetem.
chicago: Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta
Sci. Math. (Szeged). Szegedi Tudományegyetem, 2011.
ieee: B. T. Fasy, “The difference in length of curves in R^n,” Acta Sci. Math.
(Szeged), vol. 77, no. 1–2. Szegedi Tudományegyetem, pp. 359–367, 2011.
ista: Fasy BT. 2011. The difference in length of curves in R^n. Acta Sci. Math.
(Szeged). 77(1–2), 359–367.
mla: Fasy, Brittany Terese. “The Difference in Length of Curves in R^n.” Acta
Sci. Math. (Szeged), vol. 77, no. 1–2, Szegedi Tudományegyetem, 2011, pp.
359–67.
short: B.T. Fasy, Acta Sci. Math. (Szeged) 77 (2011) 359–367.
date_created: 2018-12-11T12:05:08Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:09Z
day: '01'
department:
- _id: HeEd
intvolume: ' 77'
issue: 1-2
language:
- iso: eng
month: '01'
oa_version: None
page: 359 - 367
publication: Acta Sci. Math. (Szeged)
publication_status: published
publisher: Szegedi Tudományegyetem
publist_id: '2446'
quality_controlled: '1'
status: public
title: The difference in length of curves in R^n
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2011'
...
---
_id: '3784'
abstract:
- lang: eng
text: Advanced stages of Scyllarus phyllosoma larvae were collected by demersal
trawling during fishery research surveys in the western Mediterranean Sea in 2003–2005.
Nucleotide sequence analysis of the mitochondrial 16S rDNA gene allowed the final-stage
phyllosoma of Scyllarus arctus to be identified among these larvae. Its morphology
is described and illustrated. This constitutes the second complete description
of a Scyllaridae phyllosoma with its specific identity being validated by molecular
techniques (the first was S. pygmaeus). These results also solved a long lasting
taxonomic anomaly of several species assigned to the ancient genus Phyllosoma
Leach, 1814. Detailed examination indicated that the final-stage phyllosoma of
S. arctus shows closer affinities with the American scyllarid Scyllarus depressus
or with the Australian Scyllarus sp. b (sensu Phillips et al., 1981) than to its
sympatric species S. pygmaeus.
article_processing_charge: No
article_type: original
author:
- first_name: Ferran
full_name: Palero, Ferran
id: 3F0E2A22-F248-11E8-B48F-1D18A9856A87
last_name: Palero
orcid: 0000-0002-0343-8329
- first_name: Guillermo
full_name: Guerao, Guillermo
last_name: Guerao
- first_name: Paul
full_name: Clark, Paul
last_name: Clark
- first_name: Pere
full_name: Abello, Pere
last_name: Abello
citation:
ama: 'Palero F, Guerao G, Clark P, Abello P. Scyllarus arctus (Crustacea: Decapoda:
Scyllaridae) final stage phyllosoma identified by DNA analysis, with morphological
description. Journal of the Marine Biological Association of the United Kingdom.
2011;91(2):485-492. doi:10.1017/S0025315410000287'
apa: 'Palero, F., Guerao, G., Clark, P., & Abello, P. (2011). Scyllarus arctus
(Crustacea: Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis,
with morphological description. Journal of the Marine Biological Association
of the United Kingdom. Cambridge University Press. https://doi.org/10.1017/S0025315410000287'
chicago: 'Palero, Ferran, Guillermo Guerao, Paul Clark, and Pere Abello. “Scyllarus
Arctus (Crustacea: Decapoda: Scyllaridae) Final Stage Phyllosoma Identified by
DNA Analysis, with Morphological Description.” Journal of the Marine Biological
Association of the United Kingdom. Cambridge University Press, 2011. https://doi.org/10.1017/S0025315410000287.'
ieee: 'F. Palero, G. Guerao, P. Clark, and P. Abello, “Scyllarus arctus (Crustacea:
Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with
morphological description,” Journal of the Marine Biological Association of
the United Kingdom, vol. 91, no. 2. Cambridge University Press, pp. 485–492,
2011.'
ista: 'Palero F, Guerao G, Clark P, Abello P. 2011. Scyllarus arctus (Crustacea:
Decapoda: Scyllaridae) final stage phyllosoma identified by DNA analysis, with
morphological description. Journal of the Marine Biological Association of the
United Kingdom. 91(2), 485–492.'
mla: 'Palero, Ferran, et al. “Scyllarus Arctus (Crustacea: Decapoda: Scyllaridae)
Final Stage Phyllosoma Identified by DNA Analysis, with Morphological Description.”
Journal of the Marine Biological Association of the United Kingdom, vol.
91, no. 2, Cambridge University Press, 2011, pp. 485–92, doi:10.1017/S0025315410000287.'
short: F. Palero, G. Guerao, P. Clark, P. Abello, Journal of the Marine Biological
Association of the United Kingdom 91 (2011) 485–492.
date_created: 2018-12-11T12:05:09Z
date_published: 2011-03-01T00:00:00Z
date_updated: 2021-01-12T07:52:10Z
day: '01'
department:
- _id: NiBa
doi: 10.1017/S0025315410000287
intvolume: ' 91'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://digital.csic.es/bitstream/10261/32783/3/Palero_et_al_2011.pdf
month: '03'
oa: 1
oa_version: Published Version
page: 485 - 492
publication: Journal of the Marine Biological Association of the United Kingdom
publication_status: published
publisher: Cambridge University Press
publist_id: '2443'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Scyllarus arctus (Crustacea: Decapoda: Scyllaridae) final stage phyllosoma
identified by DNA analysis, with morphological description'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 91
year: '2011'
...
---
_id: '3791'
abstract:
- lang: eng
text: During the development of multicellular organisms, cell fate specification
is followed by the sorting of different cell types into distinct domains from
where the different tissues and organs are formed. Cell sorting involves both
the segregation of a mixed population of cells with different fates and properties
into distinct domains, and the active maintenance of their segregated state. Because
of its biological importance and apparent resemblance to fluid segregation in
physics, cell sorting was extensively studied by both biologists and physicists
over the last decades. Different theories were developed that try to explain cell
sorting on the basis of the physical properties of the constituent cells. However,
only recently the molecular and cellular mechanisms that control the physical
properties driving cell sorting, have begun to be unraveled. In this review, we
will provide an overview of different cell-sorting processes in development and
discuss how these processes can be explained by the different sorting theories,
and how these theories in turn can be connected to the molecular and cellular
mechanisms driving these processes.
alternative_title:
- Current Topics in Developmental Biology
article_processing_charge: No
author:
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- 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: 'Krens G, Heisenberg C-PJ. Cell sorting in development. In: Labouesse M, ed.
Forces and Tension in Development. Vol 95. Elsevier; 2011:189-213. doi:10.1016/B978-0-12-385065-2.00006-2'
apa: Krens, G., & Heisenberg, C.-P. J. (2011). Cell sorting in development.
In M. Labouesse (Ed.), Forces and Tension in Development (Vol. 95, pp.
189–213). Elsevier. https://doi.org/10.1016/B978-0-12-385065-2.00006-2
chicago: Krens, Gabriel, and Carl-Philipp J Heisenberg. “Cell Sorting in Development.”
In Forces and Tension in Development, edited by Michel Labouesse, 95:189–213.
Elsevier, 2011. https://doi.org/10.1016/B978-0-12-385065-2.00006-2.
ieee: G. Krens and C.-P. J. Heisenberg, “Cell sorting in development,” in Forces
and Tension in Development, vol. 95, M. Labouesse, Ed. Elsevier, 2011, pp.
189–213.
ista: 'Krens G, Heisenberg C-PJ. 2011.Cell sorting in development. In: Forces and
Tension in Development. Current Topics in Developmental Biology, vol. 95, 189–213.'
mla: Krens, Gabriel, and Carl-Philipp J. Heisenberg. “Cell Sorting in Development.”
Forces and Tension in Development, edited by Michel Labouesse, vol. 95,
Elsevier, 2011, pp. 189–213, doi:10.1016/B978-0-12-385065-2.00006-2.
short: G. Krens, C.-P.J. Heisenberg, in:, M. Labouesse (Ed.), Forces and Tension
in Development, Elsevier, 2011, pp. 189–213.
date_created: 2018-12-11T12:05:11Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:13Z
day: '01'
department:
- _id: CaHe
doi: 10.1016/B978-0-12-385065-2.00006-2
editor:
- first_name: Michel
full_name: Labouesse, Michel
last_name: Labouesse
intvolume: ' 95'
language:
- iso: eng
month: '01'
oa_version: None
page: 189 - 213
publication: Forces and Tension in Development
publication_status: published
publisher: Elsevier
publist_id: '2436'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell sorting in development
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2011'
...
---
_id: '3796'
abstract:
- lang: eng
text: We address the problem of covering ℝ n with congruent balls, while minimizing
the number of balls that contain an average point. Considering the 1-parameter
family of lattices defined by stretching or compressing the integer grid in diagonal
direction, we give a closed formula for the covering density that depends on the
distortion parameter. We observe that our family contains the thinnest lattice
coverings in dimensions 2 to 5. We also consider the problem of packing congruent
balls in ℝ n , for which we give a closed formula for the packing density as well.
Again we observe that our family contains optimal configurations, this time densest
packings in dimensions 2 and 3.
alternative_title:
- LNCS
author:
- 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
citation:
ama: 'Edelsbrunner H, Kerber M. Covering and packing with spheres by diagonal distortion
in R^n. In: Calude C, Rozenberg G, Salomaa A, eds. Rainbow of Computer Science.
Vol 6570. Dedicated to Hermann Maurer on the Occasion of His 70th Birthday. Springer;
2011:20-35. doi:10.1007/978-3-642-19391-0_2'
apa: Edelsbrunner, H., & Kerber, M. (2011). Covering and packing with spheres
by diagonal distortion in R^n. In C. Calude, G. Rozenberg, & A. Salomaa (Eds.),
Rainbow of Computer Science (Vol. 6570, pp. 20–35). Springer. https://doi.org/10.1007/978-3-642-19391-0_2
chicago: Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres
by Diagonal Distortion in R^n.” In Rainbow of Computer Science, edited
by Cristian Calude, Grzegorz Rozenberg, and Arto Salomaa, 6570:20–35. Dedicated
to Hermann Maurer on the Occasion of His 70th Birthday. Springer, 2011. https://doi.org/10.1007/978-3-642-19391-0_2.
ieee: H. Edelsbrunner and M. Kerber, “Covering and packing with spheres by diagonal
distortion in R^n,” in Rainbow of Computer Science, vol. 6570, C. Calude,
G. Rozenberg, and A. Salomaa, Eds. Springer, 2011, pp. 20–35.
ista: 'Edelsbrunner H, Kerber M. 2011.Covering and packing with spheres by diagonal
distortion in R^n. In: Rainbow of Computer Science. LNCS, vol. 6570, 20–35.'
mla: Edelsbrunner, Herbert, and Michael Kerber. “Covering and Packing with Spheres
by Diagonal Distortion in R^n.” Rainbow of Computer Science, edited by
Cristian Calude et al., vol. 6570, Springer, 2011, pp. 20–35, doi:10.1007/978-3-642-19391-0_2.
short: H. Edelsbrunner, M. Kerber, in:, C. Calude, G. Rozenberg, A. Salomaa (Eds.),
Rainbow of Computer Science, Springer, 2011, pp. 20–35.
date_created: 2018-12-11T12:05:13Z
date_published: 2011-05-03T00:00:00Z
date_updated: 2021-01-12T07:52:15Z
day: '03'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-19391-0_2
editor:
- first_name: Cristian
full_name: Calude, Cristian
last_name: Calude
- first_name: Grzegorz
full_name: Rozenberg, Grzegorz
last_name: Rozenberg
- first_name: Arto
full_name: Salomaa, Arto
last_name: Salomaa
file:
- access_level: open_access
checksum: aaf22b4d7bd4277ffe8db532119cf474
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:42Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4640'
file_name: IST-2016-539-v1+1_2011-B-01-CoveringPacking.pdf
file_size: 436875
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 6570'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Submitted Version
page: 20 - 35
publication: Rainbow of Computer Science
publication_status: published
publisher: Springer
publist_id: '2427'
pubrep_id: '539'
quality_controlled: '1'
series_title: Dedicated to Hermann Maurer on the Occasion of His 70th Birthday
status: public
title: Covering and packing with spheres by diagonal distortion in R^n
type: book_chapter
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6570
year: '2011'
...
---
_id: '3965'
abstract:
- lang: eng
text: The elevation function on a smoothly embedded 2-manifold in R-3 reflects the
multiscale topography of cavities and protrusions as local maxima. The function
has been useful in identifying coarse docking configurations for protein pairs.
Transporting the concept from the smooth to the piecewise linear category, this
paper describes an algorithm for finding all local maxima. While its worst-case
running time is the same as of the algorithm used in prior work, its performance
in practice is orders of magnitudes superior. We cast light on this improvement
by relating the running time to the total absolute Gaussian curvature of the 2-manifold.
author:
- first_name: Bei
full_name: Wang, Bei
last_name: Wang
- 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
citation:
ama: Wang B, Edelsbrunner H, Morozov D. Computing elevation maxima by searching
the Gauss sphere. Journal of Experimental Algorithmics. 2011;16(2.2):1-13.
doi:10.1145/1963190.1970375
apa: Wang, B., Edelsbrunner, H., & Morozov, D. (2011). Computing elevation maxima
by searching the Gauss sphere. Journal of Experimental Algorithmics. ACM.
https://doi.org/10.1145/1963190.1970375
chicago: Wang, Bei, Herbert Edelsbrunner, and Dmitriy Morozov. “Computing Elevation
Maxima by Searching the Gauss Sphere.” Journal of Experimental Algorithmics.
ACM, 2011. https://doi.org/10.1145/1963190.1970375.
ieee: B. Wang, H. Edelsbrunner, and D. Morozov, “Computing elevation maxima by searching
the Gauss sphere,” Journal of Experimental Algorithmics, vol. 16, no. 2.2.
ACM, pp. 1–13, 2011.
ista: Wang B, Edelsbrunner H, Morozov D. 2011. Computing elevation maxima by searching
the Gauss sphere. Journal of Experimental Algorithmics. 16(2.2), 1–13.
mla: Wang, Bei, et al. “Computing Elevation Maxima by Searching the Gauss Sphere.”
Journal of Experimental Algorithmics, vol. 16, no. 2.2, ACM, 2011, pp.
1–13, doi:10.1145/1963190.1970375.
short: B. Wang, H. Edelsbrunner, D. Morozov, Journal of Experimental Algorithmics
16 (2011) 1–13.
date_created: 2018-12-11T12:06:09Z
date_published: 2011-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:31Z
day: '01'
department:
- _id: HeEd
doi: 10.1145/1963190.1970375
intvolume: ' 16'
issue: '2.2'
language:
- iso: eng
month: '05'
oa_version: None
page: 1 - 13
publication: Journal of Experimental Algorithmics
publication_status: published
publisher: ACM
publist_id: '2161'
quality_controlled: '1'
scopus_import: 1
status: public
title: Computing elevation maxima by searching the Gauss sphere
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2011'
...
---
_id: '3303'
abstract:
- lang: eng
text: 'Biological traits result in part from interactions between different genetic
loci. This can lead to sign epistasis, in which a beneficial adaptation involves
a combination of individually deleterious or neutral mutations; in this case,
a population must cross a “fitness valley” to adapt. Recombination can assist
this process by combining mutations from different individuals or retard it by
breaking up the adaptive combination. Here, we analyze the simplest fitness valley,
in which an adaptation requires one mutation at each of two loci to provide a
fitness benefit. We present a theoretical analysis of the effect of recombination
on the valley-crossing process across the full spectrum of possible parameter
regimes. We find that low recombination rates can speed up valley crossing relative
to the asexual case, while higher recombination rates slow down valley crossing,
with the transition between the two regimes occurring when the recombination rate
between the loci is approximately equal to the selective advantage provided by
the adaptation. In large populations, if the recombination rate is high and selection
against single mutants is substantial, the time to cross the valley grows exponentially
with population size, effectively meaning that the population cannot acquire the
adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing
time by up to several orders of magnitude relative to that in an asexual population. '
acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate
Fellowship and European Research Council grant 250152 (to D.B.W.) and by National
Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many
ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer
for their helpful suggestions. "
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus
last_name: Feldman
- first_name: Daniel
full_name: Fisher, Daniel
last_name: Fisher
citation:
ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual
populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240
apa: Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley
crossing in sexual populations. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.110.123240
chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley
Crossing in Sexual Populations.” Genetics. Genetics Society of America,
2010. https://doi.org/10.1534/genetics.110.123240.
ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing
in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of
America, pp. 1389–1410, 2010.
ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing
in sexual populations. Genetics. 186(4), 1389–1410.
mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.”
Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410,
doi:10.1534/genetics.110.123240.
short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.
date_created: 2018-12-11T12:02:33Z
date_published: 2010-12-01T00:00:00Z
date_updated: 2021-01-12T07:42:31Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.110.123240
ec_funded: 1
intvolume: ' 186'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1389 - 1410
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '3337'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rate of fitness-valley crossing in sexual populations
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 186
year: '2010'
...
---
_id: '10908'
abstract:
- lang: eng
text: We present ABC, a software tool for automatically computing symbolic upper
bounds on the number of iterations of nested program loops. The system combines
static analysis of programs with symbolic summation techniques to derive loop
invariant relations between program variables. Iteration bounds are obtained from
the inferred invariants, by replacing variables with bounds on their greatest
values. We have successfully applied ABC to a large number of examples. The derived
symbolic bounds express non-trivial polynomial relations over loop variables.
We also report on results to automatically infer symbolic expressions over harmonic
numbers as upper bounds on loop iteration counts.
acknowledgement: This work was supported in part by the Swiss NSF. The fourth author
is supported by an FWF Hertha Firnberg Research grant (T425-N23).
article_processing_charge: No
author:
- first_name: Régis
full_name: Blanc, Régis
last_name: Blanc
- 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
citation:
ama: 'Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation
for loops. In: Clarke EM, Voronkov A, eds. Logic for Programming, Artificial
Intelligence, and Reasoning. Vol 6355. LNCS. Berlin, Heidelberg: Springer
Nature; 2010:103-118. doi:10.1007/978-3-642-17511-4_7'
apa: 'Blanc, R., Henzinger, T. A., Hottelier, T., & Kovács, L. (2010). ABC:
Algebraic Bound Computation for loops. In E. M. Clarke & A. Voronkov (Eds.),
Logic for Programming, Artificial Intelligence, and Reasoning (Vol. 6355,
pp. 103–118). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-642-17511-4_7'
chicago: 'Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács.
“ABC: Algebraic Bound Computation for Loops.” In Logic for Programming, Artificial
Intelligence, and Reasoning, edited by Edmund M Clarke and Andrei Voronkov,
6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. https://doi.org/10.1007/978-3-642-17511-4_7.'
ieee: 'R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound
Computation for loops,” in Logic for Programming, Artificial Intelligence,
and Reasoning, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.'
ista: 'Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound
Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning.
LPAR: Conference on Logic for Programming, Artificial Intelligence and ReasoningLNCS
vol. 6355, 103–118.'
mla: 'Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” Logic
for Programming, Artificial Intelligence, and Reasoning, edited by Edmund
M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:10.1007/978-3-642-17511-4_7.'
short: R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov
(Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer
Nature, Berlin, Heidelberg, 2010, pp. 103–118.
conference:
end_date: 2010-05-01
location: Dakar, Senegal
name: 'LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning'
start_date: 2010-04-25
date_created: 2022-03-21T08:14:35Z
date_published: 2010-05-01T00:00:00Z
date_updated: 2022-06-13T07:44:21Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-642-17511-4_7
editor:
- first_name: Edmund M
full_name: Clarke, Edmund M
last_name: Clarke
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
intvolume: ' 6355'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://infoscience.epfl.ch/record/186096
month: '05'
oa: 1
oa_version: Submitted Version
page: 103-118
place: Berlin, Heidelberg
publication: Logic for Programming, Artificial Intelligence, and Reasoning
publication_identifier:
eisbn:
- '9783642175114'
eissn:
- 1611-3349
isbn:
- '9783642175107'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: 'ABC: Algebraic Bound Computation for loops'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6355
year: '2010'
...
---
_id: '10909'
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 focus
on the volume measure, that is, the 1-norm of a cycle. Two main results are presented.
First, we prove 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). A side effect is 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. We also discuss other geometric measures (diameter and radius) and show
their disadvantages in homology localization. Our work is restricted to homology
over the ℤ2 field.
acknowledgement: Partially supported by the Austrian Science Fund under grantFSP-S9103-N04
and P20134-N13.
article_processing_charge: No
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. In: Proceedings
of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for
Industrial and Applied Mathematics; 2010:1594-1604. doi:10.1137/1.9781611973075.129'
apa: 'Chen, C., & Freedman, D. (2010). Hardness results for homology localization.
In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms
(pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied
Mathematics. https://doi.org/10.1137/1.9781611973075.129'
chicago: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
In Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
1594–1604. Society for Industrial and Applied Mathematics, 2010. https://doi.org/10.1137/1.9781611973075.129.
ieee: C. Chen and D. Freedman, “Hardness results for homology localization,” in
Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
Austin, TX, United States, 2010, pp. 1594–1604.
ista: 'Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings
of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium
on Discrete Algorithms, 1594–1604.'
mla: Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.”
Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms,
Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:10.1137/1.9781611973075.129.
short: C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium
on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010,
pp. 1594–1604.
conference:
end_date: 2010-01-19
location: Austin, TX, United States
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2010-01-17
date_created: 2022-03-21T08:24:07Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2023-02-23T11:19:46Z
day: '01'
department:
- _id: HeEd
doi: 10.1137/1.9781611973075.129
language:
- iso: eng
month: '02'
oa_version: None
page: 1594-1604
publication: Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms
publication_identifier:
eisbn:
- '9781611973075'
publication_status: published
publisher: Society for Industrial and Applied Mathematics
quality_controlled: '1'
related_material:
record:
- id: '3267'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Hardness results for homology localization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '2409'
abstract:
- lang: eng
text: "Background: The availability of many gene alignments with overlapping taxon
sets raises the question of which strategy is the best to infer species phylogenies
from multiple gene information. Methods and programs abound that use the gene
alignment in different ways to reconstruct the species tree. In particular, different
methods combine the original data at different points along the way from the underlying
sequences to the final tree. Accordingly, they are classified into superalignment,
supertree and medium-level approaches. Here, we present a simulation study to
compare different methods from each of these three approaches.\r\n\r\nResults:
We observe that superalignment methods usually outperform the other approaches
over a wide range of parameters including sparse data and gene-specific evolutionary
parameters. In the presence of high incongruency among gene trees, however, other
combination methods show better performance than the superalignment approach.
Surprisingly, some supertree and medium-level methods exhibit, on average, worse
results than a single gene phylogeny with complete taxon information.\r\n\r\nConclusions:
For some methods, using the reconstructed gene tree as an estimation of the species
tree is superior to the combination of incomplete information. Superalignment
usually performs best since it is less susceptible to stochastic error. Supertree
methods can outperform superalignment in the presence of gene-tree conflict."
acknowledgement: Financial support from the Wiener Wissenschafts-, Forschungs- and
Technologiefonds (WWTF) is greatly appreciated. A.v.H. acknowledges support from
the German Research Foundation (DFG, SPP-1174).
article_number: '37'
author:
- first_name: Anne
full_name: Kupczok, Anne
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Heiko
full_name: Schmidt, Heiko
last_name: Schmidt
- first_name: Arndt
full_name: Von Haeseler, Arndt
last_name: Von Haeseler
citation:
ama: Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets . Algorithms for Molecular Biology.
2010;5(1). doi:10.1186/1748-7188-5-37
apa: Kupczok, A., Schmidt, H., & Von Haeseler, A. (2010). Accuracy of phylogeny
reconstruction methods combining overlapping gene data sets . Algorithms for
Molecular Biology. BioMed Central. https://doi.org/10.1186/1748-7188-5-37
chicago: Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny
Reconstruction Methods Combining Overlapping Gene Data Sets .” Algorithms for
Molecular Biology. BioMed Central, 2010. https://doi.org/10.1186/1748-7188-5-37.
ieee: A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets ,” Algorithms for Molecular Biology,
vol. 5, no. 1. BioMed Central, 2010.
ista: Kupczok A, Schmidt H, Von Haeseler A. 2010. Accuracy of phylogeny reconstruction
methods combining overlapping gene data sets . Algorithms for Molecular Biology.
5(1), 37.
mla: Kupczok, Anne, et al. “Accuracy of Phylogeny Reconstruction Methods Combining
Overlapping Gene Data Sets .” Algorithms for Molecular Biology, vol. 5,
no. 1, 37, BioMed Central, 2010, doi:10.1186/1748-7188-5-37.
short: A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology
5 (2010).
date_created: 2018-12-11T11:57:30Z
date_published: 2010-12-06T00:00:00Z
date_updated: 2021-01-12T06:57:18Z
day: '06'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1748-7188-5-37
file:
- access_level: open_access
checksum: e2497285388bc4da629bafb46662eb43
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:16Z
date_updated: 2020-07-14T12:45:40Z
file_id: '4739'
file_name: IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf
file_size: 723929
relation: main_file
file_date_updated: 2020-07-14T12:45:40Z
has_accepted_license: '1'
intvolume: ' 5'
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Algorithms for Molecular Biology
publication_status: published
publisher: BioMed Central
publist_id: '4517'
pubrep_id: '939'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Accuracy of phylogeny reconstruction methods combining overlapping gene data
sets '
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: 5
year: '2010'
...
---
_id: '474'
abstract:
- lang: eng
text: 'Classical models of gene flow fail in three ways: they cannot explain large-scale
patterns; they predict much more genetic diversity than is observed; and they
assume that loosely linked genetic loci evolve independently. We propose a new
model that deals with these problems. Extinction events kill some fraction of
individuals in a region. These are replaced by offspring from a small number of
parents, drawn from the preexisting population. This model of evolution forwards
in time corresponds to a backwards model, in which ancestral lineages jump to
a new location if they are hit by an event, and may coalesce with other lineages
that are hit by the same event. We derive an expression for the identity in allelic
state, and show that, over scales much larger than the largest event, this converges
to the classical value derived by Wright and Malécot. However, rare events that
cover large areas cause low genetic diversity, large-scale patterns, and correlations
in ancestry between unlinked loci.'
acknowledgement: This work has made use of the resources provided by the Edinburgh
Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative.
NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant
EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: 'Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization
in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715.
doi:10.1111/j.1558-5646.2010.01019.x'
apa: 'Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography. Evolution.
Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x'
chicago: 'Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model
for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.”
Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.'
ieee: 'N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction
and recolonization in two dimensions: Quantifying phylogeography,” Evolution,
vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.'
ista: 'Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and
recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9),
2701–2715.'
mla: 'Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization
in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no.
9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.'
short: N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.
date_created: 2018-12-11T11:46:40Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2021-01-12T08:00:52Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/j.1558-5646.2010.01019.x
intvolume: ' 64'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 2701 - 2715
publication: Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2780'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'A new model for extinction and recolonization in two dimensions: Quantifying
phylogeography'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2010'
...
---
_id: '488'
abstract:
- lang: eng
text: 'Streaming string transducers [1] define (partial) functions from input strings
to output strings. A streaming string transducer makes a single pass through the
input string and uses a finite set of variables that range over strings from the
output alphabet. At every step, the transducer processes an input symbol, and
updates all the variables in parallel using assignments whose right-hand-sides
are concatenations of output symbols and variables with the restriction that a
variable can be used at most once in a right-hand-side expression. It has been
shown that streaming string transducers operating on strings over infinite data
domains are of interest in algorithmic verification of list-processing programs,
as they lead to PSPACE decision procedures for checking pre/post conditions and
for checking semantic equivalence, for a well-defined class of heap-manipulating
programs. In order to understand the theoretical expressiveness of streaming transducers,
we focus on streaming transducers processing strings over finite alphabets, given
the existence of a robust and well-studied class of "regular" transductions
for this case. Such regular transductions can be defined either by two-way deterministic
finite-state transducers, or using a logical MSO-based characterization. Our main
result is that the expressiveness of streaming string transducers coincides exactly
with this class of regular transductions. '
alternative_title:
- LIPIcs
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Pavol
full_name: Cerny, Pavol
id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87
last_name: Cerny
citation:
ama: 'Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:10.4230/LIPIcs.FSTTCS.2010.1'
apa: 'Alur, R., & Cerny, P. (2010). Expressiveness of streaming string transducers
(Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology
and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum
für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1'
chicago: Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,”
8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1.
ieee: 'R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented
at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science,
Chennai, India, 2010, vol. 8, pp. 1–12.'
ista: 'Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS:
Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol.
8, 1–12.'
mla: Alur, Rajeev, and Pavol Cerny. Expressiveness of Streaming String Transducers.
Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:10.4230/LIPIcs.FSTTCS.2010.1.
short: R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2010, pp. 1–12.
conference:
end_date: 2010-12-18
location: Chennai, India
name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science'
start_date: 2010-12-15
date_created: 2018-12-11T11:46:45Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T08:01:00Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.FSTTCS.2010.1
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title: Expressiveness of streaming string transducers
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