---
_id: '8570'
abstract:
- lang: eng
text: 'This report presents the results of a friendly competition for formal verification
of continuous and hybrid systems with linear continuous dynamics. The friendly
competition took place as part of the workshop Applied Verification for Continuous
and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been
applied to solve six different benchmark problems in the category for linear continuous
dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx,
and XSpeed. This report is a snapshot of the current landscape of tools and the
types of benchmarks they are particularly suited for. Due to the diversity of
problems, we are not ranking tools, yet the presented results provide one of the
most complete assessments of tools for the safety verification of continuous and
hybrid systems with linear continuous dynamics up to this date.'
article_processing_charge: No
author:
- first_name: Matthias
full_name: Althoff, Matthias
last_name: Althoff
- first_name: Stanley
full_name: Bak, Stanley
last_name: Bak
- first_name: Marcelo
full_name: Forets, Marcelo
last_name: Forets
- first_name: Goran
full_name: Frehse, Goran
last_name: Frehse
- first_name: Niklas
full_name: Kochdumper, Niklas
last_name: Kochdumper
- first_name: Rajarshi
full_name: Ray, Rajarshi
last_name: Ray
- first_name: Christian
full_name: Schilling, Christian
id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87
last_name: Schilling
orcid: 0000-0003-3658-1065
- first_name: Stefan
full_name: Schupp, Stefan
last_name: Schupp
citation:
ama: 'Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous
and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing.
Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w'
apa: 'Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp,
S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear
continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40).
Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w'
chicago: 'Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper,
Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report:
Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series
in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.'
ieee: 'M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid
systems with linear continuous dynamics,” in EPiC Series in Computing,
Montreal, Canada, 2019, vol. 61, pp. 14–40.'
ista: 'Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp
S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear
continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on
Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.'
mla: 'Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid
Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol.
61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.'
short: M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling,
S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40.
conference:
end_date: 2019-04-15
location: Montreal, Canada
name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid
Systems'
start_date: 2019-04-15
corr_author: '1'
date_created: 2020-09-26T14:23:54Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2026-06-18T19:33:41Z
day: '25'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.29007/bj1w
intvolume: ' 61'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://easychair.org/publications/open/1gbP
month: '05'
oa: 1
oa_version: Published Version
page: 14-40
publication: EPiC Series in Computing
publication_identifier:
eissn:
- 2398-7340
publication_status: published
publisher: EasyChair
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous
dynamics'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2019'
...
---
_id: '8693'
abstract:
- lang: eng
text: We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s
Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation
in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp”
asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation).
All constants involved are explicitly computed.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Luigi
full_name: Chierchia, Luigi
last_name: Chierchia
- first_name: Edmond
full_name: Koudjinan, Edmond
id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E
last_name: Koudjinan
orcid: 0000-0003-2640-4049
citation:
ama: Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. Regular
and Chaotic Dynamics. 2019;24:583–606. doi:10.1134/S1560354719060017
apa: Chierchia, L., & Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem.
Regular and Chaotic Dynamics. Springer. https://doi.org/10.1134/S1560354719060017
chicago: Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM
Theorem.” Regular and Chaotic Dynamics. Springer, 2019. https://doi.org/10.1134/S1560354719060017.
ieee: L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” Regular
and Chaotic Dynamics, vol. 24. Springer, pp. 583–606, 2019.
ista: Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular
and Chaotic Dynamics. 24, 583–606.
mla: Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.”
Regular and Chaotic Dynamics, vol. 24, Springer, 2019, pp. 583–606, doi:10.1134/S1560354719060017.
short: L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606.
date_created: 2020-10-21T15:25:45Z
date_published: 2019-12-10T00:00:00Z
date_updated: 2021-01-12T08:20:34Z
day: '10'
doi: 10.1134/S1560354719060017
extern: '1'
external_id:
arxiv:
- '1908.02523'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.02523
month: '12'
oa: 1
oa_version: Preprint
page: 583–606
publication: Regular and Chaotic Dynamics
publication_status: published
publisher: Springer
quality_controlled: '1'
status: public
title: V. I. Arnold’s “pointwise” KAM theorem
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
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
license: https://creativecommons.org/licenses/by/4.0/
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
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
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'
...
---
_id: '9677'
abstract:
- lang: eng
text: Progress in the atomic-scale modeling of matter over the past decade has been
tremendous. This progress has been brought about by improvements in methods for
evaluating interatomic forces that work by either solving the electronic structure
problem explicitly, or by computing accurate approximations of the solution and
by the development of techniques that use the Born–Oppenheimer (BO) forces to
move the atoms on the BO potential energy surface. As a consequence of these developments
it is now possible to identify stable or metastable states, to sample configurations
consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics
of reactions and phase transitions. All too often, however, progress is slowed
down by the bottleneck associated with implementing new optimization algorithms
and/or sampling techniques into the many existing electronic-structure and empirical-potential
codes. To address this problem, we are thus releasing a new version of the i-PI
software. This piece of software is an easily extensible framework for implementing
advanced atomistic simulation techniques using interatomic potentials and forces
calculated by an external driver code. While the original version of the code
(Ceriotti et al., 2014) was developed with a focus on path integral molecular
dynamics techniques, this second release of i-PI not only includes several new
advanced path integral methods, but also offers other classes of algorithms. In
other words, i-PI is moving towards becoming a universal force engine that is
both modular and tightly coupled to the driver codes that evaluate the potential
energy surface and its derivatives.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Venkat
full_name: Kapil, Venkat
last_name: Kapil
- first_name: Mariana
full_name: Rossi, Mariana
last_name: Rossi
- first_name: Ondrej
full_name: Marsalek, Ondrej
last_name: Marsalek
- first_name: Riccardo
full_name: Petraglia, Riccardo
last_name: Petraglia
- first_name: Yair
full_name: Litman, Yair
last_name: Litman
- first_name: Thomas
full_name: Spura, Thomas
last_name: Spura
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Alice
full_name: Cuzzocrea, Alice
last_name: Cuzzocrea
- first_name: Robert H.
full_name: Meißner, Robert H.
last_name: Meißner
- first_name: David M.
full_name: Wilkins, David M.
last_name: Wilkins
- first_name: Benjamin A.
full_name: Helfrecht, Benjamin A.
last_name: Helfrecht
- first_name: Przemysław
full_name: Juda, Przemysław
last_name: Juda
- first_name: Sébastien P.
full_name: Bienvenue, Sébastien P.
last_name: Bienvenue
- first_name: Wei
full_name: Fang, Wei
last_name: Fang
- first_name: Jan
full_name: Kessler, Jan
last_name: Kessler
- first_name: Igor
full_name: Poltavsky, Igor
last_name: Poltavsky
- first_name: Steven
full_name: Vandenbrande, Steven
last_name: Vandenbrande
- first_name: Jelle
full_name: Wieme, Jelle
last_name: Wieme
- first_name: Clemence
full_name: Corminboeuf, Clemence
last_name: Corminboeuf
- first_name: Thomas D.
full_name: Kühne, Thomas D.
last_name: Kühne
- first_name: David E.
full_name: Manolopoulos, David E.
last_name: Manolopoulos
- first_name: Thomas E.
full_name: Markland, Thomas E.
last_name: Markland
- first_name: Jeremy O.
full_name: Richardson, Jeremy O.
last_name: Richardson
- first_name: Alexandre
full_name: Tkatchenko, Alexandre
last_name: Tkatchenko
- first_name: Gareth A.
full_name: Tribello, Gareth A.
last_name: Tribello
- first_name: Veronique
full_name: Van Speybroeck, Veronique
last_name: Van Speybroeck
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: 'Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for
advanced molecular simulations. Computer Physics Communications. 2019;236:214-223.
doi:10.1016/j.cpc.2018.09.020'
apa: 'Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T.,
… Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular
simulations. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.09.020'
chicago: 'Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair
Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine
for Advanced Molecular Simulations.” Computer Physics Communications. Elsevier,
2019. https://doi.org/10.1016/j.cpc.2018.09.020.'
ieee: 'V. Kapil et al., “i-PI 2.0: A universal force engine for advanced
molecular simulations,” Computer Physics Communications, vol. 236. Elsevier,
pp. 214–223, 2019.'
ista: 'Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea
A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler
J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos
DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti
M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations.
Computer Physics Communications. 236, 214–223.'
mla: 'Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular
Simulations.” Computer Physics Communications, vol. 236, Elsevier, 2019,
pp. 214–23, doi:10.1016/j.cpc.2018.09.020.'
short: V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng,
A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue,
W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf,
T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko,
G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications
236 (2019) 214–223.
date_created: 2021-07-16T08:53:01Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2021-08-09T12:37:16Z
day: '01'
doi: 10.1016/j.cpc.2018.09.020
extern: '1'
external_id:
arxiv:
- '1808.03824'
intvolume: ' 236'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1808.03824
month: '03'
oa: 1
oa_version: Preprint
page: 214-223
publication: Computer Physics Communications
publication_identifier:
issn:
- 0010-4655
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'i-PI 2.0: A universal force engine for advanced molecular simulations'
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 236
year: '2019'
...
---
_id: '9680'
abstract:
- lang: eng
text: Atomistic modeling of phase transitions, chemical reactions, or other rare
events that involve overcoming high free energy barriers usually entails prohibitively
long simulation times. Introducing a bias potential as a function of an appropriately
chosen set of collective variables can significantly accelerate the exploration
of phase space, albeit at the price of distorting the distribution of microstates.
Efficient reweighting to recover the unbiased distribution can be nontrivial when
employing adaptive sampling techniques such as metadynamics, variationally enhanced
sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium
manner under a time-dependent bias. We introduce an iterative unbiasing scheme
that makes efficient use of all the trajectory data and that does not require
the distribution to be evaluated on a grid. The method can thus be used even when
the bias has a high dimensionality. We benchmark this approach against some of
the existing schemes on model systems with different complexity and dimensionality.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: F.
full_name: Giberti, F.
last_name: Giberti
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: G. A.
full_name: Tribello, G. A.
last_name: Tribello
- first_name: M.
full_name: Ceriotti, M.
last_name: Ceriotti
citation:
ama: Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium
sampling. Journal of Chemical Theory and Computation. 2019;16(1):100-107.
doi:10.1021/acs.jctc.9b00907
apa: Giberti, F., Cheng, B., Tribello, G. A., & Ceriotti, M. (2019). Iterative
unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation.
American Chemical Society. https://doi.org/10.1021/acs.jctc.9b00907
chicago: Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative
Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation.
American Chemical Society, 2019. https://doi.org/10.1021/acs.jctc.9b00907.
ieee: F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing
of quasi-equilibrium sampling,” Journal of Chemical Theory and Computation,
vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019.
ista: Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of
quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1),
100–107.
mla: Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal
of Chemical Theory and Computation, vol. 16, no. 1, American Chemical Society,
2019, pp. 100–07, doi:10.1021/acs.jctc.9b00907.
short: F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory
and Computation 16 (2019) 100–107.
date_created: 2021-07-19T06:56:45Z
date_published: 2019-01-14T00:00:00Z
date_updated: 2021-08-09T12:37:37Z
day: '14'
doi: 10.1021/acs.jctc.9b00907
extern: '1'
external_id:
arxiv:
- '1911.01140'
pmid:
- '31743021'
intvolume: ' 16'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1911.01140
month: '01'
oa: 1
oa_version: Preprint
page: 100-107
pmid: 1
publication: Journal of Chemical Theory and Computation
publication_identifier:
eissn:
- 1549-9626
issn:
- 1549-9618
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Iterative unbiasing of quasi-equilibrium sampling
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 16
year: '2019'
...
---
_id: '9689'
abstract:
- lang: eng
text: A central goal of computational physics and chemistry is to predict material
properties by using first-principles methods based on the fundamental laws of
quantum mechanics. However, the high computational costs of these methods typically
prevent rigorous predictions of macroscopic quantities at finite temperatures,
such as heat capacity, density, and chemical potential. Here, we enable such predictions
by marrying advanced free-energy methods with data-driven machine-learning interatomic
potentials. We show that, for the ubiquitous and technologically essential system
of water, a first-principles thermodynamic description not only leads to excellent
agreement with experiments, but also reveals the crucial role of nuclear quantum
fluctuations in modulating the thermodynamic stabilities of different phases of
water.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
- first_name: Edgar A.
full_name: Engel, Edgar A.
last_name: Engel
- first_name: Jörg
full_name: Behler, Jörg
last_name: Behler
- first_name: Christoph
full_name: Dellago, Christoph
last_name: Dellago
- first_name: Michele
full_name: Ceriotti, Michele
last_name: Ceriotti
citation:
ama: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences.
2019;116(4):1110-1115. doi:10.1073/pnas.1815117116
apa: Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019).
Ab initio thermodynamics of liquid and solid water. Proceedings of the National
Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116
chicago: Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele
Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116.
ieee: B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio
thermodynamics of liquid and solid water,” Proceedings of the National Academy
of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115,
2019.
ista: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics
of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4),
1110–1115.
mla: Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.”
Proceedings of the National Academy of Sciences, vol. 116, no. 4, National
Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116.
short: B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of
the National Academy of Sciences 116 (2019) 1110–1115.
date_created: 2021-07-19T10:17:09Z
date_published: 2019-01-22T00:00:00Z
date_updated: 2023-02-23T14:05:08Z
day: '22'
doi: 10.1073/pnas.1815117116
extern: '1'
external_id:
arxiv:
- '1811.08630'
pmid:
- '30610171'
intvolume: ' 116'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1815117116
month: '01'
oa: 1
oa_version: Published Version
page: 1110-1115
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: Ab initio thermodynamics of liquid and solid water
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 116
year: '2019'
...
---
_id: '9726'
abstract:
- lang: eng
text: A detailed description of the two stochastic models, table of parameters,
supplementary data for Figures 4 and 5, parameter dependence of the results, and
an analysis on motors with different force–velocity functions (PDF)
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. Supplementary information - Collective force generation
by molecular motors is determined by strain-induced unbinding. 2019. doi:10.1021/acs.nanolett.9b04445.s001
apa: Ucar, M. C., & Lipowsky, R. (2019). Supplementary information - Collective
force generation by molecular motors is determined by strain-induced unbinding.
American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s001
chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Supplementary Information - Collective
Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.”
American Chemical Society , 2019. https://doi.org/10.1021/acs.nanolett.9b04445.s001.
ieee: M. C. Ucar and R. Lipowsky, “Supplementary information - Collective force
generation by molecular motors is determined by strain-induced unbinding.” American
Chemical Society , 2019.
ista: Ucar MC, Lipowsky R. 2019. Supplementary information - Collective force generation
by molecular motors is determined by strain-induced unbinding, American Chemical
Society , 10.1021/acs.nanolett.9b04445.s001.
mla: Ucar, Mehmet C., and Reinhard Lipowsky. Supplementary Information - Collective
Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.
American Chemical Society , 2019, doi:10.1021/acs.nanolett.9b04445.s001.
short: M.C. Ucar, R. Lipowsky, (2019).
date_created: 2021-07-27T09:51:46Z
date_published: 2019-12-19T00:00:00Z
date_updated: 2026-06-18T19:17:32Z
day: '19'
department:
- _id: EdHa
doi: 10.1021/acs.nanolett.9b04445.s001
month: '12'
oa_version: Published Version
publisher: 'American Chemical Society '
related_material:
record:
- id: '7166'
relation: used_in_publication
status: public
status: public
title: Supplementary information - Collective force generation by molecular motors
is determined by strain-induced unbinding
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9731'
abstract:
- lang: eng
text: OGs with putative pseudogenes by the number of affected genomes in different
chlamydial species. Frameshift and nonsense mutations located less than 60 bp
upstreamof the gene end or present in a single genome from the corresponding OG
were excluded. (CSV 31 kb)
article_processing_charge: No
author:
- first_name: Olga
full_name: Sigalova, Olga
last_name: Sigalova
- first_name: Andrei
full_name: Chaplin, Andrei
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel
full_name: Shelyakin, Pavel
last_name: Shelyakin
- first_name: Vsevolod
full_name: Filaretov, Vsevolod
last_name: Filaretov
- first_name: Evgeny
full_name: Akkuratov, Evgeny
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1
apa: Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov,
E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction.
Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1
chicago: Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod
Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional
File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation
and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1.
ieee: O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction.”
Springer Nature, 2019.
ista: Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E,
Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808772.v1.
mla: Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1.
short: O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov,
V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-07-27T14:09:11Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808772.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808772.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 11 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9783'
abstract:
- lang: eng
text: Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For
the analysis of putative pseudogenes, events located less than 60 bp. away from
gene end or present in a single genome from the corresponding OG were excluded.
(CSV 600 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808760.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1.
ieee: O. M. Sigalova et al., “Additional file 10 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1.
mla: Sigalova, Olga M., et al. Additional File 10 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808760.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-06T07:59:56Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
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department:
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doi: 10.6084/m9.figshare.9808760.v1
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month: '09'
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---
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abstract:
- lang: eng
text: 'Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either
the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1
of seeding flasks and following 6-days of continuous culture. Note: no differences
in cell numbers were observed between negative control and glyphosate treated
cultures.'
article_processing_charge: No
author:
- first_name: Michael N.
full_name: Antoniou, Michael N.
last_name: Antoniou
- first_name: Armel
full_name: Nicolas, Armel
id: 2A103192-F248-11E8-B48F-1D18A9856A87
last_name: Nicolas
- first_name: Robin
full_name: Mesnage, Robin
last_name: Mesnage
- first_name: Martina
full_name: Biserni, Martina
last_name: Biserni
- first_name: Francesco V.
full_name: Rao, Francesco V.
last_name: Rao
- first_name: Cristina Vazquez
full_name: Martin, Cristina Vazquez
last_name: Martin
citation:
ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of
Glyphosate does not substitute for glycine in proteins of actively dividing mammalian
cells. 2019. doi:10.6084/m9.figshare.9411761.v1
apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin,
C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins
of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1
chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco
V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute
for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature,
2019. https://doi.org/10.6084/m9.figshare.9411761.v1.
ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin,
“MOESM1 of Glyphosate does not substitute for glycine in proteins of actively
dividing mammalian cells.” Springer Nature, 2019.
ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1
of Glyphosate does not substitute for glycine in proteins of actively dividing
mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1.
mla: Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for
Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature,
2019, doi:10.6084/m9.figshare.9411761.v1.
short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin,
(2019).
date_created: 2021-08-06T08:14:05Z
date_published: 2019-08-09T00:00:00Z
date_updated: 2023-02-23T12:52:29Z
day: '09'
department:
- _id: LifeSc
doi: 10.6084/m9.figshare.9411761.v1
main_file_link:
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url: https://doi.org/10.6084/m9.figshare.9411761.v1
month: '08'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
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status: public
title: MOESM1 of Glyphosate does not substitute for glycine in proteins of actively
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---
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article_processing_charge: No
author:
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full_name: Ruess, Jakob
id: 4A245D00-F248-11E8-B48F-1D18A9856A87
last_name: Ruess
orcid: 0000-0003-1615-3282
- first_name: Maros
full_name: Pleska, Maros
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last_name: Pleska
orcid: 0000-0001-7460-7479
- 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
citation:
ama: Ruess J, Pleska M, Guet CC, Tkačik G. Supporting text and results. 2019. doi:10.1371/journal.pcbi.1007168.s001
apa: Ruess, J., Pleska, M., Guet, C. C., & Tkačik, G. (2019). Supporting text
and results. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007168.s001
chicago: Ruess, Jakob, Maros Pleska, Calin C Guet, and Gašper Tkačik. “Supporting
Text and Results.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007168.s001.
ieee: J. Ruess, M. Pleska, C. C. Guet, and G. Tkačik, “Supporting text and results.”
Public Library of Science, 2019.
ista: Ruess J, Pleska M, Guet CC, Tkačik G. 2019. Supporting text and results, Public
Library of Science, 10.1371/journal.pcbi.1007168.s001.
mla: Ruess, Jakob, et al. Supporting Text and Results. Public Library of
Science, 2019, doi:10.1371/journal.pcbi.1007168.s001.
short: J. Ruess, M. Pleska, C.C. Guet, G. Tkačik, (2019).
date_created: 2021-08-06T08:23:43Z
date_published: 2019-07-02T00:00:00Z
date_updated: 2025-04-15T07:33:55Z
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department:
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doi: 10.1371/journal.pcbi.1007168.s001
month: '07'
oa_version: Published Version
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---
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author:
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full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
orcid: 0000-0002-8224-4118
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
orcid: 0000-0002-7840-5062
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3
orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues.
Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple
Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010.
ieee: V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public
Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library
of Science, 10.1371/journal.pgen.1008079.s010.
mla: Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues.
Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:38:50Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2026-04-03T09:45:18Z
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department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s010
month: '04'
oa_version: Published Version
publisher: Public Library of Science
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