---
_id: '3932'
abstract:
- lang: eng
text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and
tissue content of EGFR has been directly associated with poor prognosis in patients
with ovarian cancer. The uPA system plays a role in pericellular proteolysis,
cell migration, invasion, and is over-expressed in ovarian cancer. This study
explored the effects of EGF on uPAR expression in the ovarian cancer cell line
OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration
assay, time-lapse video microscopy, real-time PCR, assays for cellular binding
of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling
using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and
uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also
for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well
as EGF-stimulated cells, is present only in the intact, not the cleaved, form.
Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas
non-occupied receptor sites were not increased. In addition, EGF treatment resulted
in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased
internalization of uPAR, since the complex is internalized together with uPAR.
Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression
of uPAR. In addition, we found an immediate increase of uPAR after exposing the
cells to EGF and this was accompanied by a transient increase of cell migration.
The increase of cell surface uPAR in response to EGF is accompanied by increased
release of the soluble form of uPAR (suPAR) to the medium as well as by increased
cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis
inhibitor colchicine even though cell migration was inhibited, suggesting that
the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased
cell surface uPAR in response to EGF stimulation results from mobilization of
uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and
decreased internalization and degradation of uPAR. Both the anti-uPAR antibody
R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa
inhibited cell migration in response to uPA as well as to EGF, suggesting that
EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.'
author:
- first_name: Emir
full_name: Henic, Emir
last_name: Henic
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Stefan
full_name: Hansson, Stefan
last_name: Hansson
- first_name: Gunilla
full_name: Høyer-Hansen, Gunilla
last_name: Høyer Hansen
- first_name: Bertil
full_name: Casslén, Bertil
last_name: Casslén
citation:
ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration
in ovarian cancer cells is associated with decreased internalization, increased
surface expression, and increased shedding of the urokinase plasminogen activator
receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038
apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006).
EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038
chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and
Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology.
Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038.
ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp.
28–39, 2006.
ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated
migration in ovarian cancer cells is associated with decreased internalization,
increased surface expression, and increased shedding of the urokinase plasminogen
activator receptor. Gynecologic Oncology. 101(1), 28–39.
mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated
with Decreased Internalization, Increased Surface Expression, and Increased Shedding
of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology,
vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038.
short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic
Oncology 101 (2006) 28–39.
date_created: 2018-12-11T12:05:57Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:53:17Z
day: '01'
doi: 10.1016/j.ygyno.2005.09.038
extern: 1
intvolume: ' 101'
issue: '1'
month: '04'
page: 28 - 39
publication: Gynecologic Oncology
publication_status: published
publisher: Elsevier
publist_id: '2194'
quality_controlled: 0
status: public
title: EGF-stimulated migration in ovarian cancer cells is associated with decreased
internalization, increased surface expression, and increased shedding of the urokinase
plasminogen activator receptor
type: journal_article
volume: 101
year: '2006'
...
---
_id: '3934'
abstract:
- lang: eng
text: T cells develop in the thymus in a highly specialized cellular and extracellular
microenvironment. The basement membrane molecule, laminin-5 (LN-5), is predominantly
found in the medulla of the human thymic lobules. Using high-resolution light
microscopy, we show here that LN-5 is localized in a bi-membranous conduit-like
structure, together with other typical basement membrane components including
collagen type IV, nidogen and perlecan. Other interstitial matrix components,
such as fibrillin-1 or -2, tenascin-C or fibrillar collagen types, were also associated
with these structures. Three-dimensional (3D) confocal microscopy suggested a
tubular structure, whereas immunoelectron and transmission electron microscopy
showed that the core of these tubes contained fibrillar collagens enwrapped by
the LN-5-containing membrane. These medullary conduits are surrounded by thymic
epithelial cells, which in vitro were found to bind LN-5, but also fibrillin and
tenascin-C. Dendritic cells were also detected in close vicinity to the conduits.
Both of these stromal cell types express major histocompatibility complex (MHC)
class II molecules capable of antigen presentation. The conduits are connected
to blood vessels but, with an average diameter of 2 mum, they are too small to
transport cells. However, evidence is provided that smaller molecules such as
a 10 kDa dextran, but not large molecules (>500 kDa), can be transported in
the conduits. These results clearly demonstrate that a conduit system, which is
also known from secondary lymphatic organs such as lymph nodes and spleen, is
present in the medulla of the human thymus, and that it might serve to transport
small blood-borne molecules or chemokines to defined locations within the medulla.
author:
- first_name: Mihaela
full_name: Drumea-Mirancea, Mihaela
last_name: Drumea Mirancea
- first_name: Johannes
full_name: Wessels, Johannes T
last_name: Wessels
- first_name: Claudia
full_name: Müller, Claudia A
last_name: Müller
- first_name: Mike
full_name: Essl, Mike
last_name: Essl
- first_name: Johannes
full_name: Eble, Johannes A
last_name: Eble
- first_name: Eva
full_name: Tolosa, Eva
last_name: Tolosa
- first_name: Manuel
full_name: Koch, Manuel
last_name: Koch
- first_name: Dieter
full_name: Reinhardt, Dieter P
last_name: Reinhardt
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Lydia
full_name: Sorokin, Lydia
last_name: Sorokin
- first_name: York
full_name: Stierhof, York-Dieter
last_name: Stierhof
- first_name: Heinz
full_name: Schwarz, Heinz
last_name: Schwarz
- first_name: Gerd
full_name: Klein, Gerd
last_name: Klein
citation:
ama: 'Drumea Mirancea M, Wessels J, Müller C, et al. Characterization of a conduit
system containing laminin-5 in the human thymus: a potential transport system
for small molecules. Journal of Cell Science. 2006;119(Pt 7):1396-1405.
doi:10.1242/jcs.02840'
apa: 'Drumea Mirancea, M., Wessels, J., Müller, C., Essl, M., Eble, J., Tolosa,
E., … Klein, G. (2006). Characterization of a conduit system containing laminin-5
in the human thymus: a potential transport system for small molecules. Journal
of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.02840'
chicago: 'Drumea Mirancea, Mihaela, Johannes Wessels, Claudia Müller, Mike Essl,
Johannes Eble, Eva Tolosa, Manuel Koch, et al. “Characterization of a Conduit
System Containing Laminin-5 in the Human Thymus: A Potential Transport System
for Small Molecules.” Journal of Cell Science. Company of Biologists, 2006.
https://doi.org/10.1242/jcs.02840.'
ieee: 'M. Drumea Mirancea et al., “Characterization of a conduit system containing
laminin-5 in the human thymus: a potential transport system for small molecules,”
Journal of Cell Science, vol. 119, no. Pt 7. Company of Biologists, pp.
1396–1405, 2006.'
ista: 'Drumea Mirancea M, Wessels J, Müller C, Essl M, Eble J, Tolosa E, Koch M,
Reinhardt D, Sixt MK, Sorokin L, Stierhof Y, Schwarz H, Klein G. 2006. Characterization
of a conduit system containing laminin-5 in the human thymus: a potential transport
system for small molecules. Journal of Cell Science. 119(Pt 7), 1396–1405.'
mla: 'Drumea Mirancea, Mihaela, et al. “Characterization of a Conduit System Containing
Laminin-5 in the Human Thymus: A Potential Transport System for Small Molecules.”
Journal of Cell Science, vol. 119, no. Pt 7, Company of Biologists, 2006,
pp. 1396–405, doi:10.1242/jcs.02840.'
short: M. Drumea Mirancea, J. Wessels, C. Müller, M. Essl, J. Eble, E. Tolosa, M.
Koch, D. Reinhardt, M.K. Sixt, L. Sorokin, Y. Stierhof, H. Schwarz, G. Klein,
Journal of Cell Science 119 (2006) 1396–1405.
date_created: 2018-12-11T12:05:58Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:53:18Z
day: '01'
doi: 10.1242/jcs.02840
extern: 1
intvolume: ' 119'
issue: Pt 7
month: '04'
page: 1396 - 1405
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '2192'
quality_controlled: 0
status: public
title: 'Characterization of a conduit system containing laminin-5 in the human thymus:
a potential transport system for small molecules'
type: journal_article
volume: 119
year: '2006'
...
---
_id: '3935'
abstract:
- lang: eng
text: Integrins regulate cell behavior through the assembly of multiprotein complexes
at the site of cell adhesion. Parvins are components of such a multiprotein complex.
They consist of three members (alpha-, beta-, and gamma-parvin), form a functional
complex with integrin-linked kinase (ILK) and PINCH, and link integrins to the
actin cytoskeleton. Whereas alpha- and beta-parvins are widely expressed, gamma-parvin
has been reported to be expressed in hematopoietic organs. In the present study,
we report the expression pattern of the parvins in hematopoietic cells and the
phenotypic analysis of gamma-parvin-deficient mice. Whereas alpha-parvin is not
expressed in hematopoietic cells, beta-parvin is only found in myeloid cells and
gamma-parvin is present in both cells of the myeloid and lymphoid lineages, where
it binds ILK. Surprisingly, loss of gamma-parvin expression had no effect on blood
cell differentiation, proliferation, and survival and no consequence for the T-cell-dependent
antibody response and lymphocyte and dendritic cell migration. These data indicate
that despite the high expression of gamma-parvin in hematopoietic cells it must
play a more subtle role for blood cell homeostasis.
author:
- first_name: Haiyan
full_name: Chu, Haiyan
last_name: Chu
- first_name: Ingo
full_name: Thievessen, Ingo
last_name: Thievessen
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Ari
full_name: Waisman, Ari
last_name: Waisman
- first_name: Attila
full_name: Braun, Attila
last_name: Braun
- first_name: Angelika
full_name: Noegel, Angelika A
last_name: Noegel
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: Chu H, Thievessen I, Sixt MK, et al. γ-Parvin is dispensable for hematopoiesis,
leukocyte trafficking, and T-cell-dependent antibody response. Molecular and
Cellular Biology. 2006;26(5):1817-1825. doi:10.1128/MCB.26.5.1817-1825.2006
apa: Chu, H., Thievessen, I., Sixt, M. K., Lämmermann, T., Waisman, A., Braun, A.,
… Fässler, R. (2006). γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking,
and T-cell-dependent antibody response. Molecular and Cellular Biology.
American Society for Microbiology. https://doi.org/10.1128/MCB.26.5.1817-1825.2006
chicago: Chu, Haiyan, Ingo Thievessen, Michael K Sixt, Tim Lämmermann, Ari Waisman,
Attila Braun, Angelika Noegel, and Reinhard Fässler. “γ-Parvin Is Dispensable
for Hematopoiesis, Leukocyte Trafficking, and T-Cell-Dependent Antibody Response.”
Molecular and Cellular Biology. American Society for Microbiology, 2006.
https://doi.org/10.1128/MCB.26.5.1817-1825.2006.
ieee: H. Chu et al., “γ-Parvin is dispensable for hematopoiesis, leukocyte
trafficking, and T-cell-dependent antibody response,” Molecular and Cellular
Biology, vol. 26, no. 5. American Society for Microbiology, pp. 1817–1825,
2006.
ista: Chu H, Thievessen I, Sixt MK, Lämmermann T, Waisman A, Braun A, Noegel A,
Fässler R. 2006. γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking,
and T-cell-dependent antibody response. Molecular and Cellular Biology. 26(5),
1817–1825.
mla: Chu, Haiyan, et al. “γ-Parvin Is Dispensable for Hematopoiesis, Leukocyte Trafficking,
and T-Cell-Dependent Antibody Response.” Molecular and Cellular Biology,
vol. 26, no. 5, American Society for Microbiology, 2006, pp. 1817–25, doi:10.1128/MCB.26.5.1817-1825.2006.
short: H. Chu, I. Thievessen, M.K. Sixt, T. Lämmermann, A. Waisman, A. Braun, A.
Noegel, R. Fässler, Molecular and Cellular Biology 26 (2006) 1817–1825.
date_created: 2018-12-11T12:05:58Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:53:18Z
day: '01'
doi: 10.1128/MCB.26.5.1817-1825.2006
extern: 1
intvolume: ' 26'
issue: '5'
month: '03'
page: 1817 - 1825
publication: Molecular and Cellular Biology
publication_status: published
publisher: American Society for Microbiology
publist_id: '2193'
quality_controlled: 0
status: public
title: γ-Parvin is dispensable for hematopoiesis, leukocyte trafficking, and T-cell-dependent
antibody response
type: journal_article
volume: 26
year: '2006'
...
---
_id: '3936'
abstract:
- lang: eng
text: At least eight of the twelve known members of the beta1 integrin family are
expressed on hematopoietic cells. Among these, the VCAM-1 receptor alpha4beta1
has received most attention as a main factor mediating firm adhesion to the endothelium
during blood cell extravasation. Therapeutic trials are ongoing into the use of
antibodies and small molecule inhibitors to target this interaction and hence
obtain anti-inflammatory effects. However, extravasation is only one possible
process that is mediated by beta1 integrins and there is evidence that they also
mediate leukocyte retention and positioning in the tissue, lymphocyte activation
and possibly migration within the interstitium. Genetic mouse models where integrins
are selectively deleted on blood cells have been used to investigate these functions
and further studies will be invaluable to critically evaluate therapeutic trials.
author:
- first_name: Michael K
full_name: Michael Sixt
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Martina
full_name: Bauer, Martina
last_name: Bauer
- first_name: Tim
full_name: Lämmermann, Tim
last_name: Lämmermann
- first_name: Reinhard
full_name: Fässler, Reinhard
last_name: Fässler
citation:
ama: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. β1 integrins: zip codes and signaling
relay for blood cells. Current Opinion in Cell Biology. 2006;18(5):482-490.
doi:10.1016/j.ceb.2006.08.007'
apa: 'Sixt, M. K., Bauer, M., Lämmermann, T., & Fässler, R. (2006). β1 integrins:
zip codes and signaling relay for blood cells. Current Opinion in Cell Biology.
Elsevier. https://doi.org/10.1016/j.ceb.2006.08.007'
chicago: 'Sixt, Michael K, Martina Bauer, Tim Lämmermann, and Reinhard Fässler.
“Β1 Integrins: Zip Codes and Signaling Relay for Blood Cells.” Current Opinion
in Cell Biology. Elsevier, 2006. https://doi.org/10.1016/j.ceb.2006.08.007.'
ieee: 'M. K. Sixt, M. Bauer, T. Lämmermann, and R. Fässler, “β1 integrins: zip codes
and signaling relay for blood cells,” Current Opinion in Cell Biology,
vol. 18, no. 5. Elsevier, pp. 482–490, 2006.'
ista: 'Sixt MK, Bauer M, Lämmermann T, Fässler R. 2006. β1 integrins: zip codes
and signaling relay for blood cells. Current Opinion in Cell Biology. 18(5), 482–490.'
mla: 'Sixt, Michael K., et al. “Β1 Integrins: Zip Codes and Signaling Relay for
Blood Cells.” Current Opinion in Cell Biology, vol. 18, no. 5, Elsevier,
2006, pp. 482–90, doi:10.1016/j.ceb.2006.08.007.'
short: M.K. Sixt, M. Bauer, T. Lämmermann, R. Fässler, Current Opinion in Cell Biology
18 (2006) 482–490.
date_created: 2018-12-11T12:05:59Z
date_published: 2006-10-01T00:00:00Z
date_updated: 2021-01-12T07:53:19Z
day: '01'
doi: 10.1016/j.ceb.2006.08.007
extern: 1
intvolume: ' 18'
issue: '5'
month: '10'
page: 482 - 490
publication: Current Opinion in Cell Biology
publication_status: published
publisher: Elsevier
publist_id: '2191'
quality_controlled: 0
status: public
title: 'β1 integrins: zip codes and signaling relay for blood cells'
type: journal_article
volume: 18
year: '2006'
...
---
_id: '3978'
abstract:
- lang: eng
text: Evaluating the quality of experimentally determined protein structural models
is an essential step toward identifying potential errors and guiding further structural
refinement. Herein, we report the use of proton local density as a sensitive measure
to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256
high-resolution crystal structures with protons added and optimized, we show that
the local density of different proton types display distinct distributions. These
distributions can be characterized by statistical moments and are used to establish
local density Z-scores for evaluating both global and local packing for individual
protons. Analysis of 546 crystal structures at various resolutions shows that
the local density Z-scores increase as the structural resolution decreases and
correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733)
generated by all atom contact analysis. Local density Z-scores for NMR structures
exhibit a significantly wider range of values than for X-ray structures and demonstrate
a combination of potentially problematic inflation and compression. Water-refined
NMR structures show improved packing quality. Our analysis of a high-quality structural
ensemble of ubiquitin refined against order parameters shows proton density distributions
that correlate nearly perfectly with our standards derived from crystal structures,
further validating our approach. We present an automated analysis and visualization
tool for proton packing to evaluate the quality of NMR structures.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
- first_name: Pei
full_name: Zhou, Pei
last_name: Zhou
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
citation:
ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures
by local density of protons. Proteins: Structure, Function and Bioinformatics.
2006;62(4):852-864. doi:10.1002/prot.20811'
apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating
the quality of NMR structures by local density of protons. Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811'
chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating
the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure,
Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.'
ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality
of NMR structures by local density of protons,” Proteins: Structure, Function
and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.'
ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of
NMR structures by local density of protons. Proteins: Structure, Function and
Bioinformatics. 62(4), 852–864.'
mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density
of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62,
no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.'
short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function
and Bioinformatics 62 (2006) 852–864.'
date_created: 2018-12-11T12:06:14Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T07:53:36Z
day: '01'
doi: 10.1002/prot.20811
extern: 1
intvolume: ' 62'
issue: '4'
month: '03'
page: 852 - 864
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2146'
quality_controlled: 0
status: public
title: Evaluating the quality of NMR structures by local density of protons
type: journal_article
volume: 62
year: '2006'
...
---
_id: '3979'
abstract:
- lang: eng
text: Protein-protein interactions, which form the basis for most cellular processes,
result in the formation of protein interfaces. Believing that the local shape
of proteins is crucial, we take a geometric approach and present a definition
of an interface surface formed by two or more proteins as a subset of their Voronoi
diagram. The definition deals with the difficult and important problem of specifying
interface boundaries by invoking methods used in the alpha shape representation
of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct
surfaces, and the assessment of the importance of topological features. We present
an algorithm to construct the surface and define a hierarchy that distinguishes
core and peripheral regions. This hierarchy is shown to have correlation with
hot-spots in protein-protein interactions. Finally, we study the geometric and
topological properties of interface surfaces and show their high degree of contortion.
author:
- first_name: Yih
full_name: Ban, Yih-En Andrew
last_name: Ban
- first_name: Herbert
full_name: Herbert Edelsbrunner
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Johannes
full_name: Rudolph, Johannes
last_name: Rudolph
citation:
ama: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes.
Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957
apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for
protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957
chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces
for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957.
ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein
complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006.
ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein
complexes. Journal of the ACM. 53(3), 361–378.
mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal
of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957.
short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378.
date_created: 2018-12-11T12:06:14Z
date_published: 2006-05-01T00:00:00Z
date_updated: 2021-01-12T07:53:37Z
day: '01'
doi: 10.1145/1147954.1147957
extern: 1
intvolume: ' 53'
issue: '3'
month: '05'
page: 361 - 378
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '2147'
quality_controlled: 0
status: public
title: Interface surfaces for protein-protein complexes
type: journal_article
volume: 53
year: '2006'
...
---
_id: '3980'
abstract:
- lang: eng
text: Given a smoothly embedded 2-manifold in R-3, we define the elevation of a
point as the height difference to a canonically defined second point on the same
manifold. Our definition is invariant under rigid motions and can be used to define
features such as lines of discontinuous or continuous but non-smooth elevation.
We give an algorithm for finding points of locally maximum elevation, which we
suggest mark cavities and protrusions and are useful in matching shapes as for
example in protein docking.
author:
- first_name: Pankaj
full_name: Agarwal, Pankaj K
last_name: Agarwal
- 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: Yusu
full_name: Wang, Yusu
last_name: Wang
citation:
ama: Agarwal P, Edelsbrunner H, Harer J, Wang Y. Extreme elevation on a 2-manifold.
Discrete & Computational Geometry. 2006;36(4):553-572. doi:10.1007/s00454-006-1265-8
apa: Agarwal, P., Edelsbrunner, H., Harer, J., & Wang, Y. (2006). Extreme elevation
on a 2-manifold. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-006-1265-8
chicago: Agarwal, Pankaj, Herbert Edelsbrunner, John Harer, and Yusu Wang. “Extreme
Elevation on a 2-Manifold.” Discrete & Computational Geometry. Springer,
2006. https://doi.org/10.1007/s00454-006-1265-8.
ieee: P. Agarwal, H. Edelsbrunner, J. Harer, and Y. Wang, “Extreme elevation on
a 2-manifold,” Discrete & Computational Geometry, vol. 36, no. 4. Springer,
pp. 553–572, 2006.
ista: Agarwal P, Edelsbrunner H, Harer J, Wang Y. 2006. Extreme elevation on a 2-manifold.
Discrete & Computational Geometry. 36(4), 553–572.
mla: Agarwal, Pankaj, et al. “Extreme Elevation on a 2-Manifold.” Discrete &
Computational Geometry, vol. 36, no. 4, Springer, 2006, pp. 553–72, doi:10.1007/s00454-006-1265-8.
short: P. Agarwal, H. Edelsbrunner, J. Harer, Y. Wang, Discrete & Computational
Geometry 36 (2006) 553–572.
date_created: 2018-12-11T12:06:15Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:53:38Z
day: '01'
doi: 10.1007/s00454-006-1265-8
extern: 1
intvolume: ' 36'
issue: '4'
month: '12'
page: 553 - 572
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '2148'
quality_controlled: 0
status: public
title: Extreme elevation on a 2-manifold
type: journal_article
volume: 36
year: '2006'
...
---
_id: '4140'
abstract:
- lang: eng
text: Wnt11 is a key signal, determining cell polarization and migration during
vertebrate gastrulation. It is known that Wnt11 functionally interacts with several
signaling components, the homologues of which control planar cell polarity in
Drosophila melanogaster. Although in D. melanogaster these components are thought
to polarize cells by asymmetrically localizing at the plasma membrane, it is not
yet clear whether their subcellular localization plays a similarly important role
in vertebrates. We show that in zebrafish embryonic cells, Wnt11 locally functions
at the plasma membrane by accumulating its receptor, Frizzled 7, on adjacent sites
of cell contacts. Wnt11-induced Frizzled 7 accumulations recruit the intracellular
Wnt signaling mediator Dishevelled, as well as Wnt11 itself, and locally increase
cell contact persistence. This increase in cell contact persistence is mediated
by the local interaction of Wnt11, Frizzled 7, and the atypical cadherin Flamingo
at the plasma membrane, and it does not require the activity of further downstream
effectors of Wnt11 signaling, such as RhoA and Rok2. We propose that Wnt11, by
interacting with Frizzled 7 and Flamingo, modulates local cell contact persistence
to coordinate cell movements during gastrulation.
article_processing_charge: No
author:
- first_name: Sabine
full_name: Witzel, Sabine
last_name: Witzel
- first_name: Vitaly
full_name: Zimyanin, Vitaly
last_name: Zimyanin
- first_name: Filipa
full_name: Carreira Barbosa, Filipa
last_name: Carreira Barbosa
- first_name: Masazumi
full_name: Tada, Masazumi
last_name: Tada
- 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: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. Wnt11 controls
cell contact persistence by local accumulation of Frizzled 7 at the plasma membrane.
Journal of Cell Biology. 2006;175(5):791-802. doi:10.1083/jcb.200606017
apa: Witzel, S., Zimyanin, V., Carreira Barbosa, F., Tada, M., & Heisenberg,
C.-P. J. (2006). Wnt11 controls cell contact persistence by local accumulation
of Frizzled 7 at the plasma membrane. Journal of Cell Biology. Rockefeller
University Press. https://doi.org/10.1083/jcb.200606017
chicago: Witzel, Sabine, Vitaly Zimyanin, Filipa Carreira Barbosa, Masazumi Tada,
and Carl-Philipp J Heisenberg. “Wnt11 Controls Cell Contact Persistence by Local
Accumulation of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology.
Rockefeller University Press, 2006. https://doi.org/10.1083/jcb.200606017.
ieee: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, and C.-P. J. Heisenberg,
“Wnt11 controls cell contact persistence by local accumulation of Frizzled 7 at
the plasma membrane,” Journal of Cell Biology, vol. 175, no. 5. Rockefeller
University Press, pp. 791–802, 2006.
ista: Witzel S, Zimyanin V, Carreira Barbosa F, Tada M, Heisenberg C-PJ. 2006. Wnt11
controls cell contact persistence by local accumulation of Frizzled 7 at the plasma
membrane. Journal of Cell Biology. 175(5), 791–802.
mla: Witzel, Sabine, et al. “Wnt11 Controls Cell Contact Persistence by Local Accumulation
of Frizzled 7 at the Plasma Membrane.” Journal of Cell Biology, vol. 175,
no. 5, Rockefeller University Press, 2006, pp. 791–802, doi:10.1083/jcb.200606017.
short: S. Witzel, V. Zimyanin, F. Carreira Barbosa, M. Tada, C.-P.J. Heisenberg,
Journal of Cell Biology 175 (2006) 791–802.
date_created: 2018-12-11T12:07:11Z
date_published: 2006-12-04T00:00:00Z
date_updated: 2021-01-12T07:54:48Z
day: '04'
doi: 10.1083/jcb.200606017
extern: '1'
intvolume: ' 175'
issue: '5'
language:
- iso: eng
month: '12'
oa_version: None
page: 791 - 802
publication: Journal of Cell Biology
publication_status: published
publisher: Rockefeller University Press
publist_id: '1980'
status: public
title: Wnt11 controls cell contact persistence by local accumulation of Frizzled 7
at the plasma membrane
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 175
year: '2006'
...
---
_id: '4145'
abstract:
- lang: eng
text: The detection of microRNAs (miRNAs) at single-cell resolution is important
for studying the role of these posttranscriptional regulators. Here, we use a
dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent
protein (mRFP)-sensor (DFRS) plasmid, injected into zebrafish blastomeres or electroporated
into defined tissues of mouse embryos in utero or ex utero, to monitor the dynamics
of specific miRNAs in individual live cells. This approach reveals, for example,
that in the developing mouse central nervous system,, miR-124a is expressed not
only in postmitotic neurons but also in neuronal progenitor cells. Collectively,
our results demonstrate that acute administration of DFRS plasmids.offers an alternative
to previous in situ hybridization and transgenic approaches and allows the monitoring
of miRNA appearance and disappearance in defined cell lineages during vertebrate
development.
article_processing_charge: No
author:
- first_name: Davide
full_name: Tonelli, Davide
last_name: Tonelli
- first_name: Frederico
full_name: Calegari, Frederico
last_name: Calegari
- first_name: Ji
full_name: Fei, Ji
last_name: Fei
- first_name: Tadashi
full_name: Nomura, Tadashi
last_name: Nomura
- first_name: Noriko
full_name: Osumi, Noriko
last_name: Osumi
- 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: Wieland
full_name: Huttner, Wieland
last_name: Huttner
citation:
ama: Tonelli D, Calegari F, Fei J, et al. Single-cell detection of microRNAs in
developing vertebrate embryos after acute administration of a dual-fluorescence
reporter/sensor plasmid. Biotechniques. 2006;41(6):727-732. doi:10.2144/000112296
apa: Tonelli, D., Calegari, F., Fei, J., Nomura, T., Osumi, N., Heisenberg, C.-P.
J., & Huttner, W. (2006). Single-cell detection of microRNAs in developing
vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor
plasmid. Biotechniques. Informa Healthcare. https://doi.org/10.2144/000112296
chicago: Tonelli, Davide, Frederico Calegari, Ji Fei, Tadashi Nomura, Noriko Osumi,
Carl-Philipp J Heisenberg, and Wieland Huttner. “Single-Cell Detection of MicroRNAs
in Developing Vertebrate Embryos after Acute Administration of a Dual-Fluorescence
Reporter/Sensor Plasmid.” Biotechniques. Informa Healthcare, 2006. https://doi.org/10.2144/000112296.
ieee: D. Tonelli et al., “Single-cell detection of microRNAs in developing
vertebrate embryos after acute administration of a dual-fluorescence reporter/sensor
plasmid,” Biotechniques, vol. 41, no. 6. Informa Healthcare, pp. 727–732,
2006.
ista: Tonelli D, Calegari F, Fei J, Nomura T, Osumi N, Heisenberg C-PJ, Huttner
W. 2006. Single-cell detection of microRNAs in developing vertebrate embryos after
acute administration of a dual-fluorescence reporter/sensor plasmid. Biotechniques.
41(6), 727–732.
mla: Tonelli, Davide, et al. “Single-Cell Detection of MicroRNAs in Developing Vertebrate
Embryos after Acute Administration of a Dual-Fluorescence Reporter/Sensor Plasmid.”
Biotechniques, vol. 41, no. 6, Informa Healthcare, 2006, pp. 727–32, doi:10.2144/000112296.
short: D. Tonelli, F. Calegari, J. Fei, T. Nomura, N. Osumi, C.-P.J. Heisenberg,
W. Huttner, Biotechniques 41 (2006) 727–732.
date_created: 2018-12-11T12:07:12Z
date_published: 2006-12-01T00:00:00Z
date_updated: 2021-01-12T07:54:50Z
day: '01'
doi: 10.2144/000112296
extern: '1'
intvolume: ' 41'
issue: '6'
language:
- iso: eng
month: '12'
oa_version: None
page: 727 - 732
publication: Biotechniques
publication_status: published
publisher: Informa Healthcare
publist_id: '1974'
status: public
title: Single-cell detection of microRNAs in developing vertebrate embryos after acute
administration of a dual-fluorescence reporter/sensor plasmid
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2006'
...
---
_id: '4173'
abstract:
- lang: eng
text: 'Background: Zebrafish (D. rerio) has become a powerful and widely used model
system for the analysis of vertebrate embryogenesis and organ development. While
genetic methods are readily available in zebrafish, protocols for two dimensional
(2D) gel electrophoresis and proteomics have yet to be developed. Results: As
a prerequisite to carry out proteomic experiments with early zebrafish embryos,
we developed a method to efficiently remove the yolk from large batches of embryos.
This method enabled high resolution 2D gel electrophoresis and improved Western
blotting considerably. Here, we provide detailed protocols for proteomics in zebrafish
from sample preparation to mass spectrometry (MS), including a comparison of databases
for MS identification of zebrafish proteins. Conclusion: The provided protocols
for proteomic analysis of early embryos enable research to be taken in novel directions
in embryogenesis.'
article_processing_charge: No
author:
- first_name: Vinzenz
full_name: Link, Vinzenz
last_name: Link
- first_name: Andrej
full_name: Shevchenko, Andrej
last_name: Shevchenko
- 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: Link V, Shevchenko A, Heisenberg C-PJ. Proteomics of early zebrafish embryos.
BMC Developmental Biology. 2006;6:1-9. doi:10.1186/1471-213X-6-1
apa: Link, V., Shevchenko, A., & Heisenberg, C.-P. J. (2006). Proteomics of
early zebrafish embryos. BMC Developmental Biology. BioMed Central. https://doi.org/10.1186/1471-213X-6-1
chicago: Link, Vinzenz, Andrej Shevchenko, and Carl-Philipp J Heisenberg. “Proteomics
of Early Zebrafish Embryos.” BMC Developmental Biology. BioMed Central,
2006. https://doi.org/10.1186/1471-213X-6-1.
ieee: V. Link, A. Shevchenko, and C.-P. J. Heisenberg, “Proteomics of early zebrafish
embryos,” BMC Developmental Biology, vol. 6. BioMed Central, pp. 1–9, 2006.
ista: Link V, Shevchenko A, Heisenberg C-PJ. 2006. Proteomics of early zebrafish
embryos. BMC Developmental Biology. 6, 1–9.
mla: Link, Vinzenz, et al. “Proteomics of Early Zebrafish Embryos.” BMC Developmental
Biology, vol. 6, BioMed Central, 2006, pp. 1–9, doi:10.1186/1471-213X-6-1.
short: V. Link, A. Shevchenko, C.-P.J. Heisenberg, BMC Developmental Biology 6 (2006)
1–9.
date_created: 2018-12-11T12:07:23Z
date_published: 2006-01-13T00:00:00Z
date_updated: 2021-01-12T07:55:02Z
day: '13'
doi: 10.1186/1471-213X-6-1
extern: '1'
intvolume: ' 6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
- open_access: '1'
url: http://www.biomedcentral.com/1471-213X/6/1
month: '01'
oa: 1
oa_version: None
page: 1 - 9
publication: BMC Developmental Biology
publication_status: published
publisher: BioMed Central
publist_id: '1945'
status: public
title: Proteomics of early zebrafish embryos
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2006'
...
---
_id: '4176'
abstract:
- lang: eng
text: 'During vertebrate gastrulation, a well-orchestrated series of morphogenetic
changes leads to the formation of the three germ layers: the ectoderm, mesoderm
and endoderm. The analysis of gene expression patterns during gastrulation has
been central to the identification of genes involved in germ layer formation.
However, many proteins are regulated on a translational or post-translational
level and are thus undetectable by gene expression analysis. Therefore, we developed
a 2D-gel-based comparative proteomic approach to target proteins involved in germ
layer morphogenesis during zebrafish gastrulation. Proteomes of ectodermal and
mesendodermal progenitor cells were compared and 35 significantly regulated proteins
were identified by mass spectrometry, including several proteins with predicted
functions in cytoskeletal organization. A comparison of our proteomic results
with data obtained in an accompanying microarray-based gene expression analysis
revealed no significant overlap, confirming the complementary nature of proteomics
and transcriptomics. The regulation of ezrin2, which was identified based on a
reduction in spot intensity in mesendodermal cells, was independently validated.
Furthermore, we show that ezrin2 is activated by phosphorylation in mesendodermal
cells and is required for proper germ layer morphogenesis. We demonstrate the
feasibility of proteomics in zebrafish, concluding that proteomics is a valuable
tool for analysis of early development.'
article_processing_charge: No
author:
- first_name: Vinzenz
full_name: Link, Vinzenz
last_name: Link
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: Irinka
full_name: Castanon, Irinka
last_name: Castanon
- first_name: Petra
full_name: Stockinger, Petra
last_name: Stockinger
- first_name: Andrej
full_name: Shevchenko, Andrej
last_name: Shevchenko
- 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: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ.
Identification of regulators of germ layer morphogenesis using proteomics in zebrafish.
Journal of Cell Science. 2006;119(10):2073-2083. doi:10.1242/jcs.02928
apa: Link, V., Carvalho, L., Castanon, I., Stockinger, P., Shevchenko, A., &
Heisenberg, C.-P. J. (2006). Identification of regulators of germ layer morphogenesis
using proteomics in zebrafish. Journal of Cell Science. Company of Biologists.
https://doi.org/10.1242/jcs.02928
chicago: Link, Vinzenz, Lara Carvalho, Irinka Castanon, Petra Stockinger, Andrej
Shevchenko, and Carl-Philipp J Heisenberg. “Identification of Regulators of Germ
Layer Morphogenesis Using Proteomics in Zebrafish.” Journal of Cell Science.
Company of Biologists, 2006. https://doi.org/10.1242/jcs.02928.
ieee: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, and C.-P.
J. Heisenberg, “Identification of regulators of germ layer morphogenesis using
proteomics in zebrafish,” Journal of Cell Science, vol. 119, no. 10. Company
of Biologists, pp. 2073–2083, 2006.
ista: Link V, Carvalho L, Castanon I, Stockinger P, Shevchenko A, Heisenberg C-PJ.
2006. Identification of regulators of germ layer morphogenesis using proteomics
in zebrafish. Journal of Cell Science. 119(10), 2073–2083.
mla: Link, Vinzenz, et al. “Identification of Regulators of Germ Layer Morphogenesis
Using Proteomics in Zebrafish.” Journal of Cell Science, vol. 119, no.
10, Company of Biologists, 2006, pp. 2073–83, doi:10.1242/jcs.02928.
short: V. Link, L. Carvalho, I. Castanon, P. Stockinger, A. Shevchenko, C.-P.J.
Heisenberg, Journal of Cell Science 119 (2006) 2073–2083.
date_created: 2018-12-11T12:07:24Z
date_published: 2006-05-15T00:00:00Z
date_updated: 2021-01-12T07:55:04Z
day: '15'
doi: 10.1242/jcs.02928
extern: '1'
intvolume: ' 119'
issue: '10'
language:
- iso: eng
month: '05'
oa_version: None
page: 2073 - 2083
publication: Journal of Cell Science
publication_status: published
publisher: Company of Biologists
publist_id: '1944'
status: public
title: Identification of regulators of germ layer morphogenesis using proteomics in
zebrafish
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2006'
...
---
_id: '4178'
abstract:
- lang: eng
text: Detailed reconstruction of the spatiotemporal history of embryonic cells is
key to understanding tissue formation processes but is often complicated by the
large number of cells involved, particularly so in vertebrates. Through a combination
of high-resolution time-lapse lineage tracing and antibody staining, we have analyzed
the movement of mesencephalic and metencephalic cell populations in the early
zebrafish embryo. To facilitate the analysis of our cell tracking data, we have
created TracePilot, a software tool that allows interactive manipulation and visualization
of tracking data. We demonstrate its utility by showing novel visualizations of
cell movement in the developing zebrafish brain. TracePilot (http://www.mpi-cbg.de/tracepilot)
is Java-based, available free of charge, and has a program structure that allows
the incorporation of additional analysis tools.
article_processing_charge: No
author:
- first_name: Tobias
full_name: Langenberg, Tobias
last_name: Langenberg
- first_name: Tadeusz
full_name: Dracz, Tadeusz
last_name: Dracz
- first_name: Andrew
full_name: Oates, Andrew
last_name: Oates
- 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: Michael
full_name: Brand, Michael
last_name: Brand
citation:
ama: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. Analysis and visualization
of cell movement in the developing zebrafish brain. Developmental Dynamics.
2006;235(4):928-933. doi:10.1002/dvdy.20692
apa: Langenberg, T., Dracz, T., Oates, A., Heisenberg, C.-P. J., & Brand, M.
(2006). Analysis and visualization of cell movement in the developing zebrafish
brain. Developmental Dynamics. Wiley-Blackwell. https://doi.org/10.1002/dvdy.20692
chicago: Langenberg, Tobias, Tadeusz Dracz, Andrew Oates, Carl-Philipp J Heisenberg,
and Michael Brand. “Analysis and Visualization of Cell Movement in the Developing
Zebrafish Brain.” Developmental Dynamics. Wiley-Blackwell, 2006. https://doi.org/10.1002/dvdy.20692.
ieee: T. Langenberg, T. Dracz, A. Oates, C.-P. J. Heisenberg, and M. Brand, “Analysis
and visualization of cell movement in the developing zebrafish brain,” Developmental
Dynamics, vol. 235, no. 4. Wiley-Blackwell, pp. 928–933, 2006.
ista: Langenberg T, Dracz T, Oates A, Heisenberg C-PJ, Brand M. 2006. Analysis and
visualization of cell movement in the developing zebrafish brain. Developmental
Dynamics. 235(4), 928–933.
mla: Langenberg, Tobias, et al. “Analysis and Visualization of Cell Movement in
the Developing Zebrafish Brain.” Developmental Dynamics, vol. 235, no.
4, Wiley-Blackwell, 2006, pp. 928–33, doi:10.1002/dvdy.20692.
short: T. Langenberg, T. Dracz, A. Oates, C.-P.J. Heisenberg, M. Brand, Developmental
Dynamics 235 (2006) 928–933.
date_created: 2018-12-11T12:07:25Z
date_published: 2006-04-01T00:00:00Z
date_updated: 2021-01-12T07:55:04Z
day: '01'
doi: 10.1002/dvdy.20692
extern: '1'
intvolume: ' 235'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 928 - 933
publication: Developmental Dynamics
publication_status: published
publisher: Wiley-Blackwell
publist_id: '1940'
status: public
title: Analysis and visualization of cell movement in the developing zebrafish brain
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 235
year: '2006'
...
---
_id: '4184'
abstract:
- lang: eng
text: Epithelial morphogenesis depends on coordinated changes in cell shape, a process
that is still poorly understood. During zebrafish epiboly and Drosophila dorsal
closure, cell-shape changes at the epithelial margin are of critical importance.
Here evidence is provided for a conserved mechanism of local actin and myosin
2 recruitment during theses events. It was found that during epiboly of the zebrafish
embryo, the movement of the outer epithelium (enveloping layer) over the yolk
cell surface involves the constriction of marginal cells. This process depends
on the recruitment of actin and myosin 2 within the yolk cytoplasm along the margin
of the enveloping layer. Actin and myosin 2 recruitment within the yolk cytoplasm
requires the Ste20-like kinase Msn1, an orthologue of Drosophila Misshapen. Similarly,
in Drosophila, actin and myosin 2 localization and cell constriction at the margin
of the epidermis mediate dorsal closure and are controlled by Misshapen. Thus,
this study has characterized a conserved mechanism underlying coordinated cell-shape
changes during epithelial morphogenesis.
article_processing_charge: No
author:
- first_name: Mathias
full_name: Köppen, Mathias
last_name: Köppen
- first_name: Beatriz
full_name: Fernández, Beatriz
last_name: Fernández
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- first_name: António
full_name: Jacinto, António
last_name: Jacinto
- 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: 'Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Coordinated
cell-shape changes control epithelial movement in zebrafish and Drosophila. Development.
2006;133(14):2671-2681. doi:doi:
10.1242/dev.02439'
apa: 'Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., & Heisenberg, C.-P.
J. (2006). Coordinated cell-shape changes control epithelial movement in zebrafish
and Drosophila. Development. Company of Biologists. https://doi.org/doi: 10.1242/dev.02439'
chicago: 'Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and
Carl-Philipp J Heisenberg. “Coordinated Cell-Shape Changes Control Epithelial
Movement in Zebrafish and Drosophila.” Development. Company of Biologists,
2006. https://doi.org/doi: 10.1242/dev.02439.'
ieee: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg,
“Coordinated cell-shape changes control epithelial movement in zebrafish and Drosophila,”
Development, vol. 133, no. 14. Company of Biologists, pp. 2671–2681, 2006.
ista: Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2006. Coordinated
cell-shape changes control epithelial movement in zebrafish and Drosophila. Development.
133(14), 2671–2681.
mla: 'Köppen, Mathias, et al. “Coordinated Cell-Shape Changes Control Epithelial
Movement in Zebrafish and Drosophila.” Development, vol. 133, no. 14, Company
of Biologists, 2006, pp. 2671–81, doi:doi:
10.1242/dev.02439.'
short: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Development
133 (2006) 2671–2681.
date_created: 2018-12-11T12:07:27Z
date_published: 2006-07-15T00:00:00Z
date_updated: 2021-01-12T07:55:08Z
day: '15'
doi: 'doi: 10.1242/dev.02439'
extern: '1'
intvolume: ' 133'
issue: '14'
language:
- iso: eng
month: '07'
oa_version: None
page: 2671 - 2681
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '1935'
status: public
title: Coordinated cell-shape changes control epithelial movement in zebrafish and
Drosophila
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 133
year: '2006'
...
---
_id: '4218'
abstract:
- lang: eng
text: The molecular and cellular mechanisms governing cell motility and directed
migration in response to the chemokine SDF-1 are largely unknown. Here, we demonstrate
that zebrafish primordial germ cells whose migration is guided by SDF-1 generate
bleb-like protrusions that are powered by cytoplasmic flow. Protrusions are formed
at sites of higher levels of free calcium where activation of myosin contraction
occurs. Separation of the acto-myosin cortex from the plasma membrane at these
sites is followed by a flow of cytoplasm into the forming bleb. We propose that
polarized activation of the receptor CXCR4 leads to a rise in free calcium that
in turn activates myosin contraction in the part of the cell responding to higher
levels of the ligand SDF-1. The biased formation of new protrusions in a particular
region of the cell in response to SDF-1 defines the leading edge and the direction
of cell migration.
article_processing_charge: No
author:
- first_name: Heiko
full_name: Blaser, Heiko
last_name: Blaser
- first_name: Michal
full_name: Reichman Fried, Michal
last_name: Reichman Fried
- first_name: Irinka
full_name: Castanon, Irinka
last_name: Castanon
- first_name: Karin
full_name: Dumstrei, Karin
last_name: Dumstrei
- first_name: Florence
full_name: Marlow, Florence
last_name: Marlow
- first_name: Koichi
full_name: Kawakami, Koichi
last_name: Kawakami
- 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: Erez
full_name: Raz, Erez
last_name: Raz
citation:
ama: 'Blaser H, Reichman Fried M, Castanon I, et al. Migration of zebrafish primordial
germ cells: A role for myosin contraction and cytoplasmic flow. Developmental
Cell. 2006;11(5):613-627. doi:10.1016/j.devcel.2006.09.023'
apa: 'Blaser, H., Reichman Fried, M., Castanon, I., Dumstrei, K., Marlow, F., Kawakami,
K., … Raz, E. (2006). Migration of zebrafish primordial germ cells: A role for
myosin contraction and cytoplasmic flow. Developmental Cell. Cell Press.
https://doi.org/10.1016/j.devcel.2006.09.023'
chicago: 'Blaser, Heiko, Michal Reichman Fried, Irinka Castanon, Karin Dumstrei,
Florence Marlow, Koichi Kawakami, Lilianna Solnica Krezel, Carl-Philipp J Heisenberg,
and Erez Raz. “Migration of Zebrafish Primordial Germ Cells: A Role for Myosin
Contraction and Cytoplasmic Flow.” Developmental Cell. Cell Press, 2006.
https://doi.org/10.1016/j.devcel.2006.09.023.'
ieee: 'H. Blaser et al., “Migration of zebrafish primordial germ cells: A
role for myosin contraction and cytoplasmic flow,” Developmental Cell,
vol. 11, no. 5. Cell Press, pp. 613–627, 2006.'
ista: 'Blaser H, Reichman Fried M, Castanon I, Dumstrei K, Marlow F, Kawakami K,
Solnica Krezel L, Heisenberg C-PJ, Raz E. 2006. Migration of zebrafish primordial
germ cells: A role for myosin contraction and cytoplasmic flow. Developmental
Cell. 11(5), 613–627.'
mla: 'Blaser, Heiko, et al. “Migration of Zebrafish Primordial Germ Cells: A Role
for Myosin Contraction and Cytoplasmic Flow.” Developmental Cell, vol.
11, no. 5, Cell Press, 2006, pp. 613–27, doi:10.1016/j.devcel.2006.09.023.'
short: H. Blaser, M. Reichman Fried, I. Castanon, K. Dumstrei, F. Marlow, K. Kawakami,
L. Solnica Krezel, C.-P.J. Heisenberg, E. Raz, Developmental Cell 11 (2006) 613–627.
date_created: 2018-12-11T12:07:39Z
date_published: 2006-11-06T00:00:00Z
date_updated: 2021-01-12T07:55:23Z
day: '06'
doi: 10.1016/j.devcel.2006.09.023
extern: '1'
intvolume: ' 11'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 613 - 627
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '1898'
status: public
title: 'Migration of zebrafish primordial germ cells: A role for myosin contraction
and cytoplasmic flow'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2006'
...
---
_id: '4235'
author:
- first_name: Harold
full_name: Harold Vladar
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: J.
full_name: González,J. A
last_name: González
citation:
ama: de Vladar H, González J. Dynamic response of cancer under the influence of
immunological activity and therapy. Journal of Theoretical Biology. 2006:91-109.
apa: de Vladar, H., & González, J. (2006). Dynamic response of cancer under
the influence of immunological activity and therapy. Journal of Theoretical
Biology. Elsevier.
chicago: Vladar, Harold de, and J. González. “Dynamic Response of Cancer under the
Influence of Immunological Activity and Therapy.” Journal of Theoretical Biology.
Elsevier, 2006.
ieee: H. de Vladar and J. González, “Dynamic response of cancer under the influence
of immunological activity and therapy,” Journal of Theoretical Biology.
Elsevier, pp. 91–109, 2006.
ista: de Vladar H, González J. 2006. Dynamic response of cancer under the influence
of immunological activity and therapy. Journal of Theoretical Biology., 91–109.
mla: de Vladar, Harold, and J. González. “Dynamic Response of Cancer under the Influence
of Immunological Activity and Therapy.” Journal of Theoretical Biology,
Elsevier, 2006, pp. 91–109.
short: H. de Vladar, J. González, Journal of Theoretical Biology (2006) 91–109.
date_created: 2018-12-11T12:07:45Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:30Z
day: '01'
extern: 1
month: '01'
page: 91 - 109
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1879'
quality_controlled: 0
status: public
title: Dynamic response of cancer under the influence of immunological activity and
therapy
type: journal_article
year: '2006'
...
---
_id: '4237'
abstract:
- lang: eng
text: The growth function of populations is central in biomathematics. The main
dogma is the existence of density-dependence mechanisms, which can be modelled
with distinct functional forms that depend on the size of the Population. One
important class of regulatory functions is the theta-logistic, which generalizes
the logistic equation. Using this model as a motivation, this paper introduces
a simple dynamical reformulation that generalizes many growth functions. The reformulation
consists of two equations, one for population size, and one for the growth rate.
Furthermore, the model shows that although population is density-dependent, the
dynamics of the growth rate does not depend either on population size, nor on
the carrying capacity. Actually, the growth equation is uncoupled from the population
size equation, and the model has only two parameters, a Malthusian parameter rho
and a competition coefficient theta. Distinct sign combinations of these parameters
reproduce not only the family of theta-logistics, but also the van Bertalanffy,
Gompertz and Potential Growth equations, among other possibilities. It is also
shown that, except for two critical points, there is a general size-scaling relation
that includes those appearing in the most important allometric theories, including
the recently proposed Metabolic Theory of Ecology. With this model, several issues
of general interest are discussed such as the growth of animal population, extinctions,
cell growth and allometry, and the effect of environment over a population. (c)
2005 Elsevier Ltd. All rights reserved.
article_processing_charge: No
author:
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
citation:
ama: de Vladar H. Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. 2006;238(2):245-256. doi:3802
apa: de Vladar, H. (2006). Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. Elsevier. https://doi.org/3802
chicago: Vladar, Harold de. “Density-Dependence as a Size-Independent Regulatory
Mechanism.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/3802.
ieee: H. de Vladar, “Density-dependence as a size-independent regulatory mechanism,”
Journal of Theoretical Biology, vol. 238, no. 2. Elsevier, pp. 245–256,
2006.
ista: de Vladar H. 2006. Density-dependence as a size-independent regulatory mechanism.
Journal of Theoretical Biology. 238(2), 245–256.
mla: de Vladar, Harold. “Density-Dependence as a Size-Independent Regulatory Mechanism.”
Journal of Theoretical Biology, vol. 238, no. 2, Elsevier, 2006, pp. 245–56,
doi:3802.
short: H. de Vladar, Journal of Theoretical Biology 238 (2006) 245–256.
date_created: 2018-12-11T12:07:46Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:55:31Z
day: '01'
doi: '3802'
extern: '1'
intvolume: ' 238'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 245 - 256
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '1878'
status: public
title: Density-dependence as a size-independent regulatory mechanism
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 238
year: '2006'
...
---
_id: '4248'
abstract:
- lang: eng
text: 'In finite populations, genetic drift generates interference between selected
loci, causing advantageous alleles to be found more often on different chromosomes
than on the same chromosome, which reduces the rate of adaptation. This “Hill–Robertson
effect” generates indirect selection to increase recombination rates. We present
a new method to quantify the strength of this selection. Our model represents
a new beneficial allele (A) entering a population as a single copy, while another
beneficial allele (B) is sweeping at another locus. A third locus affects the
recombination rate between selected loci. Using a branching process model, we
calculate the probability distribution of the number of copies of A on the different
genetic backgrounds, after it is established but while it is still rare. Then,
we use a deterministic model to express the change in frequency of the recombination
modifier, due to hitchhiking, as A goes to fixation. We show that this method
can give good estimates of selection for recombination. Moreover, it shows that
recombination is selected through two different effects: it increases the fixation
probability of new alleles, and it accelerates selective sweeps. The relative
importance of these two effects depends on the relative times of occurrence of
the beneficial alleles.'
author:
- first_name: Denis
full_name: Roze, Denis
last_name: Roze
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Roze D, Barton NH. The Hill-Robertson effect and the evolution of recombination.
Genetics. 2006;173(3):1793-1811. doi:10.1534/genetics.106.058586
apa: Roze, D., & Barton, N. H. (2006). The Hill-Robertson effect and the evolution
of recombination. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.106.058586
chicago: Roze, Denis, and Nicholas H Barton. “The Hill-Robertson Effect and the
Evolution of Recombination.” Genetics. Genetics Society of America, 2006.
https://doi.org/10.1534/genetics.106.058586
.
ieee: D. Roze and N. H. Barton, “The Hill-Robertson effect and the evolution of
recombination,” Genetics, vol. 173, no. 3. Genetics Society of America,
pp. 1793–1811, 2006.
ista: Roze D, Barton NH. 2006. The Hill-Robertson effect and the evolution of recombination.
Genetics. 173(3), 1793–1811.
mla: Roze, Denis, and Nicholas H. Barton. “The Hill-Robertson Effect and the Evolution
of Recombination.” Genetics, vol. 173, no. 3, Genetics Society of America,
2006, pp. 1793–811, doi:10.1534/genetics.106.058586
.
short: D. Roze, N.H. Barton, Genetics 173 (2006) 1793–1811.
date_created: 2018-12-11T12:07:50Z
date_published: 2006-07-01T00:00:00Z
date_updated: 2021-01-12T07:55:36Z
day: '01'
doi: '10.1534/genetics.106.058586 '
extern: 1
intvolume: ' 173'
issue: '3'
month: '07'
page: 1793 - 1811
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '1854'
quality_controlled: 0
status: public
title: The Hill-Robertson effect and the evolution of recombination
type: journal_article
volume: 173
year: '2006'
...
---
_id: '4250'
abstract:
- lang: eng
text: A recent analysis has shown that divergence between human and chimpanzee varies
greatly across the genome. Although this is consistent with ‘hybridisation’ between
the diverging human and chimp lineages, such observations can be explained more
simply by the null model of allopatric speciation.
author:
- first_name: Nicholas H
full_name: Nicholas Barton
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Evolutionary Biology: How did the human species form? Current
Biology. 2006;16(16):647-650. doi:10.1016/j.cub.2006.07.032'
apa: 'Barton, N. H. (2006). Evolutionary Biology: How did the human species form?
Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2006.07.032'
chicago: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?”
Current Biology. Cell Press, 2006. https://doi.org/10.1016/j.cub.2006.07.032.'
ieee: 'N. H. Barton, “Evolutionary Biology: How did the human species form?,” Current
Biology, vol. 16, no. 16. Cell Press, pp. 647–650, 2006.'
ista: 'Barton NH. 2006. Evolutionary Biology: How did the human species form? Current
Biology. 16(16), 647–650.'
mla: 'Barton, Nicholas H. “Evolutionary Biology: How Did the Human Species Form?”
Current Biology, vol. 16, no. 16, Cell Press, 2006, pp. 647–50, doi:10.1016/j.cub.2006.07.032.'
short: N.H. Barton, Current Biology 16 (2006) 647–650.
date_created: 2018-12-11T12:07:51Z
date_published: 2006-08-22T00:00:00Z
date_updated: 2019-04-26T07:22:41Z
day: '22'
doi: 10.1016/j.cub.2006.07.032
extern: 1
intvolume: ' 16'
issue: '16'
month: '08'
page: 647 - 650
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '1850'
quality_controlled: 0
status: public
title: 'Evolutionary Biology: How did the human species form?'
type: review
volume: 16
year: '2006'
...
---
_id: '4345'
abstract:
- lang: eng
text: Der Artikel beschäftigt sich mit dem Konzept der Bibliothek 2.0 (bzw. Library
2.0). Er skizziert anhand einiger Beispiele die Entwicklung zum Web 2.0 und beschreibt,
wie Web 2.0-Technologien und -Anwendungen in Bibliotheken eingesetzt werden. Im
Mittelpunkt stehen Social-Tagging-Systeme, benutzerorientierte Erweiterungen von
Bibliothekskatalogen und Dokumentenservern sowie der Einsatz von Weblogs an Bibliotheken.
Ferner werden neue Anforderungen an Bibliothekare diskutiert.
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 - Die Bibliothek der Zukunft? Bibliotheksdienst.
2006;40(11):1250-1271. doi:424
apa: Danowski, P., & Heller, L. (2006). Bibliothek 2.0 - Die Bibliothek der
Zukunft? Bibliotheksdienst. Zentral- und Landesbibliothek Berlin. https://doi.org/424
chicago: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek
Der Zukunft?” Bibliotheksdienst. Zentral- und Landesbibliothek Berlin,
2006. https://doi.org/424.
ieee: P. Danowski and L. Heller, “Bibliothek 2.0 - Die Bibliothek der Zukunft?,”
Bibliotheksdienst, vol. 40, no. 11. Zentral- und Landesbibliothek Berlin,
pp. 1250–1271, 2006.
ista: Danowski P, Heller L. 2006. Bibliothek 2.0 - Die Bibliothek der Zukunft? Bibliotheksdienst.
40(11), 1250–1271.
mla: Danowski, Patrick, and Lambert Heller. “Bibliothek 2.0 - Die Bibliothek Der
Zukunft?” Bibliotheksdienst, vol. 40, no. 11, Zentral- und Landesbibliothek
Berlin, 2006, pp. 1250–71, doi:424.
short: P. Danowski, L. Heller, Bibliotheksdienst 40 (2006) 1250–1271.
date_created: 2018-12-11T12:08:23Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:17Z
day: '01'
doi: '424'
extern: 1
intvolume: ' 40'
issue: '11'
main_file_link:
- open_access: '0'
url: http://www.zlb.de/aktivitaeten/bd_neu/heftinhalte2006/DigitaleBib011106.pdf
month: '01'
page: 1250 - 1271
publication: Bibliotheksdienst
publication_status: published
publisher: Zentral- und Landesbibliothek Berlin
publist_id: '1229'
quality_controlled: 0
status: public
title: Bibliothek 2.0 - Die Bibliothek der Zukunft?
type: journal_article
volume: 40
year: '2006'
...
---
_id: '4351'
abstract:
- lang: eng
text: 'BACKGROUND: Character mapping on phylogenies has played an important, if
not critical role, in our understanding of molecular, morphological, and behavioral
evolution. Until very recently we have relied on parsimony to infer character
changes. Parsimony has a number of serious limitations that are drawbacks to our
understanding. Recent statistical methods have been developed that free us from
these limitations enabling us to overcome the problems of parsimony by accommodating
uncertainty in evolutionary time, ancestral states, and the phylogeny. RESULTS:
SIMMAP has been developed to implement stochastic character mapping that is useful
to both molecular evolutionists, systematists, and bioinformaticians. Researchers
can address questions about positive selection, patterns of amino acid substitution,
character association, and patterns of morphological evolution. CONCLUSION: Stochastic
character mapping, as implemented in the SIMMAP software, enables users to address
questions that require mapping characters onto phylogenies using a probabilistic
approach that does not rely on parsimony. Analyses can be performed using a fully
Bayesian approach that is not reliant on considering a single topology, set of
substitution model parameters, or reconstruction of ancestral states. Uncertainty
in these quantities is accommodated by using MCMC samples from their respective
posterior distributions.'
author:
- first_name: Jonathan P
full_name: Jonathan Bollback
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Bollback JP. SIMMAP: stochastic character mapping of discrete traits on phylogenies.
BMC Bioinformatics. 2006;7. doi:10.1186/1471-2105-7-88'
apa: 'Bollback, J. P. (2006). SIMMAP: stochastic character mapping of discrete traits
on phylogenies. BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-7-88'
chicago: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete
Traits on Phylogenies.” BMC Bioinformatics. BioMed Central, 2006. https://doi.org/10.1186/1471-2105-7-88.'
ieee: 'J. P. Bollback, “SIMMAP: stochastic character mapping of discrete traits
on phylogenies,” BMC Bioinformatics, vol. 7. BioMed Central, 2006.'
ista: 'Bollback JP. 2006. SIMMAP: stochastic character mapping of discrete traits
on phylogenies. BMC Bioinformatics. 7.'
mla: 'Bollback, Jonathan P. “SIMMAP: Stochastic Character Mapping of Discrete Traits
on Phylogenies.” BMC Bioinformatics, vol. 7, BioMed Central, 2006, doi:10.1186/1471-2105-7-88.'
short: J.P. Bollback, BMC Bioinformatics 7 (2006).
date_created: 2018-12-11T12:08:25Z
date_published: 2006-01-01T00:00:00Z
date_updated: 2021-01-12T07:56:20Z
day: '01'
doi: 10.1186/1471-2105-7-88
extern: 1
intvolume: ' 7'
month: '01'
publication: BMC Bioinformatics
publication_status: published
publisher: BioMed Central
publist_id: '1109'
quality_controlled: 0
status: public
title: 'SIMMAP: stochastic character mapping of discrete traits on phylogenies'
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: 7
year: '2006'
...