---
_id: '3789'
abstract:
- lang: eng
text: 'The development of multicellular organisms is dependent on the tight coordination
between tissue growth and morphogenesis. The stereotypical orientation of cell
divisions has been proposed to be a fundamental mechanism by which proliferating
and growing tissues take shape. However, the actual contribution of stereotypical
division orientation (SDO) to tissue morphogenesis is unclear. In zebrafish, cell
divisions with stereotypical orientation have been implicated in both body-axis
elongation and neural rod formation [1, 2], although there is little direct evidence
for a critical function of SDO in either of these processes. Here we show that
SDO is required for formation of the neural rod midline during neurulation but
dispensable for elongation of the body axis during gastrulation. Our data indicate
that SDO during both gastrulation and neurulation is dependent on the noncanonical
Wnt receptor Frizzled 7 (Fz7) and that interfering with cell division orientation
leads to severe defects in neural rod midline formation but not body-axis elongation.
These findings suggest a novel function for Fz7-controlled cell division orientation
in neural rod midline formation during neurulation. '
acknowledgement: "This work was supported by grants from the Fundacion Caja Madrid
to E.Q.H. and the Institute of Science and Technology Austria, the Max-Planck-Society,
and the Deutsche Forschungsgemeinschaft to C.P.H.\r\nWe are grateful to Jon Clarke,
Andy Oates, and Garrett Greenan for reading earlier versions of this manuscript.
We thank J. Peychl, H. Ibarra, and P. Pitrone for excellent assistance and advice
in multi-photon microscopy and D. White for assistance during the image-processing
steps. We also thank D. Panhans for technical assistance, the whole Heisenberg laboratory
for useful comments and discussions, and E. Lehmann, J. Hückmann, and G. Junghans
for excellent fish care. "
article_processing_charge: No
author:
- first_name: Elena
full_name: Quesada-Hernández, Elena
id: EA35229E-E909-11E9-8DF8-C90C5D5AF86E
last_name: Quesada-Hernández
- first_name: Luca
full_name: Caneparo, Luca
last_name: Caneparo
- first_name: Sylvia
full_name: Schneider, Sylvia
id: 1FAC36B0-E90A-11E9-9D2F-EF31CE0C9C2F
last_name: Schneider
- first_name: Sylke
full_name: Winkler, Sylke
last_name: Winkler
- first_name: Michael
full_name: Liebling, Michael
last_name: Liebling
- first_name: Scott
full_name: Fraser, Scott
last_name: Fraser
- 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: Quesada-Hernández E, Caneparo L, Schneider S, et al. Stereotypical cell division
orientation controls neural rod midline formation in zebrafish. Current Biology.
2010;20(21):1966-1972. doi:10.1016/j.cub.2010.10.009
apa: Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, S., Liebling,
M., Fraser, S., & Heisenberg, C.-P. J. (2010). Stereotypical cell division
orientation controls neural rod midline formation in zebrafish. Current Biology.
Cell Press. https://doi.org/10.1016/j.cub.2010.10.009
chicago: Quesada-Hernández, Elena, Luca Caneparo, Sylvia Schneider, Sylke Winkler,
Michael Liebling, Scott Fraser, and Carl-Philipp J Heisenberg. “Stereotypical
Cell Division Orientation Controls Neural Rod Midline Formation in Zebrafish.”
Current Biology. Cell Press, 2010. https://doi.org/10.1016/j.cub.2010.10.009.
ieee: E. Quesada-Hernández et al., “Stereotypical cell division orientation
controls neural rod midline formation in zebrafish,” Current Biology, vol.
20, no. 21. Cell Press, pp. 1966–1972, 2010.
ista: Quesada-Hernández E, Caneparo L, Schneider S, Winkler S, Liebling M, Fraser
S, Heisenberg C-PJ. 2010. Stereotypical cell division orientation controls neural
rod midline formation in zebrafish. Current Biology. 20(21), 1966–1972.
mla: Quesada-Hernández, Elena, et al. “Stereotypical Cell Division Orientation Controls
Neural Rod Midline Formation in Zebrafish.” Current Biology, vol. 20, no.
21, Cell Press, 2010, pp. 1966–72, doi:10.1016/j.cub.2010.10.009.
short: E. Quesada-Hernández, L. Caneparo, S. Schneider, S. Winkler, M. Liebling,
S. Fraser, C.-P.J. Heisenberg, Current Biology 20 (2010) 1966–1972.
corr_author: '1'
date_created: 2018-12-11T12:05:11Z
date_published: 2010-11-09T00:00:00Z
date_updated: 2025-09-30T09:40:27Z
day: '09'
department:
- _id: CaHe
doi: 10.1016/j.cub.2010.10.009
external_id:
isi:
- '000284193900032'
intvolume: ' 20'
isi: 1
issue: '21'
language:
- iso: eng
month: '11'
oa_version: None
page: 1966 - 1972
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '2438'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stereotypical cell division orientation controls neural rod midline formation
in zebrafish
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2010'
...
---
_id: '3790'
abstract:
- lang: eng
text: Cell shape and motility are primarily controlled by cellular mechanics. The
attachment of the plasma membrane to the underlying actomyosin cortex has been
proposed to be important for cellular processes involving membrane deformation.
However, little is known about the actual function of membrane-to-cortex attachment
(MCA) in cell protrusion formation and migration, in particular in the context
of the developing embryo. Here, we use a multidisciplinary approach to study MCA
in zebrafish mesoderm and endoderm (mesendoderm) germ layer progenitor cells,
which migrate using a combination of different protrusion types, namely, lamellipodia,
filopodia, and blebs, during zebrafish gastrulation. By interfering with the activity
of molecules linking the cortex to the membrane and measuring resulting changes
in MCA by atomic force microscopy, we show that reducing MCA in mesendoderm progenitors
increases the proportion of cellular blebs and reduces the directionality of cell
migration. We propose that MCA is a key parameter controlling the relative proportions
of different cell protrusion types in mesendoderm progenitors, and thus is key
in controlling directed migration during gastrulation.
acknowledgement: "We would like to thank A. G. Clark, S. Grill, A. Oates, E. Raz,
L. Rohde, and M. Zerial for reading earlier versions of the manuscript. We are grateful
to W. Zachariae, Y. Arboleda-Estudillo, S. Schneider, P. Stockinger, D. Panhans,
M. Biro, J. C. Olaya, and the BIOTEC/MPI-CBG zebrafish and imaging facilities for
help and advice at various stages of this project and to J. Helenius for help with
programming. This work was supported by grants from the Boehringer Ingelheim Fonds
to MK, the Polish Ministry of Science and Higher Education to E. P., and the Deutsche
Forschungsgemeinschaft (HE 3231/6-1 and PA 1590/1-1) to CPH and EP.\r\n"
article_number: e1000544
article_processing_charge: No
author:
- first_name: Alba
full_name: Diz Muñoz, Alba
last_name: Diz Muñoz
- first_name: Michael
full_name: Krieg, Michael
last_name: Krieg
- first_name: Martin
full_name: Bergert, Martin
last_name: Bergert
- first_name: Itziar
full_name: Ibarlucea Benitez, Itziar
last_name: Ibarlucea Benitez
- first_name: Daniel
full_name: Müller, Daniel
last_name: Müller
- first_name: Ewa
full_name: Paluch, Ewa
last_name: Paluch
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Diz Muñoz A, Krieg M, Bergert M, et al. Control of directed cell migration
in vivo by membrane-to-cortex attachment. PLoS Biology. 2010;8(11). doi:10.1371/journal.pbio.1000544
apa: Diz Muñoz, A., Krieg, M., Bergert, M., Ibarlucea Benitez, I., Müller, D., Paluch,
E., & Heisenberg, C.-P. J. (2010). Control of directed cell migration in vivo
by membrane-to-cortex attachment. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.1000544
chicago: Diz Muñoz, Alba, Michael Krieg, Martin Bergert, Itziar Ibarlucea Benitez,
Daniel Müller, Ewa Paluch, and Carl-Philipp J Heisenberg. “Control of Directed
Cell Migration in Vivo by Membrane-to-Cortex Attachment.” PLoS Biology.
Public Library of Science, 2010. https://doi.org/10.1371/journal.pbio.1000544.
ieee: A. Diz Muñoz et al., “Control of directed cell migration in vivo by
membrane-to-cortex attachment,” PLoS Biology, vol. 8, no. 11. Public Library
of Science, 2010.
ista: Diz Muñoz A, Krieg M, Bergert M, Ibarlucea Benitez I, Müller D, Paluch E,
Heisenberg C-PJ. 2010. Control of directed cell migration in vivo by membrane-to-cortex
attachment. PLoS Biology. 8(11), e1000544.
mla: Diz Muñoz, Alba, et al. “Control of Directed Cell Migration in Vivo by Membrane-to-Cortex
Attachment.” PLoS Biology, vol. 8, no. 11, e1000544, Public Library of
Science, 2010, doi:10.1371/journal.pbio.1000544.
short: A. Diz Muñoz, M. Krieg, M. Bergert, I. Ibarlucea Benitez, D. Müller, E. Paluch,
C.-P.J. Heisenberg, PLoS Biology 8 (2010).
date_created: 2018-12-11T12:05:11Z
date_published: 2010-11-30T00:00:00Z
date_updated: 2025-09-30T09:39:58Z
day: '30'
ddc:
- '576'
department:
- _id: CaHe
doi: 10.1371/journal.pbio.1000544
external_id:
isi:
- '000284762300016'
file:
- access_level: open_access
checksum: 52d18c90ca6b02234cea5e8b399b7f46
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:24Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4685'
file_name: IST-2015-365-v1+1_journal.pbio.1000544.pdf
file_size: 799506
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '2437'
pubrep_id: '365'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Control of directed cell migration in vivo by membrane-to-cortex attachment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 8
year: '2010'
...
---
_id: '3792'
abstract:
- lang: eng
text: The yolk syncytial layer (YSL) plays crucial roles in early zebrafish development.
The YSL is a transient extra-embryonic syncytial tissue that forms during early
cleavage stages and persists until larval stages. During gastrulation, the YSL
undergoes highly dynamic movements, which are tightly coordinated with the movements
of the overlying germ layer progenitor cells, and has critical functions in cell
fate specification and morphogenesis of the early germ layers. Movement coordination
between the YSL and blastoderm cells is dependent on contact between these tissues,
and is probably required for the patterning and morphogenetic function of the
YSL. In this review, we will discuss recent advances in elucidating the molecular
and cellular mechanisms underlying the YSL morphogenesis and movement coordination
between the YSL and blastoderm during early development.
acknowledgement: "We are grateful to Valerie Virta and Jennifer Regan for reading
earlier versions of the review.\r\n"
article_processing_charge: No
author:
- first_name: Lara
full_name: Carvalho, Lara
last_name: Carvalho
- 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: Carvalho L, Heisenberg C-PJ. The yolk syncytial layer in early, zebrafish development.
Trends in Cell Biology. 2010;20(10):586-592. doi:10.1016/j.tcb.2010.06.009
apa: Carvalho, L., & Heisenberg, C.-P. J. (2010). The yolk syncytial layer in
early, zebrafish development. Trends in Cell Biology. Cell Press. https://doi.org/10.1016/j.tcb.2010.06.009
chicago: Carvalho, Lara, and Carl-Philipp J Heisenberg. “The Yolk Syncytial Layer
in Early, Zebrafish Development.” Trends in Cell Biology. Cell Press, 2010.
https://doi.org/10.1016/j.tcb.2010.06.009.
ieee: L. Carvalho and C.-P. J. Heisenberg, “The yolk syncytial layer in early, zebrafish
development,” Trends in Cell Biology, vol. 20, no. 10. Cell Press, pp.
586–592, 2010.
ista: Carvalho L, Heisenberg C-PJ. 2010. The yolk syncytial layer in early, zebrafish
development. Trends in Cell Biology. 20(10), 586–592.
mla: Carvalho, Lara, and Carl-Philipp J. Heisenberg. “The Yolk Syncytial Layer in
Early, Zebrafish Development.” Trends in Cell Biology, vol. 20, no. 10,
Cell Press, 2010, pp. 586–92, doi:10.1016/j.tcb.2010.06.009.
short: L. Carvalho, C.-P.J. Heisenberg, Trends in Cell Biology 20 (2010) 586–592.
date_created: 2018-12-11T12:05:12Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2025-09-30T09:39:30Z
day: '01'
doi: 10.1016/j.tcb.2010.06.009
external_id:
isi:
- '000283399800005'
intvolume: ' 20'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 586 - 592
publication: Trends in Cell Biology
publication_status: published
publisher: Cell Press
publist_id: '2435'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The yolk syncytial layer in early, zebrafish development
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 20
year: '2010'
...
---
_id: '3793'
abstract:
- lang: eng
text: "Recent progress in per-pixel object class labeling of natural images can
be attributed to the use of multiple types of image features and sound statistical
learning approaches. Within the latter, Conditional Random Fields (CRF) are prominently
used for their ability to represent interactions between random variables. Despite
their popularity in computer vision, parameter learning for CRFs has remained
difficult, popular approaches being cross-validation and piecewise training.\r\nIn
this work, we propose a simple yet expressive tree-structured CRF based on a recent
hierarchical image segmentation method. Our model combines and weights multiple
image features within a hierarchical representation and allows simple and efficient
globally-optimal learning of ≈ 105 parameters. The tractability of our model allows
us to pose and answer some of the open questions regarding parameter learning
applying to CRF-based approaches. The key findings for learning CRF models are,
from the obvious to the surprising, i) multiple image features always help, ii)
the limiting dimension with respect to current models is the amount of training
data, iii) piecewise training is competitive, iv) current methods for max-margin
training fail for models with many parameters.\r\n"
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Nowozin, Sebastian
last_name: Nowozin
- first_name: Peter
full_name: Gehler, Peter
last_name: Gehler
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Nowozin S, Gehler P, Lampert C. On parameter learning in CRF-based approaches
to object class image segmentation. In: Vol 6316. Springer; 2010:98-111. doi:10.1007/978-3-642-15567-3_8'
apa: 'Nowozin, S., Gehler, P., & Lampert, C. (2010). On parameter learning in
CRF-based approaches to object class image segmentation (Vol. 6316, pp. 98–111).
Presented at the ECCV: European Conference on Computer Vision, Heraklion, Crete,
Greece: Springer. https://doi.org/10.1007/978-3-642-15567-3_8'
chicago: Nowozin, Sebastian, Peter Gehler, and Christoph Lampert. “On Parameter
Learning in CRF-Based Approaches to Object Class Image Segmentation,” 6316:98–111.
Springer, 2010. https://doi.org/10.1007/978-3-642-15567-3_8.
ieee: 'S. Nowozin, P. Gehler, and C. Lampert, “On parameter learning in CRF-based
approaches to object class image segmentation,” presented at the ECCV: European
Conference on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6316, pp.
98–111.'
ista: 'Nowozin S, Gehler P, Lampert C. 2010. On parameter learning in CRF-based
approaches to object class image segmentation. ECCV: European Conference on Computer
Vision, LNCS, vol. 6316, 98–111.'
mla: Nowozin, Sebastian, et al. On Parameter Learning in CRF-Based Approaches
to Object Class Image Segmentation. Vol. 6316, Springer, 2010, pp. 98–111,
doi:10.1007/978-3-642-15567-3_8.
short: S. Nowozin, P. Gehler, C. Lampert, in:, Springer, 2010, pp. 98–111.
conference:
end_date: 2010-09-11
location: Heraklion, Crete, Greece
name: 'ECCV: European Conference on Computer Vision'
start_date: 2010-09-05
date_created: 2018-12-11T12:05:12Z
date_published: 2010-11-04T00:00:00Z
date_updated: 2021-01-12T07:52:14Z
day: '04'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1007/978-3-642-15567-3_8
file:
- access_level: open_access
checksum: 3716e10e161f7c714fd17ec193a223c3
content_type: application/pdf
creator: dernst
date_created: 2020-05-19T16:27:34Z
date_updated: 2020-07-14T12:46:16Z
file_id: '7871'
file_name: 2010_ECCV_Nowozin.pdf
file_size: 4087332
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 6316'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 98 - 111
publication_status: published
publisher: Springer
publist_id: '2431'
quality_controlled: '1'
scopus_import: 1
status: public
title: On parameter learning in CRF-based approaches to object class image segmentation
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6316
year: '2010'
...
---
OA_type: closed access
_id: '3794'
abstract:
- lang: eng
text: 'We study the problem of multimodal dimensionality reduction assuming that
data samples can be missing at training time, and not all data modalities may
be present at application time. Maximum covariance analysis, as a generalization
of PCA, has many desirable properties, but its application to practical problems
is limited by its need for perfectly paired data. We overcome this limitation
by a latent variable approach that allows working with weakly paired data and
is still able to efficiently process large datasets using standard numerical routines.
The resulting weakly paired maximum covariance analysis often finds better representations
than alternative methods, as we show in two exemplary tasks: texture discrimination
and transfer learning.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Oliver
full_name: Krömer, Oliver
last_name: Krömer
citation:
ama: 'Lampert C, Krömer O. Weakly-paired maximum covariance analysis for multimodal
dimensionality reduction and transfer learning. In: 11th European Conference
on Computer Vision. Vol 6312. Springer; 2010:566-579. doi:10.1007/978-3-642-15552-9_41'
apa: 'Lampert, C., & Krömer, O. (2010). Weakly-paired maximum covariance analysis
for multimodal dimensionality reduction and transfer learning. In 11th European
Conference on Computer Vision (Vol. 6312, pp. 566–579). Heraklion, Crete,
Greece: Springer. https://doi.org/10.1007/978-3-642-15552-9_41'
chicago: Lampert, Christoph, and Oliver Krömer. “Weakly-Paired Maximum Covariance
Analysis for Multimodal Dimensionality Reduction and Transfer Learning.” In 11th
European Conference on Computer Vision, 6312:566–79. Springer, 2010. https://doi.org/10.1007/978-3-642-15552-9_41.
ieee: C. Lampert and O. Krömer, “Weakly-paired maximum covariance analysis for multimodal
dimensionality reduction and transfer learning,” in 11th European Conference
on Computer Vision, Heraklion, Crete, Greece, 2010, vol. 6312, pp. 566–579.
ista: 'Lampert C, Krömer O. 2010. Weakly-paired maximum covariance analysis for
multimodal dimensionality reduction and transfer learning. 11th European Conference
on Computer Vision. ECCV: European Conference on Computer Vision, LNCS, vol. 6312,
566–579.'
mla: Lampert, Christoph, and Oliver Krömer. “Weakly-Paired Maximum Covariance Analysis
for Multimodal Dimensionality Reduction and Transfer Learning.” 11th European
Conference on Computer Vision, vol. 6312, Springer, 2010, pp. 566–79, doi:10.1007/978-3-642-15552-9_41.
short: C. Lampert, O. Krömer, in:, 11th European Conference on Computer Vision,
Springer, 2010, pp. 566–579.
conference:
end_date: 2010-09-11
location: Heraklion, Crete, Greece
name: 'ECCV: European Conference on Computer Vision'
start_date: 2010-09-05
date_created: 2018-12-11T12:05:12Z
date_published: 2010-11-10T00:00:00Z
date_updated: 2025-05-20T06:43:33Z
day: '10'
department:
- _id: ChLa
doi: 10.1007/978-3-642-15552-9_41
intvolume: ' 6312'
language:
- iso: eng
month: '11'
oa_version: None
page: 566 - 579
publication: 11th European Conference on Computer Vision
publication_identifier:
eisbn:
- '9783642155529'
eissn:
- 1611-3349
publication_status: published
publisher: Springer
publist_id: '2433'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Weakly-paired maximum covariance analysis for multimodal dimensionality reduction
and transfer learning
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6312
year: '2010'
...
---
_id: '3795'
abstract:
- lang: eng
text: 'The (apparent) contour of a smooth mapping from a 2-manifold to the plane,
f: M → R2 , is the set of critical values, that is, the image of the points at
which the gradients of the two component functions are linearly dependent. Assuming
M is compact and orientable and measuring difference with the erosion distance,
we prove that the contour is stable.'
acknowledgement: This research is partially supported by the Defense Advanced Research
Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.
alternative_title:
- Mathematics and Visualization
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Edelsbrunner H, Morozov D, Patel A. The stability of the apparent contour
of an orientable 2-manifold. In: Topological Data Analysis and Visualization:
Theory, Algorithms and Applications. Springer; 2010:27-42. doi:10.1007/978-3-642-15014-2_3'
apa: 'Edelsbrunner, H., Morozov, D., & Patel, A. (2010). The stability of the
apparent contour of an orientable 2-manifold. In Topological Data Analysis
and Visualization: Theory, Algorithms and Applications (pp. 27–42). Springer.
https://doi.org/10.1007/978-3-642-15014-2_3'
chicago: 'Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “The Stability
of the Apparent Contour of an Orientable 2-Manifold.” In Topological Data Analysis
and Visualization: Theory, Algorithms and Applications, 27–42. Springer, 2010.
https://doi.org/10.1007/978-3-642-15014-2_3.'
ieee: 'H. Edelsbrunner, D. Morozov, and A. Patel, “The stability of the apparent
contour of an orientable 2-manifold,” in Topological Data Analysis and Visualization:
Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.'
ista: 'Edelsbrunner H, Morozov D, Patel A. 2010.The stability of the apparent contour
of an orientable 2-manifold. In: Topological Data Analysis and Visualization:
Theory, Algorithms and Applications. Mathematics and Visualization, , 27–42.'
mla: 'Edelsbrunner, Herbert, et al. “The Stability of the Apparent Contour of an
Orientable 2-Manifold.” Topological Data Analysis and Visualization: Theory,
Algorithms and Applications, Springer, 2010, pp. 27–42, doi:10.1007/978-3-642-15014-2_3.'
short: 'H. Edelsbrunner, D. Morozov, A. Patel, in:, Topological Data Analysis and
Visualization: Theory, Algorithms and Applications, Springer, 2010, pp. 27–42.'
corr_author: '1'
date_created: 2018-12-11T12:05:13Z
date_published: 2010-12-22T00:00:00Z
date_updated: 2024-10-09T20:54:11Z
day: '22'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-15014-2_3
file:
- access_level: open_access
checksum: f03a44c3d1c3e2d4fedb3b94404f3fd5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:40Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4896'
file_name: IST-2016-538-v1+1_2011-B-02-ApparentContour.pdf
file_size: 210710
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 27 - 42
publication: 'Topological Data Analysis and Visualization: Theory, Algorithms and
Applications'
publication_status: published
publisher: Springer
publist_id: '2428'
pubrep_id: '538'
quality_controlled: '1'
scopus_import: 1
status: public
title: The stability of the apparent contour of an orientable 2-manifold
type: book_chapter
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3829'
abstract:
- lang: eng
text: To determine the number of open Ca(2+) channels necessary for transmitter
release at the inhibitory basket cell-granule cell synapse in rat hippocampus,
we combined presynaptic Ca(2+) imaging, recording of postsynaptic currents and
modeling. We found that that the opening of three or fewer Ca(2+) channels triggered
transmitter release. Furthermore, a small number of Ca(2+) channels were able
to evoke release with high temporal precision, despite stochastic Ca(2+) channel
opening.
author:
- first_name: Iancu
full_name: Bucurenciu, Iancu
last_name: Bucurenciu
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Bucurenciu I, Bischofberger J, Jonas PM. A small number of open Ca(2+) channels
trigger transmitter release at a central GABAergic synapse. Nature Neuroscience.
2010;13(1):19-21. doi:10.1038/nn.2461
apa: Bucurenciu, I., Bischofberger, J., & Jonas, P. M. (2010). A small number
of open Ca(2+) channels trigger transmitter release at a central GABAergic synapse.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2461
chicago: Bucurenciu, Iancu, Josef Bischofberger, and Peter M Jonas. “A Small Number
of Open Ca(2+) Channels Trigger Transmitter Release at a Central GABAergic Synapse.”
Nature Neuroscience. Nature Publishing Group, 2010. https://doi.org/10.1038/nn.2461 .
ieee: I. Bucurenciu, J. Bischofberger, and P. M. Jonas, “A small number of open
Ca(2+) channels trigger transmitter release at a central GABAergic synapse,” Nature
Neuroscience, vol. 13, no. 1. Nature Publishing Group, pp. 19–21, 2010.
ista: Bucurenciu I, Bischofberger J, Jonas PM. 2010. A small number of open Ca(2+)
channels trigger transmitter release at a central GABAergic synapse. Nature Neuroscience.
13(1), 19–21.
mla: Bucurenciu, Iancu, et al. “A Small Number of Open Ca(2+) Channels Trigger Transmitter
Release at a Central GABAergic Synapse.” Nature Neuroscience, vol. 13,
no. 1, Nature Publishing Group, 2010, pp. 19–21, doi:10.1038/nn.2461 .
short: I. Bucurenciu, J. Bischofberger, P.M. Jonas, Nature Neuroscience 13 (2010)
19–21.
date_created: 2018-12-11T12:05:24Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:29Z
day: '01'
doi: '10.1038/nn.2461 '
extern: 1
intvolume: ' 13'
issue: '1'
month: '01'
page: 19 - 21
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '2380'
quality_controlled: 0
status: public
title: A small number of open Ca(2+) channels trigger transmitter release at a central
GABAergic synapse
type: journal_article
volume: 13
year: '2010'
...
---
_id: '3830'
abstract:
- lang: eng
text: Fast-spiking, parvalbumin-expressing basket cells (BCs) are important for
feedforward and feedback inhibition. During network activity, BCs respond with
short latency and high temporal precision. It is thought that the specific properties
of input synapses are responsible for rapid recruitment. However, a potential
contribution of active dendritic conductances has not been addressed. We combined
confocal imaging and patch-clamp techniques to obtain simultaneous somatodendritic
recordings from BCs. Action potentials were initiated in the BC axon and backpropagated
into the dendrites with reduced amplitude and little activity dependence. These
properties were explained by a high K+ to Na+ conductance ratio in BC dendrites.
Computational analysis indicated that dendritic K+ channels convey unique integration
properties to BCs, leading to the rapid and temporally precise activation by excitatory
inputs.
author:
- first_name: Hua
full_name: Hua Hu
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Marco
full_name: Martina, Marco
last_name: Martina
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Hu H, Martina M, Jonas PM. Dendritic mechanisms underlying rapid synaptic activation
of fast-spiking hippocampal interneurons. Science. 2010;327(5961):52-58.
doi:10.1126/science.1177876
apa: Hu, H., Martina, M., & Jonas, P. M. (2010). Dendritic mechanisms underlying
rapid synaptic activation of fast-spiking hippocampal interneurons. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1177876
chicago: Hu, Hua, Marco Martina, and Peter M Jonas. “Dendritic Mechanisms Underlying
Rapid Synaptic Activation of Fast-Spiking Hippocampal Interneurons.” Science.
American Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1177876.
ieee: H. Hu, M. Martina, and P. M. Jonas, “Dendritic mechanisms underlying rapid
synaptic activation of fast-spiking hippocampal interneurons,” Science,
vol. 327, no. 5961. American Association for the Advancement of Science, pp. 52–8,
2010.
ista: Hu H, Martina M, Jonas PM. 2010. Dendritic mechanisms underlying rapid synaptic
activation of fast-spiking hippocampal interneurons. Science. 327(5961), 52–8.
mla: Hu, Hua, et al. “Dendritic Mechanisms Underlying Rapid Synaptic Activation
of Fast-Spiking Hippocampal Interneurons.” Science, vol. 327, no. 5961,
American Association for the Advancement of Science, 2010, pp. 52–58, doi:10.1126/science.1177876.
short: H. Hu, M. Martina, P.M. Jonas, Science 327 (2010) 52–8.
date_created: 2018-12-11T12:05:24Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:30Z
day: '01'
doi: 10.1126/science.1177876
extern: 1
intvolume: ' 327'
issue: '5961'
month: '01'
page: 52 - 8
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '2381'
quality_controlled: 0
status: public
title: Dendritic mechanisms underlying rapid synaptic activation of fast-spiking hippocampal
interneurons
type: journal_article
volume: 327
year: '2010'
...
---
_id: '3831'
abstract:
- lang: eng
text: Fast-spiking, parvalbumin-expressing basket cells (BCs) play a key role in
feedforward and feedback inhibition in the hippocampus. However, the dendritic
mechanisms underlying rapid interneuron recruitment have remained unclear. To
quantitatively address this question, we developed detailed passive cable models
of BCs in the dentate gyrus based on dual somatic or somatodendritic recordings
and complete morphologic reconstructions. Both specific membrane capacitance and
axial resistivity were comparable to those of pyramidal neurons, but the average
somatodendritic specific membrane resistance (R(m)) was substantially lower in
BCs. Furthermore, R(m) was markedly nonuniform, being lowest in soma and proximal
dendrites, intermediate in distal dendrites, and highest in the axon. Thus, the
somatodendritic gradient of R(m) was the reverse of that in pyramidal neurons.
Further computational analysis revealed that these unique cable properties accelerate
the time course of synaptic potentials at the soma in response to fast inputs,
while boosting the efficacy of slow distal inputs. These properties will facilitate
both rapid phasic and efficient tonic activation of BCs in hippocampal microcircuits.
author:
- first_name: Anja
full_name: Norenberg, Anja
last_name: Norenberg
- first_name: Hua
full_name: Hua Hu
id: 4AC0145C-F248-11E8-B48F-1D18A9856A87
last_name: Hu
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. Distinct nonuniform cable properties
optimize rapid and efficient activation of fast-spiking GABAergic interneurons.
PNAS. 2010;107(2):894-899. doi:10.1073/pnas.0910716107
apa: Norenberg, A., Hu, H., Vida, I., Bartos, M., & Jonas, P. M. (2010). Distinct
nonuniform cable properties optimize rapid and efficient activation of fast-spiking
GABAergic interneurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0910716107
chicago: Norenberg, Anja, Hua Hu, Imre Vida, Marlene Bartos, and Peter M Jonas.
“Distinct Nonuniform Cable Properties Optimize Rapid and Efficient Activation
of Fast-Spiking GABAergic Interneurons.” PNAS. National Academy of Sciences,
2010. https://doi.org/10.1073/pnas.0910716107.
ieee: A. Norenberg, H. Hu, I. Vida, M. Bartos, and P. M. Jonas, “Distinct nonuniform
cable properties optimize rapid and efficient activation of fast-spiking GABAergic
interneurons,” PNAS, vol. 107, no. 2. National Academy of Sciences, pp.
894–9, 2010.
ista: Norenberg A, Hu H, Vida I, Bartos M, Jonas PM. 2010. Distinct nonuniform cable
properties optimize rapid and efficient activation of fast-spiking GABAergic interneurons.
PNAS. 107(2), 894–9.
mla: Norenberg, Anja, et al. “Distinct Nonuniform Cable Properties Optimize Rapid
and Efficient Activation of Fast-Spiking GABAergic Interneurons.” PNAS,
vol. 107, no. 2, National Academy of Sciences, 2010, pp. 894–99, doi:10.1073/pnas.0910716107.
short: A. Norenberg, H. Hu, I. Vida, M. Bartos, P.M. Jonas, PNAS 107 (2010) 894–9.
date_created: 2018-12-11T12:05:24Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:31Z
day: '01'
doi: 10.1073/pnas.0910716107
extern: 1
intvolume: ' 107'
issue: '2'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818894/#!po=4.16667
month: '01'
oa: 1
page: 894 - 9
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2379'
quality_controlled: 0
status: public
title: Distinct nonuniform cable properties optimize rapid and efficient activation
of fast-spiking GABAergic interneurons
type: journal_article
volume: 107
year: '2010'
...
---
_id: '3832'
abstract:
- lang: eng
text: A recent paper by von Engelhardt et al. identifies a novel auxiliary subunit
of native AMPARs, termedCKAMP44. Unlike other auxiliary subunits, CKAMP44 accelerates
desensitization and prolongs recovery from desensitization. CKAMP44 is highly
expressed in hippocampal dentate gyrus granule cells and decreases the paired-pulse
ratio at perforant path input synapses. Thus, both principal and auxiliary AMPAR
subunits control the time course of signaling at glutamatergic synapses.
article_processing_charge: No
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Guzmán J, Jonas PM. Beyond TARPs: The growing list of auxiliary AMPAR subunits.
Neuron. 2010;66(1):8-10. doi:10.1016/j.neuron.2010.04.003'
apa: 'Guzmán, J., & Jonas, P. M. (2010). Beyond TARPs: The growing list of auxiliary
AMPAR subunits. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2010.04.003'
chicago: 'Guzmán, José, and Peter M Jonas. “Beyond TARPs: The Growing List of Auxiliary
AMPAR Subunits.” Neuron. Elsevier, 2010. https://doi.org/10.1016/j.neuron.2010.04.003.'
ieee: 'J. Guzmán and P. M. Jonas, “Beyond TARPs: The growing list of auxiliary AMPAR
subunits,” Neuron, vol. 66, no. 1. Elsevier, pp. 8–10, 2010.'
ista: 'Guzmán J, Jonas PM. 2010. Beyond TARPs: The growing list of auxiliary AMPAR
subunits. Neuron. 66(1), 8–10.'
mla: 'Guzmán, José, and Peter M. Jonas. “Beyond TARPs: The Growing List of Auxiliary
AMPAR Subunits.” Neuron, vol. 66, no. 1, Elsevier, 2010, pp. 8–10, doi:10.1016/j.neuron.2010.04.003.'
short: J. Guzmán, P.M. Jonas, Neuron 66 (2010) 8–10.
corr_author: '1'
date_created: 2018-12-11T12:05:25Z
date_published: 2010-04-15T00:00:00Z
date_updated: 2025-09-30T09:37:55Z
day: '15'
department:
- _id: PeJo
doi: 10.1016/j.neuron.2010.04.003
external_id:
isi:
- '000277016200004'
pmid:
- '20399724'
intvolume: ' 66'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/20399724
month: '04'
oa: 1
oa_version: Published Version
page: 8 - 10
pmid: 1
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2377'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond TARPs: The growing list of auxiliary AMPAR subunits'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 66
year: '2010'
...
---
_id: '3833'
article_processing_charge: No
author:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Stefan
full_name: Hefft, Stefan
last_name: Hefft
citation:
ama: 'Jonas PM, Hefft S. GABA release at terminals of CCK-interneurons: Synchrony,
asynchrony and modulation by cannabinoid receptors (commentary on Ali &
Todorova). The European Journal of Neuroscience. 2010;31(7):1194-1195.
doi:10.1111/j.1460-9568.2010.07189.x'
apa: 'Jonas, P. M., & Hefft, S. (2010). GABA release at terminals of CCK-interneurons:
Synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali
& Todorova). The European Journal of Neuroscience. Wiley-Blackwell.
https://doi.org/10.1111/j.1460-9568.2010.07189.x'
chicago: 'Jonas, Peter M, and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons:
Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali
& Todorova).” The European Journal of Neuroscience. Wiley-Blackwell,
2010. https://doi.org/10.1111/j.1460-9568.2010.07189.x.'
ieee: 'P. M. Jonas and S. Hefft, “GABA release at terminals of CCK-interneurons:
Synchrony, asynchrony and modulation by cannabinoid receptors (commentary on Ali
& Todorova),” The European Journal of Neuroscience, vol. 31, no.
7. Wiley-Blackwell, pp. 1194–1195, 2010.'
ista: 'Jonas PM, Hefft S. 2010. GABA release at terminals of CCK-interneurons: Synchrony,
asynchrony and modulation by cannabinoid receptors (commentary on Ali &
Todorova). The European Journal of Neuroscience. 31(7), 1194–1195.'
mla: 'Jonas, Peter M., and Stefan Hefft. “GABA Release at Terminals of CCK-Interneurons:
Synchrony, Asynchrony and Modulation by Cannabinoid Receptors (Commentary on Ali
& Todorova).” The European Journal of Neuroscience, vol. 31, no.
7, Wiley-Blackwell, 2010, pp. 1194–95, doi:10.1111/j.1460-9568.2010.07189.x.'
short: P.M. Jonas, S. Hefft, The European Journal of Neuroscience 31 (2010) 1194–1195.
corr_author: '1'
date_created: 2018-12-11T12:05:25Z
date_published: 2010-03-19T00:00:00Z
date_updated: 2025-09-30T09:38:44Z
day: '19'
department:
- _id: PeJo
doi: 10.1111/j.1460-9568.2010.07189.x
external_id:
isi:
- '000276245400005'
intvolume: ' 31'
isi: 1
issue: '7'
language:
- iso: eng
month: '03'
oa_version: None
page: 1194 - 1195
publication: The European Journal of Neuroscience
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2378'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'GABA release at terminals of CCK-interneurons: Synchrony, asynchrony and modulation
by cannabinoid receptors (commentary on Ali & Todorova)'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 31
year: '2010'
...
---
_id: '3834'
abstract:
- lang: eng
text: "Background\r\n\r\nThe chemical master equation (CME) is a system of ordinary
differential equations that describes the evolution of a network of chemical reactions
as a stochastic process. Its solution yields the probability density vector of
the system at each point in time. Solving the CME numerically is in many cases
computationally expensive or even infeasible as the number of reachable states
can be very large or infinite. We introduce the sliding window method, which computes
an approximate solution of the CME by performing a sequence of local analysis
steps. In each step, only a manageable subset of states is considered, representing
a "window" into the state space. In subsequent steps, the window follows
the direction in which the probability mass moves, until the time period of interest
has elapsed. We construct the window based on a deterministic approximation of
the future behavior of the system by estimating upper and lower bounds on the
populations of the chemical species.\r\nResults\r\n\r\nIn order to show the effectiveness
of our approach, we apply it to several examples previously described in the literature.
The experimental results show that the proposed method speeds up the analysis
considerably, compared to a global analysis, while still providing high accuracy.\r\n\r\n\r\nConclusions\r\n\r\nThe
sliding window method is a novel approach to address the performance problems
of numerical algorithms for the solution of the chemical master equation. The
method efficiently approximates the probability distributions at the time points
of interest for a variety of chemically reacting systems, including systems for
which no upper bound on the population sizes of the chemical species is known
a priori."
acknowledgement: This research has been partially funded by the Swiss National Science
Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal
Computing and Interaction at Saarland University.
article_processing_charge: No
author:
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
- first_name: Rushil
full_name: Goel, Rushil
last_name: Goel
- first_name: Maria
full_name: Mateescu, Maria
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
last_name: Mateescu
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Wolf V, Goel R, Mateescu M, Henzinger TA. Solving the chemical master equation
using sliding windows. BMC Systems Biology. 2010;4(42):1-19. doi:10.1186/1752-0509-4-42
apa: Wolf, V., Goel, R., Mateescu, M., & Henzinger, T. A. (2010). Solving the
chemical master equation using sliding windows. BMC Systems Biology. BioMed
Central. https://doi.org/10.1186/1752-0509-4-42
chicago: Wolf, Verena, Rushil Goel, Maria Mateescu, and Thomas A Henzinger. “Solving
the Chemical Master Equation Using Sliding Windows.” BMC Systems Biology.
BioMed Central, 2010. https://doi.org/10.1186/1752-0509-4-42.
ieee: V. Wolf, R. Goel, M. Mateescu, and T. A. Henzinger, “Solving the chemical
master equation using sliding windows,” BMC Systems Biology, vol. 4, no.
42. BioMed Central, pp. 1–19, 2010.
ista: Wolf V, Goel R, Mateescu M, Henzinger TA. 2010. Solving the chemical master
equation using sliding windows. BMC Systems Biology. 4(42), 1–19.
mla: Wolf, Verena, et al. “Solving the Chemical Master Equation Using Sliding Windows.”
BMC Systems Biology, vol. 4, no. 42, BioMed Central, 2010, pp. 1–19, doi:10.1186/1752-0509-4-42.
short: V. Wolf, R. Goel, M. Mateescu, T.A. Henzinger, BMC Systems Biology 4 (2010)
1–19.
corr_author: '1'
date_created: 2018-12-11T12:05:25Z
date_published: 2010-04-08T00:00:00Z
date_updated: 2025-09-30T09:37:27Z
day: '08'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1186/1752-0509-4-42
external_id:
isi:
- '000277612700001'
file:
- access_level: open_access
checksum: 220239fae76f7b03c4d7f05d74ef426f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:29Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5217'
file_name: IST-2012-72-v1+1_Solving_the_chemical_master_equation_using_sliding_windows.pdf
file_size: 1919130
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '42'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1 - 19
publication: BMC Systems Biology
publication_status: published
publisher: BioMed Central
publist_id: '2374'
pubrep_id: '72'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Solving the chemical master equation using sliding windows
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2010'
...
---
_id: '3838'
abstract:
- lang: eng
text: We present a numerical approximation technique for the analysis of continuous-time
Markov chains that describe net- works of biochemical reactions and play an important
role in the stochastic modeling of biological systems. Our approach is based on
the construction of a stochastic hybrid model in which certain discrete random
variables of the original Markov chain are approximated by continuous deterministic
variables. We compute the solution of the stochastic hybrid model using a numerical
algorithm that discretizes time and in each step performs a mutual update of the
transient prob- ability distribution of the discrete stochastic variables and
the values of the continuous deterministic variables. We im- plemented the algorithm
and we demonstrate its usefulness and efficiency on several case studies from
systems biology.
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
- first_name: Linar
full_name: Mikeev, Linar
last_name: Mikeev
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Henzinger TA, Mateescu M, Mikeev L, Wolf V. Hybrid numerical solution of the
chemical master equation. In: Springer; 2010:55-65. doi:10.1145/1839764.1839772'
apa: 'Henzinger, T. A., Mateescu, M., Mikeev, L., & Wolf, V. (2010). Hybrid
numerical solution of the chemical master equation (pp. 55–65). Presented at the
CMSB: Computational Methods in Systems Biology, Trento, Italy: Springer. https://doi.org/10.1145/1839764.1839772'
chicago: Henzinger, Thomas A, Maria Mateescu, Linar Mikeev, and Verena Wolf. “Hybrid
Numerical Solution of the Chemical Master Equation,” 55–65. Springer, 2010. https://doi.org/10.1145/1839764.1839772.
ieee: 'T. A. Henzinger, M. Mateescu, L. Mikeev, and V. Wolf, “Hybrid numerical solution
of the chemical master equation,” presented at the CMSB: Computational Methods
in Systems Biology, Trento, Italy, 2010, pp. 55–65.'
ista: 'Henzinger TA, Mateescu M, Mikeev L, Wolf V. 2010. Hybrid numerical solution
of the chemical master equation. CMSB: Computational Methods in Systems Biology,
55–65.'
mla: Henzinger, Thomas A., et al. Hybrid Numerical Solution of the Chemical Master
Equation. Springer, 2010, pp. 55–65, doi:10.1145/1839764.1839772.
short: T.A. Henzinger, M. Mateescu, L. Mikeev, V. Wolf, in:, Springer, 2010, pp.
55–65.
conference:
end_date: 2010-10-01
location: Trento, Italy
name: 'CMSB: Computational Methods in Systems Biology'
start_date: 2010-09-29
date_created: 2018-12-11T12:05:27Z
date_published: 2010-09-29T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '29'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.1145/1839764.1839772
file:
- access_level: open_access
checksum: 81cb6f0babd97151b171d1ce86582831
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:55Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5179'
file_name: IST-2012-68-v1+1_Hybrid_Numerical_Solution_of_the_Chemical_Master_Equation.pdf
file_size: 671790
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 55 - 65
publication_status: published
publisher: Springer
publist_id: '2356'
pubrep_id: '68'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hybrid numerical solution of the chemical master equation
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3839'
abstract:
- lang: eng
text: We present a loop property generation method for loops iterating over multi-dimensional
arrays. When used on matrices, our method is able to infer their shapes (also
called types), such as upper-triangular, diagonal, etc. To gen- erate loop properties,
we first transform a nested loop iterating over a multi- dimensional array into
an equivalent collection of unnested loops. Then, we in- fer quantified loop invariants
for each unnested loop using a generalization of a recurrence-based invariant
generation technique. These loop invariants give us conditions on matrices from
which we can derive matrix types automatically us- ing theorem provers. Invariant
generation is implemented in the software package Aligator and types are derived
by theorem provers and SMT solvers, including Vampire and Z3. When run on the
Java matrix package JAMA, our tool was able to infer automatically all matrix
types describing the matrix shapes guaranteed by JAMA’s API.
acknowledgement: The research was supported by the Swiss NSF.
alternative_title:
- LNCS
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Andrei
full_name: Voronkov, Andrei
last_name: Voronkov
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L, Voronkov A. Invariant and type inference
for matrices. In: Vol 5944. Springer; 2010:163-179. doi:10.1007/978-3-642-11319-2_14'
apa: 'Henzinger, T. A., Hottelier, T., Kovács, L., & Voronkov, A. (2010). Invariant
and type inference for matrices (Vol. 5944, pp. 163–179). Presented at the VMCAI:
Verification, Model Checking and Abstract Interpretation, Madrid, Spain: Springer.
https://doi.org/10.1007/978-3-642-11319-2_14'
chicago: Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrei Voronkov.
“Invariant and Type Inference for Matrices,” 5944:163–79. Springer, 2010. https://doi.org/10.1007/978-3-642-11319-2_14.
ieee: 'T. A. Henzinger, T. Hottelier, L. Kovács, and A. Voronkov, “Invariant and
type inference for matrices,” presented at the VMCAI: Verification, Model Checking
and Abstract Interpretation, Madrid, Spain, 2010, vol. 5944, pp. 163–179.'
ista: 'Henzinger TA, Hottelier T, Kovács L, Voronkov A. 2010. Invariant and type
inference for matrices. VMCAI: Verification, Model Checking and Abstract Interpretation,
LNCS, vol. 5944, 163–179.'
mla: Henzinger, Thomas A., et al. Invariant and Type Inference for Matrices.
Vol. 5944, Springer, 2010, pp. 163–79, doi:10.1007/978-3-642-11319-2_14.
short: T.A. Henzinger, T. Hottelier, L. Kovács, A. Voronkov, in:, Springer, 2010,
pp. 163–179.
conference:
end_date: 2010-01-19
location: Madrid, Spain
name: 'VMCAI: Verification, Model Checking and Abstract Interpretation'
start_date: 2010-01-17
date_created: 2018-12-11T12:05:27Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:33Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-11319-2_14
file:
- access_level: open_access
checksum: da69b13a2d9a7a316c909e09c1090cef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:09Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4989'
file_name: IST-2012-69-v1+1_Invariant_and_type_inference_for_matrices.pdf
file_size: 251265
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 5944'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 163 - 179
publication_status: published
publisher: Springer
publist_id: '2357'
pubrep_id: '69'
quality_controlled: '1'
scopus_import: 1
status: public
title: Invariant and type inference for matrices
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 5944
year: '2010'
...
---
_id: '3840'
abstract:
- lang: eng
text: 'Classical formalizations of systems and properties are boolean: given a system
and a property, the property is either true or false of the system. Correspondingly,
classical methods for system analysis determine the truth value of a property,
preferably giving a proof if the property is true, and a counterexample if the
property is false; classical methods for system synthesis construct a system for
which a property is true; classical methods for system transformation, composition,
and abstraction aim to preserve the truth of properties. The boolean view is prevalent
even if the system, the property, or both refer to numerical quantities, such
as the times or probabilities of events. For example, a timed automaton either
satisfies or violates a formula of a real-time logic; a stochastic process either
satisfies or violates a formula of a probabilistic logic. The classical black-and-white
view partitions the world into "correct" and "incorrect" systems, offering few
nuances. In reality, of several systems that satisfy a property in the boolean
sense, often some are more desirable than others, and of the many systems that
violate a property, usually some are less objectionable than others. For instance,
among the systems that satisfy the response property that every request be granted,
we may prefer systems that grant requests quickly (the quicker, the better), or
we may prefer systems that issue few unnecessary grants (the fewer, the better);
and among the systems that violate the response property, we may prefer systems
that serve many initial requests (the more, the better), or we may prefer systems
that serve many requests in the long run (the greater the fraction of served to
unserved requests, the better). Formally, while a boolean notion of correctness
is given by a preorder on systems and properties, a quantitative notion of correctness
is defined by a directed metric on systems and properties, where the distance
between a system and a property provides a measure of "fit" or "desirability."
There are many ways how such distances can be defined. In a linear-time framework,
one assigns numerical values to individual behaviors before assigning values to
systems and properties, which are sets of behaviors. For example, the value of
a single behavior may be a discounted value, which is largely determined by a
prefix of the behavior, e.g., by the number of requests that are granted before
the first request that is not granted; or a limit value, which is independent
of any finite prefix. A limit value may be an average, such as the average response
time over an infinite sequence of requests and grants, or a supremum, such as
the worst-case response time. Similarly, the value of a set of behaviors may be
an extremum or an average across the values of all behaviors in the set: in this
way one can measure the worst of all possible average-case response times, or
the average of all possible worst-case response times, etc. Accordingly, the distance
between two sets of behaviors may be defined as the worst or average difference
between the values of corresponding behaviors. In summary, we propagate replacing
boolean specifications for the correctness of systems with quantitative measures
for the desirability of systems. In quantitative analysis, the aim is to compute
the distance between a system and a property (or between two systems, or two properties);
in quantitative synthesis, the objective is to construct a system that has minimal
distance from a given property. Multiple quantitative measures can be prioritized
(e.g., combined lexicographically into a single measure) or studied along the
Pareto curve. Quantitative transformations, compositions, and abstractions of
systems are useful if they allow us to bound the induced change in distance from
a property. We present some initial results in some of these directions. We also
give some potential applications, which not only generalize tradiditional correctness
concerns in the functional, timed, and probabilistic domains, but also capture
such system measures as resource use, performance, cost, reliability, and robustness.'
acknowledgement: This talk surveys joint work with Roderick Bloem, Krishnendu Chatterjee,
Laurent Doyen, and Barbara Jobstmann.
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Henzinger TA. From boolean to quantitative notions of correctness. In: Vol
45. ACM; 2010:157-158. doi:10.1145/1706299.1706319'
apa: 'Henzinger, T. A. (2010). From boolean to quantitative notions of correctness
(Vol. 45, pp. 157–158). Presented at the POPL: Principles of Programming Languages,
Madrid, Spain: ACM. https://doi.org/10.1145/1706299.1706319'
chicago: Henzinger, Thomas A. “From Boolean to Quantitative Notions of Correctness,”
45:157–58. ACM, 2010. https://doi.org/10.1145/1706299.1706319.
ieee: 'T. A. Henzinger, “From boolean to quantitative notions of correctness,” presented
at the POPL: Principles of Programming Languages, Madrid, Spain, 2010, vol. 45,
no. 1, pp. 157–158.'
ista: 'Henzinger TA. 2010. From boolean to quantitative notions of correctness.
POPL: Principles of Programming Languages vol. 45, 157–158.'
mla: Henzinger, Thomas A. From Boolean to Quantitative Notions of Correctness.
Vol. 45, no. 1, ACM, 2010, pp. 157–58, doi:10.1145/1706299.1706319.
short: T.A. Henzinger, in:, ACM, 2010, pp. 157–158.
conference:
end_date: 2010-01-23
location: Madrid, Spain
name: 'POPL: Principles of Programming Languages'
start_date: 2010-01-17
corr_author: '1'
date_created: 2018-12-11T12:05:27Z
date_published: 2010-01-17T00:00:00Z
date_updated: 2025-09-30T09:36:44Z
day: '17'
department:
- _id: ToHe
doi: 10.1145/1706299.1706319
external_id:
isi:
- '000281053800014'
intvolume: ' 45'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 157 - 158
publication_status: published
publisher: ACM
publist_id: '2354'
quality_controlled: '1'
scopus_import: '1'
status: public
title: From boolean to quantitative notions of correctness
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 45
year: '2010'
...
---
_id: '3842'
abstract:
- lang: eng
text: Within systems biology there is an increasing interest in the stochastic behavior
of biochemical reaction networks. An appropriate stochastic description is provided
by the chemical master equation, which represents a continuous-time Markov chain
(CTMC). The uniformization technique is an efficient method to compute probability
distributions of a CTMC if the number of states is manageable. However, the size
of a CTMC that represents a biochemical reaction network is usually far beyond
what is feasible. In this paper we present an on-the-fly variant of uniformization,
where we improve the original algorithm at the cost of a small approximation error.
By means of several examples, we show that our approach is particularly well-suited
for biochemical reaction networks.
article_processing_charge: No
author:
- first_name: Frédéric
full_name: Didier, Frédéric
last_name: Didier
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of
the chemical master equation. IET Systems Biology. 2010;4(6):441-452. doi:10.1049/iet-syb.2010.0005
apa: Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). Fast adaptive
uniformization of the chemical master equation. IET Systems Biology. Institution
of Engineering and Technology. https://doi.org/10.1049/iet-syb.2010.0005
chicago: Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“Fast Adaptive Uniformization of the Chemical Master Equation.” IET Systems
Biology. Institution of Engineering and Technology, 2010. https://doi.org/10.1049/iet-syb.2010.0005.
ieee: F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization
of the chemical master equation,” IET Systems Biology, vol. 4, no. 6. Institution
of Engineering and Technology, pp. 441–452, 2010.
ista: Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. Fast adaptive uniformization
of the chemical master equation. IET Systems Biology. 4(6), 441–452.
mla: Didier, Frédéric, et al. “Fast Adaptive Uniformization of the Chemical Master
Equation.” IET Systems Biology, vol. 4, no. 6, Institution of Engineering
and Technology, 2010, pp. 441–52, doi:10.1049/iet-syb.2010.0005.
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, IET Systems Biology 4 (2010)
441–452.
date_created: 2018-12-11T12:05:28Z
date_published: 2010-11-15T00:00:00Z
date_updated: 2025-09-30T09:54:51Z
day: '15'
ddc:
- '570'
department:
- _id: ToHe
doi: 10.1049/iet-syb.2010.0005
external_id:
isi:
- '000284108800011'
file:
- access_level: open_access
checksum: 9a3bde48f43203991a0b3c6a277c2f5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:02Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5254'
file_name: IST-2012-66-v1+1_Fast_adaptive_uniformization_of_the_chemical_master_equation.pdf
file_size: 222890
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Submitted Version
page: 441 - 452
publication: IET Systems Biology
publication_status: published
publisher: Institution of Engineering and Technology
publist_id: '2349'
pubrep_id: '66'
quality_controlled: '1'
related_material:
record:
- id: '3843'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Fast adaptive uniformization of the chemical master equation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2010'
...
---
_id: '3845'
abstract:
- lang: eng
text: This paper presents Aligators, a tool for the generation of universally quantified
array invariants. Aligators leverages recurrence solving and algebraic techniques
to carry out inductive reasoning over array content. The Aligators’ loop extraction
module allows treatment of multi-path loops by exploiting their commutativity
and serializability properties. Our experience in applying Aligators on a collection
of loops from open source software projects indicates the applicability of recurrence
and algebraic solving techniques for reasoning about arrays.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Thibaud
full_name: Hottelier, Thibaud
last_name: Hottelier
- first_name: Laura
full_name: Kovács, Laura
last_name: Kovács
- first_name: Andrey
full_name: Rybalchenko, Andrey
last_name: Rybalchenko
citation:
ama: 'Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. Aligators for arrays.
In: Vol 6397. Springer; 2010:348-356. doi:10.1007/978-3-642-16242-8_25'
apa: 'Henzinger, T. A., Hottelier, T., Kovács, L., & Rybalchenko, A. (2010).
Aligators for arrays (Vol. 6397, pp. 348–356). Presented at the LPAR: Logic for
Programming, Artificial Intelligence, and Reasoning, Yogyakarta, Indonesia: Springer.
https://doi.org/10.1007/978-3-642-16242-8_25'
chicago: Henzinger, Thomas A, Thibaud Hottelier, Laura Kovács, and Andrey Rybalchenko.
“Aligators for Arrays,” 6397:348–56. Springer, 2010. https://doi.org/10.1007/978-3-642-16242-8_25.
ieee: 'T. A. Henzinger, T. Hottelier, L. Kovács, and A. Rybalchenko, “Aligators
for arrays,” presented at the LPAR: Logic for Programming, Artificial Intelligence,
and Reasoning, Yogyakarta, Indonesia, 2010, vol. 6397, pp. 348–356.'
ista: 'Henzinger TA, Hottelier T, Kovács L, Rybalchenko A. 2010. Aligators for arrays.
LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol.
6397, 348–356.'
mla: Henzinger, Thomas A., et al. Aligators for Arrays. Vol. 6397, Springer,
2010, pp. 348–56, doi:10.1007/978-3-642-16242-8_25.
short: T.A. Henzinger, T. Hottelier, L. Kovács, A. Rybalchenko, in:, Springer, 2010,
pp. 348–356.
conference:
end_date: 2010-10-15
location: Yogyakarta, Indonesia
name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning'
start_date: 2010-10-10
corr_author: '1'
date_created: 2018-12-11T12:05:29Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2025-09-30T09:35:47Z
day: '01'
ddc:
- '005'
department:
- _id: ToHe
doi: 10.1007/978-3-642-16242-8_25
external_id:
isi:
- '000288062700025'
file:
- access_level: open_access
checksum: 913af269da6710f2174f470b48ab7a82
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:05Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4790'
file_name: IST-2012-64-v1+1_Aligators_for_arrays.pdf
file_size: 186143
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 6397'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 348 - 356
publication_status: published
publisher: Springer
publist_id: '2342'
pubrep_id: '64'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Aligators for arrays
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 6397
year: '2010'
...
---
_id: '3847'
abstract:
- lang: eng
text: The importance of stochasticity within biological systems has been shown repeatedly
during the last years and has raised the need for efficient stochastic tools.
We present SABRE, a tool for stochastic analysis of biochemical reaction networks.
SABRE implements fast adaptive uniformization (FAU), a direct numerical approximation
algorithm for computing transient solutions of biochemical reaction networks.
Biochemical reactions networks represent biological systems studied at a molecular
level and these reactions can be modeled as transitions of a Markov chain. SABRE
accepts as input the formalism of guarded commands, which it interprets either
as continuous-time or as discrete-time Markov chains. Besides operating in a stochastic
mode, SABRE may also perform a deterministic analysis by directly computing a
mean-field approximation of the system under study. We illustrate the different
functionalities of SABRE by means of biological case studies.
author:
- first_name: Frédéric
full_name: Didier, Frédéric
last_name: Didier
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Mateescu, Maria
last_name: Mateescu
- first_name: Verena
full_name: Wolf, Verena
last_name: Wolf
citation:
ama: 'Didier F, Henzinger TA, Mateescu M, Wolf V. SABRE: A tool for the stochastic
analysis of biochemical reaction networks. In: IEEE; 2010:193-194. doi:10.1109/QEST.2010.33'
apa: 'Didier, F., Henzinger, T. A., Mateescu, M., & Wolf, V. (2010). SABRE:
A tool for the stochastic analysis of biochemical reaction networks (pp. 193–194).
Presented at the QEST: Quantitative Evaluation of Systems, Williamsburg, USA:
IEEE. https://doi.org/10.1109/QEST.2010.33'
chicago: 'Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf.
“SABRE: A Tool for the Stochastic Analysis of Biochemical Reaction Networks,”
193–94. IEEE, 2010. https://doi.org/10.1109/QEST.2010.33.'
ieee: 'F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “SABRE: A tool for
the stochastic analysis of biochemical reaction networks,” presented at the QEST:
Quantitative Evaluation of Systems, Williamsburg, USA, 2010, pp. 193–194.'
ista: 'Didier F, Henzinger TA, Mateescu M, Wolf V. 2010. SABRE: A tool for the stochastic
analysis of biochemical reaction networks. QEST: Quantitative Evaluation of Systems,
193–194.'
mla: 'Didier, Frédéric, et al. SABRE: A Tool for the Stochastic Analysis of Biochemical
Reaction Networks. IEEE, 2010, pp. 193–94, doi:10.1109/QEST.2010.33.'
short: F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2010, pp. 193–194.
conference:
end_date: 2010-09-18
location: Williamsburg, USA
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2010-09-15
date_created: 2018-12-11T12:05:29Z
date_published: 2010-10-14T00:00:00Z
date_updated: 2021-01-12T07:52:37Z
day: '14'
ddc:
- '004'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/QEST.2010.33
file:
- access_level: open_access
checksum: 38707b149d2174f01be406e794ffa849
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:09:03Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4726'
file_name: IST-2012-63-v1+1_SABRE-A_tool_for_the_stochastic_analysis_of_biochemical_reaction_networks.pdf
file_size: 433824
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 193 - 194
publication_status: published
publisher: IEEE
publist_id: '2339'
pubrep_id: '63'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'SABRE: A tool for the stochastic analysis of biochemical reaction networks'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '3848'
abstract:
- lang: eng
text: We define the robustness of a level set homology class of a function f:XR
as the magnitude of a perturbation necessary to kill the class. Casting this notion
into a group theoretic framework, we compute the robustness for each class, using
a connection to extended persistent homology. The special case X=R3 has ramifications
in medical imaging and scientific visualization.
alternative_title:
- LNCS
author:
- first_name: Paul
full_name: Bendich, Paul
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Dmitriy
full_name: Morozov, Dmitriy
last_name: Morozov
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Bendich P, Edelsbrunner H, Morozov D, Patel A. The robustness of level sets.
In: Vol 6346. Springer; 2010:1-10. doi:10.1007/978-3-642-15775-2_1'
apa: 'Bendich, P., Edelsbrunner, H., Morozov, D., & Patel, A. (2010). The robustness
of level sets (Vol. 6346, pp. 1–10). Presented at the ESA: European Symposium
on Algorithms, Liverpool, UK: Springer. https://doi.org/10.1007/978-3-642-15775-2_1'
chicago: Bendich, Paul, Herbert Edelsbrunner, Dmitriy Morozov, and Amit Patel. “The
Robustness of Level Sets,” 6346:1–10. Springer, 2010. https://doi.org/10.1007/978-3-642-15775-2_1.
ieee: 'P. Bendich, H. Edelsbrunner, D. Morozov, and A. Patel, “The robustness of
level sets,” presented at the ESA: European Symposium on Algorithms, Liverpool,
UK, 2010, vol. 6346, pp. 1–10.'
ista: 'Bendich P, Edelsbrunner H, Morozov D, Patel A. 2010. The robustness of level
sets. ESA: European Symposium on Algorithms, LNCS, vol. 6346, 1–10.'
mla: Bendich, Paul, et al. The Robustness of Level Sets. Vol. 6346, Springer,
2010, pp. 1–10, doi:10.1007/978-3-642-15775-2_1.
short: P. Bendich, H. Edelsbrunner, D. Morozov, A. Patel, in:, Springer, 2010, pp.
1–10.
conference:
end_date: 2010-09-08
location: Liverpool, UK
name: 'ESA: European Symposium on Algorithms'
start_date: 2010-09-06
corr_author: '1'
date_created: 2018-12-11T12:05:30Z
date_published: 2010-09-01T00:00:00Z
date_updated: 2024-10-09T20:54:09Z
day: '01'
department:
- _id: HeEd
doi: 10.1007/978-3-642-15775-2_1
intvolume: ' 6346'
language:
- iso: eng
month: '09'
oa_version: None
page: 1 - 10
publication_status: published
publisher: Springer
publist_id: '2336'
quality_controlled: '1'
scopus_import: 1
status: public
title: The robustness of level sets
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6346
year: '2010'
...
---
_id: '3849'
abstract:
- lang: eng
text: Using ideas from persistent homology, the robustness of a level set of a real-valued
function is defined in terms of the magnitude of the perturbation necessary to
kill the classes. Prior work has shown that the homology and robustness information
can be read off the extended persistence diagram of the function. This paper extends
these results to a non-uniform error model in which perturbations vary in their
magnitude across the domain.
alternative_title:
- LNCS
author:
- first_name: Paul
full_name: Bendich, Paul
id: 43F6EC54-F248-11E8-B48F-1D18A9856A87
last_name: Bendich
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Michael
full_name: Kerber, Michael
id: 36E4574A-F248-11E8-B48F-1D18A9856A87
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Amit
full_name: Patel, Amit
id: 34A254A0-F248-11E8-B48F-1D18A9856A87
last_name: Patel
citation:
ama: 'Bendich P, Edelsbrunner H, Kerber M, Patel A. Persistent homology under non-uniform
error. In: Vol 6281. Springer; 2010:12-23. doi:10.1007/978-3-642-15155-2_2'
apa: 'Bendich, P., Edelsbrunner, H., Kerber, M., & Patel, A. (2010). Persistent
homology under non-uniform error (Vol. 6281, pp. 12–23). Presented at the MFCS:
Mathematical Foundations of Computer Science, Brno, Czech Republic: Springer.
https://doi.org/10.1007/978-3-642-15155-2_2'
chicago: Bendich, Paul, Herbert Edelsbrunner, Michael Kerber, and Amit Patel. “Persistent
Homology under Non-Uniform Error,” 6281:12–23. Springer, 2010. https://doi.org/10.1007/978-3-642-15155-2_2.
ieee: 'P. Bendich, H. Edelsbrunner, M. Kerber, and A. Patel, “Persistent homology
under non-uniform error,” presented at the MFCS: Mathematical Foundations of Computer
Science, Brno, Czech Republic, 2010, vol. 6281, pp. 12–23.'
ista: 'Bendich P, Edelsbrunner H, Kerber M, Patel A. 2010. Persistent homology under
non-uniform error. MFCS: Mathematical Foundations of Computer Science, LNCS, vol.
6281, 12–23.'
mla: Bendich, Paul, et al. Persistent Homology under Non-Uniform Error. Vol.
6281, Springer, 2010, pp. 12–23, doi:10.1007/978-3-642-15155-2_2.
short: P. Bendich, H. Edelsbrunner, M. Kerber, A. Patel, in:, Springer, 2010, pp.
12–23.
conference:
end_date: 2010-08-27
location: Brno, Czech Republic
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2010-08-23
date_created: 2018-12-11T12:05:30Z
date_published: 2010-08-10T00:00:00Z
date_updated: 2021-01-12T07:52:38Z
day: '10'
ddc:
- '000'
department:
- _id: HeEd
doi: 10.1007/978-3-642-15155-2_2
file:
- access_level: open_access
checksum: af61e1c2bb42f3d556179d4692caeb1b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:13:13Z
date_updated: 2020-07-14T12:46:17Z
file_id: '4994'
file_name: IST-2016-537-v1+1_2010-P-05-NonuniformError.pdf
file_size: 142357
relation: main_file
file_date_updated: 2020-07-14T12:46:17Z
has_accepted_license: '1'
intvolume: ' 6281'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
page: 12 - 23
publication_status: published
publisher: Springer
publist_id: '2333'
pubrep_id: '537'
quality_controlled: '1'
scopus_import: 1
status: public
title: Persistent homology under non-uniform error
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 6281
year: '2010'
...