---
_id: '3975'
abstract:
- lang: eng
text: We study the reconstruction of a stratified space from a possibly noisy point
sample. Specifically, we use the vineyard of the distance function restricted
to a I-parameter family of neighborhoods of a point to assess the local homology
of the stratified space at that point. We prove the correctness of this assessment
under the assumption of a sufficiently dense sample. We also give an algorithm
that constructs the vineyard and makes the local assessment in time at most cubic
in the size of the Delaunay triangulation of the point sample.
author:
- first_name: Paul
full_name: Paul Bendich
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: David
full_name: Cohen-Steiner, David
last_name: Cohen Steiner
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
citation:
ama: 'Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. Inferring
local homology from sampled stratified spaces. In: IEEE; 2007:536-546. doi:10.1109/FOCS.2007.33'
apa: 'Bendich, P., Cohen Steiner, D., Edelsbrunner, H., Harer, J., & Morozov,
D. (2007). Inferring local homology from sampled stratified spaces (pp. 536–546).
Presented at the FOCS: Foundations of Computer Science, IEEE. https://doi.org/10.1109/FOCS.2007.33'
chicago: Bendich, Paul, David Cohen Steiner, Herbert Edelsbrunner, John Harer, and
Dmitriy Morozov. “Inferring Local Homology from Sampled Stratified Spaces,” 536–46.
IEEE, 2007. https://doi.org/10.1109/FOCS.2007.33.
ieee: 'P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, and D. Morozov,
“Inferring local homology from sampled stratified spaces,” presented at the FOCS:
Foundations of Computer Science, 2007, pp. 536–546.'
ista: 'Bendich P, Cohen Steiner D, Edelsbrunner H, Harer J, Morozov D. 2007. Inferring
local homology from sampled stratified spaces. FOCS: Foundations of Computer Science,
536–546.'
mla: Bendich, Paul, et al. Inferring Local Homology from Sampled Stratified Spaces.
IEEE, 2007, pp. 536–46, doi:10.1109/FOCS.2007.33.
short: P. Bendich, D. Cohen Steiner, H. Edelsbrunner, J. Harer, D. Morozov, in:,
IEEE, 2007, pp. 536–546.
conference:
name: 'FOCS: Foundations of Computer Science'
date_created: 2018-12-11T12:06:13Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:35Z
day: '01'
doi: 10.1109/FOCS.2007.33
extern: 1
month: '01'
page: 536 - 546
publication_status: published
publisher: IEEE
publist_id: '2150'
quality_controlled: 0
status: public
title: Inferring local homology from sampled stratified spaces
type: conference
year: '2007'
...
---
_id: '3976'
abstract:
- lang: eng
text: Herein, we study the interfaces of a set of 146 transient protein-protein
interfaces in order to better understand the principles of their interactions.
We define and generate the protein interface using tools from computational geometry
and topology and then apply statistical analysis to its residue composition. In
addition to counting individual occurrences, we evaluate pairing preferences,
both across and as neighbors on one side of an interface. Likelihood correction
emphasizes novel and unexpected pairs, such as the His-Cys pair found in most
complexes of serine proteases with their diverse inhibitors and the Met-Met neighbor
pair found in unrelated protein interfaces. We also present a visualization of
the protein interface that allows for facile identification of residue-residue
contacts and other biochemical properties.
author:
- first_name: Jeffrey
full_name: Headd, Jeffrey J
last_name: Headd
- first_name: Y E Andrew
full_name: Ban, Y E Andrew
last_name: Ban
- first_name: Paul
full_name: Brown, Paul
last_name: Brown
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Madhuwanti
full_name: Vaidya, Madhuwanti
last_name: Vaidya
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: 'Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. Protein-protein
interfaces: Properties, preferences, and projections. Journal of Proteome Research.
2007;6(7):2576-2586. doi:10.1021/pr070018+'
apa: 'Headd, J., Ban, Y. E. A., Brown, P., Edelsbrunner, H., Vaidya, M., & Rudolph,
J. (2007). Protein-protein interfaces: Properties, preferences, and projections.
Journal of Proteome Research. American Chemical Society. https://doi.org/10.1021/pr070018+'
chicago: 'Headd, Jeffrey, Y E Andrew Ban, Paul Brown, Herbert Edelsbrunner, Madhuwanti
Vaidya, and Johannes Rudolph. “Protein-Protein Interfaces: Properties, Preferences,
and Projections.” Journal of Proteome Research. American Chemical Society,
2007. https://doi.org/10.1021/pr070018+.'
ieee: 'J. Headd, Y. E. A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, and J. Rudolph,
“Protein-protein interfaces: Properties, preferences, and projections,” Journal
of Proteome Research, vol. 6, no. 7. American Chemical Society, pp. 2576–2586,
2007.'
ista: 'Headd J, Ban YEA, Brown P, Edelsbrunner H, Vaidya M, Rudolph J. 2007. Protein-protein
interfaces: Properties, preferences, and projections. Journal of Proteome Research.
6(7), 2576–2586.'
mla: 'Headd, Jeffrey, et al. “Protein-Protein Interfaces: Properties, Preferences,
and Projections.” Journal of Proteome Research, vol. 6, no. 7, American
Chemical Society, 2007, pp. 2576–86, doi:10.1021/pr070018+.'
short: J. Headd, Y.E.A. Ban, P. Brown, H. Edelsbrunner, M. Vaidya, J. Rudolph, Journal
of Proteome Research 6 (2007) 2576–2586.
date_created: 2018-12-11T12:06:13Z
date_published: 2007-06-02T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '02'
doi: 10.1021/pr070018+
extern: 1
intvolume: ' 6'
issue: '7'
month: '06'
page: 2576 - 2586
publication: Journal of Proteome Research
publication_status: published
publisher: American Chemical Society
publist_id: '2151'
quality_controlled: 0
status: public
title: 'Protein-protein interfaces: Properties, preferences, and projections'
type: journal_article
volume: 6
year: '2007'
...
---
_id: '3977'
abstract:
- lang: eng
text: Using inclusion-exclusion, we can write the indicator function of a union
of finitely many balls as an alternating sum of indicator functions of common
intersections of balls. We exhibit abstract simplicial complexes that correspond
to minimal inclusion-exclusion formulas. They include the dual complex, as defined
in [3], and are characterized by the independence of their simplices and by geometric
realizations with the same underlying space as the dual complex.
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: Attali D, Edelsbrunner H. Inclusion-exclusion formulas from independent complexes.
Discrete & Computational Geometry. 2007;37(1):59-77. doi:10.1007/s00454-006-1274-7
apa: Attali, D., & Edelsbrunner, H. (2007). Inclusion-exclusion formulas from
independent complexes. Discrete & Computational Geometry. Springer.
https://doi.org/10.1007/s00454-006-1274-7
chicago: Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas
from Independent Complexes.” Discrete & Computational Geometry. Springer,
2007. https://doi.org/10.1007/s00454-006-1274-7.
ieee: D. Attali and H. Edelsbrunner, “Inclusion-exclusion formulas from independent
complexes,” Discrete & Computational Geometry, vol. 37, no. 1. Springer,
pp. 59–77, 2007.
ista: Attali D, Edelsbrunner H. 2007. Inclusion-exclusion formulas from independent
complexes. Discrete & Computational Geometry. 37(1), 59–77.
mla: Attali, Dominique, and Herbert Edelsbrunner. “Inclusion-Exclusion Formulas
from Independent Complexes.” Discrete & Computational Geometry, vol.
37, no. 1, Springer, 2007, pp. 59–77, doi:10.1007/s00454-006-1274-7.
short: D. Attali, H. Edelsbrunner, Discrete & Computational Geometry 37 (2007)
59–77.
date_created: 2018-12-11T12:06:14Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '01'
doi: 10.1007/s00454-006-1274-7
extern: 1
intvolume: ' 37'
issue: '1'
month: '01'
page: 59 - 77
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2152'
quality_controlled: 0
status: public
title: Inclusion-exclusion formulas from independent complexes
type: journal_article
volume: 37
year: '2007'
...
---
_id: '3981'
abstract:
- lang: eng
text: Building on the work of Martinetz, Schulten and de Silva, Carlsson, we introduce
a 2-parameter family of witness complexes and algorithms for constructing them.
This family can be used to determine the gross topology of point cloud data in
R-d or other metric spaces. The 2-parameter family is sensitive to differences
in sampling density and thus amenable to detecting patterns within the data set.
It also lends itself to theoretical analysis. For example, we can prove that in
the limit, when the witnesses cover the entire domain, witness complexes in the
family that share the first, scale parameter have the same homotopy type.
acknowledgement: Research by the authors is partially supported by DARPA under grant
HR0011-05-1-0007, by CNRS under grant PICS-3416 and by IST Program of the EU under
Contract IST-2002-506766.
alternative_title:
- LNCS
author:
- first_name: Dominique
full_name: Attali, Dominique
last_name: Attali
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: John
full_name: Harer, John
last_name: Harer
- first_name: Yuriy
full_name: Mileyko, Yuriy
last_name: Mileyko
citation:
ama: 'Attali D, Edelsbrunner H, Harer J, Mileyko Y. Alpha-beta witness complexes.
In: Vol 4619. Springer; 2007:386-397. doi:10.1007/978-3-540-73951-7_34'
apa: 'Attali, D., Edelsbrunner, H., Harer, J., & Mileyko, Y. (2007). Alpha-beta
witness complexes (Vol. 4619, pp. 386–397). Presented at the WADS: International
Workshop on Algrithms and Data Structures, Springer. https://doi.org/10.1007/978-3-540-73951-7_34'
chicago: Attali, Dominique, Herbert Edelsbrunner, John Harer, and Yuriy Mileyko.
“Alpha-Beta Witness Complexes,” 4619:386–97. Springer, 2007. https://doi.org/10.1007/978-3-540-73951-7_34.
ieee: 'D. Attali, H. Edelsbrunner, J. Harer, and Y. Mileyko, “Alpha-beta witness
complexes,” presented at the WADS: International Workshop on Algrithms and Data
Structures, 2007, vol. 4619, pp. 386–397.'
ista: 'Attali D, Edelsbrunner H, Harer J, Mileyko Y. 2007. Alpha-beta witness complexes.
WADS: International Workshop on Algrithms and Data Structures, LNCS, vol. 4619,
386–397.'
mla: Attali, Dominique, et al. Alpha-Beta Witness Complexes. Vol. 4619, Springer,
2007, pp. 386–97, doi:10.1007/978-3-540-73951-7_34.
short: D. Attali, H. Edelsbrunner, J. Harer, Y. Mileyko, in:, Springer, 2007, pp.
386–397.
conference:
name: 'WADS: International Workshop on Algrithms and Data Structures'
date_created: 2018-12-11T12:06:15Z
date_published: 2007-08-21T00:00:00Z
date_updated: 2021-01-12T07:53:38Z
day: '21'
doi: 10.1007/978-3-540-73951-7_34
extern: 1
intvolume: ' 4619'
month: '08'
page: 386 - 397
publication_status: published
publisher: Springer
publist_id: '2149'
quality_controlled: 0
status: public
title: Alpha-beta witness complexes
type: conference
volume: 4619
year: '2007'
...
---
_id: '4152'
abstract:
- lang: eng
text: 'Gastrulation is a morphogenetic process that results in the formation of
the embryonic germ layers. Here we detail the major cell movements that occur
during zebrafish gastrulation: epiboly, internalization, and convergent extension.
Although gastrulation is known to be regulated by signaling pathways such as the
Wnt/planar cell polarity pathway, many questions remain about the underlying molecular
and cellular mechanisms. Key factors that may play a role in gastrulation cell
movements are cell adhesion and cytoskeletal rearrangement. In addition, some
of the driving force for gastrulation may derive from tissue interactions such
as those described between the enveloping layer and the yolk syncytial layer.
Future exploration of gastrulation mechanisms relies on the development of sensitive
and quantitative techniques to characterize embryonic germ-layer properties.'
author:
- first_name: Laurel
full_name: Rohde, Laurel
last_name: Rohde
- 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: 'Rohde L, Heisenberg C-PJ. Zebrafish gastrulation: Cell movements, signals,
and mechanisms. International Review of Cytology - A Survey of Cell Biology.
2007;261:159-192. doi:10.1016/S0074-7696(07)61004-3'
apa: 'Rohde, L., & Heisenberg, C.-P. J. (2007). Zebrafish gastrulation: Cell
movements, signals, and mechanisms. International Review of Cytology - A Survey
of Cell Biology. Academic Press. https://doi.org/10.1016/S0074-7696(07)61004-3'
chicago: 'Rohde, Laurel, and Carl-Philipp J Heisenberg. “Zebrafish Gastrulation:
Cell Movements, Signals, and Mechanisms.” International Review of Cytology
- A Survey of Cell Biology. Academic Press, 2007. https://doi.org/10.1016/S0074-7696(07)61004-3.'
ieee: 'L. Rohde and C.-P. J. Heisenberg, “Zebrafish gastrulation: Cell movements,
signals, and mechanisms,” International Review of Cytology - A Survey of Cell
Biology, vol. 261. Academic Press, pp. 159–192, 2007.'
ista: 'Rohde L, Heisenberg C-PJ. 2007. Zebrafish gastrulation: Cell movements, signals,
and mechanisms. International Review of Cytology - A Survey of Cell Biology. 261,
159–192.'
mla: 'Rohde, Laurel, and Carl-Philipp J. Heisenberg. “Zebrafish Gastrulation: Cell
Movements, Signals, and Mechanisms.” International Review of Cytology - A Survey
of Cell Biology, vol. 261, Academic Press, 2007, pp. 159–92, doi:10.1016/S0074-7696(07)61004-3.'
short: L. Rohde, C.-P.J. Heisenberg, International Review of Cytology - A Survey
of Cell Biology 261 (2007) 159–192.
date_created: 2018-12-11T12:07:15Z
date_published: 2007-06-06T00:00:00Z
date_updated: 2021-01-12T07:54:53Z
day: '06'
doi: 10.1016/S0074-7696(07)61004-3
extern: '1'
intvolume: ' 261'
language:
- iso: eng
month: '06'
oa_version: None
page: 159 - 192
publication: International Review of Cytology - A Survey of Cell Biology
publication_status: published
publisher: Academic Press
publist_id: '1967'
status: public
title: 'Zebrafish gastrulation: Cell movements, signals, and mechanisms'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 261
year: '2007'
...
---
_id: '4182'
abstract:
- lang: eng
text: We are interested in the cellular and molecular mechanisms underlying tissue
morphogenesis during zebrafish gastrulation. Both differential cell adhesion and
contractility have been proposed to be key mechanisms by which tissues form and
rearrange in development. To obtain insight into the potential roles of differential
cell adhesion and contraction for germ layer morphogenesis during gastrulation,
we are analyzing cell adhesion and contraction of germ layer progenitor cells
using atomic force microscopy, primary tissue culture and transplantation assays.
I will present and discuss data about the differential adhesiveness and contractility
of germ layer progenitor cells in the context of germ layer formation during vertebrate
gastrulation.
acknowledgement: Abstract for the Annual Meeting of the German Societey for Cell Biology.
article_processing_charge: No
author:
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Yohanna
full_name: Arboleda, Yohanna
last_name: Arboleda
- first_name: Daniel
full_name: Müller, Daniel
last_name: Müller
- 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: Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. The role of cell adhesion and
contractility for germ layer morphogenesis during zebrafish gastrulation. European
Journal of Cell Biology. 2007;86(Supplement 1):39-39. doi:10.1016/j.ejcb.2007.02.002
apa: Krieg, M., Arboleda, Y., Müller, D., & Heisenberg, C.-P. J. (2007). The
role of cell adhesion and contractility for germ layer morphogenesis during zebrafish
gastrulation. European Journal of Cell Biology. Elsevier. https://doi.org/10.1016/j.ejcb.2007.02.002
chicago: Krieg, Michael, Yohanna Arboleda, Daniel Müller, and Carl-Philipp J Heisenberg.
“The Role of Cell Adhesion and Contractility for Germ Layer Morphogenesis during
Zebrafish Gastrulation.” European Journal of Cell Biology. Elsevier, 2007.
https://doi.org/10.1016/j.ejcb.2007.02.002.
ieee: M. Krieg, Y. Arboleda, D. Müller, and C.-P. J. Heisenberg, “The role of cell
adhesion and contractility for germ layer morphogenesis during zebrafish gastrulation,”
European Journal of Cell Biology, vol. 86, no. Supplement 1. Elsevier,
pp. 39–39, 2007.
ista: Krieg M, Arboleda Y, Müller D, Heisenberg C-PJ. 2007. The role of cell adhesion
and contractility for germ layer morphogenesis during zebrafish gastrulation.
European Journal of Cell Biology. 86(Supplement 1), 39–39.
mla: Krieg, Michael, et al. “The Role of Cell Adhesion and Contractility for Germ
Layer Morphogenesis during Zebrafish Gastrulation.” European Journal of Cell
Biology, vol. 86, no. Supplement 1, Elsevier, 2007, pp. 39–39, doi:10.1016/j.ejcb.2007.02.002.
short: M. Krieg, Y. Arboleda, D. Müller, C.-P.J. Heisenberg, European Journal of
Cell Biology 86 (2007) 39–39.
date_created: 2018-12-11T12:07:26Z
date_published: 2007-03-22T00:00:00Z
date_updated: 2021-01-12T07:55:07Z
day: '22'
doi: 10.1016/j.ejcb.2007.02.002
extern: '1'
intvolume: ' 86'
issue: Supplement 1
language:
- iso: eng
month: '03'
oa_version: None
page: 39 - 39
publication: European Journal of Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '1937'
status: public
title: The role of cell adhesion and contractility for germ layer morphogenesis during
zebrafish gastrulation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 86
year: '2007'
...
---
_id: '4205'
abstract:
- lang: eng
text: 'Background: Bone morphogenetic proteins (Bmps) are required for the specification
of ventrolateral cell fates during embryonic dorsoventral patterning and for proper
convergence and extension gastrulation movements, but the mechanisms underlying
the latter role remained elusive. Results: Via bead implantations, we show that
the Bmp gradient determines the direction of lateral mesodermal cell migration
during dorsal convergence in the zebrafish gastrula. This effect is independent
of its role during dorsoventral patterning and of noncanonical Wnt signaling.
However, it requires Bmp signal transduction through AIk8 and Smad5 to negatively
regulate Ca2+/Cadherin-dependent cell-cell adhesiveness. In vivo, converging mesodermal
cells form lamellipodia that attach to adjacent cells. Bmp signaling diminishes
the Cadherin-dependent stability of such contact points, thereby abrogating subsequent
cell displacement during lamellipodial retraction. Conclusions: We propose that
the ventral-to-dorsal Bmp gradient has an instructive role to establish a reverse
gradient of cell-cell adhesiveness, thereby defining different migratory zones
and directing lamellipodia-driven cell migrations during dorsal convergence in
lateral regions of the zebrafish gastrula.'
article_processing_charge: No
author:
- first_name: Sophia
full_name: Von Der Hardt, Sophia
last_name: Von Der Hardt
- first_name: Jeroen
full_name: Bakkers, Jeroen
last_name: Bakkers
- first_name: Adi
full_name: Inbal, Adi
last_name: Inbal
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Lilianna
full_name: Solnica Krezel, Lilianna
last_name: Solnica Krezel
- 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: Matthias
full_name: Hammerschmidt, Matthias
last_name: Hammerschmidt
citation:
ama: Von Der Hardt S, Bakkers J, Inbal A, et al. The Bmp gradient of the zebrafish
gastrula guides migrating lateral cells by regulating cell-cell adhesion. Current
Biology. 2007;17(6):475-487. doi:10.1016/j.cub.2007.02.013
apa: Von Der Hardt, S., Bakkers, J., Inbal, A., Carvalho, L., Solnica Krezel, L.,
Heisenberg, C.-P. J., & Hammerschmidt, M. (2007). The Bmp gradient of the
zebrafish gastrula guides migrating lateral cells by regulating cell-cell adhesion.
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2007.02.013
chicago: Von Der Hardt, Sophia, Jeroen Bakkers, Adi Inbal, Lara Carvalho, Lilianna
Solnica Krezel, Carl-Philipp J Heisenberg, and Matthias Hammerschmidt. “The Bmp
Gradient of the Zebrafish Gastrula Guides Migrating Lateral Cells by Regulating
Cell-Cell Adhesion.” Current Biology. Cell Press, 2007. https://doi.org/10.1016/j.cub.2007.02.013.
ieee: S. Von Der Hardt et al., “The Bmp gradient of the zebrafish gastrula
guides migrating lateral cells by regulating cell-cell adhesion,” Current Biology,
vol. 17, no. 6. Cell Press, pp. 475–487, 2007.
ista: Von Der Hardt S, Bakkers J, Inbal A, Carvalho L, Solnica Krezel L, Heisenberg
C-PJ, Hammerschmidt M. 2007. The Bmp gradient of the zebrafish gastrula guides
migrating lateral cells by regulating cell-cell adhesion. Current Biology. 17(6),
475–487.
mla: Von Der Hardt, Sophia, et al. “The Bmp Gradient of the Zebrafish Gastrula Guides
Migrating Lateral Cells by Regulating Cell-Cell Adhesion.” Current Biology,
vol. 17, no. 6, Cell Press, 2007, pp. 475–87, doi:10.1016/j.cub.2007.02.013.
short: S. Von Der Hardt, J. Bakkers, A. Inbal, L. Carvalho, L. Solnica Krezel, C.-P.J.
Heisenberg, M. Hammerschmidt, Current Biology 17 (2007) 475–487.
date_created: 2018-12-11T12:07:34Z
date_published: 2007-03-20T00:00:00Z
date_updated: 2021-01-12T07:55:17Z
day: '20'
doi: 10.1016/j.cub.2007.02.013
extern: '1'
intvolume: ' 17'
issue: '6'
language:
- iso: eng
month: '03'
oa_version: None
page: 475 - 487
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '1910'
status: public
title: The Bmp gradient of the zebrafish gastrula guides migrating lateral cells by
regulating cell-cell adhesion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '4225'
abstract:
- lang: eng
text: The discovery of the genetic code was one of the most important advances of
modern biology. But there is more to a DNA code than protein sequence; DNA carries
signals for splicing, localization, folding, and regulation that are often embedded
within the protein-coding sequence. In this issue, Itzkovitz and Alon show that
the specific 64-to-20 mapping found in the genetic code may have been optimized
for permitting protein-coding regions to carry this extra information and suggest
that this property may have evolved as a side benefit of selection to minimize
the negative effects of frameshift errors.
article_processing_charge: No
author:
- 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: Kalin
full_name: Vetsigian, Kalin
last_name: Vetsigian
- first_name: Roy
full_name: Kishony, Roy
last_name: Kishony
citation:
ama: Bollenbach MT, Vetsigian K, Kishony R. Evolution and multilevel optimization
of the genetic code. Genome Research. 2007;17(4):401-404. doi:10.1101/gr.6144007
apa: Bollenbach, M. T., Vetsigian, K., & Kishony, R. (2007). Evolution and multilevel
optimization of the genetic code. Genome Research. Cold Spring Harbor Laboratory
Press. https://doi.org/10.1101/gr.6144007
chicago: Bollenbach, Mark Tobias, Kalin Vetsigian, and Roy Kishony. “Evolution and
Multilevel Optimization of the Genetic Code.” Genome Research. Cold Spring
Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.6144007.
ieee: M. T. Bollenbach, K. Vetsigian, and R. Kishony, “Evolution and multilevel
optimization of the genetic code,” Genome Research, vol. 17, no. 4. Cold
Spring Harbor Laboratory Press, pp. 401–404, 2007.
ista: Bollenbach MT, Vetsigian K, Kishony R. 2007. Evolution and multilevel optimization
of the genetic code. Genome Research. 17(4), 401–404.
mla: Bollenbach, Mark Tobias, et al. “Evolution and Multilevel Optimization of the
Genetic Code.” Genome Research, vol. 17, no. 4, Cold Spring Harbor Laboratory
Press, 2007, pp. 401–04, doi:10.1101/gr.6144007.
short: M.T. Bollenbach, K. Vetsigian, R. Kishony, Genome Research 17 (2007) 401–404.
date_created: 2018-12-11T12:07:42Z
date_published: 2007-03-09T00:00:00Z
date_updated: 2021-01-12T07:55:26Z
day: '09'
doi: 10.1101/gr.6144007
extern: '1'
intvolume: ' 17'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 401 - 404
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '1891'
status: public
title: Evolution and multilevel optimization of the genetic code
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2007'
...
---
_id: '4226'
abstract:
- lang: eng
text: 'In the developing fly wing, secreted morphogens such as Decapentaplegic (Dpp)
and Wingless (Wg) form gradients of concentration providing positional information.
Dpp forms a longer-range gradient than Wg. To understand how the range is controlled,
we measured the four key kinetic parameters governing morphogen spreading: the
production rate, the effective diffusion coefficient, the degradation rate, and
the immobile fraction. The four parameters had different values for Dpp versus
Wg. In addition, Dynamin-dependent endocytosis was required for spreading of Dpp,
but not Wg. Thus, the cellular mechanisms of Dpp and Wingless spreading are different:
Dpp spreading requires endocytic, intracellular trafficking.'
author:
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Periklis
full_name: Pantazis, Periklis
last_name: Pantazis
- first_name: Tobias
full_name: Bollenbach, Tobias
last_name: Bollenbach
- first_name: Yannis
full_name: Kalaidzidis, Yannis
last_name: Kalaidzidis
- first_name: Thomas
full_name: Bittig, Thomas
last_name: Bittig
- first_name: Frank
full_name: Julicher, Frank
last_name: Julicher
- first_name: Marcos
full_name: Gonzalez-Gaitan, Marcos
last_name: Gonzalez Gaitan
citation:
ama: Kicheva A, Pantazis P, Bollenbach T, et al. Kinetics of morphogen gradient
formation. Science. 2007;315(5811):521-525. doi:10.1126/science.1135774
apa: Kicheva, A., Pantazis, P., Bollenbach, T., Kalaidzidis, Y., Bittig, T., Julicher,
F., & Gonzalez Gaitan, M. (2007). Kinetics of morphogen gradient formation.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1135774
chicago: Kicheva, Anna, Periklis Pantazis, Tobias Bollenbach, Yannis Kalaidzidis,
Thomas Bittig, Frank Julicher, and Marcos Gonzalez Gaitan. “Kinetics of Morphogen
Gradient Formation.” Science. American Association for the Advancement
of Science, 2007. https://doi.org/10.1126/science.1135774.
ieee: A. Kicheva et al., “Kinetics of morphogen gradient formation,” Science,
vol. 315, no. 5811. American Association for the Advancement of Science, pp. 521–525,
2007.
ista: Kicheva A, Pantazis P, Bollenbach T, Kalaidzidis Y, Bittig T, Julicher F,
Gonzalez Gaitan M. 2007. Kinetics of morphogen gradient formation. Science. 315(5811),
521–525.
mla: Kicheva, Anna, et al. “Kinetics of Morphogen Gradient Formation.” Science,
vol. 315, no. 5811, American Association for the Advancement of Science, 2007,
pp. 521–25, doi:10.1126/science.1135774.
short: A. Kicheva, P. Pantazis, T. Bollenbach, Y. Kalaidzidis, T. Bittig, F. Julicher,
M. Gonzalez Gaitan, Science 315 (2007) 521–525.
date_created: 2018-12-11T12:07:42Z
date_published: 2007-01-26T00:00:00Z
date_updated: 2021-01-12T07:55:26Z
day: '26'
doi: 10.1126/science.1135774
extern: 1
intvolume: ' 315'
issue: '5811'
month: '01'
page: 521 - 525
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '1892'
quality_controlled: 0
status: public
title: Kinetics of morphogen gradient formation
type: journal_article
volume: 315
year: '2007'
...
---
_id: '4233'
author:
- first_name: Harold
full_name: Harold Vladar
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
citation:
ama: 'de Vladar H. Alternativas prebióticas para la síntesis de amino- ácidos y
otras moléculas relacionadas. In: Falcón N, Loyo De Sardi Y, eds. Consejo de Desarrollo
Cientifico y Tecnologico; 2007:91-109. doi:3808'
apa: 'de Vladar, H. (2007). Alternativas prebióticas para la síntesis de amino-
ácidos y otras moléculas relacionadas. In N. Falcón & Y. Loyo De Sardi (Eds.)
(pp. 91–109). Presented at the Ab Initio: Orígenes Del Universo, La Vida, Y La
Inteligencia, Consejo de Desarrollo Cientifico y Tecnologico. https://doi.org/3808'
chicago: Vladar, Harold de. “Alternativas Prebióticas Para La Síntesis de Amino-
Ácidos y Otras Moléculas Relacionadas.” edited by N. Falcón and Y. Loyo De Sardi,
91–109. Consejo de Desarrollo Cientifico y Tecnologico, 2007. https://doi.org/3808.
ieee: 'H. de Vladar, “Alternativas prebióticas para la síntesis de amino- ácidos
y otras moléculas relacionadas,” presented at the Ab Initio: Orígenes Del Universo,
La Vida, Y La Inteligencia, 2007, pp. 91–109.'
ista: 'de Vladar H. 2007. Alternativas prebióticas para la síntesis de amino- ácidos
y otras moléculas relacionadas. Ab Initio: Orígenes Del Universo, La Vida, Y La
Inteligencia, 91–109.'
mla: de Vladar, Harold. Alternativas Prebióticas Para La Síntesis de Amino- Ácidos
y Otras Moléculas Relacionadas. Edited by N. Falcón and Y. Loyo De Sardi,
Consejo de Desarrollo Cientifico y Tecnologico, 2007, pp. 91–109, doi:3808.
short: H. de Vladar, in:, N. Falcón, Y. Loyo De Sardi (Eds.), Consejo de Desarrollo
Cientifico y Tecnologico, 2007, pp. 91–109.
conference:
name: 'Ab Initio: Orígenes Del Universo, La Vida, Y La Inteligencia'
date_created: 2018-12-11T12:07:45Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:29Z
day: '01'
doi: '3808'
editor:
- first_name: N.
full_name: Falcón,N.
last_name: Falcón
- first_name: Y.
full_name: Loyo de Sardi,Y.
last_name: Loyo De Sardi
extern: 1
month: '01'
page: 91 - 109
publication_status: published
publisher: Consejo de Desarrollo Cientifico y Tecnologico
publist_id: '1880'
quality_controlled: 0
status: public
title: Alternativas prebióticas para la síntesis de amino- ácidos y otras moléculas
relacionadas
type: conference
year: '2007'
...
---
_id: '4234'
abstract:
- lang: eng
text: We study a generalised model of population growth in which the state variable
is population growth rate instead of population size. Stochastic parametric perturbations,
modelling phenotypic variability, lead to a Langevin system with two sources of
multiplicative noise. The stationary probability distributions have two characteristic
power-law scales. Numerical simulations show that noise suppresses the explosion
of the growth rate which occurs in the deterministic counterpart. Instead, in
different parameter regimes populations will grow with "anomalous" stochastic
rates and (i) stabilise at "random carrying capacities", or (ii) go
extinct in random times. Using logistic fits to reconstruct the simulated data,
we find that even highly significant estimations do not recover or reflect information
about the deterministic part of the process. Therefore, the logistic interpretation
is not biologically meaningful. These results have implications for distinct model-aided
calculations in biological situations because these kinds of estimations could
lead to spurious conclusions. (c) 2006 Elsevier B.V. All rights reserved.
article_processing_charge: No
arxiv: 1
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: I.
full_name: Pen, I.
last_name: Pen
citation:
ama: de Vladar H, Pen I. Determinism, noise, and spurious estimations in a generalised
model of population growth. Physica A. 2007;373:477-485. doi:10.1016/j.physa.2006.06.025
apa: de Vladar, H., & Pen, I. (2007). Determinism, noise, and spurious estimations
in a generalised model of population growth. Physica A. Elsevier. https://doi.org/10.1016/j.physa.2006.06.025
chicago: Vladar, Harold de, and I. Pen. “Determinism, Noise, and Spurious Estimations
in a Generalised Model of Population Growth.” Physica A. Elsevier, 2007.
https://doi.org/10.1016/j.physa.2006.06.025.
ieee: H. de Vladar and I. Pen, “Determinism, noise, and spurious estimations in
a generalised model of population growth,” Physica A, vol. 373. Elsevier,
pp. 477–485, 2007.
ista: de Vladar H, Pen I. 2007. Determinism, noise, and spurious estimations in
a generalised model of population growth. Physica A. 373, 477–485.
mla: de Vladar, Harold, and I. Pen. “Determinism, Noise, and Spurious Estimations
in a Generalised Model of Population Growth.” Physica A, vol. 373, Elsevier,
2007, pp. 477–85, doi:10.1016/j.physa.2006.06.025.
short: H. de Vladar, I. Pen, Physica A 373 (2007) 477–485.
date_created: 2018-12-11T12:07:45Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:30Z
day: '01'
doi: 10.1016/j.physa.2006.06.025
extern: '1'
external_id:
arxiv:
- abs/q-bio/0602018
intvolume: ' 373'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/q-bio/0602018
month: '01'
oa: 1
oa_version: Preprint
page: 477 - 485
publication: Physica A
publication_status: published
publisher: Elsevier
publist_id: '1881'
status: public
title: Determinism, noise, and spurious estimations in a generalised model of population
growth
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 373
year: '2007'
...
---
_id: '4246'
abstract:
- lang: eng
text: Gaia theory, which describes the life–environment system of the Earth as stable
and self-regulating, has remained at the fringes of mainstream biological science
owing to its historically inadequate definition and apparent incompatibility with
individual-level natural selection. The key issue is whether and why the biosphere
might tend towards stability and self-regulation. We review the various ways in
which these issues have been addressed by evolutionary and ecological theory,
and relate these to ‘Gaia theory’. We then ask how this theory extends the perspectives
offered by these disciplines, and how it might be tested by novel modelling approaches
and laboratory experiments using emergent technologies.
author:
- first_name: Andrew
full_name: Free, Andrew
last_name: Free
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Free A, Barton NH. Do evolution and ecology need the Gaia hypothesis? Trends
in Ecology and Evolution. 2007;22(11):611-619. doi:10.1016/j.tree.2007.07.007
apa: Free, A., & Barton, N. H. (2007). Do evolution and ecology need the Gaia
hypothesis? Trends in Ecology and Evolution. Cell Press. https://doi.org/10.1016/j.tree.2007.07.007
chicago: Free, Andrew, and Nicholas H Barton. “Do Evolution and Ecology Need the
Gaia Hypothesis?” Trends in Ecology and Evolution. Cell Press, 2007. https://doi.org/10.1016/j.tree.2007.07.007.
ieee: A. Free and N. H. Barton, “Do evolution and ecology need the Gaia hypothesis?,”
Trends in Ecology and Evolution, vol. 22, no. 11. Cell Press, pp. 611–619,
2007.
ista: Free A, Barton NH. 2007. Do evolution and ecology need the Gaia hypothesis?
Trends in Ecology and Evolution. 22(11), 611–619.
mla: Free, Andrew, and Nicholas H. Barton. “Do Evolution and Ecology Need the Gaia
Hypothesis?” Trends in Ecology and Evolution, vol. 22, no. 11, Cell Press,
2007, pp. 611–19, doi:10.1016/j.tree.2007.07.007.
short: A. Free, N.H. Barton, Trends in Ecology and Evolution 22 (2007) 611–619.
date_created: 2018-12-11T12:07:49Z
date_published: 2007-11-01T00:00:00Z
date_updated: 2021-01-12T07:55:35Z
day: '01'
doi: 10.1016/j.tree.2007.07.007
extern: 1
intvolume: ' 22'
issue: '11'
month: '11'
page: 611 - 619
publication: Trends in Ecology and Evolution
publication_status: published
publisher: Cell Press
publist_id: '1856'
quality_controlled: 0
status: public
title: Do evolution and ecology need the Gaia hypothesis?
type: journal_article
volume: 22
year: '2007'
...
---
_id: '4247'
abstract:
- lang: eng
text: Evolution at multiple gene positions is complicated. Direct selection on one
gene disturbs the evolutionary dynamics of associated genes. Recent years have
seen the development of a multilocus methodology for modeling evolution at arbitrary
numbers of gene positions with arbitrary dominance and epistatic relations, mode
of inheritance, genetic linkage, and recombination. We show that the approach
is conceptually analogous to social evolutionary methodology, which focuses on
selection acting on associated individuals. In doing so, we (1) make explicit
the links between the multilocus methodology and the foundations of social evolution
theory, namely, Price’s theorem and Hamilton’s rule; (2) relate the multilocus
approach to levels‐of‐selection and neighbor‐modulated‐fitness approaches in social
evolution; (3) highlight the equivalence between genetical hitchhiking and kin
selection; (4) demonstrate that the multilocus methodology allows for social evolutionary
analyses involving coevolution of multiple traits and genetical associations between
nonrelatives, including individuals of different species; (5) show that this methodology
helps solve problems of dynamic sufficiency in social evolution theory; (6) form
links between invasion criteria in multilocus systems and Hamilton’s rule of kin
selection; (7) illustrate the generality and exactness of Hamilton’s rule, which
has previously been described as an approximate, heuristic result.
author:
- first_name: Andy
full_name: Gardner, Andy
last_name: Gardner
- first_name: Stuart
full_name: West, Stuart A
last_name: West
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Gardner A, West S, Barton NH. The relation between multilocus population genetics
and social evolution theory. American Naturalist. 2007;169(2):207-226.
doi:10.1086/510602
apa: Gardner, A., West, S., & Barton, N. H. (2007). The relation between multilocus
population genetics and social evolution theory. American Naturalist. University
of Chicago Press. https://doi.org/10.1086/510602
chicago: Gardner, Andy, Stuart West, and Nicholas H Barton. “The Relation between
Multilocus Population Genetics and Social Evolution Theory.” American Naturalist.
University of Chicago Press, 2007. https://doi.org/10.1086/510602.
ieee: A. Gardner, S. West, and N. H. Barton, “The relation between multilocus population
genetics and social evolution theory,” American Naturalist, vol. 169, no.
2. University of Chicago Press, pp. 207–226, 2007.
ista: Gardner A, West S, Barton NH. 2007. The relation between multilocus population
genetics and social evolution theory. American Naturalist. 169(2), 207–226.
mla: Gardner, Andy, et al. “The Relation between Multilocus Population Genetics
and Social Evolution Theory.” American Naturalist, vol. 169, no. 2, University
of Chicago Press, 2007, pp. 207–26, doi:10.1086/510602.
short: A. Gardner, S. West, N.H. Barton, American Naturalist 169 (2007) 207–226.
date_created: 2018-12-11T12:07:50Z
date_published: 2007-02-01T00:00:00Z
date_updated: 2021-01-12T07:55:35Z
day: '01'
doi: 10.1086/510602
extern: 1
intvolume: ' 169'
issue: '2'
month: '02'
page: 207 - 226
publication: American Naturalist
publication_status: published
publisher: University of Chicago Press
publist_id: '1857'
quality_controlled: 0
status: public
title: The relation between multilocus population genetics and social evolution theory
type: journal_article
volume: 169
year: '2007'
...
---
_id: '4342'
abstract:
- lang: eng
text: "Library 2.0 and user-generated content are two terms, which are closely connected.
In the\r\n\r\npresentation, I will briefly define both terms. Two example projects
where user- generated content and libraries interact will be presented. The cooperation
of Wikipedia and the Personennamendatei, the German cooperative name authority
files is the first. The second will be Wikisource where users provide transcribed
source material. Another important area of user-generated content is social tagging
where users index different resources. And if the users will do so much in the
future, is there still a place for librarians? But in the future user\r\n\r\nand
librarians become partners and the library will provide the platform: the library
2.0."
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: 'Danowski P. Library 2.0 and User-Generated Content - What can the users do
for us? In: IFLA; 2007. doi:601'
apa: 'Danowski, P. (2007). Library 2.0 and User-Generated Content - What can the
users do for us? Presented at the WLIC: World Library and Information Congress,
Durban, South Africa: IFLA. https://doi.org/601'
chicago: Danowski, Patrick. “Library 2.0 and User-Generated Content - What Can the
Users Do for Us?” IFLA, 2007. https://doi.org/601.
ieee: 'P. Danowski, “Library 2.0 and User-Generated Content - What can the users
do for us?,” presented at the WLIC: World Library and Information Congress, Durban,
South Africa, 2007.'
ista: 'Danowski P. 2007. Library 2.0 and User-Generated Content - What can the users
do for us? WLIC: World Library and Information Congress.'
mla: Danowski, Patrick. Library 2.0 and User-Generated Content - What Can the
Users Do for Us? IFLA, 2007, doi:601.
short: P. Danowski, in:, IFLA, 2007.
conference:
end_date: 2007-08-23
location: Durban, South Africa
name: 'WLIC: World Library and Information Congress'
start_date: 2007-08-19
date_created: 2018-12-11T12:08:22Z
date_published: 2007-05-25T00:00:00Z
date_updated: 2021-01-12T07:56:16Z
day: '25'
doi: '601'
extern: '1'
language:
- iso: eng
main_file_link:
- url: http://www.ifla.org/IV/ifla73/papers/113-Danowski-en.pdf
month: '05'
oa_version: None
publication_status: published
publisher: IFLA
publist_id: '1232'
status: public
title: Library 2.0 and User-Generated Content - What can the users do for us?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2007'
...
---
_id: '4343'
author:
- first_name: Patrick
full_name: Patrick Danowski
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Barbara
full_name: Pfeifer,Barbara
last_name: Pfeifer
citation:
ama: 'Danowski P, Pfeifer B. Wikipedia und Normdateien: Wege der Vernetzung am Beispiel
der Kooperation mit der Personennamendatei. Bibliothek - Forschung Und Praxis.
2007;31(2):149-155. doi:485'
apa: 'Danowski, P., & Pfeifer, B. (2007). Wikipedia und Normdateien: Wege der
Vernetzung am Beispiel der Kooperation mit der Personennamendatei. Bibliothek
- Forschung Und Praxis. De Gruyter. https://doi.org/485'
chicago: 'Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege
Der Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” Bibliothek
- Forschung Und Praxis. De Gruyter, 2007. https://doi.org/485.'
ieee: 'P. Danowski and B. Pfeifer, “Wikipedia und Normdateien: Wege der Vernetzung
am Beispiel der Kooperation mit der Personennamendatei,” Bibliothek - Forschung
Und Praxis, vol. 31, no. 2. De Gruyter, pp. 149–155, 2007.'
ista: 'Danowski P, Pfeifer B. 2007. Wikipedia und Normdateien: Wege der Vernetzung
am Beispiel der Kooperation mit der Personennamendatei. Bibliothek - Forschung
Und Praxis. 31(2), 149–155.'
mla: 'Danowski, Patrick, and Barbara Pfeifer. “Wikipedia Und Normdateien: Wege Der
Vernetzung Am Beispiel Der Kooperation Mit Der Personennamendatei.” Bibliothek
- Forschung Und Praxis, vol. 31, no. 2, De Gruyter, 2007, pp. 149–55, doi:485.'
short: P. Danowski, B. Pfeifer, Bibliothek - Forschung Und Praxis 31 (2007) 149–155.
date_created: 2018-12-11T12:08:22Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:17Z
day: '01'
doi: '485'
extern: 1
intvolume: ' 31'
issue: '2'
month: '01'
page: 149 - 155
publication: Bibliothek - Forschung Und Praxis
publication_status: published
publisher: De Gruyter
publist_id: '1231'
quality_controlled: 0
status: public
title: 'Wikipedia und Normdateien: Wege der Vernetzung am Beispiel der Kooperation
mit der Personennamendatei'
type: journal_article
volume: 31
year: '2007'
...
---
_id: '4344'
author:
- first_name: Patrick
full_name: Patrick Danowski
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
- first_name: Lambert
full_name: Heller,Lambert
last_name: Heller
citation:
ama: Danowski P, Heller L. Bibliothek 2.0 ? Wird alles anders? Bibliothek - Forschung
Und Praxis. 2007;31(2007):130-136. doi:45
apa: Danowski, P., & Heller, L. (2007). Bibliothek 2.0 ? Wird alles anders?
Bibliothek - Forschung Und Praxis. De Gruyter. https://doi.org/45
chicago: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?”
Bibliothek - Forschung Und Praxis. De Gruyter, 2007. https://doi.org/45.
ieee: P. Danowski and L. Heller, “Bibliothek 2.0 ? Wird alles anders?,” Bibliothek
- Forschung Und Praxis, vol. 31, no. 2007. De Gruyter, pp. 130–136, 2007.
ista: Danowski P, Heller L. 2007. Bibliothek 2.0 ? Wird alles anders? Bibliothek
- Forschung Und Praxis. 31(2007), 130–136.
mla: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 ? Wird Alles Anders?”
Bibliothek - Forschung Und Praxis, vol. 31, no. 2007, De Gruyter, 2007,
pp. 130–36, doi:45.
short: P. Danowski, L. Heller, Bibliothek - Forschung Und Praxis 31 (2007) 130–136.
date_created: 2018-12-11T12:08:22Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:17Z
day: '01'
doi: '45'
extern: 1
intvolume: ' 31'
issue: '2007'
main_file_link:
- open_access: '0'
url: http://www.bibliothek-saur.de/2007_2/130-136.pdf
month: '01'
page: 130 - 136
publication: Bibliothek - Forschung Und Praxis
publication_status: published
publisher: De Gruyter
publist_id: '1230'
quality_controlled: 0
status: public
title: Bibliothek 2.0 ? Wird alles anders?
type: journal_article
volume: 31
year: '2007'
...
---
_id: '4353'
abstract:
- lang: eng
text: 'BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System
(454 parallel sequencing platform) has enabled the rapid and high-volume production
of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions
and subsequent sequencing runs have been unable to combine template DNA from multiple
individuals, as homologous sequences cannot be subsequently assigned to their
original sources. METHODOLOGY: We use conventional PCR with 5''-nucleotide tagged
primers to generate homologous DNA amplification products from multiple specimens,
followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing
System (GS20, Roche/454 Life Sciences). Each DNA sequence is subsequently traced
back to its individual source through 5''tag-analysis. CONCLUSIONS: We demonstrate
that this new approach enables the assignment of virtually all the generated DNA
sequences to the correct source once sequencing anomalies are accounted for (miss-assignment
rate<0.4%). Therefore, the method enables accurate sequencing and assignment
of homologous DNA sequences from multiple sources in single high-throughput GS20
run. We observe a bias in the distribution of the differently tagged primers that
is dependent on the 5'' nucleotide of the tag. In particular, primers 5'' labelled
with a cytosine are heavily overrepresented among the final sequences, while those
5'' labelled with a thymine are strongly underrepresented. A weaker bias also
exists with regards to the distribution of the sequences as sorted by the second
nucleotide of the dinucleotide tags. As the results are based on a single GS20
run, the general applicability of the approach requires confirmation. However,
our experiments demonstrate that 5''primer tagging is a useful method in which
the sequencing power of the GS20 can be applied to PCR-based assays of multiple
homologous PCR products. The new approach will be of value to a broad range of
research areas, such as those of comparative genomics, complete mitochondrial
analyses, population genetics, and phylogenetics.'
acknowledgement: JB and EW were supported by the Wellcome Trust, UK, the Carlsberg
Foundation, DK, and the National Science Foundation, DK. MTPG acknowledges the Marie
Curie Actions FP6-MEIF-CT-2005-025002 ‘FORMAPLEX’ grant for funding his research.
JPB and RN were funded by the Danish FSS and the National Science Foundation, DK.
None of the sponsors or funders have had any influence on the data or manuscript
presented here.
author:
- first_name: Jonas
full_name: Binladen, Jonas
last_name: Binladen
- first_name: M Thomas
full_name: Gilbert, M Thomas
last_name: Gilbert
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Frank
full_name: Panitz, Frank
last_name: Panitz
- first_name: Christian
full_name: Bendixen, Christian
last_name: Bendixen
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
- first_name: Eske
full_name: Willerslev, Eske
last_name: Willerslev
citation:
ama: Binladen J, Gilbert MT, Bollback JP, et al. The use of coded PCR primers enables
high-throughput sequencing of multiple homolog amplification products by 454 parallel
sequencing. PLoS One. 2007;2(2). doi:10.1371/journal.pone.0000197
apa: Binladen, J., Gilbert, M. T., Bollback, J. P., Panitz, F., Bendixen, C., Nielsen,
R., & Willerslev, E. (2007). The use of coded PCR primers enables high-throughput
sequencing of multiple homolog amplification products by 454 parallel sequencing.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0000197
chicago: Binladen, Jonas, M Thomas Gilbert, Jonathan P Bollback, Frank Panitz, Christian
Bendixen, Rasmus Nielsen, and Eske Willerslev. “The Use of Coded PCR Primers Enables
High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel
Sequencing.” PLoS One. Public Library of Science, 2007. https://doi.org/10.1371/journal.pone.0000197.
ieee: J. Binladen et al., “The use of coded PCR primers enables high-throughput
sequencing of multiple homolog amplification products by 454 parallel sequencing,”
PLoS One, vol. 2, no. 2. Public Library of Science, 2007.
ista: Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev
E. 2007. The use of coded PCR primers enables high-throughput sequencing of multiple
homolog amplification products by 454 parallel sequencing. PLoS One. 2(2).
mla: Binladen, Jonas, et al. “The Use of Coded PCR Primers Enables High-Throughput
Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing.”
PLoS One, vol. 2, no. 2, Public Library of Science, 2007, doi:10.1371/journal.pone.0000197.
short: J. Binladen, M.T. Gilbert, J.P. Bollback, F. Panitz, C. Bendixen, R. Nielsen,
E. Willerslev, PLoS One 2 (2007).
date_created: 2018-12-11T12:08:25Z
date_published: 2007-02-14T00:00:00Z
date_updated: 2021-01-12T07:56:21Z
day: '14'
doi: 10.1371/journal.pone.0000197
extern: 1
intvolume: ' 2'
issue: '2'
month: '02'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '1105'
quality_controlled: 0
status: public
title: The use of coded PCR primers enables high-throughput sequencing of multiple
homolog amplification products by 454 parallel sequencing
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
volume: 2
year: '2007'
...
---
_id: '4354'
abstract:
- lang: eng
text: Homology search is one of the most ubiquitous bioinformatic tasks, yet it
is unknown how effective the currently available tools are for identifying noncoding
RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness
of methods such as BLAST, FASTA, HMMer, and Infernal. Surprisingly, the most popular
homology search methods are often the least accurate. As a result, many studies
have used inappropriate tools for their analyses. On the basis of our results,
we suggest homology search strategies using the currently available tools and
some directions for future development.
author:
- first_name: Eva
full_name: Freyhult, Eva K
last_name: Freyhult
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Paul
full_name: Gardner, Paul P
last_name: Gardner
citation:
ama: 'Freyhult E, Bollback JP, Gardner P. Exploring genomic dark matter: a critical
assessment of the performance of homology search methods on noncoding RNA. Genome
Research. 2007;17(1):117-125. doi:10.1101/gr.5890907'
apa: 'Freyhult, E., Bollback, J. P., & Gardner, P. (2007). Exploring genomic
dark matter: a critical assessment of the performance of homology search methods
on noncoding RNA. Genome Research. Cold Spring Harbor Laboratory Press.
https://doi.org/10.1101/gr.5890907'
chicago: 'Freyhult, Eva, Jonathan P Bollback, and Paul Gardner. “Exploring Genomic
Dark Matter: A Critical Assessment of the Performance of Homology Search Methods
on Noncoding RNA.” Genome Research. Cold Spring Harbor Laboratory Press,
2007. https://doi.org/10.1101/gr.5890907.'
ieee: 'E. Freyhult, J. P. Bollback, and P. Gardner, “Exploring genomic dark matter:
a critical assessment of the performance of homology search methods on noncoding
RNA,” Genome Research, vol. 17, no. 1. Cold Spring Harbor Laboratory Press,
pp. 117–25, 2007.'
ista: 'Freyhult E, Bollback JP, Gardner P. 2007. Exploring genomic dark matter:
a critical assessment of the performance of homology search methods on noncoding
RNA. Genome Research. 17(1), 117–25.'
mla: 'Freyhult, Eva, et al. “Exploring Genomic Dark Matter: A Critical Assessment
of the Performance of Homology Search Methods on Noncoding RNA.” Genome Research,
vol. 17, no. 1, Cold Spring Harbor Laboratory Press, 2007, pp. 117–25, doi:10.1101/gr.5890907.'
short: E. Freyhult, J.P. Bollback, P. Gardner, Genome Research 17 (2007) 117–25.
date_created: 2018-12-11T12:08:25Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:21Z
day: '01'
doi: 10.1101/gr.5890907
extern: 1
intvolume: ' 17'
issue: '1'
main_file_link:
- open_access: '0'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716261
month: '01'
page: 117 - 25
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '1106'
quality_controlled: 0
status: public
title: 'Exploring genomic dark matter: a critical assessment of the performance of
homology search methods on noncoding RNA'
type: journal_article
volume: 17
year: '2007'
...
---
_id: '4355'
abstract:
- lang: eng
text: When a beneficial mutation is fixed in a population that lacks recombination,
the genetic background linked to that mutation is fixed. As a result, beneficial
mutations on different backgrounds experience competition, or "clonal interference,"
that can cause asexual populations to evolve more slowly than their sexual counterparts.
Factors such as a large population size (N) and high mutation rates (mu) increase
the number of competing beneficial mutations, and hence are expected to increase
the intensity of clonal interference. However, recent theory suggests that, with
very large values of Nmu, the severity of clonal interference may instead decline.
The reason is that, with large Nmu, genomes including both beneficial mutations
are rapidly created by recurrent mutation, obviating the need for recombination.
Here, we analyze data from experimentally evolved asexual populations of a bacteriophage
and find that, in these nonrecombining populations with very large Nmu, recurrent
mutation does appear to ameliorate this cost of asexuality.
acknowledgement: R01 GM069801-08/GM/NIGMS NIH HHS/United States
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: John
full_name: Huelsenbeck, John P
last_name: Huelsenbeck
citation:
ama: Bollback JP, Huelsenbeck J. Clonal interference is alleviated by high mutation
rates in large populations. Molecular Biology and Evolution. 2007;24(6):1397-1406.
doi:10.1093/molbev/msm056
apa: Bollback, J. P., & Huelsenbeck, J. (2007). Clonal interference is alleviated
by high mutation rates in large populations. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msm056
chicago: Bollback, Jonathan P, and John Huelsenbeck. “Clonal Interference Is Alleviated
by High Mutation Rates in Large Populations.” Molecular Biology and Evolution.
Oxford University Press, 2007. https://doi.org/10.1093/molbev/msm056.
ieee: J. P. Bollback and J. Huelsenbeck, “Clonal interference is alleviated by high
mutation rates in large populations,” Molecular Biology and Evolution,
vol. 24, no. 6. Oxford University Press, pp. 1397–1406, 2007.
ista: Bollback JP, Huelsenbeck J. 2007. Clonal interference is alleviated by high
mutation rates in large populations. Molecular Biology and Evolution. 24(6), 1397–1406.
mla: Bollback, Jonathan P., and John Huelsenbeck. “Clonal Interference Is Alleviated
by High Mutation Rates in Large Populations.” Molecular Biology and Evolution,
vol. 24, no. 6, Oxford University Press, 2007, pp. 1397–406, doi:10.1093/molbev/msm056.
short: J.P. Bollback, J. Huelsenbeck, Molecular Biology and Evolution 24 (2007)
1397–1406.
date_created: 2018-12-11T12:08:26Z
date_published: 2007-03-22T00:00:00Z
date_updated: 2021-01-12T07:56:22Z
day: '22'
doi: 10.1093/molbev/msm056
extern: 1
intvolume: ' 24'
issue: '6'
month: '03'
page: 1397 - 1406
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '1104'
quality_controlled: 0
status: public
title: Clonal interference is alleviated by high mutation rates in large populations
type: journal_article
volume: 24
year: '2007'
...
---
_id: '4356'
abstract:
- lang: eng
text: We used a comparative genomics approach to identify genes that are under positive
selection in six strains of Escherichia coli and Shigella flexneri, including
five strains that are human pathogens. We find that positive selection targets
a wide range of different functions in the E. coli genome, including cell surface
proteins such as beta barrel porins, presumably because of the involvement of
these genes in evolutionary arms races with other bacteria, phages, and/or the
host immune system. Structural mapping of positively selected sites on trans-membrane
beta barrel porins reveals that the residues under positive selection occur almost
exclusively in the extracellular region of the proteins that are enriched with
sites known to be targets of phages, colicins, or the host immune system. More
surprisingly, we also find a number of other categories of genes that show very
strong evidence for positive selection, such as the enigmatic rhs elements and
transposases. Based on structural evidence, we hypothesize that the selection
acting on transposases is related to the genomic conflict between transposable
elements and the host genome.
author:
- first_name: Lise
full_name: Petersen, Lise
last_name: Petersen
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Matt
full_name: Dimmic, Matt
last_name: Dimmic
- first_name: Melissa
full_name: Hubisz, Melissa
last_name: Hubisz
- first_name: Rasmus
full_name: Nielsen, Rasmus
last_name: Nielsen
citation:
ama: Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive
selection in Escherichia coli. Genome Research. 2007;17(9):1336-1343. doi:10.1101/gr.6254707
apa: Petersen, L., Bollback, J. P., Dimmic, M., Hubisz, M., & Nielsen, R. (2007).
Genes under positive selection in Escherichia coli. Genome Research. Cold
Spring Harbor Laboratory Press. https://doi.org/10.1101/gr.6254707
chicago: Petersen, Lise, Jonathan P Bollback, Matt Dimmic, Melissa Hubisz, and Rasmus
Nielsen. “Genes under Positive Selection in Escherichia Coli.” Genome Research.
Cold Spring Harbor Laboratory Press, 2007. https://doi.org/10.1101/gr.6254707.
ieee: L. Petersen, J. P. Bollback, M. Dimmic, M. Hubisz, and R. Nielsen, “Genes
under positive selection in Escherichia coli,” Genome Research, vol. 17,
no. 9. Cold Spring Harbor Laboratory Press, pp. 1336–1343, 2007.
ista: Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. 2007. Genes under
positive selection in Escherichia coli. Genome Research. 17(9), 1336–1343.
mla: Petersen, Lise, et al. “Genes under Positive Selection in Escherichia Coli.”
Genome Research, vol. 17, no. 9, Cold Spring Harbor Laboratory Press, 2007,
pp. 1336–43, doi:10.1101/gr.6254707.
short: L. Petersen, J.P. Bollback, M. Dimmic, M. Hubisz, R. Nielsen, Genome Research
17 (2007) 1336–1343.
date_created: 2018-12-11T12:08:26Z
date_published: 2007-08-03T00:00:00Z
date_updated: 2021-01-12T07:56:22Z
day: '03'
doi: 10.1101/gr.6254707
extern: 1
intvolume: ' 17'
issue: '9'
month: '08'
page: 1336 - 1343
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '1103'
quality_controlled: 0
status: public
title: Genes under positive selection in Escherichia coli
type: journal_article
volume: 17
year: '2007'
...