---
_id: '7459'
abstract:
- lang: eng
  text: We report the fabrication of BaTiO3-Ni magnetoelectric nanocomposites comprising
    of BaTiO3 nanotubes surrounded by Ni matrix. BaTiO3 nanotubes obtained from the
    hydrothermal transformation of TiO2 have both inner and outer surfaces, which
    facilitates greater magnetoelectric coupling with the surrounding Ni matrix. The
    magnetoelectric coupling was studied by measuring the piezoelectric behavior in
    the presence of an in-plane direct magnetic field. A higher magnetoelectric voltage
    coefficient of 110 mV/cm·Oe was obtained, because of better coupling between Ni
    and BaTiO3 through the walls of the nanotubes. Such nanocomposite developed directly
    on Ti substrate may lead to efficient fabrication of magnetoelectric devices.
article_processing_charge: No
article_type: original
author:
- first_name: Samba Siva
  full_name: Vadla, Samba Siva
  last_name: Vadla
- first_name: Tommaso
  full_name: Costanzo, Tommaso
  id: D93824F4-D9BA-11E9-BB12-F207E6697425
  last_name: Costanzo
  orcid: 0000-0001-9732-3815
- first_name: Subish
  full_name: John, Subish
  last_name: John
- first_name: Gabriel
  full_name: Caruntu, Gabriel
  last_name: Caruntu
- first_name: Somnath C.
  full_name: Roy, Somnath C.
  last_name: Roy
citation:
  ama: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. Local probing of magnetoelectric
    coupling in BaTiO3-Ni 1–3 composites. <i>Scripta Materialia</i>. 2019;159:33-36.
    doi:<a href="https://doi.org/10.1016/j.scriptamat.2018.09.003">10.1016/j.scriptamat.2018.09.003</a>
  apa: Vadla, S. S., Costanzo, T., John, S., Caruntu, G., &#38; Roy, S. C. (2019).
    Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. <i>Scripta
    Materialia</i>. Elsevier. <a href="https://doi.org/10.1016/j.scriptamat.2018.09.003">https://doi.org/10.1016/j.scriptamat.2018.09.003</a>
  chicago: Vadla, Samba Siva, Tommaso Costanzo, Subish John, Gabriel Caruntu, and
    Somnath C. Roy. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.”
    <i>Scripta Materialia</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.scriptamat.2018.09.003">https://doi.org/10.1016/j.scriptamat.2018.09.003</a>.
  ieee: S. S. Vadla, T. Costanzo, S. John, G. Caruntu, and S. C. Roy, “Local probing
    of magnetoelectric coupling in BaTiO3-Ni 1–3 composites,” <i>Scripta Materialia</i>,
    vol. 159. Elsevier, pp. 33–36, 2019.
  ista: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. 2019. Local probing of magnetoelectric
    coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 159, 33–36.
  mla: Vadla, Samba Siva, et al. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni
    1–3 Composites.” <i>Scripta Materialia</i>, vol. 159, Elsevier, 2019, pp. 33–36,
    doi:<a href="https://doi.org/10.1016/j.scriptamat.2018.09.003">10.1016/j.scriptamat.2018.09.003</a>.
  short: S.S. Vadla, T. Costanzo, S. John, G. Caruntu, S.C. Roy, Scripta Materialia
    159 (2019) 33–36.
date_created: 2020-02-05T14:19:17Z
date_published: 2019-01-15T00:00:00Z
date_updated: 2023-02-23T13:08:31Z
day: '15'
doi: 10.1016/j.scriptamat.2018.09.003
extern: '1'
fulldoi: https://doi.org/10.1016/j.scriptamat.2018.09.003
intvolume: '       159'
language:
- iso: eng
month: '01'
oa_version: None
page: 33-36
publication: Scripta Materialia
publication_identifier:
  issn:
  - 1359-6462
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2019'
...
---
_id: '7468'
abstract:
- lang: eng
  text: We present a new proximal bundle method for Maximum-A-Posteriori (MAP) inference
    in structured energy minimization problems. The method optimizes a Lagrangean
    relaxation of the original energy minimization problem using a multi plane block-coordinate
    Frank-Wolfe method that takes advantage of the specific structure of the Lagrangean
    decomposition. We show empirically that our method outperforms state-of-the-art
    Lagrangean decomposition based algorithms on some challenging Markov Random Field,
    multi-label discrete tomography and graph matching problems.
article_number: 11138-11147
article_processing_charge: No
arxiv: 1
author:
- first_name: Paul
  full_name: Swoboda, Paul
  id: 446560C6-F248-11E8-B48F-1D18A9856A87
  last_name: Swoboda
- first_name: Vladimir
  full_name: Kolmogorov, Vladimir
  id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87
  last_name: Kolmogorov
citation:
  ama: 'Swoboda P, Kolmogorov V. Map inference via block-coordinate Frank-Wolfe algorithm.
    In: <i>Proceedings of the IEEE Computer Society Conference on Computer Vision
    and Pattern Recognition</i>. Vol 2019-June. IEEE; 2019. doi:<a href="https://doi.org/10.1109/CVPR.2019.01140">10.1109/CVPR.2019.01140</a>'
  apa: 'Swoboda, P., &#38; Kolmogorov, V. (2019). Map inference via block-coordinate
    Frank-Wolfe algorithm. In <i>Proceedings of the IEEE Computer Society Conference
    on Computer Vision and Pattern Recognition</i> (Vol. 2019–June). Long Beach, CA,
    United States: IEEE. <a href="https://doi.org/10.1109/CVPR.2019.01140">https://doi.org/10.1109/CVPR.2019.01140</a>'
  chicago: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate
    Frank-Wolfe Algorithm.” In <i>Proceedings of the IEEE Computer Society Conference
    on Computer Vision and Pattern Recognition</i>, Vol. 2019–June. IEEE, 2019. <a
    href="https://doi.org/10.1109/CVPR.2019.01140">https://doi.org/10.1109/CVPR.2019.01140</a>.
  ieee: P. Swoboda and V. Kolmogorov, “Map inference via block-coordinate Frank-Wolfe
    algorithm,” in <i>Proceedings of the IEEE Computer Society Conference on Computer
    Vision and Pattern Recognition</i>, Long Beach, CA, United States, 2019, vol.
    2019–June.
  ista: 'Swoboda P, Kolmogorov V. 2019. Map inference via block-coordinate Frank-Wolfe
    algorithm. Proceedings of the IEEE Computer Society Conference on Computer Vision
    and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition
    vol. 2019–June, 11138–11147.'
  mla: Swoboda, Paul, and Vladimir Kolmogorov. “Map Inference via Block-Coordinate
    Frank-Wolfe Algorithm.” <i>Proceedings of the IEEE Computer Society Conference
    on Computer Vision and Pattern Recognition</i>, vol. 2019–June, 11138–11147, IEEE,
    2019, doi:<a href="https://doi.org/10.1109/CVPR.2019.01140">10.1109/CVPR.2019.01140</a>.
  short: P. Swoboda, V. Kolmogorov, in:, Proceedings of the IEEE Computer Society
    Conference on Computer Vision and Pattern Recognition, IEEE, 2019.
conference:
  end_date: 2019-06-20
  location: Long Beach, CA, United States
  name: 'CVPR: Conference on Computer Vision and Pattern Recognition'
  start_date: 2019-06-15
date_created: 2020-02-09T23:00:52Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2025-07-10T11:54:39Z
day: '01'
department:
- _id: VlKo
doi: 10.1109/CVPR.2019.01140
ec_funded: 1
external_id:
  arxiv:
  - '1806.05049'
  isi:
  - '000542649304076'
fulldoi: https://doi.org/10.1109/CVPR.2019.01140
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1806.05049
month: '06'
oa: 1
oa_version: Preprint
project:
- _id: 25FBA906-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '616160'
  name: 'Discrete Optimization in Computer Vision: Theory and Practice'
publication: Proceedings of the IEEE Computer Society Conference on Computer Vision
  and Pattern Recognition
publication_identifier:
  isbn:
  - '9781728132938'
  issn:
  - 1063-6919
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Map inference via block-coordinate Frank-Wolfe algorithm
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2019-June
year: '2019'
...
---
_id: '7476'
abstract:
- lang: eng
  text: The sebaceous gland (SG) is an essential component of the skin, and SG dysfunction
    is debilitating1,2. Yet, the cellular bases for its origin, development and subsequent
    maintenance remain poorly understood. Here, we apply large-scale quantitative
    fate mapping to define the patterns of cell fate behaviour during SG development
    and maintenance. We show that the SG develops from a defined number of lineage-restricted
    progenitors that undergo a programme of independent and stochastic cell fate decisions.
    Following an expansion phase, equipotent progenitors transition into a phase of
    homeostatic turnover, which is correlated with changes in the mechanical properties
    of the stroma and spatial restrictions on gland size. Expression of the oncogene
    KrasG12D results in a release from these constraints and unbridled gland expansion.
    Quantitative clonal fate analysis reveals that, during this phase, the primary
    effect of the Kras oncogene is to drive a constant fate bias with little effect
    on cell division rates. These findings provide insight into the developmental
    programme of the SG, as well as the mechanisms that drive tumour progression and
    gland dysfunction.
article_processing_charge: No
article_type: original
author:
- first_name: Marianne Stemann
  full_name: Andersen, Marianne Stemann
  last_name: Andersen
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
- first_name: Svetlana
  full_name: Ulyanchenko, Svetlana
  last_name: Ulyanchenko
- first_name: Soline
  full_name: Estrach, Soline
  last_name: Estrach
- first_name: Yasuko
  full_name: Antoku, Yasuko
  last_name: Antoku
- first_name: Sabrina
  full_name: Pisano, Sabrina
  last_name: Pisano
- first_name: Kim E.
  full_name: Boonekamp, Kim E.
  last_name: Boonekamp
- first_name: Sarah
  full_name: Sendrup, Sarah
  last_name: Sendrup
- first_name: Martti
  full_name: Maimets, Martti
  last_name: Maimets
- first_name: Marianne Terndrup
  full_name: Pedersen, Marianne Terndrup
  last_name: Pedersen
- first_name: Jens V.
  full_name: Johansen, Jens V.
  last_name: Johansen
- first_name: Ditte L.
  full_name: Clement, Ditte L.
  last_name: Clement
- first_name: Chloe C.
  full_name: Feral, Chloe C.
  last_name: Feral
- first_name: Benjamin D.
  full_name: Simons, Benjamin D.
  last_name: Simons
- first_name: Kim B.
  full_name: Jensen, Kim B.
  last_name: Jensen
citation:
  ama: Andersen MS, Hannezo EB, Ulyanchenko S, et al. Tracing the cellular dynamics
    of sebaceous gland development in normal and perturbed states. <i>Nature Cell
    Biology</i>. 2019;21(8):924-932. doi:<a href="https://doi.org/10.1038/s41556-019-0362-x">10.1038/s41556-019-0362-x</a>
  apa: Andersen, M. S., Hannezo, E. B., Ulyanchenko, S., Estrach, S., Antoku, Y.,
    Pisano, S., … Jensen, K. B. (2019). Tracing the cellular dynamics of sebaceous
    gland development in normal and perturbed states. <i>Nature Cell Biology</i>.
    Springer Nature. <a href="https://doi.org/10.1038/s41556-019-0362-x">https://doi.org/10.1038/s41556-019-0362-x</a>
  chicago: Andersen, Marianne Stemann, Edouard B Hannezo, Svetlana Ulyanchenko, Soline
    Estrach, Yasuko Antoku, Sabrina Pisano, Kim E. Boonekamp, et al. “Tracing the
    Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.”
    <i>Nature Cell Biology</i>. Springer Nature, 2019. <a href="https://doi.org/10.1038/s41556-019-0362-x">https://doi.org/10.1038/s41556-019-0362-x</a>.
  ieee: M. S. Andersen <i>et al.</i>, “Tracing the cellular dynamics of sebaceous
    gland development in normal and perturbed states,” <i>Nature Cell Biology</i>,
    vol. 21, no. 8. Springer Nature, pp. 924–932, 2019.
  ista: Andersen MS, Hannezo EB, Ulyanchenko S, Estrach S, Antoku Y, Pisano S, Boonekamp
    KE, Sendrup S, Maimets M, Pedersen MT, Johansen JV, Clement DL, Feral CC, Simons
    BD, Jensen KB. 2019. Tracing the cellular dynamics of sebaceous gland development
    in normal and perturbed states. Nature Cell Biology. 21(8), 924–932.
  mla: Andersen, Marianne Stemann, et al. “Tracing the Cellular Dynamics of Sebaceous
    Gland Development in Normal and Perturbed States.” <i>Nature Cell Biology</i>,
    vol. 21, no. 8, Springer Nature, 2019, pp. 924–32, doi:<a href="https://doi.org/10.1038/s41556-019-0362-x">10.1038/s41556-019-0362-x</a>.
  short: M.S. Andersen, E.B. Hannezo, S. Ulyanchenko, S. Estrach, Y. Antoku, S. Pisano,
    K.E. Boonekamp, S. Sendrup, M. Maimets, M.T. Pedersen, J.V. Johansen, D.L. Clement,
    C.C. Feral, B.D. Simons, K.B. Jensen, Nature Cell Biology 21 (2019) 924–932.
date_created: 2020-02-11T08:43:49Z
date_published: 2019-08-01T00:00:00Z
date_updated: 2021-01-12T08:13:47Z
day: '01'
doi: 10.1038/s41556-019-0362-x
extern: '1'
external_id:
  pmid:
  - '31358966'
fulldoi: https://doi.org/10.1038/s41556-019-0362-x
intvolume: '        21'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978139/
month: '08'
oa: 1
oa_version: Submitted Version
page: 924-932
pmid: 1
publication: Nature Cell Biology
publication_identifier:
  issn:
  - 1465-7392
  - 1476-4679
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Tracing the cellular dynamics of sebaceous gland development in normal and
  perturbed states
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2019'
...
---
_id: '7513'
abstract:
- lang: eng
  text: 'Social insects (i.e., ants, termites and the social bees and wasps) protect
    their colonies from disease using a combination of individual immunity and collectively
    performed defenses, termed social immunity. The first line of social immune defense
    is sanitary care, which is performed by colony members to protect their pathogen-exposed
    nestmates from developing an infection. If sanitary care fails and an infection
    becomes established, a second line of social immune defense is deployed to stop
    disease transmission within the colony and to protect the valuable queens, which
    together with the males are the reproductive individuals of the colony. Insect
    colonies are separated into these reproductive individuals and the sterile worker
    force, forming a superorganismal reproductive unit reminiscent of the differentiated
    germline and soma in a multicellular organism. Ultimately, the social immune response
    preserves the germline of the superorganism insect colony and increases overall
    fitness of the colony in case of disease. '
article_processing_charge: No
author:
- first_name: Sylvia
  full_name: Cremer, Sylvia
  id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
  last_name: Cremer
  orcid: 0000-0002-2193-3868
- first_name: Megan
  full_name: Kutzer, Megan
  id: 29D0B332-F248-11E8-B48F-1D18A9856A87
  last_name: Kutzer
  orcid: 0000-0002-8696-6978
citation:
  ama: 'Cremer S, Kutzer M. Social immunity. In: Choe J, ed. <i>Encyclopedia of Animal
    Behavior</i>. 2nd ed. Elsevier; 2019:747-755. doi:<a href="https://doi.org/10.1016/B978-0-12-809633-8.90721-0">10.1016/B978-0-12-809633-8.90721-0</a>'
  apa: Cremer, S., &#38; Kutzer, M. (2019). Social immunity. In J. Choe (Ed.), <i>Encyclopedia
    of Animal Behavior</i> (2nd ed., pp. 747–755). Elsevier. <a href="https://doi.org/10.1016/B978-0-12-809633-8.90721-0">https://doi.org/10.1016/B978-0-12-809633-8.90721-0</a>
  chicago: Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” In <i>Encyclopedia
    of Animal Behavior</i>, edited by Jae Choe, 2nd ed., 747–55. Elsevier, 2019. <a
    href="https://doi.org/10.1016/B978-0-12-809633-8.90721-0">https://doi.org/10.1016/B978-0-12-809633-8.90721-0</a>.
  ieee: S. Cremer and M. Kutzer, “Social immunity,” in <i>Encyclopedia of Animal Behavior</i>,
    2nd ed., J. Choe, Ed. Elsevier, 2019, pp. 747–755.
  ista: 'Cremer S, Kutzer M. 2019.Social immunity. In: Encyclopedia of Animal Behavior.
    , 747–755.'
  mla: Cremer, Sylvia, and Megan Kutzer. “Social Immunity.” <i>Encyclopedia of Animal
    Behavior</i>, edited by Jae Choe, 2nd ed., Elsevier, 2019, pp. 747–55, doi:<a
    href="https://doi.org/10.1016/B978-0-12-809633-8.90721-0">10.1016/B978-0-12-809633-8.90721-0</a>.
  short: S. Cremer, M. Kutzer, in:, J. Choe (Ed.), Encyclopedia of Animal Behavior,
    2nd ed., Elsevier, 2019, pp. 747–755.
date_created: 2020-02-23T23:00:36Z
date_published: 2019-02-06T00:00:00Z
date_updated: 2023-09-08T11:12:04Z
day: '06'
department:
- _id: SyCr
doi: 10.1016/B978-0-12-809633-8.90721-0
edition: '2'
editor:
- first_name: Jae
  full_name: Choe, Jae
  last_name: Choe
external_id:
  isi:
  - '000248989500026'
fulldoi: https://doi.org/10.1016/B978-0-12-809633-8.90721-0
isi: 1
language:
- iso: eng
month: '02'
oa_version: None
page: 747-755
publication: Encyclopedia of Animal Behavior
publication_identifier:
  eisbn:
  - '9780128132524'
  isbn:
  - '9780128132517'
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Social immunity
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
OA_place: repository
OA_type: green
_id: '7524'
abstract:
- lang: eng
  text: "We prove a lower bound for the free energy (per unit volume) of the two-dimensional
    Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$
    and inverse temperature $\\beta$ differs from the one of the non-interacting system
    by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$.
    Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ =
    \\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless
    critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho
    \\ll 1$ and if $\\beta \\rho \\gtrsim 1$."
article_number: '1910.03372'
article_processing_charge: No
arxiv: 1
author:
- first_name: Andreas
  full_name: Deuchert, Andreas
  id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87
  last_name: Deuchert
  orcid: 0000-0003-3146-6746
- first_name: Simon
  full_name: Mayer, Simon
  id: 30C4630A-F248-11E8-B48F-1D18A9856A87
  last_name: Mayer
- first_name: Robert
  full_name: Seiringer, Robert
  id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
  last_name: Seiringer
  orcid: 0000-0002-6781-0521
citation:
  ama: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute
    Bose gas. I. Lower bound. <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.1910.03372">10.48550/arXiv.1910.03372</a>
  apa: Deuchert, A., Mayer, S., &#38; Seiringer, R. (n.d.). The free energy of the
    two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv</i>. <a href="https://doi.org/10.48550/arXiv.1910.03372">https://doi.org/10.48550/arXiv.1910.03372</a>
  chicago: Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy
    of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv</i>, n.d. <a
    href="https://doi.org/10.48550/arXiv.1910.03372">https://doi.org/10.48550/arXiv.1910.03372</a>.
  ieee: A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional
    dilute Bose gas. I. Lower bound,” <i>arXiv</i>. .
  ista: Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute
    Bose gas. I. Lower bound. arXiv, 1910.03372.
  mla: Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose
    Gas. I. Lower Bound.” <i>ArXiv</i>, 1910.03372, doi:<a href="https://doi.org/10.48550/arXiv.1910.03372">10.48550/arXiv.1910.03372</a>.
  short: A. Deuchert, S. Mayer, R. Seiringer, ArXiv (n.d.).
corr_author: '1'
date_created: 2020-02-26T08:46:40Z
date_published: 2019-10-08T00:00:00Z
date_updated: 2026-04-08T07:25:40Z
day: '08'
department:
- _id: RoSe
doi: 10.48550/arXiv.1910.03372
ec_funded: 1
external_id:
  arxiv:
  - '1910.03372'
fulldoi: https://doi.org/10.48550/arXiv.1910.03372
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1910.03372
month: '10'
oa: 1
oa_version: Preprint
page: '61'
project:
- _id: 25C6DC12-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '694227'
  name: Analysis of quantum many-body systems
publication: arXiv
publication_status: draft
related_material:
  record:
  - id: '7790'
    relation: later_version
    status: public
  - id: '7514'
    relation: dissertation_contains
    status: public
status: public
title: The free energy of the two-dimensional dilute Bose gas. I. Lower bound
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7542'
abstract:
- lang: eng
  text: We present a novel class of convolutional neural networks (CNNs) for set functions,i.e.,
    data indexed with the powerset of a finite set. The convolutions are derivedas
    linear, shift-equivariant functions for various notions of shifts on set functions.The
    framework is fundamentally different from graph convolutions based on theLaplacian,
    as it provides not one but several basic shifts, one for each element inthe ground
    set. Prototypical experiments with several set function classificationtasks on
    synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate
    the potential of our new powerset CNNs.
article_processing_charge: No
arxiv: 1
author:
- first_name: Chris
  full_name: Wendler, Chris
  last_name: Wendler
- first_name: Dan-Adrian
  full_name: Alistarh, Dan-Adrian
  id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
  last_name: Alistarh
  orcid: 0000-0003-3650-940X
- first_name: Markus
  full_name: Püschel, Markus
  last_name: Püschel
citation:
  ama: 'Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks.
    In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.'
  apa: 'Wendler, C., Alistarh, D.-A., &#38; Püschel, M. (2019). Powerset convolutional
    neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural
    Information Processing Systems, Vancouver, Canada: Neural Information Processing
    Systems Foundation.'
  chicago: Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional
    Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation,
    2019.
  ieee: 'C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural
    networks,” presented at the NIPS: Conference on Neural Information Processing
    Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.'
  ista: 'Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks.
    NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.'
  mla: Wendler, Chris, et al. <i>Powerset Convolutional Neural Networks</i>. Vol.
    32, Neural Information Processing Systems Foundation, 2019, pp. 927–38.
  short: C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing
    Systems Foundation, 2019, pp. 927–938.
conference:
  end_date: 2019-12-14
  location: Vancouver, Canada
  name: 'NIPS: Conference on Neural Information Processing Systems'
  start_date: 2019-12-08
date_created: 2020-02-28T10:03:24Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2026-06-18T19:23:08Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
ec_funded: 1
external_id:
  arxiv:
  - '1909.02253'
  isi:
  - '000534424300084'
intvolume: '        32'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks
month: '12'
oa: 1
oa_version: Published Version
page: 927-938
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '805223'
  name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
  issn:
  - 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Powerset convolutional neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2019'
...
---
_id: '7547'
abstract:
- lang: eng
  text: The BH3-only family of proteins is key for initiating apoptosis in a variety
    of contexts, and may also contribute to non-apoptotic cellular processes. Historically,
    the nematode Caenorhabditis elegans has provided a powerful system for studying
    and identifying conserved regulators of BH3-only proteins. In C. elegans, the
    BH3-only protein egl-1 is expressed during development to cell-autonomously trigger
    most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed
    after development in the sensory neuron pair URX without inducing apoptosis. We
    used genetic screening and epistasis analysis to determine that its transcription
    is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein
    Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family
    proteins are also expressed in the adult nervous system of mammals, we suggest
    that studying egl-1 expression in URX may shed light on mechanisms that regulate
    conserved family members in higher organisms.
article_processing_charge: No
article_type: original
author:
- first_name: Jesse
  full_name: Cohn, Jesse
  last_name: Cohn
- first_name: Vivek
  full_name: Dwivedi, Vivek
  last_name: Dwivedi
- first_name: Giulio
  full_name: Valperga, Giulio
  last_name: Valperga
- first_name: Nicole
  full_name: Zarate, Nicole
  last_name: Zarate
- first_name: Mario
  full_name: de Bono, Mario
  id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
  last_name: de Bono
  orcid: 0000-0001-8347-0443
- first_name: H. Robert
  full_name: Horvitz, H. Robert
  last_name: Horvitz
- first_name: Jonathan T.
  full_name: Pierce, Jonathan T.
  last_name: Pierce
citation:
  ama: 'Cohn J, Dwivedi V, Valperga G, et al. Activity-dependent regulation of the
    proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans.
    <i>G3: Genes, Genomes, Genetics</i>. 2019;9(11):3703-3714. doi:<a href="https://doi.org/10.1534/g3.119.400654">10.1534/g3.119.400654</a>'
  apa: 'Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H.
    R., &#38; Pierce, J. T. (2019). Activity-dependent regulation of the proapoptotic
    BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. <i>G3:
    Genes, Genomes, Genetics</i>. Genetics Society of America. <a href="https://doi.org/10.1534/g3.119.400654">https://doi.org/10.1534/g3.119.400654</a>'
  chicago: 'Cohn, Jesse, Vivek Dwivedi, Giulio Valperga, Nicole Zarate, Mario de Bono,
    H. Robert Horvitz, and Jonathan T. Pierce. “Activity-Dependent Regulation of the
    Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.”
    <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America, 2019. <a href="https://doi.org/10.1534/g3.119.400654">https://doi.org/10.1534/g3.119.400654</a>.'
  ieee: 'J. Cohn <i>et al.</i>, “Activity-dependent regulation of the proapoptotic
    BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans,” <i>G3:
    Genes, Genomes, Genetics</i>, vol. 9, no. 11. Genetics Society of America, pp.
    3703–3714, 2019.'
  ista: 'Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT.
    2019. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in
    a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics.
    9(11), 3703–3714.'
  mla: 'Cohn, Jesse, et al. “Activity-Dependent Regulation of the Proapoptotic BH3-Only
    Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” <i>G3: Genes, Genomes,
    Genetics</i>, vol. 9, no. 11, Genetics Society of America, 2019, pp. 3703–14,
    doi:<a href="https://doi.org/10.1534/g3.119.400654">10.1534/g3.119.400654</a>.'
  short: 'J. Cohn, V. Dwivedi, G. Valperga, N. Zarate, M. de Bono, H.R. Horvitz, J.T.
    Pierce, G3: Genes, Genomes, Genetics 9 (2019) 3703–3714.'
date_created: 2020-02-28T10:44:27Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2021-01-12T08:14:07Z
day: '01'
doi: 10.1534/g3.119.400654
extern: '1'
external_id:
  pmid:
  - '31519744'
fulldoi: https://doi.org/10.1534/g3.119.400654
intvolume: '         9'
issue: '11'
language:
- iso: eng
month: '11'
oa_version: Published Version
page: 3703-3714
pmid: 1
publication: 'G3: Genes, Genomes, Genetics'
publication_identifier:
  issn:
  - 2160-1836
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a
  living neuron pair in Caenorhabditis elegans
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2019'
...
---
_id: '7548'
abstract:
- lang: eng
  text: Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils
    is a well-established hallmark of Alzheimer’s disease, the complex mechanisms
    linking this process to neurodegeneration are still incompletely understood. The
    nematode worm C. elegans is a valuable model organism through which to study these
    mechanisms because of its simple nervous system and its relatively short lifespan.
    Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study
    the toxic effects of the overexpression of Aβ in the muscle or nervous systems.
    However, the wide variety of effects associated with the tissue-level overexpression
    of Aβ makes it difficult to single out and study specific cellular mechanisms
    related to the onset of Alzheimer’s disease. Here, to better understand how to
    investigate the early events affecting neuronal signalling, we created a C. elegans
    model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion
    in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural
    assays, we found that the Aβ42-expressing animals displayed a subtle modulation
    of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG
    neurons in young Aβ42-expressing nematodes were activated more strongly than in
    control animals, and that neuronal activation remained intact until old age. Taken
    together, our results suggest that Aβ42-expression in this very subtle model of
    AD is sufficient to modulate the behavioural response but not strong enough to
    generate significant neurotoxicity, suggesting that slightly more aggressive perturbations
    will enable effectively studies of the links between the modulation of a physiological
    response and its associated neurotoxicity.
article_number: e0217746
article_processing_charge: No
article_type: original
author:
- first_name: Tessa
  full_name: Sinnige, Tessa
  last_name: Sinnige
- first_name: Prashanth
  full_name: Ciryam, Prashanth
  last_name: Ciryam
- first_name: Samuel
  full_name: Casford, Samuel
  last_name: Casford
- first_name: Christopher M.
  full_name: Dobson, Christopher M.
  last_name: Dobson
- first_name: Mario
  full_name: de Bono, Mario
  id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
  last_name: de Bono
  orcid: 0000-0001-8347-0443
- first_name: Michele
  full_name: Vendruscolo, Michele
  last_name: Vendruscolo
citation:
  ama: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression
    of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates
    the associated behavioural response. <i>PLOS ONE</i>. 2019;14(5). doi:<a href="https://doi.org/10.1371/journal.pone.0217746">10.1371/journal.pone.0217746</a>
  apa: Sinnige, T., Ciryam, P., Casford, S., Dobson, C. M., de Bono, M., &#38; Vendruscolo,
    M. (2019). Expression of the amyloid-β peptide in a single pair of C. elegans
    sensory neurons modulates the associated behavioural response. <i>PLOS ONE</i>.
    Public Library of Science. <a href="https://doi.org/10.1371/journal.pone.0217746">https://doi.org/10.1371/journal.pone.0217746</a>
  chicago: Sinnige, Tessa, Prashanth Ciryam, Samuel Casford, Christopher M. Dobson,
    Mario de Bono, and Michele Vendruscolo. “Expression of the Amyloid-β Peptide in
    a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural
    Response.” <i>PLOS ONE</i>. Public Library of Science, 2019. <a href="https://doi.org/10.1371/journal.pone.0217746">https://doi.org/10.1371/journal.pone.0217746</a>.
  ieee: T. Sinnige, P. Ciryam, S. Casford, C. M. Dobson, M. de Bono, and M. Vendruscolo,
    “Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons
    modulates the associated behavioural response,” <i>PLOS ONE</i>, vol. 14, no.
    5. Public Library of Science, 2019.
  ista: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. 2019.
    Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons
    modulates the associated behavioural response. PLOS ONE. 14(5), e0217746.
  mla: Sinnige, Tessa, et al. “Expression of the Amyloid-β Peptide in a Single Pair
    of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.”
    <i>PLOS ONE</i>, vol. 14, no. 5, e0217746, Public Library of Science, 2019, doi:<a
    href="https://doi.org/10.1371/journal.pone.0217746">10.1371/journal.pone.0217746</a>.
  short: T. Sinnige, P. Ciryam, S. Casford, C.M. Dobson, M. de Bono, M. Vendruscolo,
    PLOS ONE 14 (2019).
date_created: 2020-02-28T10:45:13Z
date_published: 2019-05-31T00:00:00Z
date_updated: 2021-01-12T08:14:08Z
day: '31'
doi: 10.1371/journal.pone.0217746
extern: '1'
fulldoi: https://doi.org/10.1371/journal.pone.0217746
intvolume: '        14'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: Published Version
publication: PLOS ONE
publication_identifier:
  issn:
  - 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
status: public
title: Expression of the amyloid-β peptide in a single pair of C. elegans sensory
  neurons modulates the associated behavioural response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2019'
...
---
OA_place: repository
OA_type: green
_id: '7550'
abstract:
- lang: eng
  text: 'We consider an optimal control problem for an abstract nonlinear dissipative
    evolution equation. The differential constraint is penalized by augmenting the
    target functional by a nonnegative global-in-time functional which is null-minimized
    in the evolution equation is satisfied. Different variational settings are presented,
    leading to the convergence of the penalization method for gradient flows, noncyclic
    and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. '
acknowledgement: This work is supported by Vienna Science and Technology Fund (WWTF)
  through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and
  I 2375.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Lorenzo
  full_name: Portinale, Lorenzo
  id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87
  last_name: Portinale
- first_name: Ulisse
  full_name: Stefanelli, Ulisse
  last_name: Stefanelli
citation:
  ama: Portinale L, Stefanelli U. Penalization via global functionals of optimal-control
    problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>.
    2019;28(2):425-447.
  apa: Portinale, L., &#38; Stefanelli, U. (2019). Penalization via global functionals
    of optimal-control problems for dissipative evolution. <i>Advances in Mathematical
    Sciences and Applications</i>. Gakko Tosho.
  chicago: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals
    of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical
    Sciences and Applications</i>. Gakko Tosho, 2019.
  ieee: L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control
    problems for dissipative evolution,” <i>Advances in Mathematical Sciences and
    Applications</i>, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.
  ista: Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control
    problems for dissipative evolution. Advances in Mathematical Sciences and Applications.
    28(2), 425–447.
  mla: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals
    of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical
    Sciences and Applications</i>, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.
  short: L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications
    28 (2019) 425–447.
corr_author: '1'
date_created: 2020-02-28T10:54:41Z
date_published: 2019-10-22T00:00:00Z
date_updated: 2025-06-26T10:23:55Z
day: '22'
department:
- _id: JaMa
external_id:
  arxiv:
  - '1910.10050'
intvolume: '        28'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: ' https://doi.org/10.48550/arXiv.1910.10050'
month: '10'
oa: 1
oa_version: Preprint
page: 425-447
project:
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
  grant_number: F6504
  name: Taming Complexity in Partial Differential Systems
publication: Advances in Mathematical Sciences and Applications
publication_identifier:
  issn:
  - 1343-4373
publication_status: published
publisher: Gakko Tosho
quality_controlled: '1'
status: public
title: Penalization via global functionals of optimal-control problems for dissipative
  evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2019'
...
---
_id: '7552'
abstract:
- lang: eng
  text: 'There is increasing evidence that protein binding to specific sites along
    DNA can activate the reading out of genetic information without coming into direct
    physical contact with the gene. There also is evidence that these distant but
    interacting sites are embedded in a liquid droplet of proteins which condenses
    out of the surrounding solution. We argue that droplet-mediated interactions can
    account for crucial features of gene regulation only if the droplet is poised
    at a non-generic point in its phase diagram. We explore a minimal model that embodies
    this idea, show that this model has a natural mechanism for self-tuning, and suggest
    direct experimental tests. '
article_number: '1912.08579'
article_processing_charge: No
arxiv: 1
author:
- first_name: William
  full_name: Bialek, William
  last_name: Bialek
- first_name: Thomas
  full_name: Gregor, Thomas
  last_name: Gregor
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
citation:
  ama: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
    <i>arXiv</i>. doi:<a href="https://doi.org/10.48550/arXiv.1912.08579">10.48550/arXiv.1912.08579</a>
  apa: Bialek, W., Gregor, T., &#38; Tkačik, G. (n.d.). Action at a distance in transcriptional
    regulation. <i>arXiv</i>. ArXiv. <a href="https://doi.org/10.48550/arXiv.1912.08579">https://doi.org/10.48550/arXiv.1912.08579</a>
  chicago: Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance
    in Transcriptional Regulation.” <i>ArXiv</i>. ArXiv, n.d. <a href="https://doi.org/10.48550/arXiv.1912.08579">https://doi.org/10.48550/arXiv.1912.08579</a>.
  ieee: W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional
    regulation,” <i>arXiv</i>. ArXiv.
  ista: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation.
    arXiv, 1912.08579.
  mla: Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.”
    <i>ArXiv</i>, 1912.08579, ArXiv, doi:<a href="https://doi.org/10.48550/arXiv.1912.08579">10.48550/arXiv.1912.08579</a>.
  short: W. Bialek, T. Gregor, G. Tkačik, ArXiv (n.d.).
date_created: 2020-02-28T10:57:08Z
date_published: 2019-12-18T00:00:00Z
date_updated: 2025-05-19T10:54:36Z
day: '18'
department:
- _id: GaTk
doi: 10.48550/arXiv.1912.08579
external_id:
  arxiv:
  - '1912.08579'
fulldoi: https://doi.org/10.48550/arXiv.1912.08579
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://arxiv.org/abs/1912.08579
month: '12'
oa: 1
oa_version: Preprint
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28844-B27
  name: Biophysics of information processing in gene regulation
publication: arXiv
publication_status: submitted
publisher: ArXiv
status: public
title: Action at a distance in transcriptional regulation
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808802.v1
fulldoi: https://doi.org/10.6084/m9.figshare.9808802.v1
main_file_link:
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month: '09'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
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    relation: used_in_publication
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status: public
title: Additional file 15 of Chlamydia pan-genomic analysis reveals balance between
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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: 2026-04-03T09:39:40Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808814.v1
fulldoi: https://doi.org/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: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808820.v1
fulldoi: https://doi.org/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: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808826.v1
fulldoi: https://doi.org/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:
  record:
  - 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: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808835.v1
fulldoi: https://doi.org/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'
...
---
_id: '9896'
abstract:
- lang: eng
  text: Summary of the analysed genomes. (CSV 24 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 1 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.9808841.v1">10.6084/m9.figshare.9808841.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 1 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.9808841.v1">https://doi.org/10.6084/m9.figshare.9808841.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 1 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.9808841.v1">https://doi.org/10.6084/m9.figshare.9808841.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 1 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 1 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.9808841.v1">10.6084/m9.figshare.9808841.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 1 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.9808841.v1">10.6084/m9.figshare.9808841.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: 2021-08-12T07:50:53Z
date_published: 2019-09-02T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '02'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808841.v1
fulldoi: https://doi.org/10.6084/m9.figshare.9808841.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808841.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 1 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: '9897'
abstract:
- lang: eng
  text: Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes.
    Only 374 genes with typical length and domain composition were considered. (CSV
    6 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 20 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.9808850.v1">10.6084/m9.figshare.9808850.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 20 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.9808850.v1">https://doi.org/10.6084/m9.figshare.9808850.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 20 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.9808850.v1">https://doi.org/10.6084/m9.figshare.9808850.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 20 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 20 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.9808850.v1">10.6084/m9.figshare.9808850.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 20 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.9808850.v1">10.6084/m9.figshare.9808850.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: 2021-08-12T07:58:15Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808850.v1
fulldoi: https://doi.org/10.6084/m9.figshare.9808850.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808850.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 20 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: '9898'
abstract:
- lang: eng
  text: All polyN tracts of length 5 or more nucleotides in sequences of genes from
    OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts
    implemented in the RAST pipeline. (CSV 133 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 21 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.9808859.v1">10.6084/m9.figshare.9808859.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 21 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.9808859.v1">https://doi.org/10.6084/m9.figshare.9808859.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 21 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.9808859.v1">https://doi.org/10.6084/m9.figshare.9808859.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 21 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 21 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.9808859.v1">10.6084/m9.figshare.9808859.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 21 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.9808859.v1">10.6084/m9.figshare.9808859.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: 2021-08-12T08:10:23Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808859.v1
fulldoi: https://doi.org/10.6084/m9.figshare.9808859.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808859.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 21 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: '9899'
abstract:
- lang: eng
  text: Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV
    362 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 2 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.9808865.v1">10.6084/m9.figshare.9808865.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 2 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.9808865.v1">https://doi.org/10.6084/m9.figshare.9808865.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 2 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.9808865.v1">https://doi.org/10.6084/m9.figshare.9808865.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 2 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 2 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.9808865.v1">10.6084/m9.figshare.9808865.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 2 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.9808865.v1">10.6084/m9.figshare.9808865.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: 2021-08-12T08:18:09Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808865.v1
fulldoi: https://doi.org/10.6084/m9.figshare.9808865.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808865.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 2 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: '9900'
abstract:
- lang: eng
  text: Pan-genome statistics by species. (CSV 3 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 5 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.9808886.v1">10.6084/m9.figshare.9808886.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 5 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.9808886.v1">https://doi.org/10.6084/m9.figshare.9808886.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 5 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.9808886.v1">https://doi.org/10.6084/m9.figshare.9808886.v1</a>.
  ieee: O. M. Sigalova <i>et al.</i>, “Additional file 5 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 5 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.9808886.v1">10.6084/m9.figshare.9808886.v1</a>.
  mla: Sigalova, Olga M., et al. <i>Additional File 5 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.9808886.v1">10.6084/m9.figshare.9808886.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: 2021-08-12T08:44:49Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-03T09:39:41Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808886.v1
fulldoi: https://doi.org/10.6084/m9.figshare.9808886.v1
main_file_link:
- open_access: '1'
  url: https://doi.org/10.6084/m9.figshare.9808886.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 5 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'
...