---
_id: '3700'
abstract:
- lang: eng
text: We propose a new method to partition an unlabeled dataset, called Discriminative
Context Partitioning (DCP). It is motivated by the idea of splitting the dataset
based only on how well the resulting parts can be separated from a context class
of disjoint data points. This is in contrast to typical clustering techniques
like K-means that are based on a generative model by implicitly or explicitly
searching for modes in the distribution of samples. The discriminative criterion
in DCP avoids the problems that density based methods have when the a priori assumption
of multimodality is violated, when the number of samples becomes small in relation
to the dimensionality of the feature space, or if the cluster sizes are strongly
unbalanced. We formulate DCP‘s separation
property as a large-margin criterion, and show how the resulting optimization
problem can be solved efficiently. Experiments on the MNIST and USPS datasets
of handwritten digits and on a subset of the Caltech256 dataset show that, given
a suitable context, DCP can achieve good results even in situation where density-based
clustering techniques fail.
acknowledgement: This work was funded in part by the EC project CLASS, IST 027978.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Lampert C. Partitioning of image datasets using discriminative context information.
In: IEEE; 2008:1-8. doi:10.1109/CVPR.2008.4587448'
apa: 'Lampert, C. (2008). Partitioning of image datasets using discriminative context
information (pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition,
IEEE. https://doi.org/10.1109/CVPR.2008.4587448'
chicago: Lampert, Christoph. “Partitioning of Image Datasets Using Discriminative
Context Information,” 1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587448.
ieee: 'C. Lampert, “Partitioning of image datasets using discriminative context
information,” presented at the CVPR: Computer Vision and Pattern Recognition,
2008, pp. 1–8.'
ista: 'Lampert C. 2008. Partitioning of image datasets using discriminative context
information. CVPR: Computer Vision and Pattern Recognition, 1–8.'
mla: Lampert, Christoph. Partitioning of Image Datasets Using Discriminative
Context Information. IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587448.
short: C. Lampert, in:, IEEE, 2008, pp. 1–8.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:41Z
date_published: 2008-09-18T00:00:00Z
date_updated: 2021-01-12T07:51:35Z
day: '18'
doi: 10.1109/CVPR.2008.4587448
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/~chl/papers/lampert-cvpr2008b.pdf
month: '09'
page: 1 - 8
publication_status: published
publisher: IEEE
publist_id: '2657'
quality_controlled: 0
status: public
title: Partitioning of image datasets using discriminative context information
type: conference
year: '2008'
...
---
_id: '3705'
abstract:
- lang: eng
text: 'Sliding window classifiers are among the most successful and widely applied
techniques for object localization. However, training is typically done in a way
that is not specific to the localization task. First a binary classifier is trained
using a sample of positive and negative examples, and this classifier is subsequently
applied to multiple regions within test images. We propose instead to treat object
localization in a principled way by posing it as a problem of predicting structured
data: we model the problem not as binary classification, but as the prediction
of the bounding box of objects located in images. The use of a joint-kernel framework
allows us to formulate the training procedure as a generalization of an SVM, which
can be solved efficiently. We further improve computational efficiency by using
a branch-and-bound strategy for localization during both training and testing.
Experimental evaluation on the PASCAL VOC and TU Darmstadt datasets show that
the structured training procedure improves pe rformance over binary training as
well as the best previously published scores.'
alternative_title:
- LNCS
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Blaschko M, Lampert C. Learning to localize objects with structured output
regression. In: Vol 5302. Springer; 2008:2-15. doi:10.1007/978-3-540-88682-2_2'
apa: 'Blaschko, M., & Lampert, C. (2008). Learning to localize objects with
structured output regression (Vol. 5302, pp. 2–15). Presented at the ECCV: European
Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-540-88682-2_2'
chicago: Blaschko, Matthew, and Christoph Lampert. “Learning to Localize Objects
with Structured Output Regression,” 5302:2–15. Springer, 2008. https://doi.org/10.1007/978-3-540-88682-2_2.
ieee: 'M. Blaschko and C. Lampert, “Learning to localize objects with structured
output regression,” presented at the ECCV: European Conference on Computer Vision,
2008, vol. 5302, pp. 2–15.'
ista: 'Blaschko M, Lampert C. 2008. Learning to localize objects with structured
output regression. ECCV: European Conference on Computer Vision, LNCS, vol. 5302,
2–15.'
mla: Blaschko, Matthew, and Christoph Lampert. Learning to Localize Objects with
Structured Output Regression. Vol. 5302, Springer, 2008, pp. 2–15, doi:10.1007/978-3-540-88682-2_2.
short: M. Blaschko, C. Lampert, in:, Springer, 2008, pp. 2–15.
conference:
name: 'ECCV: European Conference on Computer Vision'
date_created: 2018-12-11T12:04:43Z
date_published: 2008-11-17T00:00:00Z
date_updated: 2021-01-12T07:51:37Z
day: '17'
doi: 10.1007/978-3-540-88682-2_2
extern: 1
intvolume: ' 5302'
main_file_link:
- open_access: '0'
url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/ECCV2008-Blaschko_5247%5b0%5d.pdf
month: '11'
page: 2 - 15
publication_status: published
publisher: Springer
publist_id: '2653'
quality_controlled: 0
status: public
title: Learning to localize objects with structured output regression
type: conference
volume: 5302
year: '2008'
...
---
_id: '3706'
abstract:
- lang: eng
text: We present a new technique for structured prediction that works in a hybrid
generative/discriminative way, using a one-class support vector machine to model
the joint probability of (input, output)-pairs in a joint reproducing kernel Hilbert
space. Compared to discriminative techniques, like conditional random fields or
structured output SVMs?, the proposed method has the advantage that its training
time depends only on the number of training examples, not on the size of the label
space. Due to its generative aspect, it is also very tolerant against ambiguous,
incomplete or incorrect labels. Experiments on realistic data show that our method
works efficiently and robustly in situations that discriminative techniques have
problems with or that are computationally infeasible for them.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
citation:
ama: 'Lampert C, Blaschko M. Joint kernel support estimation for structured prediction.
In: Curran Associates, Inc.; 2008:1-4.'
apa: 'Lampert, C., & Blaschko, M. (2008). Joint kernel support estimation for
structured prediction (pp. 1–4). Presented at the NIPS SISO: NIPS Workshop on
“Structured Input - Structured Output,” Curran Associates, Inc.'
chicago: Lampert, Christoph, and Matthew Blaschko. “Joint Kernel Support Estimation
for Structured Prediction,” 1–4. Curran Associates, Inc., 2008.
ieee: 'C. Lampert and M. Blaschko, “Joint kernel support estimation for structured
prediction,” presented at the NIPS SISO: NIPS Workshop on “Structured Input -
Structured Output,” 2008, pp. 1–4.'
ista: 'Lampert C, Blaschko M. 2008. Joint kernel support estimation for structured
prediction. NIPS SISO: NIPS Workshop on ‘Structured Input - Structured Output’,
1–4.'
mla: Lampert, Christoph, and Matthew Blaschko. Joint Kernel Support Estimation
for Structured Prediction. Curran Associates, Inc., 2008, pp. 1–4.
short: C. Lampert, M. Blaschko, in:, Curran Associates, Inc., 2008, pp. 1–4.
conference:
name: 'NIPS SISO: NIPS Workshop on "Structured Input - Structured Output"'
date_created: 2018-12-11T12:04:43Z
date_published: 2008-12-12T00:00:00Z
date_updated: 2021-01-12T07:51:37Z
day: '12'
extern: 1
main_file_link:
- open_access: '0'
url: http://agbs.kyb.tuebingen.mpg.de/wikis/bg/siso2008/Blaschkoetal.pdf
month: '12'
page: 1 - 4
publication_status: published
publisher: Curran Associates, Inc.
publist_id: '2650'
quality_controlled: 0
status: public
title: Joint kernel support estimation for structured prediction
type: conference
year: '2008'
...
---
_id: '3712'
abstract:
- lang: eng
text: We present a new method for spectral clustering with paired data based on
kernel canonical correlation analysis, called correlational spectral clustering.
Paired data are common in real world data sources, such as images with text captions.
Traditional spectral clustering algorithms either assume that data can be represented
by a single similarity measure, or by co-occurrence matrices that are then used
in biclustering. In contrast, the proposed method uses separate similarity measures
for each data representation, and allows for projection of previously unseen data
that are only observed in one representation (e.g. images but not text). We show
that this algorithm generalizes traditional spectral clustering algorithms and
show consistent empirical improvement over spectral clustering on a variety of
datasets of images with associated text.
author:
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Blaschko M, Lampert C. Correlational spectral clustering. In: IEEE; 2008:1-8.
doi:10.1109/CVPR.2008.4587353'
apa: 'Blaschko, M., & Lampert, C. (2008). Correlational spectral clustering
(pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE.
https://doi.org/10.1109/CVPR.2008.4587353'
chicago: Blaschko, Matthew, and Christoph Lampert. “Correlational Spectral Clustering,”
1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587353.
ieee: 'M. Blaschko and C. Lampert, “Correlational spectral clustering,” presented
at the CVPR: Computer Vision and Pattern Recognition, 2008, pp. 1–8.'
ista: 'Blaschko M, Lampert C. 2008. Correlational spectral clustering. CVPR: Computer
Vision and Pattern Recognition, 1–8.'
mla: Blaschko, Matthew, and Christoph Lampert. Correlational Spectral Clustering.
IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587353.
short: M. Blaschko, C. Lampert, in:, IEEE, 2008, pp. 1–8.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:45Z
date_published: 2008-09-18T00:00:00Z
date_updated: 2021-01-12T07:51:40Z
day: '18'
doi: 10.1109/CVPR.2008.4587353
extern: 1
month: '09'
page: 1 - 8
publication_status: published
publisher: IEEE
publist_id: '2646'
quality_controlled: 0
status: public
title: Correlational spectral clustering
type: conference
year: '2008'
...
---
_id: '3714'
abstract:
- lang: eng
text: Most successful object recognition systems rely on binary classification,
deciding only if an object is present or not, but not providing information on
the actual object location. To perform localization, one can take a sliding window
approach, but this strongly increases the computational cost, because the classifier
function has to be evaluated over a large set of candidate subwindows. In this
paper, we propose a simple yet powerful branchand- bound scheme that allows efficient
maximization of a large class of classifier functions over all possible subimages.
It converges to a globally optimal solution typically in sublinear time. We show
how our method is applicable to different object detection and retrieval scenarios.
The achieved speedup allows the use of classifiers for localization that formerly
were considered too slow for this task, such as SVMs with a spatial pyramid kernel
or nearest neighbor classifiers based on the 2-distance. We demonstrate state-of-the-art
performance of the resulting systems on the UIUC Cars dataset, the PASCAL VOC
2006 dataset and in the PASCAL VOC 2007 competition.
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
- first_name: Thomas
full_name: Hofmann,Thomas
last_name: Hofmann
citation:
ama: 'Lampert C, Blaschko M, Hofmann T. Beyond sliding windows: Object localization
by efficient subwindow search. In: IEEE; 2008:1-8. doi:10.1109/CVPR.2008.4587586'
apa: 'Lampert, C., Blaschko, M., & Hofmann, T. (2008). Beyond sliding windows:
Object localization by efficient subwindow search (pp. 1–8). Presented at the
CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587586'
chicago: 'Lampert, Christoph, Matthew Blaschko, and Thomas Hofmann. “Beyond Sliding
Windows: Object Localization by Efficient Subwindow Search,” 1–8. IEEE, 2008.
https://doi.org/10.1109/CVPR.2008.4587586.'
ieee: 'C. Lampert, M. Blaschko, and T. Hofmann, “Beyond sliding windows: Object
localization by efficient subwindow search,” presented at the CVPR: Computer Vision
and Pattern Recognition, 2008, pp. 1–8.'
ista: 'Lampert C, Blaschko M, Hofmann T. 2008. Beyond sliding windows: Object localization
by efficient subwindow search. CVPR: Computer Vision and Pattern Recognition,
1–8.'
mla: 'Lampert, Christoph, et al. Beyond Sliding Windows: Object Localization
by Efficient Subwindow Search. IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587586.'
short: C. Lampert, M. Blaschko, T. Hofmann, in:, IEEE, 2008, pp. 1–8.
conference:
name: 'CVPR: Computer Vision and Pattern Recognition'
date_created: 2018-12-11T12:04:46Z
date_published: 2008-09-18T00:00:00Z
date_updated: 2021-01-12T07:51:40Z
day: '18'
doi: 10.1109/CVPR.2008.4587586
extern: 1
main_file_link:
- open_access: '0'
url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/pdfs/pdf5070.pdf
month: '09'
page: 1 - 8
publication_status: published
publisher: IEEE
publist_id: '2644'
quality_controlled: 0
status: public
title: 'Beyond sliding windows: Object localization by efficient subwindow search'
type: conference
year: '2008'
...
---
_id: '3716'
abstract:
- lang: eng
text: |
Most current methods for multi-class object classification and localization work as independent 1-vs-rest classifiers. They decide whether and where an object is visible in an image purely on a per-class basis. Joint learning of more than one object class would generally be preferable, since this would allow the use of contextual information such as co-occurrence between classes. However, this approach is usually not employed because of its computational cost.
In this paper we propose a method to combine the efficiency of single class localization with a subsequent decision process that works jointly for all given object classes. By following a multiple kernel learning (MKL) approach, we automatically obtain a sparse dependency graph of relevant object classes on which to base the decision. Experiments on the PASCAL VOC 2006 and 2007 datasets show that the subsequent joint decision step clearly improves the accuracy compared to single class detection.
alternative_title:
- LNCS
author:
- first_name: Christoph
full_name: Christoph Lampert
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Matthew
full_name: Blaschko,Matthew B
last_name: Blaschko
citation:
ama: 'Lampert C, Blaschko M. A multiple kernel learning approach to joint multi-class
object detection. In: Vol 5096. Springer; 2008:31-40. doi:10.1007/978-3-540-69321-5_4'
apa: 'Lampert, C., & Blaschko, M. (2008). A multiple kernel learning approach
to joint multi-class object detection (Vol. 5096, pp. 31–40). Presented at the
DAGM: German Association For Pattern Recognition, Springer. https://doi.org/10.1007/978-3-540-69321-5_4'
chicago: Lampert, Christoph, and Matthew Blaschko. “A Multiple Kernel Learning Approach
to Joint Multi-Class Object Detection,” 5096:31–40. Springer, 2008. https://doi.org/10.1007/978-3-540-69321-5_4.
ieee: 'C. Lampert and M. Blaschko, “A multiple kernel learning approach to joint
multi-class object detection,” presented at the DAGM: German Association For Pattern
Recognition, 2008, vol. 5096, pp. 31–40.'
ista: 'Lampert C, Blaschko M. 2008. A multiple kernel learning approach to joint
multi-class object detection. DAGM: German Association For Pattern Recognition,
LNCS, vol. 5096, 31–40.'
mla: Lampert, Christoph, and Matthew Blaschko. A Multiple Kernel Learning Approach
to Joint Multi-Class Object Detection. Vol. 5096, Springer, 2008, pp. 31–40,
doi:10.1007/978-3-540-69321-5_4.
short: C. Lampert, M. Blaschko, in:, Springer, 2008, pp. 31–40.
conference:
name: 'DAGM: German Association For Pattern Recognition'
date_created: 2018-12-11T12:04:46Z
date_published: 2008-07-07T00:00:00Z
date_updated: 2021-01-12T07:51:41Z
day: '07'
doi: 10.1007/978-3-540-69321-5_4
extern: 1
intvolume: ' 5096'
main_file_link:
- open_access: '0'
url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/DAGM2008-Lampert-Blaschko_5072%5b0%5d.pdf
month: '07'
page: 31 - 40
publication_status: published
publisher: Springer
publist_id: '2641'
quality_controlled: 0
status: public
title: A multiple kernel learning approach to joint multi-class object detection
type: conference
volume: 5096
year: '2008'
...
---
_id: '3726'
abstract:
- lang: eng
text: Single-molecule atomic force microscopy (AFM) provides novel ways to characterize
the structure-function relationship of native membrane proteins. High-resolution
AFM topographs allow observing the structure of single proteins at sub-nanometer
resolution as well as their conformational changes, oligomeric state, molecular
dynamics and assembly. We will review these feasibilities illustrating examples
of membrane proteins in native and reconstituted membranes. Classification of
individual topographs of single proteins allows understanding the principles of
motions of their extrinsic domains, to learn about their local structural flexibilities
and to find the entropy minima of certain conformations. Combined with the visualization
of functionally related conformational changes these insights allow understanding
why certain flexibilities are required for the protein to function and how structurally
flexible regions allow certain conformational changes. Complementary to AFM imaging,
single-molecule force spectroscopy (SMFS) experiments detect molecular interactions
established within and between membrane proteins. The sensitivity of this method
makes it possible to measure interactions that stabilize secondary structures
such as transmembrane α-helices, polypeptide loops and segments within. Changes
in temperature or protein-protein assembly do not change the locations of stable
structural segments, but influence their stability established by collective molecular
interactions. Such changes alter the probability of proteins to choose a certain
unfolding pathway. Recent examples have elucidated unfolding and refolding pathways
of membrane proteins as well as their energy landscapes.
author:
- first_name: Andreas
full_name: Engel, Andreas
last_name: Engel
- first_name: Harald L
full_name: Harald Janovjak
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Dimtrios
full_name: Fotiadis, Dimtrios
last_name: Fotiadis
- first_name: Alexej
full_name: Kedrov, Alexej
last_name: Kedrov
- first_name: David
full_name: Cisneros, David
last_name: Cisneros
- first_name: Daniel
full_name: Mueller, Daniel J
last_name: Mueller
citation:
ama: 'Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. Single-molecule
microscopy and force spectroscopy of membrane proteins. In: Single Molecules
and Nanotechnology. Vol 12. Springer; 2008:279-311. doi:10.1007/978-3-540-73924-1_11'
apa: Engel, A., Janovjak, H. L., Fotiadis, D., Kedrov, A., Cisneros, D., & Mueller,
D. (2008). Single-molecule microscopy and force spectroscopy of membrane proteins.
In Single Molecules and Nanotechnology (Vol. 12, pp. 279–311). Springer.
https://doi.org/10.1007/978-3-540-73924-1_11
chicago: Engel, Andreas, Harald L Janovjak, Dimtrios Fotiadis, Alexej Kedrov, David
Cisneros, and Daniel Mueller. “Single-Molecule Microscopy and Force Spectroscopy
of Membrane Proteins.” In Single Molecules and Nanotechnology, 12:279–311.
Springer, 2008. https://doi.org/10.1007/978-3-540-73924-1_11.
ieee: A. Engel, H. L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, and D. Mueller,
“Single-molecule microscopy and force spectroscopy of membrane proteins,” in Single
Molecules and Nanotechnology, vol. 12, Springer, 2008, pp. 279–311.
ista: 'Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. 2008.Single-molecule
microscopy and force spectroscopy of membrane proteins. In: Single Molecules and
Nanotechnology. vol. 12, 279–311.'
mla: Engel, Andreas, et al. “Single-Molecule Microscopy and Force Spectroscopy of
Membrane Proteins.” Single Molecules and Nanotechnology, vol. 12, Springer,
2008, pp. 279–311, doi:10.1007/978-3-540-73924-1_11.
short: A. Engel, H.L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, D. Mueller,
in:, Single Molecules and Nanotechnology, Springer, 2008, pp. 279–311.
date_created: 2018-12-11T12:04:50Z
date_published: 2008-01-08T00:00:00Z
date_updated: 2021-01-12T07:51:45Z
day: '08'
doi: 10.1007/978-3-540-73924-1_11
extern: 1
intvolume: ' 12'
month: '01'
page: 279 - 311
publication: Single Molecules and Nanotechnology
publication_status: published
publisher: Springer
publist_id: '2503'
quality_controlled: 0
status: public
title: Single-molecule microscopy and force spectroscopy of membrane proteins
type: book_chapter
volume: 12
year: '2008'
...
---
_id: '3734'
abstract:
- lang: eng
text: Gene expression levels fluctuate even under constant external conditions.
Much emphasis has usually been placed on the components of this noise that are
due to randomness in transcription and translation. Here we focus on the role
of noise associated with the inputs to transcriptional regulation; in particular,
we analyze the effects of random arrival times and binding of transcription factors
to their target sites along the genome. This contribution to the total noise sets
a fundamental physical limit to the reliability of genetic control, and has clear
signatures, but we show that these are easily obscured by experimental limitations
and even by conventional methods for plotting the variance vs. mean expression
level. We argue that simple, universal models of noise dominated by transcription
and translation are inconsistent with the embedding of gene expression in a network
of regulatory interactions. Analysis of recent experiments on transcriptional
control in the early Drosophila embryo shows that these results are quantitatively
consistent with the predicted signatures of input noise, and we discuss the experiments
needed to test the importance of input noise more generally.
acknowledgement: NSF Grant PHY-0650617; NIH grants P50 GM071508, R01 GM077599; Burroughs
Wellcome Program in Biological Dynamics
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Gregor T, Bialek W. The role of input noise in transcriptional regulation.
PLoS One. 2008;3(7). doi:10.1371/journal.pone.0002774
apa: Tkačik, G., Gregor, T., & Bialek, W. (2008). The role of input noise in
transcriptional regulation. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002774
chicago: Tkačik, Gašper, Thomas Gregor, and William Bialek. “The Role of Input Noise
in Transcriptional Regulation.” PLoS One. Public Library of Science, 2008.
https://doi.org/10.1371/journal.pone.0002774.
ieee: G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional
regulation,” PLoS One, vol. 3, no. 7. Public Library of Science, 2008.
ista: Tkačik G, Gregor T, Bialek W. 2008. The role of input noise in transcriptional
regulation. PLoS One. 3(7).
mla: Tkačik, Gašper, et al. “The Role of Input Noise in Transcriptional Regulation.”
PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774.
short: G. Tkačik, T. Gregor, W. Bialek, PLoS One 3 (2008).
date_created: 2018-12-11T12:04:52Z
date_published: 2008-07-23T00:00:00Z
date_updated: 2021-01-12T07:51:49Z
day: '23'
doi: 10.1371/journal.pone.0002774
extern: 1
intvolume: ' 3'
issue: '7'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475664
month: '07'
oa: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2498'
quality_controlled: 0
status: public
title: The role of input noise in transcriptional regulation
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: 3
year: '2008'
...
---
_id: '3739'
abstract:
- lang: eng
text: 'Changes in a cell''s external or internal conditions are usually reflected
in the concentrations of the relevant transcription factors. These proteins in
turn modulate the expression levels of the genes under their control and sometimes
need to perform nontrivial computations that integrate several inputs and affect
multiple genes. At the same time, the activities of the regulated genes would
fluctuate even if the inputs were held fixed, as a consequence of the intrinsic
noise in the system, and such noise must fundamentally limit the reliability of
any genetic computation. Here we use information theory to formalize the notion
of information transmission in simple genetic regulatory elements in the presence
of physically realistic noise sources. The dependence of this "channel capacity"
on noise parameters, cooperativity and cost of making signaling molecules is explored
systematically. We find that, in the range of parameters probed by recent in vivo
measurements, capacities higher than one bit should be achievable. It is of course
generally accepted that gene regulatory elements must, in order to function properly,
have a capacity of at least one bit. The central point of our analysis is the
demonstration that simple physical models of noisy gene transcription, with realistic
parameters, can indeed achieve this capacity: it was not self-evident that this
should be so. We also demonstrate that capacities significantly greater than one
bit are possible, so that transcriptional regulation need not be limited to simple
"on-off" components. The question whether real systems actually exploit
this richer possibility is beyond the scope of this investigation.'
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Callan C, Bialek W. Information capacity of genetic regulatory elements.
Physical Review E Statistical Nonlinear and Soft Matter Physics. 2008;78(1).
doi:10.1103/PhysRevE.78.011910
apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information capacity of genetic
regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter
Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.78.011910
chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Capacity
of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and
Soft Matter Physics. American Institute of Physics, 2008. https://doi.org/10.1103/PhysRevE.78.011910.
ieee: G. Tkačik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory
elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics,
vol. 78, no. 1. American Institute of Physics, 2008.
ista: Tkačik G, Callan C, Bialek W. 2008. Information capacity of genetic regulatory
elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 78(1).
mla: Tkačik, Gašper, et al. “Information Capacity of Genetic Regulatory Elements.”
Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78,
no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.
short: G. Tkačik, C. Callan, W. Bialek, Physical Review E Statistical Nonlinear
and Soft Matter Physics 78 (2008).
date_created: 2018-12-11T12:04:54Z
date_published: 2008-07-21T00:00:00Z
date_updated: 2021-01-12T07:51:51Z
day: '21'
doi: 10.1103/PhysRevE.78.011910
extern: 1
intvolume: ' 78'
issue: '1'
month: '07'
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '2488'
quality_controlled: 0
status: public
title: Information capacity of genetic regulatory elements
type: journal_article
volume: 78
year: '2008'
...
---
_id: '3740'
abstract:
- lang: eng
text: In the simplest view of transcriptional regulation, the expression of a gene
is turned on or off by changes in the concentration of a transcription factor
(TF). We use recent data on noise levels in gene expression to show that it should
be possible to transmit much more than just one regulatory bit. Realizing this
optimal information capacity would require that the dynamic range of TF concentrations
used by the cell, the input/output relation of the regulatory module, and the
noise in gene expression satisfy certain matching relations, which we derive.
These results provide parameter-free, quantitative predictions connecting independently
measurable quantities. Although we have considered only the simplified problem
of a single gene responding to a single TF, we find that these predictions are
in surprisingly good agreement with recent experiments on the Bicoid/Hunchback
system in the early Drosophila embryo and that this system achieves approximately
90% of its theoretical maximum information transmission.
acknowledgement: P50 GM071508/GM/NIGMS NIH HHS/United States; R01 GM077599/GM/NIGMS
NIH HHS/United States
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Curtis
full_name: Callan,Curtis G
last_name: Callan
- first_name: William
full_name: Bialek, William S
last_name: Bialek
citation:
ama: Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional
regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105
apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information flow and optimization
in transcriptional regulation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0806077105
chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and
Optimization in Transcriptional Regulation.” PNAS. National Academy of
Sciences, 2008. https://doi.org/10.1073/pnas.0806077105.
ieee: G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in
transcriptional regulation,” PNAS, vol. 105, no. 34. National Academy of
Sciences, pp. 12265–12270, 2008.
ista: Tkačik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional
regulation. PNAS. 105(34), 12265–12270.
mla: Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional
Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008,
pp. 12265–70, doi:10.1073/pnas.0806077105.
short: G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270.
date_created: 2018-12-11T12:04:54Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:52Z
day: '01'
doi: 10.1073/pnas.0806077105
extern: 1
intvolume: ' 105'
issue: '34'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527900
month: '01'
oa: 1
page: 12265 - 12270
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '2489'
quality_controlled: 0
status: public
title: Information flow and optimization in transcriptional regulation
type: journal_article
volume: 105
year: '2008'
...
---
_id: '3744'
abstract:
- lang: eng
text: It is widely acknowledged that detailed timing of action potentials is used
to encode information, for example, in auditory pathways; however, the computational
tools required to analyze encoding through timing are still in their infancy.
We present a simple example of encoding, based on a recent model of time-frequency
analysis, in which units fire action potentials when a certain condition is met,
but the timing of the action potential depends also on other features of the stimulus.
We show that, as a result, spike-triggered averages are smoothed so much that
they do not represent the true features of the encoding. Inspired by this example,
we present a simple method, differential reverse correlations, that can separate
an analysis of what causes a neuron to spike, and what controls its timing. We
analyze with this method the leaky integrate-and-fire neuron and show the method
accurately reconstructs the model's kernel.
author:
- first_name: Gasper
full_name: Gasper Tkacik
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Marcelo
full_name: Magnasco, Marcelo O
last_name: Magnasco
citation:
ama: 'Tkačik G, Magnasco M. Decoding spike timing: The differential reverse-correlation
method. Biosystems. 2008;93(1-2):90-100. doi:10.1016/j.biosystems.2008.04.011'
apa: 'Tkačik, G., & Magnasco, M. (2008). Decoding spike timing: The differential
reverse-correlation method. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2008.04.011'
chicago: 'Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential
Reverse-Correlation Method.” Biosystems. Elsevier, 2008. https://doi.org/10.1016/j.biosystems.2008.04.011.'
ieee: 'G. Tkačik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation
method,” Biosystems, vol. 93, no. 1–2. Elsevier, pp. 90–100, 2008.'
ista: 'Tkačik G, Magnasco M. 2008. Decoding spike timing: The differential reverse-correlation
method. Biosystems. 93(1–2), 90–100.'
mla: 'Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential
Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008,
pp. 90–100, doi:10.1016/j.biosystems.2008.04.011.'
short: G. Tkačik, M. Magnasco, Biosystems 93 (2008) 90–100.
date_created: 2018-12-11T12:04:56Z
date_published: 2008-07-01T00:00:00Z
date_updated: 2021-01-12T07:51:53Z
day: '01'
doi: 10.1016/j.biosystems.2008.04.011
extern: 1
intvolume: ' 93'
issue: 1-2
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792887
month: '07'
oa: 1
page: 90 - 100
publication: Biosystems
publication_status: published
publisher: Elsevier
publist_id: '2482'
quality_controlled: 0
status: public
title: 'Decoding spike timing: The differential reverse-correlation method'
type: journal_article
volume: 93
year: '2008'
...
---
_id: '3751'
abstract:
- lang: eng
text: 'Revealing the spectrum of combinatorial regulation of transcription at individual
promoters is essential for understanding the complex structure of biological networks.
However, the computations represented by the integration of various molecular
signals at complex promoters are difficult to decipher in the absence of simple
cis regulatory codes. Here we synthetically shuffle the regulatory architecture-operator
sequences binding activators and repressors-of a canonical bacterial promoter.
The resulting library of complex promoters allows for rapid exploration of promoter
encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter
encoded logics predominate. A simple transcriptional cis regulatory code determines
both logics, establishing a straightforward map between promoter structure and
logic phenotype. The regulatory code is determined solely by the type of transcriptional
regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a
repressor and an activator generate an ANDN: a AND NOT b. Three-input versions
of both logics, having an additional repressor as an input, are also present in
the library. The resulting complex promoters cover a wide dynamic range of transcriptional
strengths. Synthetic promoter shuffling represents a fast and efficient method
for exploring the spectrum of complex regulatory functions that can be encoded
by complex promoters. From an engineering point of view, synthetic promoter shuffling
enables the experimental testing of the functional properties of complex promoters
that cannot necessarily be inferred ab initio from the known properties of the
individual genetic components. Synthetic promoter shuffling may provide a useful
experimental tool for studying naturally occurring promoter shuffling.'
article_number: e2030
author:
- first_name: Ali
full_name: Kinkhabwala, Ali
last_name: Kinkhabwala
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Kinkhabwala A, Guet CC. Uncovering cis regulatory codes using synthetic promoter
shuffling. PLoS One. 2008;3(4). doi:10.1371/journal.pone.0002030
apa: Kinkhabwala, A., & Guet, C. C. (2008). Uncovering cis regulatory codes
using synthetic promoter shuffling. PLoS One. Public Library of Science.
https://doi.org/10.1371/journal.pone.0002030
chicago: Kinkhabwala, Ali, and Calin C Guet. “Uncovering Cis Regulatory Codes Using
Synthetic Promoter Shuffling.” PLoS One. Public Library of Science, 2008.
https://doi.org/10.1371/journal.pone.0002030.
ieee: A. Kinkhabwala and C. C. Guet, “Uncovering cis regulatory codes using synthetic
promoter shuffling,” PLoS One, vol. 3, no. 4. Public Library of Science,
2008.
ista: Kinkhabwala A, Guet CC. 2008. Uncovering cis regulatory codes using synthetic
promoter shuffling. PLoS One. 3(4), e2030.
mla: Kinkhabwala, Ali, and Calin C. Guet. “Uncovering Cis Regulatory Codes Using
Synthetic Promoter Shuffling.” PLoS One, vol. 3, no. 4, e2030, Public Library
of Science, 2008, doi:10.1371/journal.pone.0002030.
short: A. Kinkhabwala, C.C. Guet, PLoS One 3 (2008).
date_created: 2018-12-11T12:04:58Z
date_published: 2008-04-30T00:00:00Z
date_updated: 2021-01-12T07:51:56Z
day: '30'
ddc:
- '570'
doi: 10.1371/journal.pone.0002030
extern: '1'
external_id:
pmid:
- '18446205'
file:
- access_level: open_access
checksum: 42c26f8337298a9ecadbe34a16139466
content_type: application/pdf
creator: dernst
date_created: 2019-05-10T11:00:36Z
date_updated: 2020-07-14T12:46:15Z
file_id: '6400'
file_name: 2008_PLOS1_Kinkhabwala.PDF
file_size: 679786
relation: main_file
file_date_updated: 2020-07-14T12:46:15Z
has_accepted_license: '1'
intvolume: ' 3'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '2477'
quality_controlled: '1'
status: public
title: Uncovering cis regulatory codes using synthetic promoter shuffling
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2008'
...
---
_id: '3754'
abstract:
- lang: eng
text: Fluorescence correlation spectroscopy (FCS) has permitted the characterization
of high concentrations of noncoding RNAs in a single living bacterium. Here, we
extend the use of FCS to low concentrations of coding RNAs in single living cells.
We genetically fuse a red fluorescent protein (RFP) gene and two binding sites
for an RNA-binding protein, whose translated product is the RFP protein alone.
Using this construct, we determine in single cells both the absolute [mRNA] concentration
and the associated [RFP] expressed from an inducible plasmid. We find that the
FCS method allows us to reliably monitor in real-time [mRNA] down to similar to
40 nM (i.e. approximately two transcripts per volume of detection). To validate
these measurements, we show that [mRNA] is proportional to the associated expression
of the RFP protein. This FCS-based technique establishes a framework for minimally
invasive measurements of mRNA concentration in individual living bacteria.
acknowledgement: 'PMCID: PMC2475643 '
author:
- first_name: Calin C
full_name: Calin Guet
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Luke
full_name: Bruneaux,Luke
last_name: Bruneaux
- first_name: Taejin
full_name: Min,Taejin L
last_name: Min
- first_name: Dan
full_name: Siegal-Gaskins,Dan
last_name: Siegal Gaskins
- first_name: Israel
full_name: Figueroa,Israel
last_name: Figueroa
- first_name: Thierry
full_name: Emonet,Thierry
last_name: Emonet
- first_name: Philippe
full_name: Cluzel,Philippe
last_name: Cluzel
citation:
ama: Guet CC, Bruneaux L, Min T, et al. Minimally invasive determination of mRNA
concentration in single living bacteria. Nucleic Acids Research. 2008;36(12).
doi:10.1093/nar/gkn329
apa: Guet, C. C., Bruneaux, L., Min, T., Siegal Gaskins, D., Figueroa, I., Emonet,
T., & Cluzel, P. (2008). Minimally invasive determination of mRNA concentration
in single living bacteria. Nucleic Acids Research. Oxford University Press.
https://doi.org/10.1093/nar/gkn329
chicago: Guet, Calin C, Luke Bruneaux, Taejin Min, Dan Siegal Gaskins, Israel Figueroa,
Thierry Emonet, and Philippe Cluzel. “Minimally Invasive Determination of MRNA
Concentration in Single Living Bacteria.” Nucleic Acids Research. Oxford
University Press, 2008. https://doi.org/10.1093/nar/gkn329.
ieee: C. C. Guet et al., “Minimally invasive determination of mRNA concentration
in single living bacteria,” Nucleic Acids Research, vol. 36, no. 12. Oxford
University Press, 2008.
ista: Guet CC, Bruneaux L, Min T, Siegal Gaskins D, Figueroa I, Emonet T, Cluzel
P. 2008. Minimally invasive determination of mRNA concentration in single living
bacteria. Nucleic Acids Research. 36(12).
mla: Guet, Calin C., et al. “Minimally Invasive Determination of MRNA Concentration
in Single Living Bacteria.” Nucleic Acids Research, vol. 36, no. 12, Oxford
University Press, 2008, doi:10.1093/nar/gkn329.
short: C.C. Guet, L. Bruneaux, T. Min, D. Siegal Gaskins, I. Figueroa, T. Emonet,
P. Cluzel, Nucleic Acids Research 36 (2008).
date_created: 2018-12-11T12:04:59Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:51:57Z
day: '01'
doi: 10.1093/nar/gkn329
extern: 1
intvolume: ' 36'
issue: '12'
month: '01'
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '2474'
quality_controlled: 0
status: public
title: Minimally invasive determination of mRNA concentration in single living bacteria
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
volume: 36
year: '2008'
...
---
_id: '3760'
abstract:
- lang: eng
text: We introduce a method for efficiently animating a wide range of deformable
materials. We combine a high resolution surface mesh with a tetrahedral finite
element simulator that makes use of frequent re-meshing. This combination allows
for fast and detailed simulations of complex elastic and plastic behavior. We
significantly expand the range of physical parameters that can be simulated with
a single technique, and the results are free from common artifacts such as volume-loss,
smoothing, popping, and the absence of thin features like strands and sheets.
Our decision to couple a high resolution surface with low-resolution physics leads
to efficient simulation and detailed surface features, and our approach to creating
the tetrahedral mesh leads to an order-of-magnitude speedup over previous techniques
in the time spent re-meshing. We compute masses, collisions, and surface tension
forces on the scale of the fine mesh, which helps avoid visual artifacts due to
the differing mesh resolutions. The result is a method that can simulate a large
array of different material behaviors with high resolution features in a short
amount of time.
article_processing_charge: No
author:
- first_name: Christopher J
full_name: Wojtan, Christopher J
id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87
last_name: Wojtan
orcid: 0000-0001-6646-5546
- first_name: Greg
full_name: Turk, Greg
last_name: Turk
citation:
ama: Wojtan C, Turk G. Fast viscoelastic behavior with thin features. ACM Transactions
on Graphics. 2008;27(3). doi:10.1145/1360612.1360646
apa: Wojtan, C., & Turk, G. (2008). Fast viscoelastic behavior with thin features.
ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1360612.1360646
chicago: Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.”
ACM Transactions on Graphics. ACM, 2008. https://doi.org/10.1145/1360612.1360646.
ieee: C. Wojtan and G. Turk, “Fast viscoelastic behavior with thin features,” ACM
Transactions on Graphics, vol. 27, no. 3. ACM, 2008.
ista: Wojtan C, Turk G. 2008. Fast viscoelastic behavior with thin features. ACM
Transactions on Graphics. 27(3).
mla: Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.”
ACM Transactions on Graphics, vol. 27, no. 3, ACM, 2008, doi:10.1145/1360612.1360646.
short: C. Wojtan, G. Turk, ACM Transactions on Graphics 27 (2008).
date_created: 2018-12-11T12:05:01Z
date_published: 2008-08-01T00:00:00Z
date_updated: 2023-02-23T11:41:29Z
day: '01'
doi: 10.1145/1360612.1360646
extern: '1'
intvolume: ' 27'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://www.cc.gatech.edu/~turk/my_papers/fast_goop_2008.pdf
month: '08'
oa_version: None
publication: ACM Transactions on Graphics
publication_status: published
publisher: ACM
publist_id: '2467'
status: public
title: Fast viscoelastic behavior with thin features
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2008'
...
---
_id: '3769'
abstract:
- lang: eng
text: The geometrical representation of the space of phylogenetic trees implies
a metric on the space of weighted trees. This metric, the geodesic distance, is
the length of the shortest path through that space. We present an exact algorithm
to compute this metric. For biologically reasonable trees, the implementation
allows fast computations of the geodesic distance, although the running time of
the algorithm is worst-case exponential. The algorithm was applied to pairs of
118 gene trees of the metazoa. The results show that a special path in tree space,
the cone path, which can be computed in linear time, is a good approximation of
the geodesic distance. The program GeoMeTree is a python implementation of the
geodesic distance, and it is approximations and is available from www.cibiv.at/software/geometree.
acknowledgement: 10.1089/cmb.2008.0068
author:
- first_name: Anne
full_name: Anne Kupczok
id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87
last_name: Kupczok
- first_name: Arndt
full_name: von Haeseler,Arndt
last_name: Von Haeseler
- first_name: Steffen
full_name: Klaere,Steffen
last_name: Klaere
citation:
ama: Kupczok A, Von Haeseler A, Klaere S. An Exact Algorithm for the Geodesic Distance
between Phylogenetic Trees. Journal of Computational Biology. 2008;15(6):577-591.
doi:4200
apa: Kupczok, A., Von Haeseler, A., & Klaere, S. (2008). An Exact Algorithm
for the Geodesic Distance between Phylogenetic Trees. Journal of Computational
Biology. Mary Ann Liebert. https://doi.org/4200
chicago: Kupczok, Anne, Arndt Von Haeseler, and Steffen Klaere. “An Exact Algorithm
for the Geodesic Distance between Phylogenetic Trees.” Journal of Computational
Biology. Mary Ann Liebert, 2008. https://doi.org/4200.
ieee: A. Kupczok, A. Von Haeseler, and S. Klaere, “An Exact Algorithm for the Geodesic
Distance between Phylogenetic Trees.,” Journal of Computational Biology,
vol. 15, no. 6. Mary Ann Liebert, pp. 577–591, 2008.
ista: Kupczok A, Von Haeseler A, Klaere S. 2008. An Exact Algorithm for the Geodesic
Distance between Phylogenetic Trees. Journal of Computational Biology. 15(6),
577–591.
mla: Kupczok, Anne, et al. “An Exact Algorithm for the Geodesic Distance between
Phylogenetic Trees.” Journal of Computational Biology, vol. 15, no. 6,
Mary Ann Liebert, 2008, pp. 577–91, doi:4200.
short: A. Kupczok, A. Von Haeseler, S. Klaere, Journal of Computational Biology
15 (2008) 577–591.
date_created: 2018-12-11T12:05:04Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:04Z
day: '01'
doi: '4200'
extern: 1
intvolume: ' 15'
issue: '6'
month: '01'
page: 577 - 591
publication: Journal of Computational Biology
publication_status: published
publisher: Mary Ann Liebert
publist_id: '2458'
quality_controlled: 0
status: public
title: An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.
type: journal_article
volume: 15
year: '2008'
...
---
_id: '3822'
abstract:
- lang: eng
text: Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated
mossy fibre axons to the CA3 region. Although the initiation and propagation of
APs are fundamental steps during neural computation, little is known about the
site of AP initiation and the speed of propagation in mossy fibre axons. To address
these questions, we performed simultaneous somatic and axonal whole-cell recordings
from granule cells in acute hippocampal slices of adult mice at approximately
23 degrees C. Injection of short current pulses or synaptic stimulation evoked
axonal and somatic APs with similar amplitudes. By contrast, the time course was
significantly different, as axonal APs had a higher maximal rate of rise (464
+/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.).
Furthermore, analysis of latencies between the axonal and somatic signals showed
that APs were initiated in the proximal axon at approximately 20-30 mum distance
from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1).
Qualitatively similar results were obtained at a recording temperature of approximately
34 degrees C. Modelling of AP propagation in detailed cable models of granule
cells suggested that a approximately 4 times higher Na(+) channel density ( approximately
1000 pS mum(-2)) in the axon might account for both the higher rate of rise of
axonal APs and the robust AP initiation in the proximal mossy fibre axon. This
may be of critical importance to separate dendritic integration of thousands of
synaptic inputs from the generation and transmission of a common AP output.
author:
- first_name: Christoph
full_name: Schmidt-Hieber, Christoph
last_name: Schmidt Hieber
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Josef
full_name: Bischofberger, Josef
last_name: Bischofberger
citation:
ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Action potential initiation and
propagation in hippocampal mossy fibre axons. Journal of Physiology. 2008;586(7):1849-1857.
doi:10.1113/jphysiol.2007.150151
apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2008). Action potential
initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology.
Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.150151
chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Action
Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” Journal
of Physiology. Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.150151 .
ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Action potential initiation
and propagation in hippocampal mossy fibre axons,” Journal of Physiology,
vol. 586, no. 7. Wiley-Blackwell, pp. 1849–57, 2008.
ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2008. Action potential initiation
and propagation in hippocampal mossy fibre axons. Journal of Physiology. 586(7),
1849–57.
mla: Schmidt Hieber, Christoph, et al. “Action Potential Initiation and Propagation
in Hippocampal Mossy Fibre Axons.” Journal of Physiology, vol. 586, no.
7, Wiley-Blackwell, 2008, pp. 1849–57, doi:10.1113/jphysiol.2007.150151 .
short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Journal of Physiology 586
(2008) 1849–57.
date_created: 2018-12-11T12:05:21Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '01'
doi: '10.1113/jphysiol.2007.150151 '
extern: 1
intvolume: ' 586'
issue: '7'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375716/
month: '01'
oa: 1
page: 1849 - 57
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2387'
quality_controlled: 0
status: public
title: Action potential initiation and propagation in hippocampal mossy fibre axons
type: journal_article
volume: 586
year: '2008'
...
---
_id: '3823'
abstract:
- lang: eng
text: Two studies in this issue of Neuron (Kwon and Castillo and Rebola et al.)
show that the mossy fiber-CA3 pyramidal neuron synapse, a hippocampal synapse
well known for its presynaptic plasticity, exhibits a novel form of long-term
potentiation of NMDAR-mediated currents, which is induced and expressed postsynaptically.
author:
- first_name: Angharad
full_name: Kerr, Angharad M
last_name: Kerr
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Kerr A, Jonas PM. The two sides of hippocampal mossy fiber plasticity (Review).
Neuron. 2008;57(1):5-7. doi:10.1016/j.neuron.2007.12.015
apa: Kerr, A., & Jonas, P. M. (2008). The two sides of hippocampal mossy fiber
plasticity (Review). Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2007.12.015
chicago: Kerr, Angharad, and Peter M Jonas. “The Two Sides of Hippocampal Mossy
Fiber Plasticity (Review).” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.015.
ieee: A. Kerr and P. M. Jonas, “The two sides of hippocampal mossy fiber plasticity
(Review),” Neuron, vol. 57, no. 1. Elsevier, pp. 5–7, 2008.
ista: Kerr A, Jonas PM. 2008. The two sides of hippocampal mossy fiber plasticity
(Review). Neuron. 57(1), 5–7.
mla: Kerr, Angharad, and Peter M. Jonas. “The Two Sides of Hippocampal Mossy Fiber
Plasticity (Review).” Neuron, vol. 57, no. 1, Elsevier, 2008, pp. 5–7,
doi:10.1016/j.neuron.2007.12.015.
short: A. Kerr, P.M. Jonas, Neuron 57 (2008) 5–7.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-10T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '10'
doi: 10.1016/j.neuron.2007.12.015
extern: 1
intvolume: ' 57'
issue: '1'
month: '01'
page: 5 - 7
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2388'
quality_controlled: 0
status: public
title: The two sides of hippocampal mossy fiber plasticity (Review)
type: journal_article
volume: 57
year: '2008'
...
---
_id: '3824'
abstract:
- lang: eng
text: It is generally thought that transmitter release at mammalian central synapses
is triggered by Ca2+ microdomains, implying loose coupling between presynaptic
Ca2+ channels and Ca2+ sensors of exocytosis. Here we show that Ca2+ channel subunit
immunoreactivity is highly concentrated in the active zone of GABAergic presynaptic
terminals of putative parvalbumin-containing basket cells in the hippocampus.
Paired recording combined with presynaptic patch pipette perfusion revealed that
GABA release at basket cell-granule cell synapses is sensitive to millimolar concentrations
of the fast Ca2+ chelator BAPTA but insensitive to the slow Ca2+ chelator EGTA.
These results show that Ca2+ source and Ca2+ sensor are tightly coupled at this
synapse, with distances in the range of 10-20 nm. Models of Ca2+ inflow-exocytosis
coupling further reveal that the tightness of coupling increases efficacy, speed,
and temporal precision of transmitter release. Thus, tight coupling contributes
to fast feedforward and feedback inhibition in the hippocampal network.
author:
- first_name: Iancu
full_name: Bucurenciu, Iancu
last_name: Bucurenciu
- first_name: Ákos
full_name: Kulik, Ákos
last_name: Kulik
- first_name: Beat
full_name: Schwaller, Beat
last_name: Schwaller
- first_name: Michael
full_name: Frotscher, Michael
last_name: Frotscher
- 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, Kulik Á, Schwaller B, Frotscher M, Jonas PM. Nanodomain coupling
between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter
release at a cortical GABAergic synapse. Neuron. 2008;57(4):536-545. doi:10.1016/j.neuron.2007.12.026
apa: Bucurenciu, I., Kulik, Á., Schwaller, B., Frotscher, M., & Jonas, P. M.
(2008). Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes
fast and efficient transmitter release at a cortical GABAergic synapse. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2007.12.026
chicago: Bucurenciu, Iancu, Ákos Kulik, Beat Schwaller, Michael Frotscher, and Peter
M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes
Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” Neuron.
Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.026.
ieee: I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, and P. M. Jonas, “Nanodomain
coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient
transmitter release at a cortical GABAergic synapse,” Neuron, vol. 57,
no. 4. Elsevier, pp. 536–45, 2008.
ista: Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. 2008. Nanodomain
coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient
transmitter release at a cortical GABAergic synapse. Neuron. 57(4), 536–45.
mla: Bucurenciu, Iancu, et al. “Nanodomain Coupling between Ca(2+) Channels and
Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic
Synapse.” Neuron, vol. 57, no. 4, Elsevier, 2008, pp. 536–45, doi:10.1016/j.neuron.2007.12.026.
short: I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, P.M. Jonas, Neuron 57
(2008) 536–45.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:27Z
day: '01'
doi: 10.1016/j.neuron.2007.12.026
extern: 1
intvolume: ' 57'
issue: '4'
month: '01'
page: 536 - 45
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '2385'
quality_controlled: 0
status: public
title: Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast
and efficient transmitter release at a cortical GABAergic synapse
type: journal_article
volume: 57
year: '2008'
...
---
_id: '3825'
abstract:
- lang: eng
text: Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type
of inhibitory interneuron in the hippocampus. These cells inhibit principal cells
in a temporally precise manner and are involved in the generation of network oscillations.
Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding
proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling
in these interneurons has not been investigated. To study action potential (AP)-induced
dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings
with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously
identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2
or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients
with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that
increased linearly with AP number. Analysis of Ca(2+) transients under steady-state
conditions with different fura-2 concentrations and during loading with 200 microm
fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200
(kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the
Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1).
At approximately 23 degrees C, the decay time constant of the Ca(2+) transients
was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At
34 degrees C, the decay time constant was 203 ms and the corresponding extrusion
rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst
activity with three to five APs per theta cycle, as occurs in vivo during exploration,
led to a moderate increase in the global Ca(2+) concentration that was proportional
to AP number, whereas more intense stimulation was required to reach micromolar
Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime.
In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio,
a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion.
These specific buffering properties of BCs will sharpen the time course of local
Ca(2+) signals, while prolonging the decay of global Ca(2+) signals.
author:
- first_name: Yexica
full_name: Aponte, Yexica
last_name: Aponte
- 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: Aponte Y, Bischofberger J, Jonas PM. Efficient Ca(2+) buffering in fast-spiking
basket cells of rat hippocampus. Journal of Physiology. 2008;586(8):2061-2075.
doi:10.1113/jphysiol.2007.147298
apa: Aponte, Y., Bischofberger, J., & Jonas, P. M. (2008). Efficient Ca(2+)
buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology.
Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.147298
chicago: Aponte, Yexica, Josef Bischofberger, and Peter M Jonas. “Efficient Ca(2+)
Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” Journal of Physiology.
Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.147298.
ieee: Y. Aponte, J. Bischofberger, and P. M. Jonas, “Efficient Ca(2+) buffering
in fast-spiking basket cells of rat hippocampus,” Journal of Physiology,
vol. 586, no. 8. Wiley-Blackwell, pp. 2061–75, 2008.
ista: Aponte Y, Bischofberger J, Jonas PM. 2008. Efficient Ca(2+) buffering in fast-spiking
basket cells of rat hippocampus. Journal of Physiology. 586(8), 2061–75.
mla: Aponte, Yexica, et al. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells
of Rat Hippocampus.” Journal of Physiology, vol. 586, no. 8, Wiley-Blackwell,
2008, pp. 2061–75, doi:10.1113/jphysiol.2007.147298.
short: Y. Aponte, J. Bischofberger, P.M. Jonas, Journal of Physiology 586 (2008)
2061–75.
date_created: 2018-12-11T12:05:22Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:28Z
day: '01'
doi: 10.1113/jphysiol.2007.147298
extern: 1
intvolume: ' 586'
issue: '8'
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2465201/
month: '01'
oa: 1
page: 2061 - 75
publication: Journal of Physiology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '2386'
quality_controlled: 0
status: public
title: Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus
type: journal_article
volume: 586
year: '2008'
...
---
_id: '3826'
abstract:
- lang: eng
text: Gamma frequency (30-100 Hz) oscillations in the mature cortex underlie higher
cognitive functions. Fast signaling in GABAergic interneuron networks plays a
key role in the generation of these oscillations. During development of the rodent
brain, gamma activity appears at the end of the first postnatal week, but frequency
and synchrony reach adult levels only by the fourth week. However, the mechanisms
underlying the maturation of gamma activity are unclear. Here we demonstrate that
hippocampal basket cells (BCs), the proposed cellular substrate of gamma oscillations,
undergo marked changes in their morphological, intrinsic, and synaptic properties
between postnatal day 6 (P6) and P25. During maturation, action potential duration,
propagation time, duration of the release period, and decay time constant of IPSCs
decreases by approximately 30-60%. Thus, postnatal development converts BCs from
slow into fast signaling devices. Computational analysis reveals that BC networks
with young intrinsic and synaptic properties as well as reduced connectivity generate
oscillations with moderate coherence in the lower gamma frequency range. In contrast,
BC networks with mature properties and increased connectivity generate highly
coherent activity in the upper gamma frequency band. Thus, late postnatal maturation
of BCs enhances coherence in neuronal networks and will thereby contribute to
the development of cognitive brain functions.
author:
- first_name: Daniel
full_name: Doischer, Daniel
last_name: Doischer
- first_name: Jonas
full_name: Hosp, Jonas Aurel
last_name: Hosp
- first_name: Yuchio
full_name: Yanagawa, Yuchio
last_name: Yanagawa
- first_name: Kunihiko
full_name: Obata, Kunihiko
last_name: Obata
- first_name: Peter M
full_name: Peter Jonas
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Imre
full_name: Vida, Imre
last_name: Vida
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Doischer D, Hosp J, Yanagawa Y, et al. Postnatal differentiation of basket
cells from slow to fast signaling devices. Journal of Neuroscience. 2008;28(48):12956-12968.
doi:10.1523/JNEUROSCI.2890-08.2008
apa: Doischer, D., Hosp, J., Yanagawa, Y., Obata, K., Jonas, P. M., Vida, I., &
Bartos, M. (2008). Postnatal differentiation of basket cells from slow to fast
signaling devices. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2890-08.2008
chicago: Doischer, Daniel, Jonas Hosp, Yuchio Yanagawa, Kunihiko Obata, Peter M
Jonas, Imre Vida, and Marlene Bartos. “Postnatal Differentiation of Basket Cells
from Slow to Fast Signaling Devices.” Journal of Neuroscience. Society
for Neuroscience, 2008. https://doi.org/10.1523/JNEUROSCI.2890-08.2008.
ieee: D. Doischer et al., “Postnatal differentiation of basket cells from
slow to fast signaling devices,” Journal of Neuroscience, vol. 28, no.
48. Society for Neuroscience, pp. 12956–68, 2008.
ista: Doischer D, Hosp J, Yanagawa Y, Obata K, Jonas PM, Vida I, Bartos M. 2008.
Postnatal differentiation of basket cells from slow to fast signaling devices.
Journal of Neuroscience. 28(48), 12956–68.
mla: Doischer, Daniel, et al. “Postnatal Differentiation of Basket Cells from Slow
to Fast Signaling Devices.” Journal of Neuroscience, vol. 28, no. 48, Society
for Neuroscience, 2008, pp. 12956–68, doi:10.1523/JNEUROSCI.2890-08.2008.
short: D. Doischer, J. Hosp, Y. Yanagawa, K. Obata, P.M. Jonas, I. Vida, M. Bartos,
Journal of Neuroscience 28 (2008) 12956–68.
date_created: 2018-12-11T12:05:23Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:52:28Z
day: '01'
doi: 10.1523/JNEUROSCI.2890-08.2008
extern: 1
intvolume: ' 28'
issue: '48'
month: '01'
page: 12956 - 68
publication: Journal of Neuroscience
publication_status: published
publisher: Society for Neuroscience
publist_id: '2383'
quality_controlled: 0
status: public
title: Postnatal differentiation of basket cells from slow to fast signaling devices
type: journal_article
volume: 28
year: '2008'
...