---
_id: '2011'
abstract:
- lang: eng
text: The protection of privacy of individual-level information in genome-wide association
study (GWAS) databases has been a major concern of researchers following the publication
of “an attack” on GWAS data by Homer et al. (2008). Traditional statistical methods
for confidentiality and privacy protection of statistical databases do not scale
well to deal with GWAS data, especially in terms of guarantees regarding protection
from linkage to external information. The more recent concept of differential
privacy, introduced by the cryptographic community, is an approach that provides
a rigorous definition of privacy with meaningful privacy guarantees in the presence
of arbitrary external information, although the guarantees may come at a serious
price in terms of data utility. Building on such notions, Uhler et al. (2013)
proposed new methods to release aggregate GWAS data without compromising an individual’s
privacy. We extend the methods developed in Uhler et al. (2013) for releasing
differentially-private χ2χ2-statistics by allowing for arbitrary number of cases
and controls, and for releasing differentially-private allelic test statistics.
We also provide a new interpretation by assuming the controls’ data are known,
which is a realistic assumption because some GWAS use publicly available data
as controls. We assess the performance of the proposed methods through a risk-utility
analysis on a real data set consisting of DNA samples collected by the Wellcome
Trust Case Control Consortium and compare the methods with the differentially-private
release mechanism proposed by Johnson and Shmatikov (2013).
acknowledgement: This research was partially supported by NSF Awards EMSW21-RTG and
BCS-0941518 to the Department of Statistics at Carnegie Mellon University, and by
NSF Grant BCS-0941553 to the Department of Statistics at Pennsylvania State University.
This work was also supported in part by the National Center for Research Resources,
Grant UL1 RR033184, and is now at the National Center for Advancing Translational
Sciences, Grant UL1 TR000127 to Pennsylvania State University. The content is solely
the responsibility of the authors and does not necessarily represent the official
views of the NSF and NIH.
author:
- first_name: Fei
full_name: Yu, Fei
last_name: Yu
- first_name: Stephen
full_name: Fienberg, Stephen
last_name: Fienberg
- first_name: Alexandra
full_name: Slaković, Alexandra
last_name: Slaković
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Yu F, Fienberg S, Slaković A, Uhler C. Scalable privacy-preserving data sharing
methodology for genome-wide association studies. Journal of Biomedical Informatics.
2014;50:133-141. doi:10.1016/j.jbi.2014.01.008
apa: Yu, F., Fienberg, S., Slaković, A., & Uhler, C. (2014). Scalable privacy-preserving
data sharing methodology for genome-wide association studies. Journal of Biomedical
Informatics. Elsevier. https://doi.org/10.1016/j.jbi.2014.01.008
chicago: Yu, Fei, Stephen Fienberg, Alexandra Slaković, and Caroline Uhler. “Scalable
Privacy-Preserving Data Sharing Methodology for Genome-Wide Association Studies.”
Journal of Biomedical Informatics. Elsevier, 2014. https://doi.org/10.1016/j.jbi.2014.01.008.
ieee: F. Yu, S. Fienberg, A. Slaković, and C. Uhler, “Scalable privacy-preserving
data sharing methodology for genome-wide association studies,” Journal of Biomedical
Informatics, vol. 50. Elsevier, pp. 133–141, 2014.
ista: Yu F, Fienberg S, Slaković A, Uhler C. 2014. Scalable privacy-preserving data
sharing methodology for genome-wide association studies. Journal of Biomedical
Informatics. 50, 133–141.
mla: Yu, Fei, et al. “Scalable Privacy-Preserving Data Sharing Methodology for Genome-Wide
Association Studies.” Journal of Biomedical Informatics, vol. 50, Elsevier,
2014, pp. 133–41, doi:10.1016/j.jbi.2014.01.008.
short: F. Yu, S. Fienberg, A. Slaković, C. Uhler, Journal of Biomedical Informatics
50 (2014) 133–141.
date_created: 2018-12-11T11:55:12Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T06:54:42Z
day: '01'
department:
- _id: CaUh
doi: 10.1016/j.jbi.2014.01.008
intvolume: ' 50'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1401.5193
month: '08'
oa: 1
oa_version: Submitted Version
page: 133 - 141
publication: Journal of Biomedical Informatics
publication_status: published
publisher: Elsevier
publist_id: '5065'
quality_controlled: '1'
scopus_import: 1
status: public
title: Scalable privacy-preserving data sharing methodology for genome-wide association
studies
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '2012'
abstract:
- lang: eng
text: The classical sphere packing problem asks for the best (infinite) arrangement
of non-overlapping unit balls which cover as much space as possible. We define
a generalized version of the problem, where we allow each ball a limited amount
of overlap with other balls. We study two natural choices of overlap measures
and obtain the optimal lattice packings in a parameterized family of lattices
which contains the FCC, BCC, and integer lattice.
acknowledgement: We thank Herbert Edelsbrunner for his valuable discussions and ideas
on the topic of this paper. The second author has been supported by the Max Planck
Center for Visual Computing and Communication
article_number: '1401.0468'
article_processing_charge: No
arxiv: 1
author:
- first_name: Mabel
full_name: Iglesias Ham, Mabel
id: 41B58C0C-F248-11E8-B48F-1D18A9856A87
last_name: Iglesias Ham
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
orcid: 0000-0002-8030-9299
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
citation:
ama: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv.
doi:10.48550/arXiv.1401.0468
apa: Iglesias Ham, M., Kerber, M., & Uhler, C. (n.d.). Sphere packing with limited
overlap. arXiv. https://doi.org/10.48550/arXiv.1401.0468
chicago: Iglesias Ham, Mabel, Michael Kerber, and Caroline Uhler. “Sphere Packing
with Limited Overlap.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1401.0468.
ieee: M. Iglesias Ham, M. Kerber, and C. Uhler, “Sphere packing with limited overlap,”
arXiv. .
ista: Iglesias Ham M, Kerber M, Uhler C. Sphere packing with limited overlap. arXiv,
1401.0468.
mla: Iglesias Ham, Mabel, et al. “Sphere Packing with Limited Overlap.” ArXiv,
1401.0468, doi:10.48550/arXiv.1401.0468.
short: M. Iglesias Ham, M. Kerber, C. Uhler, ArXiv (n.d.).
date_created: 2018-12-11T11:55:12Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-10-18T08:06:45Z
day: '01'
department:
- _id: HeEd
- _id: CaUh
doi: 10.48550/arXiv.1401.0468
external_id:
arxiv:
- '1401.0468'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://cccg.ca/proceedings/2014/papers/paper23.pdf
month: '01'
oa: 1
oa_version: Submitted Version
publication: arXiv
publication_status: submitted
publist_id: '5064'
status: public
title: Sphere packing with limited overlap
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '2013'
abstract:
- lang: eng
text: "An asymptotic theory is developed for computing volumes of regions in the
parameter space of a directed Gaussian graphical model that are obtained by bounding
partial correlations. We study these volumes using the method of real log canonical
thresholds from algebraic geometry. Our analysis involves the computation of the
singular loci of correlation hypersurfaces. Statistical applications include the
strong-faithfulness assumption for the PC algorithm and the quantification of
confounder bias in causal inference. A detailed analysis is presented for trees,
bow ties, tripartite graphs, and complete graphs.\r\n"
acknowledgement: This work was supported in part by the US National Science Foundation
(DMS-0968882) and the Defense Advanced Research Projects Agency (DARPA) Deep Learning
program (FA8650-10-C-7020).
author:
- first_name: Shaowei
full_name: Lin, Shaowei
last_name: Lin
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Bernd
full_name: Sturmfels, Bernd
last_name: Sturmfels
- first_name: Peter
full_name: Bühlmann, Peter
last_name: Bühlmann
citation:
ama: Lin S, Uhler C, Sturmfels B, Bühlmann P. Hypersurfaces and their singularities
in partial correlation testing. Foundations of Computational Mathematics.
2014;14(5):1079-1116. doi:10.1007/s10208-014-9205-0
apa: Lin, S., Uhler, C., Sturmfels, B., & Bühlmann, P. (2014). Hypersurfaces
and their singularities in partial correlation testing. Foundations of Computational
Mathematics. Springer. https://doi.org/10.1007/s10208-014-9205-0
chicago: Lin, Shaowei, Caroline Uhler, Bernd Sturmfels, and Peter Bühlmann. “Hypersurfaces
and Their Singularities in Partial Correlation Testing.” Foundations of Computational
Mathematics. Springer, 2014. https://doi.org/10.1007/s10208-014-9205-0.
ieee: S. Lin, C. Uhler, B. Sturmfels, and P. Bühlmann, “Hypersurfaces and their
singularities in partial correlation testing,” Foundations of Computational
Mathematics, vol. 14, no. 5. Springer, pp. 1079–1116, 2014.
ista: Lin S, Uhler C, Sturmfels B, Bühlmann P. 2014. Hypersurfaces and their singularities
in partial correlation testing. Foundations of Computational Mathematics. 14(5),
1079–1116.
mla: Lin, Shaowei, et al. “Hypersurfaces and Their Singularities in Partial Correlation
Testing.” Foundations of Computational Mathematics, vol. 14, no. 5, Springer,
2014, pp. 1079–116, doi:10.1007/s10208-014-9205-0.
short: S. Lin, C. Uhler, B. Sturmfels, P. Bühlmann, Foundations of Computational
Mathematics 14 (2014) 1079–1116.
date_created: 2018-12-11T11:55:12Z
date_published: 2014-10-10T00:00:00Z
date_updated: 2021-01-12T06:54:43Z
day: '10'
department:
- _id: CaUh
doi: 10.1007/s10208-014-9205-0
intvolume: ' 14'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1209.0285
month: '10'
oa: 1
oa_version: Submitted Version
page: 1079 - 1116
publication: Foundations of Computational Mathematics
publication_status: published
publisher: Springer
publist_id: '5063'
quality_controlled: '1'
scopus_import: 1
status: public
title: Hypersurfaces and their singularities in partial correlation testing
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '2018'
abstract:
- lang: eng
text: Synaptic cell adhesion molecules are increasingly gaining attention for conferring
specific properties to individual synapses. Netrin-G1 and netrin-G2 are trans-synaptic
adhesion molecules that distribute on distinct axons, and their presence restricts
the expression of their cognate receptors, NGL1 and NGL2, respectively, to specific
subdendritic segments of target neurons. However, the neural circuits and functional
roles of netrin-G isoform complexes remain unclear. Here, we use netrin-G-KO and
NGL-KO mice to reveal that netrin-G1/NGL1 and netrin-G2/NGL2 interactions specify
excitatory synapses in independent hippocampal pathways. In the hippocampal CA1
area, netrin-G1/NGL1 and netrin-G2/NGL2 were expressed in the temporoammonic and
Schaffer collateral pathways, respectively. The lack of presynaptic netrin-Gs
led to the dispersion of NGLs from postsynaptic membranes. In accord, netrin-G
mutant synapses displayed opposing phenotypes in long-term and short-term plasticity
through discrete biochemical pathways. The plasticity phenotypes in netrin-G-KOs
were phenocopied in NGL-KOs, with a corresponding loss of netrin-Gs from presynaptic
membranes. Our findings show that netrin-G/NGL interactions differentially control
synaptic plasticity in distinct circuits via retrograde signaling mechanisms and
explain how synaptic inputs are diversified to control neuronal activity.
acknowledgement: This work was supported by “Funding Program for World-Leading Innovative
R&D on Science and Technology (FIRST Program)” initiated by the Council for Science
and Technology Policy.
article_processing_charge: No
article_type: original
author:
- first_name: Hiroshi
full_name: Matsukawa, Hiroshi
last_name: Matsukawa
- first_name: Sachiko
full_name: Akiyoshi Nishimura, Sachiko
last_name: Akiyoshi Nishimura
- first_name: Qi
full_name: Zhang, Qi
last_name: Zhang
- first_name: Rafael
full_name: Luján, Rafael
last_name: Luján
- first_name: Kazuhiko
full_name: Yamaguchi, Kazuhiko
last_name: Yamaguchi
- first_name: Hiromichi
full_name: Goto, Hiromichi
last_name: Goto
- first_name: Kunio
full_name: Yaguchi, Kunio
last_name: Yaguchi
- first_name: Tsutomu
full_name: Hashikawa, Tsutomu
last_name: Hashikawa
- first_name: Chie
full_name: Sano, Chie
last_name: Sano
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Toshiaki
full_name: Nakashiba, Toshiaki
last_name: Nakashiba
- first_name: Shigeyoshi
full_name: Itohara, Shigeyoshi
last_name: Itohara
citation:
ama: Matsukawa H, Akiyoshi Nishimura S, Zhang Q, et al. Netrin-G/NGL complexes encode
functional synaptic diversification. Journal of Neuroscience. 2014;34(47):15779-15792.
doi:10.1523/JNEUROSCI.1141-14.2014
apa: Matsukawa, H., Akiyoshi Nishimura, S., Zhang, Q., Luján, R., Yamaguchi, K.,
Goto, H., … Itohara, S. (2014). Netrin-G/NGL complexes encode functional synaptic
diversification. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1141-14.2014
chicago: Matsukawa, Hiroshi, Sachiko Akiyoshi Nishimura, Qi Zhang, Rafael Luján,
Kazuhiko Yamaguchi, Hiromichi Goto, Kunio Yaguchi, et al. “Netrin-G/NGL Complexes
Encode Functional Synaptic Diversification.” Journal of Neuroscience. Society
for Neuroscience, 2014. https://doi.org/10.1523/JNEUROSCI.1141-14.2014.
ieee: H. Matsukawa et al., “Netrin-G/NGL complexes encode functional synaptic
diversification,” Journal of Neuroscience, vol. 34, no. 47. Society for
Neuroscience, pp. 15779–15792, 2014.
ista: Matsukawa H, Akiyoshi Nishimura S, Zhang Q, Luján R, Yamaguchi K, Goto H,
Yaguchi K, Hashikawa T, Sano C, Shigemoto R, Nakashiba T, Itohara S. 2014. Netrin-G/NGL
complexes encode functional synaptic diversification. Journal of Neuroscience.
34(47), 15779–15792.
mla: Matsukawa, Hiroshi, et al. “Netrin-G/NGL Complexes Encode Functional Synaptic
Diversification.” Journal of Neuroscience, vol. 34, no. 47, Society for
Neuroscience, 2014, pp. 15779–92, doi:10.1523/JNEUROSCI.1141-14.2014.
short: H. Matsukawa, S. Akiyoshi Nishimura, Q. Zhang, R. Luján, K. Yamaguchi, H.
Goto, K. Yaguchi, T. Hashikawa, C. Sano, R. Shigemoto, T. Nakashiba, S. Itohara,
Journal of Neuroscience 34 (2014) 15779–15792.
date_created: 2018-12-11T11:55:14Z
date_published: 2014-11-19T00:00:00Z
date_updated: 2022-05-24T08:54:54Z
day: '19'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1523/JNEUROSCI.1141-14.2014
external_id:
pmid:
- '25411505'
file:
- access_level: open_access
checksum: 6913e9bc26e9fc1c0441a739a4199229
content_type: application/pdf
creator: dernst
date_created: 2022-05-24T08:41:41Z
date_updated: 2022-05-24T08:41:41Z
file_id: '11410'
file_name: 2014_JournNeuroscience_Matsukawa.pdf
file_size: 3963728
relation: main_file
success: 1
file_date_updated: 2022-05-24T08:41:41Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '47'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 15779 - 15792
pmid: 1
publication: Journal of Neuroscience
publication_identifier:
eissn:
- 1529-2401
issn:
- 0270-6474
publication_status: published
publisher: Society for Neuroscience
publist_id: '5054'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Netrin-G/NGL complexes encode functional synaptic diversification
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2014'
...
---
_id: '2019'
abstract:
- lang: eng
text: We prove that the empirical density of states of quantum spin glasses on arbitrary
graphs converges to a normal distribution as long as the maximal degree is negligible
compared with the total number of edges. This extends the recent results of Keating
et al. (2014) that were proved for graphs with bounded chromatic number and with
symmetric coupling distribution. Furthermore, we generalise the result to arbitrary
hypergraphs. We test the optimality of our condition on the maximal degree for
p-uniform hypergraphs that correspond to p-spin glass Hamiltonians acting on n
distinguishable spin- 1/2 particles. At the critical threshold p = n1/2 we find
a sharp classical-quantum phase transition between the normal distribution and
the Wigner semicircle law. The former is characteristic to classical systems with
commuting variables, while the latter is a signature of noncommutative random
matrix theory.
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Dominik J
full_name: Schröder, Dominik J
last_name: Schröder
citation:
ama: Erdös L, Schröder DJ. Phase transition in the density of states of quantum
spin glasses. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):441-464.
doi:10.1007/s11040-014-9164-3
apa: Erdös, L., & Schröder, D. J. (2014). Phase transition in the density of
states of quantum spin glasses. Mathematical Physics, Analysis and Geometry.
Springer. https://doi.org/10.1007/s11040-014-9164-3
chicago: Erdös, László, and Dominik J Schröder. “Phase Transition in the Density
of States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry.
Springer, 2014. https://doi.org/10.1007/s11040-014-9164-3.
ieee: L. Erdös and D. J. Schröder, “Phase transition in the density of states of
quantum spin glasses,” Mathematical Physics, Analysis and Geometry, vol.
17, no. 3–4. Springer, pp. 441–464, 2014.
ista: Erdös L, Schröder DJ. 2014. Phase transition in the density of states of quantum
spin glasses. Mathematical Physics, Analysis and Geometry. 17(3–4), 441–464.
mla: Erdös, László, and Dominik J. Schröder. “Phase Transition in the Density of
States of Quantum Spin Glasses.” Mathematical Physics, Analysis and Geometry,
vol. 17, no. 3–4, Springer, 2014, pp. 441–64, doi:10.1007/s11040-014-9164-3.
short: L. Erdös, D.J. Schröder, Mathematical Physics, Analysis and Geometry 17 (2014)
441–464.
date_created: 2018-12-11T11:55:15Z
date_published: 2014-12-17T00:00:00Z
date_updated: 2021-01-12T06:54:45Z
day: '17'
department:
- _id: LaEr
doi: 10.1007/s11040-014-9164-3
ec_funded: 1
intvolume: ' 17'
issue: 3-4
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1407.1552
month: '12'
oa: 1
oa_version: Submitted Version
page: 441 - 464
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication: Mathematical Physics, Analysis and Geometry
publication_status: published
publisher: Springer
publist_id: '5053'
quality_controlled: '1'
scopus_import: 1
status: public
title: Phase transition in the density of states of quantum spin glasses
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 17
year: '2014'
...
---
_id: '2020'
abstract:
- lang: eng
text: The mammalian heart has long been considered a postmitotic organ, implying
that the total number of cardiomyocytes is set at birth. Analysis of cell division
in the mammalian heart is complicated by cardiomyocyte binucleation shortly after
birth, which makes it challenging to interpret traditional assays of cell turnover
[Laflamme MA, Murray CE (2011) Nature 473(7347):326–335; Bergmann O, et al. (2009)
Science 324(5923):98–102]. An elegant multi-isotope imaging-mass spectrometry
technique recently calculated the low, discrete rate of cardiomyocyte generation
in mice [Senyo SE, et al. (2013) Nature 493(7432):433–436], yet our cellular-level
understanding of postnatal cardiomyogenesis remains limited. Herein, we provide
a new line of evidence for the differentiated α-myosin heavy chain-expressing
cardiomyocyte as the cell of origin of postnatal cardiomyogenesis using the “mosaic
analysis with double markers” mouse model. We show limited, life-long, symmetric
division of cardiomyocytes as a rare event that is evident in utero but significantly
diminishes after the first month of life in mice; daughter cardiomyocytes divide
very seldom, which this study is the first to demonstrate, to our knowledge. Furthermore,
ligation of the left anterior descending coronary artery, which causes a myocardial
infarction in the mosaic analysis with double-marker mice, did not increase the
rate of cardiomyocyte division above the basal level for up to 4 wk after the
injury. The clonal analysis described here provides direct evidence of postnatal
mammalian cardiomyogenesis.
author:
- first_name: Shah
full_name: Ali, Shah
last_name: Ali
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Lily
full_name: Saadat, Lily
last_name: Saadat
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Irving
full_name: Weissman, Irving
last_name: Weissman
- first_name: Reza
full_name: Ardehali, Reza
last_name: Ardehali
citation:
ama: Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. Existing cardiomyocytes
generate cardiomyocytes at a low rate after birth in mice. PNAS. 2014;111(24):8850-8855.
doi:10.1073/pnas.1408233111
apa: Ali, S., Hippenmeyer, S., Saadat, L., Luo, L., Weissman, I., & Ardehali,
R. (2014). Existing cardiomyocytes generate cardiomyocytes at a low rate after
birth in mice. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1408233111
chicago: Ali, Shah, Simon Hippenmeyer, Lily Saadat, Liqun Luo, Irving Weissman,
and Reza Ardehali. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low Rate
after Birth in Mice.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1408233111.
ieee: S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, and R. Ardehali, “Existing
cardiomyocytes generate cardiomyocytes at a low rate after birth in mice,” PNAS,
vol. 111, no. 24. National Academy of Sciences, pp. 8850–8855, 2014.
ista: Ali S, Hippenmeyer S, Saadat L, Luo L, Weissman I, Ardehali R. 2014. Existing
cardiomyocytes generate cardiomyocytes at a low rate after birth in mice. PNAS.
111(24), 8850–8855.
mla: Ali, Shah, et al. “Existing Cardiomyocytes Generate Cardiomyocytes at a Low
Rate after Birth in Mice.” PNAS, vol. 111, no. 24, National Academy of
Sciences, 2014, pp. 8850–55, doi:10.1073/pnas.1408233111.
short: S. Ali, S. Hippenmeyer, L. Saadat, L. Luo, I. Weissman, R. Ardehali, PNAS
111 (2014) 8850–8855.
date_created: 2018-12-11T11:55:15Z
date_published: 2014-06-17T00:00:00Z
date_updated: 2021-01-12T06:54:46Z
day: '17'
department:
- _id: SiHi
doi: 10.1073/pnas.1408233111
intvolume: ' 111'
issue: '24'
language:
- iso: eng
month: '06'
oa_version: None
page: 8850 - 8855
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5052'
quality_controlled: '1'
scopus_import: 1
status: public
title: Existing cardiomyocytes generate cardiomyocytes at a low rate after birth in
mice
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2014'
...
---
_id: '2021'
abstract:
- lang: eng
text: Neurotrophins regulate diverse aspects of neuronal development and plasticity,
but their precise in vivo functions during neural circuit assembly in the central
brain remain unclear. We show that the neurotrophin receptor tropomyosin-related
kinase C (TrkC) is required for dendritic growth and branching of mouse cerebellar
Purkinje cells. Sparse TrkC knockout reduced dendrite complexity, but global Purkinje
cell knockout had no effect. Removal of the TrkC ligand neurotrophin-3 (NT-3)
from cerebellar granule cells, which provide major afferent input to developing
Purkinje cell dendrites, rescued the dendrite defects caused by sparse TrkC disruption
in Purkinje cells. Our data demonstrate that NT-3 from presynaptic neurons (granule
cells) is required for TrkC-dependent competitive dendrite morphogenesis in postsynaptic
neurons (Purkinje cells)—a previously unknown mechanism of neural circuit development.
author:
- first_name: Joo
full_name: William, Joo
last_name: William
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
citation:
ama: William J, Hippenmeyer S, Luo L. Dendrite morphogenesis depends on relative
levels of NT-3/TrkC signaling. Science. 2014;346(6209):626-629. doi:10.1126/science.1258996
apa: William, J., Hippenmeyer, S., & Luo, L. (2014). Dendrite morphogenesis
depends on relative levels of NT-3/TrkC signaling. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1258996
chicago: William, Joo, Simon Hippenmeyer, and Liqun Luo. “Dendrite Morphogenesis
Depends on Relative Levels of NT-3/TrkC Signaling.” Science. American Association
for the Advancement of Science, 2014. https://doi.org/10.1126/science.1258996.
ieee: J. William, S. Hippenmeyer, and L. Luo, “Dendrite morphogenesis depends on
relative levels of NT-3/TrkC signaling,” Science, vol. 346, no. 6209. American
Association for the Advancement of Science, pp. 626–629, 2014.
ista: William J, Hippenmeyer S, Luo L. 2014. Dendrite morphogenesis depends on relative
levels of NT-3/TrkC signaling. Science. 346(6209), 626–629.
mla: William, Joo, et al. “Dendrite Morphogenesis Depends on Relative Levels of
NT-3/TrkC Signaling.” Science, vol. 346, no. 6209, American Association
for the Advancement of Science, 2014, pp. 626–29, doi:10.1126/science.1258996.
short: J. William, S. Hippenmeyer, L. Luo, Science 346 (2014) 626–629.
date_created: 2018-12-11T11:55:15Z
date_published: 2014-10-31T00:00:00Z
date_updated: 2021-01-12T06:54:47Z
day: '31'
department:
- _id: SiHi
doi: 10.1126/science.1258996
intvolume: ' 346'
issue: '6209'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631524/
month: '10'
oa: 1
oa_version: Submitted Version
page: 626 - 629
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5051'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dendrite morphogenesis depends on relative levels of NT-3/TrkC signaling
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 346
year: '2014'
...
---
_id: '2022'
abstract:
- lang: eng
text: Radial glial progenitors (RGPs) are responsible for producing nearly all neocortical
neurons. To gain insight into the patterns of RGP division and neuron production,
we quantitatively analyzed excitatory neuron genesis in the mouse neocortex using
Mosaic Analysis with Double Markers, which provides single-cell resolution of
progenitor division patterns and potential in vivo. We found that RGPs progress
through a coherent program in which their proliferative potential diminishes in
a predictable manner. Upon entry into the neurogenic phase, individual RGPs produce
∼8–9 neurons distributed in both deep and superficial layers, indicating a unitary
output in neuronal production. Removal of OTX1, a transcription factor transiently
expressed in RGPs, results in both deep- and superficial-layer neuron loss and
a reduction in neuronal unit size. Moreover, ∼1/6 of neurogenic RGPs proceed to
produce glia. These results suggest that progenitor behavior and histogenesis
in the mammalian neocortex conform to a remarkably orderly and deterministic program.
author:
- first_name: Peng
full_name: Gao, Peng
last_name: Gao
- first_name: Maria P
full_name: Postiglione, Maria P
id: 2C67902A-F248-11E8-B48F-1D18A9856A87
last_name: Postiglione
- first_name: Teresa
full_name: Krieger, Teresa
last_name: Krieger
- first_name: Luisirene
full_name: Hernandez, Luisirene
last_name: Hernandez
- first_name: Chao
full_name: Wang, Chao
last_name: Wang
- first_name: Zhi
full_name: Han, Zhi
last_name: Han
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Ekaterina
full_name: Papusheva, Ekaterina
id: 41DB591E-F248-11E8-B48F-1D18A9856A87
last_name: Papusheva
- first_name: Ryan
full_name: Insolera, Ryan
last_name: Insolera
- first_name: Kritika
full_name: Chugh, Kritika
last_name: Chugh
- first_name: Oren
full_name: Kodish, Oren
last_name: Kodish
- first_name: Kun
full_name: Huang, Kun
last_name: Huang
- first_name: Benjamin
full_name: Simons, Benjamin
last_name: Simons
- first_name: Liqun
full_name: Luo, Liqun
last_name: Luo
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Song
full_name: Shi, Song
last_name: Shi
citation:
ama: Gao P, Postiglione MP, Krieger T, et al. Deterministic progenitor behavior
and unitary production of neurons in the neocortex. Cell. 2014;159(4):775-788.
doi:10.1016/j.cell.2014.10.027
apa: Gao, P., Postiglione, M. P., Krieger, T., Hernandez, L., Wang, C., Han, Z.,
… Shi, S. (2014). Deterministic progenitor behavior and unitary production of
neurons in the neocortex. Cell. Cell Press. https://doi.org/10.1016/j.cell.2014.10.027
chicago: Gao, Peng, Maria P Postiglione, Teresa Krieger, Luisirene Hernandez, Chao
Wang, Zhi Han, Carmen Streicher, et al. “Deterministic Progenitor Behavior and
Unitary Production of Neurons in the Neocortex.” Cell. Cell Press, 2014.
https://doi.org/10.1016/j.cell.2014.10.027.
ieee: P. Gao et al., “Deterministic progenitor behavior and unitary production
of neurons in the neocortex,” Cell, vol. 159, no. 4. Cell Press, pp. 775–788,
2014.
ista: Gao P, Postiglione MP, Krieger T, Hernandez L, Wang C, Han Z, Streicher C,
Papusheva E, Insolera R, Chugh K, Kodish O, Huang K, Simons B, Luo L, Hippenmeyer
S, Shi S. 2014. Deterministic progenitor behavior and unitary production of neurons
in the neocortex. Cell. 159(4), 775–788.
mla: Gao, Peng, et al. “Deterministic Progenitor Behavior and Unitary Production
of Neurons in the Neocortex.” Cell, vol. 159, no. 4, Cell Press, 2014,
pp. 775–88, doi:10.1016/j.cell.2014.10.027.
short: P. Gao, M.P. Postiglione, T. Krieger, L. Hernandez, C. Wang, Z. Han, C. Streicher,
E. Papusheva, R. Insolera, K. Chugh, O. Kodish, K. Huang, B. Simons, L. Luo, S.
Hippenmeyer, S. Shi, Cell 159 (2014) 775–788.
date_created: 2018-12-11T11:55:16Z
date_published: 2014-11-06T00:00:00Z
date_updated: 2021-01-12T06:54:47Z
day: '06'
ddc:
- '570'
department:
- _id: SiHi
- _id: Bio
doi: 10.1016/j.cell.2014.10.027
ec_funded: 1
file:
- access_level: open_access
checksum: 6c5de8329bb2ffa71cba9fda750f14ce
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:47Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4709'
file_name: IST-2016-423-v1+1_1-s2.0-S0092867414013154-main.pdf
file_size: 4435787
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '4'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 775 - 788
project:
- _id: 25D61E48-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618444'
name: Molecular Mechanisms of Cerebral Cortex Development
- _id: 25D7962E-B435-11E9-9278-68D0E5697425
grant_number: RGP0053/2014
name: Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal
Level
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '5050'
pubrep_id: '423'
quality_controlled: '1'
scopus_import: 1
status: public
title: Deterministic progenitor behavior and unitary production of neurons in the
neocortex
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2014'
...
---
_id: '2023'
abstract:
- lang: eng
text: 'Understanding the evolution of dispersal is essential for understanding and
predicting the dynamics of natural populations. Two main factors are known to
influence dispersal evolution: spatio-temporal variation in the environment and
relatedness between individuals. However, the relation between these factors is
still poorly understood, and they are usually treated separately. In this article,
I present a theoretical framework that contains and connects effects of both environmental
variation and relatedness, and reproduces and extends their known features. Spatial
habitat variation selects for balanced dispersal strategies, whereby the population
is kept at an ideal free distribution. Within this class of dispersal strategies,
I explain how increased dispersal is promoted by perturbations to the dispersal
type frequencies. An explicit formula shows the magnitude of the selective advantage
of increased dispersal in terms of the spatial variability in the frequencies
of the different dispersal strategies present. These variances are capable of
capturing various sources of stochasticity and hence establish a common scale
for their effects on the evolution of dispersal. The results furthermore indicate
an alternative approach to identifying effects of relatedness on dispersal evolution.'
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Habitat heterogeneities versus spatial type frequency variances as
driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597.
doi:10.1002/ece3.1289
apa: Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell.
https://doi.org/10.1002/ece3.1289
chicago: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency
Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution.
Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289.
ieee: S. Novak, “Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution,” Ecology and Evolution, vol.
4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.
ista: Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.
mla: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances
as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol.
4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.
short: S. Novak, Ecology and Evolution 4 (2014) 4589–4597.
date_created: 2018-12-11T11:55:16Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2023-09-07T11:55:53Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/ece3.1289
ec_funded: 1
file:
- access_level: open_access
checksum: 9ab43db1b0fede7bfe560ed77e177b76
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:28Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4946'
file_name: IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf
file_size: 118813
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 4'
issue: '24'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 4589 - 4597
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5049'
pubrep_id: '462'
quality_controlled: '1'
related_material:
record:
- id: '1125'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Habitat heterogeneities versus spatial type frequency variances as driving
forces of dispersal evolution
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2014'
...
---
_id: '2024'
abstract:
- lang: eng
text: 'The yeast Rab5 homologue, Vps21p, is known to be involved both in the vacuolar
protein sorting (VPS) pathway from the trans-Golgi network to the vacuole, and
in the endocytic pathway from the plasma membrane to the vacuole. However, the
intracellular location at which these two pathways converge remains unclear. In
addition, the endocytic pathway is not completely blocked in yeast cells lacking
all Rab5 genes, suggesting the existence of an unidentified route that bypasses
the Rab5-dependent endocytic pathway. Here we show that convergence of the endocytic
and VPS pathways occurs upstream of the requirement for Vps21p in these pathways.
We also identify a previously unidentified endocytic pathway mediated by the AP-3
complex. Importantly, the AP-3-mediated pathway appears mostly intact in Rab5-disrupted
cells, and thus works as an alternative route to the vacuole/lysosome. We propose
that the endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent
VPS pathway and a Rab5-independent AP-3-mediated pathway.'
article_number: '3498'
author:
- first_name: Junko
full_name: Toshima, Junko
last_name: Toshima
- first_name: Show
full_name: Nishinoaki, Show
last_name: Nishinoaki
- first_name: Yoshifumi
full_name: Sato, Yoshifumi
last_name: Sato
- first_name: Wataru
full_name: Yamamoto, Wataru
last_name: Yamamoto
- first_name: Daiki
full_name: Furukawa, Daiki
last_name: Furukawa
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Akira
full_name: Sawaguchi, Akira
last_name: Sawaguchi
- first_name: Jiro
full_name: Toshima, Jiro
last_name: Toshima
citation:
ama: Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway
into Rab5-dependent and -independent transport to the vacuole. Nature Communications.
2014;5. doi:10.1038/ncomms4498
apa: Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus,
D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent
and -independent transport to the vacuole. Nature Communications. Nature
Publishing Group. https://doi.org/10.1038/ncomms4498
chicago: Toshima, Junko, Show Nishinoaki, Yoshifumi Sato, Wataru Yamamoto, Daiki
Furukawa, Daria E Siekhaus, Akira Sawaguchi, and Jiro Toshima. “Bifurcation of
the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.”
Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4498.
ieee: J. Toshima et al., “Bifurcation of the endocytic pathway into Rab5-dependent
and -independent transport to the vacuole,” Nature Communications, vol.
5. Nature Publishing Group, 2014.
ista: Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi
A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and
-independent transport to the vacuole. Nature Communications. 5, 3498.
mla: Toshima, Junko, et al. “Bifurcation of the Endocytic Pathway into Rab5-Dependent
and -Independent Transport to the Vacuole.” Nature Communications, vol.
5, 3498, Nature Publishing Group, 2014, doi:10.1038/ncomms4498.
short: J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus,
A. Sawaguchi, J. Toshima, Nature Communications 5 (2014).
date_created: 2018-12-11T11:55:16Z
date_published: 2014-03-25T00:00:00Z
date_updated: 2021-01-12T06:54:48Z
day: '25'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1038/ncomms4498
file:
- access_level: open_access
checksum: 614fb6579c86d1f95bdd95eeb9ab01b0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:11Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4864'
file_name: IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf
file_size: 4803515
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5048'
pubrep_id: '616'
quality_controlled: '1'
scopus_import: 1
status: public
title: Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport
to the vacuole
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 5
year: '2014'
...
---
_id: '2026'
abstract:
- lang: eng
text: 'We present a tool for translating LTL formulae into deterministic ω-automata.
It is the first tool that covers the whole LTL that does not use Safra’s determinization
or any of its variants. This leads to smaller automata. There are several outputs
of the tool: firstly, deterministic Rabin automata, which are the standard input
for probabilistic model checking, e.g. for the probabilistic model-checker PRISM;
secondly, deterministic generalized Rabin automata, which can also be used for
probabilistic model checking and are sometimes by orders of magnitude smaller.
We also link our tool to PRISM and show that this leads to a significant speed-up
of probabilistic LTL model checking, especially with the generalized Rabin automata.'
acknowledgement: "Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n"
alternative_title:
- LNCS
author:
- first_name: Zuzana
full_name: Komárková, Zuzana
last_name: Komárková
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
citation:
ama: 'Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small
deterministic automata. In: Cassez F, Raskin J-F, eds. Lecture Notes in Computer
Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics). Vol 8837. Springer; 2014:235-241. doi:10.1007/978-3-319-11936-6_17'
apa: 'Komárková, Z., & Kretinsky, J. (2014). Rabinizer 3: Safraless translation
of ltl to small deterministic automata. In F. Cassez & J.-F. Raskin (Eds.),
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial
Intelligence and Lecture Notes in Bioinformatics) (Vol. 8837, pp. 235–241).
Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_17'
chicago: 'Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation
of Ltl to Small Deterministic Automata.” In Lecture Notes in Computer Science
(Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, 8837:235–41.
Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_17.'
ieee: 'Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl
to small deterministic automata,” in Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
Sydney, Australia, 2014, vol. 8837, pp. 235–241.'
ista: 'Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl
to small deterministic automata. Lecture Notes in Computer Science (including
subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics).
ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241.'
mla: 'Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation
of Ltl to Small Deterministic Automata.” Lecture Notes in Computer Science
(Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes
in Bioinformatics), edited by Franck Cassez and Jean-François Raskin, vol.
8837, Springer, 2014, pp. 235–41, doi:10.1007/978-3-319-11936-6_17.'
short: Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241.
conference:
end_date: 2014-11-07
location: Sydney, Australia
name: 'ATVA: Automated Technology for Verification and Analysis'
start_date: 2014-11-03
date_created: 2018-12-11T11:55:17Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:49Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-11936-6_17
ec_funded: 1
editor:
- first_name: Franck
full_name: Cassez, Franck
last_name: Cassez
- first_name: Jean-François
full_name: Raskin, Jean-François
last_name: Raskin
intvolume: ' 8837'
language:
- iso: eng
month: '01'
oa_version: None
page: 235 - 241
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication: Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)
publication_status: published
publisher: Springer
publist_id: '5045'
quality_controlled: '1'
status: public
title: 'Rabinizer 3: Safraless translation of ltl to small deterministic automata'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8837
year: '2014'
...
---
_id: '2027'
abstract:
- lang: eng
text: We present a general framework for applying machine-learning algorithms to
the verification of Markov decision processes (MDPs). The primary goal of these
techniques is to improve performance by avoiding an exhaustive exploration of
the state space. Our framework focuses on probabilistic reachability, which is
a core property for verification, and is illustrated through two distinct instantiations.
The first assumes that full knowledge of the MDP is available, and performs a
heuristic-driven partial exploration of the model, yielding precise lower and
upper bounds on the required probability. The second tackles the case where we
may only sample the MDP, and yields probabilistic guarantees, again in terms of
both the lower and upper bounds, which provides efficient stopping criteria for
the approximation. The latter is the first extension of statistical model checking
for unbounded properties inMDPs. In contrast with other related techniques, our
approach is not restricted to time-bounded (finite-horizon) or discounted properties,
nor does it assume any particular properties of the MDP. We also show how our
methods extend to LTL objectives. We present experimental results showing the
performance of our framework on several examples.
acknowledgement: This research was funded in part by the European Research Council
(ERC) under grant agreement 246967 (VERIWARE), by the EU FP7 project HIERATIC, by
the Czech Science Foundation grant No P202/12/P612, by EPSRC project EP/K038575/1.
alternative_title:
- LNCS
author:
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Vojtěch
full_name: Forejt, Vojtěch
last_name: Forejt
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Marta
full_name: Kwiatkowska, Marta
last_name: Kwiatkowska
- first_name: David
full_name: Parker, David
last_name: Parker
- first_name: Mateusz
full_name: Ujma, Mateusz
last_name: Ujma
citation:
ama: 'Brázdil T, Chatterjee K, Chmelik M, et al. Verification of markov decision
processes using learning algorithms. In: Cassez F, Raskin J-F, eds. Lecture
Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics). Vol 8837. Society of Industrial and
Applied Mathematics; 2014:98-114. doi:10.1007/978-3-319-11936-6_8'
apa: 'Brázdil, T., Chatterjee, K., Chmelik, M., Forejt, V., Kretinsky, J., Kwiatkowska,
M., … Ujma, M. (2014). Verification of markov decision processes using learning
algorithms. In F. Cassez & J.-F. Raskin (Eds.), Lecture Notes in Computer
Science (including subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics) (Vol. 8837, pp. 98–114). Sydney, Australia: Society
of Industrial and Applied Mathematics. https://doi.org/10.1007/978-3-319-11936-6_8'
chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Vojtěch Forejt,
Jan Kretinsky, Marta Kwiatkowska, David Parker, and Mateusz Ujma. “Verification
of Markov Decision Processes Using Learning Algorithms.” In Lecture Notes
in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence
and Lecture Notes in Bioinformatics), edited by Franck Cassez and Jean-François
Raskin, 8837:98–114. Society of Industrial and Applied Mathematics, 2014. https://doi.org/10.1007/978-3-319-11936-6_8.
ieee: T. Brázdil et al., “Verification of markov decision processes using
learning algorithms,” in Lecture Notes in Computer Science (including subseries
Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics),
Sydney, Australia, 2014, vol. 8837, pp. 98–114.
ista: 'Brázdil T, Chatterjee K, Chmelik M, Forejt V, Kretinsky J, Kwiatkowska M,
Parker D, Ujma M. 2014. Verification of markov decision processes using learning
algorithms. Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics). ALENEX: Algorithm
Engineering and Experiments, LNCS, vol. 8837, 98–114.'
mla: Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning
Algorithms.” Lecture Notes in Computer Science (Including Subseries Lecture
Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), edited
by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and
Applied Mathematics, 2014, pp. 98–114, doi:10.1007/978-3-319-11936-6_8.
short: T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska,
D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer
Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture
Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014,
pp. 98–114.
conference:
end_date: 2014-11-07
location: Sydney, Australia
name: 'ALENEX: Algorithm Engineering and Experiments'
start_date: 2014-11-03
date_created: 2018-12-11T11:55:17Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2021-01-12T06:54:49Z
day: '01'
department:
- _id: KrCh
- _id: ToHe
doi: 10.1007/978-3-319-11936-6_8
ec_funded: 1
editor:
- first_name: Franck
full_name: Cassez, Franck
last_name: Cassez
- first_name: Jean-François
full_name: Raskin, Jean-François
last_name: Raskin
intvolume: ' 8837'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.2967
month: '11'
oa: 1
oa_version: Submitted Version
page: 98 - 114
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 26241A12-B435-11E9-9278-68D0E5697425
grant_number: '24696'
name: LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ' Lecture Notes in Computer Science (including subseries Lecture Notes
in Artificial Intelligence and Lecture Notes in Bioinformatics)'
publication_status: published
publisher: Society of Industrial and Applied Mathematics
publist_id: '5046'
quality_controlled: '1'
status: public
title: Verification of markov decision processes using learning algorithms
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 8837
year: '2014'
...
---
_id: '2028'
abstract:
- lang: eng
text: 'Understanding the dynamics of noisy neurons remains an important challenge
in neuroscience. Here, we describe a simple probabilistic model that accurately
describes the firing behavior in a large class (type II) of neurons. To demonstrate
the usefulness of this model, we show how it accurately predicts the interspike
interval (ISI) distributions, bursting patterns and mean firing rates found by:
(1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental
data from squid giant axon with a noisy input current and (3) experimental data
on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple
model has 6 parameters, however, in some cases, two of these parameters are coupled
and only 5 parameters account for much of the known behavior. From these parameters,
many properties of spiking can be found through simple calculation. Thus, we show
how the complex effects of noise can be understood through a simple and general
probabilistic model.'
acknowledgement: 'This work is supported by AFOSR grant FA 9550-11-1-0165, program
grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from
the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429
(KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically
Inspired Engineering. '
article_processing_charge: No
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: David
full_name: Paydarfar, David
last_name: Paydarfar
- first_name: Daniel
full_name: Forger, Daniel
last_name: Forger
citation:
ama: Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons.
Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041
apa: Bodova, K., Paydarfar, D., & Forger, D. (2014). Characterizing spiking
in noisy type II neurons. Journal of Theoretical Biology. Academic Press.
https://doi.org/10.1016/j.jtbi.2014.09.041
chicago: Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking
in Noisy Type II Neurons.” Journal of Theoretical Biology. Academic Press,
2014. https://doi.org/10.1016/j.jtbi.2014.09.041.
ieee: K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type
II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press,
pp. 40–54, 2014.
ista: Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type
II neurons. Journal of Theoretical Biology. 365, 40–54.
mla: Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.”
Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54,
doi:10.1016/j.jtbi.2014.09.041.
short: K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014)
40–54.
date_created: 2018-12-11T11:55:18Z
date_published: 2014-10-12T00:00:00Z
date_updated: 2022-08-25T14:00:47Z
day: '12'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1016/j.jtbi.2014.09.041
file:
- access_level: open_access
checksum: a9dbae18d3233b3dab6944fd3f2cd49e
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:58Z
date_updated: 2020-07-14T12:45:25Z
file_id: '5316'
file_name: IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf
file_size: 2679222
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 365'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 40 - 54
publication: ' Journal of Theoretical Biology'
publication_status: published
publisher: Academic Press
publist_id: '5043'
pubrep_id: '444'
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1016/j.jtbi.2015.03.013
scopus_import: '1'
status: public
title: Characterizing spiking in noisy type II neurons
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 365
year: '2014'
...
---
_id: '2029'
abstract:
- lang: eng
text: Spin-wave theory is a key ingredient in our comprehension of quantum spin
systems, and is used successfully for understanding a wide range of magnetic phenomena,
including magnon condensation and stability of patterns in dipolar systems. Nevertheless,
several decades of research failed to establish the validity of spin-wave theory
rigorously, even for the simplest models of quantum spins. A rigorous justification
of the method for the three-dimensional quantum Heisenberg ferromagnet at low
temperatures is presented here. We derive sharp bounds on its free energy by combining
a bosonic formulation of the model introduced by Holstein and Primakoff with probabilistic
estimates and operator inequalities.
acknowledgement: 239694; ERC; European Research Council
article_number: '20003'
author:
- first_name: Michele
full_name: Correggi, Michele
last_name: Correggi
- first_name: Alessandro
full_name: Giuliani, Alessandro
last_name: Giuliani
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum
Heisenberg model. EPL. 2014;108(2). doi:10.1209/0295-5075/108/20003
apa: Correggi, M., Giuliani, A., & Seiringer, R. (2014). Validity of spin-wave
theory for the quantum Heisenberg model. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/108/20003
chicago: Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity
of Spin-Wave Theory for the Quantum Heisenberg Model.” EPL. IOP Publishing
Ltd., 2014. https://doi.org/10.1209/0295-5075/108/20003.
ieee: M. Correggi, A. Giuliani, and R. Seiringer, “Validity of spin-wave theory
for the quantum Heisenberg model,” EPL, vol. 108, no. 2. IOP Publishing
Ltd., 2014.
ista: Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for
the quantum Heisenberg model. EPL. 108(2), 20003.
mla: Correggi, Michele, et al. “Validity of Spin-Wave Theory for the Quantum Heisenberg
Model.” EPL, vol. 108, no. 2, 20003, IOP Publishing Ltd., 2014, doi:10.1209/0295-5075/108/20003.
short: M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014).
date_created: 2018-12-11T11:55:18Z
date_published: 2014-10-13T00:00:00Z
date_updated: 2021-01-12T06:54:50Z
day: '13'
department:
- _id: RoSe
doi: 10.1209/0295-5075/108/20003
intvolume: ' 108'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.4717
month: '10'
oa: 1
oa_version: Submitted Version
publication: EPL
publication_status: published
publisher: IOP Publishing Ltd.
publist_id: '5044'
quality_controlled: '1'
scopus_import: 1
status: public
title: Validity of spin-wave theory for the quantum Heisenberg model
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2014'
...
---
_id: '2031'
abstract:
- lang: eng
text: A puzzling property of synaptic transmission, originally established at the
neuromuscular junction, is that the time course of transmitter release is independent
of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release
is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory
basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o.
Modeling of Ca2+-dependent transmitter release suggests that the invariant time
course of release critically depends on tight coupling between Ca2+ channels and
release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor
coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance
of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation
for the apparent [Ca2+]o independence of the time course of release.
author:
- first_name: Itaru
full_name: Arai, Itaru
id: 32A73F6C-F248-11E8-B48F-1D18A9856A87
last_name: Arai
- 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: Arai itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter
release time course at a fast central synapse. eLife. 2014;3. doi:10.7554/eLife.04057
apa: Arai, itaru, & Jonas, P. M. (2014). Nanodomain coupling explains Ca^2+
independence of transmitter release time course at a fast central synapse. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.04057
chicago: Arai, itaru, and Peter M Jonas. “Nanodomain Coupling Explains Ca^2+ Independence
of Transmitter Release Time Course at a Fast Central Synapse.” ELife. eLife
Sciences Publications, 2014. https://doi.org/10.7554/eLife.04057.
ieee: itaru Arai and P. M. Jonas, “Nanodomain coupling explains Ca^2+ independence
of transmitter release time course at a fast central synapse,” eLife, vol.
3. eLife Sciences Publications, 2014.
ista: Arai itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence
of transmitter release time course at a fast central synapse. eLife. 3.
mla: Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence
of Transmitter Release Time Course at a Fast Central Synapse.” ELife, vol.
3, eLife Sciences Publications, 2014, doi:10.7554/eLife.04057.
short: itaru Arai, P.M. Jonas, ELife 3 (2014).
date_created: 2018-12-11T11:55:19Z
date_published: 2014-12-09T00:00:00Z
date_updated: 2021-01-12T06:54:51Z
day: '09'
ddc:
- '570'
department:
- _id: PeJo
doi: 10.7554/eLife.04057
ec_funded: 1
file:
- access_level: open_access
checksum: c240f915450d4ebe8f95043a2a8c7b1a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:41Z
date_updated: 2020-07-14T12:45:26Z
file_id: '5094'
file_name: IST-2016-421-v1+1_e04057.full.pdf
file_size: 2239563
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
project:
- _id: 25C26B1E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P24909-B24
name: Mechanisms of transmitter release at GABAergic synapses
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '5041'
pubrep_id: '421'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nanodomain coupling explains Ca^2+ independence of transmitter release time
course at a fast central synapse
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '2032'
abstract:
- lang: eng
text: As light-based control of fundamental signaling pathways is becoming a reality,
the field of optogenetics is rapidly moving beyond neuroscience. We have recently
developed receptor tyrosine kinases that are activated by light and control cell
proliferation, epithelial–mesenchymal transition, and angiogenic sprouting—cell
behaviors central to cancer progression.
article_number: e964045
author:
- first_name: Álvaro
full_name: Inglés Prieto, Álvaro
id: 2A9DB292-F248-11E8-B48F-1D18A9856A87
last_name: Inglés Prieto
orcid: 0000-0002-5409-8571
- first_name: Eva
full_name: Gschaider-Reichhart, Eva
id: 3FEE232A-F248-11E8-B48F-1D18A9856A87
last_name: Gschaider-Reichhart
orcid: 0000-0002-7218-7738
- first_name: Karin
full_name: Schelch, Karin
last_name: Schelch
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Michael
full_name: Grusch, Michael
last_name: Grusch
citation:
ama: 'Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M.
The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology.
2014;1(4). doi:10.4161/23723548.2014.964045'
apa: 'Inglés Prieto, Á., Gschaider-Reichhart, E., Schelch, K., Janovjak, H. L.,
& Grusch, M. (2014). The optogenetic promise for oncology: Episode I. Molecular
and Cellular Oncology. Taylor & Francis. https://doi.org/10.4161/23723548.2014.964045'
chicago: 'Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Karin Schelch, Harald
L Janovjak, and Michael Grusch. “The Optogenetic Promise for Oncology: Episode
I.” Molecular and Cellular Oncology. Taylor & Francis, 2014. https://doi.org/10.4161/23723548.2014.964045.'
ieee: 'Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H. L. Janovjak, and
M. Grusch, “The optogenetic promise for oncology: Episode I,” Molecular and
Cellular Oncology, vol. 1, no. 4. Taylor & Francis, 2014.'
ista: 'Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M.
2014. The optogenetic promise for oncology: Episode I. Molecular and Cellular
Oncology. 1(4), e964045.'
mla: 'Inglés Prieto, Álvaro, et al. “The Optogenetic Promise for Oncology: Episode
I.” Molecular and Cellular Oncology, vol. 1, no. 4, e964045, Taylor &
Francis, 2014, doi:10.4161/23723548.2014.964045.'
short: Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch,
Molecular and Cellular Oncology 1 (2014).
date_created: 2018-12-11T11:55:19Z
date_published: 2014-12-31T00:00:00Z
date_updated: 2021-01-12T06:54:51Z
day: '31'
ddc:
- '570'
department:
- _id: HaJa
doi: 10.4161/23723548.2014.964045
file:
- access_level: open_access
checksum: 44e17ad40577ab46eb602e88a8b0b8fd
content_type: application/pdf
creator: kschuh
date_created: 2019-05-16T13:39:11Z
date_updated: 2020-07-14T12:45:26Z
file_id: '6464'
file_name: 2014_Taylor_Alvaro.pdf
file_size: 1765933
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '4'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
publication: Molecular and Cellular Oncology
publication_status: published
publisher: Taylor & Francis
publist_id: '5040'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The optogenetic promise for oncology: Episode I'
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
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2014'
...
---
_id: '2033'
abstract:
- lang: eng
text: 'The learning with privileged information setting has recently attracted a
lot of attention within the machine learning community, as it allows the integration
of additional knowledge into the training process of a classifier, even when this
comes in the form of a data modality that is not available at test time. Here,
we show that privileged information can naturally be treated as noise in the latent
function of a Gaussian process classifier (GPC). That is, in contrast to the standard
GPC setting, the latent function is not just a nuisance but a feature: it becomes
a natural measure of confidence about the training data by modulating the slope
of the GPC probit likelihood function. Extensive experiments on public datasets
show that the proposed GPC method using privileged noise, called GPC+, improves
over a standard GPC without privileged knowledge, and also over the current state-of-the-art
SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep
learning methods can be compressed as privileged information.'
author:
- first_name: Daniel
full_name: Hernandez Lobato, Daniel
last_name: Hernandez Lobato
- first_name: Viktoriia
full_name: Sharmanska, Viktoriia
id: 2EA6D09E-F248-11E8-B48F-1D18A9856A87
last_name: Sharmanska
orcid: 0000-0003-0192-9308
- first_name: Kristian
full_name: Kersting, Kristian
last_name: Kersting
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
citation:
ama: 'Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. Mind
the nuisance: Gaussian process classification using privileged noise. In: Advances
in Neural Information Processing Systems. Vol 1. Neural Information Processing
Systems; 2014:837-845.'
apa: 'Hernandez Lobato, D., Sharmanska, V., Kersting, K., Lampert, C., & Quadrianto,
N. (2014). Mind the nuisance: Gaussian process classification using privileged
noise. In Advances in Neural Information Processing Systems (Vol. 1, pp.
837–845). Montreal, Canada: Neural Information Processing Systems.'
chicago: 'Hernandez Lobato, Daniel, Viktoriia Sharmanska, Kristian Kersting, Christoph
Lampert, and Novi Quadrianto. “Mind the Nuisance: Gaussian Process Classification
Using Privileged Noise.” In Advances in Neural Information Processing Systems,
1:837–45. Neural Information Processing Systems, 2014.'
ieee: 'D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, and N. Quadrianto,
“Mind the nuisance: Gaussian process classification using privileged noise,” in
Advances in Neural Information Processing Systems, Montreal, Canada, 2014,
vol. 1, no. January, pp. 837–845.'
ista: 'Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. 2014.
Mind the nuisance: Gaussian process classification using privileged noise. Advances
in Neural Information Processing Systems. NIPS: Neural Information Processing
Systems vol. 1, 837–845.'
mla: 'Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification
Using Privileged Noise.” Advances in Neural Information Processing Systems,
vol. 1, no. January, Neural Information Processing Systems, 2014, pp. 837–45.'
short: D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto,
in:, Advances in Neural Information Processing Systems, Neural Information Processing
Systems, 2014, pp. 837–845.
conference:
end_date: 2014-12-13
location: Montreal, Canada
name: 'NIPS: Neural Information Processing Systems'
start_date: 2014-12-08
date_created: 2018-12-11T11:55:20Z
date_published: 2014-12-08T00:00:00Z
date_updated: 2023-02-23T10:25:24Z
day: '08'
department:
- _id: ChLa
intvolume: ' 1'
issue: January
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise
month: '12'
oa: 1
oa_version: Submitted Version
page: 837-845
publication: Advances in Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems
publist_id: '5038'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Mind the nuisance: Gaussian process classification using privileged noise'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 1
year: '2014'
...
---
_id: '2036'
abstract:
- lang: eng
text: ' In rapidly changing environments, selection history may impact the dynamics
of adaptation. Mutations selected in one environment may result in pleiotropic
fitness trade-offs in subsequent novel environments, slowing the rates of adaptation.
Epistatic interactions between mutations selected in sequential stressful environments
may slow or accelerate subsequent rates of adaptation, depending on the nature
of that interaction. We explored the dynamics of adaptation during sequential
exposure to herbicides with different modes of action in Chlamydomonas reinhardtii.
Evolution of resistance to two of the herbicides was largely independent of selection
history. For carbetamide, previous adaptation to other herbicide modes of action
positively impacted the likelihood of adaptation to this herbicide. Furthermore,
while adaptation to all individual herbicides was associated with pleiotropic
fitness costs in stress-free environments, we observed that accumulation of resistance
mechanisms was accompanied by a reduction in overall fitness costs. We suggest
that antagonistic epistasis may be a driving mechanism that enables populations
to more readily adapt in novel environments. These findings highlight the potential
for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug
and -pesticide resistance, as well as the potential for epistatic interactions
between adaptive mutations to facilitate evolutionary rescue in rapidly changing
environments. '
acknowledgement: The project was supported by Leverhulme Trust.
article_number: '20141679'
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Nick
full_name: Colegrave, Nick
last_name: Colegrave
- first_name: Paul
full_name: Neve, Paul
last_name: Neve
citation:
ama: Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses. Proceedings
of the Royal Society of London Series B Biological Sciences. 2014;281(1794).
doi:10.1098/rspb.2014.1679
apa: Lagator, M., Colegrave, N., & Neve, P. (2014). Selection history and epistatic
interactions impact dynamics of adaptation to novel environmental stresses. Proceedings
of the Royal Society of London Series B Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rspb.2014.1679
chicago: Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic
Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings
of the Royal Society of London Series B Biological Sciences. Royal Society,
The, 2014. https://doi.org/10.1098/rspb.2014.1679.
ieee: M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 281, no.
1794. Royal Society, The, 2014.
ista: Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions
impact dynamics of adaptation to novel environmental stresses. Proceedings of
the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.
mla: Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact
Dynamics of Adaptation to Novel Environmental Stresses.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 281, no. 1794,
20141679, Royal Society, The, 2014, doi:10.1098/rspb.2014.1679.
short: M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London
Series B Biological Sciences 281 (2014).
date_created: 2018-12-11T11:55:21Z
date_published: 2014-09-17T00:00:00Z
date_updated: 2023-02-23T14:06:44Z
day: '17'
department:
- _id: CaGu
doi: 10.1098/rspb.2014.1679
intvolume: ' 281'
issue: '1794'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/
month: '09'
oa: 1
oa_version: Submitted Version
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '5019'
quality_controlled: '1'
related_material:
record:
- id: '9741'
relation: research_data
status: public
scopus_import: 1
status: public
title: Selection history and epistatic interactions impact dynamics of adaptation
to novel environmental stresses
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 281
year: '2014'
...
---
_id: '2038'
abstract:
- lang: eng
text: Recently, there has been an effort to add quantitative objectives to formal
verification and synthesis. We introduce and investigate the extension of temporal
logics with quantitative atomic assertions. At the heart of quantitative objectives
lies the accumulation of values along a computation. It is often the accumulated
sum, as with energy objectives, or the accumulated average, as with mean-payoff
objectives. We investigate the extension of temporal logics with the prefix-accumulation
assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable
of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the
accumulated sum and average of the values of v from the beginning of the computation
up to the current point in time. We also allow the path-accumulation assertions
LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an
entire infinite computation. We study the border of decidability for such quantitative
extensions of various temporal logics. In particular, we show that extending the
fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with
both prefix-accumulation assertions, or extending LTL with both path-accumulation
assertions, results in temporal logics whose model-checking problem is decidable.
Moreover, the prefix-accumulation assertions may be generalized with "controlled
accumulation," allowing, for example, to specify constraints on the average
waiting time between a request and a grant. On the negative side, we show that
this branching-time logic is, in a sense, the maximal logic with one or both of
the prefix-accumulation assertions that permits a decidable model-checking procedure.
Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL,
makes the problem undecidable.
acknowledgement: The research was supported in part by ERC Starting grant 278410 (QUALITY).
article_number: '27'
article_processing_charge: No
article_type: original
author:
- first_name: Udi
full_name: Boker, Udi
id: 31E297B6-F248-11E8-B48F-1D18A9856A87
last_name: Boker
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- 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: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with
accumulative values. ACM Transactions on Computational Logic (TOCL). 2014;15(4).
doi:10.1145/2629686
apa: Boker, U., Chatterjee, K., Henzinger, T. A., & Kupferman, O. (2014). Temporal
specifications with accumulative values. ACM Transactions on Computational
Logic (TOCL). ACM. https://doi.org/10.1145/2629686
chicago: Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman.
“Temporal Specifications with Accumulative Values.” ACM Transactions on Computational
Logic (TOCL). ACM, 2014. https://doi.org/10.1145/2629686.
ieee: U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications
with accumulative values,” ACM Transactions on Computational Logic (TOCL),
vol. 15, no. 4. ACM, 2014.
ista: Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications
with accumulative values. ACM Transactions on Computational Logic (TOCL). 15(4),
27.
mla: Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” ACM
Transactions on Computational Logic (TOCL), vol. 15, no. 4, 27, ACM, 2014,
doi:10.1145/2629686.
short: U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on
Computational Logic (TOCL) 15 (2014).
date_created: 2018-12-11T11:55:21Z
date_published: 2014-09-16T00:00:00Z
date_updated: 2023-02-23T12:23:54Z
day: '16'
ddc:
- '000'
- '004'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1145/2629686
ec_funded: 1
file:
- access_level: open_access
checksum: 354c41d37500b56320afce94cf9a99c2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:59Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4851'
file_name: IST-2014-192-v1+1_AccumulativeValues.pdf
file_size: 346184
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 15'
issue: '4'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: ACM Transactions on Computational Logic (TOCL)
publication_status: published
publisher: ACM
publist_id: '5013'
pubrep_id: '192'
quality_controlled: '1'
related_material:
record:
- id: '3356'
relation: earlier_version
status: public
- id: '5385'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Temporal specifications with accumulative values
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2014'
...
---
_id: '2039'
abstract:
- lang: eng
text: 'A fundamental question in biology is the following: what is the time scale
that is needed for evolutionary innovations? There are many results that characterize
single steps in terms of the fixation time of new mutants arising in populations
of certain size and structure. But here we ask a different question, which is
concerned with the much longer time scale of evolutionary trajectories: how long
does it take for a population exploring a fitness landscape to find target sequences
that encode new biological functions? Our key variable is the length, (Formula
presented.) of the genetic sequence that undergoes adaptation. In computer science
there is a crucial distinction between problems that require algorithms which
take polynomial or exponential time. The latter are considered to be intractable.
Here we develop a theoretical approach that allows us to estimate the time of
evolution as function of (Formula presented.) We show that adaptation on many
fitness landscapes takes time that is exponential in (Formula presented.) even
if there are broad selection gradients and many targets uniformly distributed
in sequence space. These negative results lead us to search for specific mechanisms
that allow evolution to work on polynomial time scales. We study a regeneration
process and show that it enables evolution to work in polynomial time.'
article_number: 7p
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
- first_name: Ben
full_name: Adlam, Ben
last_name: Adlam
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary
innovation. PLoS Computational Biology. 2014;10(9). doi:10.1371/journal.pcbi.1003818
apa: Chatterjee, K., Pavlogiannis, A., Adlam, B., & Nowak, M. (2014). The time
scale of evolutionary innovation. PLoS Computational Biology. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1003818
chicago: Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak.
“The Time Scale of Evolutionary Innovation.” PLoS Computational Biology.
Public Library of Science, 2014. https://doi.org/10.1371/journal.pcbi.1003818.
ieee: K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of
evolutionary innovation,” PLoS Computational Biology, vol. 10, no. 9. Public
Library of Science, 2014.
ista: Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary
innovation. PLoS Computational Biology. 10(9), 7p.
mla: Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.”
PLoS Computational Biology, vol. 10, no. 9, 7p, Public Library of Science,
2014, doi:10.1371/journal.pcbi.1003818.
short: K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology
10 (2014).
date_created: 2018-12-11T11:55:22Z
date_published: 2014-09-11T00:00:00Z
date_updated: 2023-02-23T14:06:36Z
day: '11'
ddc:
- '510'
department:
- _id: KrCh
doi: 10.1371/journal.pcbi.1003818
ec_funded: 1
file:
- access_level: open_access
checksum: 712d4c5787ddf97809cfc962507f0738
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:35Z
date_updated: 2020-07-14T12:45:26Z
file_id: '4890'
file_name: IST-2016-440-v1+1_journal.pcbi.1003818.pdf
file_size: 1399093
relation: main_file
file_date_updated: 2020-07-14T12:45:26Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5012'
pubrep_id: '440'
quality_controlled: '1'
related_material:
record:
- id: '9739'
relation: research_data
status: public
scopus_import: 1
status: public
title: The time scale of evolutionary innovation
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...