---
_id: '9892'
abstract:
- lang: eng
text: Distribution of OGs with mosaic phyletic patterns across species (all genomes).
(CSV 10 kb)
article_processing_charge: No
author:
- first_name: Olga M.
full_name: Sigalova, Olga M.
last_name: Sigalova
- first_name: Andrei V
full_name: Chaplin, Andrei V
last_name: Chaplin
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Pavel V.
full_name: Shelyakin, Pavel V.
last_name: Shelyakin
- first_name: Vsevolod A.
full_name: Filaretov, Vsevolod A.
last_name: Filaretov
- first_name: Evgeny E.
full_name: Akkuratov, Evgeny E.
last_name: Akkuratov
- first_name: Valentina
full_name: Burskaia, Valentina
last_name: Burskaia
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 16 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808814.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 16 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808814.v1
chicago: Sigalova, Olga M., Andrei V Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 16 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808814.v1.
ieee: O. M. Sigalova et al., “Additional file 16 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 16 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808814.v1.
mla: Sigalova, Olga M., et al. Additional File 16 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808814.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:11:53Z
date_published: 2019-09-12T00:00:00Z
date_updated: 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:10.6084/m9.figshare.9808820.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 17 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808820.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 17 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808820.v1.
ieee: O. M. Sigalova et al., “Additional file 17 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction.” Springer Nature, 2019.
ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov
EE, Burskaia V, Gelfand MS. 2019. Additional file 17 of Chlamydia pan-genomic
analysis reveals balance between host adaptation and selective pressure to genome
reduction, Springer Nature, 10.6084/m9.figshare.9808820.v1.
mla: Sigalova, Olga M., et al. Additional File 17 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808820.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:20:10Z
date_published: 2019-09-12T00:00:00Z
date_updated: 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:10.6084/m9.figshare.9808826.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 18 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808826.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 18 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808826.v1.
ieee: O. M. Sigalova et al., “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, 10.6084/m9.figshare.9808826.v1.
mla: Sigalova, Olga M., et al. Additional File 18 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808826.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:25:07Z
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:
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:10.6084/m9.figshare.9808835.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 19 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808835.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 19 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808835.v1.
ieee: O. M. Sigalova et al., “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, 10.6084/m9.figshare.9808835.v1.
mla: Sigalova, Olga M., et al. Additional File 19 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808835.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:44:52Z
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'
...
---
_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:10.6084/m9.figshare.9808841.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 1 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808841.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 1 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808841.v1.
ieee: O. M. Sigalova et al., “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, 10.6084/m9.figshare.9808841.v1.
mla: Sigalova, Olga M., et al. Additional File 1 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808841.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T07:50:53Z
date_published: 2019-09-02T00:00:00Z
date_updated: 2023-08-30T06:20:21Z
day: '02'
department:
- _id: FyKo
doi: 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: '6899'
abstract:
- lang: eng
text: Intra-organ communication guides morphogenetic processes that are essential
for an organ to carry out complex physiological functions. In the heart, the growth
of the myocardium is tightly coupled to that of the endocardium, a specialized
endothelial tissue that lines its interior. Several molecular pathways have been
implicated in the communication between these tissues including secreted factors,
components of the extracellular matrix, or proteins involved in cell-cell communication.
Yet, it is unknown how the growth of the endocardium is coordinated with that
of the myocardium. Here, we show that an increased expansion of the myocardial
atrial chamber volume generates higher junctional forces within endocardial cells.
This leads to biomechanical signaling involving VE-cadherin, triggering nuclear
localization of the Hippo pathway transcriptional regulator Yap1 and endocardial
proliferation. Our work suggests that the growth of the endocardium results from
myocardial chamber volume expansion and ends when the tension on the tissue is
relaxed.
article_processing_charge: No
author:
- first_name: Dorothee
full_name: Bornhorst, Dorothee
last_name: Bornhorst
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- first_name: Hiroyuki
full_name: Nakajima, Hiroyuki
last_name: Nakajima
- first_name: Chaitanya
full_name: Dingare, Chaitanya
last_name: Dingare
- first_name: Wiebke
full_name: Herzog, Wiebke
last_name: Herzog
- first_name: Virginie
full_name: Lecaudey, Virginie
last_name: Lecaudey
- first_name: Naoki
full_name: Mochizuki, Naoki
last_name: Mochizuki
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Deborah
full_name: Yelon, Deborah
last_name: Yelon
- first_name: Salim
full_name: Abdelilah-Seyfried, Salim
last_name: Abdelilah-Seyfried
citation:
ama: Bornhorst D, Xia P, Nakajima H, et al. Biomechanical signaling within the developing
zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature
communications. 2019;10(1):4113. doi:10.1038/s41467-019-12068-x
apa: Bornhorst, D., Xia, P., Nakajima, H., Dingare, C., Herzog, W., Lecaudey, V.,
… Abdelilah-Seyfried, S. (2019). Biomechanical signaling within the developing
zebrafish heart attunes endocardial growth to myocardial chamber dimensions. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-019-12068-x
chicago: Bornhorst, Dorothee, Peng Xia, Hiroyuki Nakajima, Chaitanya Dingare, Wiebke
Herzog, Virginie Lecaudey, Naoki Mochizuki, Carl-Philipp J Heisenberg, Deborah
Yelon, and Salim Abdelilah-Seyfried. “Biomechanical Signaling within the Developing
Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.”
Nature Communications. Nature Publishing Group, 2019. https://doi.org/10.1038/s41467-019-12068-x.
ieee: D. Bornhorst et al., “Biomechanical signaling within the developing
zebrafish heart attunes endocardial growth to myocardial chamber dimensions,”
Nature communications, vol. 10, no. 1. Nature Publishing Group, p. 4113,
2019.
ista: Bornhorst D, Xia P, Nakajima H, Dingare C, Herzog W, Lecaudey V, Mochizuki
N, Heisenberg C-PJ, Yelon D, Abdelilah-Seyfried S. 2019. Biomechanical signaling
within the developing zebrafish heart attunes endocardial growth to myocardial
chamber dimensions. Nature communications. 10(1), 4113.
mla: Bornhorst, Dorothee, et al. “Biomechanical Signaling within the Developing
Zebrafish Heart Attunes Endocardial Growth to Myocardial Chamber Dimensions.”
Nature Communications, vol. 10, no. 1, Nature Publishing Group, 2019, p.
4113, doi:10.1038/s41467-019-12068-x.
short: D. Bornhorst, P. Xia, H. Nakajima, C. Dingare, W. Herzog, V. Lecaudey, N.
Mochizuki, C.-P.J. Heisenberg, D. Yelon, S. Abdelilah-Seyfried, Nature Communications
10 (2019) 4113.
date_created: 2019-09-22T22:00:37Z
date_published: 2019-09-11T00:00:00Z
date_updated: 2023-08-30T06:21:23Z
day: '11'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1038/s41467-019-12068-x
external_id:
isi:
- '000485216800009'
pmid:
- '31511517'
file:
- access_level: open_access
checksum: 62c2512712e16d27c1797d318d14ba9f
content_type: application/pdf
creator: kschuh
date_created: 2019-10-01T11:18:50Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6926'
file_name: 2019_Nature_Bornhorst.pdf
file_size: 3905793
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '4113'
pmid: 1
publication: Nature communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Biomechanical signaling within the developing zebrafish heart attunes endocardial
growth to myocardial chamber dimensions
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: 10
year: '2019'
...
---
_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.
BMC Genomics. 2019;20(1). doi:10.1186/s12864-019-6059-5
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.
BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-019-6059-5
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.” BMC Genomics. BioMed Central,
2019. https://doi.org/10.1186/s12864-019-6059-5.
ieee: O. M. Sigalova et al., “Chlamydia pan-genomic analysis reveals balance
between host adaptation and selective pressure to genome reduction,” BMC Genomics,
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.” BMC Genomics,
vol. 20, no. 1, 710, BioMed Central, 2019, doi:10.1186/s12864-019-6059-5.
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
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- 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: '6920'
article_processing_charge: No
article_type: original
author:
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Artner C, Benková E. Ethylene and cytokinin - partners in root growth regulation.
Molecular Plant. 2019;12(10):1312-1314. doi:10.1016/j.molp.2019.09.003
apa: Artner, C., & Benková, E. (2019). Ethylene and cytokinin - partners in
root growth regulation. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2019.09.003
chicago: Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners
in Root Growth Regulation.” Molecular Plant. Cell Press, 2019. https://doi.org/10.1016/j.molp.2019.09.003.
ieee: C. Artner and E. Benková, “Ethylene and cytokinin - partners in root growth
regulation,” Molecular Plant, vol. 12, no. 10. Cell Press, pp. 1312–1314,
2019.
ista: Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth
regulation. Molecular Plant. 12(10), 1312–1314.
mla: Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root
Growth Regulation.” Molecular Plant, vol. 12, no. 10, Cell Press, 2019,
pp. 1312–14, doi:10.1016/j.molp.2019.09.003.
short: C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314.
date_created: 2019-09-30T10:00:40Z
date_published: 2019-10-07T00:00:00Z
date_updated: 2023-08-30T06:55:02Z
day: '07'
department:
- _id: EvBe
doi: 10.1016/j.molp.2019.09.003
external_id:
isi:
- '000489132500002'
pmid:
- '31541740'
intvolume: ' 12'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 1312-1314
pmid: 1
project:
- _id: 2685A872-B435-11E9-9278-68D0E5697425
name: Hormonal regulation of plant adaptive responses to environmental signals
publication: Molecular Plant
publication_identifier:
issn:
- 1674-2052
- 1752-9867
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Ethylene and cytokinin - partners in root growth regulation
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
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:10.6084/m9.figshare.9808859.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808859.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808859.v1.
ieee: O. M. Sigalova et al., “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, 10.6084/m9.figshare.9808859.v1.
mla: Sigalova, Olga M., et al. Additional File 21 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808859.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T08:10:23Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 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: '9901'
abstract:
- lang: eng
text: Clusters of Orthologous Genes (COGs) and corresponding functional categories
assigned to OGs. (CSV 117 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 9 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. 2019. doi:10.6084/m9.figshare.9808907.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808907.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808907.v1.
ieee: O. M. Sigalova et al., “Additional file 9 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 9 of Chlamydia pan-genomic analysis
reveals balance between host adaptation and selective pressure to genome reduction,
Springer Nature, 10.6084/m9.figshare.9808907.v1.
mla: Sigalova, Olga M., et al. Additional File 9 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808907.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T10:54:03Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.9808907.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.9808907.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 9 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:10.6084/m9.figshare.9808865.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 2 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808865.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808865.v1.
ieee: O. M. Sigalova et al., “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, 10.6084/m9.figshare.9808865.v1.
mla: Sigalova, Olga M., et al. Additional File 2 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808865.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T08:18:09Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 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:10.6084/m9.figshare.9808886.v1
apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov,
V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia
pan-genomic analysis reveals balance between host adaptation and selective pressure
to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808886.v1
chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin,
Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S.
Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance
between Host Adaptation and Selective Pressure to Genome Reduction.” Springer
Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1.
ieee: O. M. Sigalova et al., “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, 10.6084/m9.figshare.9808886.v1.
mla: Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis
Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.
Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1.
short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov,
E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019).
date_created: 2021-08-12T08:44:49Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2023-08-30T06:20:22Z
day: '12'
department:
- _id: FyKo
doi: 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'
...
---
_id: '6936'
abstract:
- lang: eng
text: "A key challenge for community ecology is to understand to what extent observational
data can be used to infer the underlying community assembly processes. As different
processes can lead to similar or even identical patterns, statistical analyses
of non‐manipulative observational data never yield undisputable causal inference
on the underlying processes. Still, most empirical studies in community ecology
are based on observational data, and hence understanding under which circumstances
such data can shed light on assembly processes is a central concern for community
ecologists. We simulated a spatial agent‐based model that generates variation
in metacommunity dynamics across multiple axes, including the four classic metacommunity
paradigms as special cases. We further simulated a virtual ecologist who analysed
snapshot data sampled from the simulations using eighteen output metrics derived
from beta‐diversity and habitat variation indices, variation partitioning and
joint species distribution modelling. Our results indicated two main axes of variation
in the output metrics. The first axis of variation described whether the landscape
has patchy or continuous variation, and thus was essentially independent of the
properties of the species community. The second axis of variation related to the
level of predictability of the metacommunity. The most predictable communities
were niche‐based metacommunities inhabiting static landscapes with marked environmental
heterogeneity, such as metacommunities following the species sorting paradigm
or the mass effects paradigm. The most unpredictable communities were neutral‐based
metacommunities inhabiting dynamics landscapes with little spatial heterogeneity,
such as metacommunities following the neutral or patch sorting paradigms. The
output metrics from joint species distribution modelling yielded generally the
highest resolution to disentangle among the simulated scenarios. Yet, the different
types of statistical approaches utilized in this study carried complementary information,
and thus our results suggest that the most comprehensive evaluation of metacommunity
structure can be obtained by combining them.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: Otso
full_name: Ovaskainen, Otso
last_name: Ovaskainen
- first_name: Joel
full_name: Rybicki, Joel
id: 334EFD2E-F248-11E8-B48F-1D18A9856A87
last_name: Rybicki
orcid: 0000-0002-6432-6646
- first_name: Nerea
full_name: Abrego, Nerea
last_name: Abrego
citation:
ama: Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about
metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444
apa: Ovaskainen, O., Rybicki, J., & Abrego, N. (2019). What can observational
data reveal about metacommunity processes? Ecography. Wiley. https://doi.org/10.1111/ecog.04444
chicago: Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational
Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444.
ieee: O. Ovaskainen, J. Rybicki, and N. Abrego, “What can observational data reveal
about metacommunity processes?,” Ecography, vol. 42, no. 11. Wiley, pp.
1877–1886, 2019.
ista: Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal
about metacommunity processes? Ecography. 42(11), 1877–1886.
mla: Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity
Processes?” Ecography, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:10.1111/ecog.04444.
short: O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886.
date_created: 2019-10-08T13:01:24Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-30T06:57:25Z
day: '01'
ddc:
- '577'
department:
- _id: DaAl
doi: 10.1111/ecog.04444
ec_funded: 1
external_id:
isi:
- '000486348700001'
file:
- access_level: open_access
checksum: 6c9fbbd5ea8ce10ae93e55ad560a7bf9
content_type: application/pdf
creator: jrybicki
date_created: 2019-10-08T13:07:44Z
date_updated: 2020-07-14T12:47:45Z
file_id: '6937'
file_name: ecog.04444.pdf
file_size: 1682718
relation: main_file
file_date_updated: 2020-07-14T12:47:45Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1877-1886
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Ecography
publication_identifier:
eissn:
- 1600-0587
issn:
- 0906-7590
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: What can observational data reveal about metacommunity processes?
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: 42
year: '2019'
...
---
_id: '6857'
abstract:
- lang: eng
text: "Gene Drives are regarded as future tools with a high potential for population
control. Due to their inherent ability to overcome the rules of Mendelian inheritance,
gene drives (GD) may spread genes rapidly through populations of sexually reproducing
organisms. A release of organisms carrying a GD would constitute a paradigm shift
in the handling of genetically modified organisms because gene drive organisms
(GDO) are designed to drive their transgenes into wild populations and thereby
increase the number of GDOs. The rapid development in this field and its focus
on wild populations demand a prospective risk assessment with a focus on exposure
related aspects. Presently, it is unclear how adequate risk management could be
guaranteed to limit the spread of GDs in time and space, in order to avoid potential
adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the
“Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute
of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight
into the potential population dynamic behavior of GDs and appropriate measures
of control. Scientists from France, Germany, England, and the USA discussed both
topics in this meeting on April 4–5, 2019. This article summarizes results of
the workshop."
article_number: '1900151'
article_processing_charge: No
article_type: original
author:
- first_name: B
full_name: Giese, B
last_name: Giese
- first_name: J L
full_name: Friess, J L
last_name: Friess
- first_name: 'M F '
full_name: 'Schetelig, M F '
last_name: Schetelig
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Philip
full_name: Messer, Philip
last_name: Messer
- first_name: Florence
full_name: Debarre, Florence
last_name: Debarre
- first_name: H
full_name: Meimberg, H
last_name: Meimberg
- first_name: N
full_name: Windbichler, N
last_name: Windbichler
- first_name: C
full_name: Boete, C
last_name: Boete
citation:
ama: 'Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory
matters – A report from the workshop “Evaluation of spatial and temporal control
of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151'
apa: 'Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre,
F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report
from the workshop “Evaluation of spatial and temporal control of Gene Drives”,
4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151'
chicago: 'Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer,
Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics
and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and
Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays.
Wiley, 2019. https://doi.org/10.1002/bies.201900151.'
ieee: 'B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A
report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’,
4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.'
ista: 'Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg
H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters
– A report from the workshop “Evaluation of spatial and temporal control of Gene
Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.'
mla: 'Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report
from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’,
4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley,
2019, doi:10.1002/bies.201900151.'
short: B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre,
H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).
date_created: 2019-09-07T14:40:03Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-30T06:56:26Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/bies.201900151
external_id:
isi:
- '000489502000001'
file:
- access_level: open_access
checksum: 8cc7551bff70b2658f8d5630f228ee12
content_type: application/pdf
creator: dernst
date_created: 2019-10-11T06:59:26Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6939'
file_name: 2019_BioEssays_Giese.pdf
file_size: 193248
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: BioEssays
publication_identifier:
eissn:
- 1521-1878
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Gene Drives: Dynamics and regulatory matters – A report from the workshop
“Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna'
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: '2019'
...
---
_id: '6890'
abstract:
- lang: eng
text: Describing the protein interactions that form pleomorphic and asymmetric viruses
represents a considerable challenge to most structural biology techniques, including
X-ray crystallography and single particle cryo-electron microscopy. Obtaining
a detailed understanding of these interactions is nevertheless important, considering
the number of relevant human pathogens that do not follow strict icosahedral or
helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide
structural insights into complex biological environments and are well suited to
go beyond structures of perfectly symmetric viruses. This chapter discusses recent
developments showing that cryo-ET and subtomogram averaging can provide high-resolution
insights into hitherto unknown structural features of pleomorphic and asymmetric
virus particles. It also describes how these methods have significantly added
to our understanding of retrovirus capsid assemblies in immature and mature viruses.
Additional examples of irregular viruses and their associated proteins, whose
structures have been studied via cryo-ET and subtomogram averaging, further support
the versatility of these methods.
article_processing_charge: No
author:
- first_name: Martin
full_name: Obr, Martin
id: 4741CA5A-F248-11E8-B48F-1D18A9856A87
last_name: Obr
orcid: 0000-0003-1756-6564
- first_name: Florian KM
full_name: Schur, Florian KM
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
citation:
ama: 'Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses
using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary
Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus
Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008'
apa: Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and
asymmetric viruses using cryo-electron tomography and subtomogram averaging. In
F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function
(Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008
chicago: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic
and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.”
In Complementary Strategies to Study Virus Structure and Function, edited
by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008.
ieee: M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric
viruses using cryo-electron tomography and subtomogram averaging,” in Complementary
Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed.
Elsevier, 2019, pp. 117–159.
ista: 'Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses
using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies
to Study Virus Structure and Function. vol. 105, 117–159.'
mla: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and
Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.”
Complementary Strategies to Study Virus Structure and Function, edited
by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008.
short: M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study
Virus Structure and Function, Elsevier, 2019, pp. 117–159.
date_created: 2019-09-18T08:15:37Z
date_published: 2019-08-27T00:00:00Z
date_updated: 2023-08-30T06:56:00Z
day: '27'
department:
- _id: FlSc
doi: 10.1016/bs.aivir.2019.07.008
editor:
- first_name: Félix A.
full_name: Rey, Félix A.
last_name: Rey
external_id:
isi:
- '000501594500006'
pmid:
- ' 31522703'
intvolume: ' 105'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 117-159
pmid: 1
publication: Complementary Strategies to Study Virus Structure and Function
publication_identifier:
isbn:
- '9780128184561'
issn:
- 0065-3527
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
series_title: Advances in Virus Research
status: public
title: Structural analysis of pleomorphic and asymmetric viruses using cryo-electron
tomography and subtomogram averaging
type: book_chapter
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 105
year: '2019'
...
---
_id: '6940'
abstract:
- lang: eng
text: "We study the effect of a linear tunneling coupling between two-dimensional
systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless
(BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the
one-body correlation functions are algebraically decaying and the other with\r\nexponential
decay. When the linear coupling is turned on, a third BKT-paired phase emerges,
in which one-body correlations are exponentially decaying, while two-body correlation
functions exhibit power-law\r\ndecay. We perform numerical simulations in the
paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences
that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent.
We provide a picture of the phase diagram using a renormalization group approach."
acknowledgement: "We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio
and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from
the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport
from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1
- 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative
Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021
Joint Project “Strongly interacting systems in confined geometries” is gratefully
acknowledged."
article_number: '100601'
article_processing_charge: No
article_type: original
author:
- first_name: Giacomo
full_name: Bighin, Giacomo
id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87
last_name: Bighin
orcid: 0000-0001-8823-9777
- first_name: Nicolò
full_name: Defenu, Nicolò
last_name: Defenu
- first_name: István
full_name: Nándori, István
last_name: Nándori
- first_name: Luca
full_name: Salasnich, Luca
last_name: Salasnich
- first_name: Andrea
full_name: Trombettoni, Andrea
last_name: Trombettoni
citation:
ama: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models. Physical Review Letters. 2019;123(10).
doi:10.1103/physrevlett.123.100601
apa: Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019).
Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601
chicago: Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea
Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.”
Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.100601.
ieee: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models,” Physical Review Letters, vol. 123,
no. 10. American Physical Society, 2019.
ista: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless
paired phase in coupled XY models. Physical Review Letters. 123(10), 100601.
mla: Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled
XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American
Physical Society, 2019, doi:10.1103/physrevlett.123.100601.
short: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical
Review Letters 123 (2019).
date_created: 2019-10-14T06:31:13Z
date_published: 2019-09-06T00:00:00Z
date_updated: 2023-08-30T06:57:53Z
day: '06'
department:
- _id: MiLe
doi: 10.1103/physrevlett.123.100601
external_id:
arxiv:
- '1907.06253'
isi:
- '000483587200004'
intvolume: ' 123'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.06253
month: '09'
oa: 1
oa_version: Preprint
project:
- _id: 26986C82-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02641
name: A path-integral approach to composite impurities
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
related_material:
link:
- description: News auf IST Website
relation: press_release
url: https://ist.ac.at/en/news/new-form-of-magnetism-found/
scopus_import: '1'
status: public
title: Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 123
year: '2019'
...
---
_id: '6919'
article_number: eaaw6490
article_processing_charge: No
author:
- first_name: Chao
full_name: Qi, Chao
last_name: Qi
- first_name: Giulio Di
full_name: Minin, Giulio Di
last_name: Minin
- first_name: Irene
full_name: Vercellino, Irene
id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87
last_name: Vercellino
orcid: 0000-0001-5618-3449
- first_name: Anton
full_name: Wutz, Anton
last_name: Wutz
- first_name: Volodymyr M.
full_name: Korkhov, Volodymyr M.
last_name: Korkhov
citation:
ama: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol
recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9).
doi:10.1126/sciadv.aaw6490
apa: Qi, C., Minin, G. D., Vercellino, I., Wutz, A., & Korkhov, V. M. (2019).
Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science
Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw6490
chicago: Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr
M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor
PTCH1.” Science Advances. American Association for the Advancement of Science,
2019. https://doi.org/10.1126/sciadv.aaw6490.
ieee: C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural
basis of sterol recognition by human hedgehog receptor PTCH1,” Science Advances,
vol. 5, no. 9. American Association for the Advancement of Science, 2019.
ista: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of
sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490.
mla: Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog
Receptor PTCH1.” Science Advances, vol. 5, no. 9, eaaw6490, American Association
for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw6490.
short: C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances
5 (2019).
date_created: 2019-09-29T22:00:45Z
date_published: 2019-09-18T00:00:00Z
date_updated: 2023-08-30T06:55:31Z
day: '18'
ddc:
- '570'
department:
- _id: LeSa
doi: 10.1126/sciadv.aaw6490
external_id:
isi:
- '000491128800062'
file:
- access_level: open_access
checksum: b2256c9117655bc15f621ba0babf219f
content_type: application/pdf
creator: kschuh
date_created: 2019-10-02T11:13:54Z
date_updated: 2020-07-14T12:47:44Z
file_id: '6928'
file_name: 2019_AAAS_Qi.pdf
file_size: 1236101
relation: main_file
file_date_updated: 2020-07-14T12:47:44Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '09'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
eissn:
- '23752548'
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of sterol recognition by human hedgehog receptor PTCH1
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: 5
year: '2019'
...
---
_id: '6983'
abstract:
- lang: eng
text: Malaria, a disease caused by parasites of the Plasmodium genus, begins when
Plasmodium-infected mosquitoes inject malaria sporozoites while searching for
blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes,
and form liver stages which in mice 48 h later escape into blood and cause clinical
malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating
and eliminating all liver stages in 48 h, thus preventing the blood-stage disease.
However, the rules of how CD8 T cells are able to locate all liver stages within
a relatively short time period remains poorly understood. We recently reported
formation of clusters consisting of variable numbers of activated CD8 T cells
around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental
data and mathematical models we now provide additional insights into mechanisms
of formation of these clusters. First, we show that a model in which cluster formation
is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness”
of different liver stages, cannot explain distribution of cluster sizes in different
experimental conditions. In contrast, the model in which cluster formation is
driven by the positive feedback loop (i.e., larger clusters attract more CD8 T
cells) can accurately explain the available data. Second, while both Py-specific
CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are
attracted to the clusters, we found no evidence that non-specific CD8 T cells
play a role in cluster formation. Third and finally, mathematical modeling suggested
that formation of clusters occurs rapidly, within few hours after adoptive transfer
of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their
targets in complex peripheral organs, such as the liver. Taken together, our analysis
provides novel insights into and attempts to discriminate between alternative
mechanisms driving the formation of clusters of antigen-specific CD8 T cells in
the liver.
article_number: '2153'
article_processing_charge: No
article_type: original
author:
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: H
full_name: Rajakaruna, H
last_name: Rajakaruna
- first_name: IA
full_name: Cockburn, IA
last_name: Cockburn
- first_name: VV
full_name: Ganusov, VV
last_name: Ganusov
citation:
ama: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8
T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific
cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153
apa: Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering
of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven
by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153
chicago: Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering
of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven
by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153.
ieee: R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of
activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven
by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers,
2019.
ista: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated
CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific
cells. Frontiers in Immunology. 10, 2153.
mla: Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected
Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in
Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153.
short: R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology
10 (2019).
date_created: 2019-11-04T15:50:06Z
date_published: 2019-09-20T00:00:00Z
date_updated: 2023-08-30T07:18:23Z
day: '20'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.3389/fimmu.2019.02153
external_id:
isi:
- '000487187000001'
pmid:
- '31616407'
file:
- access_level: open_access
checksum: 68d1708f7aa412544159b498ef17a6b9
content_type: application/pdf
creator: dernst
date_created: 2019-11-04T15:54:00Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6984'
file_name: 2019_FrontiersImmonology_Kelemen.pdf
file_size: 2083061
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Immunology
publication_identifier:
issn:
- 1664-3224
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Clustering of activated CD8 T cells around Malaria-infected hepatocytes is
rapid and is driven by antigen-specific cells
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: 10
year: '2019'
...
---
_id: '6972'
abstract:
- lang: eng
text: 'We give fault-tolerant algorithms for establishing synchrony in distributed
systems in which each of thennodes has its own clock. Our algorithms operate in
a very strong fault model: we require self-stabilisation, i.e.,the initial state
of the system may be arbitrary, and there can be up to fJournal of the ACM. 2019;66(5). doi:10.1145/3339471
apa: Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471
chicago: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock
Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM,
2019. https://doi.org/10.1145/3339471.
ieee: C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM,
2019.
ista: Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation
is almost as easy as consensus. Journal of the ACM. 66(5), 32.
mla: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation
Is Almost as Easy as Consensus.” Journal of the ACM, vol. 66, no. 5, 32,
ACM, 2019, doi:10.1145/3339471.
short: C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019).
date_created: 2019-10-24T17:12:48Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-30T07:07:23Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
doi: 10.1145/3339471
ec_funded: 1
external_id:
arxiv:
- '1705.06173'
isi:
- '000496514100001'
file:
- access_level: open_access
checksum: 7e5d95c478e0e393f4927fcf7e48194e
content_type: application/pdf
creator: dernst
date_created: 2019-10-25T12:58:38Z
date_updated: 2020-07-14T12:47:46Z
file_id: '6975'
file_name: 2019_JACM_Lenzen.pdf
file_size: 2183085
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 66'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-stabilising Byzantine clock synchronisation is almost as easy as consensus
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: 66
year: '2019'
...
---
_id: '6942'
abstract:
- lang: eng
text: "Graph games and Markov decision processes (MDPs) are standard models in reactive
synthesis and verification of probabilistic systems with nondeterminism. The class
of \U0001D714 -regular winning conditions; e.g., safety, reachability, liveness,
parity conditions; provides a robust and expressive specification formalism for
properties that arise in analysis of reactive systems. The resolutions of nondeterminism
in games and MDPs are represented as strategies, and we consider succinct representation
of such strategies. The decision-tree data structure from machine learning retains
the flavor of decisions of strategies and allows entropy-based minimization to
obtain succinct trees. However, in contrast to traditional machine-learning problems
where small errors are allowed, for winning strategies in graph games and MDPs
no error is allowed, and the decision tree must represent the entire strategy.
In this work we propose decision trees with linear classifiers for representation
of strategies in graph games and MDPs. We have implemented strategy representation
using this data structure and we present experimental results for problems on
graph games and MDPs, which show that this new data structure presents a much
more efficient strategy representation as compared to standard decision trees."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Pranav
full_name: Ashok, Pranav
last_name: Ashok
- first_name: Tomáš
full_name: Brázdil, Tomáš
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jan
full_name: Křetínský, Jan
last_name: Křetínský
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Viktor
full_name: Toman, Viktor
id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87
last_name: Toman
orcid: 0000-0001-9036-063X
citation:
ama: 'Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy
representation by decision trees with linear classifiers. In: 16th International
Conference on Quantitative Evaluation of Systems. Vol 11785. Springer Nature;
2019:109-128. doi:10.1007/978-3-030-30281-8_7'
apa: 'Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., &
Toman, V. (2019). Strategy representation by decision trees with linear classifiers.
In 16th International Conference on Quantitative Evaluation of Systems
(Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-30281-8_7'
chicago: Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph
Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear
Classifiers.” In 16th International Conference on Quantitative Evaluation of
Systems, 11785:109–28. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-30281-8_7.
ieee: P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman,
“Strategy representation by decision trees with linear classifiers,” in 16th
International Conference on Quantitative Evaluation of Systems, Glasgow, United
Kingdom, 2019, vol. 11785, pp. 109–128.
ista: 'Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019.
Strategy representation by decision trees with linear classifiers. 16th International
Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation
of Systems, LNCS, vol. 11785, 109–128.'
mla: Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear
Classifiers.” 16th International Conference on Quantitative Evaluation of Systems,
vol. 11785, Springer Nature, 2019, pp. 109–28, doi:10.1007/978-3-030-30281-8_7.
short: P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman,
in:, 16th International Conference on Quantitative Evaluation of Systems, Springer
Nature, 2019, pp. 109–128.
conference:
end_date: 2019-09-12
location: Glasgow, United Kingdom
name: 'QEST: Quantitative Evaluation of Systems'
start_date: 2019-09-10
date_created: 2019-10-14T06:57:49Z
date_published: 2019-09-04T00:00:00Z
date_updated: 2023-08-30T06:59:36Z
day: '04'
department:
- _id: KrCh
- _id: ChLa
doi: 10.1007/978-3-030-30281-8_7
external_id:
arxiv:
- '1906.08178'
isi:
- '000679281300007'
intvolume: ' 11785'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1906.08178
month: '09'
oa: 1
oa_version: Preprint
page: 109-128
project:
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
publication: 16th International Conference on Quantitative Evaluation of Systems
publication_identifier:
eisbn:
- '9783030302818'
isbn:
- '9783030302801'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Strategy representation by decision trees with linear classifiers
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11785
year: '2019'
...