---
_id: '9910'
abstract:
- lang: eng
text: Adult height inspired the first biometrical and quantitative genetic studies
and is a test-case trait for understanding heritability. The studies of height
led to formulation of the classical polygenic model, that has a profound influence
on the way we view and analyse complex traits. An essential part of the classical
model is an assumption of additivity of effects and normality of the distribution
of the residuals. However, it may be expected that the normal approximation will
become insufficient in bigger studies. Here, we demonstrate that when the height
of hundreds of thousands of individuals is analysed, the model complexity needs
to be increased to include non-additive interactions between sex, environment
and genes. Alternatively, the use of log-normal approximation allowed us to still
use the additive effects model. These findings are important for future genetic
and methodologic studies that make use of adult height as an exemplar trait.
acknowledgement: "We are grateful to Marianna Bevova and Pavel Borodin for fruitful
discussion and help with conceptualising our findings and to Lennart C. Karssen
for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has
been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects
in control of complex human traits”). The work of SAS, IAK, and TIS were supported
by Russian Ministry of Science and Education under the 5–100 Excellence Programme.
The work of YSA and TIA was supported by the Ministry of Education and Science of
the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4).
FAK is supported by the ERC Consolidator Grant (ChrFL: 771209)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sergei A.
full_name: Slavskii, Sergei A.
last_name: Slavskii
- first_name: Ivan A.
full_name: Kuznetsov, Ivan A.
last_name: Kuznetsov
- first_name: Tatiana I.
full_name: Shashkova, Tatiana I.
last_name: Shashkova
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Tatiana I.
full_name: Axenovich, Tatiana I.
last_name: Axenovich
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yurii S.
full_name: Aulchenko, Yurii S.
last_name: Aulchenko
citation:
ama: Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation
for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091.
doi:10.1038/s41431-021-00836-7
apa: Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich,
T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation
for adult height. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-021-00836-7
chicago: Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A.
Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The
Limits of Normal Approximation for Adult Height.” European Journal of Human
Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7.
ieee: S. A. Slavskii et al., “The limits of normal approximation for adult
height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature,
pp. 1082–1091, 2021.
ista: Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov
F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European
Journal of Human Genetics. 29(7), 1082–1091.
mla: Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.”
European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021,
pp. 1082–91, doi:10.1038/s41431-021-00836-7.
short: S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich,
F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2025-07-10T12:02:05Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1038/s41431-021-00836-7
ec_funded: 1
external_id:
isi:
- '000625853200001'
pmid:
- '33664501'
file:
- access_level: open_access
checksum: a676d76f91b0dbe0504c63e469129c2a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:14:36Z
date_updated: 2021-08-16T09:14:36Z
file_id: '9921'
file_name: 2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf
file_size: 1079395
relation: main_file
success: 1
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- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1082-1091
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- 1476-5438
issn:
- 1018-4813
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The limits of normal approximation for adult height
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: 29
year: '2021'
...
---
_id: '9905'
abstract:
- lang: eng
text: Vaccines are thought to be the best available solution for controlling the
ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains
may come too rapidly for current vaccine developments to alleviate the health,
economic and social consequences of the pandemic. To quantify and characterize
the risk of such a scenario, we created a SIR-derived model with initial stochastic
dynamics of the vaccine-resistant strain to study the probability of its emergence
and establishment. Using parameters realistically resembling SARS-CoV-2 transmission,
we model a wave-like pattern of the pandemic and consider the impact of the rate
of vaccination and the strength of non-pharmaceutical intervention measures on
the probability of emergence of a resistant strain. As expected, we found that
a fast rate of vaccination decreases the probability of emergence of a resistant
strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions
happened at a time when most individuals of the population have already been vaccinated
the probability of emergence of a resistant strain was greatly increased. Consequently,
we show that a period of transmission reduction close to the end of the vaccination
campaign can substantially reduce the probability of resistant strain establishment.
Our results suggest that policymakers and individuals should consider maintaining
non-pharmaceutical interventions and transmission-reducing behaviours throughout
the entire vaccination period.
acknowledgement: We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta,
Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants
of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España
for useful comments. The opinions expressed in this document are exclusively of
the authors and, therefore, do not necessarily coincide with those of the Banco
de España or the Eurosystem. ETD is supported by the Swiss National Science and
Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator
Grant (771209-CharFL).
article_number: '15729'
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Yuliya A.
full_name: Kulikova, Yuliya A.
last_name: Kulikova
- first_name: Emmanouil T.
full_name: Dermitzakis, Emmanouil T.
last_name: Dermitzakis
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission
and vaccination impact the fate of vaccine-resistant strains. Scientific Reports.
2021;11(1). doi:10.1038/s41598-021-95025-3
apa: Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021).
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3
chicago: Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor
Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate
of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021.
https://doi.org/10.1038/s41598-021-95025-3.
ieee: S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of
SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,”
Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.
ista: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2
transmission and vaccination impact the fate of vaccine-resistant strains. Scientific
Reports. 11(1), 15729.
mla: Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact
the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no.
1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.
short: S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports
11 (2021).
date_created: 2021-08-15T22:01:26Z
date_published: 2021-07-30T00:00:00Z
date_updated: 2026-04-07T12:34:57Z
day: '30'
ddc:
- '570'
- '610'
department:
- _id: FyKo
doi: 10.1038/s41598-021-95025-3
ec_funded: 1
external_id:
isi:
- '000683329100001'
pmid:
- '34330988'
file:
- access_level: open_access
checksum: ac86892ed17e6724c7251844da5cef5c
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T11:36:49Z
date_updated: 2021-08-16T11:36:49Z
file_id: '9927'
file_name: 2021_ScientificReports_Rella.pdf
file_size: 3432001
relation: main_file
success: 1
file_date_updated: 2021-08-16T11:36:49Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/
record:
- id: '20811'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains
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: 11
year: '2021'
...
---
_id: '15071'
abstract:
- lang: eng
text: "A mesophilic methanogenic culture, designated JL01, was isolated from Holocene
permafrost in the Russian Arctic [1]. After long-term extensive cultivation at
15°C it turned out to be a tied binary culture of archaeal (JL01) and bacterial
(Sphaerochaeta associata GLS2) strains.\r\nStrain JL01 was a strict anaerobe and
grew on methanol, acetate and methylamines as energy and carbon sources. Cells
were irregular coccoid, non-motile, non-spore-forming, and Gram-stainpositive.
Optimum conditions for growth were 24-28 oC, pH 6.8–7.3 and 0.075-0.1 M NaCl.\r\nPhylogenetic
tree reconstructions based on 16S rRNA and concatenated alignment of broadly\r\nconserved
protein-coding genes revealed its close relation to Methanosarcina mazei S-6\r\nT
(similarity 99.5%). The comparison of whole genomic sequences (ANI) of the isolate
and the type strain of M.mazei was 98.5%, which is higher than the values recommended
for new species. Thus strain JL01 (=VKM B-2370=JCM 31898) represents the first
M. mazei isolated from permanently subzero Arcticsediments. The long-term co-cultivation
of JL01 with S. associata GLS2T showed the methane production without any additional
carbon and energy sources. Genome analysis of S. associata GLS2T revealed putative
genes involved in methanochondroithin catabolism."
acknowledgement: "The work was supported by of Russian Foundation of Basic Research:
grant № 19-04-00831 for Viktoria Shcherbakova and Olga Troshina, grant № 18-34-00334
for Viktoriia Oshurkova and Vladimir Trubitsyn. \r\nWe thank Dr Natalia Suzina (IBPM
RAS, Federal Research Center Pushchino Center for\r\nBiological Research RAS) for
the help with the microscopic studies, respectively; Dr. Margarita Meyer (Division
of Genetics, Department of Medicine, BWH and HMS, USA) and Dr Fedor Kondrashov (IST,
Austria) for their help in obtaining the genomic sequence of strain JL01. "
article_processing_charge: Yes
author:
- first_name: Viktoriia
full_name: Oshurkova, Viktoriia
last_name: Oshurkova
- first_name: Olga
full_name: Troshina, Olga
last_name: Troshina
- first_name: Vladimir
full_name: Trubitsyn, Vladimir
last_name: Trubitsyn
- first_name: Yana
full_name: Ryzhmanova, Yana
last_name: Ryzhmanova
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Viktoria
full_name: Shcherbakova, Viktoria
last_name: Shcherbakova
citation:
ama: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova
V. Characterization of methanosarcina mazei JL01 isolated from holocene arctic
permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta
associata GLS2T. In: Proceedings of 1st International Electronic Conference
on Microbiology. MDPI; 2020. doi:10.3390/ecm2020-07116'
apa: 'Oshurkova, V., Troshina, O., Trubitsyn, V., Ryzhmanova, Y., Bochkareva, O.,
& Shcherbakova, V. (2020). Characterization of methanosarcina mazei JL01 isolated
from holocene arctic permafrost and study of the archaeon cooperation with bacterium
Sphaerochaeta associata GLS2T. In Proceedings of 1st International Electronic
Conference on Microbiology. Virtual: MDPI. https://doi.org/10.3390/ecm2020-07116'
chicago: Oshurkova, Viktoriia, Olga Troshina, Vladimir Trubitsyn, Yana Ryzhmanova,
Olga Bochkareva, and Viktoria Shcherbakova. “Characterization of Methanosarcina
Mazei JL01 Isolated from Holocene Arctic Permafrost and Study of the Archaeon
Cooperation with Bacterium Sphaerochaeta Associata GLS2T.” In Proceedings of
1st International Electronic Conference on Microbiology. MDPI, 2020. https://doi.org/10.3390/ecm2020-07116.
ieee: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, and
V. Shcherbakova, “Characterization of methanosarcina mazei JL01 isolated from
holocene arctic permafrost and study of the archaeon cooperation with bacterium
Sphaerochaeta associata GLS2T,” in Proceedings of 1st International Electronic
Conference on Microbiology, Virtual, 2020.
ista: 'Oshurkova V, Troshina O, Trubitsyn V, Ryzhmanova Y, Bochkareva O, Shcherbakova
V. 2020. Characterization of methanosarcina mazei JL01 isolated from holocene
arctic permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta
associata GLS2T. Proceedings of 1st International Electronic Conference on Microbiology.
ECM: Electronic Conference on Microbiology.'
mla: Oshurkova, Viktoriia, et al. “Characterization of Methanosarcina Mazei JL01
Isolated from Holocene Arctic Permafrost and Study of the Archaeon Cooperation
with Bacterium Sphaerochaeta Associata GLS2T.” Proceedings of 1st International
Electronic Conference on Microbiology, MDPI, 2020, doi:10.3390/ecm2020-07116.
short: V. Oshurkova, O. Troshina, V. Trubitsyn, Y. Ryzhmanova, O. Bochkareva, V.
Shcherbakova, in:, Proceedings of 1st International Electronic Conference on Microbiology,
MDPI, 2020.
conference:
end_date: 2020-11-30
location: Virtual
name: 'ECM: Electronic Conference on Microbiology'
start_date: 2020-11-02
date_created: 2024-03-04T11:41:31Z
date_published: 2020-11-02T00:00:00Z
date_updated: 2024-03-20T08:06:22Z
day: '02'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.3390/ecm2020-07116
file:
- access_level: open_access
checksum: d1914af7811a21a4b2744eb51b5834e3
content_type: application/pdf
creator: dernst
date_created: 2024-03-20T08:05:46Z
date_updated: 2024-03-20T08:05:46Z
file_id: '15127'
file_name: 2020_ECM_Oshurkova.pdf
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language:
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month: '11'
oa: 1
oa_version: Published Version
publication: Proceedings of 1st International Electronic Conference on Microbiology
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: Characterization of methanosarcina mazei JL01 isolated from holocene arctic
permafrost and study of the archaeon cooperation with bacterium Sphaerochaeta associata
GLS2T
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
year: '2020'
...
---
_id: '8320'
abstract:
- lang: eng
text: The genetic code is considered to use five nucleic bases (adenine, guanine,
cytosine, thymine and uracil), which form two pairs for encoding information in
DNA and two pairs for encoding information in RNA. Nevertheless, in recent years
several artificial base pairs have been developed in attempts to expand the genetic
code. Employment of these additional base pairs increases the information capacity
and variety of DNA sequences, and provides a platform for the site-specific, enzymatic
incorporation of extra functional components into DNA and RNA. As a result, of
the development of such expanded systems, many artificial base pairs have been
synthesized and tested under various conditions. Following many stages of enhancement,
unnatural base pairs have been modified to eliminate their weak points, qualifying
them for specific research needs. Moreover, the first attempts to create a semi-synthetic
organism containing DNA with unnatural base pairs seem to have been successful.
This further extends the possible applications of these kinds of pairs. Herein,
we describe the most significant qualities of unnatural base pairs and their actual
applications.
acknowledgement: We would like to thank our co-workers and members of the Alkalaeva
lab for participating in discussions about the topics covered in this essay.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mukba, S. A.
last_name: Mukba
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: P. M.
full_name: Kolosov, P. M.
last_name: Kolosov
- first_name: E. Y.
full_name: Shuvalova, E. Y.
last_name: Shuvalova
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding
the genetic code: Unnatural base pairs in biological systems. Molecular Biology.
2020;54(4):475-484. doi:10.1134/S0026893320040111'
apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V.,
& Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs
in biological systems. Molecular Biology. Springer Nature. https://doi.org/10.1134/S0026893320040111'
chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova,
and E. Z. Alkalaeva. “Expanding the Genetic Code: Unnatural Base Pairs in Biological
Systems.” Molecular Biology. Springer Nature, 2020. https://doi.org/10.1134/S0026893320040111.'
ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and
E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological
systems,” Molecular Biology, vol. 54, no. 4. Springer Nature, pp. 475–484,
2020.'
ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020.
Expanding the genetic code: Unnatural base pairs in biological systems. Molecular
Biology. 54(4), 475–484.'
mla: 'Mukba, S. A., et al. “Expanding the Genetic Code: Unnatural Base Pairs in
Biological Systems.” Molecular Biology, vol. 54, no. 4, Springer Nature,
2020, pp. 475–84, doi:10.1134/S0026893320040111.'
short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
Molecular Biology 54 (2020) 475–484.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-08-19T00:00:00Z
date_updated: 2025-07-10T11:57:02Z
day: '19'
department:
- _id: FyKo
doi: 10.1134/S0026893320040111
external_id:
isi:
- '000562110300001'
intvolume: ' 54'
isi: 1
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 475-484
publication: Molecular Biology
publication_identifier:
eissn:
- 1608-3245
issn:
- 0026-8933
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8321'
relation: original
status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2020'
...
---
_id: '8321'
abstract:
- lang: eng
text: The genetic code is considered to use five nucleic bases (adenine, guanine,
cytosine, thymine and uracil), which form two pairs for encoding information in
DNA and two pairs for encoding information in RNA. Nevertheless, in recent years
several artificial base pairs have been developed in attempts to expand the genetic
code. Employment of these additional base pairs increases the information capacity
and variety of DNA sequences, and provides a platform for the site-specific, enzymatic
incorporation of extra functional components into DNA and RNA. As a result, of
the development of such expanded systems, many artificial base pairs have been
synthesized and tested under various conditions. Following many stages of enhancement,
unnatural base pairs have been modified to eliminate their weak points, qualifying
them for specific research needs. Moreover, the first attempts to create a semi-synthetic
organism containing DNA with unnatural base pairs seem to have been successful.
This further extends the possible applications of these kinds of pairs. Herein,
we describe the most significant qualities of unnatural base pairs and their actual
applications.
article_processing_charge: No
article_type: original
author:
- first_name: S. A.
full_name: Mukba, S. A.
last_name: Mukba
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: P. M.
full_name: Kolosov, P. M.
last_name: Kolosov
- first_name: E. Y.
full_name: Shuvalova, E. Y.
last_name: Shuvalova
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. Expanding
the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia
biologiia. 2020;54(4):531-541. doi:10.31857/S0026898420040126'
apa: 'Mukba, S. A., Vlasov, P., Kolosov, P. M., Shuvalova, E. Y., Egorova, T. V.,
& Alkalaeva, E. Z. (2020). Expanding the genetic code: Unnatural base pairs
in biological systems. Molekuliarnaia biologiia. Russian Academy of Sciences.
https://doi.org/10.31857/S0026898420040126'
chicago: 'Mukba, S. A., Petr Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova,
and E. Z. Alkalaeva. “Expanding the genetic code: Unnatural base pairs in biological
systems.” Molekuliarnaia biologiia. Russian Academy of Sciences, 2020.
https://doi.org/10.31857/S0026898420040126.'
ieee: 'S. A. Mukba, P. Vlasov, P. M. Kolosov, E. Y. Shuvalova, T. V. Egorova, and
E. Z. Alkalaeva, “Expanding the genetic code: Unnatural base pairs in biological
systems,” Molekuliarnaia biologiia, vol. 54, no. 4. Russian Academy of
Sciences, pp. 531–541, 2020.'
ista: 'Mukba SA, Vlasov P, Kolosov PM, Shuvalova EY, Egorova TV, Alkalaeva EZ. 2020.
Expanding the genetic code: Unnatural base pairs in biological systems. Molekuliarnaia
biologiia. 54(4), 531–541.'
mla: 'Mukba, S. A., et al. “Expanding the genetic code: Unnatural base pairs in
biological systems.” Molekuliarnaia biologiia, vol. 54, no. 4, Russian
Academy of Sciences, 2020, pp. 531–41, doi:10.31857/S0026898420040126.'
short: S.A. Mukba, P. Vlasov, P.M. Kolosov, E.Y. Shuvalova, T.V. Egorova, E.Z. Alkalaeva,
Molekuliarnaia biologiia 54 (2020) 531–541.
date_created: 2020-08-30T22:01:11Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2025-07-10T11:57:03Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420040126
external_id:
pmid:
- '32799218'
intvolume: ' 54'
issue: '4'
language:
- iso: rus
month: '07'
oa_version: None
page: 531-541
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
issn:
- 0026-8984
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '8320'
relation: translation
status: public
scopus_import: '1'
status: public
title: 'Expanding the genetic code: Unnatural base pairs in biological systems'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2020'
...
---
_id: '8645'
abstract:
- lang: eng
text: 'Epistasis, the context-dependence of the contribution of an amino acid substitution
to fitness, is common in evolution. To detect epistasis, fitness must be measured
for at least four genotypes: the reference genotype, two different single mutants
and a double mutant with both of the single mutations. For higher-order epistasis
of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional
hypercube in genotype space forming a ‘combinatorially complete dataset’. So far,
only a handful of such datasets have been produced by manual curation. Concurrently,
random mutagenesis experiments have produced measurements of fitness and other
phenotypes in a high-throughput manner, potentially containing a number of combinatorially
complete datasets. We present an effective recursive algorithm for finding all
hypercube structures in random mutagenesis experimental data. To test the algorithm,
we applied it to the data from a recent HIS3 protein dataset and found all 199
847 053 unique combinatorially complete genotype combinations of dimensionality
ranging from 2 to 12. The algorithm may be useful for researchers looking for
higher-order epistasis in their high-throughput experimental data.'
acknowledgement: 'This work was supported by the European Research Council under the
European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement
335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute
of Science and Technology. The work was started at the School of Molecular and Theoretical
Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman
Scientists Support Grant in Centre for Genomic Regulation (CRG). '
article_processing_charge: No
article_type: original
author:
- first_name: Laura A
full_name: Esteban, Laura A
last_name: Esteban
- first_name: Lyubov R
full_name: Lonishin, Lyubov R
last_name: Lonishin
- first_name: Daniil M
full_name: Bobrovskiy, Daniil M
last_name: Bobrovskiy
- first_name: Gregory
full_name: Leleytner, Gregory
last_name: Leleytner
- first_name: Natalya S
full_name: Bogatyreva, Natalya S
last_name: Bogatyreva
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: 'Dmitry N '
full_name: 'Ivankov, Dmitry N '
last_name: Ivankov
citation:
ama: 'Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million
combinatorially complete datasets from a single experiment. Bioinformatics.
2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841'
apa: 'Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva,
N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million
combinatorially complete datasets from a single experiment. Bioinformatics.
Oxford University Press. https://doi.org/10.1093/bioinformatics/btz841'
chicago: 'Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner,
Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME:
Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.”
Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btz841.'
ieee: 'L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially
complete datasets from a single experiment,” Bioinformatics, vol. 36, no.
6. Oxford University Press, pp. 1960–1962, 2020.'
ista: 'Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov
F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete
datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.'
mla: 'Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially
Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no.
6, Oxford University Press, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.'
short: L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva,
F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.
date_created: 2020-10-11T22:01:14Z
date_published: 2020-03-15T00:00:00Z
date_updated: 2025-05-14T11:04:01Z
day: '15'
ddc:
- '000'
- '570'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/btz841
ec_funded: 1
external_id:
isi:
- '000538696800054'
pmid:
- '31742320'
file:
- access_level: open_access
checksum: 21d6f71839deb3b83e4a356193f72767
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T12:02:09Z
date_updated: 2020-10-12T12:02:09Z
file_id: '8649'
file_name: 2020_Bioinformatics_Esteban.pdf
file_size: 308341
relation: main_file
success: 1
file_date_updated: 2020-10-12T12:02:09Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1960-1962
pmid: 1
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Bioinformatics
publication_identifier:
eissn:
- 1460-2059
issn:
- 1367-4803
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'HypercubeME: Two hundred million combinatorially complete datasets from a
single experiment'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2020'
...
---
_id: '8700'
abstract:
- lang: eng
text: Translation termination is a finishing step of protein biosynthesis. The significant
role in this process belongs not only to protein factors of translation termination
but also to the nearest nucleotide environment of stop codons. There are numerous
descriptions of stop codons readthrough, which is due to specific nucleotide sequences
behind them. However, represented data are segmental and don’t explain the mechanism
of the nucleotide context influence on translation termination. It is well known
that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for
G/C-rich genes, which is related to an expression level of these genes. We investigated
the connection between a frequency of nucleotides occurrence in 3' area of stop
codons in the human genome and their influence on translation termination efficiency.
We found that 3' context motif, which is cognate to the sequence of a stop codon,
stimulates translation termination. At the same time, the nucleotide composition
of 3' sequence that differs from stop codon, decreases translation termination
efficiency.
acknowledgement: We would like to thank the staff of CCU Genome for sequencing, Tat’yana
Pestova, Christopher Helen, and Lyudmila Yur’evna Frolova for the plasmids provided,
as well as the laboratory staff for productive discussion of the results. We also
thank former laboratory employees Yuliya Vladimirovna Bocharova and Polina Nikolaevna
Kryuchkova for the exceptional contribution to the present work.
article_processing_charge: No
article_type: original
author:
- first_name: E. E.
full_name: Sokolova, E. E.
last_name: Sokolova
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: A. V.
full_name: Shuvalov, A. V.
last_name: Shuvalov
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molecular Biology. 2020;54(5):739-748. doi:10.1134/S0026893320050088
apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva,
E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes. Molecular Biology. Springer Nature.
https://doi.org/10.1134/S0026893320050088
chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z.
Alkalaeva. “The Influence of A/G Composition of 3’ Stop Codon Contexts on Translation
Termination Efficiency in Eukaryotes.” Molecular Biology. Springer Nature,
2020. https://doi.org/10.1134/S0026893320050088.
ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva,
“The influence of A/G composition of 3’ stop codon contexts on translation termination
efficiency in eukaryotes,” Molecular Biology, vol. 54, no. 5. Springer
Nature, pp. 739–748, 2020.
ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molecular Biology. 54(5), 739–748.
mla: Sokolova, E. E., et al. “The Influence of A/G Composition of 3’ Stop Codon
Contexts on Translation Termination Efficiency in Eukaryotes.” Molecular Biology,
vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:10.1134/S0026893320050088.
short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molecular
Biology 54 (2020) 739–748.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2025-07-10T12:01:20Z
day: '01'
department:
- _id: FyKo
doi: 10.1134/S0026893320050088
external_id:
isi:
- '000579441200009'
intvolume: ' 54'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 739-748
publication: Molecular Biology
publication_identifier:
eissn:
- 1608-3245
issn:
- 0026-8933
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '8701'
relation: original
status: public
scopus_import: '1'
status: public
title: The influence of A/G composition of 3' stop codon contexts on translation termination
efficiency in eukaryotes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2020'
...
---
_id: '8701'
abstract:
- lang: eng
text: Translation termination is a finishing step of protein biosynthesis. The significant
role in this process belongs not only to protein factors of translation termination
but also to the nearest nucleotide environment of stop codons. There are numerous
descriptions of stop codons readthrough, which is due to specific nucleotide sequences
behind them. However, represented data are segmental and don’t explain the mechanism
of the nucleotide context influence on translation termination. It is well known
that stop codon UAA usage is preferential for A/T-rich genes, and UAG, UGA—for
G/C-rich genes, which is related to an expression level of these genes. We investigated
the connection between a frequency of nucleotides occurrence in 3' area of stop
codons in the human genome and their influence on translation termination efficiency.
We found that 3' context motif, which is cognate to the sequence of a stop codon,
stimulates translation termination. At the same time, the nucleotide composition
of 3' sequence that differs from stop codon, decreases translation termination
efficiency.
article_processing_charge: No
article_type: original
author:
- first_name: E. E.
full_name: Sokolova, E. E.
last_name: Sokolova
- first_name: Petr
full_name: Vlasov, Petr
id: 38BB9AC4-F248-11E8-B48F-1D18A9856A87
last_name: Vlasov
- first_name: T. V.
full_name: Egorova, T. V.
last_name: Egorova
- first_name: A. V.
full_name: Shuvalov, A. V.
last_name: Shuvalov
- first_name: E. Z.
full_name: Alkalaeva, E. Z.
last_name: Alkalaeva
citation:
ama: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molekuliarnaia biologiia. 2020;54(5):837-848. doi:10.31857/S0026898420050080
apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., & Alkalaeva,
E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes. Molekuliarnaia biologiia. Russian
Academy of Sciences. https://doi.org/10.31857/S0026898420050080
chicago: Sokolova, E. E., Petr Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z.
Alkalaeva. “The influence of A/G composition of 3’ stop codon contexts on translation
termination efficiency in eukaryotes.” Molekuliarnaia biologiia. Russian
Academy of Sciences, 2020. https://doi.org/10.31857/S0026898420050080.
ieee: E. E. Sokolova, P. Vlasov, T. V. Egorova, A. V. Shuvalov, and E. Z. Alkalaeva,
“The influence of A/G composition of 3’ stop codon contexts on translation termination
efficiency in eukaryotes,” Molekuliarnaia biologiia, vol. 54, no. 5. Russian
Academy of Sciences, pp. 837–848, 2020.
ista: Sokolova EE, Vlasov P, Egorova TV, Shuvalov AV, Alkalaeva EZ. 2020. The influence
of A/G composition of 3’ stop codon contexts on translation termination efficiency
in eukaryotes. Molekuliarnaia biologiia. 54(5), 837–848.
mla: Sokolova, E. E., et al. “The influence of A/G composition of 3’ stop codon
contexts on translation termination efficiency in eukaryotes.” Molekuliarnaia
biologiia, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48,
doi:10.31857/S0026898420050080.
short: E.E. Sokolova, P. Vlasov, T.V. Egorova, A.V. Shuvalov, E.Z. Alkalaeva, Molekuliarnaia
biologiia 54 (2020) 837–848.
date_created: 2020-10-25T23:01:17Z
date_published: 2020-09-01T00:00:00Z
date_updated: 2025-07-10T12:01:20Z
day: '01'
department:
- _id: FyKo
doi: 10.31857/S0026898420050080
external_id:
pmid:
- '33009793'
intvolume: ' 54'
issue: '5'
language:
- iso: rus
month: '09'
oa_version: None
page: 837-848
pmid: 1
publication: Molekuliarnaia biologiia
publication_identifier:
issn:
- 0026-8984
publication_status: published
publisher: Russian Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '8700'
relation: translation
status: public
scopus_import: '1'
status: public
title: The influence of A/G composition of 3' stop codon contexts on translation termination
efficiency in eukaryotes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2020'
...
---
_id: '7622'
abstract:
- lang: eng
text: The International Young Physicists' Tournament (IYPT) continued in 2018 in
Beijing, China and 2019 in Warsaw, Poland with its 31st and 32nd editions. The
IYPT is a modern scientific competition for teams of high school students, also
known as the Physics World Cup. It involves long-term theoretical and experimental
work focused on solving 17 publicly announced open-ended problems in teams of
five. On top of that, teams have to present their solutions in front of other
teams and a scientific jury, and get opposed and reviewed by their peers. Here
we present a brief information about the competition with a specific focus on
one of the IYPT 2018 tasks, the 'Ring Oiler'. This seemingly simple mechanical
problem appeared to be of such a complexity that even the dozens of participating
teams and jurying scientists were not able to solve all of its subtleties.
article_number: '034001'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Martin
full_name: Plesch, Martin
last_name: Plesch
- first_name: Samuel
full_name: Plesník, Samuel
last_name: Plesník
- first_name: Natalia
full_name: Ruzickova, Natalia
id: D2761128-D73D-11E9-A1BF-BA0DE6697425
last_name: Ruzickova
citation:
ama: Plesch M, Plesník S, Ruzickova N. The IYPT and the “Ring Oiler” problem. European
Journal of Physics. 2020;41(3). doi:10.1088/1361-6404/ab6414
apa: Plesch, M., Plesník, S., & Ruzickova, N. (2020). The IYPT and the “Ring
Oiler” problem. European Journal of Physics. IOP Publishing. https://doi.org/10.1088/1361-6404/ab6414
chicago: Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the
‘Ring Oiler’ Problem.” European Journal of Physics. IOP Publishing, 2020.
https://doi.org/10.1088/1361-6404/ab6414.
ieee: M. Plesch, S. Plesník, and N. Ruzickova, “The IYPT and the ‘Ring Oiler’ problem,”
European Journal of Physics, vol. 41, no. 3. IOP Publishing, 2020.
ista: Plesch M, Plesník S, Ruzickova N. 2020. The IYPT and the ‘Ring Oiler’ problem.
European Journal of Physics. 41(3), 034001.
mla: Plesch, Martin, et al. “The IYPT and the ‘Ring Oiler’ Problem.” European
Journal of Physics, vol. 41, no. 3, 034001, IOP Publishing, 2020, doi:10.1088/1361-6404/ab6414.
short: M. Plesch, S. Plesník, N. Ruzickova, European Journal of Physics 41 (2020).
date_created: 2020-03-31T11:25:04Z
date_published: 2020-02-24T00:00:00Z
date_updated: 2026-04-02T14:22:29Z
day: '24'
ddc:
- '530'
department:
- _id: FyKo
doi: 10.1088/1361-6404/ab6414
external_id:
arxiv:
- '1910.03290'
isi:
- '000537425400001'
file:
- access_level: open_access
checksum: 47dda164e33b6c0c6c3ed14aad298376
content_type: application/pdf
creator: dernst
date_created: 2020-04-06T08:53:53Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7641'
file_name: 2020_EuropJourPhysics_Plesch.pdf
file_size: 1533672
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '3'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: European Journal of Physics
publication_identifier:
eissn:
- 1361-6404
issn:
- 0143-0807
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: The IYPT and the 'Ring Oiler' problem
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: 41
year: '2020'
...
---
_id: '7931'
abstract:
- lang: eng
text: In the course of sample preparation for Next Generation Sequencing (NGS),
DNA is fragmented by various methods. Fragmentation shows a persistent bias with
regard to the cleavage rates of various dinucleotides. With the exception of CpG
dinucleotides the previously described biases were consistent with results of
the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides
including the methylated CpG and unmethylated CpG dinucleotides using data of
the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that
the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides.
Using this information, we developed a classifier for distinguishing cancer and
healthy tissues based on their CpG islands statuses of the fragmentation. A simple
Support Vector Machine classifier based on this algorithm shows an accuracy of
84%. The proposed method allows the detection of epigenetic markers purely based
on mechanochemical DNA fragmentation, which can be detected by a simple analysis
of the NGS sequencing data.
article_number: '8635'
article_processing_charge: No
article_type: original
author:
- first_name: Leonid A.
full_name: Uroshlev, Leonid A.
last_name: Uroshlev
- first_name: Eldar T.
full_name: Abdullaev, Eldar T.
last_name: Abdullaev
- first_name: Iren R.
full_name: Umarova, Iren R.
last_name: Umarova
- first_name: Irina A.
full_name: Il’Icheva, Irina A.
last_name: Il’Icheva
- first_name: Larisa A.
full_name: Panchenko, Larisa A.
last_name: Panchenko
- first_name: Robert V.
full_name: Polozov, Robert V.
last_name: Polozov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yury D.
full_name: Nechipurenko, Yury D.
last_name: Nechipurenko
- first_name: Sergei L.
full_name: Grokhovsky, Sergei L.
last_name: Grokhovsky
citation:
ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of
the methylation level of CpG islands from NGS data. Scientific Reports.
2020;10. doi:10.1038/s41598-020-65406-1
apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko,
L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports.
Springer Nature. https://doi.org/10.1038/s41598-020-65406-1
chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva,
Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko,
and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level
of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020.
https://doi.org/10.1038/s41598-020-65406-1.
ieee: L. A. Uroshlev et al., “A method for identification of the methylation
level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer
Nature, 2020.
ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov
RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports. 10,
8635.
mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation
Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635,
Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.
short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko,
R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports
10 (2020).
date_created: 2020-06-07T22:00:51Z
date_published: 2020-05-25T00:00:00Z
date_updated: 2026-04-03T09:26:06Z
day: '25'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-020-65406-1
external_id:
isi:
- '000560774200007'
pmid:
- '32451390'
file:
- access_level: open_access
checksum: 099e51611a5b7ca04244d03b2faddf33
content_type: application/pdf
creator: dernst
date_created: 2020-06-08T06:27:32Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7947'
file_name: 2020_ScientificReports_Uroshlev.pdf
file_size: 1001724
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Scientific Reports
publication_identifier:
eissn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A method for identification of the methylation level of CpG islands from NGS
data
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: 10
year: '2020'
...
---
_id: '7603'
abstract:
- lang: eng
text: Plants are exposed to a variety of abiotic and biotic stresses that may result
in DNA damage. Endogenous processes - such as DNA replication, DNA recombination,
respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore
essential to understand the strategies plants have developed for DNA damage detection,
signaling, and repair. Alternative splicing (AS) is a key post-transcriptional
process with a role in regulation of gene expression. Recent studies demonstrate
that the majority of intron-containing genes in plants are alternatively spliced,
highlighting the importance of AS in plant development and stress response. Not
only does AS ensure a versatile proteome and influence the abundance and availability
of proteins greatly, it has also emerged as an important player in the DNA damage
response (DDR) in animals. Despite extensive studies of DDR carried out in plants,
its regulation at the level of AS has not been comprehensively addressed. Here,
we provide some insights into the interplay between AS and DDR in plants.
article_number: '91'
article_processing_charge: No
article_type: original
author:
- first_name: Barbara Anna
full_name: Nimeth, Barbara Anna
last_name: Nimeth
- first_name: Stefan
full_name: Riegler, Stefan
id: FF6018E0-D806-11E9-8E43-0B14E6697425
last_name: Riegler
orcid: 0000-0003-3413-1343
- first_name: Maria
full_name: Kalyna, Maria
last_name: Kalyna
citation:
ama: Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response
in plants. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.00091
apa: Nimeth, B. A., Riegler, S., & Kalyna, M. (2020). Alternative splicing and
DNA damage response in plants. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.00091
chicago: Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing
and DNA Damage Response in Plants.” Frontiers in Plant Science. Frontiers,
2020. https://doi.org/10.3389/fpls.2020.00091.
ieee: B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage
response in plants,” Frontiers in Plant Science, vol. 11. Frontiers, 2020.
ista: Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage
response in plants. Frontiers in Plant Science. 11, 91.
mla: Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response
in Plants.” Frontiers in Plant Science, vol. 11, 91, Frontiers, 2020, doi:10.3389/fpls.2020.00091.
short: B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).
date_created: 2020-03-22T23:00:46Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2026-04-16T08:28:17Z
day: '19'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.3389/fpls.2020.00091
external_id:
isi:
- '000518903600001'
file:
- access_level: open_access
checksum: 57c37209f7b6712ced86c0f11b2be74e
content_type: application/pdf
creator: dernst
date_created: 2020-03-23T09:03:40Z
date_updated: 2020-07-14T12:48:01Z
file_id: '7607'
file_name: 2020_FrontiersPlants_Nimeth.pdf
file_size: 507414
relation: main_file
file_date_updated: 2020-07-14T12:48:01Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664-462X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Alternative splicing and DNA damage response in plants
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: 11
year: '2020'
...
---
_id: '7889'
abstract:
- lang: eng
text: Autoluminescent plants engineered to express a bacterial bioluminescence gene
cluster in plastids have not been widely adopted because of low light output.
We engineered tobacco plants with a fungal bioluminescence system that converts
caffeic acid (present in all plants) into luciferin and report self-sustained
luminescence that is visible to the naked eye. Our findings could underpin development
of a suite of imaging tools for plants.
acknowledgement: "This study was designed, performed and funded by Planta LLC. We
thank K. Wood for assisting in manuscript development. Planta acknowledges support
from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography
equipment. The Synthetic Biology Group is funded by the MRC London Institute of
Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial
College Research Fellowship. Experiments were partially carried out using equipment
provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences
Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science
Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL.
This project received funding from the European Union’s Horizon 2020 Research and
Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S.
acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of
some of the plasmids was supported by Russian Science Foundation grant 19-74-10102.
Imaging experiments were partially supported by Russian Science Foundation grant
17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science
Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported
by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the
Russian Federation allocated to the Center for Precision Genome Editing and Genetic
Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work
of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which
performed the sequencing and bioinformatic analysis."
article_processing_charge: No
article_type: original
author:
- first_name: Tatiana
full_name: Mitiouchkina, Tatiana
last_name: Mitiouchkina
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Tatiana V.
full_name: Chepurnyh, Tatiana V.
last_name: Chepurnyh
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Tatiana A.
full_name: Karataeva, Tatiana A.
last_name: Karataeva
- first_name: Kseniia A.
full_name: Palkina, Kseniia A.
last_name: Palkina
- first_name: Ekaterina S.
full_name: Shakhova, Ekaterina S.
last_name: Shakhova
- first_name: Liliia I.
full_name: Fakhranurova, Liliia I.
last_name: Fakhranurova
- first_name: Sofia V.
full_name: Chekova, Sofia V.
last_name: Chekova
- first_name: Aleksandra S.
full_name: Tsarkova, Aleksandra S.
last_name: Tsarkova
- first_name: Yaroslav V.
full_name: Golubev, Yaroslav V.
last_name: Golubev
- first_name: Vadim V.
full_name: Negrebetsky, Vadim V.
last_name: Negrebetsky
- first_name: Sergey A.
full_name: Dolgushin, Sergey A.
last_name: Dolgushin
- first_name: Pavel V.
full_name: Shalaev, Pavel V.
last_name: Shalaev
- first_name: Dmitry
full_name: Shlykov, Dmitry
last_name: Shlykov
- first_name: Olesya A.
full_name: Melnik, Olesya A.
last_name: Melnik
- first_name: Victoria O.
full_name: Shipunova, Victoria O.
last_name: Shipunova
- first_name: Sergey M.
full_name: Deyev, Sergey M.
last_name: Deyev
- first_name: Andrey I.
full_name: Bubyrev, Andrey I.
last_name: Bubyrev
- first_name: Alexander S.
full_name: Pushin, Alexander S.
last_name: Pushin
- first_name: Vladimir V.
full_name: Choob, Vladimir V.
last_name: Choob
- first_name: Sergey V.
full_name: Dolgov, Sergey V.
last_name: Dolgov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
- first_name: Karen S.
full_name: Sarkisyan, Karen S.
last_name: Sarkisyan
citation:
ama: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically
encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9
apa: Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh,
T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded
autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9
chicago: Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer,
Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva,
et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology.
Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.
ieee: T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,”
Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020.
ista: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV,
Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV,
Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D,
Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV,
Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded
autoluminescence. Nature Biotechnology. 38, 944–946.
mla: Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.”
Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9.
short: T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V.
Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova,
S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V.
Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S.
Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan,
Nature Biotechnology 38 (2020) 944–946.
date_created: 2020-05-25T15:02:00Z
date_published: 2020-04-27T00:00:00Z
date_updated: 2025-04-14T07:49:47Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41587-020-0500-9
ec_funded: 1
external_id:
isi:
- '000529298800003'
pmid:
- '32341562'
file:
- access_level: open_access
checksum: 1b30467500ec6277229a875b06e196d0
content_type: application/pdf
creator: dernst
date_created: 2020-08-28T08:57:07Z
date_updated: 2021-03-02T23:30:03Z
embargo: 2021-03-01
file_id: '8316'
file_name: 2020_NatureBiotech_Mitiouchkina.pdf
file_size: 1180086
relation: main_file
file_date_updated: 2021-03-02T23:30:03Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Submitted Version
page: 944-946
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41587-020-0578-0
scopus_import: '1'
status: public
title: Plants with genetically encoded autoluminescence
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2020'
...
---
OA_place: repository
OA_type: green
_id: '8707'
abstract:
- lang: eng
text: Dynamic changes in the three-dimensional (3D) organization of chromatin are
associated with central biological processes, such as transcription, replication
and development. Therefore, the comprehensive identification and quantification
of these changes is fundamental to understanding of evolutionary and regulatory
mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity
(CHESS), an algorithm for the comparison of chromatin contact maps and automatic
differential feature extraction. We demonstrate the robustness of CHESS to experimental
variability and showcase its biological applications on (1) interspecies comparisons
of syntenic regions in human and mouse models; (2) intraspecies identification
of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific
aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and
(4) the systematic identification of chromatin contact differences in high-resolution
Capture-C data. In summary, CHESS is a computationally efficient method for the
comparison and classification of changes in chromatin contact data.
acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society,
the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome
Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the
DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project
no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN
to J.M.V.) and the Medical Research Council in the UK. This research was partially
funded by the European Union’s H2020 Framework Programme through the European Research
Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio
de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R.
The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia,
Innovación y Universidades to the European Molecular Biology Laboratory partnership,
the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208,
the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación
y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya
through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing
by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from
the European Regional Development Fund corresponding to the 2014–2020 Smart Growth
Operating Program. S.G. thanks the support from the Company of Biologists (grant
no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship
programme.'
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: ' Galan, Silvia'
last_name: ' Galan'
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
- first_name: Kai
full_name: Kruse, Kai
last_name: Kruse
- first_name: Noelia
full_name: Díaz, Noelia
last_name: Díaz
- first_name: Marc A
full_name: Marti-Renom, Marc A
last_name: Marti-Renom
- first_name: Juan M
full_name: Vaquerizas, Juan M
last_name: Vaquerizas
citation:
ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS
enables quantitative comparison of chromatin contact data and automatic feature
extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y
apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas,
J. M. (2020). CHESS enables quantitative comparison of chromatin contact data
and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y
chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom,
and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature,
2020. https://doi.org/10.1038/s41588-020-00712-y.
ieee: S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M.
Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and
automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature,
pp. 1247–1255, 2020.
ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020.
CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction. Nature Genetics. 52, 1247–1255.
mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer
Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.
short: S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas,
Nature Genetics 52 (2020) 1247–1255.
date_created: 2020-10-25T23:01:20Z
date_published: 2020-10-19T00:00:00Z
date_updated: 2026-06-06T22:30:29Z
day: '19'
department:
- _id: FyKo
doi: 10.1038/s41588-020-00712-y
external_id:
isi:
- '000579693500004'
pmid:
- '33077914'
intvolume: ' 52'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://pmc.ncbi.nlm.nih.gov/articles/PMC7610641/
month: '10'
oa: 1
oa_version: Submitted Version
page: 1247-1255
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '18642'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 52
year: '2020'
...
---
_id: '6506'
abstract:
- lang: eng
text: How does environmental complexity affect the evolution of single genes? Here,
we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase
mutants across 19 different environments—from phenotypically homogeneous single-cell
populations in liquid media to heterogeneous biofilms, plant roots and soil populations.
The effects of individual gene mutations on organismal fitness were highly reproducible
in liquid cultures. However, 84% of the tested alleles showed opposing fitness
effects under different growth conditions (sign environmental pleiotropy). In
colony biofilms and soil samples, different alleles dominated in parallel replica
experiments. Accordingly, we found that in these heterogeneous cell populations
the fate of mutations was dictated by a combination of selection and drift. The
latter relates to programmed prophage excisions that occurred during biofilm development.
Overall, for each condition, a wide range of glutamate dehydrogenase mutations
persisted and sometimes fixated as a result of the combined action of selection,
pleiotropy and chance. However, over longer periods and in multiple environments,
nearly all of this diversity would be lost—across all the environments and conditions
that we tested, the wild type was the fittest allele.
article_processing_charge: No
article_type: original
author:
- first_name: Lianet
full_name: Noda-García, Lianet
last_name: Noda-García
- first_name: Dan
full_name: Davidi, Dan
last_name: Davidi
- first_name: Elisa
full_name: Korenblum, Elisa
last_name: Korenblum
- first_name: Assaf
full_name: Elazar, Assaf
last_name: Elazar
- first_name: Ekaterina
full_name: Putintseva, Ekaterina
id: 2EF67C84-F248-11E8-B48F-1D18A9856A87
last_name: Putintseva
- first_name: Asaph
full_name: Aharoni, Asaph
last_name: Aharoni
- first_name: Dan S.
full_name: Tawfik, Dan S.
last_name: Tawfik
citation:
ama: Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate
genetic diversity in complex bacterial environments. Nature Microbiology.
2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y
apa: Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni,
A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity
in complex bacterial environments. Nature Microbiology. Springer Nature.
https://doi.org/10.1038/s41564-019-0412-y
chicago: Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina
Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate
Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology.
Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y.
ieee: L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity
in complex bacterial environments,” Nature Microbiology, vol. 4, no. 7.
Springer Nature, pp. 1221–1230, 2019.
ista: Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik
DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial
environments. Nature Microbiology. 4(7), 1221–1230.
mla: Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity
in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7,
Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y.
short: L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni,
D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230.
date_created: 2019-05-29T13:03:30Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-28T08:39:47Z
day: '01'
department:
- _id: FyKo
doi: 10.1038/s41564-019-0412-y
external_id:
isi:
- '000480348200017'
intvolume: ' 4'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/340828v2
month: '07'
oa: 1
oa_version: Preprint
page: 1221–1230
publication: Nature Microbiology
publication_identifier:
issn:
- 2058-5276
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chance and pleiotropy dominate genetic diversity in complex bacterial environments
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 4
year: '2019'
...
---
_id: '7181'
abstract:
- lang: eng
text: Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary
predictions1,2, but the complexity of aligning large datasets requires the use
of approximate solutions3, including the progressive algorithm4. Progressive MSA
methods start by aligning the most similar sequences and subsequently incorporate
the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy
declines substantially as the number of sequences is scaled up5. We introduce
a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard
workstation and substantially improves accuracy on datasets larger than 10,000
sequences. Our regressive algorithm works the other way around to the progressive
algorithm and begins by aligning the most dissimilar sequences. It uses an efficient
divide-and-conquer strategy to run third-party alignment methods in linear time,
regardless of their original complexity. Our approach will enable analyses of
extremely large genomic datasets such as the recently announced Earth BioGenome
Project, which comprises 1.5 million eukaryotic genomes6.
article_processing_charge: No
article_type: original
author:
- first_name: Edgar
full_name: Garriga, Edgar
last_name: Garriga
- first_name: Paolo
full_name: Di Tommaso, Paolo
last_name: Di Tommaso
- first_name: Cedrik
full_name: Magis, Cedrik
last_name: Magis
- first_name: Ionas
full_name: Erb, Ionas
last_name: Erb
- first_name: Leila
full_name: Mansouri, Leila
last_name: Mansouri
- first_name: Athanasios
full_name: Baltzis, Athanasios
last_name: Baltzis
- first_name: Hafid
full_name: Laayouni, Hafid
last_name: Laayouni
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Evan
full_name: Floden, Evan
last_name: Floden
- first_name: Cedric
full_name: Notredame, Cedric
last_name: Notredame
citation:
ama: Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470.
doi:10.1038/s41587-019-0333-6
apa: Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,
… Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf
regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6
chicago: Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri,
Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric
Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive
Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.
ieee: E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf
regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature,
pp. 1466–1470, 2019.
ista: Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H,
Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.
mla: Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf
Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature,
2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.
short: E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H.
Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019)
1466–1470.
date_created: 2019-12-15T23:00:43Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2025-07-10T11:54:19Z
day: '01'
department:
- _id: FyKo
doi: 10.1038/s41587-019-0333-6
ec_funded: 1
external_id:
isi:
- '000500748900021'
pmid:
- '31792410'
intvolume: ' 37'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1466-1470
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
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relation: research_data
status: public
scopus_import: '1'
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title: Large multiple sequence alignments with a root-to-leaf regressive method
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2019'
...
---
_id: '9731'
abstract:
- lang: eng
text: OGs with putative pseudogenes by the number of affected genomes in different
chlamydial species. Frameshift and nonsense mutations located less than 60 bp
upstreamof the gene end or present in a single genome from the corresponding OG
were excluded. (CSV 31 kb)
article_processing_charge: No
author:
- first_name: Olga
full_name: Sigalova, Olga
last_name: Sigalova
- first_name: Andrei
full_name: Chaplin, Andrei
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel
full_name: Shelyakin, Pavel
last_name: Shelyakin
- first_name: Vsevolod
full_name: Filaretov, Vsevolod
last_name: Filaretov
- first_name: Evgeny
full_name: Akkuratov, Evgeny
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova O, Chaplin A, Bochkareva O, et al. Additional file 11 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808772.v1
apa: Sigalova, O., Chaplin, A., Bochkareva, O., Shelyakin, P., Filaretov, V., Akkuratov,
E., … Gelfand, M. S. (2019). Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction.
Springer Nature. https://doi.org/10.6084/m9.figshare.9808772.v1
chicago: Sigalova, Olga, Andrei Chaplin, Olga Bochkareva, Pavel Shelyakin, Vsevolod
Filaretov, Evgeny Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional
File 11 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation
and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808772.v1.
ieee: O. Sigalova et al., “Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction.”
Springer Nature, 2019.
ista: Sigalova O, Chaplin A, Bochkareva O, Shelyakin P, Filaretov V, Akkuratov E,
Burskaia V, Gelfand MS. 2019. Additional file 11 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808772.v1.
mla: Sigalova, Olga, et al. Additional File 11 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808772.v1.
short: O. Sigalova, A. Chaplin, O. Bochkareva, P. Shelyakin, V. Filaretov, E. Akkuratov,
V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-07-27T14:09:11Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808772.v1
main_file_link:
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url: https://doi.org/10.6084/m9.figshare.9808772.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
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- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 11 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9783'
abstract:
- lang: eng
text: Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For
the analysis of putative pseudogenes, events located less than 60 bp. away from
gene end or present in a single genome from the corresponding OG were excluded.
(CSV 600 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808760.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 10 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808760.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 10 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808760.v1.
ieee: O. M. Sigalova et al., “Additional file 10 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 10 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808760.v1.
mla: Sigalova, Olga M., et al. Additional File 10 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808760.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-06T07:59:56Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808760.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808760.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 10 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9890'
abstract:
- lang: eng
text: Distribution of OGs with mosaic phyletic patterns across species (complete
genomes only). (CSV 7 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 15 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808802.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 15 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808802.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 15 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808802.v1.
ieee: O. M. Sigalova et al., “Additional file 15 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 15 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808802.v1.
mla: Sigalova, Olga M., et al. Additional File 15 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808802.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-11T14:26:40Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808802.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808802.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 15 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9892'
abstract:
- lang: eng
text: Distribution of OGs with mosaic phyletic patterns across species (all genomes).
(CSV 10 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V
full_name: Chaplin, Andrei V
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 16 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808814.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 16 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808814.v1
chicago: Sigalova, Olga M., Andrei V Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808814.v1.
ieee: O. M. Sigalova et al., “Additional file 16 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 16 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808814.v1.
mla: Sigalova, Olga M., et al. Additional File 16 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808814.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:11:53Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808814.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808814.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 16 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9893'
abstract:
- lang: eng
text: Summary of peripheral genesa phyletic patterns and tree concordance. (CSV
26 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V.
full_name: Chaplin, Andrei V.
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 17 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808820.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 17 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808820.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 17 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808820.v1.
ieee: O. M. Sigalova et al., “Additional file 17 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 17 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808820.v1.
mla: Sigalova, Olga M., et al. Additional File 17 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808820.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:20:10Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808820.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808820.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '6898'
relation: used_in_publication
status: public
status: public
title: Additional file 17 of Chlamydia pan-genomic analysis reveals balance between
host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...