---
_id: '287'
abstract:
- lang: eng
text: In this paper, we discuss biological effects of electromagnetic (EM) fields
in the context of cancer biology. In particular, we review the nanomechanical
properties of microtubules (MTs), the latter being one of the most successful
targets for cancer therapy. We propose an investigation on the coupling of electromagnetic
radiation to mechanical vibrations of MTs as an important basis for biological
and medical applications. In our opinion, optomechanical methods can accurately
monitor and control the mechanical properties of isolated MTs in a liquid environment.
Consequently, studying nanomechanical properties of MTs may give useful information
for future applications to diagnostic and therapeutic technologies involving non-invasive
externally applied physical fields. For example, electromagnetic fields or high
intensity ultrasound can be used therapeutically avoiding harmful side effects
of chemotherapeutic agents or classical radiation therapy.
acknowledgement: The work of SB has been supported by the European Unions Horizon
2020 research and innovation program under the Marie Sklodowska Curie grant agreement
No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC
(Canada) for his research. MC acknowledges support from the Czech Science Foundation,
projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211
and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.
article_processing_charge: No
author:
- first_name: Vahid
full_name: Salari, Vahid
last_name: Salari
- first_name: Shabir
full_name: Barzanjeh, Shabir
id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87
last_name: Barzanjeh
orcid: 0000-0003-0415-1423
- first_name: Michal
full_name: Cifra, Michal
last_name: Cifra
- first_name: Christoph
full_name: Simon, Christoph
last_name: Simon
- first_name: Felix
full_name: Scholkmann, Felix
last_name: Scholkmann
- first_name: Zahra
full_name: Alirezaei, Zahra
last_name: Alirezaei
- first_name: Jack
full_name: Tuszynski, Jack
last_name: Tuszynski
citation:
ama: Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics
In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark.
2018;23(8):1391-1406. doi:10.2741/4651
apa: Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei,
Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer
diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers
in Bioscience. https://doi.org/10.2741/4651
chicago: Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann,
Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics
In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark.
Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651.
ieee: V. Salari et al., “Electromagnetic fields and optomechanics In cancer
diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23,
no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.
ista: Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski
J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment.
Frontiers in Bioscience - Landmark. 23(8), 1391–1406.
mla: Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics
and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers
in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651.
short: V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei,
J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.
date_created: 2018-12-11T11:45:37Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:38:14Z
day: '01'
department:
- _id: JoFi
doi: 10.2741/4651
ec_funded: 1
external_id:
isi:
- '000439042800001'
pmid:
- '29293441'
intvolume: ' 23'
isi: 1
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.bioscience.org/2018/v23/af/4651/fulltext.htm
month: '03'
oa: 1
oa_version: Submitted Version
page: 1391 - 1406
pmid: 1
project:
- _id: 258047B6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '707438'
name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination
with cavity Optomechanics SUPEREOM'
publication: Frontiers in Bioscience - Landmark
publication_status: published
publisher: Frontiers in Bioscience
quality_controlled: '1'
scopus_import: '1'
status: public
title: Electromagnetic fields and optomechanics In cancer diagnostics and treatment
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2018'
...
---
_id: '425'
abstract:
- lang: eng
text: 'We show that the following algorithmic problem is decidable: given a 2-dimensional
simplicial complex, can it be embedded (topologically, or equivalently, piecewise
linearly) in R3? By a known reduction, it suffices to decide the embeddability
of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which
allows us to simplify X and recurse, is in proving that if X can be embedded in
S3, then there is also an embedding in which X has a short meridian, that is,
an essential curve in the boundary of X bounding a disk in S3 \ X with length
bounded by a computable function of the number of tetrahedra of X.'
article_number: '5'
article_processing_charge: No
article_type: original
author:
- first_name: Jiří
full_name: Matoušek, Jiří
last_name: Matoušek
- first_name: Eric
full_name: Sedgwick, Eric
last_name: Sedgwick
- first_name: Martin
full_name: Tancer, Martin
id: 38AC689C-F248-11E8-B48F-1D18A9856A87
last_name: Tancer
orcid: 0000-0002-1191-6714
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is
decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632
apa: Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability
in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632
chicago: Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability
in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632.
ieee: J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the
3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018.
ista: Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere
is decidable. Journal of the ACM. 65(1), 5.
mla: Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal
of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632.
short: J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).
date_created: 2018-12-11T11:46:24Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-11T13:38:49Z
day: '01'
department:
- _id: UlWa
doi: 10.1145/3078632
ec_funded: 1
external_id:
arxiv:
- '1402.0815'
isi:
- '000425685900006'
intvolume: ' 65'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1402.0815
month: '01'
oa: 1
oa_version: Preprint
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Journal of the ACM
publication_status: published
publisher: ACM
publist_id: '7398'
quality_controlled: '1'
related_material:
record:
- id: '2157'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Embeddability in the 3-Sphere is decidable
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 65
year: '2018'
...
---
_id: '564'
abstract:
- lang: eng
text: "Maladapted individuals can only colonise a new habitat if they can evolve
a\r\npositive growth rate fast enough to avoid extinction, a process known as
evolutionary\r\nrescue. We treat log fitness at low density in the new habitat
as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow
the evolution\r\nof the growth rate; this assumes that the trait values of offspring
of a\r\nsexual union are normally distributed around the mean of the parents’
trait\r\nvalues, with variance that depends only on the parents’ relatedness.
The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe
mean and genetic variance of the trait in the source population.\r\nThe chance
of success becomes small if migrants come from a population\r\nwith mean growth
rate in the new habitat more than a few standard deviations\r\nbelow zero; this
chance depends roughly equally on the probability\r\nthat the initial founder
is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring
as a result of selection. The loss of genetic variation\r\nduring the founding
event is substantial, but highly variable. With\r\ncontinued migration at rate
M, establishment is inevitable; when migration\r\nis rare, the expected time to
establishment decreases inversely with M.\r\nHowever, above a threshold migration
rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation
is held back by gene flow; above this\r\nthreshold, the expected time to establishment
increases exponentially with M. This threshold behaviour is captured by a deterministic
approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder
population\r\nwith mean and variance evolving deterministically. By assuming a
constant\r\ngenetic variance, we also develop a diffusion approximation for the
joint distribution\r\nof population size and trait mean, which extends to include
stabilising\r\nselection and density regulation. Divergence of the population
from its\r\nancestors causes partial reproductive isolation, which we measure
through\r\nthe reproductive value of migrants into the newly established population."
article_processing_charge: No
article_type: original
author:
- 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: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation.
Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007
apa: Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by
polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007
chicago: Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat
by Polygenic Adaptation.” Theoretical Population Biology. Academic Press,
2018. https://doi.org/10.1016/j.tpb.2017.11.007.
ieee: N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic
adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic
Press, pp. 110–127, 2018.
ista: Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic
adaptation. Theoretical Population Biology. 122(7), 110–127.
mla: Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat
by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no.
7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.
short: N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.
date_created: 2018-12-11T11:47:12Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-11T13:41:22Z
day: '01'
ddc:
- '519'
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.11.007
ec_funded: 1
external_id:
isi:
- '000440392900014'
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checksum: 0b96f6db47e3e91b5e7d103b847c239d
content_type: application/pdf
creator: nbarton
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file_id: '7199'
file_name: bartonetheridge.pdf
file_size: 2287682
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has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '07'
oa: 1
oa_version: Submitted Version
page: 110-127
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '7250'
quality_controlled: '1'
related_material:
record:
- id: '9842'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Establishment in a new habitat by polygenic adaptation
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 122
year: '2018'
...
---
_id: '157'
abstract:
- lang: eng
text: 'Social dilemmas occur when incentives for individuals are misaligned with
group interests 1-7 . According to the ''tragedy of the commons'', these misalignments
can lead to overexploitation and collapse of public resources. The resulting behaviours
can be analysed with the tools of game theory 8 . The theory of direct reciprocity
9-15 suggests that repeated interactions can alleviate such dilemmas, but previous
work has assumed that the public resource remains constant over time. Here we
introduce the idea that the public resource is instead changeable and depends
on the strategic choices of individuals. An intuitive scenario is that cooperation
increases the public resource, whereas defection decreases it. Thus, cooperation
allows the possibility of playing a more valuable game with higher payoffs, whereas
defection leads to a less valuable game. We analyse this idea using the theory
of stochastic games 16-19 and evolutionary game theory. We find that the dependence
of the public resource on previous interactions can greatly enhance the propensity
for cooperation. For these results, the interaction between reciprocity and payoff
feedback is crucial: neither repeated interactions in a constant environment nor
single interactions in a changing environment yield similar cooperation rates.
Our framework shows which feedbacks between exploitation and environment - either
naturally occurring or designed - help to overcome social dilemmas.'
acknowledgement: "European Research Council Start Grant 279307, Austrian Science Fund
(FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme."
article_processing_charge: No
author:
- first_name: Christian
full_name: Hilbe, Christian
id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87
last_name: Hilbe
orcid: 0000-0001-5116-955X
- first_name: Štepán
full_name: Šimsa, Štepán
last_name: Šimsa
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic
games. Nature. 2018;559(7713):246-249. doi:10.1038/s41586-018-0277-x
apa: Hilbe, C., Šimsa, Š., Chatterjee, K., & Nowak, M. (2018). Evolution of
cooperation in stochastic games. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0277-x
chicago: Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak.
“Evolution of Cooperation in Stochastic Games.” Nature. Nature Publishing
Group, 2018. https://doi.org/10.1038/s41586-018-0277-x.
ieee: C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation
in stochastic games,” Nature, vol. 559, no. 7713. Nature Publishing Group,
pp. 246–249, 2018.
ista: Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in
stochastic games. Nature. 559(7713), 246–249.
mla: Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” Nature,
vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:10.1038/s41586-018-0277-x.
short: C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.
date_created: 2018-12-11T11:44:56Z
date_published: 2018-07-04T00:00:00Z
date_updated: 2023-09-11T13:43:22Z
day: '04'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1038/s41586-018-0277-x
ec_funded: 1
external_id:
isi:
- '000438240900054'
file:
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content_type: application/pdf
creator: dernst
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file_id: '7049'
file_name: 2018_Nature_Hilbe.pdf
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language:
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month: '07'
oa: 1
oa_version: Submitted Version
page: 246 - 249
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '7764'
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/engineering-cooperation/
scopus_import: '1'
status: public
title: Evolution of cooperation in stochastic games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 559
year: '2018'
...
---
_id: '384'
abstract:
- lang: eng
text: Can orthologous proteins differ in terms of their ability to be secreted?
To answer this question, we investigated the distribution of signal peptides within
the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons
revealed a large number of signal peptide gain and loss events, in which signal
peptides emerge or disappear in the course of evolution. Signal peptide losses
prevail over gains, an effect which is especially pronounced in the transition
from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate
decline in the number of signal peptide-containing proteins in endosymbionts cannot
be explained by the overall reduction of their genomes. Signal peptides can be
gained and lost either by acquisition/elimination of the corresponding N-terminal
regions or by gradual accumulation of mutations. The evolutionary dynamics of
signal peptides in bacterial proteins represents a powerful mechanism of functional
diversification.
acknowledgement: "his work was supported by the Deutsche Forschungsgemeinschaft (grant
\ number FR 1411/9-1). This work was supported by the German Research Foundation
(DFG) and the Technical University of Munich within the fund- ing programme Open
Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont
status of the organisms and Michael Galperin for\r\nuseful comments. T"
article_processing_charge: No
author:
- first_name: Peter
full_name: Hönigschmid, Peter
last_name: Hönigschmid
- first_name: Nadya
full_name: Bykova, Nadya
last_name: Bykova
- first_name: René
full_name: Schneider, René
last_name: Schneider
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Dmitrij
full_name: Frishman, Dmitrij
last_name: Frishman
citation:
ama: Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay
between symbiotic relationships and patterns of signal peptide gain and loss.
Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049
apa: Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D.
(2018). Evolutionary interplay between symbiotic relationships and patterns of
signal peptide gain and loss. Genome Biology and Evolution. Oxford University
Press. https://doi.org/10.1093/gbe/evy049
chicago: Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij
Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns
of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford
University Press, 2018. https://doi.org/10.1093/gbe/evy049.
ieee: P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary
interplay between symbiotic relationships and patterns of signal peptide gain
and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University
Press, pp. 928–938, 2018.
ista: Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary
interplay between symbiotic relationships and patterns of signal peptide gain
and loss. Genome Biology and Evolution. 10(3), 928–938.
mla: Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships
and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution,
vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.
short: P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome
Biology and Evolution 10 (2018) 928–938.
date_created: 2018-12-11T11:46:10Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:56:52Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1093/gbe/evy049
external_id:
isi:
- '000429483700022'
file:
- access_level: open_access
checksum: 458a7c2c2e79528567edfeb0f326cbe0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:07Z
date_updated: 2020-07-14T12:46:16Z
file_id: '4667'
file_name: IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf
file_size: 691602
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file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '03'
oa: 1
oa_version: Published Version
page: 928 - 938
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7445'
pubrep_id: '999'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary interplay between symbiotic relationships and patterns of signal
peptide gain and loss
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: 10
year: '2018'
...