---
_id: '6060'
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation
on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019.
doi:10.15479/AT:ISTA:6060
apa: Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al.,
2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060
chicago: Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and
Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et
Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.
ieee: B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al.,
2019). .” Institute of Science and Technology Austria, 2019.
ista: Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al.,
2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.
mla: Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and
Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et
Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.
short: B. Vicoso, (2019).
date_created: 2019-02-28T10:55:15Z
date_published: 2019-02-28T00:00:00Z
date_updated: 2024-02-21T12:45:42Z
day: '28'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:6060
file:
- access_level: open_access
checksum: a338a622d728af0e3199cb07e6dd64d3
content_type: application/zip
creator: bvicoso
date_created: 2019-02-28T10:54:27Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6061'
file_name: SupData.zip
file_size: 36646050
relation: main_file
file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6418'
relation: research_paper
status: public
status: public
title: 'Supplementary data for "Sex-biased gene expression and dosage compensation
on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). '
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6074'
abstract:
- lang: eng
text: "This dataset contains the supplementary data for the research paper \"Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary
Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary
Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary
Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential
gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro
(ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene
Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment
analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro
(GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro
samples were split into upregulated and downregulated genes (up/down) and the
analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary
Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults
for the differential gene expression analysis for samples from adult mice before
(HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively).
Each sheet shows the results for a different comparison. Sheets 1-3 show results
for comparisons between timepoints for wild type (WT) samples only and sheets
4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results
for comparisons between genotypes at each time point and sheet 10 contains the
results for the analysis of differential expression trajectories between wild
type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults
for k-means clustering of genes by expression. Sheet 1 shows clustering of just
the genes with significantly different expression trajectories between genotypes.
Sheet 2 shows clustering of all genes that are significantly differentially expressed
in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary
Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment
analysis and EWCE analysis for enrichment of cell type specific genes for each
cluster identified by clustering genes with different expression trajectories
(see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults
showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet
1 shows protein protein interaction data generated from these results (combined
with data from the STRING database. Sheet 2 shows the results of the statistical
analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults
for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows
results for differential binding of PolII at the transcription start site (TSS)
between genotypes and sheets 2+3 show the corresponding GO enrichment analysis
for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with
increased binding of PolII at the TSS."
article_processing_charge: No
author:
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition.” 2019. doi:10.15479/AT:ISTA:6074
apa: Dotter, C., & Novarino, G. (2019). Supplementary data for the research
paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental
gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074
chicago: Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research
Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental
Gene Expression and Cognition.’” Institute of Science and Technology Austria,
2019. https://doi.org/10.15479/AT:ISTA:6074.
ieee: C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition.’” Institute of Science and Technology Austria, 2019.
ista: Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.
mla: Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research
Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental
Gene Expression and Cognition.” Institute of Science and Technology Austria,
2019, doi:10.15479/AT:ISTA:6074.
short: C. Dotter, G. Novarino, (2019).
date_created: 2019-03-07T13:32:35Z
date_published: 2019-01-09T00:00:00Z
date_updated: 2024-02-21T13:41:01Z
day: '09'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:6074
file:
- access_level: open_access
checksum: bc1b285edca9e98a2c63d153c79bb75b
content_type: application/zip
creator: dernst
date_created: 2019-03-07T13:37:19Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6084'
file_name: Setd5_paper.zip
file_size: 33202743
relation: supplementary_material
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '3'
relation: research_paper
status: public
status: public
title: Supplementary data for the research paper "Haploinsufficiency of the intellectual
disability gene SETD5 disturbs developmental gene expression and cognition"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6062'
abstract:
- lang: eng
text: Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section
with Python 3.7).
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
citation:
ama: Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive
Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062
apa: Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal
Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:6062
chicago: Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal
Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria,
2019. https://doi.org/10.15479/AT:ISTA:6062.
ieee: M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive
Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.
ista: Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal
Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:6062.
mla: Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal
Cognitive Map Is Attracted to Goals.” Institute of Science and Technology
Austria, 2019, doi:10.15479/AT:ISTA:6062.
short: M. Nardin, (2019).
date_created: 2019-03-04T14:20:58Z
date_published: 2019-03-29T00:00:00Z
date_updated: 2024-02-21T12:46:04Z
day: '29'
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6062
file:
- access_level: open_access
checksum: 48e7b9a02939b763417733239522a236
content_type: application/zip
creator: mnardin
date_created: 2019-03-05T09:29:37Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6068'
file_name: Online_data.zip
file_size: 37002186
relation: main_file
title: Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals"
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6194'
relation: research_paper
status: public
status: public
title: Supplementary Code and Data for the paper "The Entorhinal Cognitive Map is
Attracted to Goals"
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6089'
abstract:
- lang: eng
text: Pleiotropy is the well-established idea that a single mutation affects multiple
phenotypes. If a mutation has opposite effects on fitness when expressed in different
contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce
the efficacy of selection by limiting the fixation of beneficial mutations through
adaptation, and the removal of deleterious mutations through purifying selection.
Although this has been widely discussed, in particular in the context of a putative
“gender load,” it has yet to be systematically quantified. In this work, we empirically
estimate to which extent different pleiotropic regimes impede the efficacy of
selection in Drosophila melanogaster. We use whole-genome polymorphism data from
a single African population and divergence data from D. simulans to estimate the
fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction
of selection (DoS). After controlling for confounding covariates, we find that
the different pleiotropic regimes have a relatively small, but significant, effect
on selection efficacy. Specifically, our results suggest that pleiotropic sexual
antagonism may restrict the efficacy of selection, but that this conflict can
be resolved by limiting the expression of genes to the sex where they are beneficial.
Intermediate levels of pleiotropy across tissues and life stages can also lead
to maladaptation in D. melanogaster, due to inefficient purifying selection combined
with low frequency of mutations that confer a selective advantage. Thus, our study
highlights the need to consider the efficacy of selection in the context of antagonistic
pleiotropy, and of genetic conflict in general.
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection
in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515.
doi:10.1093/molbev/msy246
apa: Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates
the efficacy of selection in drosophila melanogaster. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246
chicago: Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy
Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular
Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.
ieee: C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy
of selection in drosophila melanogaster,” Molecular biology and evolution,
vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.
ista: Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy
of selection in drosophila melanogaster. Molecular biology and evolution. 36(3),
500–515.
mla: Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection
in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36,
no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.
short: C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36
(2019) 500–515.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2024-02-21T13:59:17Z
day: '01'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/molbev/msy246
external_id:
isi:
- '000462585100006'
pmid:
- '30590559'
intvolume: ' 36'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30590559
month: '03'
oa: 1
oa_version: Submitted Version
page: 500-515
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular biology and evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '5757'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Pleiotropy modulates the efficacy of selection in drosophila melanogaster
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2019'
...
---
_id: '6179'
abstract:
- lang: eng
text: "In the first part of this thesis we consider large random matrices with arbitrary
expectation and a general slowly decaying correlation among its entries. We prove
universality of the local eigenvalue statistics and optimal local laws for the
resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic
control of a multivariate cumulant expansion.\r\nIn the second part we consider
Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue
distribution the local eigenvalue statistics are uni- versal and form a Pearcey
process. Since the density of states typically exhibits only square root or cubic
root cusp singularities, our work complements previous results on the bulk and
edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta
universality conjecture for the last remaining universality type. Our analysis
holds not only for exact cusps, but approximate cusps as well, where an ex- tended
Pearcey process emerges. As a main technical ingredient we prove an optimal local
law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow-
nian motion to the cusp regime.\r\nIn the third and final part we explore the
entrywise linear statistics of Wigner ma- trices and identify the fluctuations
for a large class of test functions with little regularity. This enables us to
study the rectangular Young diagram obtained from the interlacing eigenvalues
of the random matrix and its minor, and we find that, despite having the same
limit, the fluctuations differ from those of the algebraic Young tableaux equipped
with the Plancharel measure."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: 'Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix
theory. 2019. doi:10.15479/AT:ISTA:th6179'
apa: 'Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in
random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179'
chicago: 'Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random
Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179.'
ieee: 'D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix
theory,” Institute of Science and Technology Austria, 2019.'
ista: 'Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random
matrix theory. Institute of Science and Technology Austria.'
mla: 'Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random
Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.'
short: 'D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix
Theory, Institute of Science and Technology Austria, 2019.'
date_created: 2019-03-28T08:58:59Z
date_published: 2019-03-18T00:00:00Z
date_updated: 2024-02-22T14:34:33Z
day: '18'
ddc:
- '515'
- '519'
degree_awarded: PhD
department:
- _id: LaEr
doi: 10.15479/AT:ISTA:th6179
ec_funded: 1
file:
- access_level: closed
checksum: 6926f66f28079a81c4937e3764be00fc
content_type: application/x-gzip
creator: dernst
date_created: 2019-03-28T08:53:52Z
date_updated: 2020-07-14T12:47:21Z
file_id: '6180'
file_name: 2019_Schroeder_Thesis.tar.gz
file_size: 7104482
relation: source_file
- access_level: open_access
checksum: 7d0ebb8d1207e89768cdd497a5bf80fb
content_type: application/pdf
creator: dernst
date_created: 2019-03-28T08:53:52Z
date_updated: 2020-07-14T12:47:21Z
file_id: '6181'
file_name: 2019_Schroeder_Thesis.pdf
file_size: 4228794
relation: main_file
file_date_updated: 2020-07-14T12:47:21Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '375'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1144'
relation: part_of_dissertation
status: public
- id: '6186'
relation: part_of_dissertation
status: public
- id: '6185'
relation: part_of_dissertation
status: public
- id: '6182'
relation: part_of_dissertation
status: public
- id: '1012'
relation: part_of_dissertation
status: public
- id: '6184'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
title: 'From Dyson to Pearcey: Universal statistics in random matrix theory'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...