---
_id: '9445'
abstract:
- lang: eng
text: Cytosine methylation regulates essential genome functions across eukaryotes,
but the fundamental question of whether nucleosomal or naked DNA is the preferred
substrate of plant and animal methyltransferases remains unresolved. Here, we
show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler
biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana
and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome,
suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases
in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone
H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of
species that diverged from flowering plants and animals over a billion years ago.
Our results indicate that in the absence of remodeling, nucleosomes are strong
barriers to DNA methyltransferases. Linker-specific methylation can evolve simply
by breaking the connection between nucleosome remodeling and DNA methylation.
article_number: e30674
article_processing_charge: No
article_type: original
author:
- first_name: David B
full_name: Lyons, David B
last_name: Lyons
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped
in nucleosomes. eLife. 2017;6. doi:10.7554/elife.30674
apa: Lyons, D. B., & Zilberman, D. (2017). DDM1 and Lsh remodelers allow methylation
of DNA wrapped in nucleosomes. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.30674
chicago: Lyons, David B, and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30674.
ieee: D. B. Lyons and D. Zilberman, “DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes,” eLife, vol. 6. eLife Sciences Publications,
2017.
ista: Lyons DB, Zilberman D. 2017. DDM1 and Lsh remodelers allow methylation of
DNA wrapped in nucleosomes. eLife. 6, e30674.
mla: Lyons, David B., and Daniel Zilberman. “DDM1 and Lsh Remodelers Allow Methylation
of DNA Wrapped in Nucleosomes.” ELife, vol. 6, e30674, eLife Sciences Publications,
2017, doi:10.7554/elife.30674.
short: D.B. Lyons, D. Zilberman, ELife 6 (2017).
date_created: 2021-06-02T14:28:58Z
date_published: 2017-11-15T00:00:00Z
date_updated: 2021-12-14T07:54:36Z
day: '15'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.7554/elife.30674
extern: '1'
external_id:
pmid:
- '29140247'
file:
- access_level: open_access
checksum: 4cfcdd67511ae4aed3d993550e46e146
content_type: application/pdf
creator: cziletti
date_created: 2021-06-02T14:33:36Z
date_updated: 2021-06-02T14:33:36Z
file_id: '9446'
file_name: 2017_eLife_Lyons.pdf
file_size: 1603102
relation: main_file
success: 1
file_date_updated: 2021-06-02T14:33:36Z
fulldoi: https://doi.org/10.7554/elife.30674
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes
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: 6
year: '2017'
...
---
_id: '945'
abstract:
- lang: eng
text: While chromosome-wide dosage compensation of the X chromosome has been found
in many species, studies in ZW clades have indicated that compensation of the
Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show
complete compensation of the Z chromosome, while others lack full equalization,
but what drives these inconsistencies is unclear. Here, we compare patterns of
male and female gene expression on the Z chromosome of two closely related butterfly
species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths
species, Plodia interpunctella and Bombyx mori, which were previously found to
differ in the extent to which they equalize Z-linked gene expression between the
sexes. We find that, while some species and tissues seem to have incomplete dosage
compensation, this is in fact due to the accumulation of male-biased genes and
the depletion of female-biased genes on the Z chromosome. Once this is accounted
for, the Z chromosome is fully compensated in all four species, through the up-regulation
of Z expression in females and in some cases additional down-regulation in males.
We further find that both sex-biased genes and Z-linked genes have increased rates
of expression divergence in this clade, and that this can lead to fast shifts
in patterns of gene expression even between closely related species. Taken together,
these results show that the uneven distribution of sex-biased genes on sex chromosomes
can confound conclusions about dosage compensation and that Z chromosome-wide
dosage compensation is not only possible but ubiquitous among Lepidoptera.
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in
Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular
Biology and Evolution. 2017;34(10):2637-2649. doi:10.1093/molbev/msx190
apa: Huylmans, A. K., Macon, A., & Vicoso, B. (2017). Global dosage compensation
is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z
chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msx190
chicago: Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation
Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z
Chromosome.” Molecular Biology and Evolution. Oxford University Press,
2017. https://doi.org/10.1093/molbev/msx190.
ieee: A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous
in Lepidoptera, but counteracted by the masculinization of the Z chromosome,”
Molecular Biology and Evolution, vol. 34, no. 10. Oxford University Press,
pp. 2637–2649, 2017.
ista: Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous
in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular
Biology and Evolution. 34(10), 2637–2649.
mla: Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera,
but Counteracted by the Masculinization of the Z Chromosome.” Molecular Biology
and Evolution, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49,
doi:10.1093/molbev/msx190.
short: A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017)
2637–2649.
date_created: 2018-12-11T11:49:20Z
date_published: 2017-07-06T00:00:00Z
date_updated: 2026-04-16T09:58:19Z
day: '06'
ddc:
- '570'
- '576'
department:
- _id: BeVi
doi: 10.1093/molbev/msx190
external_id:
isi:
- '000411814800016'
file:
- access_level: open_access
checksum: 009fd68043211d645ceb9d1de28274f2
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:23Z
date_updated: 2020-07-14T12:48:15Z
file_id: '4810'
file_name: IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf
file_size: 462863
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
fulldoi: https://doi.org/10.1093/molbev/msx190
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '10'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 2637 - 2649
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular Biology and Evolution
publication_identifier:
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '6472'
pubrep_id: '848'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by
the masculinization of the Z chromosome
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 34
year: '2017'
...
---
_id: '946'
abstract:
- lang: eng
text: Roots navigate through soil integrating environmental signals to orient their
growth. The Arabidopsis root is a widely used model for developmental, physiological
and cell biological studies. Live imaging greatly aids these efforts, but the
horizontal sample position and continuous root tip displacement present significant
difficulties. Here, we develop a confocal microscope setup for vertical sample
mounting and integrated directional illumination. We present TipTracker – a custom
software for automatic tracking of diverse moving objects usable on various microscope
setups. Combined, this enables observation of root tips growing along the natural
gravity vector over prolonged periods of time, as well as the ability to induce
rapid gravity or light stimulation. We also track migrating cells in the developing
zebrafish embryo, demonstrating the utility of this system in the acquisition
of high-resolution data sets of dynamic samples. We provide detailed descriptions
of the tools enabling the easy implementation on other microscopes.
acknowledged_ssus:
- _id: M-Shop
- _id: Bio
acknowledgement: "Funding: Marie Curie Actions (FP7/2007-2013 no 291734) to Daniel
von Wangenheim; Austrian Science Fund (M 2128-B21) to Matyáš Fendrych; Austrian
Science Fund (FWF01_I1774S) to Eva Benková; European Research Council (FP7/2007-2013
no 282300) to Jiří Friml. \r\nThe authors are grateful to the Miba Machine Shop
at IST Austria for their contribution to the microscope setup and to Yvonne Kemper
for reading, understanding and correcting the manuscript.\r\n#BioimagingFacility"
article_number: e26792
article_processing_charge: Yes
author:
- first_name: Daniel
full_name: Von Wangenheim, Daniel
id: 49E91952-F248-11E8-B48F-1D18A9856A87
last_name: Von Wangenheim
orcid: 0000-0002-6862-1247
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Matyas
full_name: Fendrych, Matyas
id: 43905548-F248-11E8-B48F-1D18A9856A87
last_name: Fendrych
orcid: 0000-0002-9767-8699
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. Live
tracking of moving samples in confocal microscopy for vertically grown roots.
eLife. 2017;6. doi:10.7554/eLife.26792
apa: von Wangenheim, D., Hauschild, R., Fendrych, M., Barone, V., Benková, E., &
Friml, J. (2017). Live tracking of moving samples in confocal microscopy for vertically
grown roots. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.26792
chicago: Wangenheim, Daniel von, Robert Hauschild, Matyas Fendrych, Vanessa Barone,
Eva Benková, and Jiří Friml. “Live Tracking of Moving Samples in Confocal Microscopy
for Vertically Grown Roots.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/eLife.26792.
ieee: D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, and J.
Friml, “Live tracking of moving samples in confocal microscopy for vertically
grown roots,” eLife, vol. 6. eLife Sciences Publications, 2017.
ista: von Wangenheim D, Hauschild R, Fendrych M, Barone V, Benková E, Friml J. 2017.
Live tracking of moving samples in confocal microscopy for vertically grown roots.
eLife. 6, e26792.
mla: von Wangenheim, Daniel, et al. “Live Tracking of Moving Samples in Confocal
Microscopy for Vertically Grown Roots.” ELife, vol. 6, e26792, eLife Sciences
Publications, 2017, doi:10.7554/eLife.26792.
short: D. von Wangenheim, R. Hauschild, M. Fendrych, V. Barone, E. Benková, J. Friml,
ELife 6 (2017).
date_created: 2018-12-11T11:49:21Z
date_published: 2017-06-19T00:00:00Z
date_updated: 2025-04-15T06:37:26Z
day: '19'
ddc:
- '570'
department:
- _id: JiFr
- _id: Bio
- _id: CaHe
- _id: EvBe
doi: 10.7554/eLife.26792
ec_funded: 1
external_id:
isi:
- '000404728300001'
file:
- access_level: open_access
checksum: 9af3398cb0d81f99d79016a616df22e9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:57Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5315'
file_name: IST-2017-847-v1+1_elife-26792-v2.pdf
file_size: 19581847
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
fulldoi: https://doi.org/10.7554/eLife.26792
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2572ED28-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02128
name: Molecular basis of root growth inhibition by auxin
- _id: 2542D156-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I 1774-B16
name: Hormone cross-talk drives nutrient dependent plant development
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6471'
pubrep_id: '847'
quality_controlled: '1'
related_material:
record:
- id: '5566'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Live tracking of moving samples in confocal microscopy for vertically grown
roots
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2017'
...
---
_id: '950'
abstract:
- lang: eng
text: "Two-player games on graphs are widely studied in formal methods as they model
the interaction between a system and its environment. The game is played by moving
a token throughout a graph to produce an infinite path. There are several common
modes to determine how the players move the token through the graph; e.g., in
turn-based games the players alternate turns in moving the token. We study the
bidding mode of moving the token, which, to the best of our knowledge, has never
been studied in infinite-duration games. Both players have separate budgets, which
sum up to $1$. In each turn, a bidding takes place. Both players submit bids simultaneously,
and a bid is legal if it does not exceed the available budget. The winner of the
bidding pays his bid to the other player and moves the token. For reachability
objectives, repeated bidding games have been studied and are called Richman games.
There, a central question is the existence and computation of threshold budgets;
namely, a value t\\in [0,1] such that if\\PO's budget exceeds $t$, he can win
the game, and if\\PT's budget exceeds 1-t, he can win the game. We focus on parity
games and mean-payoff games. We show the existence of threshold budgets in these
games, and reduce the problem of finding them to Richman games. We also determine
the strategy-complexity of an optimal strategy. Our most interesting result shows
that memoryless strategies suffice for mean-payoff bidding games. \r\n"
alternative_title:
- LIPIcs
article_number: '17'
arxiv: 1
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ventsislav K
full_name: Chonev, Ventsislav K
id: 36CBE2E6-F248-11E8-B48F-1D18A9856A87
last_name: Chonev
citation:
ama: 'Avni G, Henzinger TA, Chonev VK. Infinite-duration bidding games. In: Vol
85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.CONCUR.2017.21'
apa: 'Avni, G., Henzinger, T. A., & Chonev, V. K. (2017). Infinite-duration
bidding games (Vol. 85). Presented at the CONCUR: Concurrency Theory, Berlin,
Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2017.21'
chicago: Avni, Guy, Thomas A Henzinger, and Ventsislav K Chonev. “Infinite-Duration
Bidding Games,” Vol. 85. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.
https://doi.org/10.4230/LIPIcs.CONCUR.2017.21.
ieee: 'G. Avni, T. A. Henzinger, and V. K. Chonev, “Infinite-duration bidding games,”
presented at the CONCUR: Concurrency Theory, Berlin, Germany, 2017, vol. 85.'
ista: 'Avni G, Henzinger TA, Chonev VK. 2017. Infinite-duration bidding games. CONCUR:
Concurrency Theory, LIPIcs, vol. 85, 17.'
mla: Avni, Guy, et al. Infinite-Duration Bidding Games. Vol. 85, 17, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.CONCUR.2017.21.
short: G. Avni, T.A. Henzinger, V.K. Chonev, in:, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2017.
conference:
end_date: 2017-09-07
location: Berlin, Germany
name: 'CONCUR: Concurrency Theory'
start_date: 2017-09-05
date_created: 2018-12-11T11:49:22Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2025-07-10T11:53:48Z
day: '01'
ddc:
- '000'
department:
- _id: ToHe
- _id: KrCh
doi: 10.4230/LIPIcs.CONCUR.2017.21
external_id:
arxiv:
- '1705.01433'
file:
- access_level: open_access
checksum: 6d5cccf755207b91ccbef95d8275b013
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:18:00Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5318'
file_name: IST-2017-844-v1+1_concur-cr.pdf
file_size: 335170
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
fulldoi: https://doi.org/10.4230/LIPIcs.CONCUR.2017.21
has_accepted_license: '1'
intvolume: ' 85'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6466'
pubrep_id: '844'
quality_controlled: '1'
related_material:
record:
- id: '6752'
relation: later_version
status: public
scopus_import: 1
status: public
title: Infinite-duration bidding games
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 85
year: '2017'
...
---
_id: '9506'
abstract:
- lang: eng
text: Methylation in the bodies of active genes is common in animals and vascular
plants. Evolutionary patterns indicate homeostatic functions for this type of
methylation.
article_number: '87'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. An evolutionary case for functional gene body methylation in plants
and animals. Genome Biology. 2017;18(1). doi:10.1186/s13059-017-1230-2
apa: Zilberman, D. (2017). An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-017-1230-2
chicago: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology. Springer Nature, 2017. https://doi.org/10.1186/s13059-017-1230-2.
ieee: D. Zilberman, “An evolutionary case for functional gene body methylation in
plants and animals,” Genome Biology, vol. 18, no. 1. Springer Nature, 2017.
ista: Zilberman D. 2017. An evolutionary case for functional gene body methylation
in plants and animals. Genome Biology. 18(1), 87.
mla: Zilberman, Daniel. “An Evolutionary Case for Functional Gene Body Methylation
in Plants and Animals.” Genome Biology, vol. 18, no. 1, 87, Springer Nature,
2017, doi:10.1186/s13059-017-1230-2.
short: D. Zilberman, Genome Biology 18 (2017).
date_created: 2021-06-07T12:27:39Z
date_published: 2017-05-09T00:00:00Z
date_updated: 2021-12-14T07:55:02Z
day: '09'
ddc:
- '570'
department:
- _id: DaZi
doi: 10.1186/s13059-017-1230-2
extern: '1'
external_id:
pmid:
- '28486944'
file:
- access_level: open_access
checksum: 5a455ad914e7d225b1baa4ab07fd925e
content_type: application/pdf
creator: asandaue
date_created: 2021-06-07T12:31:36Z
date_updated: 2021-06-07T12:31:36Z
file_id: '9507'
file_name: 2017_GenomeBiology_Zilberman.pdf
file_size: 278183
relation: main_file
success: 1
file_date_updated: 2021-06-07T12:31:36Z
fulldoi: https://doi.org/10.1186/s13059-017-1230-2
has_accepted_license: '1'
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: An evolutionary case for functional gene body methylation in plants and animals
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: 18
year: '2017'
...
---
_id: '952'
abstract:
- lang: eng
text: A novel strategy for controlling the spread of arboviral diseases such as
dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing
Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness
costs through lower viability or fecundity. These maternally inherited bacteria
also produce a frequency-dependent advantage for infected females by inducing
cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected
females mated to infected males. These competing effects, a frequency-dependent
advantage and frequency-independent costs, produce bistable Wolbachia frequency
dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing
Wolbachia transinfections through local populations; but below pˆ, infection frequencies
tend to decline to zero. If pˆ is not too high, CI also drives spatial spread
once infections become established over sufficiently large areas. We illustrate
how simple models provide testable predictions concerning the spatial and temporal
dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape
of spreading waves, and the conditions for initiating spread from local introductions.
First, we consider the robustness of diffusion-based predictions to incorporating
two important features of wMel-Aedes aegypti biology that may be inconsistent
with the diffusion approximations, namely fast local dynamics induced by complete
CI (i.e., all embryos produced from incompatible crosses die) and long-tailed,
non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed
dispersal changes wave-width predictions only slightly; but it can significantly
reduce wave speed relative to the diffusion prediction; it also allows smaller
local introductions to initiate spatial spread. Second, we use approximations
for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected
Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti
populations near Cairns, Australia that demonstrate long-distance dispersal and
provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally,
we apply our analyses to produce operational guidelines for efficient transformation
of vector populations over large areas. We demonstrate that even very slow spatial
spread, on the order of 10-20 m/month (as predicted), can produce area-wide population
transformation within a few years following initial releases covering about 20-30%
of the target area.
article_processing_charge: No
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models
predict slow but effective spatial spread in Aedes aegypti. Theoretical Population
Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003'
apa: 'Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia:
Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing
Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.”
Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.'
ieee: 'M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti,” Theoretical
Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.'
ista: 'Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. 115, 45–60.'
mla: 'Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia:
Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical
Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.'
short: M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.
date_created: 2018-12-11T11:49:22Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-07-10T12:01:49Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.03.003
external_id:
pmid:
- '28411063'
file:
- access_level: open_access
checksum: 9aeff86fa7de69f7a15cf4fc60d57d01
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T06:39:45Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6327'
file_name: 2017_TheoreticalPopulationBio_Turelli.pdf
file_size: 2073856
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
fulldoi: https://doi.org/10.1016/j.tpb.2017.03.003
has_accepted_license: '1'
intvolume: ' 115'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
oa: 1
oa_version: Submitted Version
page: 45 - 60
pmid: 1
publication: Theoretical Population Biology
publication_identifier:
issn:
- 0040-5809
publication_status: published
publisher: Elsevier
publist_id: '6463'
pubrep_id: '972'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective
spatial spread in Aedes aegypti'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
year: '2017'
...
---
_id: '954'
abstract:
- lang: eng
text: Understanding the relation between genotype and phenotype remains a major
challenge. The difficulty of predicting individual mutation effects, and particularly
the interactions between them, has prevented the development of a comprehensive
theory that links genotypic changes to their phenotypic effects. We show that
a general thermodynamic framework for gene regulation, based on a biophysical
understanding of protein-DNA binding, accurately predicts the sign of epistasis
in a canonical cis-regulatory element consisting of overlapping RNA polymerase
and repressor binding sites. Sign and magnitude of individual mutation effects
are sufficient to predict the sign of epistasis and its environmental dependence.
Thus, the thermodynamic model offers the correct null prediction for epistasis
between mutations across DNA-binding sites. Our results indicate that a predictive
theory for the effects of cis-regulatory mutations is possible from first principles,
as long as the essential molecular mechanisms and the constraints these impose
on a biological system are accounted for.
article_number: e25192
article_processing_charge: Yes
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature
of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C.
(2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and
Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory
Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.
ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the
mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic
nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical
Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications,
2017, doi:10.7554/eLife.25192.
short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2025-07-10T12:01:50Z
day: '18'
ddc:
- '576'
department:
- _id: CaGu
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.25192
ec_funded: 1
external_id:
isi:
- '000404024800001'
file:
- access_level: open_access
checksum: 59cdd4400fb41280122d414fea971546
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:49Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5306'
file_name: IST-2017-841-v1+1_elife-25192-v2.pdf
file_size: 2441529
relation: main_file
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checksum: b69024880558b858eb8c5d47a92b6377
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:50Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5307'
file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf
file_size: 3752660
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
fulldoi: https://doi.org/10.7554/eLife.25192
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6460'
pubrep_id: '841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mechanistic nature of epistasis in a canonical cis-regulatory element
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '955'
abstract:
- lang: eng
text: 'Gene expression is controlled by networks of regulatory proteins that interact
specifically with external signals and DNA regulatory sequences. These interactions
force the network components to co-evolve so as to continually maintain function.
Yet, existing models of evolution mostly focus on isolated genetic elements. In
contrast, we study the essential process by which regulatory networks grow: the
duplication and subsequent specialization of network components. We synthesize
a biophysical model of molecular interactions with the evolutionary framework
to find the conditions and pathways by which new regulatory functions emerge.
We show that specialization of new network components is usually slow, but can
be drastically accelerated in the presence of regulatory crosstalk and mutations
that promote promiscuous interactions between network components.'
article_number: '216'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions
on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1).
doi:10.1038/s41467-017-00238-8
apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution
of new regulatory functions on biophysically realistic fitness landscapes. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8
chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik.
“Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.
ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new
regulatory functions on biophysically realistic fitness landscapes,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory
functions on biophysically realistic fitness landscapes. Nature Communications.
8(1), 216.
mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically
Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216,
Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications
8 (2017).
corr_author: '1'
date_created: 2018-12-11T11:49:23Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2026-04-08T13:54:24Z
day: '09'
ddc:
- '539'
- '576'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1038/s41467-017-00238-8
ec_funded: 1
external_id:
isi:
- '000407198800005'
file:
- access_level: open_access
checksum: 29a1b5db458048d3bd5c67e0e2a56818
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:14Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5064'
file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf
file_size: 998157
relation: main_file
- access_level: open_access
checksum: 7b78401e52a576cf3e6bbf8d0abadc17
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:15Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5065'
file_name: IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf
file_size: 9715993
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
fulldoi: https://doi.org/10.1038/s41467-017-00238-8
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Nature Publishing Group
publist_id: '6459'
pubrep_id: '864'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Evolution of new regulatory functions on biophysically realistic fitness landscapes
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '956'
abstract:
- lang: eng
text: We study a class of ergodic quantum Markov semigroups on finite-dimensional
unital C⁎-algebras. These semigroups have a unique stationary state σ, and we
are concerned with those that satisfy a quantum detailed balance condition with
respect to σ. We show that the evolution on the set of states that is given by
such a quantum Markov semigroup is gradient flow for the relative entropy with
respect to σ in a particular Riemannian metric on the set of states. This metric
is a non-commutative analog of the 2-Wasserstein metric, and in several interesting
cases we are able to show, in analogy with work of Otto on gradient flows with
respect to the classical 2-Wasserstein metric, that the relative entropy is strictly
and uniformly convex with respect to the Riemannian metric introduced here. As
a consequence, we obtain a number of new inequalities for the decay of relative
entropy for ergodic quantum Markov semigroups with detailed balance.
article_processing_charge: No
arxiv: 1
author:
- first_name: Eric
full_name: Carlen, Eric
last_name: Carlen
- first_name: Jan
full_name: Maas, Jan
id: 4C5696CE-F248-11E8-B48F-1D18A9856A87
last_name: Maas
orcid: 0000-0002-0845-1338
citation:
ama: Carlen E, Maas J. Gradient flow and entropy inequalities for quantum Markov
semigroups with detailed balance. Journal of Functional Analysis. 2017;273(5):1810-1869.
doi:10.1016/j.jfa.2017.05.003
apa: Carlen, E., & Maas, J. (2017). Gradient flow and entropy inequalities for
quantum Markov semigroups with detailed balance. Journal of Functional Analysis.
Academic Press. https://doi.org/10.1016/j.jfa.2017.05.003
chicago: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for
Quantum Markov Semigroups with Detailed Balance.” Journal of Functional Analysis.
Academic Press, 2017. https://doi.org/10.1016/j.jfa.2017.05.003.
ieee: E. Carlen and J. Maas, “Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance,” Journal of Functional Analysis,
vol. 273, no. 5. Academic Press, pp. 1810–1869, 2017.
ista: Carlen E, Maas J. 2017. Gradient flow and entropy inequalities for quantum
Markov semigroups with detailed balance. Journal of Functional Analysis. 273(5),
1810–1869.
mla: Carlen, Eric, and Jan Maas. “Gradient Flow and Entropy Inequalities for Quantum
Markov Semigroups with Detailed Balance.” Journal of Functional Analysis,
vol. 273, no. 5, Academic Press, 2017, pp. 1810–69, doi:10.1016/j.jfa.2017.05.003.
short: E. Carlen, J. Maas, Journal of Functional Analysis 273 (2017) 1810–1869.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2025-06-04T08:14:53Z
day: '01'
department:
- _id: JaMa
doi: 10.1016/j.jfa.2017.05.003
external_id:
arxiv:
- '1609.01254'
isi:
- '000406082300005'
fulldoi: https://doi.org/10.1016/j.jfa.2017.05.003
intvolume: ' 273'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1609.01254
month: '09'
oa: 1
oa_version: Submitted Version
page: 1810 - 1869
publication: Journal of Functional Analysis
publication_identifier:
issn:
- 0022-1236
publication_status: published
publisher: Academic Press
publist_id: '6452'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Gradient flow and entropy inequalities for quantum Markov semigroups with detailed
balance
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 273
year: '2017'
...
---
_id: '957'
abstract:
- lang: eng
text: Small molecule biosensors based on Forster resonance energy transfer (FRET)
enable small molecule signaling to be monitored with high spatial and temporal
resolution in complex cellular environments. FRET sensors can be constructed by
fusing a pair of fluorescent proteins to a suitable recognition domain, such as
a member of the solute-binding protein (SBP) superfamily. However, naturally occurring
SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability,
which may preclude imaging under physiological conditions, or because the positions
of their N- and C-termini may be suboptimal for fusion of fluorescent proteins,
which may limit the dynamic range of the resulting sensors. Here, we show how
these problems can be overcome using ancestral protein reconstruction and circular
permutation. Ancestral protein reconstruction, used as a protein engineering strategy,
leverages phylogenetic information to improve the thermostability of proteins,
while circular permutation enables the termini of an SBP to be repositioned to
maximize the dynamic range of the resulting FRET sensor. We also provide a protocol
for cloning the engineered SBPs into FRET sensor constructs using Golden Gate
assembly and discuss considerations for in situ characterization of the FRET sensors.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Ben
full_name: Clifton, Ben
last_name: Clifton
- first_name: Jason
full_name: Whitfield, Jason
last_name: Whitfield
- first_name: Inmaculada
full_name: Sanchez Romero, Inmaculada
id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87
last_name: Sanchez Romero
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Clifton B, Whitfield J, Sanchez-Romero I, et al. Ancestral protein reconstruction
and circular permutation for improving the stability and dynamic range of FRET
sensors. In: Stein V, ed. Synthetic Protein Switches. Vol 1596. Synthetic
Protein Switches. Springer; 2017:71-87. doi:10.1007/978-1-4939-6940-1_5'
apa: Clifton, B., Whitfield, J., Sanchez-Romero, I., Herde, M., Henneberger, C.,
Janovjak, H. L., & Jackson, C. (2017). Ancestral protein reconstruction and
circular permutation for improving the stability and dynamic range of FRET sensors.
In V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 71–87). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_5
chicago: Clifton, Ben, Jason Whitfield, Inmaculada Sanchez-Romero, Michel Herde,
Christian Henneberger, Harald L Janovjak, and Colin Jackson. “Ancestral Protein
Reconstruction and Circular Permutation for Improving the Stability and Dynamic
Range of FRET Sensors.” In Synthetic Protein Switches, edited by Viktor
Stein, 1596:71–87. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_5.
ieee: B. Clifton et al., “Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors,” in Synthetic
Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017, pp. 71–87.
ista: 'Clifton B, Whitfield J, Sanchez-Romero I, Herde M, Henneberger C, Janovjak
HL, Jackson C. 2017.Ancestral protein reconstruction and circular permutation
for improving the stability and dynamic range of FRET sensors. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 71–87.'
mla: Clifton, Ben, et al. “Ancestral Protein Reconstruction and Circular Permutation
for Improving the Stability and Dynamic Range of FRET Sensors.” Synthetic Protein
Switches, edited by Viktor Stein, vol. 1596, Springer, 2017, pp. 71–87, doi:10.1007/978-1-4939-6940-1_5.
short: B. Clifton, J. Whitfield, I. Sanchez-Romero, M. Herde, C. Henneberger, H.L.
Janovjak, C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer,
2017, pp. 71–87.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-03-15T00:00:00Z
date_updated: 2025-07-10T12:01:52Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_5
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
fulldoi: https://doi.org/10.1007/978-1-4939-6940-1_5
intvolume: ' 1596'
language:
- iso: eng
month: '03'
oa_version: None
page: 71 - 87
project:
- _id: 255BFFFA-B435-11E9-9278-68D0E5697425
grant_number: RGY0084/2012
name: In situ real-time imaging of neurotransmitter signaling using designer optical
sensors
publication: Synthetic Protein Switches
publication_identifier:
issn:
- 1064-3745
publication_status: published
publisher: Springer
publist_id: '6451'
quality_controlled: '1'
scopus_import: '1'
series_title: Synthetic Protein Switches
status: public
title: Ancestral protein reconstruction and circular permutation for improving the
stability and dynamic range of FRET sensors
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
_id: '958'
abstract:
- lang: eng
text: Biosensors that exploit Forster resonance energy transfer (FRET) can be used
to visualize biological and physiological processes and are capable of providing
detailed information in both spatial and temporal dimensions. In a FRET-based
biosensor, substrate binding is associated with a change in the relative positions
of two fluorophores, leading to a change in FRET efficiency that may be observed
in the fluorescence spectrum. As a result, their design requires a ligand-binding
protein that exhibits a conformational change upon binding. However, not all ligand-binding
proteins produce responsive sensors upon conjugation to fluorescent proteins or
dyes, and identifying the optimum locations for the fluorophores often involves
labor-intensive iterative design or high-throughput screening. Combining the genetic
fusion of a fluorescent protein to the ligand-binding protein with site-specific
covalent attachment of a fluorescent dye can allow fine control over the positions
of the two fluorophores, allowing the construction of very sensitive sensors.
This relies upon the accurate prediction of the locations of the two fluorophores
in bound and unbound states. In this chapter, we describe a method for computational
identification of dye-attachment sites that allows the use of cysteine modification
to attach synthetic dyes that can be paired with a fluorescent protein for the
purposes of creating FRET sensors.
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Joshua
full_name: Mitchell, Joshua
last_name: Mitchell
- first_name: William
full_name: Zhang, William
last_name: Zhang
- first_name: Michel
full_name: Herde, Michel
last_name: Herde
- first_name: Christian
full_name: Henneberger, Christian
last_name: Henneberger
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
- first_name: Megan
full_name: O'Mara, Megan
last_name: O'Mara
- first_name: Colin
full_name: Jackson, Colin
last_name: Jackson
citation:
ama: 'Mitchell J, Zhang W, Herde M, et al. Method for developing optical sensors
using a synthetic dye fluorescent protein FRET pair and computational modeling
and assessment. In: Stein V, ed. Synthetic Protein Switches. Vol 1596.
Synthetic Protein Switches. Springer; 2017:89-99. doi:10.1007/978-1-4939-6940-1_6'
apa: Mitchell, J., Zhang, W., Herde, M., Henneberger, C., Janovjak, H. L., O’Mara,
M., & Jackson, C. (2017). Method for developing optical sensors using a synthetic
dye fluorescent protein FRET pair and computational modeling and assessment. In
V. Stein (Ed.), Synthetic Protein Switches (Vol. 1596, pp. 89–99). Springer.
https://doi.org/10.1007/978-1-4939-6940-1_6
chicago: Mitchell, Joshua, William Zhang, Michel Herde, Christian Henneberger, Harald
L Janovjak, Megan O’Mara, and Colin Jackson. “Method for Developing Optical Sensors
Using a Synthetic Dye Fluorescent Protein FRET Pair and Computational Modeling
and Assessment.” In Synthetic Protein Switches, edited by Viktor Stein,
1596:89–99. Synthetic Protein Switches. Springer, 2017. https://doi.org/10.1007/978-1-4939-6940-1_6.
ieee: J. Mitchell et al., “Method for developing optical sensors using a
synthetic dye fluorescent protein FRET pair and computational modeling and assessment,”
in Synthetic Protein Switches, vol. 1596, V. Stein, Ed. Springer, 2017,
pp. 89–99.
ista: 'Mitchell J, Zhang W, Herde M, Henneberger C, Janovjak HL, O’Mara M, Jackson
C. 2017.Method for developing optical sensors using a synthetic dye fluorescent
protein FRET pair and computational modeling and assessment. In: Synthetic Protein
Switches. Methods in Molecular Biology, vol. 1596, 89–99.'
mla: Mitchell, Joshua, et al. “Method for Developing Optical Sensors Using a Synthetic
Dye Fluorescent Protein FRET Pair and Computational Modeling and Assessment.”
Synthetic Protein Switches, edited by Viktor Stein, vol. 1596, Springer,
2017, pp. 89–99, doi:10.1007/978-1-4939-6940-1_6.
short: J. Mitchell, W. Zhang, M. Herde, C. Henneberger, H.L. Janovjak, M. O’Mara,
C. Jackson, in:, V. Stein (Ed.), Synthetic Protein Switches, Springer, 2017, pp.
89–99.
date_created: 2018-12-11T11:49:24Z
date_published: 2017-05-15T00:00:00Z
date_updated: 2025-07-10T12:01:54Z
day: '15'
department:
- _id: HaJa
doi: 10.1007/978-1-4939-6940-1_6
editor:
- first_name: Viktor
full_name: Stein, Viktor
last_name: Stein
fulldoi: https://doi.org/10.1007/978-1-4939-6940-1_6
intvolume: ' 1596'
language:
- iso: eng
month: '05'
oa_version: None
page: 89 - 99
publication: Synthetic Protein Switches
publication_identifier:
issn:
- 1064-3745
publication_status: published
publisher: Springer
publist_id: '6450'
quality_controlled: '1'
scopus_import: '1'
series_title: Synthetic Protein Switches
status: public
title: Method for developing optical sensors using a synthetic dye fluorescent protein
FRET pair and computational modeling and assessment
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 1596
year: '2017'
...
---
OA_place: publisher
_id: '961'
abstract:
- lang: eng
text: Cell-cell contact formation constitutes the first step in the emergence of multicellularity in
evolution, thereby allowing the differentiation of specialized cell types. In metazoan
development, cell-cell contact formation is thought to influence cell fate specification,
and cell fate specification has been implicated in cell-cell contact
formation. However, remarkably little is yet known about whether and how the
interaction and feedback between cell-cell contact formation and cell fate specification
affect development. Here we identify a positive feedback loop between cell-cell contact duration, morphogen signaling and
mesendoderm cell fate specification during zebrafish gastrulation. We show that long
lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor
cells to respond to Nodal signaling, required for proper ppl cell fate specification. We further
show that Nodal signalling romotes ppl cell-cell contact duration, thereby generating an
effective positive feedback loop between ppl cell-cell contact duration and cell fate
specification. Finally, by using a combination of theoretical modeling and experimentation,
we show that this feedback loop determines whether anterior axial mesendoderm cells
become ppl progenitors or, instead, turn into endoderm progenitors. Our findings reveal
that the gene regulatory networks leading to cell fate diversification within the developing
embryo are controlled by the interdependent activities of cell-cell signaling and contact
formation.
acknowledgement: "Many people accompanied me during this trip: I would not have reached
my destination nor \r\nenjoyed the travelling without them. First of all, thanks
to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting
and incredibly competent people and thanks for \r\nall the good science I witnessed
\ and participated in. It has been a \r\nblast, an incredibly \r\nexciting
\ one! Thanks to JLo, for teaching me how to master my pipettes and
\ showing me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching
me basically everything \r\nabout zebrafish and being always there to advice,
\ sugge\r\nst, support...and play fussball! \r\nThank you to Julien, for the
critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing
kicker matches, and Keisuke, for showing me the light, and to the three of them
\r\ntogether for all the good laughs we\r\nhad. My start in Vienna would
\ have been a lot more \r\ndifficult without you guys. Also it would not
\ have been possible without Elena and Inês: \r\nthanks for helping setting
\ up this lab and for the dinners in Gugging. Thanks to Martin, for
\r\nhelping me understand \r\nthe physics behind biology. Thanks to Philipp,
\ for the interest and \r\nadvice, and to Michael, for the Viennise take on things.
Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend
in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel
for the enthusiasm and the neverending energy and for all your \r\nhelp over the
years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat.
\ To Shayan, for being such a motivated student. To Matt, for helping
\ out\r\nwith coding \r\nand for finding punk solutions to data analysis problems.
Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla,
Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza, for the wonderful
\ atmosphere in the lab. Many than\r\nks to Koni and Deborah: doing \r\nexperiments
would have been much more difficult without your help. Special thanks to Katjia
\r\nfor setting up an amazing imaging facility and for building the best
\ team, Robert, Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith
all the late sortings and for helping with all \r\nthe technical problems. Thanks
to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald
Janovjak for being a present and helpful committee member over the years \r\nand
\ to Patrick Lemaire f\r\nor the helpful insight and extremely interesting
\ discussion we had \r\nabout the project. Also, this journey would not
\ have been the same without all the friends \r\nthat I met in Dresden and
then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne,
Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph,
\r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled
my days with \r\nfun and support. A special thank to my family, always close even
if they are \r\nkilometers away. \r\nGrazie ai miei fratelli, Nunzio e William,
\ e alla mia mamma, per essermi sempre vicini pur \r\nvivendo a chilometri
di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe
crazy life of a scientist, the living apart for\r\nso long, never knowing when things
are going \r\nto happen. Thanks for being a great partner and my number one fan!"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
citation:
ama: 'Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish
gastrulation. 2017. doi:10.15479/AT:ISTA:th_825'
apa: 'Barone, V. (2017). Cell adhesion and cell fate: An effective feedback loop
during zebrafish gastrulation. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:th_825'
chicago: 'Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop
during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017.
https://doi.org/10.15479/AT:ISTA:th_825.'
ieee: 'V. Barone, “Cell adhesion and cell fate: An effective feedback loop during
zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.'
ista: 'Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during
zebrafish gastrulation. Institute of Science and Technology Austria.'
mla: 'Barone, Vanessa. Cell Adhesion and Cell Fate: An Effective Feedback Loop
during Zebrafish Gastrulation. Institute of Science and Technology Austria,
2017, doi:10.15479/AT:ISTA:th_825.'
short: 'V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during
Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.'
corr_author: '1'
date_created: 2018-12-11T11:49:25Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2026-06-18T18:12:40Z
day: '01'
ddc:
- '570'
- '590'
degree_awarded: PhD
department:
- _id: CaHe
doi: 10.15479/AT:ISTA:th_825
file:
- access_level: closed
checksum: 242f88c87f2cf267bf05049fa26a687b
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:36:52Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6205'
file_name: 2017_Barone_thesis_final.docx
file_size: 14497822
relation: source_file
- access_level: open_access
checksum: ba5b0613ed8bade73a409acdd880fb8a
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:36:52Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6206'
file_name: 2017_Barone_thesis_.pdf
file_size: 14995941
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
fulldoi: https://doi.org/10.15479/AT:ISTA:th_825
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '109'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6444'
pubrep_id: '825'
related_material:
record:
- id: '735'
relation: part_of_dissertation
status: public
- id: '1100'
relation: part_of_dissertation
status: public
- id: '1537'
relation: part_of_dissertation
status: public
- id: '3246'
relation: part_of_dissertation
status: public
- id: '2926'
relation: part_of_dissertation
status: public
- id: '676'
relation: part_of_dissertation
status: public
- id: '1912'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
title: 'Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation'
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2017'
...
---
_id: '962'
abstract:
- lang: eng
text: 'We present a new algorithm for model counting of a class of string constraints.
In addition to the classic operation of concatenation, our class includes some
recursively defined operations such as Kleene closure, and replacement of substrings.
Additionally, our class also includes length constraints on the string expressions,
which means, by requiring reasoning about numbers, that we face a multi-sorted
logic. In the end, our string constraints are motivated by their use in programming
for web applications. Our algorithm comprises two novel features: the ability
to use a technique of (1) partial derivatives for constraints that are already
in a solved form, i.e. a form where its (string) satisfiability is clearly displayed,
and (2) non-progression, where cyclic reasoning in the reduction process may be
terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally
compare our model counter with two recent works on model counting of similar constraints,
SMC [18] and ABC [5], to demonstrate its superior performance.'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Minh
full_name: Trinh, Minh
last_name: Trinh
- first_name: Duc Hiep
full_name: Chu, Duc Hiep
id: 3598E630-F248-11E8-B48F-1D18A9856A87
last_name: Chu
- first_name: Joxan
full_name: Jaffar, Joxan
last_name: Jaffar
citation:
ama: 'Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings.
In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:10.1007/978-3-319-63390-9_21'
apa: 'Trinh, M., Chu, D. H., & Jaffar, J. (2017). Model counting for recursively-defined
strings. In R. Majumdar & V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented
at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. https://doi.org/10.1007/978-3-319-63390-9_21'
chicago: Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined
Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer,
2017. https://doi.org/10.1007/978-3-319-63390-9_21.
ieee: 'M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined
strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany,
2017, vol. 10427, pp. 399–418.'
ista: 'Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings.
CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418.'
mla: Trinh, Minh, et al. Model Counting for Recursively-Defined Strings.
Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418,
doi:10.1007/978-3-319-63390-9_21.
short: M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer,
2017, pp. 399–418.
conference:
end_date: 2017-07-28
location: Heidelberg, Germany
name: 'CAV: Computer Aided Verification'
start_date: 2017-07-24
date_created: 2018-12-11T11:49:26Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2026-04-16T09:58:05Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-319-63390-9_21
editor:
- first_name: Rupak
full_name: Majumdar, Rupak
last_name: Majumdar
- first_name: Viktor
full_name: Kunčak, Viktor
last_name: Kunčak
external_id:
isi:
- '000431900900021'
fulldoi: https://doi.org/10.1007/978-3-319-63390-9_21
intvolume: ' 10427'
isi: 1
language:
- iso: eng
month: '01'
oa_version: None
page: 399 - 418
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: Formal methods for the design and analysis of complex systems
publication_identifier:
issn:
- 0302-9743
publication_status: published
publisher: Springer
publist_id: '6443'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Model counting for recursively-defined strings
type: conference
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 10427
year: '2017'
...
---
_id: '963'
abstract:
- lang: eng
text: 'Network games are widely used as a model for selfish resource-allocation
problems. In the classical model, each player selects a path connecting her source
and target vertex. The cost of traversing an edge depends on the number of players
that traverse it. Thus, it abstracts the fact that different users may use a resource
at different times and for different durations, which plays an important role
in defining the costs of the users in reality. For example, when transmitting
packets in a communication network, routing traffic in a road network, or processing
a task in a production system, the traversal of the network involves an inherent
delay, and so sharing and congestion of resources crucially depends on time. We
study timed network games , which add a time component to network games. Each
vertex v in the network is associated with a cost function, mapping the load on
v to the price that a player pays for staying in v for one time unit with this
load. In addition, each edge has a guard, describing time intervals in which the
edge can be traversed, forcing the players to spend time on vertices. Unlike earlier
work that add a time component to network games, the time in our model is continuous
and cannot be discretized. In particular, players have uncountably many strategies,
and a game may have uncountably many pure Nash equilibria. We study properties
of timed network games with cost-sharing or congestion cost functions: their stability,
equilibrium inefficiency, and complexity. In particular, we show that the answer
to the question whether we can restrict attention to boundary strategies, namely
ones in which edges are traversed only at the boundaries of guards, is mixed. '
alternative_title:
- LIPIcs
article_number: '37'
article_processing_charge: No
author:
- first_name: Guy
full_name: Avni, Guy
id: 463C8BC2-F248-11E8-B48F-1D18A9856A87
last_name: Avni
orcid: 0000-0001-5588-8287
- first_name: Shibashis
full_name: Guha, Shibashis
last_name: Guha
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: 'Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83.
Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:10.4230/LIPIcs.MFCS.2017.37'
apa: 'Avni, G., Guha, S., & Kupferman, O. (2017). Timed network games with clocks
(Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science,
Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2017.37'
chicago: Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with
Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. https://doi.org/10.4230/LIPIcs.MFCS.2017.37.
ieee: 'G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented
at the MFCS: Mathematical Foundations of Computer Science, Aalborg, Denmark, 2017,
vol. 83.'
ista: 'Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS:
Mathematical Foundations of Computer Science, LIPIcs, vol. 83, 37.'
mla: Avni, Guy, et al. Timed Network Games with Clocks. Vol. 83, 37, Schloss
Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:10.4230/LIPIcs.MFCS.2017.37.
short: G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für
Informatik, 2017.
conference:
end_date: 2017-08-25
location: Aalborg, Denmark
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2017-08-21
date_created: 2018-12-11T11:49:26Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2025-07-10T12:01:59Z
day: '01'
ddc:
- '004'
department:
- _id: ToHe
doi: 10.4230/LIPIcs.MFCS.2017.37
file:
- access_level: open_access
checksum: f55eaf7f3c36ea07801112acfedd17d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:10Z
date_updated: 2020-07-14T12:48:18Z
file_id: '5059'
file_name: IST-2017-829-v1+1_mfcs-cr.pdf
file_size: 369730
relation: main_file
file_date_updated: 2020-07-14T12:48:18Z
fulldoi: https://doi.org/10.4230/LIPIcs.MFCS.2017.37
has_accepted_license: '1'
intvolume: ' 83'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 25F5A88A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Moderne Concurrency Paradigms
publication_identifier:
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
publist_id: '6438'
pubrep_id: '829'
quality_controlled: '1'
related_material:
record:
- id: '6005'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Timed network games with clocks
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: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 83
year: '2017'
...
---
_id: '9707'
abstract:
- lang: eng
text: Branching morphogenesis of the epithelial ureteric bud forms the renal collecting
duct system and is critical for normal nephron number, while low nephron number
is implicated in hypertension and renal disease. Ureteric bud growth and branching
requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric
bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling
up-regulates transcription factors Etv4 and Etv5, which are also critical for
branching. Despite extensive knowledge of the genetic control of these events,
it is not understood, at the cellular level, how renal branching morphogenesis
is achieved or how Ret signaling influences epithelial cell behaviors to promote
this process. Analysis of chimeric embryos previously suggested a role for Ret
signaling in promoting cell rearrangements in the nephric duct, but this method
was unsuited to study individual cell behaviors during ureteric bud branching.
Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture
and time-lapse imaging, to trace the movements and divisions of individual ureteric
bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type
clones in which the mutant and wild-type sister cells are differentially and heritably
marked by green and red fluorescent proteins. We find that, in normal kidneys,
most individual tip cells behave as self-renewing progenitors, some of whose progeny
remain at the tips while others populate the growing UB trunks. In Ret or Etv4
MADM clones, the wild-type cells generated at a UB tip are much more likely to
remain at, or move to, the new tips during branching and elongation, while their
Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks.
By tracking successive mitoses in a cell lineage, we find that Ret signaling has
little effect on proliferation, in contrast to its effects on cell movement. Our
results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric
bud tips, and suggest a model in which these cell movements mediate branching
morphogenesis.
article_processing_charge: No
author:
- first_name: Paul
full_name: Riccio, Paul
last_name: Riccio
- first_name: Christina
full_name: Cebrián, Christina
last_name: Cebrián
- first_name: Hui
full_name: Zong, Hui
last_name: Zong
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Frank
full_name: Costantini, Frank
last_name: Costantini
citation:
ama: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and
Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.
2017. doi:10.5061/dryad.pk16b'
apa: 'Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., & Costantini, F. (2017).
Data from: Ret and Etv4 promote directed movements of progenitor cells during
renal branching morphogenesis. Dryad. https://doi.org/10.5061/dryad.pk16b'
chicago: 'Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank
Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor
Cells during Renal Branching Morphogenesis.” Dryad, 2017. https://doi.org/10.5061/dryad.pk16b.'
ieee: 'P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data
from: Ret and Etv4 promote directed movements of progenitor cells during renal
branching morphogenesis.” Dryad, 2017.'
ista: 'Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from:
Ret and Etv4 promote directed movements of progenitor cells during renal branching
morphogenesis, Dryad, 10.5061/dryad.pk16b.'
mla: 'Riccio, Paul, et al. Data from: Ret and Etv4 Promote Directed Movements
of Progenitor Cells during Renal Branching Morphogenesis. Dryad, 2017, doi:10.5061/dryad.pk16b.'
short: P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017).
date_created: 2021-07-23T09:39:34Z
date_published: 2017-01-14T00:00:00Z
date_updated: 2022-08-25T13:34:55Z
day: '14'
department:
- _id: SiHi
doi: 10.5061/dryad.pk16b
fulldoi: https://doi.org/10.5061/dryad.pk16b
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.pk16b
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '9702'
relation: used_in_publication
status: deleted
status: public
title: 'Data from: Ret and Etv4 promote directed movements of progenitor cells during
renal branching morphogenesis'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9709'
abstract:
- lang: eng
text: Across the nervous system, certain population spiking patterns are observed
far more frequently than others. A hypothesis about this structure is that these
collective activity patterns function as population codewords–collective modes–carrying
information distinct from that of any single cell. We investigate this phenomenon
in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop
a novel statistical model that decomposes the population response into modes;
it predicts the distribution of spiking activity in the ganglion cell population
with high accuracy. We found that the modes represent localized features of the
visual stimulus that are distinct from the features represented by single neurons.
Modes form clusters of activity states that are readily discriminated from one
another. When we repeated the same visual stimulus, we found that the same mode
was robustly elicited. These results suggest that retinal ganglion cells’ collective
signaling is endowed with a form of error-correcting code–a principle that may
hold in brain areas beyond retina.
article_processing_charge: No
author:
- first_name: Jason
full_name: Prentice, Jason
last_name: Prentice
- first_name: Olivier
full_name: Marre, Olivier
last_name: Marre
- first_name: Mark
full_name: Ioffe, Mark
last_name: Ioffe
- first_name: Adrianna
full_name: Loback, Adrianna
last_name: Loback
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Michael
full_name: Berry, Michael
last_name: Berry
citation:
ama: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust
modes of the retinal population code. 2017. doi:10.5061/dryad.1f1rc'
apa: 'Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M.
(2017). Data from: Error-robust modes of the retinal population code. Dryad. https://doi.org/10.5061/dryad.1f1rc'
chicago: 'Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik,
and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.”
Dryad, 2017. https://doi.org/10.5061/dryad.1f1rc.'
ieee: 'J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data
from: Error-robust modes of the retinal population code.” Dryad, 2017.'
ista: 'Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from:
Error-robust modes of the retinal population code, Dryad, 10.5061/dryad.1f1rc.'
mla: 'Prentice, Jason, et al. Data from: Error-Robust Modes of the Retinal Population
Code. Dryad, 2017, doi:10.5061/dryad.1f1rc.'
short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).
date_created: 2021-07-23T11:34:34Z
date_published: 2017-10-18T00:00:00Z
date_updated: 2025-09-22T09:43:12Z
day: '18'
department:
- _id: GaTk
doi: 10.5061/dryad.1f1rc
fulldoi: https://doi.org/10.5061/dryad.1f1rc
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.1f1rc
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1197'
relation: used_in_publication
status: public
status: public
title: 'Data from: Error-robust modes of the retinal population code'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9842'
abstract:
- lang: eng
text: Mathematica notebooks used to generate figures.
article_processing_charge: No
author:
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic
adaptation. 2017. doi:10.17632/nw68fxzjpm.1'
apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new
habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1'
chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in
a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.'
ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat
by polygenic adaptation.” Mendeley Data, 2017.'
ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by
polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.'
mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a
New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.'
short: A. Etheridge, N.H. Barton, (2017).
date_created: 2021-08-09T13:18:55Z
date_published: 2017-12-29T00:00:00Z
date_updated: 2025-04-15T07:11:04Z
day: '29'
department:
- _id: NiBa
doi: 10.17632/nw68fxzjpm.1
fulldoi: https://doi.org/10.17632/nw68fxzjpm.1
main_file_link:
- open_access: '1'
url: https://doi.org/10.17632/nw68fxzjpm.1
month: '12'
oa: 1
oa_version: Published Version
publisher: Mendeley Data
related_material:
record:
- id: '564'
relation: used_in_publication
status: public
status: public
title: 'Data for: Establishment in a new habitat by polygenic adaptation'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '642'
abstract:
- lang: eng
text: Cauchy problems with SPDEs on the whole space are localized to Cauchy problems
on a ball of radius R. This localization reduces various kinds of spatial approximation
schemes to finite dimensional problems. The error is shown to be exponentially
small. As an application, a numerical scheme is presented which combines the localization
and the space and time discretization, and thus is fully implementable.
article_processing_charge: No
arxiv: 1
author:
- first_name: Mate
full_name: Gerencser, Mate
id: 44ECEDF2-F248-11E8-B48F-1D18A9856A87
last_name: Gerencser
- first_name: István
full_name: Gyöngy, István
last_name: Gyöngy
citation:
ama: Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential
equations in the whole space. Mathematics of Computation. 2017;86(307):2373-2397.
doi:10.1090/mcom/3201
apa: Gerencser, M., & Gyöngy, I. (2017). Localization errors in solving stochastic
partial differential equations in the whole space. Mathematics of Computation.
American Mathematical Society. https://doi.org/10.1090/mcom/3201
chicago: Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic
Partial Differential Equations in the Whole Space.” Mathematics of Computation.
American Mathematical Society, 2017. https://doi.org/10.1090/mcom/3201.
ieee: M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial
differential equations in the whole space,” Mathematics of Computation,
vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017.
ista: Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial
differential equations in the whole space. Mathematics of Computation. 86(307),
2373–2397.
mla: Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic
Partial Differential Equations in the Whole Space.” Mathematics of Computation,
vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:10.1090/mcom/3201.
short: M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.
corr_author: '1'
date_created: 2018-12-11T11:47:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2025-09-11T07:20:20Z
day: '01'
department:
- _id: JaMa
doi: 10.1090/mcom/3201
external_id:
arxiv:
- '1508.05535'
isi:
- '000400929100013'
fulldoi: https://doi.org/10.1090/mcom/3201
intvolume: ' 86'
isi: 1
issue: '307'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1508.05535
month: '01'
oa: 1
oa_version: Submitted Version
page: 2373 - 2397
publication: Mathematics of Computation
publication_identifier:
issn:
- 0025-5718
publication_status: published
publisher: American Mathematical Society
publist_id: '7144'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Localization errors in solving stochastic partial differential equations in
the whole space
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 86
year: '2017'
...
---
_id: '6426'
abstract:
- lang: eng
text: Synchronous programs are easy to specify because the side effects of an operation
are finished by the time the invocation of the operation returns to the caller.
Asynchronous programs, on the other hand, are difficult to specify because there
are side effects due to pending computation scheduled as a result of the invocation
of an operation. They are also difficult to verify because of the large number
of possible interleavings of concurrent asynchronous computation threads. We show
that specifications and correctness proofs for asynchronous programs can be structured
by introducing the fiction, for proof purposes, that intermediate, non-quiescent
states of asynchronous operations can be ignored. Then, the task of specification
becomes relatively simple and the task of verification can be naturally decomposed
into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure
of an asynchronous program, the atomic effect of non-atomic operations and the
synchronous effect of asynchronous operations. This structuring of specifications
and proofs corresponds to the introduction of multiple layers of stepwise refinement
for asynchronous programs. We present the first proof rule, called synchronization,
to reduce asynchronous invocations on a lower layer to synchronous invocations
on a higher layer. We implemented our proof method in CIVL and evaluated it on
a collection of benchmark programs.
alternative_title:
- IST Austria Technical Report
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Bernhard
full_name: Kragl, Bernhard
id: 320FC952-F248-11E8-B48F-1D18A9856A87
last_name: Kragl
orcid: 0000-0001-7745-9117
- first_name: Shaz
full_name: Qadeer, Shaz
last_name: Qadeer
citation:
ama: Henzinger TA, Kragl B, Qadeer S. Synchronizing the Asynchronous. IST
Austria; 2017. doi:10.15479/AT:IST-2018-853-v2-2
apa: Henzinger, T. A., Kragl, B., & Qadeer, S. (2017). Synchronizing the
asynchronous. IST Austria. https://doi.org/10.15479/AT:IST-2018-853-v2-2
chicago: Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. Synchronizing
the Asynchronous. IST Austria, 2017. https://doi.org/10.15479/AT:IST-2018-853-v2-2.
ieee: T. A. Henzinger, B. Kragl, and S. Qadeer, Synchronizing the asynchronous.
IST Austria, 2017.
ista: Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST
Austria, 28p.
mla: Henzinger, Thomas A., et al. Synchronizing the Asynchronous. IST Austria,
2017, doi:10.15479/AT:IST-2018-853-v2-2.
short: T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST
Austria, 2017.
date_created: 2019-05-13T08:15:55Z
date_published: 2017-08-04T00:00:00Z
date_updated: 2025-04-15T08:11:53Z
day: '04'
ddc:
- '000'
department:
- _id: ToHe
doi: 10.15479/AT:IST-2018-853-v2-2
file:
- access_level: open_access
checksum: b48d42725182d7ca10107a118815f4cf
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T08:14:44Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6431'
file_name: main(1).pdf
file_size: 971347
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
fulldoi: https://doi.org/10.15479/AT:IST-2018-853-v2-2
has_accepted_license: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '28'
publication_identifier:
issn:
- 2664-1690
publication_status: published
publisher: IST Austria
related_material:
record:
- id: '133'
relation: later_version
status: public
status: public
title: Synchronizing the asynchronous
type: technical_report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
OA_type: closed access
_id: '643'
abstract:
- lang: eng
text: It has been reported that nicotinamide-overload induces oxidative stress associated
with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This
study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance
tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without
cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT)
were also carried out in adult Sprague-Dawley rats treated with or without cumulative
doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration
significantly increased the plasma H2O2 levels associated with high insulin levels.
Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration
of nicotinic acid, another form of Vitamin B3, also significantly increased plasma
insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic
acid or nicotinamide impaired glucose metabolism. This study suggested that excess
Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance.
article_processing_charge: No
article_type: original
author:
- first_name: Wuping
full_name: Sun, Wuping
last_name: Sun
- first_name: Ming-Zhu
full_name: Zhai, Ming-Zhu
id: 34009CFA-F248-11E8-B48F-1D18A9856A87
last_name: Zhai
- first_name: Qian
full_name: Zhou, Qian
last_name: Zhou
- first_name: Chengrui
full_name: Qian, Chengrui
last_name: Qian
- first_name: Changyu
full_name: Jiang, Changyu
last_name: Jiang
citation:
ama: Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on
plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal
of Physiology. 2017;60(4):207-214. doi:10.4077/CJP.2017.BAF469
apa: Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., & Jiang, C. (2017). Effects of
B vitamins overload on plasma insulin level and hydrogen peroxide generation in
rats. Chinese Journal of Physiology. Chinese Physiological Society. https://doi.org/10.4077/CJP.2017.BAF469
chicago: Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang.
“Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide
Generation in Rats.” Chinese Journal of Physiology. Chinese Physiological
Society, 2017. https://doi.org/10.4077/CJP.2017.BAF469.
ieee: W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins
overload on plasma insulin level and hydrogen peroxide generation in rats,” Chinese
Journal of Physiology, vol. 60, no. 4. Chinese Physiological Society, pp.
207–214, 2017.
ista: Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload
on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal
of Physiology. 60(4), 207–214.
mla: Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level
and Hydrogen Peroxide Generation in Rats.” Chinese Journal of Physiology,
vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:10.4077/CJP.2017.BAF469.
short: W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology
60 (2017) 207–214.
date_created: 2018-12-11T11:47:40Z
date_published: 2017-08-31T00:00:00Z
date_updated: 2025-09-11T07:19:13Z
day: '31'
ddc:
- '570'
department:
- _id: RySh
doi: 10.4077/CJP.2017.BAF469
external_id:
isi:
- '000409566300002'
pmid:
- '28847140'
fulldoi: https://doi.org/10.4077/CJP.2017.BAF469
intvolume: ' 60'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 207 - 214
pmid: 1
publication: Chinese Journal of Physiology
publication_identifier:
issn:
- 0304-4920
publication_status: published
publisher: Chinese Physiological Society
publist_id: '7142'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Effects of B vitamins overload on plasma insulin level and hydrogen peroxide
generation in rats
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 60
year: '2017'
...