---
_id: '18255'
abstract:
- lang: eng
text: Learning an object detection or retrieval system requires a large data set
with manual annotations. Such data sets are expensive and time consuming to create
and therefore difficult to obtain on a large scale. In this work, we propose to
exploit the natural correlation in narrations and the visual presence of objects
in video, to learn an object detector and retrieval without any manual labeling
involved. We pose the problem as weakly supervised learning with noisy labels,
and propose a novel object detection paradigm under these constraints. We handle
the background rejection by using contrastive samples and confront the high level
of label noise with a new clustering score. Our evaluation is based on a set of
11 manually annotated objects in over 5000 frames. We show comparison to a weakly-supervised
approach as baseline and provide a strongly labeled upper bound.
article_number: '9022341'
article_processing_charge: No
arxiv: 1
author:
- first_name: Elad
full_name: Amrani, Elad
last_name: Amrani
- first_name: Rami
full_name: Ben-Ari, Rami
last_name: Ben-Ari
- first_name: Tal
full_name: Hakim, Tal
last_name: Hakim
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: 'Amrani E, Ben-Ari R, Hakim T, Bronstein AM. Learning to detect and retrieve
objects from unlabeled videos. In: 2019 IEEE/CVF International Conference on
Computer Vision Workshop (ICCVW). IEEE; 2020. doi:10.1109/iccvw.2019.00567'
apa: 'Amrani, E., Ben-Ari, R., Hakim, T., & Bronstein, A. M. (2020). Learning
to detect and retrieve objects from unlabeled videos. In 2019 IEEE/CVF International
Conference on Computer Vision Workshop (ICCVW). Seoul, Korea (South): IEEE.
https://doi.org/10.1109/iccvw.2019.00567'
chicago: Amrani, Elad, Rami Ben-Ari, Tal Hakim, and Alex M. Bronstein. “Learning
to Detect and Retrieve Objects from Unlabeled Videos.” In 2019 IEEE/CVF International
Conference on Computer Vision Workshop (ICCVW). IEEE, 2020. https://doi.org/10.1109/iccvw.2019.00567.
ieee: E. Amrani, R. Ben-Ari, T. Hakim, and A. M. Bronstein, “Learning to detect
and retrieve objects from unlabeled videos,” in 2019 IEEE/CVF International
Conference on Computer Vision Workshop (ICCVW), Seoul, Korea (South), 2020.
ista: Amrani E, Ben-Ari R, Hakim T, Bronstein AM. 2020. Learning to detect and retrieve
objects from unlabeled videos. 2019 IEEE/CVF International Conference on Computer
Vision Workshop (ICCVW). 17th IEEE/CVF International Conference on Computer Vision
Workshop, 9022341.
mla: Amrani, Elad, et al. “Learning to Detect and Retrieve Objects from Unlabeled
Videos.” 2019 IEEE/CVF International Conference on Computer Vision Workshop
(ICCVW), 9022341, IEEE, 2020, doi:10.1109/iccvw.2019.00567.
short: E. Amrani, R. Ben-Ari, T. Hakim, A.M. Bronstein, in:, 2019 IEEE/CVF International
Conference on Computer Vision Workshop (ICCVW), IEEE, 2020.
conference:
end_date: 2019-10-28
location: Seoul, Korea (South)
name: 17th IEEE/CVF International Conference on Computer Vision Workshop
start_date: 2019-10-27
date_created: 2024-10-08T13:07:16Z
date_published: 2020-03-05T00:00:00Z
date_updated: 2024-12-05T16:04:03Z
day: '05'
doi: 10.1109/iccvw.2019.00567
extern: '1'
external_id:
arxiv:
- '1905.11137'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1905.11137
month: '03'
oa: 1
oa_version: Preprint
publication: 2019 IEEE/CVF International Conference on Computer Vision Workshop (ICCVW)
publication_identifier:
eissn:
- 2473-9944
isbn:
- '9781728150246'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Learning to detect and retrieve objects from unlabeled videos
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '18258'
abstract:
- lang: eng
text: Distance metric learning (DML) has been successfully applied to object classification,
both in the standard regime of rich training data and in the few-shot scenario,
where each category is represented by only a few examples. In this work, we propose
a new method for DML that simultaneously learns the backbone network parameters,
the embedding space, and the multi-modal distribution of each of the training
categories in that space, in a single end-to-end training process. Our approach
outperforms state-of-the-art methods for DML-based object classification on a
variety of standard fine-grained datasets. Furthermore, we demonstrate the effectiveness
of our approach on the problem of few-shot object detection, by incorporating
the proposed DML architecture as a classification head into a standard object
detection model. We achieve the best results on the ImageNet-LOC dataset compared
to strong baselines, when only a few training examples are available. We also
offer the community a new episodic benchmark based on the ImageNet dataset for
the few-shot object detection task.
article_number: '8953439'
article_processing_charge: No
author:
- first_name: Leonid
full_name: Karlinsky, Leonid
last_name: Karlinsky
- first_name: Joseph
full_name: Shtok, Joseph
last_name: Shtok
- first_name: Sivan
full_name: Harary, Sivan
last_name: Harary
- first_name: Eli
full_name: Schwartz, Eli
last_name: Schwartz
- first_name: Amit
full_name: Aides, Amit
last_name: Aides
- first_name: Rogerio
full_name: Feris, Rogerio
last_name: Feris
- first_name: Raja
full_name: Giryes, Raja
last_name: Giryes
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: 'Karlinsky L, Shtok J, Harary S, et al. Repmet: Representative-based metric
learning for classification and few-shot object detection. In: 2019 IEEE/CVF
Conference on Computer Vision and Pattern Recognition (CVPR). IEEE; 2020.
doi:10.1109/cvpr.2019.00534'
apa: 'Karlinsky, L., Shtok, J., Harary, S., Schwartz, E., Aides, A., Feris, R.,
… Bronstein, A. M. (2020). Repmet: Representative-based metric learning for classification
and few-shot object detection. In 2019 IEEE/CVF Conference on Computer Vision
and Pattern Recognition (CVPR). Long Beach, CA, United States: IEEE. https://doi.org/10.1109/cvpr.2019.00534'
chicago: 'Karlinsky, Leonid, Joseph Shtok, Sivan Harary, Eli Schwartz, Amit Aides,
Rogerio Feris, Raja Giryes, and Alex M. Bronstein. “Repmet: Representative-Based
Metric Learning for Classification and Few-Shot Object Detection.” In 2019
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). IEEE,
2020. https://doi.org/10.1109/cvpr.2019.00534.'
ieee: 'L. Karlinsky et al., “Repmet: Representative-based metric learning
for classification and few-shot object detection,” in 2019 IEEE/CVF Conference
on Computer Vision and Pattern Recognition (CVPR), Long Beach, CA, United
States, 2020.'
ista: 'Karlinsky L, Shtok J, Harary S, Schwartz E, Aides A, Feris R, Giryes R, Bronstein
AM. 2020. Repmet: Representative-based metric learning for classification and
few-shot object detection. 2019 IEEE/CVF Conference on Computer Vision and Pattern
Recognition (CVPR). 32nd IEEE/CVF Conference on Computer Vision and Pattern Recognition,
8953439.'
mla: 'Karlinsky, Leonid, et al. “Repmet: Representative-Based Metric Learning for
Classification and Few-Shot Object Detection.” 2019 IEEE/CVF Conference on
Computer Vision and Pattern Recognition (CVPR), 8953439, IEEE, 2020, doi:10.1109/cvpr.2019.00534.'
short: L. Karlinsky, J. Shtok, S. Harary, E. Schwartz, A. Aides, R. Feris, R. Giryes,
A.M. Bronstein, in:, 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition
(CVPR), IEEE, 2020.
conference:
end_date: 2019-06-20
location: Long Beach, CA, United States
name: 32nd IEEE/CVF Conference on Computer Vision and Pattern Recognition
start_date: 2019-06-15
date_created: 2024-10-08T13:08:09Z
date_published: 2020-01-09T00:00:00Z
date_updated: 2024-12-05T15:38:16Z
day: '09'
doi: 10.1109/cvpr.2019.00534
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)
publication_identifier:
eissn:
- 2575-7075
isbn:
- '9781728132945'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Repmet: Representative-based metric learning for classification and few-shot
object detection'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '18259'
abstract:
- lang: eng
text: Example synthesis is one of the leading methods to tackle the problem of few-shot
learning, where only a small number of samples per class are available. However,
current synthesis approaches only address the scenario of a single category label
per image. In this work, we propose a novel technique for synthesizing samples
with multiple labels for the (yet unhandled) multi-label few-shot classification
scenario. We propose to combine pairs of given examples in feature space, so that
the resulting synthesized feature vectors will correspond to examples whose label
sets are obtained through certain set operations on the label sets of the corresponding
input pairs. Thus, our method is capable of producing a sample containing the
intersection, union or set-difference of labels present in two input samples.
As we show, these set operations generalize to labels unseen during training.
This enables performing augmentation on examples of novel categories, thus, facilitating
multi-label few-shot classifier learning. We conduct numerous experiments showing
promising results for the label-set manipulation capabilities of the proposed
approach, both directly (using the classification and retrieval metrics), and
in the context of performing data augmentation for multi-label few-shot learning.
We propose a benchmark for this new and challenging task and show that our method
compares favorably to all the common baselines.
article_number: '8954088'
article_processing_charge: No
arxiv: 1
author:
- first_name: Amit
full_name: Alfassy, Amit
last_name: Alfassy
- first_name: Leonid
full_name: Karlinsky, Leonid
last_name: Karlinsky
- first_name: Amit
full_name: Aides, Amit
last_name: Aides
- first_name: Joseph
full_name: Shtok, Joseph
last_name: Shtok
- first_name: Sivan
full_name: Harary, Sivan
last_name: Harary
- first_name: Rogerio
full_name: Feris, Rogerio
last_name: Feris
- first_name: Raja
full_name: Giryes, Raja
last_name: Giryes
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
citation:
ama: 'Alfassy A, Karlinsky L, Aides A, et al. Laso: Label-set operations networks
for multi-label few-shot learning. In: 2019 IEEE/CVF Conference on Computer
Vision and Pattern Recognition (CVPR). IEEE; 2020. doi:10.1109/cvpr.2019.00671'
apa: 'Alfassy, A., Karlinsky, L., Aides, A., Shtok, J., Harary, S., Feris, R., …
Bronstein, A. M. (2020). Laso: Label-set operations networks for multi-label few-shot
learning. In 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition
(CVPR). Long Beach, CA, United States: IEEE. https://doi.org/10.1109/cvpr.2019.00671'
chicago: 'Alfassy, Amit, Leonid Karlinsky, Amit Aides, Joseph Shtok, Sivan Harary,
Rogerio Feris, Raja Giryes, and Alex M. Bronstein. “Laso: Label-Set Operations
Networks for Multi-Label Few-Shot Learning.” In 2019 IEEE/CVF Conference on
Computer Vision and Pattern Recognition (CVPR). IEEE, 2020. https://doi.org/10.1109/cvpr.2019.00671.'
ieee: 'A. Alfassy et al., “Laso: Label-set operations networks for multi-label
few-shot learning,” in 2019 IEEE/CVF Conference on Computer Vision and Pattern
Recognition (CVPR), Long Beach, CA, United States, 2020.'
ista: 'Alfassy A, Karlinsky L, Aides A, Shtok J, Harary S, Feris R, Giryes R, Bronstein
AM. 2020. Laso: Label-set operations networks for multi-label few-shot learning.
2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). 32nd
IEEE/CVF Conference on Computer Vision and Pattern Recognition, 8954088.'
mla: 'Alfassy, Amit, et al. “Laso: Label-Set Operations Networks for Multi-Label
Few-Shot Learning.” 2019 IEEE/CVF Conference on Computer Vision and Pattern
Recognition (CVPR), 8954088, IEEE, 2020, doi:10.1109/cvpr.2019.00671.'
short: A. Alfassy, L. Karlinsky, A. Aides, J. Shtok, S. Harary, R. Feris, R. Giryes,
A.M. Bronstein, in:, 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition
(CVPR), IEEE, 2020.
conference:
end_date: 2019-06-20
location: Long Beach, CA, United States
name: 32nd IEEE/CVF Conference on Computer Vision and Pattern Recognition
start_date: 2019-06-15
date_created: 2024-10-08T13:08:26Z
date_published: 2020-01-09T00:00:00Z
date_updated: 2024-12-05T15:33:21Z
day: '09'
doi: 10.1109/cvpr.2019.00671
extern: '1'
external_id:
arxiv:
- '1902.09811'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1902.09811
month: '01'
oa: 1
oa_version: Preprint
publication: 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)
publication_identifier:
eissn:
- 2575-7075
isbn:
- '9781728132945'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Laso: Label-set operations networks for multi-label few-shot learning'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '18260'
abstract:
- lang: eng
text: We introduce the first completely unsupervised correspondence learning approach
for deformable 3D shapes. Key to our model is the understanding that natural deformations
(such as changes in pose) approximately preserve the metric structure of the surface,
yielding a natural criterion to drive the learning process toward distortion-minimizing
predictions. On this basis, we overcome the need for annotated data and replace
it by a purely geometric criterion. The resulting learning model is class-agnostic,
and is able to leverage any type of deformable geometric data for the training
phase. In contrast to existing supervised approaches which specialize on the class
seen at training time, we demonstrate stronger generalization as well as applicability
to a variety of challenging settings. We showcase our method on a wide selection
of correspondence benchmarks, where we outperform other methods in terms of accuracy,
generalization, and efficiency.
article_number: '8953366'
article_processing_charge: No
author:
- first_name: Oshri
full_name: Halimi, Oshri
last_name: Halimi
- first_name: Or
full_name: Litany, Or
last_name: Litany
- first_name: Emanuele Rodola
full_name: Rodola, Emanuele Rodola
last_name: Rodola
- first_name: Alexander
full_name: Bronstein, Alexander
id: 58f3726e-7cba-11ef-ad8b-e6e8cb3904e6
last_name: Bronstein
orcid: 0000-0001-9699-8730
- first_name: Ron
full_name: Kimmel, Ron
last_name: Kimmel
citation:
ama: 'Halimi O, Litany O, Rodola ER, Bronstein AM, Kimmel R. Unsupervised learning
of dense shape correspondence. In: 2019 IEEE/CVF Conference on Computer Vision
and Pattern Recognition (CVPR). IEEE; 2020. doi:10.1109/cvpr.2019.00450'
apa: 'Halimi, O., Litany, O., Rodola, E. R., Bronstein, A. M., & Kimmel, R.
(2020). Unsupervised learning of dense shape correspondence. In 2019 IEEE/CVF
Conference on Computer Vision and Pattern Recognition (CVPR). Long Beach,
CA, United States: IEEE. https://doi.org/10.1109/cvpr.2019.00450'
chicago: Halimi, Oshri, Or Litany, Emanuele Rodola Rodola, Alex M. Bronstein, and
Ron Kimmel. “Unsupervised Learning of Dense Shape Correspondence.” In 2019
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR). IEEE,
2020. https://doi.org/10.1109/cvpr.2019.00450.
ieee: O. Halimi, O. Litany, E. R. Rodola, A. M. Bronstein, and R. Kimmel, “Unsupervised
learning of dense shape correspondence,” in 2019 IEEE/CVF Conference on Computer
Vision and Pattern Recognition (CVPR), Long Beach, CA, United States, 2020.
ista: Halimi O, Litany O, Rodola ER, Bronstein AM, Kimmel R. 2020. Unsupervised
learning of dense shape correspondence. 2019 IEEE/CVF Conference on Computer Vision
and Pattern Recognition (CVPR). 32nd IEEE/CVF Conference on Computer Vision and
Pattern Recognition, 8953366.
mla: Halimi, Oshri, et al. “Unsupervised Learning of Dense Shape Correspondence.”
2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR),
8953366, IEEE, 2020, doi:10.1109/cvpr.2019.00450.
short: O. Halimi, O. Litany, E.R. Rodola, A.M. Bronstein, R. Kimmel, in:, 2019 IEEE/CVF
Conference on Computer Vision and Pattern Recognition (CVPR), IEEE, 2020.
conference:
end_date: 2019-06-20
location: Long Beach, CA, United States
name: 32nd IEEE/CVF Conference on Computer Vision and Pattern Recognition
start_date: 2019-06-15
date_created: 2024-10-08T13:08:43Z
date_published: 2020-01-09T00:00:00Z
date_updated: 2024-12-05T15:19:01Z
day: '09'
doi: 10.1109/cvpr.2019.00450
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)
publication_identifier:
eissn:
- 2575-7075
isbn:
- '9781728132945'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unsupervised learning of dense shape correspondence
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '22054'
abstract:
- lang: eng
text: We consider the Korteweg–de Vries equation with white noise initial data,
posed on the whole real line, and prove the almost sure existence of solutions.
Moreover, we show that the solutions obey the group property and follow a white
noise law at all times, past or future. As an offshoot of our methods, we also
obtain a new proof of the existence of solutions and the invariance of white noise
measure in the torus setting.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Rowan
full_name: Killip, Rowan
last_name: Killip
- first_name: Jason
full_name: Murphy, Jason
last_name: Murphy
- first_name: Monica
full_name: Visan, Monica
id: 056daca0-b8d1-11f0-964f-f91054abf8ca
last_name: Visan
citation:
ama: Killip R, Murphy J, Vişan M. Invariance of white noise for KdV on the line.
Inventiones mathematicae. 2020;222(1):203-282. doi:10.1007/s00222-020-00964-9
apa: Killip, R., Murphy, J., & Vişan, M. (2020). Invariance of white noise for
KdV on the line. Inventiones Mathematicae. Springer Nature. https://doi.org/10.1007/s00222-020-00964-9
chicago: Killip, Rowan, Jason Murphy, and Monica Vişan. “Invariance of White Noise
for KdV on the Line.” Inventiones Mathematicae. Springer Nature, 2020.
https://doi.org/10.1007/s00222-020-00964-9.
ieee: R. Killip, J. Murphy, and M. Vişan, “Invariance of white noise for KdV on
the line,” Inventiones mathematicae, vol. 222, no. 1. Springer Nature,
pp. 203–282, 2020.
ista: Killip R, Murphy J, Vişan M. 2020. Invariance of white noise for KdV on the
line. Inventiones mathematicae. 222(1), 203–282.
mla: Killip, Rowan, et al. “Invariance of White Noise for KdV on the Line.” Inventiones
Mathematicae, vol. 222, no. 1, Springer Nature, 2020, pp. 203–82, doi:10.1007/s00222-020-00964-9.
short: R. Killip, J. Murphy, M. Vişan, Inventiones Mathematicae 222 (2020) 203–282.
das_tickbox: '1'
date_created: 2026-06-19T07:56:16Z
date_published: 2020-10-01T00:00:00Z
date_updated: 2026-06-25T08:39:30Z
day: '01'
doi: 10.1007/s00222-020-00964-9
extern: '1'
external_id:
arxiv:
- '1904.11910'
intvolume: ' 222'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1904.11910
month: '10'
oa: 1
oa_version: Preprint
page: 203-282
publication: Inventiones mathematicae
publication_identifier:
eissn:
- 1432-1297
issn:
- 0020-9910
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Invariance of white noise for KdV on the line
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 222
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '22080'
abstract:
- lang: eng
text: We consider discrete analogues of two well-known open problems regarding invariant
measures for dispersive PDE, namely, the invariance of the Gibbs measure for the
continuum (classical) Heisenberg model and the invariance of white noise under
focusing cubic nonlinear Schrödinger equation. These continuum models are completely
integrable and connected by the Hasimoto transform; correspondingly, we focus
our attention on discretizations that are also completely integrable and also
connected by a discrete Hasimoto transform. We consider these models on the infinite
lattice ℤ. Concretely, for a completely integrable variant of the classical Heisenberg
spin chain model (introduced independently by Haldane, Ishimori, and Sklyanin)
we prove the existence and uniqueness of solutions for initial data following
a Gibbs law (which we show is unique) and show that the Gibbs measure is preserved
under these dynamics. In the setting of the focusing Ablowitz--Ladik system, we
prove invariance of a measure that we will show is the appropriate discrete analogue
of white noise. We also include a thorough discussion of the Poisson geometry
associated to the discrete Hasimoto transform introduced by Ishimori that connects
the two models studied in this article.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yannis
full_name: Angelopoulos, Yannis
last_name: Angelopoulos
- first_name: Rowan
full_name: Killip, Rowan
last_name: Killip
- first_name: Monica
full_name: Visan, Monica
id: 056daca0-b8d1-11f0-964f-f91054abf8ca
last_name: Visan
citation:
ama: Angelopoulos Y, Killip R, Vişan M. Invariant measures for integrable spin chains
and an integrable discrete nonlinear Schrödinger equation. SIAM Journal on
Mathematical Analysis. 2020;52(1):135-163. doi:10.1137/19m1265314
apa: Angelopoulos, Y., Killip, R., & Vişan, M. (2020). Invariant measures for
integrable spin chains and an integrable discrete nonlinear Schrödinger equation.
SIAM Journal on Mathematical Analysis. Society for Industrial & Applied
Mathematics. https://doi.org/10.1137/19m1265314
chicago: Angelopoulos, Yannis, Rowan Killip, and Monica Vişan. “Invariant Measures
for Integrable Spin Chains and an Integrable Discrete Nonlinear Schrödinger Equation.”
SIAM Journal on Mathematical Analysis. Society for Industrial & Applied
Mathematics, 2020. https://doi.org/10.1137/19m1265314.
ieee: Y. Angelopoulos, R. Killip, and M. Vişan, “Invariant measures for integrable
spin chains and an integrable discrete nonlinear Schrödinger equation,” SIAM
Journal on Mathematical Analysis, vol. 52, no. 1. Society for Industrial &
Applied Mathematics, pp. 135–163, 2020.
ista: Angelopoulos Y, Killip R, Vişan M. 2020. Invariant measures for integrable
spin chains and an integrable discrete nonlinear Schrödinger equation. SIAM Journal
on Mathematical Analysis. 52(1), 135–163.
mla: Angelopoulos, Yannis, et al. “Invariant Measures for Integrable Spin Chains
and an Integrable Discrete Nonlinear Schrödinger Equation.” SIAM Journal on
Mathematical Analysis, vol. 52, no. 1, Society for Industrial & Applied
Mathematics, 2020, pp. 135–63, doi:10.1137/19m1265314.
short: Y. Angelopoulos, R. Killip, M. Vişan, SIAM Journal on Mathematical Analysis
52 (2020) 135–163.
das_tickbox: '1'
date_created: 2026-06-19T08:26:32Z
date_published: 2020-01-01T00:00:00Z
date_updated: 2026-06-30T12:21:20Z
day: '01'
doi: 10.1137/19m1265314
extern: '1'
external_id:
arxiv:
- '1807.08801'
intvolume: ' 52'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1807.08801
mathsc:
- 35Q55
- 35Q51
- 35Q82
month: '01'
oa: 1
oa_version: Preprint
page: 135-163
publication: SIAM Journal on Mathematical Analysis
publication_identifier:
eissn:
- 1095-7154
issn:
- 0036-1410
publication_status: published
publisher: Society for Industrial & Applied Mathematics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Invariant measures for integrable spin chains and an integrable discrete nonlinear
Schrödinger equation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2020'
...
---
_id: '15079'
abstract:
- lang: eng
text: "Large complex systems tend to develop universal patterns that often represent
their essential characteristics. For example, the cumulative effects of independent
or weakly dependent random variables often yield the Gaussian universality class
via the central limit theorem. For non-commutative random variables, e.g. matrices,
the Gaussian behavior is often replaced by another universality class, commonly
called random matrix statistics. Nearby eigenvalues are strongly correlated, and,
remarkably, their correlation structure is universal, depending only on the symmetry
type of the matrix. Even more surprisingly, this feature is not restricted to
matrices; in fact Eugene Wigner, the pioneer of the field, discovered in the 1950s
that distributions of the gaps between energy levels of complicated quantum systems
universally follow the same random matrix statistics. This claim has never been
rigorously proved for any realistic physical system but experimental data and
extensive numerics leave no doubt as to its correctness. Since then random matrices
have proved to be extremely useful phenomenological models in a wide range of
applications beyond quantum physics that include number theory, statistics, neuroscience,
population dynamics, wireless communication and mathematical finance. The ubiquity
of random matrices in natural sciences is still a mystery, but recent years have
witnessed a breakthrough in the mathematical description of the statistical structure
of their spectrum. Random matrices and closely related areas such as log-gases
have become an extremely active research area in probability theory.\r\nThis workshop
brought together outstanding researchers from a variety of mathematical backgrounds
whose areas of research are linked to random matrices. While there are strong
links between their motivations, the techniques used by these researchers span
a large swath of mathematics, ranging from purely algebraic techniques to stochastic
analysis, classical probability theory, operator algebra, supersymmetry, orthogonal
polynomials, etc."
article_processing_charge: No
article_type: original
author:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
- first_name: Friedrich
full_name: Götze, Friedrich
last_name: Götze
- first_name: Alice
full_name: Guionnet, Alice
last_name: Guionnet
citation:
ama: Erdös L, Götze F, Guionnet A. Random matrices. Oberwolfach Reports.
2020;16(4):3459-3527. doi:10.4171/owr/2019/56
apa: Erdös, L., Götze, F., & Guionnet, A. (2020). Random matrices. Oberwolfach
Reports. EMS Press. https://doi.org/10.4171/owr/2019/56
chicago: Erdös, László, Friedrich Götze, and Alice Guionnet. “Random Matrices.”
Oberwolfach Reports. EMS Press, 2020. https://doi.org/10.4171/owr/2019/56.
ieee: L. Erdös, F. Götze, and A. Guionnet, “Random matrices,” Oberwolfach Reports,
vol. 16, no. 4. EMS Press, pp. 3459–3527, 2020.
ista: Erdös L, Götze F, Guionnet A. 2020. Random matrices. Oberwolfach Reports.
16(4), 3459–3527.
mla: Erdös, László, et al. “Random Matrices.” Oberwolfach Reports, vol. 16,
no. 4, EMS Press, 2020, pp. 3459–527, doi:10.4171/owr/2019/56.
short: L. Erdös, F. Götze, A. Guionnet, Oberwolfach Reports 16 (2020) 3459–3527.
das_tickbox: '1'
date_created: 2024-03-05T07:54:44Z
date_published: 2020-11-19T00:00:00Z
date_updated: 2026-07-06T11:53:24Z
day: '19'
department:
- _id: LaEr
doi: 10.4171/owr/2019/56
intvolume: ' 16'
issue: '4'
language:
- iso: eng
month: '11'
oa_version: None
page: 3459-3527
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: EMS Press
quality_controlled: '1'
status: public
title: Random matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '8042'
abstract:
- lang: eng
text: We consider systems of N bosons in a box of volume one, interacting through
a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for
sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov
theory, identifying the ground state energy and the low-lying excitation spectrum
up to errors that vanish in the limit of large N.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Chiara
full_name: Boccato, Chiara
id: 342E7E22-F248-11E8-B48F-1D18A9856A87
last_name: Boccato
- first_name: Christian
full_name: Brennecke, Christian
last_name: Brennecke
- first_name: Serena
full_name: Cenatiempo, Serena
last_name: Cenatiempo
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
citation:
ama: Boccato C, Brennecke C, Cenatiempo S, Schlein B. The excitation spectrum of
Bose gases interacting through singular potentials. Journal of the European
Mathematical Society. 2020;22(7):2331-2403. doi:10.4171/JEMS/966
apa: Boccato, C., Brennecke, C., Cenatiempo, S., & Schlein, B. (2020). The excitation
spectrum of Bose gases interacting through singular potentials. Journal of
the European Mathematical Society. EMS Press. https://doi.org/10.4171/JEMS/966
chicago: Boccato, Chiara, Christian Brennecke, Serena Cenatiempo, and Benjamin Schlein.
“The Excitation Spectrum of Bose Gases Interacting through Singular Potentials.”
Journal of the European Mathematical Society. EMS Press, 2020. https://doi.org/10.4171/JEMS/966.
ieee: C. Boccato, C. Brennecke, S. Cenatiempo, and B. Schlein, “The excitation spectrum
of Bose gases interacting through singular potentials,” Journal of the European
Mathematical Society, vol. 22, no. 7. EMS Press, pp. 2331–2403, 2020.
ista: Boccato C, Brennecke C, Cenatiempo S, Schlein B. 2020. The excitation spectrum
of Bose gases interacting through singular potentials. Journal of the European
Mathematical Society. 22(7), 2331–2403.
mla: Boccato, Chiara, et al. “The Excitation Spectrum of Bose Gases Interacting
through Singular Potentials.” Journal of the European Mathematical Society,
vol. 22, no. 7, EMS Press, 2020, pp. 2331–403, doi:10.4171/JEMS/966.
short: C. Boccato, C. Brennecke, S. Cenatiempo, B. Schlein, Journal of the European
Mathematical Society 22 (2020) 2331–2403.
das_tickbox: '1'
date_created: 2020-06-29T07:59:35Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2026-07-06T11:53:41Z
day: '01'
department:
- _id: RoSe
doi: 10.4171/JEMS/966
external_id:
arxiv:
- '1704.04819'
isi:
- '000548174700006'
intvolume: ' 22'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.04819
month: '07'
oa: 1
oa_version: Preprint
page: 2331-2403
publication: Journal of the European Mathematical Society
publication_identifier:
issn:
- 1435-9855
publication_status: published
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The excitation spectrum of Bose gases interacting through singular potentials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2020'
...
---
_id: '9007'
abstract:
- lang: eng
text: Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle
method to count “sufficiently free” rational points of bounded height on arbitrary
smooth projective hypersurfaces of low degree that are defined over the rationals.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Timothy D
full_name: Browning, Timothy D
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Will
full_name: Sawin, Will
last_name: Sawin
citation:
ama: Browning TD, Sawin W. Free rational points on smooth hypersurfaces. Commentarii
Mathematici Helvetici. 2020;95(4):635-659. doi:10.4171/CMH/499
apa: Browning, T. D., & Sawin, W. (2020). Free rational points on smooth hypersurfaces.
Commentarii Mathematici Helvetici. EMS Press. https://doi.org/10.4171/CMH/499
chicago: Browning, Timothy D, and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.”
Commentarii Mathematici Helvetici. EMS Press, 2020. https://doi.org/10.4171/CMH/499.
ieee: T. D. Browning and W. Sawin, “Free rational points on smooth hypersurfaces,”
Commentarii Mathematici Helvetici, vol. 95, no. 4. EMS Press, pp. 635–659,
2020.
ista: Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces.
Commentarii Mathematici Helvetici. 95(4), 635–659.
mla: Browning, Timothy D., and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.”
Commentarii Mathematici Helvetici, vol. 95, no. 4, EMS Press, 2020, pp.
635–59, doi:10.4171/CMH/499.
short: T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.
das_tickbox: '1'
date_created: 2021-01-17T23:01:11Z
date_published: 2020-12-07T00:00:00Z
date_updated: 2026-07-06T11:54:01Z
day: '07'
department:
- _id: TiBr
doi: 10.4171/CMH/499
external_id:
arxiv:
- '1906.08463'
isi:
- '000596833300001'
intvolume: ' 95'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1906.08463
month: '12'
oa: 1
oa_version: Preprint
page: 635-659
publication: Commentarii Mathematici Helvetici
publication_identifier:
eissn:
- 1420-8946
issn:
- 0010-2571
publication_status: published
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Free rational points on smooth hypersurfaces
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2020'
...
---
_id: '15070'
abstract:
- lang: eng
text: This workshop focused on interactions between the various perspectives on
the moduli space of Higgs bundles over a Riemann surface. This subject draws on
algebraic geometry, geometric topology, geometric analysis and mathematical physics,
and the goal was to promote interactions between these various branches of the
subject. The main current directions of research were well represented by the
participants, and the talks included many from both senior and junior participants.
article_processing_charge: No
article_type: original
author:
- first_name: Lara
full_name: Anderson, Lara
last_name: Anderson
- first_name: Tamás
full_name: Hausel, Tamás
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
orcid: 0000-0002-9582-2634
- first_name: Rafe
full_name: Mazzeo, Rafe
last_name: Mazzeo
- first_name: Laura
full_name: Schaposnik, Laura
last_name: Schaposnik
citation:
ama: Anderson L, Hausel T, Mazzeo R, Schaposnik L. Geometry and physics of Higgs
bundles. Oberwolfach Reports. 2020;16(2):1357-1417. doi:10.4171/owr/2019/23
apa: Anderson, L., Hausel, T., Mazzeo, R., & Schaposnik, L. (2020). Geometry
and physics of Higgs bundles. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2019/23
chicago: Anderson, Lara, Tamás Hausel, Rafe Mazzeo, and Laura Schaposnik. “Geometry
and Physics of Higgs Bundles.” Oberwolfach Reports. EMS Press, 2020. https://doi.org/10.4171/owr/2019/23.
ieee: L. Anderson, T. Hausel, R. Mazzeo, and L. Schaposnik, “Geometry and physics
of Higgs bundles,” Oberwolfach Reports, vol. 16, no. 2. EMS Press, pp.
1357–1417, 2020.
ista: Anderson L, Hausel T, Mazzeo R, Schaposnik L. 2020. Geometry and physics of
Higgs bundles. Oberwolfach Reports. 16(2), 1357–1417.
mla: Anderson, Lara, et al. “Geometry and Physics of Higgs Bundles.” Oberwolfach
Reports, vol. 16, no. 2, EMS Press, 2020, pp. 1357–417, doi:10.4171/owr/2019/23.
short: L. Anderson, T. Hausel, R. Mazzeo, L. Schaposnik, Oberwolfach Reports 16
(2020) 1357–1417.
das_tickbox: '1'
date_created: 2024-03-04T11:36:31Z
date_published: 2020-06-04T00:00:00Z
date_updated: 2026-07-06T11:52:54Z
day: '04'
department:
- _id: TaHa
doi: 10.4171/owr/2019/23
intvolume: ' 16'
issue: '2'
keyword:
- Organic Chemistry
- Biochemistry
language:
- iso: eng
month: '06'
oa_version: None
page: 1357-1417
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: EMS Press
quality_controlled: '1'
status: public
title: Geometry and physics of Higgs bundles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '15072'
abstract:
- lang: eng
text: The interaction among fundamental particles in nature leads to many interesting
effects in quantum statistical mechanics; examples include superconductivity for
charged systems and superfluidity in cold gases. It is a huge challenge for mathematical
physics to understand the collective behavior of systems containing a large number
of particles, emerging from known microscopic interactions. In this workshop we
brought together researchers working on different aspects of many-body quantum
mechanics to discuss recent developments, exchange ideas and propose new challenges
and research directions.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Hainzl, Christian
last_name: Hainzl
- first_name: Benjamin
full_name: Schlein, Benjamin
last_name: Schlein
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
- first_name: Simone
full_name: Warzel, Simone
last_name: Warzel
citation:
ama: Hainzl C, Schlein B, Seiringer R, Warzel S. Many-body quantum systems. Oberwolfach
Reports. 2020;16(3):2541-2603. doi:10.4171/owr/2019/41
apa: Hainzl, C., Schlein, B., Seiringer, R., & Warzel, S. (2020). Many-body
quantum systems. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2019/41
chicago: Hainzl, Christian, Benjamin Schlein, Robert Seiringer, and Simone Warzel.
“Many-Body Quantum Systems.” Oberwolfach Reports. EMS Press, 2020. https://doi.org/10.4171/owr/2019/41.
ieee: C. Hainzl, B. Schlein, R. Seiringer, and S. Warzel, “Many-body quantum systems,”
Oberwolfach Reports, vol. 16, no. 3. EMS Press, pp. 2541–2603, 2020.
ista: Hainzl C, Schlein B, Seiringer R, Warzel S. 2020. Many-body quantum systems.
Oberwolfach Reports. 16(3), 2541–2603.
mla: Hainzl, Christian, et al. “Many-Body Quantum Systems.” Oberwolfach Reports,
vol. 16, no. 3, EMS Press, 2020, pp. 2541–603, doi:10.4171/owr/2019/41.
short: C. Hainzl, B. Schlein, R. Seiringer, S. Warzel, Oberwolfach Reports 16 (2020)
2541–2603.
das_tickbox: '1'
date_created: 2024-03-04T11:46:12Z
date_published: 2020-09-10T00:00:00Z
date_updated: 2026-07-06T11:53:09Z
day: '10'
department:
- _id: RoSe
doi: 10.4171/owr/2019/41
intvolume: ' 16'
issue: '3'
language:
- iso: eng
month: '09'
oa_version: None
page: 2541-2603
publication: Oberwolfach Reports
publication_identifier:
issn:
- 1660-8933
publication_status: published
publisher: EMS Press
quality_controlled: '1'
status: public
title: Many-body quantum systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '8973'
abstract:
- lang: eng
text: We consider the symmetric simple exclusion process in Zd with quenched bounded
dynamic random conductances and prove its hydrodynamic limit in path space. The
main tool is the connection, due to the self-duality of the process, between the
invariance principle for single particles starting from all points and the macroscopic
behavior of the density field. While the hydrodynamic limit at fixed macroscopic
times is obtained via a generalization to the time-inhomogeneous context of the
strategy introduced in [41], in order to prove tightness for the sequence of empirical
density fields we develop a new criterion based on the notion of uniform conditional
stochastic continuity, following [50]. In conclusion, we show that uniform elliptic
dynamic conductances provide an example of environments in which the so-called
arbitrary starting point invariance principle may be derived from the invariance
principle of a single particle starting from the origin. Therefore, our hydrodynamics
result applies to the examples of quenched environments considered in, e.g., [1],
[3], [6] in combination with the hypothesis of uniform ellipticity.
acknowledgement: "We warmly thank S.R.S. Varadhan for many enlightening discussions
at an early stage of this work. We are indebted to Francesca Collet for fruitful
discussions and constant support all throughout this work. We thank Simone Floreani\r\nand
Alberto Chiarini for helpful conversations on the final part of this paper as well
as both referees for their careful reading and for raising relevant issues on some
weak points contained in a previous version of this manuscript; we believe this
helped us to improve it.\r\nPart of this work was done during the authors’ stay
at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile
Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank
this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01).
F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University,
for financial support and hospitality. F.S. acknowledges NWO for financial support
via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon
2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement
No. 754411. This research has been conducted within the FP2M federation (CNRS FR
2036)."
article_number: '138'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Frank
full_name: Redig, Frank
last_name: Redig
- first_name: Ellen
full_name: Saada, Ellen
last_name: Saada
- first_name: Federico
full_name: Sau, Federico
id: E1836206-9F16-11E9-8814-AEFDE5697425
last_name: Sau
citation:
ama: 'Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment:
Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536'
apa: 'Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process
in dynamic environment: Hydrodynamics. Electronic Journal of Probability.
Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536'
chicago: 'Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion
Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability.
Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536.'
ieee: 'F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic
environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25.
Institute of Mathematical Statistics, 2020.'
ista: 'Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic
environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.'
mla: 'Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment:
Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute
of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.'
short: F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).
das_tickbox: '1'
date_created: 2020-12-27T23:01:17Z
date_published: 2020-10-21T00:00:00Z
date_updated: 2026-07-06T12:04:40Z
day: '21'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1214/20-EJP536
ec_funded: 1
external_id:
arxiv:
- '1811.01366'
isi:
- '000591737500001'
file:
- access_level: open_access
checksum: d75359b9814e78d57c0a481b7cde3751
content_type: application/pdf
creator: dernst
date_created: 2020-12-28T08:24:08Z
date_updated: 2020-12-28T08:24:08Z
file_id: '8976'
file_name: 2020_ElectronJProbab_Redig.pdf
file_size: 696653
relation: main_file
success: 1
file_date_updated: 2020-12-28T08:24:08Z
has_accepted_license: '1'
intvolume: ' 25'
isi: 1
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Electronic Journal of Probability
publication_identifier:
eissn:
- 1083-6489
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Symmetric simple exclusion process in dynamic environment: Hydrodynamics'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2020'
...
---
_id: '8040'
abstract:
- lang: eng
text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes
energy from catabolic processes to synthesize ATP. Complex I, the first and the
largest protein complex of the chain, harvests electrons from NADH to reduce quinone,
while pumping protons across the mitochondrial membrane. Detailed knowledge of
the working principle of such coupled charge-transfer processes remains, however,
fragmentary due to bottlenecks in understanding redox-driven conformational transitions
and their interplay with the hydrated proton pathways. Complex I from Thermus
thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons
from NADH. Here, employing the latest crystal structure of T. thermophilus complex
I, we have used microsecond-scale molecular dynamics simulations to study the
chemo-mechanical coupling between redox changes of the iron–sulfur clusters and
conformational transitions across complex I. First, we identify the redox switches
within complex I, which allosterically couple the dynamics of the quinone binding
pocket to the site of NADH reduction. Second, our free-energy calculations reveal
that the affinity of the quinone, specifically menaquinone, for the binding-site
is higher than that of its reduced, menaquinol form—a design essential for menaquinol
release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser
than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup
of the former furnishes stronger binding interactions with the pocket, favoring
menaquinone for charge transport in T. thermophilus. Our computations are consistent
with experimentally validated mutations and hierarchize the key residues into
three functional classes, identifying new mutation targets. Third, long-range
hydrogen-bond networks connecting the quinone-binding site to the transmembrane
subunits are found to be responsible for proton pumping. Put together, the simulations
reveal the molecular design principles linking redox reactions to quinone turnover
to proton translocation in complex I.
article_processing_charge: No
article_type: original
author:
- first_name: Chitrak
full_name: Gupta, Chitrak
last_name: Gupta
- first_name: Umesh
full_name: Khaniya, Umesh
last_name: Khaniya
- first_name: Chun Kit
full_name: Chan, Chun Kit
last_name: Chan
- first_name: Francois
full_name: Dehez, Francois
last_name: Dehez
- first_name: Mrinal
full_name: Shekhar, Mrinal
last_name: Shekhar
- first_name: M. R.
full_name: Gunner, M. R.
last_name: Gunner
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: Abhishek
full_name: Singharoy, Abhishek
last_name: Singharoy
citation:
ama: Gupta C, Khaniya U, Chan CK, et al. Charge transfer and chemo-mechanical coupling
in respiratory complex I. Journal of the American Chemical Society. 2020;142(20):9220-9230.
doi:10.1021/jacs.9b13450
apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R.,
… Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory
complex I. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/jacs.9b13450
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar,
M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge
Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” Journal of
the American Chemical Society. American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.
ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in
respiratory complex I,” Journal of the American Chemical Society, vol.
142, no. 20. American Chemical Society, pp. 9220–9230, 2020.
ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory
complex I. Journal of the American Chemical Society. 142(20), 9220–9230.
mla: Gupta, Chitrak, et al. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory
Complex I.” Journal of the American Chemical Society, vol. 142, no. 20,
American Chemical Society, 2020, pp. 9220–30, doi:10.1021/jacs.9b13450.
short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A.
Sazanov, C. Chipot, A. Singharoy, Journal of the American Chemical Society 142
(2020) 9220–9230.
corr_author: '1'
date_created: 2020-06-29T07:59:35Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2026-07-06T12:16:34Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450
external_id:
isi:
- '000537415600020'
pmid:
- '32347721'
intvolume: ' 142'
isi: 1
issue: '20'
language:
- iso: eng
month: '05'
oa_version: None
page: 9220-9230
pmid: 1
publication: Journal of the American Chemical Society
publication_identifier:
eissn:
- 1520-5126
issn:
- 0002-7863
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '9878'
relation: research_data
status: public
- id: '9326'
relation: research_data
status: public
- id: '9713'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Charge transfer and chemo-mechanical coupling in respiratory complex I
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 142
year: '2020'
...
---
_id: '7166'
abstract:
- lang: eng
text: In the living cell, we encounter a large variety of motile processes such
as organelle transport and cytoskeleton remodeling. These processes are driven
by motor proteins that generate force by transducing chemical free energy into
mechanical work. In many cases, the molecular motors work in teams to collectively
generate larger forces. Recent optical trapping experiments on small teams of
cytoskeletal motors indicated that the collectively generated force increases
with the size of the motor team but that this increase depends on the motor type
and on whether the motors are studied in vitro or in vivo. Here, we use the theory
of stochastic processes to describe the motion of N motors in a stationary optical
trap and to compute the N-dependence of the collectively generated forces. We
consider six distinct motor types, two kinesins, two dyneins, and two myosins.
We show that the force increases always linearly with N but with a prefactor that
depends on the performance of the single motor. Surprisingly, this prefactor increases
for weaker motors with a lower stall force. This counter-intuitive behavior reflects
the increased probability with which stronger motors detach from the filament
during strain generation. Our theoretical results are in quantitative agreement
with experimental data on small teams of kinesin-1 motors.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Reinhard
full_name: Lipowsky, Reinhard
last_name: Lipowsky
citation:
ama: Ucar MC, Lipowsky R. Collective force generation by molecular motors is determined
by strain-induced unbinding. Nano Letters. 2020;20(1):669-676. doi:10.1021/acs.nanolett.9b04445
apa: Ucar, M. C., & Lipowsky, R. (2020). Collective force generation by molecular
motors is determined by strain-induced unbinding. Nano Letters. American
Chemical Society. https://doi.org/10.1021/acs.nanolett.9b04445
chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Collective Force Generation by
Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters.
American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.9b04445.
ieee: M. C. Ucar and R. Lipowsky, “Collective force generation by molecular motors
is determined by strain-induced unbinding,” Nano Letters, vol. 20, no.
1. American Chemical Society, pp. 669–676, 2020.
ista: Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors
is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676.
mla: Ucar, Mehmet C., and Reinhard Lipowsky. “Collective Force Generation by Molecular
Motors Is Determined by Strain-Induced Unbinding.” Nano Letters, vol. 20,
no. 1, American Chemical Society, 2020, pp. 669–76, doi:10.1021/acs.nanolett.9b04445.
short: M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676.
corr_author: '1'
date_created: 2019-12-10T15:36:05Z
date_published: 2020-01-08T00:00:00Z
date_updated: 2026-07-06T12:14:33Z
day: '08'
ddc:
- '570'
department:
- _id: EdHa
doi: 10.1021/acs.nanolett.9b04445
external_id:
isi:
- '000507151600087'
pmid:
- '31797672'
intvolume: ' 20'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1021/acs.nanolett.9b04445
month: '01'
oa: 1
oa_version: Published Version
page: 669-676
pmid: 1
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
related_material:
record:
- id: '9726'
relation: research_data
status: public
- id: '9885'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Collective force generation by molecular motors is determined by strain-induced
unbinding
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2020'
...
---
_id: '9713'
abstract:
- lang: eng
text: Additional analyses of the trajectories
article_processing_charge: No
author:
- first_name: Chitrak
full_name: Gupta, Chitrak
last_name: Gupta
- first_name: Umesh
full_name: Khaniya, Umesh
last_name: Khaniya
- first_name: Chun Kit
full_name: Chan, Chun Kit
last_name: Chan
- first_name: Francois
full_name: Dehez, Francois
last_name: Dehez
- first_name: Mrinal
full_name: Shekhar, Mrinal
last_name: Shekhar
- first_name: M.R.
full_name: Gunner, M.R.
last_name: Gunner
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: Abhishek
full_name: Singharoy, Abhishek
last_name: Singharoy
citation:
ama: Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001
apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R.,
… Singharoy, A. (2020). Supporting information. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s001
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar,
M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting
Information.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s001.
ieee: C. Gupta et al., “Supporting information.” American Chemical Society,
2020.
ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Supporting information, American Chemical Society, 10.1021/jacs.9b13450.s001.
mla: Gupta, Chitrak, et al. Supporting Information. American Chemical Society,
2020, doi:10.1021/jacs.9b13450.s001.
short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A.
Sazanov, C. Chipot, A. Singharoy, (2020).
date_created: 2021-07-23T12:02:39Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2026-07-06T12:16:34Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450.s001
month: '05'
oa_version: Published Version
publisher: American Chemical Society
related_material:
record:
- id: '8040'
relation: used_in_publication
status: public
status: public
title: Supporting information
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '9885'
abstract:
- lang: eng
text: Data obtained from the fine-grained simulations used in Figures 2-5, data
obtained from the coarse-grained numerical calculations used in Figure 6, and
a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)
article_processing_charge: No
author:
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Reinhard
full_name: Lipowsky, Reinhard
last_name: Lipowsky
citation:
ama: Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002
apa: Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society.
https://doi.org/10.1021/acs.nanolett.9b04445.s002
chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical
Society, 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002.
ieee: M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society, 2020.
ista: Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society, 10.1021/acs.nanolett.9b04445.s002.
mla: Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical
Society, 2020, doi:10.1021/acs.nanolett.9b04445.s002.
short: M.C. Ucar, R. Lipowsky, (2020).
date_created: 2021-08-11T13:16:03Z
date_published: 2020-01-08T00:00:00Z
date_updated: 2026-07-06T12:14:33Z
day: '08'
department:
- _id: EdHa
doi: 10.1021/acs.nanolett.9b04445.s002
month: '01'
oa_version: Published Version
publisher: American Chemical Society
related_material:
record:
- id: '7166'
relation: used_in_publication
status: public
status: public
title: MURL_Dataz
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
OA_place: publisher
_id: '8155'
abstract:
- lang: eng
text: "In the thesis we focus on the interplay of the biophysics and evolution of
gene regulation. We start by addressing how the type of prokaryotic gene regulation
– activation and repression – affects spurious binding to DNA, also known as\r\ntranscriptional
crosstalk. We propose that regulatory interference caused by excess regulatory
proteins in the dense cellular medium – global crosstalk – could be a factor in
determining which type of gene regulatory network is evolutionarily preferred.
Next,we use a normative approach in eukaryotic gene regulation to describe minimal\r\nnon-equilibrium
enhancer models that optimize so-called regulatory phenotypes. We find a class
of models that differ from standard thermodynamic equilibrium models by a single
parameter that notably increases the regulatory performance. Next chapter addresses
the question of genotype-phenotype-fitness maps of higher dimensional phenotypes.
We show that our biophysically realistic approach allows us to understand how
the mechanisms of promoter function constrain genotypephenotype maps, and how
they affect the evolutionary trajectories of promoters.\r\nIn the last chapter
we ask whether the intrinsic instability of gene duplication and amplification
provides a generic alternative to canonical gene regulation. Using mathematical
modeling, we show that amplifications can tune gene expression in many environments,
including those where transcription factor-based schemes are\r\nhard to evolve
or maintain. "
acknowledgement: For the duration of his PhD, Rok was a recipient of a DOC fellowship
of the Austrian Academy of Sciences.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
citation:
ama: Grah R. Gene regulation across scales – how biophysical constraints shape evolution.
2020. doi:10.15479/AT:ISTA:8155
apa: Grah, R. (2020). Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8155
chicago: Grah, Rok. “Gene Regulation across Scales – How Biophysical Constraints
Shape Evolution.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8155.
ieee: R. Grah, “Gene regulation across scales – how biophysical constraints shape
evolution,” Institute of Science and Technology Austria, 2020.
ista: Grah R. 2020. Gene regulation across scales – how biophysical constraints
shape evolution. Institute of Science and Technology Austria.
mla: Grah, Rok. Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8155.
short: R. Grah, Gene Regulation across Scales – How Biophysical Constraints Shape
Evolution, Institute of Science and Technology Austria, 2020.
corr_author: '1'
date_created: 2020-07-23T09:51:28Z
date_published: 2020-07-24T00:00:00Z
date_updated: 2026-07-06T12:43:42Z
day: '24'
ddc:
- '530'
- '570'
degree_awarded: PhD
department:
- _id: CaGu
- _id: GaTk
doi: 10.15479/AT:ISTA:8155
file:
- access_level: open_access
content_type: application/pdf
creator: rgrah
date_created: 2020-07-27T12:00:07Z
date_updated: 2020-07-27T12:00:07Z
file_id: '8176'
file_name: Thesis_RokGrah_200727_convertedNew.pdf
file_size: 16638998
relation: main_file
success: 1
- access_level: closed
content_type: application/zip
creator: rgrah
date_created: 2020-07-27T12:02:23Z
date_updated: 2020-07-30T13:04:55Z
file_id: '8177'
file_name: Thesis_new.zip
file_size: 347459978
relation: main_file
file_date_updated: 2020-07-30T13:04:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '310'
project:
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7569'
relation: part_of_dissertation
status: public
- id: '7652'
relation: part_of_dissertation
status: public
- id: '7675'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Gene regulation across scales – how biophysical constraints shape evolution
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2020'
...
---
_id: '7675'
abstract:
- lang: eng
text: 'In prokaryotes, thermodynamic models of gene regulation provide a highly
quantitative mapping from promoter sequences to gene expression levels that is
compatible with in vivo and in vitro bio-physical measurements. Such concordance
has not been achieved for models of enhancer function in eukaryotes. In equilibrium
models, it is difficult to reconcile the reported short transcription factor (TF)
residence times on the DNA with the high specificity of regulation. In non-equilibrium
models, progress is difficult due to an explosion in the number of parameters.
Here, we navigate this complexity by looking for minimal non-equilibrium enhancer
models that yield desired regulatory phenotypes: low TF residence time, high specificity
and tunable cooperativity. We find that a single extra parameter, interpretable
as the “linking rate” by which bound TFs interact with Mediator components, enables
our models to escape equilibrium bounds and access optimal regulatory phenotypes,
while remaining consistent with the reported phenomenology and simple enough to
be inferred from upcoming experiments. We further find that high specificity in
non-equilibrium models is in a tradeoff with gene expression noise, predicting
bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription.
By drastically reducing the vast parameter space to a much smaller subspace that
optimally realizes biological function prior to inference from data, our normative
approach holds promise for mathematical models in systems biology.'
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Benjamin
full_name: Zoller, Benjamin
last_name: Zoller
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
biorxivid: 1
citation:
ama: Grah R, Zoller B, Tkačik G. Normative models of enhancer function. bioRxiv.
2020. doi:10.1101/2020.04.08.029405
apa: Grah, R., Zoller, B., & Tkačik, G. (2020). Normative models of enhancer
function. bioRxiv. https://doi.org/10.1101/2020.04.08.029405
chicago: Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer
Function.” BioRxiv, 2020. https://doi.org/10.1101/2020.04.08.029405.
ieee: R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,”
bioRxiv. 2020.
ista: Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv,
10.1101/2020.04.08.029405.
mla: Grah, Rok, et al. “Normative Models of Enhancer Function.” BioRxiv,
2020, doi:10.1101/2020.04.08.029405.
short: R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).
corr_author: '1'
das_tickbox: '1'
date_created: 2020-04-23T10:12:51Z
date_published: 2020-04-09T00:00:00Z
date_updated: 2026-07-06T12:43:43Z
day: '09'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1101/2020.04.08.029405
external_id:
biorxivid:
- 10.1101/2020.04.08.029405
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2020.04.08.029405 '
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
- _id: 267C84F4-B435-11E9-9278-68D0E5697425
name: Biophysically realistic genotype-phenotype maps for regulatory networks
publication: bioRxiv
publication_status: published
related_material:
record:
- id: '8155'
relation: dissertation_contains
status: public
status: public
title: Normative models of enhancer function
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8813'
abstract:
- lang: eng
text: 'In mammals, chromatin marks at imprinted genes are asymmetrically inherited
to control parentally-biased gene expression. This control is thought predominantly
to involve parent-specific differentially methylated regions (DMR) in genomic
DNA. However, neither parent-of-origin-specific transcription nor DMRs have been
comprehensively mapped. We here address this by integrating transcriptomic and
epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis
identified 71 genes expressed with previously unknown parent-of-origin-specific
expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental
expression of nBiX genes disappeared soon after implantation. Micro-whole-genome
bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859
DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated
with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated
imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted
gene, and five novel clusters contained exclusively nBiX-genes. These data suggest
a complex program of stage-specific imprinting involving different tiers of regulation.'
article_processing_charge: No
author:
- first_name: Laura
full_name: Santini, Laura
last_name: Santini
- first_name: Florian
full_name: Halbritter, Florian
last_name: Halbritter
- first_name: Fabian
full_name: Titz-Teixeira, Fabian
last_name: Titz-Teixeira
- first_name: Toru
full_name: Suzuki, Toru
last_name: Suzuki
- first_name: Maki
full_name: Asami, Maki
last_name: Asami
- first_name: Julia
full_name: Ramesmayer, Julia
last_name: Ramesmayer
- first_name: Xiaoyan
full_name: Ma, Xiaoyan
last_name: Ma
- first_name: Andreas
full_name: Lackner, Andreas
last_name: Lackner
- first_name: Nick
full_name: Warr, Nick
last_name: Warr
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Ernest
full_name: Laue, Ernest
last_name: Laue
- first_name: Matthias
full_name: Farlik, Matthias
last_name: Farlik
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Andreas
full_name: Beyer, Andreas
last_name: Beyer
- first_name: Anthony C. F.
full_name: Perry, Anthony C. F.
last_name: Perry
- first_name: Martin
full_name: Leeb, Martin
last_name: Leeb
citation:
ama: Santini L, Halbritter F, Titz-Teixeira F, et al. Novel imprints in mouse blastocysts
are predominantly DNA methylation independent. bioRxiv. doi:10.1101/2020.11.03.366948
apa: Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ramesmayer,
J., … Leeb, M. (n.d.). Novel imprints in mouse blastocysts are predominantly DNA
methylation independent. bioRxiv. https://doi.org/10.1101/2020.11.03.366948
chicago: Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki,
Maki Asami, Julia Ramesmayer, Xiaoyan Ma, et al. “Novel Imprints in Mouse Blastocysts
Are Predominantly DNA Methylation Independent.” BioRxiv, n.d. https://doi.org/10.1101/2020.11.03.366948.
ieee: L. Santini et al., “Novel imprints in mouse blastocysts are predominantly
DNA methylation independent,” bioRxiv. .
ista: Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J,
Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer
A, Perry ACF, Leeb M. Novel imprints in mouse blastocysts are predominantly DNA
methylation independent. bioRxiv, 10.1101/2020.11.03.366948.
mla: Santini, Laura, et al. “Novel Imprints in Mouse Blastocysts Are Predominantly
DNA Methylation Independent.” BioRxiv, doi:10.1101/2020.11.03.366948.
short: L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, J. Ramesmayer,
X. Ma, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C.
Bock, A. Beyer, A.C.F. Perry, M. Leeb, BioRxiv (n.d.).
das_tickbox: '1'
date_created: 2020-11-26T07:17:19Z
date_published: 2020-11-05T00:00:00Z
date_updated: 2026-07-06T12:45:07Z
day: '05'
department:
- _id: SiHi
doi: 10.1101/2020.11.03.366948
external_id:
pmid:
- 'PPR234457 '
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.11.03.366948
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
publication: bioRxiv
publication_status: submitted
status: public
title: Novel imprints in mouse blastocysts are predominantly DNA methylation independent
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7601'
abstract:
- lang: eng
text: Plasmodesmata (PD) are crucial structures for intercellular communication
in multicellular plants with remorins being their crucial plant-specific structural
and functional constituents. The PD biogenesis is an intriguing but poorly understood
process. By expressing an Arabidopsis remorin protein in mammalian cells, we have
reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting
neighboring cells physically and physiologically. Notably, RFs are capable of
transporting macromolecules intercellularly, in a way similar to plant PD. With
further super-resolution microscopic analysis and biochemical characterization,
we found that RFs are also composed of actin filaments, forming the core skeleton
structure, aligned with the remorin protein. This unique heterologous filamentous
structure might explain the molecular mechanism for remorin function as well as
PD construction. Furthermore, remorin protein exhibits a specific distribution
manner in the plasma membrane in mammalian cells, representing a lipid nanodomain,
depending on its lipid modification status. Our studies not only provide crucial
insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental
mechanistic and evolutionary links between intercellular communication systems
of plants and animals.
article_processing_charge: No
author:
- first_name: Zhuang
full_name: Wei, Zhuang
last_name: Wei
- first_name: Shutang
full_name: Tan, Shutang
id: 2DE75584-F248-11E8-B48F-1D18A9856A87
last_name: Tan
orcid: 0000-0002-0471-8285
- first_name: Tao
full_name: Liu, Tao
last_name: Liu
- first_name: Yuan
full_name: Wu, Yuan
last_name: Wu
- first_name: Ji-Gang
full_name: Lei, Ji-Gang
last_name: Lei
- first_name: ZhengJun
full_name: Chen, ZhengJun
last_name: Chen
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Hong-Wei
full_name: Xue, Hong-Wei
last_name: Xue
- first_name: Kan
full_name: Liao, Kan
last_name: Liao
citation:
ama: Wei Z, Tan S, Liu T, et al. Plasmodesmata-like intercellular connections by
plant remorin in animal cells. bioRxiv. 2020. doi:10.1101/791137
apa: Wei, Z., Tan, S., Liu, T., Wu, Y., Lei, J.-G., Chen, Z., … Liao, K. (2020).
Plasmodesmata-like intercellular connections by plant remorin in animal cells.
bioRxiv. https://doi.org/10.1101/791137
chicago: Wei, Zhuang, Shutang Tan, Tao Liu, Yuan Wu, Ji-Gang Lei, ZhengJun Chen,
Jiří Friml, Hong-Wei Xue, and Kan Liao. “Plasmodesmata-like Intercellular Connections
by Plant Remorin in Animal Cells.” BioRxiv, 2020. https://doi.org/10.1101/791137.
ieee: Z. Wei et al., “Plasmodesmata-like intercellular connections by plant
remorin in animal cells,” bioRxiv. 2020.
ista: Wei Z, Tan S, Liu T, Wu Y, Lei J-G, Chen Z, Friml J, Xue H-W, Liao K. 2020.
Plasmodesmata-like intercellular connections by plant remorin in animal cells.
bioRxiv, 10.1101/791137.
mla: Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant
Remorin in Animal Cells.” BioRxiv, 2020, doi:10.1101/791137.
short: Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K.
Liao, BioRxiv (2020).
das_tickbox: '1'
date_created: 2020-03-21T16:34:42Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2026-07-06T12:53:37Z
day: '19'
department:
- _id: JiFr
doi: 10.1101/791137
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/791137
month: '02'
oa: 1
oa_version: Preprint
page: '22'
publication: bioRxiv
publication_status: published
status: public
title: Plasmodesmata-like intercellular connections by plant remorin in animal cells
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...