---
DOAJ_listed: '1'
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OA_type: gold
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_id: '22229'
abstract:
- lang: eng
text: Hippocampal CA3 pyramidal neurons (PNs) form the largest autoassociative network
in the mammalian brain. Whether CA3–CA3 recurrent connectivity is genetically
preconfigured or environmentally shaped during ongoing memory storage is currently
unknown. To address this question, we performed multicellular patch-clamp-based
circuit mapping of up to eight CA3 PNs in the mouse hippocampus at multiple postnatal
time points (P7–8, P18–25, and P45–50). Here, we show that the hippocampal CA3
network undergoes a developmental transformation from local, dense, and random
connectivity to a distributed, sparse, and structured configuration. Thus, sparse
and structured connectivity may emerge via experience-dependent mechanisms. In
parallel, the strength of single synapses is downregulated; single synaptic events
are sufficient to trigger postsynaptic spiking early in development, whereas spatial
summation of several inputs is required at later time points. Biologically inspired
models of memory storage by Hebbian synaptic plasticity and retrieval via pattern
completion suggest that developmental changes improve specific aspects of memory
storage and retrieval. Our results imply a developmental transformation of the
neuronal code and the memory functions in the hippocampal CA3 network.
acknowledged_ssus:
- _id: PreCl
- _id: Bio
- _id: M-Shop
- _id: ScienComp
acknowledgement: 'We thank Jose Guzman, Simon Hippenmeyer, and Tim Vogels for critically
reading the manuscript, Jozsef Csicsvari for useful discussions, Florian Marr for
technical assistance, and Eleftheria Kralli-Beller for manuscript editing. This
research was supported by the Scientific Services Units (SSUs) of ISTA: the preclinical
facility (PCF) provided housing and breeding of the animals, the imaging and optics
facility (IOF) offered technical training and state of the art equipment, the Miba
machine shop contributed to the construction and maintenance of multicellular recording
setups, and the scientific computing unit helped with the large-scale simulations.
The project received funding from the European Union’s Horizon 2020 research and
innovation programme (ERC Advanced Grants No 692692 GIANTSYN and 101199096 CA3-SYNGRAM
to P.J.; Marie Skłodowska-Curie Grant 754411 to V.V.B.; Marie Skłodowska-Curie Grant
101026635 to J.F.W.), the Fond zur Förderung der Wissenschaftlichen Forschung (P
36232-B, PAT4178023, and 10.55776/CoE16 to P.J.), and the Nomis Foundation (fellowship
to A.N.-O.). V.V.B. received funding from a CONACyT fellowship (289638).'
article_number: '5540'
article_processing_charge: Yes
article_type: original
author:
- first_name: Victor M
full_name: Vargas Barroso, Victor M
id: 2F55A9DE-F248-11E8-B48F-1D18A9856A87
last_name: Vargas Barroso
- first_name: Jake
full_name: Watson, Jake
id: 63836096-4690-11EA-BD4E-32803DDC885E
last_name: Watson
orcid: 0000-0002-8698-3823
- first_name: Andrea C
full_name: Navas Olivé, Andrea C
id: 739d26c9-52e8-11ee-8d72-f14d3893b4ce
last_name: Navas Olivé
orcid: 0000-0002-9280-8597
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Vargas Barroso VM, Watson J, Navas Olivé AC, Schlögl A, Jonas PM. Developmental
emergence of sparse and structured synaptic connectivity in the hippocampal CA3
memory circuit. Nature Communications. 2026;17. doi:10.1038/s41467-026-71914-x
apa: Vargas Barroso, V. M., Watson, J., Navas Olivé, A. C., Schlögl, A., & Jonas,
P. M. (2026). Developmental emergence of sparse and structured synaptic connectivity
in the hippocampal CA3 memory circuit. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-026-71914-x
chicago: Vargas Barroso, Victor M, Jake Watson, Andrea C Navas Olivé, Alois Schlögl,
and Peter M Jonas. “Developmental Emergence of Sparse and Structured Synaptic
Connectivity in the Hippocampal CA3 Memory Circuit.” Nature Communications.
Springer Nature, 2026. https://doi.org/10.1038/s41467-026-71914-x.
ieee: V. M. Vargas Barroso, J. Watson, A. C. Navas Olivé, A. Schlögl, and P. M.
Jonas, “Developmental emergence of sparse and structured synaptic connectivity
in the hippocampal CA3 memory circuit,” Nature Communications, vol. 17.
Springer Nature, 2026.
ista: Vargas Barroso VM, Watson J, Navas Olivé AC, Schlögl A, Jonas PM. 2026. Developmental
emergence of sparse and structured synaptic connectivity in the hippocampal CA3
memory circuit. Nature Communications. 17, 5540.
mla: Vargas Barroso, Victor M., et al. “Developmental Emergence of Sparse and Structured
Synaptic Connectivity in the Hippocampal CA3 Memory Circuit.” Nature Communications,
vol. 17, 5540, Springer Nature, 2026, doi:10.1038/s41467-026-71914-x.
short: V.M. Vargas Barroso, J. Watson, A.C. Navas Olivé, A. Schlögl, P.M. Jonas,
Nature Communications 17 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: Source data are provided with this paper. Additional original
data are available from the corresponding author upon request. Code is available
from https://doi.org/10.15479/AT-ISTA-21442 under the link https://research-explorer.ista.ac.at/download/21442/21443/ca3simu-vargas2026v1.tar.gz
date_created: 2026-06-30T13:05:52Z
date_published: 2026-06-23T00:00:00Z
date_updated: 2026-07-01T06:47:49Z
day: '23'
ddc:
- '570'
department:
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- _id: ScienComp
doi: 10.1038/s41467-026-71914-x
ec_funded: 1
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- '42014695'
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call_identifier: H2020
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name: Synaptic computations of the hippocampal CA3 circuitry
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grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
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name: Synaptic networks of human brain
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name: Reglas de Conectividad funcional en el hipocampo
publication: Nature Communications
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publisher: Springer Nature
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supplementarymaterial: yes
title: Developmental emergence of sparse and structured synaptic connectivity in the
hippocampal CA3 memory circuit
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
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type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
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...
---
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author:
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full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
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citation:
ama: Schlögl A. CA3Simu v1.06 (vargas2026v1). 2026. doi:10.15479/AT-ISTA-21442
apa: Schlögl, A. (2026). CA3Simu v1.06 (vargas2026v1). Institute of Science and
Technology Austria. https://doi.org/10.15479/AT-ISTA-21442
chicago: Schlögl, Alois. “CA3Simu v1.06 (Vargas2026v1).” Institute of Science and
Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21442.
ieee: A. Schlögl, “CA3Simu v1.06 (vargas2026v1).” Institute of Science and Technology
Austria, 2026.
ista: Schlögl A. 2026. CA3Simu v1.06 (vargas2026v1), Institute of Science and Technology
Austria, 10.15479/AT-ISTA-21442.
mla: Schlögl, Alois. CA3Simu v1.06 (Vargas2026v1). Institute of Science and
Technology Austria, 2026, doi:10.15479/AT-ISTA-21442.
short: A. Schlögl, (2026).
corr_author: '1'
date_created: 2026-03-12T08:20:46Z
date_published: 2026-03-12T00:00:00Z
date_updated: 2026-07-01T06:47:49Z
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keyword:
- hypocampus
- ca3 simulations
- modelling
license: https://opensource.org/licenses/GPL-3.0
month: '03'
oa: 1
project:
- _id: e62b56fe-ab3c-11f0-94c7-d181dd352b3b
grant_number: '101199096'
name: Synaptic mechanisms of engram storage and retrieval in CA3 hippocampal microcircuits
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grant_number: P36232
name: Mechanisms of GABA release in hippocampal circuits
- _id: 8d9195e9-16d5-11f0-9cad-d075be887a1e
grant_number: PAT 4178023
name: Synaptic networks of human brain
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
publisher: Institute of Science and Technology Austria
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title: CA3Simu v1.06 (vargas2026v1)
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name: GNU General Public License 3.0
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...
---
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_id: '22295'
abstract:
- lang: eng
text: 'Despite the functional diversity of over 100 causal genes1,2,3, phenotypic
convergence across models may reveal common neurobiological processes in autism
spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse
models of ASD using single-nucleus multi-omic sequencing across three developmental
stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked
mutations converged on perturbations of the radial glial cell lineage. These alterations
reflect a transient developmental delay rather than lasting lineage misspecification
and resolve by postnatal stages. Molecularly, the largest transcriptional differences
emerged in neurons at early postnatal stages. These changes included downregulation
of synaptic and ion channel-related genes, consistent with homeostatic adaptation
or delayed maturation. Network analysis showed molecular convergence across models
within each developmental stage, suggesting that diverse mutations linked to ASD
impinge on common, stage-specific processes. Convergence becomes less pronounced
by postnatal day 14, highlighting the dynamic nature of ASD-associated changes.
Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology
corroborated this pattern: mutants generally showed altered neuronal excitability
and synaptic properties with model-specific nuances. Our study also highlighted
sex-specific gene expression alterations, with female mice often displaying larger
effect sizes than male mice. Together, our findings provide a comprehensive view
of developmental cellular and molecular dynamics across models of ASD.'
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: We thank F. Freeman, V. Voronin and M. Ladron de Guevara for technical
assistance; A. Stichelberger and S. Liegenfeld for the management of our animal
colony; M. Schunn, C. Gold and the Preclinical Facility team for technical assistance;
C. Jansen and the Scientific Computing Facility for bioinformatics support and technical
assistance; the Biomedical Sequencing Facility at CeMM for assistance with next-generation
sequencing; and J. Lin and T. Krausgruber in the laboratory of C. Bock for support
with flow cytometry; J. Kirchner for illustrating the multi-omics approach depicted
in Fig. 1; and all members of the laboratory of G.N. for their support and discussions.
This study was supported by the Scientific Service Units of ISTA through resources
provided by the Imaging & Optics Facility and the Laboratory Support Facility. Bulk
RNA-seq was performed by the Next Generation Sequencing Facility at Vienna BioCenter
Core Facilities, member of the Vienna BioCenter. This work was supported by a European
Research Council Consolidator Grant (PR1028ERC02), by SFARI (PR1028SIM02) and by
the Austrian Science Fund (PE1028W1232 and PR1028FG1803) to G.N. Open access funding
provided by Institute of Science and Technology (IST Austria).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lena A
full_name: Schwarz, Lena A
id: 29A8453C-F248-11E8-B48F-1D18A9856A87
last_name: Schwarz
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Sergey
full_name: Isaev, Sergey
last_name: Isaev
- first_name: Michela
full_name: Lisi, Michela
id: 39383c1b-d3eb-11ef-8d6c-c8cdf4e10c8c
last_name: Lisi
- first_name: Daniel
full_name: Malzl, Daniel
last_name: Malzl
- first_name: Christoph
full_name: Büschl, Christoph
id: 2a8c054c-0913-11ee-9159-f8ef515809ed
last_name: Büschl
- first_name: Sabrina
full_name: Ladstätter, Sabrina
last_name: Ladstätter
- first_name: Bárbara
full_name: Oliveira, Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- first_name: Matteo
full_name: Barel, Matteo
id: 8959927b-2236-11ed-bd6e-ea83d94ade0e
last_name: Barel
- first_name: Bernadette
full_name: Basilico, Bernadette
id: 36035796-5ACA-11E9-A75E-7AF2E5697425
last_name: Basilico
orcid: 0000-0003-1843-3173
- first_name: Chaitanya
full_name: Chintaluri, Chaitanya
id: BA06AFEE-A4BA-11EA-AE5C-14673DDC885E
last_name: Chintaluri
orcid: 0000-0003-4252-1608
- first_name: Sarah
full_name: Gorkiewicz, Sarah
id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f
last_name: Gorkiewicz
- first_name: Mohammad
full_name: Goudarzi, Mohammad
id: 3384113A-F248-11E8-B48F-1D18A9856A87
last_name: Goudarzi
- first_name: Tereza
full_name: Belinova, Tereza
id: 0bf89b6a-d28b-11eb-8bd6-f43768e4d368
last_name: Belinova
- first_name: Stephan
full_name: Reichl, Stephan
last_name: Reichl
- first_name: Gintarė
full_name: Sendžikaitė, Gintarė
id: dd6d52f2-c50d-11eb-9548-bcf0ff82b344
last_name: Sendžikaitė
- first_name: Satish
full_name: Arcot Jayaram, Satish
id: b0bbee33-09f7-11eb-909c-8b358058d28a
last_name: Arcot Jayaram
orcid: 0000-0002-2479-2669
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Christoph M
full_name: Sommer, Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Jörg
full_name: Menche, Jörg
last_name: Menche
- first_name: Igor
full_name: Adameyko, Igor
last_name: Adameyko
- first_name: Peter Vasili
full_name: Kharchenko, Peter Vasili
id: 0095641e-7eb7-11f1-8665-aec51a2ab5e0
last_name: Kharchenko
- first_name: Christoph
full_name: Bock, Christoph
last_name: Bock
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Schwarz LA, Dotter C, Isaev S, et al. Cortical development dynamics across
autism spectrum disorder mouse models. Nature. 2026. doi:10.1038/s41586-026-10679-1
apa: Schwarz, L. A., Dotter, C., Isaev, S., Lisi, M., Malzl, D., Büschl, C., … Novarino,
G. (2026). Cortical development dynamics across autism spectrum disorder mouse
models. Nature. Springer Nature. https://doi.org/10.1038/s41586-026-10679-1
chicago: Schwarz, Lena A, Christoph Dotter, Sergey Isaev, Michela Lisi, Daniel Malzl,
Christoph Büschl, Sabrina Ladstätter, et al. “Cortical Development Dynamics across
Autism Spectrum Disorder Mouse Models.” Nature. Springer Nature, 2026.
https://doi.org/10.1038/s41586-026-10679-1.
ieee: L. A. Schwarz et al., “Cortical development dynamics across autism
spectrum disorder mouse models,” Nature. Springer Nature, 2026.
ista: Schwarz LA, Dotter C, Isaev S, Lisi M, Malzl D, Büschl C, Ladstätter S, Oliveira
B, Barel M, Basilico B, Chintaluri C, Gorkiewicz S, Goudarzi M, Belinova T, Reichl
S, Sendžikaitė G, Arcot Jayaram S, Koppensteiner P, Sommer CM, Vogels TP, Menche
J, Adameyko I, Kharchenko PV, Bock C, Novarino G. 2026. Cortical development dynamics
across autism spectrum disorder mouse models. Nature.
mla: Schwarz, Lena A., et al. “Cortical Development Dynamics across Autism Spectrum
Disorder Mouse Models.” Nature, Springer Nature, 2026, doi:10.1038/s41586-026-10679-1.
short: L.A. Schwarz, C. Dotter, S. Isaev, M. Lisi, D. Malzl, C. Büschl, S. Ladstätter,
B. Oliveira, M. Barel, B. Basilico, C. Chintaluri, S. Gorkiewicz, M. Goudarzi,
T. Belinova, S. Reichl, G. Sendžikaitė, S. Arcot Jayaram, P. Koppensteiner, C.M.
Sommer, T.P. Vogels, J. Menche, I. Adameyko, P.V. Kharchenko, C. Bock, G. Novarino,
Nature (2026).
corr_author: '1'
dataavailabilitystatement: Single-nucleus multiomics data are available from the Gene
Expression Omnibus (GSE328363). The mm10 reference genome was used for the alignment
(refdata-cellranger-arc-mm10-2020-A-2.0.0, obtained from https://cf.10xgenomics.com/supp/cell-arc/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz).
Single-cell data can be accessed and visualized through a CELLxGENE database (https://adameykolab.hifo.meduniwien.ac.at/cellxgene_public/filecrawl/.2026_Nature_Schwarz).
Source data are provided with this paper. Scripts and analyses that support the
main findings of this study are accessible in a GitHub repository (https://git.ista.ac.at/research-sofware/mouseome).
date_created: 2026-07-13T09:47:21Z
date_published: 2026-06-17T00:00:00Z
date_updated: 2026-08-04T09:29:55Z
day: '17'
ddc:
- '570'
department:
- _id: AnKi
- _id: GaNo
- _id: TiVo
- _id: ScienComp
- _id: GradSch
- _id: Bio
- _id: PreCl
doi: 10.1038/s41586-026-10679-1
external_id:
pmid:
- '42310454'
fulldoi: https://doi.org/10.1038/s41586-026-10679-1
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-026-10679-1
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ba8964-11ca-11ed-8bc3-e15864e7e9a6
grant_number: '101044865'
name: Toward an understanding of the brain interstitial system and the extracellular
proteome in health and autism spectrum disorders
- _id: 9B91375C-BA93-11EA-9121-9846C619BF3A
grant_number: '707964'
name: Critical windows and reversibility of ASD associated with mutations in chromatin
remodelers
- _id: 2548AE96-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W1232
name: Molecular Drug Targets
- _id: ebb38b5d-77a9-11ec-83b8-a42e08120a88
grant_number: FG1803 49015
name: Neurobiology of anxiety in autism spectrum disorders
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/patterns-in-genetic-chaos/
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Cortical development dynamics across autism spectrum disorder mouse models
tmp:
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short: CC BY (4.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
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_id: '22951'
abstract:
- lang: eng
text: Anesthesia recovery is critical for resuming normal physiological and neuronal
functions; however, the mechanisms involved remain elusive. Here, we identify
a female-selective corticosterone-mediated microglia-neuron interaction during
ketamine anesthesia recovery, absent in males. This microglia-neuron interaction
induces plastic and functional neuronal changes, as evidenced by increased mEPSC
frequency, which was occluded upon microglia depletion. We showed that this process
is driven through up-regulation of the stress-responsive co-chaperone Fkbp5 mRNA
and its protein, Fkbp51, in female microglia. Fkbp5/Fkbp51 is a key intermediary
in a corticosteroid-induced stress response, and its involvement points toward
a critical interface between endocrine signaling and microglia. To counteract
the observed ketamine anesthesia-mediated increase in blood corticosterone during
recovery, we removed the primary source of corticosterone by adrenalectomy. Close
microglia-neuron interaction was reduced and increased again following corticosterone
injection. Our findings identify a sex-specific microglia-mediated mechanism of
neuronal plasticity during anesthesia recovery, driven by corticosterone, thereby
enhancing our understanding of sex differences in brain function.
acknowledged_ssus:
- _id: Bio
- _id: M-Shop
- _id: PreCl
- _id: LifeSc
acknowledgement: "We thank the scientific service units at ISTA, especially the imaging
optic facility (IOF), the machine shop (Miba), specifically T. Asenov, the preclinical
facility (PCF), specifically M. Schunn and S. Haslinger, C. Jansen for bioinformatic
support, and the laboratory support facility (LSF). We also thank M. Benevento for
supporting the design and partial performance of electrophysiology and fluorescence
in situ hybridization experiments and for extensive discussions about the manuscript
draft, R. Schulz and G. Colombo for advice on morphological reconstruction, M. Schmidt
for valuable discussions about Fkbp5, and all Siegert team members for constant
feedback on the project and manuscript. Grammarly was used to assist with grammatical
revisions. We specifically acknowledge the following experimental contributions:
R.J.A.C. (Multiome quality control), P.K. (electrophysiology), B.T., C.T.J.V., K.J.
(multiome), J.Y. (KXA estimates), M.A. and T.N. (morphOMICs).\r\nA.V., M.A., T.N.,
R.J.A.C., J.Y., P.K., and S.S. were supported by the Institute of Science and Technology
Austria. C.T.J.V., K.J., and B.T. were supported by the Allen Institute."
article_number: eadz6517
article_processing_charge: Yes
article_type: original
author:
- first_name: Alessandro
full_name: Venturino, Alessandro
id: 41CB84B2-F248-11E8-B48F-1D18A9856A87
last_name: Venturino
orcid: 0000-0003-2356-9403
- first_name: Amin
full_name: Alam, Amin
id: 65a3f615-b651-11f1-9c4b-da4396a4174a
last_name: Alam
- first_name: Thomas
full_name: Negrello, Thomas
id: 37d68bf2-b651-11f1-b680-ec86ff9a70f3
last_name: Negrello
- first_name: Kelly
full_name: Jin, Kelly
last_name: Jin
- first_name: Cindy T. J.
full_name: van Velthoven, Cindy T. J.
last_name: van Velthoven
- first_name: Ryan J
full_name: Cubero, Ryan J
id: 850B2E12-9CD4-11E9-837F-E719E6697425
last_name: Cubero
orcid: 0000-0003-0002-1867
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Peter
full_name: Koppensteiner, Peter
id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87
last_name: Koppensteiner
orcid: 0000-0002-3509-1948
- first_name: Bosiljka
full_name: Tasic, Bosiljka
last_name: Tasic
- first_name: Sandra
full_name: Siegert, Sandra
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
citation:
ama: Venturino A, Alam A, Negrello T, et al. Corticosterone-linked microglial activity
underpins sexually dimorphic neuroplasticity after ketamine anesthesia. Science
Advances. 2026;12(31). doi:10.1126/sciadv.adz6517
apa: Venturino, A., Alam, A., Negrello, T., Jin, K., van Velthoven, C. T. J., Cubero,
R. J., … Siegert, S. (2026). Corticosterone-linked microglial activity underpins
sexually dimorphic neuroplasticity after ketamine anesthesia. Science Advances.
AAAS. https://doi.org/10.1126/sciadv.adz6517
chicago: Venturino, Alessandro, Amin Alam, Thomas Negrello, Kelly Jin, Cindy T.
J. van Velthoven, Ryan J Cubero, Jake Yeung, Peter Koppensteiner, Bosiljka Tasic,
and Sandra Siegert. “Corticosterone-Linked Microglial Activity Underpins Sexually
Dimorphic Neuroplasticity after Ketamine Anesthesia.” Science Advances.
AAAS, 2026. https://doi.org/10.1126/sciadv.adz6517.
ieee: A. Venturino et al., “Corticosterone-linked microglial activity underpins
sexually dimorphic neuroplasticity after ketamine anesthesia,” Science Advances,
vol. 12, no. 31. AAAS, 2026.
ista: Venturino A, Alam A, Negrello T, Jin K, van Velthoven CTJ, Cubero RJ, Yeung
J, Koppensteiner P, Tasic B, Siegert S. 2026. Corticosterone-linked microglial
activity underpins sexually dimorphic neuroplasticity after ketamine anesthesia.
Science Advances. 12(31), eadz6517.
mla: Venturino, Alessandro, et al. “Corticosterone-Linked Microglial Activity Underpins
Sexually Dimorphic Neuroplasticity after Ketamine Anesthesia.” Science Advances,
vol. 12, no. 31, eadz6517, AAAS, 2026, doi:10.1126/sciadv.adz6517.
short: A. Venturino, A. Alam, T. Negrello, K. Jin, C.T.J. van Velthoven, R.J. Cubero,
J. Yeung, P. Koppensteiner, B. Tasic, S. Siegert, Science Advances 12 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: 'All data and code needed to evaluate and reproduce the
results in the paper are present in the paper and/or the Supplementary Materials.
This study did not generate new materials. Transcriptional data can be accessed
at the NCBI GEO accession GSE298669. The code for the morphological analysis is
available under DOI: https://doi.org/10.5281/zenodo.19057068. The codes for the
single-nucleus analysis are accessible under DOI: 10.5281/zenodo.19019013 and DOI:
10.5281/zenodo.19071467.'
date_created: 2026-09-17T11:05:39Z
date_published: 2026-07-01T00:00:00Z
date_updated: 2026-09-22T06:56:26Z
day: '01'
ddc:
- '570'
department:
- _id: SaSi
- _id: ScienComp
- _id: PreCl
doi: 10.1126/sciadv.adz6517
external_id:
pmid:
- '42536755 '
file:
- access_level: open_access
checksum: 715a1f35a0805be85ef90556205a2cbc
content_type: application/pdf
creator: dernst
date_created: 2026-09-22T06:50:16Z
date_updated: 2026-09-22T06:50:16Z
file_id: '22980'
file_name: 2026_ScienceAdv_Venturino.pdf
file_size: 4556377
relation: main_file
success: 1
file_date_updated: 2026-09-22T06:50:16Z
fulldoi: https://doi.org/10.1126/sciadv.adz6517
has_accepted_license: '1'
intvolume: ' 12'
issue: '31'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Corticosterone-linked microglial activity underpins sexually dimorphic neuroplasticity
after ketamine anesthesia
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2026'
...
---
OA_place: repository
OA_type: green
_id: '21920'
abstract:
- lang: eng
text: 'Vertebrates display remarkable diversity of sensorimotor behaviors, each
adapted to distinct ecological and survival demands. This diversity raises fundamental
questions about the evolutionary origin of motor control: do conserved spinal
circuits underlie these behaviors, and how have they diverged across species.
Recent studies detail spinal cell-type architecture in mammals but comparable,
high-resolution atlases of the non-mammalian spinal cord are lacking. Here, we
compare spinal cord cell types between fish, frogs, mice and humans, spanning
∼450 million years of evolution. Across species, we define highly conserved programs
of cell type specification that segregate spinal neurons into nearly identical
cardinal classes during development. This contrasts with adult stages, when spinal
cell-type composition selectively diverges for excitatory neuron subpopulations.
Using spatial transcriptomics, we localize this species divergence to the superficial,
dorsal spinal cord, where variant neuropeptide expression defines mammalian-specific
cell types. The most dorsal spinal cord thus emerges as a recently evolved hub
for sensory integration in mammals, a neospinal cord analogous to the neocortex.'
acknowledgement: "We would like to thank the members of the Sweeney Lab for discussion
and support; Andrey\r\nBydanov for technical assistance with single-cell sequencing
processing; and Jay Bikoff,\r\nNikos Konstantinides, Maria Tosches, and Graziana
Gatto for comments on the manuscript. \r\nThis research was supported by: Horizon
Europe ERC Starting Grant 101041551 (L.B.S,\r\nY.I., S.P.); Special Research Program
(SFB) of the Austrian Science Fund (FWF) F7814-B\r\n(L.B.S., S.P., E.M.T); Austrian
Science Fund (FWF) 10.55776/COE16 (L.B.S., Y.I., E.M.T.);\r\nAustrian Academy of
Sciences DOC Fellowship 27229 (S.P.); ERC Advanced Grant 742046\r\n(E.M.T.); NIH
award R24 OD031956 (L.P.); and in part by the Intramural Research\r\nProgram of
the National Institutes of Health (NIH) through 1ZIA NS003153 to A.J.L.\r\nThe contributions
of the NIH author are considered Works of the United States\r\nGovernment. The findings
and conclusions presented in this paper are those of\r\nthe authors and do not necessarily
reflect the views of the NIH or the U.S. Department\r\nof Health and Human Services. "
article_processing_charge: No
author:
- first_name: Yuri
full_name: Ignatyev, Yuri
last_name: Ignatyev
- first_name: Stavros
full_name: Papadopoulos, Stavros
id: 40606b92-f128-11eb-9611-bf66a98cfa5c
last_name: Papadopoulos
- first_name: Mateja
full_name: Soretić, Mateja
last_name: Soretić
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Tzi-Yang
full_name: Lin, Tzi-Yang
last_name: Lin
- first_name: Elly M
full_name: Tanaka, Elly M
last_name: Tanaka
- first_name: Leonid
full_name: Peshkin, Leonid
last_name: Peshkin
- first_name: Ariel J
full_name: Levine, Ariel J
last_name: Levine
- first_name: Mariano I
full_name: Gabitto, Mariano I
last_name: Gabitto
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
citation:
ama: Ignatyev Y, Papadopoulos S, Soretić M, et al. Innovations in spinal cord cell
type heterogeneity across vertebrate evolution. bioRxiv. doi:10.1101/2025.10.09.680955
apa: Ignatyev, Y., Papadopoulos, S., Soretić, M., Yeung, J., Lin, T.-Y., Tanaka,
E. M., … Sweeney, L. B. (n.d.). Innovations in spinal cord cell type heterogeneity
across vertebrate evolution. bioRxiv. https://doi.org/10.1101/2025.10.09.680955
chicago: Ignatyev, Yuri, Stavros Papadopoulos, Mateja Soretić, Jake Yeung, Tzi-Yang
Lin, Elly M Tanaka, Leonid Peshkin, Ariel J Levine, Mariano I Gabitto, and Lora
B. Sweeney. “Innovations in Spinal Cord Cell Type Heterogeneity across Vertebrate
Evolution.” BioRxiv, n.d. https://doi.org/10.1101/2025.10.09.680955.
ieee: Y. Ignatyev et al., “Innovations in spinal cord cell type heterogeneity
across vertebrate evolution,” bioRxiv. .
ista: Ignatyev Y, Papadopoulos S, Soretić M, Yeung J, Lin T-Y, Tanaka EM, Peshkin
L, Levine AJ, Gabitto MI, Sweeney LB. Innovations in spinal cord cell type heterogeneity
across vertebrate evolution. bioRxiv, 10.1101/2025.10.09.680955.
mla: Ignatyev, Yuri, et al. “Innovations in Spinal Cord Cell Type Heterogeneity
across Vertebrate Evolution.” BioRxiv, doi:10.1101/2025.10.09.680955.
short: Y. Ignatyev, S. Papadopoulos, M. Soretić, J. Yeung, T.-Y. Lin, E.M. Tanaka,
L. Peshkin, A.J. Levine, M.I. Gabitto, L.B. Sweeney, BioRxiv (n.d.).
corr_author: '1'
date_created: 2026-05-27T06:54:04Z
date_published: 2025-10-11T00:00:00Z
date_updated: 2026-05-27T07:25:41Z
day: '11'
department:
- _id: LoSw
- _id: ScienComp
doi: 10.1101/2025.10.09.680955
fulldoi: https://doi.org/10.1101/2025.10.09.680955
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.10.09.680955
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae
grant_number: '101041551'
name: Development and Evolution of Tetrapod Motor Circuits
- _id: 907b765e-16d5-11f0-9cad-fef108a945b1
grant_number: '27229'
name: 'A Tale of Two Circuits: Rostrocaudal spinal cord patterning during the swim-to-limb
transition of Xenopus metamorphosis'
publication: bioRxiv
publication_status: submitted
status: public
title: Innovations in spinal cord cell type heterogeneity across vertebrate evolution
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
_id: '17139'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Waleed
full_name: Khalid, Waleed
id: 097c0562-3cf0-11ee-8fd3-e7a79c1e2fd1
last_name: Khalid
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Khalid W, Elefante S, Stadlbauer S. How much memory per CPU core
is requested? In: ASHPC24 - Austrian-Slovenian HPC Meeting 2024. EuroCC
Austria; 2024:46. doi:10.25365/phaidra.463'
apa: 'Schlögl, A., Khalid, W., Elefante, S., & Stadlbauer, S. (2024). How much
memory per CPU core is requested? In ASHPC24 - Austrian-Slovenian HPC Meeting
2024 (p. 46). Grundlsee, Austria: EuroCC Austria. https://doi.org/10.25365/phaidra.463'
chicago: Schlögl, Alois, Waleed Khalid, Stefano Elefante, and Stephan Stadlbauer.
“How Much Memory per CPU Core Is Requested?” In ASHPC24 - Austrian-Slovenian
HPC Meeting 2024, 46. EuroCC Austria, 2024. https://doi.org/10.25365/phaidra.463.
ieee: A. Schlögl, W. Khalid, S. Elefante, and S. Stadlbauer, “How much memory per
CPU core is requested?,” in ASHPC24 - Austrian-Slovenian HPC Meeting 2024,
Grundlsee, Austria, 2024, p. 46.
ista: 'Schlögl A, Khalid W, Elefante S, Stadlbauer S. 2024. How much memory per
CPU core is requested? ASHPC24 - Austrian-Slovenian HPC Meeting 2024. ASHPC: Austrian-Slovenian
HPC Meeting, 46.'
mla: Schlögl, Alois, et al. “How Much Memory per CPU Core Is Requested?” ASHPC24
- Austrian-Slovenian HPC Meeting 2024, EuroCC Austria, 2024, p. 46, doi:10.25365/phaidra.463.
short: A. Schlögl, W. Khalid, S. Elefante, S. Stadlbauer, in:, ASHPC24 - Austrian-Slovenian
HPC Meeting 2024, EuroCC Austria, 2024, p. 46.
conference:
end_date: 2024-06-13
location: Grundlsee, Austria
name: 'ASHPC: Austrian-Slovenian HPC Meeting'
start_date: 2024-06-10
date_created: 2024-06-14T09:06:36Z
date_published: 2024-06-13T00:00:00Z
date_updated: 2024-06-17T09:40:37Z
day: '13'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.25365/phaidra.463
file:
- access_level: open_access
checksum: f7d3dded6df2dcdb4818904cf2e1c183
content_type: application/pdf
creator: dernst
date_created: 2024-06-17T09:36:51Z
date_updated: 2024-06-17T09:36:51Z
file_id: '17153'
file_name: 2024_ASHPC_Schloegl.pdf
file_size: 206746
relation: main_file
success: 1
file_date_updated: 2024-06-17T09:36:51Z
fulldoi: https://doi.org/10.25365/phaidra.463
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '46'
publication: ASHPC24 - Austrian-Slovenian HPC Meeting 2024
publication_identifier:
isbn:
- '9783200096455'
publication_status: published
publisher: EuroCC Austria
quality_controlled: '1'
status: public
title: How much memory per CPU core is requested?
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: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
APC_amount: 11700 EUR
OA_place: publisher
OA_type: hybrid
_id: '14979'
abstract:
- lang: eng
text: Poxviruses are among the largest double-stranded DNA viruses, with members
such as variola virus, monkeypox virus and the vaccination strain vaccinia virus
(VACV). Knowledge about the structural proteins that form the viral core has remained
sparse. While major core proteins have been annotated via indirect experimental
evidence, their structures have remained elusive and they could not be assigned
to individual core features. Hence, which proteins constitute which layers of
the core, such as the palisade layer and the inner core wall, has remained enigmatic.
Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach
in combination with AlphaFold molecular modeling, that trimers formed by the cleavage
product of VACV protein A10 are the key component of the palisade layer. This
allows us to place previously obtained descriptions of protein interactions within
the core wall into perspective and to provide a detailed model of poxvirus core
architecture. Importantly, we show that interactions within A10 trimers are likely
generalizable over members of orthopox- and parapoxviruses.
acknowledged_ssus:
- _id: ScienComp
- _id: LifeSc
- _id: EM-Fac
acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of
the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and
his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific
Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel
and other members of the Schur group for support and helpful discussions. We also
thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help
optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map
with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S.
also received support from the Austrian Science Fund (FWF) grant P31445. This publication
has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg
from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community
Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis
research was also supported by the Scientific Service Units (SSUs) of ISTA through
resources provided by Scientific Computing (SciComp), the Life Science Facility
(LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of
COSMIC45 and Colabfold46."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Julia
full_name: Datler, Julia
id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87
last_name: Datler
orcid: 0000-0002-3616-8580
- first_name: Jesse
full_name: Hansen, Jesse
id: 1063c618-6f9b-11ec-9123-f912fccded63
last_name: Hansen
orcid: 0000-0001-7967-2085
- first_name: Andreas
full_name: Thader, Andreas
id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87
last_name: Thader
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Lukas W
full_name: Bauer, Lukas W
id: 0c894dcf-897b-11ed-a09c-8186353224b0
last_name: Bauer
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
- 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: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of
protein A10 to form the palisade layer in poxvirus cores. Nature Structural
& Molecular Biology. 2024;31:1114-1123. doi:10.1038/s41594-023-01201-6
apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V.,
& Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores. Nature Structural & Molecular
Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6
chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer,
Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers
of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural
& Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.
ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10
to form the palisade layer in poxvirus cores,” Nature Structural & Molecular
Biology, vol. 31. Springer Nature, pp. 1114–1123, 2024.
ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK.
2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade
layer in poxvirus cores. Nature Structural & Molecular Biology. 31, 1114–1123.
mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to
Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular
Biology, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:10.1038/s41594-023-01201-6.
short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau,
F.K. Schur, Nature Structural & Molecular Biology 31 (2024) 1114–1123.
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: "The electron microscopy density maps of the A10 trimer
and the hexameric flower-shaped pore, the subtomogram average of the palisade layer
and representative tomograms for complete viruses as well as isolated cores have
been deposited in the Electron Microscopy Data Bank under accession codes: EMD-17410,
EMD-17411, EMD-17412, EMD-17413, EMD-17414 and EMD-18452.\r\n\r\nThe refined model
of the A10 trimer has been deposited in the Protein Data Bank accession code: PDB
8P4K.\r\n\r\nThe UniProt codes of VACV core proteins used for structure prediction
are: A10 (P16715), A3 (P06440), A4 (P29191) and L4 (P03295).\r\n\r\nGenBank Protein
IDs of variola virus A10 (ABF23487.1), monkeypox virus A10 (YP_010377118.1), rabbitpox
virus A10 (AAS49831.1), cowpox virus A10 (ADZ29251.1), ectromelia virus A10 (NP_671631.1),
orf virus P4a (AY386264.1), Amsacta moorei entomopoxvirus AMV139 (NP_064921.1) and
Melanoplus sanguinipes entomopoxvirus putative core protein P4a homolog (AF063866.1)
were used for protein sequence alignment. Source data for MS experiments are provided
as Supplementary Information accompanying this manuscript."
date_created: 2024-02-12T09:59:45Z
date_published: 2024-07-01T00:00:00Z
date_updated: 2026-10-02T11:21:19Z
day: '01'
ddc:
- '570'
department:
- _id: FlSc
- _id: ScienComp
- _id: EM-Fac
doi: 10.1038/s41594-023-01201-6
external_id:
isi:
- '001158144600002'
pmid:
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creator: dernst
date_created: 2024-07-22T11:27:22Z
date_updated: 2024-07-22T11:27:22Z
file_id: '17307'
file_name: 2024_NatureStrucBio_Datler.pdf
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success: 1
file_date_updated: 2024-07-22T11:27:22Z
fulldoi: https://doi.org/10.1038/s41594-023-01201-6
has_accepted_license: '1'
intvolume: ' 31'
isi: 1
keyword:
- Molecular Biology
- Structural Biology
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1114-1123
pmid: 1
project:
- _id: 26736D6A-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31445
name: Structural conservation and diversity in retroviral capsid
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on ISTA Website
relation: press_release
url: https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/
record:
- id: '18766'
relation: dissertation_contains
status: public
researchdata_availability: yes
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer
in poxvirus cores
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 31
year: '2024'
...
---
_id: '12106'
abstract:
- lang: eng
text: Regulation of chromatin states involves the dynamic interplay between different
histone modifications to control gene expression. Recent advances have enabled
mapping of histone marks in single cells, but most methods are constrained to
profile only one histone mark per cell. Here, we present an integrated experimental
and computational framework, scChIX-seq (single-cell chromatin immunocleavage
and unmixing sequencing), to map several histone marks in single cells. scChIX-seq
multiplexes two histone marks together in single cells, then computationally deconvolves
the signal using training data from respective histone mark profiles. This framework
learns the cell-type-specific correlation structure between histone marks, and
therefore does not require a priori assumptions of their genomic distributions.
Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single
cells across a range of mark combinations. Modeling dynamics of in vitro macrophage
differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq
unlocks systematic interrogation of the interplay between histone modifications
in single cells.
acknowledgement: We thank M. van Loenhout for experimental advice on purifying cell
types from the bone marrow, R. van der Linden for expertise with FACS and M. Blotenburg
for help with cell typing the mouse organogenesis dataset. We thank M. Saraswat
and O. Stegle for discussions on multinomial distributions. This work was supported
by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics); Nederlandse
Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP grant (NWO CW 714.016.001)
and NWO grant (OCENW.GROOT.2019.017); the Swiss National Science Foundation Early
Postdoc Mobility (P2ELP3-184488 to P.Z. and P2BSP3-174991 to J.Y.); Marie Sklodowska-Curie
Actions Postdoc (798573 to P.Z.) and the Human Frontier for Science Program Long-Term
Fellowships (LT000209-2018-L to P.Z. and LT000097-2019-L to J.Y.). This work is
part of the Oncode Institute which is financed partly by the Dutch Cancer Society.
article_processing_charge: No
article_type: original
author:
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Buys Anton
full_name: De Barbanson, Buys Anton
last_name: De Barbanson
- first_name: Max D.
full_name: Wellenstein, Max D.
last_name: Wellenstein
- first_name: Alexander
full_name: Van Oudenaarden, Alexander
last_name: Van Oudenaarden
citation:
ama: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. scChIX-seq infers dynamic relationships between histone modifications in single
cells. Nature Biotechnology. 2023;41:813–823. doi:10.1038/s41587-022-01560-3
apa: Yeung, J., Florescu, M., Zeller, P., De Barbanson, B. A., Wellenstein, M. D.,
& Van Oudenaarden, A. (2023). scChIX-seq infers dynamic relationships between
histone modifications in single cells. Nature Biotechnology. Springer Nature.
https://doi.org/10.1038/s41587-022-01560-3
chicago: Yeung, Jake, Maria Florescu, Peter Zeller, Buys Anton De Barbanson, Max
D. Wellenstein, and Alexander Van Oudenaarden. “ScChIX-Seq Infers Dynamic Relationships
between Histone Modifications in Single Cells.” Nature Biotechnology. Springer
Nature, 2023. https://doi.org/10.1038/s41587-022-01560-3.
ieee: J. Yeung, M. Florescu, P. Zeller, B. A. De Barbanson, M. D. Wellenstein, and
A. Van Oudenaarden, “scChIX-seq infers dynamic relationships between histone modifications
in single cells,” Nature Biotechnology, vol. 41. Springer Nature, pp. 813–823,
2023.
ista: Yeung J, Florescu M, Zeller P, De Barbanson BA, Wellenstein MD, Van Oudenaarden
A. 2023. scChIX-seq infers dynamic relationships between histone modifications
in single cells. Nature Biotechnology. 41, 813–823.
mla: Yeung, Jake, et al. “ScChIX-Seq Infers Dynamic Relationships between Histone
Modifications in Single Cells.” Nature Biotechnology, vol. 41, Springer
Nature, 2023, pp. 813–823, doi:10.1038/s41587-022-01560-3.
short: J. Yeung, M. Florescu, P. Zeller, B.A. De Barbanson, M.D. Wellenstein, A.
Van Oudenaarden, Nature Biotechnology 41 (2023) 813–823.
corr_author: '1'
date_created: 2023-01-08T23:00:53Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2025-04-23T08:45:24Z
day: '01'
ddc:
- '570'
department:
- _id: ScienComp
doi: 10.1038/s41587-022-01560-3
external_id:
isi:
- '000909067600003'
pmid:
- '36593403'
file:
- access_level: open_access
checksum: 668447a1c8d360b68f8aaf9e08ed644f
content_type: application/pdf
creator: dernst
date_created: 2023-08-16T11:30:45Z
date_updated: 2023-08-16T11:30:45Z
file_id: '14066'
file_name: 2023_NatureBioTech_Yeung.pdf
file_size: 12040976
relation: main_file
success: 1
file_date_updated: 2023-08-16T11:30:45Z
fulldoi: https://doi.org/10.1038/s41587-022-01560-3
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 813–823
pmid: 1
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: scChIX-seq infers dynamic relationships between histone modifications in single
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 41
year: '2023'
...
---
_id: '12158'
abstract:
- lang: eng
text: 'Post-translational histone modifications modulate chromatin activity to affect
gene expression. How chromatin states underlie lineage choice in single cells
is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage
(sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3)
histone modifications in the mouse bone marrow. During differentiation, hematopoietic
stem and progenitor cells (HSPCs) acquire active chromatin states mediated by
cell-type-specifying transcription factors, which are unique for each lineage.
By contrast, most alterations in repressive marks during differentiation occur
independent of the final cell type. Chromatin trajectory analysis shows that lineage
choice at the chromatin level occurs at the progenitor stage. Joint profiling
of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage
have distinct active chromatin but share similar myeloid-specific heterochromatin
states. This implies a hierarchical regulation of chromatin during hematopoiesis:
heterochromatin dynamics distinguish differentiation trajectories and lineages,
while euchromatin dynamics reflect cell types within lineages.'
acknowledgement: We thank A. Giladi for sharing mRNA abundance tables of cell types
together with J. van den Berg for critical reading of the manuscript. We thank M.
Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich
Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973).
Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström
under CC-BY-SA 3.0 license. This work was supported by European Research Council
Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor
Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991),
HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z.
The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF
(ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which
is partly financed by the Dutch Cancer Society. The funders had no role in study
design, data collection and analysis, decision to publish or preparation of the
manuscript.
article_processing_charge: No
article_type: review
author:
- first_name: Peter
full_name: Zeller, Peter
last_name: Zeller
- first_name: Jake
full_name: Yeung, Jake
id: 123012b2-db30-11eb-b4d8-a35840c0551b
last_name: Yeung
orcid: 0000-0003-1732-1559
- first_name: Helena
full_name: Viñas Gaza, Helena
last_name: Viñas Gaza
- first_name: Buys Anton
full_name: de Barbanson, Buys Anton
last_name: de Barbanson
- first_name: Vivek
full_name: Bhardwaj, Vivek
last_name: Bhardwaj
- first_name: Maria
full_name: Florescu, Maria
last_name: Florescu
- first_name: Reinier
full_name: van der Linden, Reinier
last_name: van der Linden
- first_name: Alexander
full_name: van Oudenaarden, Alexander
last_name: van Oudenaarden
citation:
ama: Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345.
doi:10.1038/s41588-022-01260-3
apa: Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu,
M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature.
https://doi.org/10.1038/s41588-022-01260-3
chicago: Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson,
Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden.
“Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.”
Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.
ieee: P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin
dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature,
pp. 333–345, 2023.
ista: Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M,
van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical
chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345.
mla: Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin
Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature,
2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.
short: P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu,
R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.
date_created: 2023-01-12T12:09:09Z
date_published: 2023-02-01T00:00:00Z
date_updated: 2025-04-23T08:45:00Z
day: '01'
ddc:
- '570'
- '000'
department:
- _id: ScienComp
doi: 10.1038/s41588-022-01260-3
external_id:
pmid:
- '36539617'
file:
- access_level: open_access
checksum: 6fdb8e34fbeea63edd0f2c6c2cc5823e
content_type: application/pdf
creator: dernst
date_created: 2023-02-27T07:46:45Z
date_updated: 2023-02-27T07:46:45Z
file_id: '12688'
file_name: 2023_NatureGenetics_Zeller.pdf
file_size: 21484855
relation: main_file
success: 1
file_date_updated: 2023-02-27T07:46:45Z
fulldoi: https://doi.org/10.1038/s41588-022-01260-3
has_accepted_license: '1'
intvolume: ' 55'
keyword:
- Genetics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 333-345
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: Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2023'
...
---
_id: '14449'
abstract:
- lang: eng
text: The rapid development of machine learning (ML) techniques has opened up the
data-dense field of microbiome research for novel therapeutic, diagnostic, and
prognostic applications targeting a wide range of disorders, which could substantially
improve healthcare practices in the era of precision medicine. However, several
challenges must be addressed to exploit the benefits of ML in this field fully.
In particular, there is a need to establish “gold standard” protocols for conducting
ML analysis experiments and improve interactions between microbiome researchers
and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome)
COST Action CA18131 is a European network established in 2019 to promote collaboration
between discovery-oriented microbiome researchers and data-driven ML experts to
optimize and standardize ML approaches for microbiome analysis. This perspective
paper presents the key achievements of ML4Microbiome, which include identifying
predictive and discriminatory ‘omics’ features, improving repeatability and comparability,
developing automation procedures, and defining priority areas for the novel development
of ML methods targeting the microbiome. The insights gained from ML4Microbiome
will help to maximize the potential of ML in microbiome research and pave the
way for new and improved healthcare practices.
acknowledgement: "This study is based upon work from COST Action ML4Microbiome “Statistical
and machine learning techniques in human microbiome studies” (CA18131), supported
by COST (European Cooperation in Science and Technology), www.cost.eu. MB acknowledges
support through the Metagenopolis grant ANR-11-DPBS-0001. IM-I acknowledges support
by the “Miguel Servet Type II” program (CPII21/00013) of the ISCIII-Madrid (Spain),
co-financed by the FEDER.\r\nThe authors are grateful to all COST Action CA18131
“Statistical and machine learning techniques in human microbiome studies” members
for their contribution to the COST Action objectives, and to COST (European Cooperation
in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank
Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis,
78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset."
article_number: '1257002'
article_processing_charge: Yes
article_type: original
author:
- first_name: Domenica
full_name: D’Elia, Domenica
last_name: D’Elia
- first_name: Jaak
full_name: Truu, Jaak
last_name: Truu
- first_name: Leo
full_name: Lahti, Leo
last_name: Lahti
- first_name: Magali
full_name: Berland, Magali
last_name: Berland
- first_name: Georgios
full_name: Papoutsoglou, Georgios
last_name: Papoutsoglou
- first_name: Michelangelo
full_name: Ceci, Michelangelo
last_name: Ceci
- first_name: Aldert
full_name: Zomer, Aldert
last_name: Zomer
- first_name: Marta B.
full_name: Lopes, Marta B.
last_name: Lopes
- first_name: Eliana
full_name: Ibrahimi, Eliana
last_name: Ibrahimi
- first_name: Aleksandra
full_name: Gruca, Aleksandra
last_name: Gruca
- first_name: Alina
full_name: Nechyporenko, Alina
last_name: Nechyporenko
- first_name: Marcus
full_name: Frohme, Marcus
last_name: Frohme
- first_name: Thomas
full_name: Klammsteiner, Thomas
last_name: Klammsteiner
- first_name: Enrique Carrillo De Santa
full_name: Pau, Enrique Carrillo De Santa
last_name: Pau
- first_name: Laura Judith
full_name: Marcos-Zambrano, Laura Judith
last_name: Marcos-Zambrano
- first_name: Karel
full_name: Hron, Karel
last_name: Hron
- first_name: Gianvito
full_name: Pio, Gianvito
last_name: Pio
- first_name: Andrea
full_name: Simeon, Andrea
last_name: Simeon
- first_name: Ramona
full_name: Suharoschi, Ramona
last_name: Suharoschi
- first_name: Isabel
full_name: Moreno-Indias, Isabel
last_name: Moreno-Indias
- first_name: Andriy
full_name: Temko, Andriy
last_name: Temko
- first_name: Miroslava
full_name: Nedyalkova, Miroslava
last_name: Nedyalkova
- first_name: Elena Simona
full_name: Apostol, Elena Simona
last_name: Apostol
- first_name: Ciprian Octavian
full_name: Truică, Ciprian Octavian
last_name: Truică
- first_name: Rajesh
full_name: Shigdel, Rajesh
last_name: Shigdel
- first_name: Jasminka Hasić
full_name: Telalović, Jasminka Hasić
last_name: Telalović
- first_name: Erik
full_name: Bongcam-Rudloff, Erik
last_name: Bongcam-Rudloff
- first_name: Piotr
full_name: Przymus, Piotr
last_name: Przymus
- first_name: Naida Babić
full_name: Jordamović, Naida Babić
last_name: Jordamović
- first_name: Laurent
full_name: Falquet, Laurent
last_name: Falquet
- first_name: Sonia
full_name: Tarazona, Sonia
last_name: Tarazona
- first_name: Alexia
full_name: Sampri, Alexia
last_name: Sampri
- first_name: Gaetano
full_name: Isola, Gaetano
last_name: Isola
- first_name: David
full_name: Pérez-Serrano, David
last_name: Pérez-Serrano
- first_name: Vladimir
full_name: Trajkovik, Vladimir
last_name: Trajkovik
- first_name: Lubos
full_name: Klucar, Lubos
last_name: Klucar
- first_name: Tatjana
full_name: Loncar-Turukalo, Tatjana
last_name: Loncar-Turukalo
- first_name: Aki S.
full_name: Havulinna, Aki S.
last_name: Havulinna
- first_name: Christian
full_name: Jansen, Christian
id: 837b2259-bcc9-11ed-a196-ae55927bc6e2
last_name: Jansen
- first_name: Randi J.
full_name: Bertelsen, Randi J.
last_name: Bertelsen
- first_name: Marcus Joakim
full_name: Claesson, Marcus Joakim
last_name: Claesson
citation:
ama: 'D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine
learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology.
2023;14. doi:10.3389/fmicb.2023.1257002'
apa: 'D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M.,
… Claesson, M. J. (2023). Advancing microbiome research with machine learning:
Key findings from the ML4Microbiome COST action. Frontiers in Microbiology.
Frontiers. https://doi.org/10.3389/fmicb.2023.1257002'
chicago: 'D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou,
Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine
Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology.
Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1257002.'
ieee: 'D. D’Elia et al., “Advancing microbiome research with machine learning:
Key findings from the ML4Microbiome COST action,” Frontiers in Microbiology,
vol. 14. Frontiers, 2023.'
ista: 'D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes
MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano
LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova
M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus
P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik
V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson
MJ. 2023. Advancing microbiome research with machine learning: Key findings from
the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.'
mla: 'D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning:
Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology,
vol. 14, 1257002, Frontiers, 2023, doi:10.3389/fmicb.2023.1257002.'
short: D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer,
M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner,
E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi,
I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel,
J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S.
Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo,
A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology
14 (2023).
date_created: 2023-10-22T22:01:16Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2023-12-13T13:07:21Z
day: '25'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.3389/fmicb.2023.1257002
external_id:
isi:
- '001080536000001'
pmid:
- '37808321'
file:
- access_level: open_access
checksum: 6c0acdd8fa111a699826957b8dff19d5
content_type: application/pdf
creator: dernst
date_created: 2023-10-30T13:38:48Z
date_updated: 2023-10-30T13:38:48Z
file_id: '14471'
file_name: 2023_FrontiersMicrobiology_DElia.pdf
file_size: 505078
relation: main_file
success: 1
file_date_updated: 2023-10-30T13:38:48Z
fulldoi: https://doi.org/10.3389/fmicb.2023.1257002
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Microbiology
publication_identifier:
eissn:
- 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Advancing microbiome research with machine learning: Key findings from the
ML4Microbiome COST action'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13162'
article_processing_charge: No
author:
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
- first_name: Michael F
full_name: Alexander, Michael F
id: 3A02A8FA-F248-11E8-B48F-1D18A9856A87
last_name: Alexander
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
citation:
ama: 'Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages:
A sys-admins point of view. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023.
EuroCC Austria; 2023:42-42.'
apa: 'Elefante, S., Stadlbauer, S., Alexander, M. F., & Schlögl, A. (2023).
Cryo-EM software packages: A sys-admins point of view. In ASHPC23 - Austrian-Slovenian
HPC Meeting 2023 (pp. 42–42). Maribor, Slovenia: EuroCC Austria.'
chicago: 'Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois
Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In ASHPC23
- Austrian-Slovenian HPC Meeting 2023, 42–42. EuroCC Austria, 2023.'
ieee: 'S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software
packages: A sys-admins point of view,” in ASHPC23 - Austrian-Slovenian HPC
Meeting 2023, Maribor, Slovenia, 2023, pp. 42–42.'
ista: 'Elefante S, Stadlbauer S, Alexander MF, Schlögl A. 2023. Cryo-EM software
packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting
2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.'
mla: 'Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of
View.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023,
pp. 42–42.'
short: S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian
HPC Meeting 2023, EuroCC Austria, 2023, pp. 42–42.
conference:
end_date: 2023-06-15
location: Maribor, Slovenia
name: 'ASHPC: Austrian-Slovenian HPC Meeting'
start_date: 2023-06-12
corr_author: '1'
date_created: 2023-06-23T11:03:18Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2026-07-06T13:01:58Z
day: '01'
ddc:
- '000'
department:
- _id: ScienComp
file:
- access_level: open_access
checksum: 0ab6173cd5c5634ed773cd37ff012681
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T09:28:30Z
date_updated: 2023-07-18T09:28:30Z
file_id: '13250'
file_name: 2023_ASHPC_Elefante.pdf
file_size: 380354
relation: main_file
success: 1
file_date_updated: 2023-07-18T09:28:30Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 42-42
publication: ASHPC23 - Austrian-Slovenian HPC Meeting 2023
publication_status: published
publisher: EuroCC Austria
quality_controlled: '1'
status: public
title: 'Cryo-EM software packages: A sys-admins point of view'
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: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13161'
acknowledgement: Thanks to Jesse Hansen for his suggestions on improving the abstract.
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
- first_name: Victor-Valentin
full_name: Hodirnau, Victor-Valentin
id: 3661B498-F248-11E8-B48F-1D18A9856A87
last_name: Hodirnau
orcid: 0000-0003-3904-947X
citation:
ama: 'Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux
HPC cluster using WINE. In: ASHPC23 - Austrian-Slovenian HPC Meeting 2023.
EuroCC Austria; 2023:59-59.'
apa: 'Schlögl, A., Elefante, S., & Hodirnau, V.-V. (2023). Running Windows-applications
on a Linux HPC cluster using WINE. In ASHPC23 - Austrian-Slovenian HPC Meeting
2023 (pp. 59–59). Maribor, Slovenia: EuroCC Austria.'
chicago: Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running
Windows-Applications on a Linux HPC Cluster Using WINE.” In ASHPC23 - Austrian-Slovenian
HPC Meeting 2023, 59–59. EuroCC Austria, 2023.
ieee: A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications
on a Linux HPC cluster using WINE,” in ASHPC23 - Austrian-Slovenian HPC Meeting
2023, Maribor, Slovenia, 2023, pp. 59–59.
ista: 'Schlögl A, Elefante S, Hodirnau V-V. 2023. Running Windows-applications on
a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023.
ASHPC: Austrian-Slovenian HPC Meeting, 59–59.'
mla: Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster
Using WINE.” ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria,
2023, pp. 59–59.
short: A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian
HPC Meeting 2023, EuroCC Austria, 2023, pp. 59–59.
conference:
end_date: 2023-06-15
location: Maribor, Slovenia
name: 'ASHPC: Austrian-Slovenian HPC Meeting'
start_date: 2023-06-13
corr_author: '1'
date_created: 2023-06-23T11:01:23Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2026-07-06T13:01:46Z
day: '01'
ddc:
- '000'
department:
- _id: ScienComp
- _id: EM-Fac
file:
- access_level: open_access
checksum: ec8e4295d54171032cdd1b01423eb4a6
content_type: application/pdf
creator: dernst
date_created: 2023-07-18T09:18:55Z
date_updated: 2023-07-18T09:18:55Z
file_id: '13249'
file_name: 2023_ASHPC_Schloegl.pdf
file_size: 316959
relation: main_file
success: 1
file_date_updated: 2023-07-18T09:18:55Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 59-59
publication: ASHPC23 - Austrian-Slovenian HPC Meeting 2023
publication_status: published
publisher: EuroCC Austria
quality_controlled: '1'
status: public
title: Running Windows-applications on a Linux HPC cluster using WINE
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: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12894'
acknowledgement: "The abstracts in this booklet are licenced under a CC BY 4.0 licence
(https://creativecommons.org/licenses/by/4.0/legalcode), except Markus Wallerberger’s
contribution at page 21, licenced under a CC BY-SA 4.0 licence (https://creativecommons.org/licenses/by-sa/4.0/legalcode).\r\n"
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Andrei
full_name: Hornoiu, Andrei
id: 77129392-B450-11EA-8745-D4653DDC885E
last_name: Hornoiu
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. Where is the sweet spot? A
procurement story of general purpose compute nodes. In: ASHPC22 - Austrian-Slovenian
HPC Meeting 2022. EuroCC Austria; 2022:7. doi:10.25365/phaidra.337'
apa: 'Schlögl, A., Hornoiu, A., Elefante, S., & Stadlbauer, S. (2022). Where
is the sweet spot? A procurement story of general purpose compute nodes. In ASHPC22
- Austrian-Slovenian HPC Meeting 2022 (p. 7). Grundlsee, Austria: EuroCC Austria.
https://doi.org/10.25365/phaidra.337'
chicago: Schlögl, Alois, Andrei Hornoiu, Stefano Elefante, and Stephan Stadlbauer.
“Where Is the Sweet Spot? A Procurement Story of General Purpose Compute Nodes.”
In ASHPC22 - Austrian-Slovenian HPC Meeting 2022, 7. EuroCC Austria, 2022.
https://doi.org/10.25365/phaidra.337.
ieee: A. Schlögl, A. Hornoiu, S. Elefante, and S. Stadlbauer, “Where is the sweet
spot? A procurement story of general purpose compute nodes,” in ASHPC22 - Austrian-Slovenian
HPC Meeting 2022, Grundlsee, Austria, 2022, p. 7.
ista: 'Schlögl A, Hornoiu A, Elefante S, Stadlbauer S. 2022. Where is the sweet
spot? A procurement story of general purpose compute nodes. ASHPC22 - Austrian-Slovenian
HPC Meeting 2022. ASHPC: Austrian-Slovenian HPC Meeting, 7.'
mla: Schlögl, Alois, et al. “Where Is the Sweet Spot? A Procurement Story of General
Purpose Compute Nodes.” ASHPC22 - Austrian-Slovenian HPC Meeting 2022,
EuroCC Austria, 2022, p. 7, doi:10.25365/phaidra.337.
short: A. Schlögl, A. Hornoiu, S. Elefante, S. Stadlbauer, in:, ASHPC22 - Austrian-Slovenian
HPC Meeting 2022, EuroCC Austria, 2022, p. 7.
conference:
end_date: 2022-06-02
location: Grundlsee, Austria
name: 'ASHPC: Austrian-Slovenian HPC Meeting'
start_date: 2022-05-31
corr_author: '1'
date_created: 2023-05-05T09:13:42Z
date_published: 2022-06-02T00:00:00Z
date_updated: 2026-07-06T13:02:13Z
day: '02'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.25365/phaidra.337
file:
- access_level: open_access
checksum: e3f8c240b85422ce2190e7b203cc2563
content_type: application/pdf
creator: schloegl
date_created: 2023-05-05T09:06:00Z
date_updated: 2023-05-05T09:06:00Z
file_id: '12895'
file_name: BOOKLET_ASHPC22.pdf
file_size: 7180531
relation: main_file
success: 1
file_date_updated: 2023-05-05T09:06:00Z
fulldoi: https://doi.org/10.25365/phaidra.337
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '7'
publication: ASHPC22 - Austrian-Slovenian HPC Meeting 2022
publication_identifier:
isbn:
- 978-3-200-08499-5
publication_status: published
publisher: EuroCC Austria
status: public
title: Where is the sweet spot? A procurement story of general purpose compute nodes
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: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2022'
...
---
_id: '15285'
abstract:
- lang: eng
text: Ever since the first publication of the standard communication protocol for
computer-assisted electrocardiography (SCP-ECG), prENV 1064, in 1993, by the European
Committee for Standardization (CEN), SCP-ECG has become a leading example in health
informatics, enabling open, secure, and well-documented digital data exchange
at a low cost, for quick and efficient cardiovascular disease detection and management.
Based on the experiences gained, since the 1970s, in computerized electrocardiology,
and on the results achieved by the pioneering, international cooperative research
on common standards for quantitative electrocardiography (CSE), SCP-ECG was designed,
from the beginning, to empower personalized medicine, thanks to serial ECG analysis.
The fundamental concept behind SCP-ECG is to convey the necessary information
for ECG re-analysis, serial comparison, and interpretation, and to structure the
ECG data and metadata in sections that are mostly optional in order to fit all
use cases. SCP-ECG is open to the storage of the ECG signal and ECG measurement
data, whatever the ECG recording modality or computation method, and can store
the over-reading trails and ECG annotations, as well as any computerized or medical
interpretation reports. Only the encoding syntax and the semantics of the ECG
descriptors and of the diagnosis codes are standardized. We present all of the
landmarks in the development and publication of SCP-ECG, from the early 1990s
to the 2009 International Organization for Standardization (ISO) SCP-ECG standards,
including the latest version published by CEN in 2020, which now encompasses rest
and stress ECGs, Holter recordings, and protocol-based trials.
acknowledgement: This research received no external funding. The authors thank the
large number of researchers, engineers, cardiologists, and clinicians from academia,
industry, and normalization organizations who contributed to the development and
testing of the SCP-ECG standards.
article_processing_charge: Yes
article_type: review
author:
- first_name: Paul
full_name: Rubel, Paul
last_name: Rubel
- first_name: Jocelyne
full_name: Fayn, Jocelyne
last_name: Fayn
- first_name: Peter W.
full_name: Macfarlane, Peter W.
last_name: Macfarlane
- first_name: Danilo
full_name: Pani, Danilo
last_name: Pani
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Alpo
full_name: Värri, Alpo
last_name: Värri
citation:
ama: 'Rubel P, Fayn J, Macfarlane PW, Pani D, Schlögl A, Värri A. The history and
challenges of SCP-ECG: The standard communication protocol for computer-assisted
electrocardiography. Hearts. 2021;2(3):384-409. doi:10.3390/hearts2030031'
apa: 'Rubel, P., Fayn, J., Macfarlane, P. W., Pani, D., Schlögl, A., & Värri,
A. (2021). The history and challenges of SCP-ECG: The standard communication protocol
for computer-assisted electrocardiography. Hearts. MDPI. https://doi.org/10.3390/hearts2030031'
chicago: 'Rubel, Paul, Jocelyne Fayn, Peter W. Macfarlane, Danilo Pani, Alois Schlögl,
and Alpo Värri. “The History and Challenges of SCP-ECG: The Standard Communication
Protocol for Computer-Assisted Electrocardiography.” Hearts. MDPI, 2021.
https://doi.org/10.3390/hearts2030031.'
ieee: 'P. Rubel, J. Fayn, P. W. Macfarlane, D. Pani, A. Schlögl, and A. Värri, “The
history and challenges of SCP-ECG: The standard communication protocol for computer-assisted
electrocardiography,” Hearts, vol. 2, no. 3. MDPI, pp. 384–409, 2021.'
ista: 'Rubel P, Fayn J, Macfarlane PW, Pani D, Schlögl A, Värri A. 2021. The history
and challenges of SCP-ECG: The standard communication protocol for computer-assisted
electrocardiography. Hearts. 2(3), 384–409.'
mla: 'Rubel, Paul, et al. “The History and Challenges of SCP-ECG: The Standard Communication
Protocol for Computer-Assisted Electrocardiography.” Hearts, vol. 2, no.
3, MDPI, 2021, pp. 384–409, doi:10.3390/hearts2030031.'
short: P. Rubel, J. Fayn, P.W. Macfarlane, D. Pani, A. Schlögl, A. Värri, Hearts
2 (2021) 384–409.
date_created: 2024-04-03T09:03:31Z
date_published: 2021-08-24T00:00:00Z
date_updated: 2024-04-09T06:51:50Z
day: '24'
ddc:
- '610'
department:
- _id: ScienComp
doi: 10.3390/hearts2030031
file:
- access_level: open_access
checksum: f67142b1e1e8ca5cd7a6a6798f46375e
content_type: application/pdf
creator: dernst
date_created: 2024-04-09T06:49:47Z
date_updated: 2024-04-09T06:49:47Z
file_id: '15302'
file_name: 2021_Hearts_Rubel.pdf
file_size: 3539897
relation: main_file
success: 1
file_date_updated: 2024-04-09T06:49:47Z
fulldoi: https://doi.org/10.3390/hearts2030031
has_accepted_license: '1'
intvolume: ' 2'
issue: '3'
keyword:
- General Medicine
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 384-409
publication: Hearts
publication_identifier:
issn:
- 2673-3846
publication_status: published
publisher: MDPI
quality_controlled: '1'
status: public
title: 'The history and challenges of SCP-ECG: The standard communication protocol
for computer-assisted electrocardiography'
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2021'
...
---
_id: '9329'
abstract:
- lang: eng
text: "Background: To understand information coding in single neurons, it is necessary
to analyze subthreshold synaptic events, action potentials (APs), and their interrelation
in different behavioral states. However, detecting excitatory postsynaptic potentials
(EPSPs) or currents (EPSCs) in behaving animals remains challenging, because of
unfavorable signal-to-noise ratio, high frequency, fluctuating amplitude, and
variable time course of synaptic events.\r\nNew method: We developed a method
for synaptic event detection, termed MOD (Machine-learning Optimal-filtering Detection-procedure),
which combines concepts of supervised machine learning and optimal Wiener filtering.
Experts were asked to manually score short epochs of data. The algorithm was trained
to obtain the optimal filter coefficients of a Wiener filter and the optimal detection
threshold. Scored and unscored data were then processed with the optimal filter,
and events were detected as peaks above threshold.\r\nResults: We challenged MOD
with EPSP traces in vivo in mice during spatial navigation and EPSC traces in
vitro in slices under conditions of enhanced transmitter release. The area under
the curve (AUC) of the receiver operating characteristics (ROC) curve was, on
average, 0.894 for in vivo and 0.969 for in vitro data sets, indicating high detection
accuracy and efficiency.\r\nComparison with existing methods: When benchmarked
using a (1 − AUC)−1 metric, MOD outperformed previous methods (template-fit, deconvolution,
and Bayesian methods) by an average factor of 3.13 for in vivo data sets, but
showed comparable (template-fit, deconvolution) or higher (Bayesian) computational
efficacy.\r\nConclusions: MOD may become an important new tool for large-scale,
real-time analysis of synaptic activity."
acknowledged_ssus:
- _id: SSU
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement number 692692 to P.J.) and the Fond zur Förderung der Wissenschaftlichen
Forschung (Z 312-B27, Wittgenstein award to P.J.). We thank Drs. Jozsef Csicsvari,
Christoph Lampert, and Federico Stella for critically reading previous manuscript
versions. We are also grateful to Drs. Josh Merel and Ben Shababo for their help
with applying the Bayesian detection method to our data. We also thank Florian Marr
for technical assistance, Eleftheria Kralli-Beller for manuscript editing, and the
Scientific Service Units of IST Austria for efficient support.
article_number: '109125'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: David H
full_name: Vandael, David H
id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87
last_name: Vandael
orcid: 0000-0001-7577-1676
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Zhang X, Schlögl A, Vandael DH, Jonas PM. MOD: A novel machine-learning optimal-filtering
method for accurate and efficient detection of subthreshold synaptic events in
vivo. Journal of Neuroscience Methods. 2021;357(6). doi:10.1016/j.jneumeth.2021.109125'
apa: 'Zhang, X., Schlögl, A., Vandael, D. H., & Jonas, P. M. (2021). MOD: A
novel machine-learning optimal-filtering method for accurate and efficient detection
of subthreshold synaptic events in vivo. Journal of Neuroscience Methods.
Elsevier. https://doi.org/10.1016/j.jneumeth.2021.109125'
chicago: 'Zhang, Xiaomin, Alois Schlögl, David H Vandael, and Peter M Jonas. “MOD:
A Novel Machine-Learning Optimal-Filtering Method for Accurate and Efficient Detection
of Subthreshold Synaptic Events in Vivo.” Journal of Neuroscience Methods.
Elsevier, 2021. https://doi.org/10.1016/j.jneumeth.2021.109125.'
ieee: 'X. Zhang, A. Schlögl, D. H. Vandael, and P. M. Jonas, “MOD: A novel machine-learning
optimal-filtering method for accurate and efficient detection of subthreshold
synaptic events in vivo,” Journal of Neuroscience Methods, vol. 357, no.
6. Elsevier, 2021.'
ista: 'Zhang X, Schlögl A, Vandael DH, Jonas PM. 2021. MOD: A novel machine-learning
optimal-filtering method for accurate and efficient detection of subthreshold
synaptic events in vivo. Journal of Neuroscience Methods. 357(6), 109125.'
mla: 'Zhang, Xiaomin, et al. “MOD: A Novel Machine-Learning Optimal-Filtering Method
for Accurate and Efficient Detection of Subthreshold Synaptic Events in Vivo.”
Journal of Neuroscience Methods, vol. 357, no. 6, 109125, Elsevier, 2021,
doi:10.1016/j.jneumeth.2021.109125.'
short: X. Zhang, A. Schlögl, D.H. Vandael, P.M. Jonas, Journal of Neuroscience Methods
357 (2021).
date_created: 2021-04-18T22:01:39Z
date_published: 2021-03-09T00:00:00Z
date_updated: 2025-06-12T06:39:15Z
day: '09'
ddc:
- '570'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.1016/j.jneumeth.2021.109125
ec_funded: 1
external_id:
isi:
- '000661088500005'
pmid:
- '33711356'
file:
- access_level: open_access
checksum: 2a5800d91b96d08b525e17319dcd5e44
content_type: application/pdf
creator: dernst
date_created: 2021-04-19T08:30:22Z
date_updated: 2021-04-19T08:30:22Z
file_id: '9339'
file_name: 2021_JourNeuroscienceMeth_Zhang.pdf
file_size: 6924738
relation: main_file
success: 1
file_date_updated: 2021-04-19T08:30:22Z
fulldoi: https://doi.org/10.1016/j.jneumeth.2021.109125
has_accepted_license: '1'
intvolume: ' 357'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication: Journal of Neuroscience Methods
publication_identifier:
eissn:
- 1872-678X
issn:
- 0165-0270
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'MOD: A novel machine-learning optimal-filtering method for accurate and efficient
detection of subthreshold synaptic events in vivo'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 357
year: '2021'
...
---
_id: '12909'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
- first_name: Andrei
full_name: Hornoiu, Andrei
id: 77129392-B450-11EA-8745-D4653DDC885E
last_name: Hornoiu
- first_name: Stephan
full_name: Stadlbauer, Stephan
id: 4D0BC184-F248-11E8-B48F-1D18A9856A87
last_name: Stadlbauer
citation:
ama: 'Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. Managing software on a heterogenous
HPC cluster. In: ASHPC21 – Austrian-Slovenian HPC Meeting 2021. University
of Ljubljana; 2021:5. doi:10.3359/2021hpc'
apa: 'Schlögl, A., Elefante, S., Hornoiu, A., & Stadlbauer, S. (2021). Managing
software on a heterogenous HPC cluster. In ASHPC21 – Austrian-Slovenian HPC
Meeting 2021 (p. 5). Virtual: University of Ljubljana. https://doi.org/10.3359/2021hpc'
chicago: Schlögl, Alois, Stefano Elefante, Andrei Hornoiu, and Stephan Stadlbauer.
“Managing Software on a Heterogenous HPC Cluster.” In ASHPC21 – Austrian-Slovenian
HPC Meeting 2021, 5. University of Ljubljana, 2021. https://doi.org/10.3359/2021hpc.
ieee: A. Schlögl, S. Elefante, A. Hornoiu, and S. Stadlbauer, “Managing software
on a heterogenous HPC cluster,” in ASHPC21 – Austrian-Slovenian HPC Meeting
2021, Virtual, 2021, p. 5.
ista: 'Schlögl A, Elefante S, Hornoiu A, Stadlbauer S. 2021. Managing software on
a heterogenous HPC cluster. ASHPC21 – Austrian-Slovenian HPC Meeting 2021. ASHPC:
Austrian-Slovenian HPC Meeting, 5.'
mla: Schlögl, Alois, et al. “Managing Software on a Heterogenous HPC Cluster.” ASHPC21
– Austrian-Slovenian HPC Meeting 2021, University of Ljubljana, 2021, p. 5,
doi:10.3359/2021hpc.
short: A. Schlögl, S. Elefante, A. Hornoiu, S. Stadlbauer, in:, ASHPC21 – Austrian-Slovenian
HPC Meeting 2021, University of Ljubljana, 2021, p. 5.
conference:
end_date: 2021-06-02
location: Virtual
name: 'ASHPC: Austrian-Slovenian HPC Meeting'
start_date: 2021-05-31
corr_author: '1'
date_created: 2023-05-05T13:17:36Z
date_published: 2021-06-02T00:00:00Z
date_updated: 2026-10-14T09:47:31Z
day: '02'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.3359/2021hpc
file:
- access_level: open_access
checksum: ba73f85858fb9d5737ebc7724646dd45
content_type: application/pdf
creator: dernst
date_created: 2023-05-16T07:36:34Z
date_updated: 2023-05-16T07:36:34Z
file_id: '12971'
file_name: 2021_ASHPC_Schloegl.pdf
file_size: 422761
relation: main_file
success: 1
file_date_updated: 2023-05-16T07:36:34Z
fulldoi: https://doi.org/10.3359/2021hpc
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ashpc21/BOOKLET_ASHPC21.pdf
month: '06'
oa: 1
oa_version: Published Version
page: '5'
publication: ASHPC21 – Austrian-Slovenian HPC Meeting 2021
publication_identifier:
isbn:
- 978-961-6980-77-7
- 978-961-6133-48-7
publication_status: published
publisher: University of Ljubljana
status: public
title: Managing software on a heterogenous HPC cluster
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2021'
...
---
_id: '10110'
abstract:
- lang: eng
text: Pattern separation is a fundamental brain computation that converts small
differences in input patterns into large differences in output patterns. Several
synaptic mechanisms of pattern separation have been proposed, including code expansion,
inhibition and plasticity; however, which of these mechanisms play a role in the
entorhinal cortex (EC)–dentate gyrus (DG)–CA3 circuit, a classical pattern separation
circuit, remains unclear. Here we show that a biologically realistic, full-scale
EC–DG–CA3 circuit model, including granule cells (GCs) and parvalbumin-positive
inhibitory interneurons (PV+-INs) in the DG, is an efficient pattern separator.
Both external gamma-modulated inhibition and internal lateral inhibition mediated
by PV+-INs substantially contributed to pattern separation. Both local connectivity
and fast signaling at GC–PV+-IN synapses were important for maximum effectiveness.
Similarly, mossy fiber synapses with conditional detonator properties contributed
to pattern separation. By contrast, perforant path synapses with Hebbian synaptic
plasticity and direct EC–CA3 connection shifted the network towards pattern completion.
Our results demonstrate that the specific properties of cells and synapses optimize
higher-order computations in biological networks and might be useful to improve
the deep learning capabilities of technical networks.
author:
- first_name: José
full_name: Guzmán, José
id: 30CC5506-F248-11E8-B48F-1D18A9856A87
last_name: Guzmán
orcid: 0000-0003-2209-5242
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
orcid: 0000-0003-0256-6529
- first_name: Benjamin
full_name: Suter, Benjamin
id: 4952F31E-F248-11E8-B48F-1D18A9856A87
last_name: Suter
orcid: 0000-0002-9885-6936
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. How connectivity
rules and synaptic properties shape the efficacy of pattern separation in the
entorhinal cortex–dentate gyrus–CA3 network. 2021. doi:10.15479/AT:ISTA:10110
apa: Guzmán, J., Schlögl, A., Espinoza Martinez, C., Zhang, X., Suter, B., &
Jonas, P. M. (2021). How connectivity rules and synaptic properties shape the
efficacy of pattern separation in the entorhinal cortex–dentate gyrus–CA3 network.
IST Austria. https://doi.org/10.15479/AT:ISTA:10110
chicago: Guzmán, José, Alois Schlögl, Claudia Espinoza Martinez, Xiaomin Zhang,
Benjamin Suter, and Peter M Jonas. “How Connectivity Rules and Synaptic Properties
Shape the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network.” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:10110.
ieee: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, and P. M.
Jonas, “How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network.” IST Austria, 2021.
ista: Guzmán J, Schlögl A, Espinoza Martinez C, Zhang X, Suter B, Jonas PM. 2021.
How connectivity rules and synaptic properties shape the efficacy of pattern separation
in the entorhinal cortex–dentate gyrus–CA3 network, IST Austria, 10.15479/AT:ISTA:10110.
mla: Guzmán, José, et al. How Connectivity Rules and Synaptic Properties Shape
the Efficacy of Pattern Separation in the Entorhinal Cortex–Dentate Gyrus–CA3
Network. IST Austria, 2021, doi:10.15479/AT:ISTA:10110.
short: J. Guzmán, A. Schlögl, C. Espinoza Martinez, X. Zhang, B. Suter, P.M. Jonas,
(2021).
date_created: 2021-10-08T06:44:22Z
date_published: 2021-12-16T00:00:00Z
date_updated: 2026-10-15T22:30:57Z
day: '16'
ddc:
- '005'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.15479/AT:ISTA:10110
file:
- access_level: open_access
checksum: f92f8931cad0aa7e411c1715337bf408
content_type: application/x-zip-compressed
creator: cchlebak
date_created: 2021-10-08T08:46:04Z
date_updated: 2021-10-08T08:46:04Z
file_id: '10114'
file_name: patternseparation-main (1).zip
file_size: 332990101
relation: main_file
success: 1
file_date_updated: 2021-10-08T08:46:04Z
fulldoi: https://doi.org/10.15479/AT:ISTA:10110
has_accepted_license: '1'
month: '12'
oa: 1
publisher: IST Austria
related_material:
link:
- description: News on IST Webpage
relation: press_release
url: https://ist.ac.at/en/news/spot-the-difference/
record:
- id: '10816'
relation: used_for_analysis_in
status: public
status: public
title: How connectivity rules and synaptic properties shape the efficacy of pattern
separation in the entorhinal cortex–dentate gyrus–CA3 network
tmp:
legal_code_url: https://www.gnu.org/licenses/gpl-3.0.en.html
name: GNU General Public License 3.0
short: GPL 3.0
type: software
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2021'
...
---
_id: '8261'
abstract:
- lang: eng
text: Dentate gyrus granule cells (GCs) connect the entorhinal cortex to the hippocampal
CA3 region, but how they process spatial information remains enigmatic. To examine
the role of GCs in spatial coding, we measured excitatory postsynaptic potentials
(EPSPs) and action potentials (APs) in head-fixed mice running on a linear belt.
Intracellular recording from morphologically identified GCs revealed that most
cells were active, but activity level varied over a wide range. Whereas only ∼5%
of GCs showed spatially tuned spiking, ∼50% received spatially tuned input. Thus,
the GC population broadly encodes spatial information, but only a subset relays
this information to the CA3 network. Fourier analysis indicated that GCs received
conjunctive place-grid-like synaptic input, suggesting code conversion in single
neurons. GC firing was correlated with dendritic complexity and intrinsic excitability,
but not extrinsic excitatory input or dendritic cable properties. Thus, functional
maturation may control input-output transformation and spatial code conversion.
acknowledged_ssus:
- _id: M-Shop
- _id: ScienComp
- _id: PreCl
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation program (grant
agreement 692692, P.J.) and the Fond zur Förderung der Wissenschaftlichen Forschung
(Z 312-B27, Wittgenstein award, P.J.). We thank Gyorgy Buzsáki, Jozsef Csicsvari,
Juan Ramirez Villegas, and Federico Stella for commenting on earlier versions of
this manuscript. We also thank Katie Bittner, Michael Brecht, Albert Lee, Jeffery
Magee, and Alejandro Pernía-Andrade for sharing expertise in in vivo patch-clamp
recording. We are grateful to Florian Marr for cell labeling, cell reconstruction,
and technical assistance; Ben Suter for helpful discussions; Christina Altmutter
for technical support; Eleftheria Kralli-Beller for manuscript editing; and Todor
Asenov (Machine Shop) for device construction. We also thank the Scientific Service
Units (SSUs) of IST Austria (Machine Shop, Scientific Computing, and Preclinical
Facility) for efficient support.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaomin
full_name: Zhang, Xiaomin
id: 423EC9C2-F248-11E8-B48F-1D18A9856A87
last_name: Zhang
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: Zhang X, Schlögl A, Jonas PM. Selective routing of spatial information flow
from input to output in hippocampal granule cells. Neuron. 2020;107(6):1212-1225.
doi:10.1016/j.neuron.2020.07.006
apa: Zhang, X., Schlögl, A., & Jonas, P. M. (2020). Selective routing of spatial
information flow from input to output in hippocampal granule cells. Neuron.
Elsevier. https://doi.org/10.1016/j.neuron.2020.07.006
chicago: Zhang, Xiaomin, Alois Schlögl, and Peter M Jonas. “Selective Routing of
Spatial Information Flow from Input to Output in Hippocampal Granule Cells.” Neuron.
Elsevier, 2020. https://doi.org/10.1016/j.neuron.2020.07.006.
ieee: X. Zhang, A. Schlögl, and P. M. Jonas, “Selective routing of spatial information
flow from input to output in hippocampal granule cells,” Neuron, vol. 107,
no. 6. Elsevier, pp. 1212–1225, 2020.
ista: Zhang X, Schlögl A, Jonas PM. 2020. Selective routing of spatial information
flow from input to output in hippocampal granule cells. Neuron. 107(6), 1212–1225.
mla: Zhang, Xiaomin, et al. “Selective Routing of Spatial Information Flow from
Input to Output in Hippocampal Granule Cells.” Neuron, vol. 107, no. 6,
Elsevier, 2020, pp. 1212–25, doi:10.1016/j.neuron.2020.07.006.
short: X. Zhang, A. Schlögl, P.M. Jonas, Neuron 107 (2020) 1212–1225.
corr_author: '1'
date_created: 2020-08-14T09:36:05Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2025-04-15T08:29:03Z
day: '23'
ddc:
- '570'
department:
- _id: PeJo
- _id: ScienComp
doi: 10.1016/j.neuron.2020.07.006
ec_funded: 1
external_id:
isi:
- '000579698700009'
pmid:
- '32763145'
file:
- access_level: open_access
checksum: 44a5960fc083a4cb3488d22224859fdc
content_type: application/pdf
creator: dernst
date_created: 2020-12-04T09:29:21Z
date_updated: 2020-12-04T09:29:21Z
file_id: '8920'
file_name: 2020_Neuron_Zhang.pdf
file_size: 3011120
relation: main_file
success: 1
file_date_updated: 2020-12-04T09:29:21Z
fulldoi: https://doi.org/10.1016/j.neuron.2020.07.006
has_accepted_license: '1'
intvolume: ' 107'
isi: 1
issue: '6'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1212-1225
pmid: 1
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glutamatergic synapse
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: Synaptic communication in neuronal microcircuits
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/the-bouncer-in-the-brain/
scopus_import: '1'
status: public
title: Selective routing of spatial information flow from input to output in hippocampal
granule cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 107
year: '2020'
...
---
_id: '7474'
abstract:
- lang: eng
text: This booklet is a collection of abstracts presented at the AHPC conference.
article_processing_charge: No
citation:
ama: 'Schlögl A, Kiss J, Elefante S, eds. Austrian High-Performance-Computing
Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria; 2020. doi:10.15479/AT:ISTA:7474'
apa: 'Schlögl, A., Kiss, J., & Elefante, S. (Eds.). (2020). Austrian High-Performance-Computing
meeting (AHPC2020). Presented at the AHPC: Austrian High-Performance-Computing
Meeting, Klosterneuburg, Austria: IST Austria. https://doi.org/10.15479/AT:ISTA:7474'
chicago: 'Schlögl, Alois, Janos Kiss, and Stefano Elefante, eds. Austrian High-Performance-Computing
Meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020. https://doi.org/10.15479/AT:ISTA:7474.'
ieee: 'A. Schlögl, J. Kiss, and S. Elefante, Eds., Austrian High-Performance-Computing
meeting (AHPC2020). Klosterneuburg, Austria: IST Austria, 2020.'
ista: 'Schlögl A, Kiss J, Elefante S eds. 2020. Austrian High-Performance-Computing
meeting (AHPC2020), Klosterneuburg, Austria: IST Austria, 72p.'
mla: Schlögl, Alois, et al., editors. Austrian High-Performance-Computing Meeting
(AHPC2020). IST Austria, 2020, doi:10.15479/AT:ISTA:7474.
short: A. Schlögl, J. Kiss, S. Elefante, eds., Austrian High-Performance-Computing
Meeting (AHPC2020), IST Austria, Klosterneuburg, Austria, 2020.
conference:
end_date: 2020-02-21
location: Klosterneuburg, Austria
name: 'AHPC: Austrian High-Performance-Computing Meeting'
start_date: 2020-02-19
date_created: 2020-02-11T07:59:04Z
date_published: 2020-02-19T00:00:00Z
date_updated: 2023-05-16T07:48:28Z
day: '19'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.15479/AT:ISTA:7474
editor:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Janos
full_name: Kiss, Janos
id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87
last_name: Kiss
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
file:
- access_level: open_access
checksum: 49798edb9e57bbd6be18362d1d7b18a9
content_type: application/pdf
creator: schloegl
date_created: 2020-02-19T06:53:38Z
date_updated: 2020-07-14T12:47:59Z
file_id: '7504'
file_name: BOOKLET_AHPC2020.final.pdf
file_size: 90899507
relation: main_file
file_date_updated: 2020-07-14T12:47:59Z
fulldoi: https://doi.org/10.15479/AT:ISTA:7474
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '72'
place: Klosterneuburg, Austria
publication_identifier:
isbn:
- 978-3-99078-004-6
publication_status: published
publisher: IST Austria
quality_controlled: '1'
status: public
title: Austrian High-Performance-Computing meeting (AHPC2020)
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: book_editor
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '12901'
article_processing_charge: No
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Janos
full_name: Kiss, Janos
id: 3D3A06F8-F248-11E8-B48F-1D18A9856A87
last_name: Kiss
- first_name: Stefano
full_name: Elefante, Stefano
id: 490F40CE-F248-11E8-B48F-1D18A9856A87
last_name: Elefante
citation:
ama: 'Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster?
In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches
Rechnen der Universität Graz; 2019:25.'
apa: 'Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running
an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee,
Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität
Graz.'
chicago: Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for
Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut
für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.
ieee: A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC
Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria,
2019, p. 25.
ista: 'Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC
Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25.'
mla: Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19
- Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches
Rechnen der Universität Graz, 2019, p. 25.
short: A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019
, Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz,
2019, p. 25.
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