---
_id: '14689'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Elizabeth
full_name: Ing-Simmons, Elizabeth
last_name: Ing-Simmons
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
- first_name: Juan M.
full_name: Vaquerizas, Juan M.
last_name: Vaquerizas
citation:
ama: 'Ing-Simmons E, Machnik NN, Vaquerizas JM. Reply to: Revisiting the use of
structural similarity index in Hi-C. Nature Genetics. 2023;55(12):2053-2055.
doi:10.1038/s41588-023-01595-5'
apa: 'Ing-Simmons, E., Machnik, N. N., & Vaquerizas, J. M. (2023). Reply to:
Revisiting the use of structural similarity index in Hi-C. Nature Genetics.
Springer Nature. https://doi.org/10.1038/s41588-023-01595-5'
chicago: 'Ing-Simmons, Elizabeth, Nick N Machnik, and Juan M. Vaquerizas. “Reply
to: Revisiting the Use of Structural Similarity Index in Hi-C.” Nature Genetics.
Springer Nature, 2023. https://doi.org/10.1038/s41588-023-01595-5.'
ieee: 'E. Ing-Simmons, N. N. Machnik, and J. M. Vaquerizas, “Reply to: Revisiting
the use of structural similarity index in Hi-C,” Nature Genetics, vol.
55, no. 12. Springer Nature, pp. 2053–2055, 2023.'
ista: 'Ing-Simmons E, Machnik NN, Vaquerizas JM. 2023. Reply to: Revisiting the
use of structural similarity index in Hi-C. Nature Genetics. 55(12), 2053–2055.'
mla: 'Ing-Simmons, Elizabeth, et al. “Reply to: Revisiting the Use of Structural
Similarity Index in Hi-C.” Nature Genetics, vol. 55, no. 12, Springer Nature,
2023, pp. 2053–55, doi:10.1038/s41588-023-01595-5.'
short: E. Ing-Simmons, N.N. Machnik, J.M. Vaquerizas, Nature Genetics 55 (2023)
2053–2055.
date_created: 2023-12-17T23:00:53Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2023-12-18T08:51:38Z
day: '01'
department:
- _id: MaRo
doi: 10.1038/s41588-023-01595-5
external_id:
pmid:
- '38052961'
intvolume: ' 55'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 2053-2055
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Reply to: Revisiting the use of structural similarity index in Hi-C'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2023'
...
---
_id: '8151'
abstract:
- lang: eng
text: The main idea behind the Core Project is to teach first year students at IST
scientific communication skills and let them practice by presenting their research
within an interdisciplinary environment. Over the course of the first semester,
students participated in seminars, where they shared their results with the colleagues
from other fields and took part in discussions on relevant subjects. The main
focus during this sessions was on delivering the information in a simplified and
comprehensible way, going into the very basics of a subject if necessary. At the
end, the students were asked to present their research in the written form to
exercise their writing skills. The reports were gathered in this document. All
of them were reviewed by the teaching assistants and write-ups illustrating unique
stylistic features and, in general, an outstanding level of writing skills, were
honorably mentioned in the section "Selected Reports".
article_processing_charge: No
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Mike
full_name: Hennessey-Wesen, Mike
id: 3F338C72-F248-11E8-B48F-1D18A9856A87
last_name: Hennessey-Wesen
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
- first_name: Roshan K
full_name: Satapathy, Roshan K
id: 46046B7A-F248-11E8-B48F-1D18A9856A87
last_name: Satapathy
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Maslov M, Kondrashov F, Artner C, et al. Core Project Proceedings. IST
Austria; 2020.
apa: Maslov, M., Kondrashov, F., Artner, C., Hennessey-Wesen, M., Kavcic, B., Machnik,
N. N., … Tomanek, I. (2020). Core Project Proceedings. IST Austria.
chicago: Maslov, Mikhail, Fyodor Kondrashov, Christina Artner, Mike Hennessey-Wesen,
Bor Kavcic, Nick N Machnik, Roshan K Satapathy, and Isabella Tomanek. Core
Project Proceedings. IST Austria, 2020.
ieee: M. Maslov et al., Core Project Proceedings. IST Austria, 2020.
ista: Maslov M, Kondrashov F, Artner C, Hennessey-Wesen M, Kavcic B, Machnik NN,
Satapathy RK, Tomanek I. 2020. Core Project Proceedings, IST Austria, 425p.
mla: Maslov, Mikhail, et al. Core Project Proceedings. IST Austria, 2020.
short: M. Maslov, F. Kondrashov, C. Artner, M. Hennessey-Wesen, B. Kavcic, N.N.
Machnik, R.K. Satapathy, I. Tomanek, Core Project Proceedings, IST Austria, 2020.
date_created: 2020-07-22T14:48:14Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-02-23T13:26:00Z
day: '01'
ddc:
- '510'
- '530'
- '570'
extern: '1'
file:
- access_level: local
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T14:45:07Z
date_updated: 2020-07-22T14:45:07Z
file_id: '8152'
file_name: Core_Project_Proceedings_mod.pdf
file_size: 169620437
relation: main_file
file_date_updated: 2020-07-22T14:45:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: '425'
publication_status: published
publisher: IST Austria
status: public
title: Core Project Proceedings
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '8707'
abstract:
- lang: eng
text: Dynamic changes in the three-dimensional (3D) organization of chromatin are
associated with central biological processes, such as transcription, replication
and development. Therefore, the comprehensive identification and quantification
of these changes is fundamental to understanding of evolutionary and regulatory
mechanisms. Here, we present Comparison of Hi-C Experiments using Structural Similarity
(CHESS), an algorithm for the comparison of chromatin contact maps and automatic
differential feature extraction. We demonstrate the robustness of CHESS to experimental
variability and showcase its biological applications on (1) interspecies comparisons
of syntenic regions in human and mouse models; (2) intraspecies identification
of conformational changes in Zelda-depleted Drosophila embryos; (3) patient-specific
aberrant chromatin conformation in a diffuse large B-cell lymphoma sample; and
(4) the systematic identification of chromatin contact differences in high-resolution
Capture-C data. In summary, CHESS is a computationally efficient method for the
comparison and classification of changes in chromatin contact data.
acknowledgement: 'Work in the Vaquerizas laboratory is funded by the Max Planck Society,
the Deutsche Forschungsgemeinschaft (DFG) Priority Programme SPP 2202 ‘Spatial Genome
Architecture in Development and Disease’ (project no. 422857230 to J.M.V.), the
DFG Clinical Research Unit CRU326 ‘Male Germ Cells: from Genes to Function’ (project
no. 329621271 to J.M.V.), the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie grant agreement no. 643062—ZENCODE-ITN
to J.M.V.) and the Medical Research Council in the UK. This research was partially
funded by the European Union’s H2020 Framework Programme through the European Research
Council (grant no. 609989 to M.A.M.-R.). We thank the support of the Spanish Ministerio
de Ciencia, Innovación y Universidades through grant no. BFU2017-85926-P to M.A.M.-R.
The Centre for Genomic Regulation thanks the support of the Ministerio de Ciencia,
Innovación y Universidades to the European Molecular Biology Laboratory partnership,
the ‘Centro de Excelencia Severo Ochoa 2013–2017’, agreement no. SEV-2012-0208,
the CERCA Programme/Generalitat de Catalunya, Spanish Ministerio de Ciencia, Innovación
y Universidades through the Instituto de Salud Carlos III, the Generalitat de Catalunya
through the Departament de Salut and Departament d’Empresa i Coneixement and cofinancing
by the Spanish Ministerio de Ciencia, Innovación y Universidades with funds from
the European Regional Development Fund corresponding to the 2014–2020 Smart Growth
Operating Program. S.G. thanks the support from the Company of Biologists (grant
no. JCSTF181158) and the European Molecular Biology Organization Short-Term Fellowship
programme.'
article_processing_charge: No
article_type: original
author:
- first_name: Silvia
full_name: ' Galan, Silvia'
last_name: ' Galan'
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
orcid: 0000-0001-6617-9742
- first_name: Kai
full_name: Kruse, Kai
last_name: Kruse
- first_name: Noelia
full_name: Díaz, Noelia
last_name: Díaz
- first_name: Marc A
full_name: Marti-Renom, Marc A
last_name: Marti-Renom
- first_name: Juan M
full_name: Vaquerizas, Juan M
last_name: Vaquerizas
citation:
ama: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. CHESS
enables quantitative comparison of chromatin contact data and automatic feature
extraction. Nature Genetics. 2020;52:1247-1255. doi:10.1038/s41588-020-00712-y
apa: Galan, S., Machnik, N. N., Kruse, K., Díaz, N., Marti-Renom, M. A., & Vaquerizas,
J. M. (2020). CHESS enables quantitative comparison of chromatin contact data
and automatic feature extraction. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-020-00712-y
chicago: Galan, Silvia, Nick N Machnik, Kai Kruse, Noelia Díaz, Marc A Marti-Renom,
and Juan M Vaquerizas. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics. Springer Nature,
2020. https://doi.org/10.1038/s41588-020-00712-y.
ieee: S. Galan, N. N. Machnik, K. Kruse, N. Díaz, M. A. Marti-Renom, and J. M.
Vaquerizas, “CHESS enables quantitative comparison of chromatin contact data and
automatic feature extraction,” Nature Genetics, vol. 52. Springer Nature,
pp. 1247–1255, 2020.
ista: Galan S, Machnik NN, Kruse K, Díaz N, Marti-Renom MA, Vaquerizas JM. 2020.
CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction. Nature Genetics. 52, 1247–1255.
mla: Galan, Silvia, et al. “CHESS Enables Quantitative Comparison of Chromatin Contact
Data and Automatic Feature Extraction.” Nature Genetics, vol. 52, Springer
Nature, 2020, pp. 1247–55, doi:10.1038/s41588-020-00712-y.
short: S. Galan, N.N. Machnik, K. Kruse, N. Díaz, M.A. Marti-Renom, J.M. Vaquerizas,
Nature Genetics 52 (2020) 1247–1255.
date_created: 2020-10-25T23:01:20Z
date_published: 2020-10-19T00:00:00Z
date_updated: 2023-08-22T10:37:10Z
day: '19'
department:
- _id: FyKo
doi: 10.1038/s41588-020-00712-y
external_id:
isi:
- '000579693500004'
pmid:
- '33077914'
intvolume: ' 52'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 1247-1255
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- '15461718'
issn:
- '10614036'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: CHESS enables quantitative comparison of chromatin contact data and automatic
feature extraction
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2020'
...