---
_id: '3996'
abstract:
- lang: eng
text: We formalize a notion of topological simplification within the framework of
a filtration, which is the history of a growing complex. We classify a topological
change that happens during growth as either a feature or noise depending on its
lifetime or persistence within the filtration. We give fast algorithms for computing
persistence and experimental evidence for their speed and utility.
acknowledgement: "We thank Jeff Erickson and John Harer for helpful discussions during
early stages of this\r\npaper. We also thank Daniel Huson for the zeolite dataset
Z, Thomas LaBean for the DNA\r\ndataset D, and the Stanford Graphics Lab for the
Buddha dataset S. To generate the bone\r\ndataset B, we sampled an iso-surface generated
by Dominique Attali. The volume data\r\nTopological Persistence and Simplification
533 was provided by Francoise Peyrin from CNRS CREATIS in Lyon and was issued from
¸ Synchrotron Radiation Microtomography from the ID19 beamline at ESRF in Grenoble.\r\nWe
generated Fig. 17 using the Protein Explorer [6]."
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: David
full_name: Letscher, David
last_name: Letscher
- first_name: Afra
full_name: Zomorodian, Afra
last_name: Zomorodian
citation:
ama: Edelsbrunner H, Letscher D, Zomorodian A. Topological persistence and simplification.
Discrete & Computational Geometry. 2002;28(4):511-533. doi:10.1007/s00454-002-2885-2
apa: Edelsbrunner, H., Letscher, D., & Zomorodian, A. (2002). Topological persistence
and simplification. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-002-2885-2
chicago: Edelsbrunner, Herbert, David Letscher, and Afra Zomorodian. “Topological
Persistence and Simplification.” Discrete & Computational Geometry.
Springer, 2002. https://doi.org/10.1007/s00454-002-2885-2.
ieee: H. Edelsbrunner, D. Letscher, and A. Zomorodian, “Topological persistence
and simplification,” Discrete & Computational Geometry, vol. 28, no.
4. Springer, pp. 511–533, 2002.
ista: Edelsbrunner H, Letscher D, Zomorodian A. 2002. Topological persistence and
simplification. Discrete & Computational Geometry. 28(4), 511–533.
mla: Edelsbrunner, Herbert, et al. “Topological Persistence and Simplification.”
Discrete & Computational Geometry, vol. 28, no. 4, Springer, 2002,
pp. 511–33, doi:10.1007/s00454-002-2885-2.
short: H. Edelsbrunner, D. Letscher, A. Zomorodian, Discrete & Computational
Geometry 28 (2002) 511–533.
date_created: 2018-12-11T12:06:20Z
date_published: 2002-12-01T00:00:00Z
date_updated: 2023-06-13T11:41:19Z
day: '01'
doi: 10.1007/s00454-002-2885-2
extern: '1'
intvolume: ' 28'
issue: '4'
language:
- iso: eng
month: '12'
oa_version: None
page: 511 - 533
publication: Discrete & Computational Geometry
publication_identifier:
issn:
- 0179-5376
publication_status: published
publisher: Springer
publist_id: '2130'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topological persistence and simplification
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 28
year: '2002'
...
---
_id: '3998'
abstract:
- lang: eng
text: We present results on a two-step improvement of mesh quality in three-dimensional
Delaunay triangulations. The first step refines the triangulation by inserting
sinks and eliminates tetrahedra with large circumradius over shortest edge length
ratio. The second step assigns weights to the vertices to eliminate slivers. Our
experimental findings provide evidence for the practical effectiveness of sliver
exudation.
acknowledgement: NSF under grants CCR-97-12088 and DMS 98-73945, NSF under grands
EIA-9972879 and CCR-00-86013 and by ARO under grant DAAG55-98-1- 0177.
article_processing_charge: No
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Damrong
full_name: Guoy, Damrong
last_name: Guoy
citation:
ama: Edelsbrunner H, Guoy D. An experimental study of sliver exudation. Engineering
with Computers. 2002;18(3):229-240. doi:10.1007/s003660200020
apa: Edelsbrunner, H., & Guoy, D. (2002). An experimental study of sliver exudation.
Engineering with Computers. Springer. https://doi.org/10.1007/s003660200020
chicago: Edelsbrunner, Herbert, and Damrong Guoy. “An Experimental Study of Sliver
Exudation.” Engineering with Computers. Springer, 2002. https://doi.org/10.1007/s003660200020.
ieee: H. Edelsbrunner and D. Guoy, “An experimental study of sliver exudation,”
Engineering with Computers, vol. 18, no. 3. Springer, pp. 229–240, 2002.
ista: Edelsbrunner H, Guoy D. 2002. An experimental study of sliver exudation. Engineering
with Computers. 18(3), 229–240.
mla: Edelsbrunner, Herbert, and Damrong Guoy. “An Experimental Study of Sliver Exudation.”
Engineering with Computers, vol. 18, no. 3, Springer, 2002, pp. 229–40,
doi:10.1007/s003660200020.
short: H. Edelsbrunner, D. Guoy, Engineering with Computers 18 (2002) 229–240.
date_created: 2018-12-11T12:06:21Z
date_published: 2002-10-01T00:00:00Z
date_updated: 2023-06-13T11:14:44Z
day: '01'
doi: 10.1007/s003660200020
extern: '1'
intvolume: ' 18'
issue: '3'
language:
- iso: eng
month: '10'
oa_version: None
page: 229 - 240
publication: Engineering with Computers
publication_identifier:
issn:
- 0177-0667
publication_status: published
publisher: Springer
publist_id: '2126'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An experimental study of sliver exudation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 18
year: '2002'
...
---
_id: '4000'
abstract:
- lang: eng
text: We present fast implementations of a hybrid algorithm for reporting box and
cube intersections. Our algorithm initially takes a divide-and-conquer approach
and switches to simpler algorithms for low numbers of boxes. We use our implementations
as engines to solve problems about geometric primitives. We look at two such problems
in the category of quality analysis of surface triangulations.
acknowledgement: Center for Simulation of Advanced Rockets funded by the U.S. Department
of Energy under Subcontract B341494, NSF under grant CCR-96-19542 and ARO under
grant DAAG55-98-1-0177.
article_processing_charge: No
article_type: original
author:
- first_name: Afra
full_name: Zomorodian, Afra
last_name: Zomorodian
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Zomorodian A, Edelsbrunner H. Fast software for box intersections. International
Journal of Computational Geometry and Applications. 2002;12(1-2):143-172.
doi:10.1142/S0218195902000785
apa: Zomorodian, A., & Edelsbrunner, H. (2002). Fast software for box intersections.
International Journal of Computational Geometry and Applications. World
Scientific Publishing. https://doi.org/10.1142/S0218195902000785
chicago: Zomorodian, Afra, and Herbert Edelsbrunner. “Fast Software for Box Intersections.”
International Journal of Computational Geometry and Applications. World
Scientific Publishing, 2002. https://doi.org/10.1142/S0218195902000785.
ieee: A. Zomorodian and H. Edelsbrunner, “Fast software for box intersections,”
International Journal of Computational Geometry and Applications, vol.
12, no. 1–2. World Scientific Publishing, pp. 143–172, 2002.
ista: Zomorodian A, Edelsbrunner H. 2002. Fast software for box intersections. International
Journal of Computational Geometry and Applications. 12(1–2), 143–172.
mla: Zomorodian, Afra, and Herbert Edelsbrunner. “Fast Software for Box Intersections.”
International Journal of Computational Geometry and Applications, vol.
12, no. 1–2, World Scientific Publishing, 2002, pp. 143–72, doi:10.1142/S0218195902000785.
short: A. Zomorodian, H. Edelsbrunner, International Journal of Computational Geometry
and Applications 12 (2002) 143–172.
date_created: 2018-12-11T12:06:22Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-06-13T11:20:09Z
day: '01'
doi: 10.1142/S0218195902000785
extern: '1'
intvolume: ' 12'
issue: 1-2
language:
- iso: eng
month: '01'
oa_version: None
page: 143 - 172
publication: International Journal of Computational Geometry and Applications
publication_identifier:
issn:
- 0218-1959
publication_status: published
publisher: World Scientific Publishing
publist_id: '2128'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fast software for box intersections
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 12
year: '2002'
...
---
_id: '4003'
abstract:
- lang: eng
text: The writhing number measures the global geometry of a closed space curve or
knot. We show that this measure is related to the average winding number of its
Gauss map. Using this relationship, we give an algorithm for computing the writhing
number for a polygonal knot with n edges in time roughly proportional to n(1.6).
We also implement a different, simple algorithm and provide experimental evidence
for its practical efficiency.
acknowledgement: NSF under grants CCR-00-86013 and EIA-9972879, NSF under grant CCR-97-12088.
article_processing_charge: No
author:
- first_name: Pankaj
full_name: Agarwal, Pankaj
last_name: Agarwal
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: 'Agarwal P, Edelsbrunner H, Wang Y. Computing the writhing number of a polygonal
knot. In: Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms.
SIAM; 2002:791-799.'
apa: 'Agarwal, P., Edelsbrunner, H., & Wang, Y. (2002). Computing the writhing
number of a polygonal knot. In Proceedings of the 13th annual ACM-SIAM symposium
on Discrete algorithms (pp. 791–799). San Francisco, CA, USA: SIAM.'
chicago: Agarwal, Pankaj, Herbert Edelsbrunner, and Yusu Wang. “Computing the Writhing
Number of a Polygonal Knot.” In Proceedings of the 13th Annual ACM-SIAM Symposium
on Discrete Algorithms, 791–99. SIAM, 2002.
ieee: P. Agarwal, H. Edelsbrunner, and Y. Wang, “Computing the writhing number of
a polygonal knot,” in Proceedings of the 13th annual ACM-SIAM symposium on
Discrete algorithms, San Francisco, CA, USA, 2002, pp. 791–799.
ista: 'Agarwal P, Edelsbrunner H, Wang Y. 2002. Computing the writhing number of
a polygonal knot. Proceedings of the 13th annual ACM-SIAM symposium on Discrete
algorithms. SODA: Symposium on Discrete Algorithms, 791–799.'
mla: Agarwal, Pankaj, et al. “Computing the Writhing Number of a Polygonal Knot.”
Proceedings of the 13th Annual ACM-SIAM Symposium on Discrete Algorithms,
SIAM, 2002, pp. 791–99.
short: P. Agarwal, H. Edelsbrunner, Y. Wang, in:, Proceedings of the 13th Annual
ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2002, pp. 791–799.
conference:
end_date: 2002-01-08
location: San Francisco, CA, USA
name: 'SODA: Symposium on Discrete Algorithms'
start_date: 2002-01-06
date_created: 2018-12-11T12:06:23Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-06-07T13:50:04Z
day: '01'
extern: '1'
language:
- iso: eng
main_file_link:
- url: https://dl.acm.org/doi/10.5555/545381.545485
month: '01'
oa_version: None
page: 791 - 799
publication: Proceedings of the 13th annual ACM-SIAM symposium on Discrete algorithms
publication_identifier:
isbn:
- '9780898715132'
publication_status: published
publisher: SIAM
publist_id: '2125'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Computing the writhing number of a polygonal knot
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '2002'
...
---
_id: '4139'
abstract:
- lang: eng
text: Pilot studies in England by Stopka and Macdonald revealed that allogrooming
in the Old World wood mouse, Apodemus sylvaticus, is a commodity that males can
trade for reproductive benefits with females. This study, which used a combination
of field study and observations in experimental enclosures, revealed that specific
experimental conditions such as group-size and sex-ratio manipulations have a
significant effect on the pattern of allogrooming exchanged between individuals.
Furthermore, females from the Czech population were more likely to associate with
each other as revealed by the clustering of activity centers of females (i.e.,
as opposed to almost exclusive ranges in English populations), and also by the
higher intensity of allogrooming exchanged between females (i.e., virtually lacking
in the previous experiment with English mice). Therefore, geographic variation
and specific social conditions seem to be important driving factors for allogrooming
behavior. Together with changes in overall grooming patterns, allogrooming between
males and females remained invariably asymmetrical over all four experimental
groups (i.e., two conditions for each sex) in that males provided more allogrooming
to females than they received from them.
article_processing_charge: No
article_type: original
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
- first_name: P.
full_name: Stopka, P.
last_name: Stopka
citation:
ama: Polechova J, Stopka P. Geometry of social relationships in the Old World wood
mouse, Apodemus sylvaticus. Canadian Journal of Zoology. 2002;80(8):1383-1388.
doi:10.1139/z02-128
apa: Polechova, J., & Stopka, P. (2002). Geometry of social relationships in
the Old World wood mouse, Apodemus sylvaticus. Canadian Journal of Zoology.
NRC Research Press. https://doi.org/10.1139/z02-128
chicago: Polechova, Jitka, and P. Stopka. “Geometry of Social Relationships in the
Old World Wood Mouse, Apodemus Sylvaticus.” Canadian Journal of Zoology.
NRC Research Press, 2002. https://doi.org/10.1139/z02-128.
ieee: J. Polechova and P. Stopka, “Geometry of social relationships in the Old World
wood mouse, Apodemus sylvaticus,” Canadian Journal of Zoology, vol. 80,
no. 8. NRC Research Press, pp. 1383–1388, 2002.
ista: Polechova J, Stopka P. 2002. Geometry of social relationships in the Old World
wood mouse, Apodemus sylvaticus. Canadian Journal of Zoology. 80(8), 1383–1388.
mla: Polechova, Jitka, and P. Stopka. “Geometry of Social Relationships in the Old
World Wood Mouse, Apodemus Sylvaticus.” Canadian Journal of Zoology, vol.
80, no. 8, NRC Research Press, 2002, pp. 1383–88, doi:10.1139/z02-128.
short: J. Polechova, P. Stopka, Canadian Journal of Zoology 80 (2002) 1383–1388.
date_created: 2018-12-11T12:07:10Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-06-07T12:53:35Z
day: '01'
doi: 10.1139/z02-128
extern: '1'
intvolume: ' 80'
issue: '8'
language:
- iso: eng
month: '01'
oa_version: None
page: 1383 - 1388
publication: Canadian Journal of Zoology
publication_identifier:
issn:
- 0008-4301
publication_status: published
publisher: NRC Research Press
publist_id: '1981'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometry of social relationships in the Old World wood mouse, Apodemus sylvaticus
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 80
year: '2002'
...
---
_id: '4148'
abstract:
- lang: eng
text: Members of the Wnt family have been implicated in a variety of developmental
processes including axis formation, Patterning of the central nervous system and
tissue morphogenesis. Recent studies have shown that a Wnt signalling pathway
similar to that involved in the establishment of planar cell polarity in Drosophila
regulates convergent extension movements during zebrafish and Xenopus gastrulation.
This finding provides a good starting point to dissect the complex cell biology
and genetic regulation of vertebrate gastrulation movements.
acknowledgement: We would like to thank Steve Wilson for encouraging us to write this
article and for critical comments on this manuscript, and Lila Solnica-Krezel for
communicating results prior to publication. MT is supported by an MRC Career Development
Award, MLC by a Wellcome Trust Fellowship and CPH by an Emmy–Noether–Fellowship
from the DFG.
article_processing_charge: No
article_type: original
author:
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- first_name: Miguel
full_name: Concha, Miguel
last_name: Concha
- 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: Tada M, Concha M, Heisenberg C-PJ. Non-canonical Wnt signalling and regulation
of gastrulation movements. Seminars in Cell & Developmental Biology.
2002;13(3):251-260. doi:10.1016/S1084-9521(02)00052-6
apa: Tada, M., Concha, M., & Heisenberg, C.-P. J. (2002). Non-canonical Wnt
signalling and regulation of gastrulation movements. Seminars in Cell &
Developmental Biology. Academic Press. https://doi.org/10.1016/S1084-9521(02)00052-6
chicago: Tada, Masazumi, Miguel Concha, and Carl-Philipp J Heisenberg. “Non-Canonical
Wnt Signalling and Regulation of Gastrulation Movements.” Seminars in Cell
& Developmental Biology. Academic Press, 2002. https://doi.org/10.1016/S1084-9521(02)00052-6.
ieee: M. Tada, M. Concha, and C.-P. J. Heisenberg, “Non-canonical Wnt signalling
and regulation of gastrulation movements,” Seminars in Cell & Developmental
Biology, vol. 13, no. 3. Academic Press, pp. 251–260, 2002.
ista: Tada M, Concha M, Heisenberg C-PJ. 2002. Non-canonical Wnt signalling and
regulation of gastrulation movements. Seminars in Cell & Developmental Biology.
13(3), 251–260.
mla: Tada, Masazumi, et al. “Non-Canonical Wnt Signalling and Regulation of Gastrulation
Movements.” Seminars in Cell & Developmental Biology, vol. 13, no.
3, Academic Press, 2002, pp. 251–60, doi:10.1016/S1084-9521(02)00052-6.
short: M. Tada, M. Concha, C.-P.J. Heisenberg, Seminars in Cell & Developmental
Biology 13 (2002) 251–260.
date_created: 2018-12-11T12:07:13Z
date_published: 2002-06-01T00:00:00Z
date_updated: 2023-06-07T09:50:14Z
day: '01'
doi: 10.1016/S1084-9521(02)00052-6
extern: '1'
external_id:
pmid:
- '12137734'
intvolume: ' 13'
issue: '3'
language:
- iso: eng
month: '06'
oa_version: None
page: 251 - 260
pmid: 1
publication: Seminars in Cell & Developmental Biology
publication_identifier:
issn:
- 1084-9521
publication_status: published
publisher: Academic Press
publist_id: '1973'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Non-canonical Wnt signalling and regulation of gastrulation movements
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 13
year: '2002'
...
---
_id: '4194'
abstract:
- lang: eng
text: Cells at the anterior boundary of the neural plate (ANB) can induce telencephalic
gene expression when transplanted to more posterior regions. Here, we identify
a secreted Frizzled-related Wnt antagonist, Tic, that is expressed in ANB cells
and can cell nonautonomously promote telencephalic gene expression in a concentration-dependent
manner. Moreover, abrogation of Tlc function compromises telencephalic development.
We also identify Wnt8b as a locally acting modulator of regional fate in the anterior
neural plate and a likely target for antagonism by Tic. Finally, we show that
tlc expression is regulated by signals that establish early antero-posterior and
dorso-ventral ectodermal pattern. From these studies, we propose that local antagonism
of Wnt activity within the anterior ectoderm is required to establish the telencephalon.
acknowledgement: We thank many of our colleagues, especially Randy Moon, for providing reagents used
in this study. This study was supported by the Wellcome Trust, MRC, and BBSRC to
S.W.W. and C.H. S.W.W. is a Wellcome Trust Senior Research Fellow.
article_processing_charge: No
article_type: original
author:
- first_name: Corinne
full_name: Houart, Corinne
last_name: Houart
- first_name: Luca
full_name: Caneparo, Luca
last_name: Caneparo
- 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: K Anukampa
full_name: Barth, K Anukampa
last_name: Barth
- first_name: Masaya
full_name: Take Uchi, Masaya
last_name: Take Uchi
- first_name: Stephen
full_name: Wilson, Stephen
last_name: Wilson
citation:
ama: Houart C, Caneparo L, Heisenberg C-PJ, Barth KA, Take Uchi M, Wilson S. Establishment
of the telencephalon during gastrulation by local antagonism of Wnt signaling.
Neuron. 2002;35(2):255-265. doi:10.1016/S0896-6273(02)00751-1
apa: Houart, C., Caneparo, L., Heisenberg, C.-P. J., Barth, K. A., Take Uchi, M.,
& Wilson, S. (2002). Establishment of the telencephalon during gastrulation
by local antagonism of Wnt signaling. Neuron. Elsevier. https://doi.org/10.1016/S0896-6273(02)00751-1
chicago: Houart, Corinne, Luca Caneparo, Carl-Philipp J Heisenberg, K Anukampa Barth,
Masaya Take Uchi, and Stephen Wilson. “Establishment of the Telencephalon during
Gastrulation by Local Antagonism of Wnt Signaling.” Neuron. Elsevier, 2002.
https://doi.org/10.1016/S0896-6273(02)00751-1.
ieee: C. Houart, L. Caneparo, C.-P. J. Heisenberg, K. A. Barth, M. Take Uchi, and
S. Wilson, “Establishment of the telencephalon during gastrulation by local antagonism
of Wnt signaling,” Neuron, vol. 35, no. 2. Elsevier, pp. 255–265, 2002.
ista: Houart C, Caneparo L, Heisenberg C-PJ, Barth KA, Take Uchi M, Wilson S. 2002.
Establishment of the telencephalon during gastrulation by local antagonism of
Wnt signaling. Neuron. 35(2), 255–265.
mla: Houart, Corinne, et al. “Establishment of the Telencephalon during Gastrulation
by Local Antagonism of Wnt Signaling.” Neuron, vol. 35, no. 2, Elsevier,
2002, pp. 255–65, doi:10.1016/S0896-6273(02)00751-1.
short: C. Houart, L. Caneparo, C.-P.J. Heisenberg, K.A. Barth, M. Take Uchi, S.
Wilson, Neuron 35 (2002) 255–265.
date_created: 2018-12-11T12:07:30Z
date_published: 2002-07-18T00:00:00Z
date_updated: 2023-06-07T09:43:19Z
day: '18'
doi: 10.1016/S0896-6273(02)00751-1
extern: '1'
external_id:
pmid:
- '12160744'
intvolume: ' 35'
issue: '2'
language:
- iso: eng
month: '07'
oa_version: None
page: 255 - 265
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
publist_id: '1925'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Establishment of the telencephalon during gastrulation by local antagonism
of Wnt signaling
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 35
year: '2002'
...
---
_id: '4196'
abstract:
- lang: eng
text: During vertebrate gastrulation, large cellular rearrangements lead to the
formation of the three germ layers, ectoderm, mesoderm and endoderm. Zebrafish
offer many genetic and experimental advantages for studying vertebrate gastrulation
movements. For instance, several mutants, including silberblick, knypek and trilobite,
exhibit defects in morphogenesis during gastrulation. The identification of the
genes mutated in these lines together with the analysis of the mutant phenotypes
has provided new insights into the molecular and cellular mechanisms that underlie
vertebrate gastrulation movements.
acknowledgement: We would like to thank Miguel Concha, Will Norton, Tim Geach, Suzanne
Eaton, Kimbo Kotovic, Jenny Geiger and Steve Wilson for critical comments on this
manuscript, and Lila Solnica-Krezel for providing results prior to publication.
C.-P.H. is supported by an Emmy-Noether-Fellowship from the DFG and M.T. by an MRC
Career Development Award.
article_processing_charge: No
article_type: original
author:
- 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: Masazumi
full_name: Tada, Masazumi
last_name: Tada
citation:
ama: 'Heisenberg C-PJ, Tada M. Zebrafish gastrulation movements: bridging cell and
developmental biology. Seminars in Cell & Developmental Biology. 2002;13(6):471-479.
doi:10.1016/S1084952102001003'
apa: 'Heisenberg, C.-P. J., & Tada, M. (2002). Zebrafish gastrulation movements:
bridging cell and developmental biology. Seminars in Cell & Developmental
Biology. Academic Press. https://doi.org/10.1016/S1084952102001003'
chicago: 'Heisenberg, Carl-Philipp J, and Masazumi Tada. “Zebrafish Gastrulation
Movements: Bridging Cell and Developmental Biology.” Seminars in Cell &
Developmental Biology. Academic Press, 2002. https://doi.org/10.1016/S1084952102001003.'
ieee: 'C.-P. J. Heisenberg and M. Tada, “Zebrafish gastrulation movements: bridging
cell and developmental biology,” Seminars in Cell & Developmental Biology,
vol. 13, no. 6. Academic Press, pp. 471–479, 2002.'
ista: 'Heisenberg C-PJ, Tada M. 2002. Zebrafish gastrulation movements: bridging
cell and developmental biology. Seminars in Cell & Developmental Biology.
13(6), 471–479.'
mla: 'Heisenberg, Carl-Philipp J., and Masazumi Tada. “Zebrafish Gastrulation Movements:
Bridging Cell and Developmental Biology.” Seminars in Cell & Developmental
Biology, vol. 13, no. 6, Academic Press, 2002, pp. 471–79, doi:10.1016/S1084952102001003.'
short: C.-P.J. Heisenberg, M. Tada, Seminars in Cell & Developmental Biology
13 (2002) 471–479.
date_created: 2018-12-11T12:07:31Z
date_published: 2002-12-01T00:00:00Z
date_updated: 2023-06-07T09:28:48Z
day: '01'
doi: 10.1016/S1084952102001003
extern: '1'
external_id:
pmid:
- '12468250'
intvolume: ' 13'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 471 - 479
pmid: 1
publication: Seminars in Cell & Developmental Biology
publication_identifier:
issn:
- 1084-9521
publication_status: published
publisher: Academic Press
publist_id: '1920'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Zebrafish gastrulation movements: bridging cell and developmental biology'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 13
year: '2002'
...
---
_id: '4199'
abstract:
- lang: eng
text: Recent studies on vertebrate homologues of the van gogh/strabismus (vang/stbm)
gene, a key player in planar cell polarity signalling in Drosophila, show that
vang/stbm is involved in patterning and morphogenesis during vertebrate gastrulation
where it modulates two distinct Wnt signals.
article_processing_charge: No
article_type: original
author:
- 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: Masazumi
full_name: Tada, Masazumi
last_name: Tada
citation:
ama: 'Heisenberg C-PJ, Tada M. Wnt signalling: A moving picture emerges from van
gogh. Current Biology. 2002;12(4):R126-R128. doi:10.1016/S0960-9822(02)00704-2'
apa: 'Heisenberg, C.-P. J., & Tada, M. (2002). Wnt signalling: A moving picture
emerges from van gogh. Current Biology. Cell Press. https://doi.org/10.1016/S0960-9822(02)00704-2'
chicago: 'Heisenberg, Carl-Philipp J, and Masazumi Tada. “Wnt Signalling: A Moving
Picture Emerges from van Gogh.” Current Biology. Cell Press, 2002. https://doi.org/10.1016/S0960-9822(02)00704-2.'
ieee: 'C.-P. J. Heisenberg and M. Tada, “Wnt signalling: A moving picture emerges
from van gogh,” Current Biology, vol. 12, no. 4. Cell Press, pp. R126–R128,
2002.'
ista: 'Heisenberg C-PJ, Tada M. 2002. Wnt signalling: A moving picture emerges from
van gogh. Current Biology. 12(4), R126–R128.'
mla: 'Heisenberg, Carl-Philipp J., and Masazumi Tada. “Wnt Signalling: A Moving
Picture Emerges from van Gogh.” Current Biology, vol. 12, no. 4, Cell Press,
2002, pp. R126–28, doi:10.1016/S0960-9822(02)00704-2.'
short: C.-P.J. Heisenberg, M. Tada, Current Biology 12 (2002) R126–R128.
date_created: 2018-12-11T12:07:32Z
date_published: 2002-02-19T00:00:00Z
date_updated: 2023-06-07T08:54:35Z
day: '19'
doi: 10.1016/S0960-9822(02)00704-2
extern: '1'
external_id:
pmid:
- '11864583'
intvolume: ' 12'
issue: '4'
language:
- iso: eng
month: '02'
oa_version: None
page: R126 - R128
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
publist_id: '1919'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Wnt signalling: A moving picture emerges from van gogh'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 12
year: '2002'
...
---
_id: '4207'
abstract:
- lang: eng
text: Vertebrate homologues of the Strabismus/van Gogh (stbm/vang) gene have been
implicated in patterning and morphogenesis during gastrulation. Recent work shows
that stbm/vang is mutated in zebrafish trilobite mutants and that stbm/vang is
required for morphogenesis but not patterning during zebrafish gastrulation.
article_processing_charge: No
article_type: original
author:
- 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: 'Heisenberg C-PJ. Wnt signalling: Refocusing on Strabismus. Current Biology.
2002;12(19):R657-R659. doi:10.1016/S0960-9822(02)01160-0'
apa: 'Heisenberg, C.-P. J. (2002). Wnt signalling: Refocusing on Strabismus. Current
Biology. Cell Press. https://doi.org/10.1016/S0960-9822(02)01160-0'
chicago: 'Heisenberg, Carl-Philipp J. “Wnt Signalling: Refocusing on Strabismus.”
Current Biology. Cell Press, 2002. https://doi.org/10.1016/S0960-9822(02)01160-0.'
ieee: 'C.-P. J. Heisenberg, “Wnt signalling: Refocusing on Strabismus,” Current
Biology, vol. 12, no. 19. Cell Press, pp. R657–R659, 2002.'
ista: 'Heisenberg C-PJ. 2002. Wnt signalling: Refocusing on Strabismus. Current
Biology. 12(19), R657–R659.'
mla: 'Heisenberg, Carl-Philipp J. “Wnt Signalling: Refocusing on Strabismus.” Current
Biology, vol. 12, no. 19, Cell Press, 2002, pp. R657–59, doi:10.1016/S0960-9822(02)01160-0.'
short: C.-P.J. Heisenberg, Current Biology 12 (2002) R657–R659.
date_created: 2018-12-11T12:07:35Z
date_published: 2002-10-01T00:00:00Z
date_updated: 2023-06-06T15:09:53Z
day: '01'
doi: 10.1016/S0960-9822(02)01160-0
extern: '1'
external_id:
pmid:
- '12361585'
intvolume: ' 12'
issue: '19'
language:
- iso: eng
month: '10'
oa_version: None
page: R657 - R659
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Cell Press
publist_id: '1912'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Wnt signalling: Refocusing on Strabismus'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 12
year: '2002'
...
---
_id: '4209'
abstract:
- lang: eng
text: We have identified widerborst (wdb), a B' regulatory subunit of PP2A, as a
conserved component of planar cell polarization mechanisms in both Drosophila
and in zebrafish. In Drosophila, wdb acts at two steps during planar polarization
of wing epithelial cells. It is required to organize tissue polarity proteins
into proximal and distal cortical domains, thus determining wing hair orientation.
It is also needed to generate the polarized membrane outgrowth that becomes the
wing hair. Widerborst activates the catalytic subunit of PP2A and localizes to
the distal side of a planar microtubule web that lies at the level of apical cell
junctions. This suggests that polarized PP2A activation along the planar microtubule
web is important for planar polarization. In zebrafish, two wdb homologs are required
for convergent extension during gastrulation, supporting the conjecture that Drosophila
planar cell polarization and vertebrate gastrulation movements are regulated by
similar mechanisms.
acknowledgement: We gratefully acknowledge Bianca Habermann for assistance with bioinformatics,
Jens Rietdorf and Arshad Desai for help with deconvolution, and Tadashi Uemura and
Rick Fehon for providing antibodies. Arshad Desai, Christian Dahmann, Tony Hyman
and Elly Tanaka provided helpful comments on the manuscript. Part of this work was
performed at the EMBL in Heidelberg.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Hannus, Michael
last_name: Hannus
- first_name: Fabian
full_name: Feiguin, Fabian
last_name: Feiguin
- 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: Suzanne
full_name: Eaton, Suzanne
last_name: Eaton
citation:
ama: Hannus M, Feiguin F, Heisenberg C-PJ, Eaton S. Planar cell polarization requires
Widerborst, a B′ regulatory subunit of protein phosphatase 2A. Development.
2002;129(14):3493-3503. doi:10.1242/dev.129.14.3493
apa: Hannus, M., Feiguin, F., Heisenberg, C.-P. J., & Eaton, S. (2002). Planar
cell polarization requires Widerborst, a B′ regulatory subunit of protein phosphatase
2A. Development. Company of Biologists. https://doi.org/10.1242/dev.129.14.3493
chicago: Hannus, Michael, Fabian Feiguin, Carl-Philipp J Heisenberg, and Suzanne
Eaton. “Planar Cell Polarization Requires Widerborst, a B′ Regulatory Subunit
of Protein Phosphatase 2A.” Development. Company of Biologists, 2002. https://doi.org/10.1242/dev.129.14.3493.
ieee: M. Hannus, F. Feiguin, C.-P. J. Heisenberg, and S. Eaton, “Planar cell polarization
requires Widerborst, a B′ regulatory subunit of protein phosphatase 2A,” Development,
vol. 129, no. 14. Company of Biologists, pp. 3493–3503, 2002.
ista: Hannus M, Feiguin F, Heisenberg C-PJ, Eaton S. 2002. Planar cell polarization
requires Widerborst, a B′ regulatory subunit of protein phosphatase 2A. Development.
129(14), 3493–3503.
mla: Hannus, Michael, et al. “Planar Cell Polarization Requires Widerborst, a B′
Regulatory Subunit of Protein Phosphatase 2A.” Development, vol. 129, no.
14, Company of Biologists, 2002, pp. 3493–503, doi:10.1242/dev.129.14.3493.
short: M. Hannus, F. Feiguin, C.-P.J. Heisenberg, S. Eaton, Development 129 (2002)
3493–3503.
date_created: 2018-12-11T12:07:36Z
date_published: 2002-07-15T00:00:00Z
date_updated: 2023-06-06T14:07:49Z
day: '15'
doi: 10.1242/dev.129.14.3493
extern: '1'
external_id:
pmid:
- '12091318'
intvolume: ' 129'
issue: '14'
language:
- iso: eng
month: '07'
oa_version: None
page: 3493 - 3503
pmid: 1
publication: Development
publication_identifier:
issn:
- 0950-1991
publication_status: published
publisher: Company of Biologists
publist_id: '1909'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Planar cell polarization requires Widerborst, a B′ regulatory subunit of protein
phosphatase 2A
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 129
year: '2002'
...
---
_id: '4258'
abstract:
- lang: eng
text: We studied the effect of multilocus balancing selection on neutral nucleotide
variability at linked sites by simulating a model where diallelic polymorphisms
are maintained at an arbitrary number of selected loci by means of symmetric overdominance.
Different combinations of alleles define different genetic backgrounds that subdivide
the population and strongly affect variability. Several multilocus fitness regimes
with different degrees of epistasis and gametic disequilibrium are allowed. Analytical
results based on a multilocus extension of the structured coalescent predict that
the expected linked neutral diversity increases exponentially with the number
of selected loci and can become extremely large. Our simulation results show that
although variability increases with the number of genetic backgrounds that are
maintained in the population, it is reduced by random fluctuations in the frequencies
of those backgrounds and does not reach high levels even in very large populations.
We also show that previous results on balancing selection in single-locus systems
do not extend to the multilocus scenario in a straightforward way. Different patterns
of linkage disequilibrium and of the frequency spectrum of neutral mutations are
expected under different degrees of epistasis. Interestingly, the power to detect
balancing selection using deviations from a neutral distribution of allele frequencies
seems to be diminished under the fitness regime that leads to the largest increase
of variability over the neutral case. This and other results are discussed in
the light of data from the Mhc.
acknowledgement: We thank P. Andolfatto, P. Awadalla, B. Charlesworth, D. Charles-
Guillaudeux, T., M. Janer, G. K. S. Wong, T. Spies and D. E. Geraghty, F. Depaulis,
S. Otto, J. Rozas, and three anonymous reviewers for valuable discussion and criticism.
A.N. is grateful to F. Depaulis, whose comments were particularly helpful (and extremely
funny), and to D. Charlesworth, whose ideas made this work readable. This work was
supported by Biotechnology and Biological Sciences Research Council/Engineering
and Physical Sciences Research Council.
article_processing_charge: No
article_type: original
author:
- first_name: Arcadio
full_name: Navarro, Arcadio
last_name: Navarro
- 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: Navarro A, Barton NH. The effects of multilocus balancing selection on neutral
variability. Genetics. 2002;161(2):849-863. doi:10.1093/genetics/161.2.849
apa: Navarro, A., & Barton, N. H. (2002). The effects of multilocus balancing
selection on neutral variability. Genetics. Genetics Society of America.
https://doi.org/10.1093/genetics/161.2.849
chicago: Navarro, Arcadio, and Nicholas H Barton. “The Effects of Multilocus Balancing
Selection on Neutral Variability.” Genetics. Genetics Society of America,
2002. https://doi.org/10.1093/genetics/161.2.849.
ieee: A. Navarro and N. H. Barton, “The effects of multilocus balancing selection
on neutral variability,” Genetics, vol. 161, no. 2. Genetics Society of
America, pp. 849–863, 2002.
ista: Navarro A, Barton NH. 2002. The effects of multilocus balancing selection
on neutral variability. Genetics. 161(2), 849–863.
mla: Navarro, Arcadio, and Nicholas H. Barton. “The Effects of Multilocus Balancing
Selection on Neutral Variability.” Genetics, vol. 161, no. 2, Genetics
Society of America, 2002, pp. 849–63, doi:10.1093/genetics/161.2.849.
short: A. Navarro, N.H. Barton, Genetics 161 (2002) 849–863.
date_created: 2018-12-11T12:07:53Z
date_published: 2002-06-01T00:00:00Z
date_updated: 2023-06-06T12:02:32Z
day: '01'
doi: 10.1093/genetics/161.2.849
extern: '1'
external_id:
pmid:
- '12072479'
intvolume: ' 161'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462137/
month: '06'
oa: 1
oa_version: Published Version
page: 849 - 863
pmid: 1
publication: Genetics
publication_identifier:
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
publist_id: '1835'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The effects of multilocus balancing selection on neutral variability
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 161
year: '2002'
...
---
_id: '4259'
abstract:
- lang: eng
text: 'We extend current multilocus models to describe the effects of migration,
recombination, selection, and nonrandom mating on sets of genes in diploids with
varied modes of inheritance, allowing us to consider the patterns of nuclear and
cytonuclear associations (disequilibria) under various models of migration. We
show the relationship between the multilocus notation recently presented by Kirkpatrick,
Johnson, and Barton (developed from previous work by Barton and Turelli) and the
cytonuclear parameterization of Asmussen, Arnold, and Avise and extend this notation
to describe associations between cytoplasmic elements and multiple nuclear genes.
Under models with sexual symmetry, both nuclear-nuclear and cytonuclear disequilibria
are equivalent. They differ, however, in cases involving some type of sexual asymmetry,
which is then reflected in the asymmetric inheritance of cytoplasmic markers.
An example given is the case of different migration rates in males and females;
simulations using 2, 3, 4, or 5 unlinked autosomal markers with a maternally inherited
cytoplasmic marker illustrate how nuclear-nuclear and cytonuclear associations
can be used to separately estimate female and male migration rates. The general
framework developed here allows us to investigate conditions where associations
between loci with different modes of inheritance are not equivalent and to use
this nonequivalence to test for deviations from simple models of admixture. '
acknowledgement: The authors thank Toby Johnson for his helpful comments on this manuscript.
This work was supported by a National Science Foundation NATO postdoctoral fellowship
and National Science Foundation grants DEB-9813335 and DEB-0108242 to M.E.O.; N.H.B.
gratefully acknowledges the support of the Darwin Trust of Edinburgh and the National
Environmental Research Council.
article_processing_charge: No
article_type: original
author:
- first_name: Maria
full_name: Orive, Maria
last_name: Orive
- 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: Orive M, Barton NH. Associations between cytoplasmic and nuclear loci in hybridizing
populations. Genetics. 2002;162(3):1469-1485. doi:10.1093/genetics/162.3.1469
apa: Orive, M., & Barton, N. H. (2002). Associations between cytoplasmic and
nuclear loci in hybridizing populations. Genetics. Genetics Society of
America. https://doi.org/10.1093/genetics/162.3.1469
chicago: Orive, Maria, and Nicholas H Barton. “Associations between Cytoplasmic
and Nuclear Loci in Hybridizing Populations.” Genetics. Genetics Society
of America, 2002. https://doi.org/10.1093/genetics/162.3.1469.
ieee: M. Orive and N. H. Barton, “Associations between cytoplasmic and nuclear loci
in hybridizing populations,” Genetics, vol. 162, no. 3. Genetics Society
of America, pp. 1469–1485, 2002.
ista: Orive M, Barton NH. 2002. Associations between cytoplasmic and nuclear loci
in hybridizing populations. Genetics. 162(3), 1469–1485.
mla: Orive, Maria, and Nicholas H. Barton. “Associations between Cytoplasmic and
Nuclear Loci in Hybridizing Populations.” Genetics, vol. 162, no. 3, Genetics
Society of America, 2002, pp. 1469–85, doi:10.1093/genetics/162.3.1469.
short: M. Orive, N.H. Barton, Genetics 162 (2002) 1469–1485.
date_created: 2018-12-11T12:07:54Z
date_published: 2002-11-01T00:00:00Z
date_updated: 2023-06-06T12:19:54Z
day: '01'
doi: 10.1093/genetics/162.3.1469
extern: '1'
external_id:
pmid:
- '12454089'
intvolume: ' 162'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462324/
month: '11'
oa: 1
oa_version: Published Version
page: 1469 - 1485
pmid: 1
publication: Genetics
publication_identifier:
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
publist_id: '1836'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Associations between cytoplasmic and nuclear loci in hybridizing populations
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 162
year: '2002'
...
---
_id: '4260'
abstract:
- lang: eng
text: 'We calculate the fixation probability of a beneficial allele that arises
as the result of a unique mutation in an asexual population that is subject to
recurrent deleterious mutation at rate U. Our analysis is an extension of previous
works, which make a biologically restrictive assumption that selection against
deleterious alleles is stronger than that on the beneficial allele of interest.
We show that when selection against deleterious alleles is weak, beneficial alleles
that confer a selective advantage that is small relative to U have greatly reduced
probabilities of fixation. We discuss the consequences of this effect for the
distribution of effects of alleles fixed during adaptation. We show that a selective
sweep will increase the fixation probabilities of other beneficial mutations arising
during some short interval afterward. We use the calculated fixation probabilities
to estimate the expected rate of fitness improvement in an asexual population
when beneficial alleles arise continually at some low rate proportional to U.
We estimate the rate of mutation that is optimal in the sense that it maximizes
this rate of fitness improvement. Again, this analysis relaxes the assumption
made previously that selection against deleterious alleles is stronger than on
beneficial alleles. '
acknowledgement: "We thank Brian Charlesworth, Arcadi Navarro, Allen Orr, Sally Otto,
Mario Pineda-Krch, Rosie Redfield, Olivier Tenaillon, and two anonymous reviewers
for discussions and/or helpful comments on the\r\nmanuscript. T.J. is supported
by Wellcome Trust International Prize Travelling Research Fellowship no. 061530.
N.B. is supported by the Biotechnology and Biological Sciences Research Council
and by the Natural Environment Research Council."
article_processing_charge: No
article_type: original
author:
- first_name: Toby
full_name: Johnson, Toby
last_name: Johnson
- 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: Johnson T, Barton NH. The effect of deleterious alleles on adaptation in asexual
populations. Genetics. 2002;162(1):395-411. doi:10.1093/genetics/162.1.395
apa: Johnson, T., & Barton, N. H. (2002). The effect of deleterious alleles
on adaptation in asexual populations. Genetics. Genetics Society of America.
https://doi.org/10.1093/genetics/162.1.395
chicago: Johnson, Toby, and Nicholas H Barton. “The Effect of Deleterious Alleles
on Adaptation in Asexual Populations.” Genetics. Genetics Society of America,
2002. https://doi.org/10.1093/genetics/162.1.395.
ieee: T. Johnson and N. H. Barton, “The effect of deleterious alleles on adaptation
in asexual populations,” Genetics, vol. 162, no. 1. Genetics Society of
America, pp. 395–411, 2002.
ista: Johnson T, Barton NH. 2002. The effect of deleterious alleles on adaptation
in asexual populations. Genetics. 162(1), 395–411.
mla: Johnson, Toby, and Nicholas H. Barton. “The Effect of Deleterious Alleles on
Adaptation in Asexual Populations.” Genetics, vol. 162, no. 1, Genetics
Society of America, 2002, pp. 395–411, doi:10.1093/genetics/162.1.395.
short: T. Johnson, N.H. Barton, Genetics 162 (2002) 395–411.
date_created: 2018-12-11T12:07:54Z
date_published: 2002-09-01T00:00:00Z
date_updated: 2023-06-06T11:45:48Z
day: '01'
doi: 10.1093/genetics/162.1.395
extern: '1'
external_id:
pmid:
- '12242249'
intvolume: ' 162'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462245/
month: '09'
oa: 1
oa_version: None
page: 395 - 411
pmid: 1
publication: Genetics
publication_identifier:
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
publist_id: '1833'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The effect of deleterious alleles on adaptation in asexual populations
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 162
year: '2002'
...
---
_id: '4261'
abstract:
- lang: eng
text: Until recently, it was impracticable to identify the genes that are responsible
for variation in continuous traits, or to directly observe the effects of their
different alleles. Now, the abundance of genetic markers has made it possible
to identify quantitative trait loci (QTL) — the regions of a chromosome or, ideally,
individual sequence variants that are responsible for trait variation. What kind
of QTL do we expect to find and what can our observations of QTL tell us about
how organisms evolve? The key to understanding the evolutionary significance of
QTL is to understand the nature of inherited variation, not in the immediate mechanistic
sense of how genes influence phenotype, but, rather, to know what evolutionary
forces maintain genetic variability.
article_processing_charge: No
article_type: original
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: Peter
full_name: Keightley, Peter
last_name: Keightley
citation:
ama: Barton NH, Keightley P. Understanding quantitative genetic variation. Nature
Reviews Genetics. 2002;3:11-21. doi:10.1038/nrg700
apa: Barton, N. H., & Keightley, P. (2002). Understanding quantitative genetic
variation. Nature Reviews Genetics. Nature Publishing Group. https://doi.org/10.1038/nrg700
chicago: Barton, Nicholas H, and Peter Keightley. “Understanding Quantitative Genetic
Variation.” Nature Reviews Genetics. Nature Publishing Group, 2002. https://doi.org/10.1038/nrg700.
ieee: N. H. Barton and P. Keightley, “Understanding quantitative genetic variation,”
Nature Reviews Genetics, vol. 3. Nature Publishing Group, pp. 11–21, 2002.
ista: Barton NH, Keightley P. 2002. Understanding quantitative genetic variation.
Nature Reviews Genetics. 3, 11–21.
mla: Barton, Nicholas H., and Peter Keightley. “Understanding Quantitative Genetic
Variation.” Nature Reviews Genetics, vol. 3, Nature Publishing Group, 2002,
pp. 11–21, doi:10.1038/nrg700.
short: N.H. Barton, P. Keightley, Nature Reviews Genetics 3 (2002) 11–21.
date_created: 2018-12-11T12:07:55Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-06-06T10:07:00Z
day: '01'
doi: 10.1038/nrg700
extern: '1'
external_id:
pmid:
- '11823787'
intvolume: ' 3'
language:
- iso: eng
month: '01'
oa_version: None
page: 11 - 21
pmid: 1
publication: Nature Reviews Genetics
publication_identifier:
issn:
- 1471-0056
publication_status: published
publisher: Nature Publishing Group
publist_id: '1831'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Understanding quantitative genetic variation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 3
year: '2002'
...
---
_id: '4262'
abstract:
- lang: eng
text: Natural populations are structured spatially into local populations and genetically
into diverse ‘genetic backgrounds’ defined by different combinations of selected
alleles. If selection maintains genetic backgrounds at constant frequency then
neutral diversity is enhanced. By contrast, if background frequencies fluctuate
then diversity is reduced. Provided that the population size of each background
is large enough, these effects can be described by the structured coalescent process.
Almost all the extant results based on the coalescent deal with a single selected
locus. Yet we know that very large numbers of genes are under selection and that
any substantial effects are likely to be due to the cumulative effects of many
loci. Here, we set up a general framework for the extension of the coalescent
to multilocus scenarios and we use it to study the simplest model, where strong
balancing selection acting on a set of n loci maintains 2n backgrounds at constant
frequencies and at linkage equilibrium. Analytical results show that the expected
linked neutral diversity increases exponentially with the number of selected loci
and can become extremely large. However, simulation results reveal that the structured
coalescent approach breaks down when the number of backgrounds approaches the
population size, because of stochastic fluctuations in background frequencies.
A new method is needed to extend the structured coalescent to cases with large
numbers of backgrounds.
acknowledgement: "We thank B. Charlesworth, D. Charlesworth and F. Depaulis for valuable
discussion and criticism. We are also\r\ngrateful to an anonymous reviewer, who
pointed out an imprecision in the original manuscript. This work was\r\nsupported
by the BBSRC."
article_processing_charge: No
article_type: original
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: Arcadio
full_name: Navarro, Arcadio
last_name: Navarro
citation:
ama: 'Barton NH, Navarro A. Extending the coalescent to multilocus systems: the
case of balancing selection. Genetical Research. 2002;79(2):129-139. doi:10.1017/S0016672301005493'
apa: 'Barton, N. H., & Navarro, A. (2002). Extending the coalescent to multilocus
systems: the case of balancing selection. Genetical Research. Cambridge
University Press. https://doi.org/10.1017/S0016672301005493'
chicago: 'Barton, Nicholas H, and Arcadio Navarro. “Extending the Coalescent to
Multilocus Systems: The Case of Balancing Selection.” Genetical Research.
Cambridge University Press, 2002. https://doi.org/10.1017/S0016672301005493.'
ieee: 'N. H. Barton and A. Navarro, “Extending the coalescent to multilocus systems:
the case of balancing selection,” Genetical Research, vol. 79, no. 2. Cambridge
University Press, pp. 129–139, 2002.'
ista: 'Barton NH, Navarro A. 2002. Extending the coalescent to multilocus systems:
the case of balancing selection. Genetical Research. 79(2), 129–139.'
mla: 'Barton, Nicholas H., and Arcadio Navarro. “Extending the Coalescent to Multilocus
Systems: The Case of Balancing Selection.” Genetical Research, vol. 79,
no. 2, Cambridge University Press, 2002, pp. 129–39, doi:10.1017/S0016672301005493.'
short: N.H. Barton, A. Navarro, Genetical Research 79 (2002) 129–139.
date_created: 2018-12-11T12:07:55Z
date_published: 2002-05-23T00:00:00Z
date_updated: 2023-06-06T11:23:19Z
day: '23'
doi: 10.1017/S0016672301005493
extern: '1'
external_id:
pmid:
- '12073551'
intvolume: ' 79'
issue: '2'
language:
- iso: eng
month: '05'
oa_version: None
page: 129 - 139
pmid: 1
publication: Genetical Research
publication_identifier:
issn:
- 0016-6723
publication_status: published
publisher: Cambridge University Press
publist_id: '1832'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Extending the coalescent to multilocus systems: the case of balancing selection'
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 79
year: '2002'
...
---
_id: '4263'
abstract:
- lang: eng
text: 'We introduce a general recursion for the probability of identity in state
of two individuals sampled from a population subject to mutation, migration, and
random drift in a two-dimensional continuum. The recursion allows for the interactions
induced by density-dependent regulation of the population, which are inevitable
in a continuous population. We give explicit series expansions for large neighbourhood
size and for low mutation rates respectively and investigate the accuracy of the
classical Malécot formula for these general models. When neighbourhood size is
small, this formula does not give the identity even over large scales. However,
for large neighbourhood size, it is an accurate approximation which summarises
the local population structure in terms of three quantities: the effective dispersal
rate, σe; the effective population density, ρe; and a local scale, κ, at which
local interactions become significant. The results are illustrated by simulations.'
acknowledgement: This work was supported by grants from the EPSRC (GR/L10048 and an
advanced fellowship for A.M.E.) and NERC (GR3/11635) and by the Darwin Trust of
Edinburgh. We thank Anja Sturm for her assistance with the project and anonymous
reviewers for helpful comments. This paper is dedicated to Charlotte, A.M.E.’s daughter
born during the gestation of the manuscript.
article_processing_charge: No
article_type: original
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: Frantz
full_name: Depaulis, Frantz
last_name: Depaulis
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Barton NH, Depaulis F, Etheridge A. Neutral evolution in spatially continuous
populations. Theoretical Population Biology. 2002;61(1):31-48. doi:10.1006/tpbi.2001.1557
apa: Barton, N. H., Depaulis, F., & Etheridge, A. (2002). Neutral evolution
in spatially continuous populations. Theoretical Population Biology. Academic
Press. https://doi.org/10.1006/tpbi.2001.1557
chicago: Barton, Nicholas H, Frantz Depaulis, and Alison Etheridge. “Neutral Evolution
in Spatially Continuous Populations.” Theoretical Population Biology. Academic
Press, 2002. https://doi.org/10.1006/tpbi.2001.1557.
ieee: N. H. Barton, F. Depaulis, and A. Etheridge, “Neutral evolution in spatially
continuous populations,” Theoretical Population Biology, vol. 61, no. 1.
Academic Press, pp. 31–48, 2002.
ista: Barton NH, Depaulis F, Etheridge A. 2002. Neutral evolution in spatially continuous
populations. Theoretical Population Biology. 61(1), 31–48.
mla: Barton, Nicholas H., et al. “Neutral Evolution in Spatially Continuous Populations.”
Theoretical Population Biology, vol. 61, no. 1, Academic Press, 2002, pp.
31–48, doi:10.1006/tpbi.2001.1557.
short: N.H. Barton, F. Depaulis, A. Etheridge, Theoretical Population Biology 61
(2002) 31–48.
date_created: 2018-12-11T12:07:55Z
date_published: 2002-02-01T00:00:00Z
date_updated: 2023-06-06T09:57:49Z
day: '01'
doi: 10.1006/tpbi.2001.1557
extern: '1'
external_id:
pmid:
- '11895381'
intvolume: ' 61'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 31 - 48
pmid: 1
publication: Theoretical Population Biology
publication_identifier:
issn:
- 0040-5809
publication_status: published
publisher: Academic Press
publist_id: '1830'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neutral evolution in spatially continuous populations
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 61
year: '2002'
...
---
_id: '4347'
abstract:
- lang: eng
text: 'Phylogenetic trees can be rooted by a number of criteria. Here, we introduce
a Bayesian method for inferring the root of a phylogenetic tree by using one of
several criteria: the outgroup, molecular clock, and nonreversible model of DNA
substitution. We perform simulation analyses to examine the relative ability of
these three criteria to correctly identify the root of the tree. The outgroup
and molecular clock criteria were best able to identify the root of the tree,
whereas the nonreversible model was able to identify the root only when the substitution
process was highly nonreversible. We also examined the performance of the criteria
for a tree of four species for which the topology and root position are well supported.
Results of the analyses of these data are consistent with the simulation results.'
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Huelsenbeck, John
last_name: Huelsenbeck
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Amy
full_name: Levine, Amy
last_name: Levine
citation:
ama: Huelsenbeck J, Bollback JP, Levine A. Inferring the root of a phylogenetic
tree. Systematic Biology. 2002;51(1):32-43. doi:10.1080/106351502753475862
apa: Huelsenbeck, J., Bollback, J. P., & Levine, A. (2002). Inferring the root
of a phylogenetic tree. Systematic Biology. Oxford University Press. https://doi.org/10.1080/106351502753475862
chicago: Huelsenbeck, John, Jonathan P Bollback, and Amy Levine. “Inferring the
Root of a Phylogenetic Tree.” Systematic Biology. Oxford University Press,
2002. https://doi.org/10.1080/106351502753475862.
ieee: J. Huelsenbeck, J. P. Bollback, and A. Levine, “Inferring the root of a phylogenetic
tree,” Systematic Biology, vol. 51, no. 1. Oxford University Press, pp.
32–43, 2002.
ista: Huelsenbeck J, Bollback JP, Levine A. 2002. Inferring the root of a phylogenetic
tree. Systematic Biology. 51(1), 32–43.
mla: Huelsenbeck, John, et al. “Inferring the Root of a Phylogenetic Tree.” Systematic
Biology, vol. 51, no. 1, Oxford University Press, 2002, pp. 32–43, doi:10.1080/106351502753475862.
short: J. Huelsenbeck, J.P. Bollback, A. Levine, Systematic Biology 51 (2002) 32–43.
date_created: 2018-12-11T12:08:23Z
date_published: 2002-02-01T00:00:00Z
date_updated: 2023-06-06T09:53:27Z
day: '01'
doi: 10.1080/106351502753475862
extern: '1'
external_id:
pmid:
- '11943091'
intvolume: ' 51'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 32 - 43
pmid: 1
publication: Systematic Biology
publication_identifier:
issn:
- 0039-7989
publication_status: published
publisher: Oxford University Press
publist_id: '1113'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring the root of a phylogenetic tree
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 51
year: '2002'
...
---
_id: '4349'
abstract:
- lang: eng
text: 'Bayesian inference is becoming a common statistical approach to phylogenetic
estimation because, among other reasons, it allows for rapid analysis of large
data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic
methods use currently available stochastic models of sequence evolution. However,
as with other model-based approaches, the results of Bayesian inference are conditional
on the assumed model of evolution: inadequate models (models that poorly fit the
data) may result in erroneous inferences. In this article, I present a Bayesian
phylogenetic method that evaluates the adequacy of evolutionary models using posterior
predictive distributions. By evaluating a model''s posterior predictive performance,
an adequate model can be selected for a Bayesian phylogenetic study. Although
I present a single test statistic that assesses the overall (global) performance
of a phylogenetic model, a variety of test statistics can be tailored to evaluate
specific features (local performance) of evolutionary models to identify sources
failure. The method presented here, unlike the likelihood-ratio test and parametric
bootstrap, accounts for uncertainty in the phylogeny and model parameters.'
acknowledgement: "This work was supported by grants from the NSF to John Huelsenbeck
(MCB-0075404 and DEB0075406), to whom I am grateful for his support throughout this
project. Also, I would like to express my deep thanks to Andrea Betancourt, John
Huelsenbeck, Kelly Dyer, Rasmus Nielsen, and Frederick Ronquist for taking the time
to read early versions of the\r\nmanuscript. Each and every one of them provided
invaluable comments, that ultimately made the manuscript better. John Huelsenbeck,
Bret Larget, Rasmus Nielsen, Ken Karol, and Andrea Betancourt patiently listened
to me drone on about this project, and offered insightful comments that benefited
this work, and for this they have my deepest gratitude. And finally, I would like
to thank two anonymous reviewers who gave critical attention to the manuscript and
provided valuable comments."
article_processing_charge: No
article_type: original
author:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Bollback JP. Bayesian model adequacy and choice in phylogenetics. Molecular
Biology and Evolution. 2002;19(7):1171-1180. doi:10.1093/oxfordjournals.molbev.a004175
apa: Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics.
Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/oxfordjournals.molbev.a004175
chicago: Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.”
Molecular Biology and Evolution. Oxford University Press, 2002. https://doi.org/10.1093/oxfordjournals.molbev.a004175.
ieee: J. P. Bollback, “Bayesian model adequacy and choice in phylogenetics,” Molecular
Biology and Evolution, vol. 19, no. 7. Oxford University Press, pp. 1171–80,
2002.
ista: Bollback JP. 2002. Bayesian model adequacy and choice in phylogenetics. Molecular
Biology and Evolution. 19(7), 1171–80.
mla: Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.”
Molecular Biology and Evolution, vol. 19, no. 7, Oxford University Press,
2002, pp. 1171–80, doi:10.1093/oxfordjournals.molbev.a004175.
short: J.P. Bollback, Molecular Biology and Evolution 19 (2002) 1171–80.
date_created: 2018-12-11T12:08:24Z
date_published: 2002-03-25T00:00:00Z
date_updated: 2023-06-06T09:18:18Z
day: '25'
doi: 10.1093/oxfordjournals.molbev.a004175
extern: '1'
external_id:
pmid:
- '12082136 '
intvolume: ' 19'
issue: '7'
language:
- iso: eng
month: '03'
oa_version: None
page: 1171 - 80
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '1112'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Bayesian model adequacy and choice in phylogenetics
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 19
year: '2002'
...
---
_id: '4407'
abstract:
- lang: eng
text: 'This paper presents a complete axiomatization of two decidable propositional
real-time linear temporal logics: Event Clock Logic (EventClockTL) and Metric
Interval Temporal Logic with past (MetricIntervalTL). The completeness proof consists
of an effective proof building procedure for EventClockTL. From this result we
obtain a complete axiomatization of MetricIntervalTL by providing axioms translating
MetricIntervalTL formulae into EventClockTL formulae, the two logics being equally
expressive. Our proof is structured to yield axiomatizations also for interesting
fragments of these logics, such as the linear temporal logic of the real numbers
(TLR).'
article_processing_charge: No
article_type: original
author:
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
- first_name: Pierre
full_name: Schobbens, Pierre
last_name: Schobbens
- 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: Raskin J, Schobbens P, Henzinger TA. Axioms for real-time logics. Theoretical
Computer Science. 2002;274(1-2):151-182. doi:10.1016/S0304-3975(00)00308-X
apa: Raskin, J., Schobbens, P., & Henzinger, T. A. (2002). Axioms for real-time
logics. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/S0304-3975(00)00308-X
chicago: Raskin, Jean, Pierre Schobbens, and Thomas A Henzinger. “Axioms for Real-Time
Logics.” Theoretical Computer Science. Elsevier, 2002. https://doi.org/10.1016/S0304-3975(00)00308-X.
ieee: J. Raskin, P. Schobbens, and T. A. Henzinger, “Axioms for real-time logics,”
Theoretical Computer Science, vol. 274, no. 1–2. Elsevier, pp. 151–182,
2002.
ista: Raskin J, Schobbens P, Henzinger TA. 2002. Axioms for real-time logics. Theoretical
Computer Science. 274(1–2), 151–182.
mla: Raskin, Jean, et al. “Axioms for Real-Time Logics.” Theoretical Computer
Science, vol. 274, no. 1–2, Elsevier, 2002, pp. 151–82, doi:10.1016/S0304-3975(00)00308-X.
short: J. Raskin, P. Schobbens, T.A. Henzinger, Theoretical Computer Science 274
(2002) 151–182.
date_created: 2018-12-11T12:08:42Z
date_published: 2002-03-01T00:00:00Z
date_updated: 2023-06-06T09:10:56Z
day: '01'
doi: 10.1016/S0304-3975(00)00308-X
extern: '1'
intvolume: ' 274'
issue: 1-2
language:
- iso: eng
month: '03'
oa_version: None
page: 151 - 182
publication: Theoretical Computer Science
publication_identifier:
issn:
- 0304-3975
publication_status: published
publisher: Elsevier
publist_id: '324'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Axioms for real-time logics
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 274
year: '2002'
...