---
_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. <i>Bioinformatics</i>.
    2020;36(6):1960-1962. doi:<a href="https://doi.org/10.1093/bioinformatics/btz841">10.1093/bioinformatics/btz841</a>'
  apa: 'Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva,
    N. S., Kondrashov, F., &#38; Ivankov, D. N. (2020). HypercubeME: Two hundred million
    combinatorially complete datasets from a single experiment. <i>Bioinformatics</i>.
    Oxford Academic. <a href="https://doi.org/10.1093/bioinformatics/btz841">https://doi.org/10.1093/bioinformatics/btz841</a>'
  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.”
    <i>Bioinformatics</i>. Oxford Academic, 2020. <a href="https://doi.org/10.1093/bioinformatics/btz841">https://doi.org/10.1093/bioinformatics/btz841</a>.'
  ieee: 'L. A. Esteban <i>et al.</i>, “HypercubeME: Two hundred million combinatorially
    complete datasets from a single experiment,” <i>Bioinformatics</i>, vol. 36, no.
    6. Oxford Academic, 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.” <i>Bioinformatics</i>, vol. 36, no.
    6, Oxford Academic, 2020, pp. 1960–62, doi:<a href="https://doi.org/10.1093/bioinformatics/btz841">10.1093/bioinformatics/btz841</a>.'
  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: 2023-08-22T09:57:29Z
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
license: https://creativecommons.org/licenses/by-nc/4.0/
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 Academic
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. <i>Molecular Biology</i>. 2020;54(5):739-748. doi:<a href="https://doi.org/10.1134/S0026893320050088">10.1134/S0026893320050088</a>
  apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &#38; Alkalaeva,
    E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation
    termination efficiency in eukaryotes. <i>Molecular Biology</i>. Springer Nature.
    <a href="https://doi.org/10.1134/S0026893320050088">https://doi.org/10.1134/S0026893320050088</a>
  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.” <i>Molecular Biology</i>. Springer Nature,
    2020. <a href="https://doi.org/10.1134/S0026893320050088">https://doi.org/10.1134/S0026893320050088</a>.
  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,” <i>Molecular Biology</i>, 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.” <i>Molecular Biology</i>,
    vol. 54, no. 5, Springer Nature, 2020, pp. 739–48, doi:<a href="https://doi.org/10.1134/S0026893320050088">10.1134/S0026893320050088</a>.
  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: 2023-08-22T10:39:38Z
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:
  - '16083245'
  issn:
  - '00268933'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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. <i>Molekuliarnaia biologiia</i>. 2020;54(5):837-848. doi:<a href="https://doi.org/10.31857/S0026898420050080">10.31857/S0026898420050080</a>
  apa: Sokolova, E. E., Vlasov, P., Egorova, T. V., Shuvalov, A. V., &#38; Alkalaeva,
    E. Z. (2020). The influence of A/G composition of 3’ stop codon contexts on translation
    termination efficiency in eukaryotes. <i>Molekuliarnaia biologiia</i>. Russian
    Academy of Sciences. <a href="https://doi.org/10.31857/S0026898420050080">https://doi.org/10.31857/S0026898420050080</a>
  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.” <i>Molekuliarnaia biologiia</i>. Russian
    Academy of Sciences, 2020. <a href="https://doi.org/10.31857/S0026898420050080">https://doi.org/10.31857/S0026898420050080</a>.
  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,” <i>Molekuliarnaia biologiia</i>, 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.” <i>Molekuliarnaia
    biologiia</i>, vol. 54, no. 5, Russian Academy of Sciences, 2020, pp. 837–48,
    doi:<a href="https://doi.org/10.31857/S0026898420050080">10.31857/S0026898420050080</a>.
  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: 2023-08-22T10:39:37Z
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:
  - '00268984'
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 54
year: '2020'
...
---
_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. <i>Nature Genetics</i>. 2020;52:1247-1255. doi:<a href="https://doi.org/10.1038/s41588-020-00712-y">10.1038/s41588-020-00712-y</a>
  apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., &#38; Vaquerizas,
    J. M. (2020). CHESS enables quantitative comparison of chromatin contact data
    and automatic feature extraction. <i>Nature Genetics</i>. Springer Nature. <a
    href="https://doi.org/10.1038/s41588-020-00712-y">https://doi.org/10.1038/s41588-020-00712-y</a>
  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.” <i>Nature Genetics</i>. Springer Nature,
    2020. <a href="https://doi.org/10.1038/s41588-020-00712-y">https://doi.org/10.1038/s41588-020-00712-y</a>.
  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,” <i>Nature Genetics</i>, 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.” <i>Nature Genetics</i>, vol. 52, Springer
    Nature, 2020, pp. 1247–55, doi:<a href="https://doi.org/10.1038/s41588-020-00712-y">10.1038/s41588-020-00712-y</a>.
  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: 2023-08-22T10:37:10Z
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
month: '10'
oa_version: None
page: 1247-1255
pmid: 1
publication: Nature Genetics
publication_identifier:
  eissn:
  - '15461718'
  issn:
  - '10614036'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: CHESS enables quantitative comparison of chromatin contact data and automatic
  feature extraction
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
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. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href="https://doi.org/10.3389/fpls.2020.00091">10.3389/fpls.2020.00091</a>
  apa: Nimeth, B. A., Riegler, S., &#38; Kalyna, M. (2020). Alternative splicing and
    DNA damage response in plants. <i>Frontiers in Plant Science</i>. Frontiers. <a
    href="https://doi.org/10.3389/fpls.2020.00091">https://doi.org/10.3389/fpls.2020.00091</a>
  chicago: Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing
    and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>. Frontiers,
    2020. <a href="https://doi.org/10.3389/fpls.2020.00091">https://doi.org/10.3389/fpls.2020.00091</a>.
  ieee: B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage
    response in plants,” <i>Frontiers in Plant Science</i>, 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.” <i>Frontiers in Plant Science</i>, vol. 11, 91, Frontiers, 2020, doi:<a
    href="https://doi.org/10.3389/fpls.2020.00091">10.3389/fpls.2020.00091</a>.
  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: 2023-08-18T07:05:18Z
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:
  - 1664462X
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
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. <i>European
    Journal of Physics</i>. 2020;41(3). doi:<a href="https://doi.org/10.1088/1361-6404/ab6414">10.1088/1361-6404/ab6414</a>
  apa: Plesch, M., Plesník, S., &#38; Ruzickova, N. (2020). The IYPT and the “Ring
    Oiler” problem. <i>European Journal of Physics</i>. IOP Publishing. <a href="https://doi.org/10.1088/1361-6404/ab6414">https://doi.org/10.1088/1361-6404/ab6414</a>
  chicago: Plesch, Martin, Samuel Plesník, and Natalia Ruzickova. “The IYPT and the
    ‘Ring Oiler’ Problem.” <i>European Journal of Physics</i>. IOP Publishing, 2020.
    <a href="https://doi.org/10.1088/1361-6404/ab6414">https://doi.org/10.1088/1361-6404/ab6414</a>.
  ieee: M. Plesch, S. Plesník, and N. Ruzickova, “The IYPT and the ‘Ring Oiler’ problem,”
    <i>European Journal of Physics</i>, 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.” <i>European
    Journal of Physics</i>, vol. 41, no. 3, 034001, IOP Publishing, 2020, doi:<a href="https://doi.org/10.1088/1361-6404/ab6414">10.1088/1361-6404/ab6414</a>.
  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: 2023-08-18T10:18:29Z
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:
  - '13616404'
  issn:
  - '01430807'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2020'
...
---
_id: '6898'
abstract:
- lang: eng
  text: "Background\r\n\r\nChlamydia are ancient intracellular pathogens with reduced,
    though strikingly conserved genome. Despite their parasitic lifestyle and isolated
    intracellular environment, these bacteria managed to avoid accumulation of deleterious
    mutations leading to subsequent genome degradation characteristic for many parasitic
    bacteria.\r\nResults\r\n\r\nWe report pan-genomic analysis of sixteen species
    from genus Chlamydia including identification and functional annotation of orthologous
    genes, and characterization of gene gains, losses, and rearrangements. We demonstrate
    the overall genome stability of these bacteria as indicated by a large fraction
    of common genes with conserved genomic locations. On the other hand, extreme evolvability
    is confined to several paralogous gene families such as polymorphic membrane proteins
    and phospholipase D, and likely is caused by the pressure from the host immune
    system.\r\nConclusions\r\n\r\nThis combination of a large, conserved core genome
    and a small, evolvable periphery likely reflect the balance between the selective
    pressure towards genome reduction and the need to adapt to escape from the host
    immunity."
article_number: '710'
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. Chlamydia pan-genomic analysis
    reveals balance between host adaptation and selective pressure to genome reduction.
    <i>BMC Genomics</i>. 2019;20(1). doi:<a href="https://doi.org/10.1186/s12864-019-6059-5">10.1186/s12864-019-6059-5</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Chlamydia pan-genomic analysis
    reveals balance between host adaptation and selective pressure to genome reduction.
    <i>BMC Genomics</i>. BioMed Central. <a href="https://doi.org/10.1186/s12864-019-6059-5">https://doi.org/10.1186/s12864-019-6059-5</a>
  chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
    Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
    Gelfand. “Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation
    and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>. BioMed Central,
    2019. <a href="https://doi.org/10.1186/s12864-019-6059-5">https://doi.org/10.1186/s12864-019-6059-5</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Chlamydia pan-genomic analysis reveals balance
    between host adaptation and selective pressure to genome reduction,” <i>BMC Genomics</i>,
    vol. 20, no. 1. BioMed Central, 2019.
  ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
    EE, Burskaia V, Gelfand MS. 2019. Chlamydia pan-genomic analysis reveals balance
    between host adaptation and selective pressure to genome reduction. BMC Genomics.
    20(1), 710.
  mla: Sigalova, Olga M., et al. “Chlamydia Pan-Genomic Analysis Reveals Balance between
    Host Adaptation and Selective Pressure to Genome Reduction.” <i>BMC Genomics</i>,
    vol. 20, no. 1, 710, BioMed Central, 2019, doi:<a href="https://doi.org/10.1186/s12864-019-6059-5">10.1186/s12864-019-6059-5</a>.
  short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
    E.E. Akkuratov, V. Burskaia, M.S. Gelfand, BMC Genomics 20 (2019).
date_created: 2019-09-22T22:00:36Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s12864-019-6059-5
external_id:
  isi:
  - '000485256100001'
file:
- access_level: open_access
  checksum: b798773c5823012d31c812c9f7975da2
  content_type: application/pdf
  creator: kschuh
  date_created: 2019-10-01T10:33:17Z
  date_updated: 2020-07-14T12:47:44Z
  file_id: '6924'
  file_name: 2019_BioMed_Sigalova.pdf
  file_size: 4157175
  relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: '        20'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_identifier:
  eissn:
  - '14712164'
publication_status: published
publisher: BioMed Central
quality_controlled: '1'
related_material:
  record:
  - id: '9731'
    relation: research_data
    status: public
  - id: '9783'
    relation: research_data
    status: public
  - id: '9890'
    relation: research_data
    status: public
  - id: '9892'
    relation: research_data
    status: public
  - id: '9893'
    relation: research_data
    status: public
  - id: '9894'
    relation: research_data
    status: public
  - id: '9895'
    relation: research_data
    status: public
  - id: '9896'
    relation: research_data
    status: public
  - id: '9897'
    relation: research_data
    status: public
  - id: '9898'
    relation: research_data
    status: public
  - id: '9899'
    relation: research_data
    status: public
  - id: '9900'
    relation: research_data
    status: public
  - id: '9901'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Chlamydia pan-genomic analysis reveals balance between host adaptation and
  selective pressure to genome reduction
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
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. <i>Nature Biotechnology</i>. 2019;37(12):1466-1470.
    doi:<a href="https://doi.org/10.1038/s41587-019-0333-6">10.1038/s41587-019-0333-6</a>
  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. <i>Nature Biotechnology</i>. Springer Nature. <a href="https://doi.org/10.1038/s41587-019-0333-6">https://doi.org/10.1038/s41587-019-0333-6</a>
  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.” <i>Nature Biotechnology</i>. Springer Nature, 2019. <a href="https://doi.org/10.1038/s41587-019-0333-6">https://doi.org/10.1038/s41587-019-0333-6</a>.
  ieee: E. Garriga <i>et al.</i>, “Large multiple sequence alignments with a root-to-leaf
    regressive method,” <i>Nature Biotechnology</i>, 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.” <i>Nature Biotechnology</i>, vol. 37, no. 12, Springer Nature,
    2019, pp. 1466–70, doi:<a href="https://doi.org/10.1038/s41587-019-0333-6">10.1038/s41587-019-0333-6</a>.
  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: 2023-09-06T14:32:52Z
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:
  - '15461696'
  issn:
  - '10870156'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
  record:
  - id: '13059'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Large multiple sequence alignments with a root-to-leaf regressive method
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2019'
...
---
_id: '6419'
abstract:
- lang: eng
  text: Characterizing the fitness landscape, a representation of fitness for a large
    set of genotypes, is key to understanding how genetic information is interpreted
    to create functional organisms. Here we determined the evolutionarily-relevant
    segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine
    synthesis pathway, focusing on combinations of amino acid states found at orthologous
    sites of extant species. Just 15% of amino acids found in yeast His3 orthologues
    were always neutral while the impact on fitness of the remaining 85% depended
    on the genetic background. Furthermore, at 67% of sites, amino acid replacements
    were under sign epistasis, having both strongly positive and negative effect in
    different genetic backgrounds. 46% of sites were under reciprocal sign epistasis.
    The fitness impact of amino acid replacements was influenced by only a few genetic
    backgrounds but involved interaction of multiple sites, shaping a rugged fitness
    landscape in which many of the shortest paths between highly fit genotypes are
    inaccessible.
article_number: e1008079
article_processing_charge: No
author:
- first_name: Victoria
  full_name: Pokusaeva, Victoria
  id: 3184041C-F248-11E8-B48F-1D18A9856A87
  last_name: Pokusaeva
  orcid: 0000-0001-7660-444X
- first_name: Dinara R.
  full_name: Usmanova, Dinara R.
  last_name: Usmanova
- first_name: Ekaterina V.
  full_name: Putintseva, Ekaterina V.
  last_name: Putintseva
- first_name: Lorena
  full_name: Espinar, Lorena
  last_name: Espinar
- first_name: Karen
  full_name: Sarkisyan, Karen
  id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
  last_name: Sarkisyan
  orcid: 0000-0002-5375-6341
- first_name: Alexander S.
  full_name: Mishin, Alexander S.
  last_name: Mishin
- first_name: Natalya S.
  full_name: Bogatyreva, Natalya S.
  last_name: Bogatyreva
- first_name: Dmitry
  full_name: Ivankov, Dmitry
  id: 49FF1036-F248-11E8-B48F-1D18A9856A87
  last_name: Ivankov
- first_name: Arseniy
  full_name: Akopyan, Arseniy
  id: 430D2C90-F248-11E8-B48F-1D18A9856A87
  last_name: Akopyan
  orcid: 0000-0002-2548-617X
- first_name: Sergey
  full_name: Avvakumov, Sergey
  id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
  last_name: Avvakumov
- first_name: Inna S.
  full_name: Povolotskaya, Inna S.
  last_name: Povolotskaya
- first_name: Guillaume J.
  full_name: Filion, Guillaume J.
  last_name: Filion
- first_name: Lucas B.
  full_name: Carey, Lucas B.
  last_name: Carey
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
citation:
  ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the
    interactions of amino acids from orthologous sequences shaping a complex fitness
    landscape. <i>PLoS Genetics</i>. 2019;15(4). doi:<a href="https://doi.org/10.1371/journal.pgen.1008079">10.1371/journal.pgen.1008079</a>
  apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
    K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions
    of amino acids from orthologous sequences shaping a complex fitness landscape.
    <i>PLoS Genetics</i>. Public Library of Science. <a href="https://doi.org/10.1371/journal.pgen.1008079">https://doi.org/10.1371/journal.pgen.1008079</a>
  chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
    Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An
    Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences
    Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>. Public Library of
    Science, 2019. <a href="https://doi.org/10.1371/journal.pgen.1008079">https://doi.org/10.1371/journal.pgen.1008079</a>.
  ieee: V. Pokusaeva <i>et al.</i>, “An experimental assay of the interactions of
    amino acids from orthologous sequences shaping a complex fitness landscape,” <i>PLoS
    Genetics</i>, vol. 15, no. 4. Public Library of Science, 2019.
  ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
    Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
    Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino
    acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics.
    15(4), e1008079.
  mla: Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino
    Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS
    Genetics</i>, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:<a
    href="https://doi.org/10.1371/journal.pgen.1008079">10.1371/journal.pgen.1008079</a>.
  short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
    Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
    G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:37Z
day: '10'
ddc:
- '570'
department:
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doi: 10.1371/journal.pgen.1008079
ec_funded: 1
external_id:
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  name: International IST Doctoral Program
publication: PLoS Genetics
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quality_controlled: '1'
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    status: public
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    relation: research_data
    status: public
scopus_import: '1'
status: public
title: An experimental assay of the interactions of amino acids from orthologous sequences
  shaping a complex fitness landscape
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_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. <i>Nature Microbiology</i>.
    2019;4(7):1221–1230. doi:<a href="https://doi.org/10.1038/s41564-019-0412-y">10.1038/s41564-019-0412-y</a>
  apa: Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni,
    A., &#38; Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity
    in complex bacterial environments. <i>Nature Microbiology</i>. Springer Nature.
    <a href="https://doi.org/10.1038/s41564-019-0412-y">https://doi.org/10.1038/s41564-019-0412-y</a>
  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.” <i>Nature Microbiology</i>.
    Springer Nature, 2019. <a href="https://doi.org/10.1038/s41564-019-0412-y">https://doi.org/10.1038/s41564-019-0412-y</a>.
  ieee: L. Noda-García <i>et al.</i>, “Chance and pleiotropy dominate genetic diversity
    in complex bacterial environments,” <i>Nature Microbiology</i>, 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.” <i>Nature Microbiology</i>, vol. 4, no. 7,
    Springer Nature, 2019, pp. 1221–1230, doi:<a href="https://doi.org/10.1038/s41564-019-0412-y">10.1038/s41564-019-0412-y</a>.
  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: '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:<a href="https://doi.org/10.6084/m9.figshare.9808772.v1">10.6084/m9.figshare.9808772.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808772.v1">https://doi.org/10.6084/m9.figshare.9808772.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808772.v1">https://doi.org/10.6084/m9.figshare.9808772.v1</a>.
  ieee: O. Sigalova <i>et al.</i>, “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, <a href="https://doi.org/10.6084/m9.figshare.9808772.v1">10.6084/m9.figshare.9808772.v1</a>.
  mla: Sigalova, Olga, et al. <i>Additional File 11 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808772.v1">10.6084/m9.figshare.9808772.v1</a>.
  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: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808772.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808772.v1
month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
  record:
  - id: '6898'
    relation: used_in_publication
    status: public
status: public
title: Additional file 11 of Chlamydia pan-genomic analysis reveals balance between
  host adaptation and selective pressure to genome reduction
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9783'
abstract:
- lang: eng
  text: Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For
    the analysis of putative pseudogenes, events located less than 60 bp. away from
    gene end or present in a single genome from the corresponding OG were excluded.
    (CSV 600 kb)
article_processing_charge: No
author:
- first_name: Olga M.
  full_name: Sigalova, Olga M.
  last_name: Sigalova
- first_name: Andrei V.
  full_name: Chaplin, Andrei V.
  last_name: Chaplin
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
- first_name: Pavel V.
  full_name: Shelyakin, Pavel V.
  last_name: Shelyakin
- first_name: Vsevolod A.
  full_name: Filaretov, Vsevolod A.
  last_name: Filaretov
- first_name: Evgeny E.
  full_name: Akkuratov, Evgeny E.
  last_name: Akkuratov
- first_name: Valentina
  full_name: Burskaia, Valentina
  last_name: Burskaia
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
citation:
  ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 10 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808760.v1">10.6084/m9.figshare.9808760.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808760.v1">https://doi.org/10.6084/m9.figshare.9808760.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808760.v1">https://doi.org/10.6084/m9.figshare.9808760.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “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, <a href="https://doi.org/10.6084/m9.figshare.9808760.v1">10.6084/m9.figshare.9808760.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 10 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808760.v1">10.6084/m9.figshare.9808760.v1</a>.
  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: 2023-08-30T06:20:21Z
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:
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  - 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: '9789'
article_processing_charge: No
author:
- first_name: Victoria
  full_name: Pokusaeva, Victoria
  id: 3184041C-F248-11E8-B48F-1D18A9856A87
  last_name: Pokusaeva
  orcid: 0000-0001-7660-444X
- first_name: Dinara R.
  full_name: Usmanova, Dinara R.
  last_name: Usmanova
- first_name: Ekaterina V.
  full_name: Putintseva, Ekaterina V.
  last_name: Putintseva
- first_name: Lorena
  full_name: Espinar, Lorena
  last_name: Espinar
- first_name: Karen
  full_name: Sarkisyan, Karen
  id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
  last_name: Sarkisyan
  orcid: 0000-0002-5375-6341
- first_name: Alexander S.
  full_name: Mishin, Alexander S.
  last_name: Mishin
- first_name: Natalya S.
  full_name: Bogatyreva, Natalya S.
  last_name: Bogatyreva
- first_name: Dmitry
  full_name: Ivankov, Dmitry
  id: 49FF1036-F248-11E8-B48F-1D18A9856A87
  last_name: Ivankov
- first_name: Arseniy
  full_name: Akopyan, Arseniy
  id: 430D2C90-F248-11E8-B48F-1D18A9856A87
  last_name: Akopyan
  orcid: 0000-0002-2548-617X
- first_name: Sergey
  full_name: Avvakumov, Sergey
  id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
  last_name: Avvakumov
- first_name: Inna S.
  full_name: Povolotskaya, Inna S.
  last_name: Povolotskaya
- first_name: Guillaume J.
  full_name: Filion, Guillaume J.
  last_name: Filion
- first_name: Lucas B.
  full_name: Carey, Lucas B.
  last_name: Carey
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
citation:
  ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3
    orthologues. 2019. doi:<a href="https://doi.org/10.1371/journal.pgen.1008079.s010">10.1371/journal.pgen.1008079.s010</a>
  apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
    K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues.
    Public Library of Science. <a href="https://doi.org/10.1371/journal.pgen.1008079.s010">https://doi.org/10.1371/journal.pgen.1008079.s010</a>
  chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
    Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple
    Alignment of His3 Orthologues.” Public Library of Science, 2019. <a href="https://doi.org/10.1371/journal.pgen.1008079.s010">https://doi.org/10.1371/journal.pgen.1008079.s010</a>.
  ieee: V. Pokusaeva <i>et al.</i>, “Multiple alignment of His3 orthologues.” Public
    Library of Science, 2019.
  ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
    Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
    Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library
    of Science, <a href="https://doi.org/10.1371/journal.pgen.1008079.s010">10.1371/journal.pgen.1008079.s010</a>.
  mla: Pokusaeva, Victoria, et al. <i>Multiple Alignment of His3 Orthologues</i>.
    Public Library of Science, 2019, doi:<a href="https://doi.org/10.1371/journal.pgen.1008079.s010">10.1371/journal.pgen.1008079.s010</a>.
  short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
    Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
    G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:38:50Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s010
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
  record:
  - id: '6419'
    relation: used_in_publication
    status: public
status: public
title: Multiple alignment of His3 orthologues
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9790'
article_processing_charge: No
author:
- first_name: Victoria
  full_name: Pokusaeva, Victoria
  id: 3184041C-F248-11E8-B48F-1D18A9856A87
  last_name: Pokusaeva
  orcid: 0000-0001-7660-444X
- first_name: Dinara R.
  full_name: Usmanova, Dinara R.
  last_name: Usmanova
- first_name: Ekaterina V.
  full_name: Putintseva, Ekaterina V.
  last_name: Putintseva
- first_name: Lorena
  full_name: Espinar, Lorena
  last_name: Espinar
- first_name: Karen
  full_name: Sarkisyan, Karen
  id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
  last_name: Sarkisyan
  orcid: 0000-0002-5375-6341
- first_name: Alexander S.
  full_name: Mishin, Alexander S.
  last_name: Mishin
- first_name: Natalya S.
  full_name: Bogatyreva, Natalya S.
  last_name: Bogatyreva
- first_name: Dmitry
  full_name: Ivankov, Dmitry
  id: 49FF1036-F248-11E8-B48F-1D18A9856A87
  last_name: Ivankov
- first_name: Arseniy
  full_name: Akopyan, Arseniy
  id: 430D2C90-F248-11E8-B48F-1D18A9856A87
  last_name: Akopyan
  orcid: 0000-0002-2548-617X
- first_name: Sergey
  full_name: Avvakumov, Sergey
  id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
  last_name: Avvakumov
- first_name: Inna S.
  full_name: Povolotskaya, Inna S.
  last_name: Povolotskaya
- first_name: Guillaume J.
  full_name: Filion, Guillaume J.
  last_name: Filion
- first_name: Lucas B.
  full_name: Carey, Lucas B.
  last_name: Carey
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
citation:
  ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
    libraries and sequencing results. 2019. doi:<a href="https://doi.org/10.1371/journal.pgen.1008079.s011">10.1371/journal.pgen.1008079.s011</a>
  apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
    K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
    and sequencing results. Public Library of Science. <a href="https://doi.org/10.1371/journal.pgen.1008079.s011">https://doi.org/10.1371/journal.pgen.1008079.s011</a>
  chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
    Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
    Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
    of Science, 2019. <a href="https://doi.org/10.1371/journal.pgen.1008079.s011">https://doi.org/10.1371/journal.pgen.1008079.s011</a>.
  ieee: V. Pokusaeva <i>et al.</i>, “A statistical summary of segment libraries and
    sequencing results.” Public Library of Science, 2019.
  ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
    Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
    Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing
    results, Public Library of Science, <a href="https://doi.org/10.1371/journal.pgen.1008079.s011">10.1371/journal.pgen.1008079.s011</a>.
  mla: Pokusaeva, Victoria, et al. <i>A Statistical Summary of Segment Libraries and
    Sequencing Results</i>. Public Library of Science, 2019, doi:<a href="https://doi.org/10.1371/journal.pgen.1008079.s011">10.1371/journal.pgen.1008079.s011</a>.
  short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
    Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
    G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:50:15Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
  record:
  - id: '6419'
    relation: used_in_publication
    status: public
status: public
title: A statistical summary of segment libraries and sequencing results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9797'
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author:
- first_name: Victoria
  full_name: Pokusaeva, Victoria
  id: 3184041C-F248-11E8-B48F-1D18A9856A87
  last_name: Pokusaeva
  orcid: 0000-0001-7660-444X
- first_name: Dinara R.
  full_name: Usmanova, Dinara R.
  last_name: Usmanova
- first_name: Ekaterina V.
  full_name: Putintseva, Ekaterina V.
  last_name: Putintseva
- first_name: Lorena
  full_name: Espinar, Lorena
  last_name: Espinar
- first_name: Karen
  full_name: Sarkisyan, Karen
  id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
  last_name: Sarkisyan
  orcid: 0000-0002-5375-6341
- first_name: Alexander S.
  full_name: Mishin, Alexander S.
  last_name: Mishin
- first_name: Natalya S.
  full_name: Bogatyreva, Natalya S.
  last_name: Bogatyreva
- first_name: Dmitry
  full_name: Ivankov, Dmitry
  id: 49FF1036-F248-11E8-B48F-1D18A9856A87
  last_name: Ivankov
- first_name: Arseniy
  full_name: Akopyan, Arseniy
  id: 430D2C90-F248-11E8-B48F-1D18A9856A87
  last_name: Akopyan
  orcid: 0000-0002-2548-617X
- first_name: Inna S.
  full_name: Povolotskaya, Inna S.
  last_name: Povolotskaya
- first_name: Guillaume J.
  full_name: Filion, Guillaume J.
  last_name: Filion
- first_name: Lucas B.
  full_name: Carey, Lucas B.
  last_name: Carey
- first_name: Fyodor
  full_name: Kondrashov, Fyodor
  id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
  last_name: Kondrashov
  orcid: 0000-0001-8243-4694
citation:
  ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
    libraries and sequencing results. 2019. doi:<a href="https://doi.org/10.1371/journal.pgen.1008079.s011">10.1371/journal.pgen.1008079.s011</a>
  apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
    K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
    and sequencing results. Public Library of Science. <a href="https://doi.org/10.1371/journal.pgen.1008079.s011">https://doi.org/10.1371/journal.pgen.1008079.s011</a>
  chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
    Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
    Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
    of Science, 2019. <a href="https://doi.org/10.1371/journal.pgen.1008079.s011">https://doi.org/10.1371/journal.pgen.1008079.s011</a>.
  ieee: V. Pokusaeva <i>et al.</i>, “A statistical summary of segment libraries and
    sequencing results.” Public Library of Science, 2019.
  ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
    Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov
    F. 2019. A statistical summary of segment libraries and sequencing results, Public
    Library of Science, <a href="https://doi.org/10.1371/journal.pgen.1008079.s011">10.1371/journal.pgen.1008079.s011</a>.
  mla: Pokusaeva, Victoria, et al. <i>A Statistical Summary of Segment Libraries and
    Sequencing Results</i>. Public Library of Science, 2019, doi:<a href="https://doi.org/10.1371/journal.pgen.1008079.s011">10.1371/journal.pgen.1008079.s011</a>.
  short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
    Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion,
    L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T11:08:20Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
  record:
  - id: '6419'
    relation: used_in_publication
    status: public
status: public
title: A statistical summary of segment libraries and sequencing results
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:<a href="https://doi.org/10.6084/m9.figshare.9808802.v1">10.6084/m9.figshare.9808802.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808802.v1">https://doi.org/10.6084/m9.figshare.9808802.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808802.v1">https://doi.org/10.6084/m9.figshare.9808802.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “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, <a href="https://doi.org/10.6084/m9.figshare.9808802.v1">10.6084/m9.figshare.9808802.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 15 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808802.v1">10.6084/m9.figshare.9808802.v1</a>.
  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: 2023-08-30T06:20:21Z
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:<a href="https://doi.org/10.6084/m9.figshare.9808814.v1">10.6084/m9.figshare.9808814.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808814.v1">https://doi.org/10.6084/m9.figshare.9808814.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808814.v1">https://doi.org/10.6084/m9.figshare.9808814.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “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, <a href="https://doi.org/10.6084/m9.figshare.9808814.v1">10.6084/m9.figshare.9808814.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 16 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808814.v1">10.6084/m9.figshare.9808814.v1</a>.
  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: 2023-08-30T06:20:21Z
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:<a href="https://doi.org/10.6084/m9.figshare.9808820.v1">10.6084/m9.figshare.9808820.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808820.v1">https://doi.org/10.6084/m9.figshare.9808820.v1</a>
  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. <a href="https://doi.org/10.6084/m9.figshare.9808820.v1">https://doi.org/10.6084/m9.figshare.9808820.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “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, <a href="https://doi.org/10.6084/m9.figshare.9808820.v1">10.6084/m9.figshare.9808820.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 17 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808820.v1">10.6084/m9.figshare.9808820.v1</a>.
  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: 2023-08-30T06:20:21Z
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'
...
---
_id: '9894'
abstract:
- lang: eng
  text: Orthologous families (OFs) derived by MCL clustering of OGs. (CSV 189 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 18 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808826.v1">10.6084/m9.figshare.9808826.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 18 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808826.v1">https://doi.org/10.6084/m9.figshare.9808826.v1</a>
  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 18 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808826.v1">https://doi.org/10.6084/m9.figshare.9808826.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 18 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 18 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808826.v1">10.6084/m9.figshare.9808826.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 18 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808826.v1">10.6084/m9.figshare.9808826.v1</a>.
  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: 2021-08-12T07:25:07Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808826.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808826.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 18 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: '9895'
abstract:
- lang: eng
  text: Additional information on proteins from OG1. (CSV 30 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 19 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. 2019. doi:<a href="https://doi.org/10.6084/m9.figshare.9808835.v1">10.6084/m9.figshare.9808835.v1</a>
  apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
    V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 19 of Chlamydia
    pan-genomic analysis reveals balance between host adaptation and selective pressure
    to genome reduction. Springer Nature. <a href="https://doi.org/10.6084/m9.figshare.9808835.v1">https://doi.org/10.6084/m9.figshare.9808835.v1</a>
  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 19 of Chlamydia Pan-Genomic Analysis Reveals Balance
    between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
    Nature, 2019. <a href="https://doi.org/10.6084/m9.figshare.9808835.v1">https://doi.org/10.6084/m9.figshare.9808835.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 19 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 19 of Chlamydia pan-genomic
    analysis reveals balance between host adaptation and selective pressure to genome
    reduction, Springer Nature, <a href="https://doi.org/10.6084/m9.figshare.9808835.v1">10.6084/m9.figshare.9808835.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 19 of Chlamydia Pan-Genomic Analysis
    Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction</i>.
    Springer Nature, 2019, doi:<a href="https://doi.org/10.6084/m9.figshare.9808835.v1">10.6084/m9.figshare.9808835.v1</a>.
  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: 2021-08-12T07:44:52Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808835.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808835.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 19 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'
...