---
_id: '138'
abstract:
- lang: eng
text: Autoregulation is the direct modulation of gene expression by the product
of the corresponding gene. Autoregulation of bacterial gene expression has been
mostly studied at the transcriptional level, when a protein acts as the cognate
transcriptional repressor. A recent study investigating dynamics of the bacterial
toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional
and post-transcriptional levels affects the heterogeneity of Escherichia coli
populations. Toxin–antitoxin systems hold a crucial but still elusive part in
bacterial response to stress. This perspective highlights how these modules can
also serve as a great model system for investigating basic concepts in gene regulation.
However, as the genomic background and environmental conditions substantially
influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin
systems in well-defined setups as well as in conditions that resemble the environmental
niche.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Nela
full_name: Nikolic, Nela
id: 42D9CABC-F248-11E8-B48F-1D18A9856A87
last_name: Nikolic
orcid: 0000-0001-9068-6090
citation:
ama: 'Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF
toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8'
apa: 'Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from
the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8'
chicago: 'Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from
the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.'
ieee: 'N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the
MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer,
pp. 133–138, 2019.'
ista: 'Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from
the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.'
mla: 'Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from
the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer,
2019, pp. 133–38, doi:10.1007/s00294-018-0879-8.'
short: N. Nikolic, Current Genetics 65 (2019) 133–138.
date_created: 2018-12-11T11:44:50Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-09-08T13:23:42Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.1007/s00294-018-0879-8
ec_funded: 1
external_id:
isi:
- '000456958800017'
file:
- access_level: open_access
checksum: 6779708b0b632a1a6ed28c56f5161142
content_type: application/pdf
creator: dernst
date_created: 2019-02-06T07:50:58Z
date_updated: 2020-07-14T12:44:47Z
file_id: '5930'
file_name: 2019_CurrentGenetics_Nikolic.pdf
file_size: 776399
relation: main_file
file_date_updated: 2020-07-14T12:44:47Z
has_accepted_license: '1'
intvolume: ' 65'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 133-138
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Current Genetics
publication_status: published
publisher: Springer
publist_id: '7785'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin
system'
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2019'
...
---
_id: '14001'
abstract:
- lang: eng
text: Chiral molecules interact and react differently with other chiral objects,
depending on their handedness. Therefore, it is essential to understand and ultimately
control the evolution of molecular chirality during chemical reactions. Although
highly sophisticated techniques for the controlled synthesis of chiral molecules
have been developed, the observation of chirality on the natural femtosecond time
scale of a chemical reaction has so far remained out of reach in the gas phase.
Here, we demonstrate a general experimental technique, based on high-harmonic
generation in tailored laser fields, and apply it to probe the time evolution
of molecular chirality during the photodissociation of 2-iodobutane. These measurements
show a change in sign and a pronounced increase in the magnitude of the chiral
response over the first 100 fs, followed by its decay within less than 500 fs,
revealing the photodissociation to achiral products. The observed time evolution
is explained in terms of the variation of the electric and magnetic transition-dipole
moments between the lowest electronic states of the cation as a function of the
reaction coordinate. These results open the path to investigations of the chirality
of molecular-reaction pathways, light-induced chirality in chemical processes,
and the control of molecular chirality through tailored laser pulses.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Daniel
full_name: Zindel, Daniel
last_name: Zindel
- first_name: Vít
full_name: Svoboda, Vít
last_name: Svoboda
- first_name: Elias
full_name: Bommeli, Elias
last_name: Bommeli
- first_name: Manuel
full_name: Ochsner, Manuel
last_name: Ochsner
- first_name: Andres
full_name: Tehlar, Andres
last_name: Tehlar
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Zindel D, Svoboda V, et al. Real-time probing of chirality during
a chemical reaction. Proceedings of the National Academy of Sciences. 2019;116(48):23923-23929.
doi:10.1073/pnas.1907189116
apa: Baykusheva, D. R., Zindel, D., Svoboda, V., Bommeli, E., Ochsner, M., Tehlar,
A., & Wörner, H. J. (2019). Real-time probing of chirality during a chemical
reaction. Proceedings of the National Academy of Sciences. Proceedings
of the National Academy of Sciences. https://doi.org/10.1073/pnas.1907189116
chicago: Baykusheva, Denitsa Rangelova, Daniel Zindel, Vít Svoboda, Elias Bommeli,
Manuel Ochsner, Andres Tehlar, and Hans Jakob Wörner. “Real-Time Probing of Chirality
during a Chemical Reaction.” Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1907189116.
ieee: D. R. Baykusheva et al., “Real-time probing of chirality during a chemical
reaction,” Proceedings of the National Academy of Sciences, vol. 116, no.
48. Proceedings of the National Academy of Sciences, pp. 23923–23929, 2019.
ista: Baykusheva DR, Zindel D, Svoboda V, Bommeli E, Ochsner M, Tehlar A, Wörner
HJ. 2019. Real-time probing of chirality during a chemical reaction. Proceedings
of the National Academy of Sciences. 116(48), 23923–23929.
mla: Baykusheva, Denitsa Rangelova, et al. “Real-Time Probing of Chirality during
a Chemical Reaction.” Proceedings of the National Academy of Sciences,
vol. 116, no. 48, Proceedings of the National Academy of Sciences, 2019, pp. 23923–29,
doi:10.1073/pnas.1907189116.
short: D.R. Baykusheva, D. Zindel, V. Svoboda, E. Bommeli, M. Ochsner, A. Tehlar,
H.J. Wörner, Proceedings of the National Academy of Sciences 116 (2019) 23923–23929.
date_created: 2023-08-09T13:10:36Z
date_published: 2019-11-13T00:00:00Z
date_updated: 2023-08-22T07:40:05Z
day: '13'
doi: 10.1073/pnas.1907189116
extern: '1'
external_id:
arxiv:
- '1906.10818'
pmid:
- '31723044'
intvolume: ' 116'
issue: '48'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1907189116
month: '11'
oa: 1
oa_version: Published Version
page: 23923-23929
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Real-time probing of chirality during a chemical reaction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2019'
...
---
_id: '14002'
abstract:
- lang: eng
text: The advancement of attosecond chronoscopy has made it possible to reveal ultrashort
time dynamics of photoionization [1]. Ionization delay measurements in atomic
targets provide a wealth of information about the timing of the photoelectric
effect [2], resonances, electron correlations and transport. The extension of
this approach to molecules, however, presents great challenges. In addition to
the difficulty of identifying correct ionization channels, it is hard to disentangle
the role of the anisotropic molecular landscape from the delays inherent to the
excitation process itself. Here, we present the measurements of ionization delays
from ethyl iodide around the 4d giant dipole resonance of iodine. We employ attosecond
streaking spectroscopy, which enables to disentangle the contribution to the delay
from the functional ethyl group, being responsible for the characteristic chemical
reactivity of the molecule. An attosecond extreme ultraviolet (XUV) pulse ionizes
the molecule around the energy of the giant resonance and the released electron
is exposed to the ponderomotive force of a synchronized near-infrared (NIR) field,
which yields a streaking spectrogram (see figure). Comparative phase analysis
of the spectrograms corresponding to iodine 4d and neon 2p emission permits extracting
overall photoemission delays for ethyl iodide. The data is recorded for multiple
photon energies around the iodine 4d resonance and compared to classical Wigner
propagation [3] and quantum scattering [4] calculations. Here the outgoing electron,
produced via inner shell ionization of the iodine atom in ethyl iodide, and thereby
hardly influenced by the molecular potential during the birth process, acquires
the necessary information about the influence of the functional ethyl group during
its propagation. We find significant delay contributions that can distinguish
between different functional groups, providing a sensitive probe of the local
molecular environment [5]. This would stimulate to perform further angle resolved
measurements in molecules to probe the potential landscape in three dimension.
article_number: '8871819'
article_processing_charge: No
author:
- first_name: Shubhadeep
full_name: Biswas, Shubhadeep
last_name: Biswas
- first_name: I.
full_name: Liontos, I.
last_name: Liontos
- first_name: A. M.
full_name: Kamal, A. M.
last_name: Kamal
- first_name: N. G.
full_name: Kling, N. G.
last_name: Kling
- first_name: A. F.
full_name: Alharbi, A. F.
last_name: Alharbi
- first_name: M.
full_name: Alharbi, M.
last_name: Alharbi
- first_name: A. M.
full_name: Azzeer, A. M.
last_name: Azzeer
- first_name: H. J.
full_name: Worner, H. J.
last_name: Worner
- first_name: A. S.
full_name: Landsman, A. S.
last_name: Landsman
- first_name: M. F.
full_name: Kling, M. F.
last_name: Kling
- first_name: B.
full_name: Forg, B.
last_name: Forg
- first_name: J.
full_name: Schotz, J.
last_name: Schotz
- first_name: W.
full_name: Schweinberger, W.
last_name: Schweinberger
- first_name: L.
full_name: Ortmann, L.
last_name: Ortmann
- first_name: T.
full_name: Zimmermann, T.
last_name: Zimmermann
- first_name: L.-W.
full_name: Pi, L.-W.
last_name: Pi
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: H. A.
full_name: Masood, H. A.
last_name: Masood
citation:
ama: 'Biswas S, Liontos I, Kamal AM, et al. Probing molecular influence on photoemission
delays. In: 2019 Conference on Lasers and Electro-Optics Europe & European
Quantum Electronics Conference. Institute of Electrical and Electronics Engineers;
2019. doi:10.1109/cleoe-eqec.2019.8871819'
apa: 'Biswas, S., Liontos, I., Kamal, A. M., Kling, N. G., Alharbi, A. F., Alharbi,
M., … Masood, H. A. (2019). Probing molecular influence on photoemission delays.
In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference. Munich, Germany: Institute of Electrical and Electronics
Engineers. https://doi.org/10.1109/cleoe-eqec.2019.8871819'
chicago: Biswas, Shubhadeep, I. Liontos, A. M. Kamal, N. G. Kling, A. F. Alharbi,
M. Alharbi, A. M. Azzeer, et al. “Probing Molecular Influence on Photoemission
Delays.” In 2019 Conference on Lasers and Electro-Optics Europe & European
Quantum Electronics Conference. Institute of Electrical and Electronics Engineers,
2019. https://doi.org/10.1109/cleoe-eqec.2019.8871819.
ieee: S. Biswas et al., “Probing molecular influence on photoemission delays,”
in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference, Munich, Germany, 2019.
ista: 'Biswas S, Liontos I, Kamal AM, Kling NG, Alharbi AF, Alharbi M, Azzeer AM,
Worner HJ, Landsman AS, Kling MF, Forg B, Schotz J, Schweinberger W, Ortmann L,
Zimmermann T, Pi L-W, Baykusheva DR, Masood HA. 2019. Probing molecular influence
on photoemission delays. 2019 Conference on Lasers and Electro-Optics Europe &
European Quantum Electronics Conference. CLEO: European Conference on Lasers and
Electro-Optics, 8871819.'
mla: Biswas, Shubhadeep, et al. “Probing Molecular Influence on Photoemission Delays.”
2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference, 8871819, Institute of Electrical and Electronics Engineers,
2019, doi:10.1109/cleoe-eqec.2019.8871819.
short: S. Biswas, I. Liontos, A.M. Kamal, N.G. Kling, A.F. Alharbi, M. Alharbi,
A.M. Azzeer, H.J. Worner, A.S. Landsman, M.F. Kling, B. Forg, J. Schotz, W. Schweinberger,
L. Ortmann, T. Zimmermann, L.-W. Pi, D.R. Baykusheva, H.A. Masood, in:, 2019 Conference
on Lasers and Electro-Optics Europe & European Quantum Electronics Conference,
Institute of Electrical and Electronics Engineers, 2019.
conference:
end_date: 2019-06-27
location: Munich, Germany
name: 'CLEO: European Conference on Lasers and Electro-Optics'
start_date: 2019-06-23
date_created: 2023-08-09T13:10:49Z
date_published: 2019-10-17T00:00:00Z
date_updated: 2023-08-22T09:32:56Z
day: '17'
doi: 10.1109/cleoe-eqec.2019.8871819
extern: '1'
language:
- iso: eng
month: '10'
oa_version: None
publication: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum
Electronics Conference
publication_identifier:
eisbn:
- '9781728104690'
isbn:
- '9781728104706'
publication_status: published
publisher: Institute of Electrical and Electronics Engineers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Probing molecular influence on photoemission delays
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '14184'
abstract:
- lang: eng
text: "Learning disentangled representations is considered a cornerstone problem
in\r\nrepresentation learning. Recently, Locatello et al. (2019) demonstrated
that\r\nunsupervised disentanglement learning without inductive biases is theoretically\r\nimpossible
and that existing inductive biases and unsupervised methods do not\r\nallow to
consistently learn disentangled representations. However, in many\r\npractical
settings, one might have access to a limited amount of supervision,\r\nfor example
through manual labeling of (some) factors of variation in a few\r\ntraining examples.
In this paper, we investigate the impact of such supervision\r\non state-of-the-art
disentanglement methods and perform a large scale study,\r\ntraining over 52000
models under well-defined and reproducible experimental\r\nconditions. We observe
that a small number of labeled examples (0.01--0.5\\% of\r\nthe data set), with
potentially imprecise and incomplete labels, is sufficient\r\nto perform model
selection on state-of-the-art unsupervised models. Further, we\r\ninvestigate
the benefit of incorporating supervision into the training process.\r\nOverall,
we empirically validate that with little and imprecise supervision it\r\nis possible
to reliably learn disentangled representations."
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
citation:
ama: 'Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling
factors of variation using few labels. In: 8th International Conference on
Learning Representations. ; 2019.'
apa: Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem,
O. (2019). Disentangling factors of variation using few labels. In 8th International
Conference on Learning Representations. Virtual.
chicago: Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard
Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.”
In 8th International Conference on Learning Representations, 2019.
ieee: F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem,
“Disentangling factors of variation using few labels,” in 8th International
Conference on Learning Representations, Virtual, 2019.
ista: 'Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. 2019.
Disentangling factors of variation using few labels. 8th International Conference
on Learning Representations. ICLR: International Conference on Learning Representations.'
mla: Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few
Labels.” 8th International Conference on Learning Representations, 2019.
short: F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem,
in:, 8th International Conference on Learning Representations, 2019.
conference:
end_date: 2020-05-01
location: Virtual
name: 'ICLR: International Conference on Learning Representations'
start_date: 2020-04-26
date_created: 2023-08-22T14:06:37Z
date_published: 2019-12-20T00:00:00Z
date_updated: 2023-09-12T07:01:34Z
day: '20'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1905.01258'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.01258
month: '12'
oa: 1
oa_version: Preprint
publication: 8th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Disentangling factors of variation using few labels
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '14189'
abstract:
- lang: eng
text: "We consider the problem of recovering a common latent source with independent\r\ncomponents
from multiple views. This applies to settings in which a variable is\r\nmeasured
with multiple experimental modalities, and where the goal is to\r\nsynthesize
the disparate measurements into a single unified representation. We\r\nconsider
the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions
of the sources. When the views are considered\r\nseparately, this reduces to nonlinear
Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to
undo the mixing. We present novel\r\nidentifiability proofs that this is possible
when the multiple views are\r\nconsidered jointly, showing that the mixing can
theoretically be undone using\r\nfunction approximators such as deep neural networks.
In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that
independent latent\r\nsources with arbitrary mixing can be recovered as long as
multiple,\r\nsufficiently different noisy views are available."
alternative_title:
- PMLR
article_processing_charge: No
arxiv: 1
author:
- first_name: Luigi
full_name: Gresele, Luigi
last_name: Gresele
- first_name: Paul K.
full_name: Rubenstein, Paul K.
last_name: Rubenstein
- first_name: Arash
full_name: Mehrjou, Arash
last_name: Mehrjou
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
citation:
ama: 'Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete
Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In:
Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence.
Vol 115. ML Research Press; 2019:217-227.'
apa: 'Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., & Schölkopf,
B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view
nonlinear ICA. In Proceedings of the 35th Conference on Uncertainty in Artificial
Intelligence (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press.'
chicago: 'Gresele, Luigi, Paul K. Rubenstein, Arash Mehrjou, Francesco Locatello,
and Bernhard Schölkopf. “The Incomplete Rosetta Stone Problem: Identifiability
Results for Multi-View Nonlinear ICA.” In Proceedings of the 35th Conference
on Uncertainty in Artificial Intelligence, 115:217–27. ML Research Press,
2019.'
ieee: 'L. Gresele, P. K. Rubenstein, A. Mehrjou, F. Locatello, and B. Schölkopf,
“The incomplete Rosetta Stone problem: Identifiability results for multi-view
nonlinear ICA,” in Proceedings of the 35th Conference on Uncertainty in Artificial
Intelligence, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.'
ista: 'Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. 2019. The
incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear
ICA. Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence.
UAI: Uncertainty in Artificial Intelligence, PMLR, vol. 115, 217–227.'
mla: 'Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability
Results for Multi-View Nonlinear ICA.” Proceedings of the 35th Conference on
Uncertainty in Artificial Intelligence, vol. 115, ML Research Press, 2019,
pp. 217–27.'
short: L. Gresele, P.K. Rubenstein, A. Mehrjou, F. Locatello, B. Schölkopf, in:,
Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence,
ML Research Press, 2019, pp. 217–227.
conference:
end_date: 2019-07-25
location: Tel Aviv, Israel
name: 'UAI: Uncertainty in Artificial Intelligence'
start_date: 2019-07-22
date_created: 2023-08-22T14:08:35Z
date_published: 2019-05-16T00:00:00Z
date_updated: 2023-09-12T08:07:38Z
day: '16'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1905.06642'
intvolume: ' 115'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.06642
month: '05'
oa: 1
oa_version: Preprint
page: 217-227
publication: Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The incomplete Rosetta Stone problem: Identifiability results for multi-view
nonlinear ICA'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2019'
...
---
_id: '14190'
abstract:
- lang: eng
text: "Learning meaningful and compact representations with disentangled semantic\r\naspects
is considered to be of key importance in representation learning. Since\r\nreal-world
data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement
models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose
a novel data-set which consists of over one million images of\r\nphysical 3D objects
with seven factors of variation, such as object color,\r\nshape, size and position.
In order to be able to control all the factors of\r\nvariation precisely, we built
an experimental platform where the objects are\r\nbeing moved by a robotic arm.
In addition, we provide two more datasets which\r\nconsist of simulations of the
experimental setup. These datasets provide for\r\nthe first time the possibility
to systematically investigate how well different\r\ndisentanglement methods perform
on real data in comparison to simulation, and\r\nhow simulated data can be leveraged
to build better representations of the real\r\nworld. We provide a first experimental
study of these questions and our results\r\nindicate that learned models transfer
poorly, but that model and hyperparameter\r\nselection is an effective means of
transferring information to the real world."
article_processing_charge: No
arxiv: 1
author:
- first_name: Muhammad Waleed
full_name: Gondal, Muhammad Waleed
last_name: Gondal
- first_name: Manuel
full_name: Wüthrich, Manuel
last_name: Wüthrich
- first_name: Đorđe
full_name: Miladinović, Đorđe
last_name: Miladinović
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Martin
full_name: Breidt, Martin
last_name: Breidt
- first_name: Valentin
full_name: Volchkov, Valentin
last_name: Volchkov
- first_name: Joel
full_name: Akpo, Joel
last_name: Akpo
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
citation:
ama: 'Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive
bias from simulation to the real world: a new disentanglement dataset. In: Advances
in Neural Information Processing Systems. Vol 32. ; 2019.'
apa: 'Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov,
V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the
real world: a new disentanglement dataset. In Advances in Neural Information
Processing Systems (Vol. 32). Vancouver, Canada.'
chicago: 'Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco
Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard
Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation
to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information
Processing Systems, Vol. 32, 2019.'
ieee: 'M. W. Gondal et al., “On the transfer of inductive bias from simulation
to the real world: a new disentanglement dataset,” in Advances in Neural Information
Processing Systems, Vancouver, Canada, 2019, vol. 32.'
ista: 'Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V,
Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias
from simulation to the real world: a new disentanglement dataset. Advances in
Neural Information Processing Systems. NeurIPS: Neural Information Processing
Systems vol. 32.'
mla: 'Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation
to the Real World: A New Disentanglement Dataset.” Advances in Neural Information
Processing Systems, vol. 32, 2019.'
short: M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov,
J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information
Processing Systems, 2019.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2023-08-22T14:09:13Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-09-13T09:46:38Z
day: '07'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1906.03292'
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1906.03292
month: '06'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713807933'
publication_status: published
quality_controlled: '1'
status: public
title: 'On the transfer of inductive bias from simulation to the real world: a new
disentanglement dataset'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 32
year: '2019'
...
---
_id: '14191'
abstract:
- lang: eng
text: A broad class of convex optimization problems can be formulated as a semidefinite
program (SDP), minimization of a convex function over the positive-semidefinite
cone subject to some affine constraints. The majority of classical SDP solvers
are designed for the deterministic setting where problem data is readily available.
In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type
methods) provide scalable solutions by leveraging the so-called linear minimization
oracle instead of the projection onto the semidefinite cone. Most problems in
machine learning and modern engineering applications, however, contain some degree
of stochasticity. In this work, we propose the first conditional-gradient-type
method for solving stochastic optimization problems under affine constraints.
Our method guarantees O(k−1/3) convergence rate in expectation on the objective
residual and O(k−5/12) on the feasibility gap.
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Alp
full_name: Yurtsever, Alp
last_name: Yurtsever
- first_name: Olivier
full_name: Fercoq, Olivier
last_name: Fercoq
- first_name: Volkan
full_name: Cevher, Volkan
last_name: Cevher
citation:
ama: 'Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite
convex minimization. In: Advances in Neural Information Processing Systems.
Vol 32. ; 2019:14291–14301.'
apa: Locatello, F., Yurtsever, A., Fercoq, O., & Cevher, V. (2019). Stochastic
Frank-Wolfe for composite convex minimization. In Advances in Neural Information
Processing Systems (Vol. 32, pp. 14291–14301). Vancouver, Canada.
chicago: Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher.
“Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in
Neural Information Processing Systems, 32:14291–14301, 2019.
ieee: F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe
for composite convex minimization,” in Advances in Neural Information Processing
Systems, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301.
ista: 'Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe
for composite convex minimization. Advances in Neural Information Processing Systems.
NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301.'
mla: Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.”
Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.
short: F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural
Information Processing Systems, 2019, pp. 14291–14301.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2023-08-22T14:09:35Z
date_published: 2019-12-29T00:00:00Z
date_updated: 2023-09-12T08:48:45Z
day: '29'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1901.10348'
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1901.10348
month: '12'
oa: 1
oa_version: Preprint
page: 14291–14301
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713807933'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stochastic Frank-Wolfe for composite convex minimization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '14193'
abstract:
- lang: eng
text: "A disentangled representation encodes information about the salient factors\r\nof
variation in the data independently. Although it is often argued that this\r\nrepresentational
format is useful in learning to solve many real-world\r\ndown-stream tasks, there
is little empirical evidence that supports this claim.\r\nIn this paper, we conduct
a large-scale study that investigates whether\r\ndisentangled representations
are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar
to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations
learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based
on these representations, we train 3600 abstract\r\nreasoning models and observe
that disentangled representations do in fact lead\r\nto better down-stream performance.
In particular, they enable quicker learning\r\nusing fewer samples."
article_processing_charge: No
arxiv: 1
author:
- first_name: Sjoerd van
full_name: Steenkiste, Sjoerd van
last_name: Steenkiste
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Jürgen
full_name: Schmidhuber, Jürgen
last_name: Schmidhuber
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
citation:
ama: 'Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations
helpful for abstract visual reasoning? In: Advances in Neural Information Processing
Systems. Vol 32. ; 2019.'
apa: Steenkiste, S. van, Locatello, F., Schmidhuber, J., & Bachem, O. (2019).
Are disentangled representations helpful for abstract visual reasoning? In Advances
in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.
chicago: Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier
Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?”
In Advances in Neural Information Processing Systems, Vol. 32, 2019.
ieee: S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled
representations helpful for abstract visual reasoning?,” in Advances in Neural
Information Processing Systems, Vancouver, Canada, 2019, vol. 32.
ista: 'Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. 2019. Are disentangled
representations helpful for abstract visual reasoning? Advances in Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.'
mla: Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for
Abstract Visual Reasoning?” Advances in Neural Information Processing Systems,
vol. 32, 2019.
short: S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances
in Neural Information Processing Systems, 2019.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2023-08-22T14:09:53Z
date_published: 2019-05-29T00:00:00Z
date_updated: 2023-09-12T09:02:43Z
day: '29'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1905.12506'
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1905.12506
month: '05'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713807933'
publication_status: published
quality_controlled: '1'
status: public
title: Are disentangled representations helpful for abstract visual reasoning?
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '14197'
abstract:
- lang: eng
text: "Recently there has been a significant interest in learning disentangled\r\nrepresentations,
as they promise increased interpretability, generalization to\r\nunseen scenarios
and faster learning on downstream tasks. In this paper, we\r\ninvestigate the
usefulness of different notions of disentanglement for\r\nimproving the fairness
of downstream prediction tasks based on representations.\r\nWe consider the setting
where the goal is to predict a target variable based on\r\nthe learned representation
of high-dimensional observations (such as images)\r\nthat depend on both the target
variable and an \\emph{unobserved} sensitive\r\nvariable. We show that in this
setting both the optimal and empirical\r\npredictions can be unfair, even if the
target variable and the sensitive\r\nvariable are independent. Analyzing the representations
of more than\r\n\\num{12600} trained state-of-the-art disentangled models, we
observe that\r\nseveral disentanglement scores are consistently correlated with
increased\r\nfairness, suggesting that disentanglement may be a useful property
to encourage\r\nfairness when sensitive variables are not observed."
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Gabriele
full_name: Abbati, Gabriele
last_name: Abbati
- first_name: Tom
full_name: Rainforth, Tom
last_name: Rainforth
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
citation:
ama: 'Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the
fairness of disentangled representations. In: Advances in Neural Information
Processing Systems. Vol 32. ; 2019:14611–14624.'
apa: Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., & Bachem,
O. (2019). On the fairness of disentangled representations. In Advances in
Neural Information Processing Systems (Vol. 32, pp. 14611–14624). Vancouver,
Canada.
chicago: Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard
Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.”
In Advances in Neural Information Processing Systems, 32:14611–14624, 2019.
ieee: F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem,
“On the fairness of disentangled representations,” in Advances in Neural Information
Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14611–14624.
ista: 'Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. 2019.
On the fairness of disentangled representations. Advances in Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14611–14624.'
mla: Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.”
Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14611–14624.
short: F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem,
in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624.
conference:
end_date: 2019-12-14
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2019-12-08
date_created: 2023-08-22T14:12:28Z
date_published: 2019-12-08T00:00:00Z
date_updated: 2023-09-12T09:37:22Z
day: '08'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1905.13662'
intvolume: ' 32'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1905.13662
month: '12'
oa: 1
oa_version: Preprint
page: 14611–14624
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781713807933'
publication_status: published
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the fairness of disentangled representations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '14200'
abstract:
- lang: eng
text: "The key idea behind the unsupervised learning of disentangled representations\r\nis
that real-world data is generated by a few explanatory factors of variation\r\nwhich
can be recovered by unsupervised learning algorithms. In this paper, we\r\nprovide
a sober look at recent progress in the field and challenge some common\r\nassumptions.
We first theoretically show that the unsupervised learning of\r\ndisentangled
representations is fundamentally impossible without inductive\r\nbiases on both
the models and the data. Then, we train more than 12000 models\r\ncovering most
prominent methods and evaluation metrics in a reproducible\r\nlarge-scale experimental
study on seven different data sets. We observe that\r\nwhile the different methods
successfully enforce properties ``encouraged'' by\r\nthe corresponding losses,
well-disentangled models seemingly cannot be\r\nidentified without supervision.
Furthermore, increased disentanglement does not\r\nseem to lead to a decreased
sample complexity of learning for downstream tasks.\r\nOur results suggest that
future work on disentanglement learning should be\r\nexplicit about the role of
inductive biases and (implicit) supervision,\r\ninvestigate concrete benefits
of enforcing disentanglement of the learned\r\nrepresentations, and consider a
reproducible experimental setup covering\r\nseveral data sets."
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Stefan
full_name: Bauer, Stefan
last_name: Bauer
- first_name: Mario
full_name: Lucic, Mario
last_name: Lucic
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Sylvain
full_name: Gelly, Sylvain
last_name: Gelly
- first_name: Bernhard
full_name: Schölkopf, Bernhard
last_name: Schölkopf
- first_name: Olivier
full_name: Bachem, Olivier
last_name: Bachem
citation:
ama: 'Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the
unsupervised learning of disentangled representations. In: Proceedings of the
36th International Conference on Machine Learning. Vol 97. ML Research Press;
2019:4114-4124.'
apa: 'Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B.,
& Bachem, O. (2019). Challenging common assumptions in the unsupervised learning
of disentangled representations. In Proceedings of the 36th International Conference
on Machine Learning (Vol. 97, pp. 4114–4124). Long Beach, CA, United States:
ML Research Press.'
chicago: Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain
Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions
in the Unsupervised Learning of Disentangled Representations.” In Proceedings
of the 36th International Conference on Machine Learning, 97:4114–24. ML Research
Press, 2019.
ieee: F. Locatello et al., “Challenging common assumptions in the unsupervised
learning of disentangled representations,” in Proceedings of the 36th International
Conference on Machine Learning, Long Beach, CA, United States, 2019, vol.
97, pp. 4114–4124.
ista: Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2019.
Challenging common assumptions in the unsupervised learning of disentangled representations.
Proceedings of the 36th International Conference on Machine Learning. International
Conference on Machine Learning vol. 97, 4114–4124.
mla: Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised
Learning of Disentangled Representations.” Proceedings of the 36th International
Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 4114–24.
short: F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem,
in:, Proceedings of the 36th International Conference on Machine Learning, ML
Research Press, 2019, pp. 4114–4124.
conference:
end_date: 2019-06-15
location: Long Beach, CA, United States
name: International Conference on Machine Learning
start_date: 2019-06-10
date_created: 2023-08-22T14:13:08Z
date_published: 2019-06-09T00:00:00Z
date_updated: 2023-09-13T07:45:30Z
day: '09'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1811.12359'
intvolume: ' 97'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.12359
month: '06'
oa: 1
oa_version: Preprint
page: 4114-4124
publication: Proceedings of the 36th International Conference on Machine Learning
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Challenging common assumptions in the unsupervised learning of disentangled
representations
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 97
year: '2019'
...
---
_id: '14299'
abstract:
- lang: eng
text: DNA origami nano-objects are usually designed around generic single-stranded
“scaffolds”. Many properties of the target object are determined by details of
those generic scaffold sequences. Here, we enable designers to fully specify the
target structure not only in terms of desired 3D shape but also in terms of the
sequences used. To this end, we built design tools to construct scaffold sequences
de novo based on strand diagrams, and we developed scalable production methods
for creating design-specific scaffold strands with fully user-defined sequences.
We used 17 custom scaffolds having different lengths and sequence properties to
study the influence of sequence redundancy and sequence composition on multilayer
DNA origami assembly and to realize efficient one-pot assembly of multiscaffold
DNA origami objects. Furthermore, as examples for functionalized scaffolds, we
created a scaffold that enables direct, covalent cross-linking of DNA origami
via UV irradiation, and we built DNAzyme-containing scaffolds that allow postfolding
DNA origami domain separation.
article_processing_charge: No
article_type: original
author:
- first_name: Engelhardt
full_name: FAS, Engelhardt
last_name: FAS
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: CH
full_name: Wachauf, CH
last_name: Wachauf
- first_name: G
full_name: Brüggenthies, G
last_name: Brüggenthies
- first_name: F
full_name: Kohler, F
last_name: Kohler
- first_name: B
full_name: Kick, B
last_name: Kick
- first_name: KL
full_name: Kadletz, KL
last_name: Kadletz
- first_name: PN
full_name: Pham, PN
last_name: Pham
- first_name: KL
full_name: Behler, KL
last_name: Behler
- first_name: T
full_name: Gerling, T
last_name: Gerling
- first_name: H
full_name: Dietz, H
last_name: Dietz
citation:
ama: FAS E, Praetorius FM, Wachauf C, et al. Custom-size, functional, and durable
DNA origami with design-specific scaffolds. ACS Nano. 2019;13(5):5015-5027.
doi:10.1021/acsnano.9b01025
apa: FAS, E., Praetorius, F. M., Wachauf, C., Brüggenthies, G., Kohler, F., Kick,
B., … Dietz, H. (2019). Custom-size, functional, and durable DNA origami with
design-specific scaffolds. ACS Nano. ACS Publications. https://doi.org/10.1021/acsnano.9b01025
chicago: FAS, Engelhardt, Florian M Praetorius, CH Wachauf, G Brüggenthies, F Kohler,
B Kick, KL Kadletz, et al. “Custom-Size, Functional, and Durable DNA Origami with
Design-Specific Scaffolds.” ACS Nano. ACS Publications, 2019. https://doi.org/10.1021/acsnano.9b01025.
ieee: E. FAS et al., “Custom-size, functional, and durable DNA origami with
design-specific scaffolds,” ACS Nano, vol. 13, no. 5. ACS Publications,
pp. 5015–5027, 2019.
ista: FAS E, Praetorius FM, Wachauf C, Brüggenthies G, Kohler F, Kick B, Kadletz
K, Pham P, Behler K, Gerling T, Dietz H. 2019. Custom-size, functional, and durable
DNA origami with design-specific scaffolds. ACS Nano. 13(5), 5015–5027.
mla: FAS, Engelhardt, et al. “Custom-Size, Functional, and Durable DNA Origami with
Design-Specific Scaffolds.” ACS Nano, vol. 13, no. 5, ACS Publications,
2019, pp. 5015–27, doi:10.1021/acsnano.9b01025.
short: E. FAS, F.M. Praetorius, C. Wachauf, G. Brüggenthies, F. Kohler, B. Kick,
K. Kadletz, P. Pham, K. Behler, T. Gerling, H. Dietz, ACS Nano 13 (2019) 5015–5027.
date_created: 2023-09-06T12:48:47Z
date_published: 2019-04-16T00:00:00Z
date_updated: 2023-11-07T12:17:31Z
day: '16'
doi: 10.1021/acsnano.9b01025
extern: '1'
external_id:
pmid:
- '30990672'
intvolume: ' 13'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acsnano.9b01025
month: '04'
oa: 1
oa_version: Published Version
page: 5015-5027
pmid: 1
publication: ACS Nano
publication_identifier:
eissn:
- 1936-086x
issn:
- 1936-0851
publication_status: published
publisher: ACS Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Custom-size, functional, and durable DNA origami with design-specific scaffolds
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2019'
...
---
_id: '9016'
abstract:
- lang: eng
text: Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein
interaction (PPI) represents a potential approach for treating numerous cancers.
As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135)
is a strategy through which chemical probes might be elaborated to test this hypothesis.
In this work, variant H3118–135 peptides bearing pentenylglycine residues at the
i and i+4 positions were constrained by olefin metathesis. Biophysical analyses
revealed that promotion of a bioactive helical conformation depends on the position
at which the constraint is introduced, but that the potency of binding towards
ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation
occurs.
article_processing_charge: No
article_type: original
author:
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Silvia
full_name: Rodriguez‐Marin, Silvia
last_name: Rodriguez‐Marin
- first_name: Zsófia
full_name: Hegedüs, Zsófia
last_name: Hegedüs
- first_name: Marie E.
full_name: Perrin, Marie E.
last_name: Perrin
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
- first_name: Andrew J.
full_name: Wilson, Andrew J.
last_name: Wilson
citation:
ama: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ.
Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem.
2019;20(7):891-895. doi:10.1002/cbic.201800633
apa: Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein,
F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained
peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633
chicago: Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin,
Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained
Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633.
ieee: M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein,
and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,”
ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019.
ista: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ.
2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem.
20(7), 891–895.
mla: Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained
Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633.
short: M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein,
A.J. Wilson, ChemBioChem 20 (2019) 891–895.
date_created: 2021-01-19T10:59:14Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-02-23T13:46:48Z
day: '01'
doi: 10.1002/cbic.201800633
extern: '1'
intvolume: ' 20'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.1002/cbic.201800633'
month: '04'
oa: 1
oa_version: Published Version
page: 891-895
publication: ChemBioChem
publication_identifier:
issn:
- 1439-4227
- 1439-7633
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Recognition of ASF1 by using hydrocarbon‐constrained peptides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2019'
...
---
_id: '9018'
abstract:
- lang: eng
text: Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved
in histone dynamics during replication, transcription, and DNA repair. Overexpressed
in proliferating tissues including many tumors, ASF1 has emerged as a promising
therapeutic target. Here, we combine structural, computational, and biochemical
approaches to design peptides that inhibit the ASF1-histone interaction. Starting
from the structure of the human ASF1-histone complex, we developed a rational
design strategy combining epitope tethering and optimization of interface contacts
to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When
introduced into cultured cells, the inhibitors impair cell proliferation, perturb
cell-cycle progression, and reduce cell migration and invasion in a manner commensurate
with their affinity for ASF1. Finally, we find that direct injection of the most
potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results
open new avenues to use ASF1 inhibitors as promising leads for cancer therapy.
article_processing_charge: No
article_type: original
author:
- first_name: May M
full_name: Bakail, May M
id: FB3C3F8E-522F-11EA-B186-22963DDC885E
last_name: Bakail
orcid: 0000-0002-9592-1587
- first_name: Albane
full_name: Gaubert, Albane
last_name: Gaubert
- first_name: Jessica
full_name: Andreani, Jessica
last_name: Andreani
- first_name: Gwenaëlle
full_name: Moal, Gwenaëlle
last_name: Moal
- first_name: Guillaume
full_name: Pinna, Guillaume
last_name: Pinna
- first_name: Ekaterina
full_name: Boyarchuk, Ekaterina
last_name: Boyarchuk
- first_name: Marie-Cécile
full_name: Gaillard, Marie-Cécile
last_name: Gaillard
- first_name: Regis
full_name: Courbeyrette, Regis
last_name: Courbeyrette
- first_name: Carl
full_name: Mann, Carl
last_name: Mann
- first_name: Jean-Yves
full_name: Thuret, Jean-Yves
last_name: Thuret
- first_name: Bérengère
full_name: Guichard, Bérengère
last_name: Guichard
- first_name: Brice
full_name: Murciano, Brice
last_name: Murciano
- first_name: Nicolas
full_name: Richet, Nicolas
last_name: Richet
- first_name: Adeline
full_name: Poitou, Adeline
last_name: Poitou
- first_name: Claire
full_name: Frederic, Claire
last_name: Frederic
- first_name: Marie-Hélène
full_name: Le Du, Marie-Hélène
last_name: Le Du
- first_name: Morgane
full_name: Agez, Morgane
last_name: Agez
- first_name: Caroline
full_name: Roelants, Caroline
last_name: Roelants
- first_name: Zachary A.
full_name: Gurard-Levin, Zachary A.
last_name: Gurard-Levin
- first_name: Geneviève
full_name: Almouzni, Geneviève
last_name: Almouzni
- first_name: Nadia
full_name: Cherradi, Nadia
last_name: Cherradi
- first_name: Raphael
full_name: Guerois, Raphael
last_name: Guerois
- first_name: Françoise
full_name: Ochsenbein, Françoise
last_name: Ochsenbein
citation:
ama: Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity
peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology.
2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002
apa: Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E.,
… Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides
inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier.
https://doi.org/10.1016/j.chembiol.2019.09.002
chicago: Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume
Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational
Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell
Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002.
ieee: M. M. Bakail et al., “Design on a rational basis of high-affinity peptides
inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26,
no. 11. Elsevier, p. 1573–1585.e10, 2019.
ista: Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C,
Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A,
Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi
N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity
peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11),
1573–1585.e10.
mla: Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides
Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26,
no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002.
short: M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C.
Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N.
Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin,
G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26
(2019) 1573–1585.e10.
date_created: 2021-01-19T11:04:50Z
date_published: 2019-11-21T00:00:00Z
date_updated: 2023-02-23T13:46:53Z
day: '21'
doi: 10.1016/j.chembiol.2019.09.002
extern: '1'
external_id:
pmid:
- '31543461'
intvolume: ' 26'
issue: '11'
keyword:
- Clinical Biochemistry
- Molecular Medicine
- Biochemistry
- Molecular Biology
- Pharmacology
- Drug Discovery
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.chembiol.2019.09.002
month: '11'
oa: 1
oa_version: Published Version
page: 1573-1585.e10
pmid: 1
publication: Cell Chemical Biology
publication_identifier:
issn:
- 2451-9456
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Design on a rational basis of high-affinity peptides inhibiting the histone
chaperone ASF1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2019'
...
---
_id: '9060'
abstract:
- lang: eng
text: Molecular motors are essential to the living, generating fluctuations that
boost transport and assist assembly. Active colloids, that consume energy to move,
hold similar potential for man-made materials controlled by forces generated from
within. Yet, their use as a powerhouse in materials science lacks. Here we show
a massive acceleration of the annealing of a monolayer of passive beads by moderate
addition of self-propelled microparticles. We rationalize our observations with
a model of collisions that drive active fluctuations and activate the annealing.
The experiment is quantitatively compared with Brownian dynamic simulations that
further unveil a dynamical transition in the mechanism of annealing. Active dopants
travel uniformly in the system or co-localize at the grain boundaries as a result
of the persistence of their motion. Our findings uncover the potential of internal
activity to control materials and lay the groundwork for the rise of materials
science beyond equilibrium.
article_number: '3380'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sophie
full_name: Ramananarivo, Sophie
last_name: Ramananarivo
- first_name: Etienne
full_name: Ducrot, Etienne
last_name: Ducrot
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal
monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y
apa: Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled
annealing of colloidal monolayers. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-11362-y
chicago: Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled
Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature,
2019. https://doi.org/10.1038/s41467-019-11362-y.
ieee: S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing
of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer
Nature, 2019.
ista: Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing
of colloidal monolayers. Nature Communications. 10(1), 3380.
mla: Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.”
Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.
short: S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).
date_created: 2021-02-02T13:43:36Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-02-23T13:47:59Z
day: '29'
ddc:
- '530'
doi: 10.1038/s41467-019-11362-y
extern: '1'
external_id:
arxiv:
- '1909.07382'
pmid:
- '31358762'
file:
- access_level: open_access
checksum: 70c6e5d6fbea0932b0669505ab6633ec
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:47:21Z
date_updated: 2021-02-02T13:47:21Z
file_id: '9061'
file_name: 2019_NatureComm_Ramananarivo.pdf
file_size: 2820337
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:47:21Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Activity-controlled annealing of colloidal monolayers
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2019'
...
---
_id: '9261'
abstract:
- lang: eng
text: 'Bending-active structures are able to efficiently produce complex curved
shapes starting from flat panels. The desired deformation of the panels derives
from the proper selection of their elastic properties. Optimized panels, called
FlexMaps, are designed such that, once they are bent and assembled, the resulting
static equilibrium configuration matches a desired input 3D shape. The FlexMaps
elastic properties are controlled by locally varying spiraling geometric mesostructures,
which are optimized in size and shape to match the global curvature (i.e., bending
requests) of the target shape. The design pipeline starts from a quad mesh representing
the input 3D shape, which defines the edge size and the total amount of spirals:
every quad will embed one spiral. Then, an optimization algorithm tunes the geometry
of the spirals by using a simplified pre-computed rod model. This rod model is
derived from a non-linear regression algorithm which approximates the non-linear
behavior of solid FEM spiral models subject to hundreds of load combinations.
This innovative pipeline has been applied to the project of a lightweight plywood
pavilion named FlexMaps Pavilion, which is a single-layer piecewise twisted arc
that fits a bounding box of 3.90x3.96x3.25 meters.'
article_processing_charge: No
author:
- first_name: Francesco
full_name: Laccone, Francesco
last_name: Laccone
- first_name: Luigi
full_name: Malomo, Luigi
last_name: Malomo
- first_name: Jesus
full_name: Perez Rodriguez, Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Nico
full_name: Pietroni, Nico
last_name: Pietroni
- first_name: Federico
full_name: Ponchio, Federico
last_name: Ponchio
- first_name: Bernd
full_name: Bickel, Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
- first_name: Paolo
full_name: Cignoni, Paolo
last_name: Cignoni
citation:
ama: 'Laccone F, Malomo L, Perez Rodriguez J, et al. FlexMaps Pavilion: A twisted
arc made of mesostructured flat flexible panels. In: IASS Symposium 2019 -
60th Anniversary Symposium of the International Association for Shell and Spatial
Structures; Structural Membranes 2019 - 9th International Conference on Textile
Composites and Inflatable Structures, FORM and FORCE. International Center
for Numerical Methods in Engineering; 2019:509-515.'
apa: 'Laccone, F., Malomo, L., Perez Rodriguez, J., Pietroni, N., Ponchio, F., Bickel,
B., & Cignoni, P. (2019). FlexMaps Pavilion: A twisted arc made of mesostructured
flat flexible panels. In IASS Symposium 2019 - 60th Anniversary Symposium of
the International Association for Shell and Spatial Structures; Structural Membranes
2019 - 9th International Conference on Textile Composites and Inflatable Structures,
FORM and FORCE (pp. 509–515). Barcelona, Spain: International Center for Numerical
Methods in Engineering.'
chicago: 'Laccone, Francesco, Luigi Malomo, Jesus Perez Rodriguez, Nico Pietroni,
Federico Ponchio, Bernd Bickel, and Paolo Cignoni. “FlexMaps Pavilion: A Twisted
Arc Made of Mesostructured Flat Flexible Panels.” In IASS Symposium 2019 -
60th Anniversary Symposium of the International Association for Shell and Spatial
Structures; Structural Membranes 2019 - 9th International Conference on Textile
Composites and Inflatable Structures, FORM and FORCE, 509–15. International
Center for Numerical Methods in Engineering, 2019.'
ieee: 'F. Laccone et al., “FlexMaps Pavilion: A twisted arc made of mesostructured
flat flexible panels,” in IASS Symposium 2019 - 60th Anniversary Symposium
of the International Association for Shell and Spatial Structures; Structural
Membranes 2019 - 9th International Conference on Textile Composites and Inflatable
Structures, FORM and FORCE, Barcelona, Spain, 2019, pp. 509–515.'
ista: 'Laccone F, Malomo L, Perez Rodriguez J, Pietroni N, Ponchio F, Bickel B,
Cignoni P. 2019. FlexMaps Pavilion: A twisted arc made of mesostructured flat
flexible panels. IASS Symposium 2019 - 60th Anniversary Symposium of the International
Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th
International Conference on Textile Composites and Inflatable Structures, FORM
and FORCE. IASS: International Association for Shell and Spatial Structures, 509–515.'
mla: 'Laccone, Francesco, et al. “FlexMaps Pavilion: A Twisted Arc Made of Mesostructured
Flat Flexible Panels.” IASS Symposium 2019 - 60th Anniversary Symposium of
the International Association for Shell and Spatial Structures; Structural Membranes
2019 - 9th International Conference on Textile Composites and Inflatable Structures,
FORM and FORCE, International Center for Numerical Methods in Engineering,
2019, pp. 509–15.'
short: F. Laccone, L. Malomo, J. Perez Rodriguez, N. Pietroni, F. Ponchio, B. Bickel,
P. Cignoni, in:, IASS Symposium 2019 - 60th Anniversary Symposium of the International
Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th
International Conference on Textile Composites and Inflatable Structures, FORM
and FORCE, International Center for Numerical Methods in Engineering, 2019, pp.
509–515.
conference:
end_date: 2019-10-10
location: Barcelona, Spain
name: 'IASS: International Association for Shell and Spatial Structures'
start_date: 2019-10-07
date_created: 2021-03-21T23:01:21Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-09-08T11:21:54Z
day: '10'
department:
- _id: BeBi
external_id:
isi:
- '000563497600059'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 509-515
publication: IASS Symposium 2019 - 60th Anniversary Symposium of the International
Association for Shell and Spatial Structures; Structural Membranes 2019 - 9th International
Conference on Textile Composites and Inflatable Structures, FORM and FORCE
publication_identifier:
isbn:
- '9788412110104'
issn:
- 2518-6582
publication_status: published
publisher: International Center for Numerical Methods in Engineering
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'FlexMaps Pavilion: A twisted arc made of mesostructured flat flexible panels'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '9460'
abstract:
- lang: eng
text: Epigenetic reprogramming is required for proper regulation of gene expression
in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for
seed viability, pollen function, and successful reproduction. The DEMETER (DME)
DNA glycosylase initiates localized DNA demethylation in vegetative and central
cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively.
In rice, the central cell genome displays local DNA hypomethylation, suggesting
that active DNA demethylation also occurs in rice; however, the enzyme responsible
for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING
1a (ROS1a) gene, which is related to DME and is essential for rice seed viability
and pollen function. Here, we report genome-wide analyses of DNA methylation in
wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative
cell genome is locally hypomethylated compared with sperm by a process that requires
ROS1a activity. We show that many ROS1a target sequences in the vegetative cell
are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates
the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation
is indirectly promoted by DNA demethylation in the vegetative cell. These results
reveal that DNA glycosylase-mediated DNA demethylation processes are conserved
in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally,
although global non-CG methylation levels of sperm and egg differ, the maternal
and paternal embryo genomes show similar non-CG methylation levels, suggesting
that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell
fusion.
article_processing_charge: No
article_type: original
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Akemi
full_name: Ono, Akemi
last_name: Ono
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
- first_name: Tetsu
full_name: Kinoshita, Tetsu
last_name: Kinoshita
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative
cells promotes methylation in sperm. Proceedings of the National Academy of
Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116
apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T.,
& Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm. Proceedings of the National Academy of Sciences.
National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116
chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman,
Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative
Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116.
ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells
promotes methylation in sperm,” Proceedings of the National Academy of Sciences,
vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019.
ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL.
2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation
in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657.
mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells
Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences,
vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116.
short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L.
Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657.
date_created: 2021-06-04T12:38:20Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2021-12-14T07:52:30Z
day: '07'
ddc:
- '580'
department:
- _id: DaZi
doi: 10.1073/pnas.1821435116
extern: '1'
external_id:
pmid:
- '31000601'
file:
- access_level: open_access
checksum: 5b0ae3779b8b21b5223bd2d3cceede3a
content_type: application/pdf
creator: asandaue
date_created: 2021-06-04T12:50:47Z
date_updated: 2021-06-04T12:50:47Z
file_id: '9461'
file_name: 2019_PNAS_Kim.pdf
file_size: 1142540
relation: main_file
success: 1
file_date_updated: 2021-06-04T12:50:47Z
has_accepted_license: '1'
intvolume: ' 116'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 9652-9657
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in
sperm
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 116
year: '2019'
...
---
_id: '9530'
abstract:
- lang: eng
text: "Background\r\nDNA methylation of active genes, also known as gene body methylation,
is found in many animal and plant genomes. Despite this, the transcriptional and
developmental role of such methylation remains poorly understood. Here, we explore
the dynamic range of DNA methylation in honey bee, a model organism for gene body
methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies
globally fluctuates during honey bee development. However, these changes cause
no gene expression alterations. Intriguingly, despite the global alterations,
tissue-specific CG methylation patterns of complete genes or exons are rare, implying
robust maintenance of genic methylation during development. Additionally, we show
that CG methylation maintenance fluctuates in somatic cells, while reaching maximum
fidelity in sperm cells. Finally, unlike universally present CG methylation, we
discovered non-CG methylation specifically in bee heads that resembles such methylation
in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose
that gene body CG methylation can oscillate during development if it is kept to
a level adequate to preserve function. Additionally, our data suggest that heightened
non-CG methylation is a conserved regulator of animal nervous systems."
article_number: '62'
article_processing_charge: No
article_type: original
author:
- first_name: Keith D.
full_name: Harris, Keith D.
last_name: Harris
- first_name: James P. B.
full_name: Lloyd, James P. B.
last_name: Lloyd
- first_name: Katherine
full_name: Domb, Katherine
last_name: Domb
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
citation:
ama: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained
with high fidelity in the honey bee germline and exhibits global non-functional
fluctuations during somatic development. Epigenetics and Chromatin. 2019;12.
doi:10.1186/s13072-019-0307-4
apa: Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019).
DNA methylation is maintained with high fidelity in the honey bee germline and
exhibits global non-functional fluctuations during somatic development. Epigenetics
and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4
chicago: Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman,
and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey
Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.”
Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4.
ieee: K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation
is maintained with high fidelity in the honey bee germline and exhibits global
non-functional fluctuations during somatic development,” Epigenetics and Chromatin,
vol. 12. Springer Nature, 2019.
ista: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation
is maintained with high fidelity in the honey bee germline and exhibits global
non-functional fluctuations during somatic development. Epigenetics and Chromatin.
12, 62.
mla: Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity
in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during
Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer
Nature, 2019, doi:10.1186/s13072-019-0307-4.
short: K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics
and Chromatin 12 (2019).
date_created: 2021-06-08T09:21:51Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2021-12-14T07:53:00Z
day: '10'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13072-019-0307-4
extern: '1'
external_id:
pmid:
- '31601251'
file:
- access_level: open_access
checksum: 86ff50a7517891511af2733c76c81b67
content_type: application/pdf
creator: asandaue
date_created: 2021-06-08T09:29:19Z
date_updated: 2021-06-08T09:29:19Z
file_id: '9531'
file_name: 2019_EpigeneticsAndChromatin_Harris.pdf
file_size: 3221067
relation: main_file
success: 1
file_date_updated: 2021-06-08T09:29:19Z
has_accepted_license: '1'
intvolume: ' 12'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Epigenetics and Chromatin
publication_identifier:
eissn:
- 1756-8935
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation is maintained with high fidelity in the honey bee germline
and exhibits global non-functional fluctuations during somatic development
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 12
year: '2019'
...
---
_id: '9580'
abstract:
- lang: eng
text: An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H
into r parts and the size of the cut is the number of edges which have a vertex
in each part. A classical result of Edwards says that every m-edge graph has a
2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts
which exceed the expected size of a random cut by some multiple of the standard
deviation. We study analogues of this and related results in hypergraphs. First,
we observe that similarly to graphs, every m-edge k-uniform hypergraph has an
r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover,
in the case where k = 3 and r = 2 this bound is best possible and is attained
by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥
4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose
size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant
difference in behaviour, since the amount by which the size of the largest cut
exceeds the expected size of a random cut is now considerably larger than the
standard deviation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: David
full_name: Conlon, David
last_name: Conlon
- first_name: Jacob
full_name: Fox, Jacob
last_name: Fox
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel
Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z
apa: Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts
above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z
chicago: Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph
Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019.
https://doi.org/10.1007/s11856-019-1897-z.
ieee: D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the
average,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp.
67–111, 2019.
ista: Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average.
Israel Journal of Mathematics. 233(1), 67–111.
mla: Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal
of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z.
short: D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233
(2019) 67–111.
date_created: 2021-06-21T13:36:02Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2023-02-23T14:01:41Z
day: '01'
doi: 10.1007/s11856-019-1897-z
extern: '1'
external_id:
arxiv:
- '1803.08462'
intvolume: ' 233'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1803.08462
month: '08'
oa: 1
oa_version: Preprint
page: 67-111
publication: Israel Journal of Mathematics
publication_identifier:
eissn:
- 1565-8511
issn:
- 0021-2172
publication_status: published
publisher: Springer
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hypergraph cuts above the average
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 233
year: '2019'
...
---
_id: '9585'
abstract:
- lang: eng
text: An n-vertex graph is called C-Ramsey if it has no clique or independent set
of size C log n. All known constructions of Ramsey graphs involve randomness in
an essential way, and there is an ongoing line of research towards showing that
in fact all Ramsey graphs must obey certain “richness” properties characteristic
of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that
in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have
the same numbers of vertices and edges. Improving on earlier results of Alon,
Balogh, Kostochka and Samotij, in this paper we prove this conjecture.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
citation:
ama: Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs.
Transactions of the American Mathematical Society. 2019;372(8):5571-5594.
doi:10.1090/tran/7729
apa: Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs
of Ramsey graphs. Transactions of the American Mathematical Society. American
Mathematical Society. https://doi.org/10.1090/tran/7729
chicago: Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced
Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society.
American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729.
ieee: M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of
Ramsey graphs,” Transactions of the American Mathematical Society, vol.
372, no. 8. American Mathematical Society, pp. 5571–5594, 2019.
ista: Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey
graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594.
mla: Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs
of Ramsey Graphs.” Transactions of the American Mathematical Society, vol.
372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729.
short: M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society
372 (2019) 5571–5594.
date_created: 2021-06-22T09:31:45Z
date_published: 2019-10-15T00:00:00Z
date_updated: 2023-02-23T14:01:50Z
day: '15'
doi: 10.1090/tran/7729
extern: '1'
external_id:
arxiv:
- '1712.05656'
intvolume: ' 372'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1090/tran/7729
month: '10'
oa: 1
oa_version: Submitted Version
page: 5571-5594
publication: Transactions of the American Mathematical Society
publication_identifier:
eissn:
- 1088-6850
issn:
- 0002-9947
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Proof of a conjecture on induced subgraphs of Ramsey graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 372
year: '2019'
...
---
_id: '9586'
abstract:
- lang: eng
text: "Consider integers \U0001D458,ℓ such that 0⩽ℓ⩽(\U0001D4582) . Given a large
graph \U0001D43A , what is the fraction of \U0001D458 -vertex subsets of \U0001D43A
\ which span exactly ℓ edges? When \U0001D43A is empty or complete, and ℓ
\ is zero or (\U0001D4582) , this fraction can be exactly 1. On the other hand,
if ℓ is far from these extreme values, one might expect that this fraction is
substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich,
and Tyomkyn who initiated the systematic study of this question and proposed several
natural conjectures.\r\nLet ℓ∗=min{ℓ,(\U0001D4582)−ℓ} . Our main result is that
for any \U0001D458 and ℓ , the fraction of \U0001D458 -vertex subsets that
span ℓ edges is at most log\U0001D442(1)(ℓ∗/\U0001D458)√ \U0001D458/ℓ∗, which
is best-possible up to the logarithmic factor. This improves on multiple results
of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures.
In addition, we also make some first steps towards some analogous questions for
hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of
different probabilistic tools, such as polynomial anticoncentration inequalities,
hypercontractivity, and a coupling trick for random variables defined on a ‘slice’
of the Boolean hypercube."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: Benny
full_name: Sudakov, Benny
last_name: Sudakov
- first_name: Tuan
full_name: Tran, Tuan
last_name: Tran
citation:
ama: Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal
of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192
apa: Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph
statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192
chicago: Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for
Subgraph Statistics.” Journal of the London Mathematical Society. Wiley,
2019. https://doi.org/10.1112/jlms.12192.
ieee: M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,”
Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp.
757–777, 2019.
ista: Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics.
Journal of the London Mathematical Society. 99(3), 757–777.
mla: Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal
of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77,
doi:10.1112/jlms.12192.
short: M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society
99 (2019) 757–777.
date_created: 2021-06-22T09:46:03Z
date_published: 2019-05-03T00:00:00Z
date_updated: 2023-02-23T14:01:53Z
day: '03'
doi: 10.1112/jlms.12192
extern: '1'
external_id:
arxiv:
- '1807.05202'
intvolume: ' 99'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.05202
month: '05'
oa: 1
oa_version: Preprint
page: 757-777
publication: Journal of the London Mathematical Society
publication_identifier:
eissn:
- 1469-7750
issn:
- 0024-6107
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anticoncentration for subgraph statistics
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 99
year: '2019'
...