---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21727'
abstract:
- lang: eng
text: We present a comprehensive analysis of the MIRI Extremely Red Object Virgil,
a Lyα emitter at zspec = 6.6379 ± 0.0035 with the photometric properties of a
Little Red Dot. Leveraging new JWST/MIRI imaging from the MIDIS and PAHSPECS programs,
we confirm Virgil’s extraordinary nature among galaxies in JADES/GOODS-South,
exhibiting a strikingly red NIRCam-to-MIRI color (F444W–F1500W = 2.84 ± 0.04 mag).
Deep NIRSpec/PRISM spectroscopy from the OASIS program offers key insights into
the host galaxy, revealing properties of an average star-forming galaxy during
Cosmic Reionization, such as a subsolar metallicity, low-to-moderate dust content,
and a relatively high ionization parameter and electron temperature. By estimating
the star formation rate of Virgil from UV and Hα, we find evidence that the galaxy
is either entering or fading out of a bursty episode. Although line-ratio diagnostics
employed at high z would classify Virgil as an active galactic nucleus (AGN),
this classification becomes ambiguous once redshift evolution is considered. Nonetheless,
Virgil occupies the same parameter space as recently confirmed AGNs at similar
redshifts. The new deep MIRI data at 15 μm reinforce the AGN nature of Virgil,
as inferred from multiple spectral energy distribution (SED) fitting codes. Virgil’s
rising infrared SED and UV excess resemble those of Dust-Obscured Galaxies (DOGs)
studied with Spitzer at Cosmic Noon, particularly blue-excess HotDOGs. Our results
highlight the need for a multiwavelength approach incorporating MIRI to uncover
such extreme sources at z ≳ 6 and to shed light on the interplay between galaxy
evolution and early black hole growth during Cosmic Reionization.
acknowledgement: "The authors are deeply grateful to Antonello Calabrò for valuable
insights on CLOUDY and pyCloudy, and for publicly sharing their SFG and AGN models,
which were used as a reference to verify the consistency of our photoionization
models. The authors also thank Adam Carnall for insightful input on bagpipes and
for assistance with the implementation of the two-population model adopted in this
work. Finally, they also thank Camilla Pacifici, Vasily Kokorev, and Cristian Vignali
for their insightful discussions.\r\n\r\nThis work is based on observations made
with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for
Space Telescopes (MAST) at the Space Telescope Science Institute, which is operated
by the Association of Universities for Research in Astronomy, Inc., under NASA contract
NAS 5-03127 for JWST. These observations are associated with JWST programs GTO #1180,
GO #1210, GTO#1283, GO #1963, GO #1895, GO# 3215, and GO#6511.\r\n\r\nThe authors
acknowledge the FRESCO, JEMS, and #3215 teams led by co-PIs P. Oesch, C. C. Williams,
M. Maseda, D. Eisenstein, and R. Maiolino for developing their observing program
with a zero-exclusive-access period. Processing for the JADES NIRCam data release
was performed on the lux cluster at the University of California, Santa Cruz, funded
by NSF MRI grant AST 1828315. Also based on observations made with the NASA/ESA
Hubble Space Telescope obtained from the Space Telescope Science Institute, which
is operated by the Association of Universities for Research in Astronomy, Inc.,
under NASA contract NAS 526555. The data presented in this article were obtained
from MAST at the Space Telescope Science Institute. The specific observations analyzed
can be accessed via doi: 10.17909/1rq3-8048 P. Oesch & D. Magee (2023), C. Williams
et al. (2023), G. Illingworth (2015), and M. Rieke et al. (2023).\r\n\r\nA.J.B.
acknowledges funding from the “FirstGalaxies” Advanced Grant from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation program
(grant agreement No. 789056).\r\n\r\nP.G.P.-G. acknowledges support from grant PID2022-139567NB-I00
funded by the Spanish Ministerio de Ciencia e Innovación MCIN/AEI/10.13039/501100011033,
FEDER, UE.\r\n\r\nB.E.R. acknowledges support from the NIRCam Science Team contract
to the University of Arizona, NAS5-02015, and JWST Program 3215.\r\n\r\nS.T. acknowledges
support by the Royal Society Research Grant G125142.\r\n\r\nThe research of C.C.W.
is supported by NOIRLab, which is managed by the Association of Universities for
Research in Astronomy (AURA) under a cooperative agreement with the National Science
Foundation.\r\n\r\nJ.W. gratefully acknowledges support from the Cosmic Dawn Center
through the DAWN Fellowship. The Cosmic Dawn Center (DAWN) is funded by the Danish
National Research Foundation under grant No. 140.\r\n\r\nY.Z., Z.J., and P.L. gratefully
acknowledge the JWST/NIRCam contract to the University of Arizona NAS5-02015.\r\n\r\nThe
work of G.H.R. and P.L. was also supported by grant 80NSSC18K0555, from the NASA
Goddard Space Flight Center to the University of Arizona.\r\n\r\nH.Ü. acknowledges
funding by the European Union (ERC APEX, 101164796). Views and opinions expressed
are however those of the authors only and do not necessarily reflect those of the
European Union or the European Research Council Executive Agency. Neither the European
Union nor the granting authority can be held responsible for them.\r\n\r\nG.C.J.
acknowledges support by the Science and Technology Facilities Council (STFC), ERC
Advanced grant 695671 “QUENCH.”\r\n\r\nA.C.G. acknowledges support by JWST contract
B0215/JWST-GO-02926.\r\n\r\nG.O. acknowledges support from the Swedish National
Space Agency (SNSA).\r\n\r\nH.I. acknowledges support from JSPS KAKENHI grant No.
JP21H01129.\r\n\r\nM.A. gratefully acknowledges support from ANID Basal Project
FB210003 and ANID MILENIO NCN2024_112.\r\n\r\nT.D.S. acknowledges the research project
was supported by the Hellenic Foundation for Research and Innovation (HFRI) under
the “2nd Call for HFRI Research Projects to Support Faculty Members and Researchers”
(project No.: 03382).\r\n\r\nR.M. acknowledges support by the Science and Technology
Facilities Council (STFC), by the ERC through Advanced grant 695671 “QUENCH,” and
by the UKRI Frontier Research grant RISEandFALL. R.M. also acknowledges funding
from a research professorship from the Royal Society.\r\n\r\nI.S. acknowledges funding
from the Atraccíon de Talento grant No. 2022-T1/TIC-20472 of the Comunidad de Madrid,
Spain, and the European Research Council (ERC) under the European Union’s Horizon
2020 research and innovation program (grant No. 101117541, DistantDust).\r\n\r\nK.I.C.
acknowledges funding from the Dutch Research Council (NWO) through the award of
the Vici grant VI.C.212.036.\r\n\r\nFacilities: HST - Hubble Space Telescope satellite,
JWST. -\r\n\r\nSoftware: Astropy (Astropy Collaboration et al. 2022), Bagpipes (A.
C. Carnall et al. 2019), MSAEXP (G. Brammer 2023) NumPy (C. R. Harris et al. 2020),
pandas (The pandas development team 2024) Photutils (L. Bradley et al. 2016), TOPCAT
(M. Taylor 2022)."
article_number: '86'
article_processing_charge: Yes
article_type: original
author:
- first_name: Pierluigi
full_name: Rinaldi, Pierluigi
last_name: Rinaldi
- first_name: Pablo G.
full_name: Pérez-González, Pablo G.
last_name: Pérez-González
- first_name: George H.
full_name: Rieke, George H.
last_name: Rieke
- first_name: Jianwei
full_name: Lyu, Jianwei
last_name: Lyu
- first_name: Francesco
full_name: D’Eugenio, Francesco
last_name: D’Eugenio
- first_name: Zihao
full_name: Wu, Zihao
last_name: Wu
- first_name: Stefano
full_name: Carniani, Stefano
last_name: Carniani
- first_name: Tobias J.
full_name: Looser, Tobias J.
last_name: Looser
- first_name: Irene
full_name: Shivaei, Irene
last_name: Shivaei
- first_name: Leindert A.
full_name: Boogaard, Leindert A.
last_name: Boogaard
- first_name: Tanio
full_name: Diaz-Santos, Tanio
last_name: Diaz-Santos
- first_name: Luis
full_name: Colina, Luis
last_name: Colina
- first_name: Göran
full_name: Östlin, Göran
last_name: Östlin
- first_name: Stacey
full_name: Alberts, Stacey
last_name: Alberts
- first_name: Javier
full_name: Álvarez-Márquez, Javier
last_name: Álvarez-Márquez
- first_name: Marianna
full_name: Annuziatella, Marianna
last_name: Annuziatella
- first_name: Manuel
full_name: Aravena, Manuel
last_name: Aravena
- first_name: Rachana
full_name: Bhatawdekar, Rachana
last_name: Bhatawdekar
- first_name: Andrew J.
full_name: Bunker, Andrew J.
last_name: Bunker
- first_name: Karina I.
full_name: Caputi, Karina I.
last_name: Caputi
- first_name: Stéphane
full_name: Charlot, Stéphane
last_name: Charlot
- first_name: Alejandro
full_name: Crespo Gómez, Alejandro
last_name: Crespo Gómez
- first_name: Mirko
full_name: Curti, Mirko
last_name: Curti
- first_name: Andreas
full_name: Eckart, Andreas
last_name: Eckart
- first_name: Steven
full_name: Gillman, Steven
last_name: Gillman
- first_name: Kevin
full_name: Hainline, Kevin
last_name: Hainline
- first_name: Nimisha
full_name: Kumari, Nimisha
last_name: Kumari
- first_name: Jens
full_name: Hjorth, Jens
last_name: Hjorth
- first_name: Edoardo
full_name: Iani, Edoardo
id: 4053390a-6b68-11ef-9828-a3b8adef8d0a
last_name: Iani
orcid: 0000-0001-8386-3546
- first_name: Hanae
full_name: Inami, Hanae
last_name: Inami
- first_name: Zhiyuan
full_name: Ji, Zhiyuan
last_name: Ji
- first_name: Benjamin D.
full_name: Johnson, Benjamin D.
last_name: Johnson
- first_name: Gareth C.
full_name: Jones, Gareth C.
last_name: Jones
- first_name: Álvaro
full_name: Labiano, Álvaro
last_name: Labiano
- first_name: Roberto
full_name: Maiolino, Roberto
last_name: Maiolino
- first_name: Jens
full_name: Melinder, Jens
last_name: Melinder
- first_name: Thibaud
full_name: Moutard, Thibaud
last_name: Moutard
- first_name: Florian
full_name: Peissker, Florian
last_name: Peissker
- first_name: Marcia
full_name: Rieke, Marcia
last_name: Rieke
- first_name: Brant
full_name: Robertson, Brant
last_name: Robertson
- first_name: Jan
full_name: Scholtz, Jan
last_name: Scholtz
- first_name: Sandro
full_name: Tacchella, Sandro
last_name: Tacchella
- first_name: Paul P.
full_name: Van Der Werf, Paul P.
last_name: Van Der Werf
- first_name: Fabian
full_name: Walter, Fabian
last_name: Walter
- first_name: Christina C.
full_name: Williams, Christina C.
last_name: Williams
- first_name: Chris
full_name: Willott, Chris
last_name: Willott
- first_name: Joris
full_name: Witstok, Joris
last_name: Witstok
- first_name: Hannah
full_name: Übler, Hannah
last_name: Übler
- first_name: Yongda
full_name: Zhu, Yongda
last_name: Zhu
citation:
ama: 'Rinaldi P, Pérez-González PG, Rieke GH, et al. Deciphering the nature of Virgil:
An obscured active galactic nucleus lurking within an apparently normal Lyα emitter
during cosmic reionization. The Astrophysical Journal. 2025;994(1). doi:10.3847/1538-4357/ae089c'
apa: 'Rinaldi, P., Pérez-González, P. G., Rieke, G. H., Lyu, J., D’Eugenio, F.,
Wu, Z., … Zhu, Y. (2025). Deciphering the nature of Virgil: An obscured active
galactic nucleus lurking within an apparently normal Lyα emitter during cosmic
reionization. The Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ae089c'
chicago: 'Rinaldi, Pierluigi, Pablo G. Pérez-González, George H. Rieke, Jianwei
Lyu, Francesco D’Eugenio, Zihao Wu, Stefano Carniani, et al. “Deciphering the
Nature of Virgil: An Obscured Active Galactic Nucleus Lurking within an Apparently
Normal Lyα Emitter during Cosmic Reionization.” The Astrophysical Journal.
IOP Publishing, 2025. https://doi.org/10.3847/1538-4357/ae089c.'
ieee: 'P. Rinaldi et al., “Deciphering the nature of Virgil: An obscured
active galactic nucleus lurking within an apparently normal Lyα emitter during
cosmic reionization,” The Astrophysical Journal, vol. 994, no. 1. IOP Publishing,
2025.'
ista: 'Rinaldi P, Pérez-González PG, Rieke GH, Lyu J, D’Eugenio F, Wu Z, Carniani
S, Looser TJ, Shivaei I, Boogaard LA, Diaz-Santos T, Colina L, Östlin G, Alberts
S, Álvarez-Márquez J, Annuziatella M, Aravena M, Bhatawdekar R, Bunker AJ, Caputi
KI, Charlot S, Crespo Gómez A, Curti M, Eckart A, Gillman S, Hainline K, Kumari
N, Hjorth J, Iani E, Inami H, Ji Z, Johnson BD, Jones GC, Labiano Á, Maiolino
R, Melinder J, Moutard T, Peissker F, Rieke M, Robertson B, Scholtz J, Tacchella
S, Van Der Werf PP, Walter F, Williams CC, Willott C, Witstok J, Übler H, Zhu
Y. 2025. Deciphering the nature of Virgil: An obscured active galactic nucleus
lurking within an apparently normal Lyα emitter during cosmic reionization. The
Astrophysical Journal. 994(1), 86.'
mla: 'Rinaldi, Pierluigi, et al. “Deciphering the Nature of Virgil: An Obscured
Active Galactic Nucleus Lurking within an Apparently Normal Lyα Emitter during
Cosmic Reionization.” The Astrophysical Journal, vol. 994, no. 1, 86, IOP
Publishing, 2025, doi:10.3847/1538-4357/ae089c.'
short: P. Rinaldi, P.G. Pérez-González, G.H. Rieke, J. Lyu, F. D’Eugenio, Z. Wu,
S. Carniani, T.J. Looser, I. Shivaei, L.A. Boogaard, T. Diaz-Santos, L. Colina,
G. Östlin, S. Alberts, J. Álvarez-Márquez, M. Annuziatella, M. Aravena, R. Bhatawdekar,
A.J. Bunker, K.I. Caputi, S. Charlot, A. Crespo Gómez, M. Curti, A. Eckart, S.
Gillman, K. Hainline, N. Kumari, J. Hjorth, E. Iani, H. Inami, Z. Ji, B.D. Johnson,
G.C. Jones, Á. Labiano, R. Maiolino, J. Melinder, T. Moutard, F. Peissker, M.
Rieke, B. Robertson, J. Scholtz, S. Tacchella, P.P. Van Der Werf, F. Walter, C.C.
Williams, C. Willott, J. Witstok, H. Übler, Y. Zhu, The Astrophysical Journal
994 (2025).
date_created: 2026-04-12T22:01:53Z
date_published: 2025-11-20T00:00:00Z
date_updated: 2026-04-13T07:54:11Z
day: '20'
ddc:
- '520'
department:
- _id: JoMa
doi: 10.3847/1538-4357/ae089c
file:
- access_level: open_access
checksum: 5d13b0ad3e9f56cbe29c5de0ba5757c8
content_type: application/pdf
creator: dernst
date_created: 2026-04-13T07:53:00Z
date_updated: 2026-04-13T07:53:00Z
file_id: '21731'
file_name: 2025_AstrophysicalJournal_Rinaldi.pdf
file_size: 10298729
relation: main_file
success: 1
file_date_updated: 2026-04-13T07:53:00Z
fulldoi: https://doi.org/10.3847/1538-4357/ae089c
has_accepted_license: '1'
intvolume: ' 994'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deciphering the nature of Virgil: An obscured active galactic nucleus lurking
within an apparently normal Lyα emitter during cosmic reionization'
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: 994
year: '2025'
...
---
OA_type: closed access
_id: '21885'
abstract:
- lang: eng
text: Symbolic datatypes have proved to be central for automated reasoning about
dynamical systems. In its basic form, a symbolic datatype for a class of dynamical
systems supports the representation of state and transition sets, boolean operations
and emptiness checks on such sets, and the transformation of a state set by a
transition set. Successful examples of symbolic datatypes include BDDs and SAT
for reasoning about finitestate systems, as well as polyhedra and SMT for reasoning
about discrete dynamical systems over multidimensional realvalued state spaces.
Most automated verification engines are based on such symbolic datatypes.
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000-0002-2985-7724
citation:
ama: 'Henzinger TA. Neural Certificates. In: Proceedings of the 27th International
Symposium on Symbolic and Numeric Algorithms for Scientific Computing. IEEE;
2025. doi:10.1109/SYNASC69064.2025.00008'
apa: 'Henzinger, T. A. (2025). Neural Certificates. In Proceedings of the 27th
International Symposium on Symbolic and Numeric Algorithms for Scientific Computing.
Timisoara, Romania: IEEE. https://doi.org/10.1109/SYNASC69064.2025.00008'
chicago: Henzinger, Thomas A. “Neural Certificates.” In Proceedings of the 27th
International Symposium on Symbolic and Numeric Algorithms for Scientific Computing.
IEEE, 2025. https://doi.org/10.1109/SYNASC69064.2025.00008.
ieee: T. A. Henzinger, “Neural Certificates,” in Proceedings of the 27th International
Symposium on Symbolic and Numeric Algorithms for Scientific Computing, Timisoara,
Romania, 2025.
ista: 'Henzinger TA. 2025. Neural Certificates. Proceedings of the 27th International
Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC:
Symposium on Symbolic and Numeric Algorithms for Scientific Computing.'
mla: Henzinger, Thomas A. “Neural Certificates.” Proceedings of the 27th International
Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE,
2025, doi:10.1109/SYNASC69064.2025.00008.
short: T.A. Henzinger, in:, Proceedings of the 27th International Symposium on Symbolic
and Numeric Algorithms for Scientific Computing, IEEE, 2025.
conference:
end_date: 2025-09-25
location: Timisoara, Romania
name: 'SYNASC: Symposium on Symbolic and Numeric Algorithms for Scientific Computing'
start_date: 2025-09-22
corr_author: '1'
date_created: 2026-05-17T22:02:11Z
date_published: 2025-10-01T00:00:00Z
date_updated: 2026-05-18T08:34:15Z
day: '01'
department:
- _id: ToHe
doi: 10.1109/SYNASC69064.2025.00008
fulldoi: https://doi.org/10.1109/SYNASC69064.2025.00008
language:
- iso: eng
month: '10'
oa_version: None
publication: Proceedings of the 27th International Symposium on Symbolic and Numeric
Algorithms for Scientific Computing
publication_identifier:
eisbn:
- '9798331590116'
eissn:
- 2470-881X
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neural Certificates
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
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'
...
---
OA_place: publisher
OA_type: gold
_id: '14647'
abstract:
- lang: eng
text: "In the developing vertebrate central nervous system, neurons and glia typically
arise\r\nsequentially from common progenitors. Here, we report that the transcription
factor Forkhead\r\nBox G1 (Foxg1) regulates gliogenesis in the mouse neocortex
via distinct cell-autonomous roles in progenitors and postmitotic neurons that
regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate
that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature
astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway
component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis.
Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the
augmentation of FGF signalling. We identify a second novel function of FOXG1 in
regulating the expression of gliogenic cues in newborn neocortical upper-layer
neurons. Loss of FOXG1 in postmitotic neurons non-autonomously enhances gliogenesis
in the progenitors via FGF signalling. These results fit well with the model that
newborn neurons secrete cues that trigger progenitors to produce the next wave
of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors,
they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions
the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes
depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic
signalling via the FGF pathway to regulate the sequential generation of neurons,
astrocytes, and oligodendrocytes in the cerebral cortex. "
acknowledgement: "We thank the animal house staff of the Tata Institute of Fundamental
Research, Mumbai (TIFR), for their excellent support; Gordon Fishell (Harvard Medical
School, USA), and Goichi Miyoshi (Gunma University, Japan) for the Foxg1 floxed
mouse line; Hiroshi Kawasaki (Kanazawa University, Japan) for the plasmids pCAG-FGF8
and pCAG-sFgfr3c; Soo Kyung Lee (University at Buffalo, The State University of
New York, USA) for the Foxg1lox/lox genotyping primers and protocol. We thank Deepak
Modi and Vainav Patel (National Institute for Research in Reproductive and Child
Health, NIRRCH, Mumbai, India) for the use of the NIRRCH FACS Facility, and the
staff of the NIRRCH and TIFR FACS facilities for their assistance. We thank Denis
Jabaudon (University of Geneva, Switzerland) for his critical comments on the manuscript
and members of the Jabaudon lab for helpful discussions. This work was funded by
the Department of Atomic Energy (DAE), Govt. of India (Project Identification no.
RTI4003,\r\nDAE OM no. 1303/2/2019/R&D-II/DAE/2079). "
article_number: '101851'
article_processing_charge: Yes
article_type: original
author:
- first_name: Mahima
full_name: Bose, Mahima
last_name: Bose
- first_name: Varun
full_name: Suresh, Varun
last_name: Suresh
- first_name: Urvi
full_name: Mishra, Urvi
last_name: Mishra
- first_name: Ishita
full_name: Talwar, Ishita
last_name: Talwar
- first_name: Anuradha
full_name: Yadav, Anuradha
last_name: Yadav
- first_name: Shiona
full_name: Biswas, Shiona
last_name: Biswas
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Shubha
full_name: Tole, Shubha
last_name: Tole
citation:
ama: Bose M, Suresh V, Mishra U, et al. Dual role of FOXG1 in regulating gliogenesis
in the developing neocortex via the FGF signalling pathway. eLife. 2025;13.
doi:10.7554/elife.101851.3
apa: Bose, M., Suresh, V., Mishra, U., Talwar, I., Yadav, A., Biswas, S., … Tole,
S. (2025). Dual role of FOXG1 in regulating gliogenesis in the developing neocortex
via the FGF signalling pathway. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.101851.3
chicago: Bose, Mahima, Varun Suresh, Urvi Mishra, Ishita Talwar, Anuradha Yadav,
Shiona Biswas, Simon Hippenmeyer, and Shubha Tole. “Dual Role of FOXG1 in Regulating
Gliogenesis in the Developing Neocortex via the FGF Signalling Pathway.” ELife.
eLife Sciences Publications, 2025. https://doi.org/10.7554/elife.101851.3.
ieee: M. Bose et al., “Dual role of FOXG1 in regulating gliogenesis in the
developing neocortex via the FGF signalling pathway,” eLife, vol. 13. eLife
Sciences Publications, 2025.
ista: Bose M, Suresh V, Mishra U, Talwar I, Yadav A, Biswas S, Hippenmeyer S, Tole
S. 2025. Dual role of FOXG1 in regulating gliogenesis in the developing neocortex
via the FGF signalling pathway. eLife. 13, 101851.
mla: Bose, Mahima, et al. “Dual Role of FOXG1 in Regulating Gliogenesis in the Developing
Neocortex via the FGF Signalling Pathway.” ELife, vol. 13, 101851, eLife
Sciences Publications, 2025, doi:10.7554/elife.101851.3.
short: M. Bose, V. Suresh, U. Mishra, I. Talwar, A. Yadav, S. Biswas, S. Hippenmeyer,
S. Tole, ELife 13 (2025).
date_created: 2023-12-06T13:07:01Z
date_published: 2025-03-14T00:00:00Z
date_updated: 2025-05-14T11:41:52Z
day: '14'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.7554/elife.101851.3
external_id:
pmid:
- '40085500'
file:
- access_level: open_access
checksum: 64a6a6f86e24b21fe72c7a7fd6056fed
content_type: application/pdf
creator: dernst
date_created: 2025-04-03T11:19:26Z
date_updated: 2025-04-03T11:19:26Z
file_id: '19467'
file_name: 2025_eLife_Bose.pdf
file_size: 17462771
relation: main_file
success: 1
file_date_updated: 2025-04-03T11:19:26Z
fulldoi: https://doi.org/10.7554/elife.101851.3
has_accepted_license: '1'
intvolume: ' 13'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via
the FGF signalling pathway
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: 13
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '15128'
abstract:
- lang: eng
text: We prove a universal mesoscopic central limit theorem for linear eigenvalue
statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly
supported twice continuously differentiable test functions. The main novel ingredient
is an optimal local law for the two-point function $T(z,\zeta)$ and a general
class of related quantities involving two resolvents at nearby spectral parameters.
- lang: fre
text: "On établit un théorème limite central universel pour les statistiques linéaires
mésoscopiques des valeurs propres d’une matrice de type Wigner au milieu du spectre,
avec des fonctions de classe \r\n et à support compact. La principale nouveauté
de cette approche est qu’elle repose sur une loi locale optimale pour la fonction
à deux points $T(z,\\zeta)$ , ainsi que pour une classe plus générale d’observables
impliquant deux résolvantes évaluées en des paramètres proches."
acknowledgement: "I would like to express my gratitude to László Erdős for suggesting
the project and supervising my work. I am also thankful to Yuanyuan Xu and Oleksii
Kolupaiev for many helpful discussions. Furthermore, I am grateful to Guillaume
Dubach for translating the abstract into French.\r\nThe author was supported by
the ERC Advanced Grant “RMTBeyond” No. 101020331."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Volodymyr
full_name: Riabov, Volodymyr
id: 1949f904-edfb-11eb-afb5-e2dfddabb93b
last_name: Riabov
citation:
ama: Riabov V. Mesoscopic eigenvalue statistics for Wigner-type matrices. Annales
de l’institut Henri Poincare (B) Probability and Statistics. 2025;61(1):129-154.
doi:10.1214/23-AIHP1438
apa: Riabov, V. (2025). Mesoscopic eigenvalue statistics for Wigner-type matrices.
Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute
of Mathematical Statistics. https://doi.org/10.1214/23-AIHP1438
chicago: Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.”
Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute
of Mathematical Statistics, 2025. https://doi.org/10.1214/23-AIHP1438.
ieee: V. Riabov, “Mesoscopic eigenvalue statistics for Wigner-type matrices,” Annales
de l’institut Henri Poincare (B) Probability and Statistics, vol. 61, no.
1. Institute of Mathematical Statistics, pp. 129–154, 2025.
ista: Riabov V. 2025. Mesoscopic eigenvalue statistics for Wigner-type matrices.
Annales de l’institut Henri Poincare (B) Probability and Statistics. 61(1), 129–154.
mla: Riabov, Volodymyr. “Mesoscopic Eigenvalue Statistics for Wigner-Type Matrices.”
Annales de l’institut Henri Poincare (B) Probability and Statistics, vol.
61, no. 1, Institute of Mathematical Statistics, 2025, pp. 129–54, doi:10.1214/23-AIHP1438.
short: V. Riabov, Annales de l’institut Henri Poincare (B) Probability and Statistics
61 (2025) 129–154.
corr_author: '1'
date_created: 2024-03-20T09:41:04Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-05-19T13:54:31Z
day: '01'
department:
- _id: GradSch
- _id: LaEr
doi: 10.1214/23-AIHP1438
ec_funded: 1
external_id:
arxiv:
- '2301.01712'
isi:
- '001427953600004'
fulldoi: https://doi.org/10.1214/23-AIHP1438
intvolume: ' 61'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2301.01712
month: '02'
oa: 1
oa_version: Preprint
page: 129-154
project:
- _id: 62796744-2b32-11ec-9570-940b20777f1d
call_identifier: H2020
grant_number: '101020331'
name: Random matrices beyond Wigner-Dyson-Mehta
publication: Annales de l'institut Henri Poincare (B) Probability and Statistics
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mesoscopic eigenvalue statistics for Wigner-type matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 61
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18478'
abstract:
- lang: eng
text: For a given graph G=(V,E), we define its \emph{nth subdivision} as the graph
obtained from G by replacing every edge by a path of length n. We also define
the \emph{mth power} of G as the graph on vertex set V where we connect every
pair of vertices at distance at most m in G. In this paper, we study the chromatic
number of powers of subdivisions of graphs and resolve the case m=n asymptotically.
In particular, our result confirms a conjecture of Mozafari-Nia and Iradmusa in
the case m=n=3 in a strong sense.
acknowledgement: "This work was initiated at the annual workshop of the Combinatorics
and Graph Theory group of Freie Universität Berlin in Wilhelmsaue in September 2023.
The authors would like to thank the institution for enabling this research. Finally,
the fourth author would like to thank Tibor Szabó and the Combinatorics and Graph
Theory group at Freie Universität Berlin for their hospitality during the research
visit. Additionally, we thank Moharram Iradmusa for bringing the papers [5], [7]
to our attention. Finally, we thank the anonymous referees for their suggestions
on the manuscript, which have improved the quality of the document.\r\nM.A.: This
project has received funding from the European Union’s Horizon 2020 research and
innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413
.\r\nS.B.: The research leading to these results was supported by EPSRC, UK, grant
no. EP/V048287/1. There are no additional data beyond that contained within the
main manuscript.\r\nS.R.: Funded by the Deutsche Forschungsgemeinschaft (DFG, German
Research Foundation) under Germany’s Excellence Strategy – The Berlin Mathematics
Research Center MATH+ (EXC-2046/1, project ID: 390685689).\r\nJ.R. acknowledges
the support of the Grant PID2020-113082GB-I00 funded by MICIU/AEI/10.13039/501100011033,
Spain, and the Severo Ochoa and María de Maeztu Program for Centers and Units of
Excellence in R&D, Spain (CEX2020-001084-M)."
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Michael
full_name: Anastos, Michael
id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb
last_name: Anastos
- first_name: Simona
full_name: Boyadzhiyska, Simona
last_name: Boyadzhiyska
- first_name: Silas
full_name: Rathke, Silas
last_name: Rathke
- first_name: Juanjo
full_name: Rué, Juanjo
last_name: Rué
citation:
ama: Anastos M, Boyadzhiyska S, Rathke S, Rué J. On the chromatic number of powers
of subdivisions of graphs. Discrete Applied Mathematics. 2025;360:506-511.
doi:10.1016/j.dam.2024.10.002
apa: Anastos, M., Boyadzhiyska, S., Rathke, S., & Rué, J. (2025). On the chromatic
number of powers of subdivisions of graphs. Discrete Applied Mathematics.
Elsevier. https://doi.org/10.1016/j.dam.2024.10.002
chicago: Anastos, Michael, Simona Boyadzhiyska, Silas Rathke, and Juanjo Rué. “On
the Chromatic Number of Powers of Subdivisions of Graphs.” Discrete Applied
Mathematics. Elsevier, 2025. https://doi.org/10.1016/j.dam.2024.10.002.
ieee: M. Anastos, S. Boyadzhiyska, S. Rathke, and J. Rué, “On the chromatic number
of powers of subdivisions of graphs,” Discrete Applied Mathematics, vol.
360. Elsevier, pp. 506–511, 2025.
ista: Anastos M, Boyadzhiyska S, Rathke S, Rué J. 2025. On the chromatic number
of powers of subdivisions of graphs. Discrete Applied Mathematics. 360, 506–511.
mla: Anastos, Michael, et al. “On the Chromatic Number of Powers of Subdivisions
of Graphs.” Discrete Applied Mathematics, vol. 360, Elsevier, 2025, pp.
506–11, doi:10.1016/j.dam.2024.10.002.
short: M. Anastos, S. Boyadzhiyska, S. Rathke, J. Rué, Discrete Applied Mathematics
360 (2025) 506–511.
corr_author: '1'
date_created: 2024-10-27T23:01:44Z
date_published: 2025-01-15T00:00:00Z
date_updated: 2025-04-14T07:54:56Z
day: '15'
ddc:
- '510'
department:
- _id: MaKw
doi: 10.1016/j.dam.2024.10.002
ec_funded: 1
external_id:
arxiv:
- '2404.05542'
isi:
- '001343647000001'
file:
- access_level: open_access
checksum: bd20a13e56b3ea01daf5e7aca5247c60
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T09:25:59Z
date_updated: 2025-01-13T09:25:59Z
file_id: '18836'
file_name: 2025_DiscreteApplMath_Anastos.pdf
file_size: 441060
relation: main_file
success: 1
file_date_updated: 2025-01-13T09:25:59Z
fulldoi: https://doi.org/10.1016/j.dam.2024.10.002
has_accepted_license: '1'
intvolume: ' 360'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 506-511
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Discrete Applied Mathematics
publication_identifier:
issn:
- 0166-218X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the chromatic number of powers of subdivisions of graphs
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: 360
year: '2025'
...
---
OA_type: closed access
_id: '18529'
abstract:
- lang: eng
text: Temporal networks are obtained from time-dependent interactions among individuals,
whereas the interactions can be emails, phone calls, face-to-face meetings, or
work collaboration. In this article, a temporal game framework is established,
in which interactions among rational individuals are embedded into two-player
games in a time-dependent manner. This allows studying the time-dependent complexity
and variability of interactions, and the way they affect prosocial behaviors.
Based on this simple mathematical model, it is found that the level of cooperation
is promoted when the time of collaboration is equally limited for every individual.
This observation is confirmed by a series of systematic human experiments on over
1,400 subjects, forming a foundation for comprehensively describing human temporal
interactions in collaboration. The research results reveal an important incentive
for human cooperation, leading to a better understanding of a fascinating aspect
of human nature in society.
article_processing_charge: No
article_type: original
author:
- first_name: Yichao
full_name: Zhang, Yichao
last_name: Zhang
- first_name: Jiasheng
full_name: Wang, Jiasheng
last_name: Wang
- first_name: Guanghui
full_name: Wen, Guanghui
last_name: Wen
- first_name: Jihong
full_name: Guan, Jihong
last_name: Guan
- first_name: Shuigeng
full_name: Zhou, Shuigeng
last_name: Zhou
- first_name: Guanrong
full_name: Chen, Guanrong
last_name: Chen
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Matjaz
full_name: Perc, Matjaz
last_name: Perc
citation:
ama: Zhang Y, Wang J, Wen G, et al. Limitation of time promotes cooperation in structured
collaboration systems. IEEE Transactions on Network Science and Engineering.
2025;12(1):4-12. doi:10.1109/TNSE.2024.3481434
apa: Zhang, Y., Wang, J., Wen, G., Guan, J., Zhou, S., Chen, G., … Perc, M. (2025).
Limitation of time promotes cooperation in structured collaboration systems. IEEE
Transactions on Network Science and Engineering. IEEE. https://doi.org/10.1109/TNSE.2024.3481434
chicago: Zhang, Yichao, Jiasheng Wang, Guanghui Wen, Jihong Guan, Shuigeng Zhou,
Guanrong Chen, Krishnendu Chatterjee, and Matjaz Perc. “Limitation of Time Promotes
Cooperation in Structured Collaboration Systems.” IEEE Transactions on Network
Science and Engineering. IEEE, 2025. https://doi.org/10.1109/TNSE.2024.3481434.
ieee: Y. Zhang et al., “Limitation of time promotes cooperation in structured
collaboration systems,” IEEE Transactions on Network Science and Engineering,
vol. 12, no. 1. IEEE, pp. 4–12, 2025.
ista: Zhang Y, Wang J, Wen G, Guan J, Zhou S, Chen G, Chatterjee K, Perc M. 2025.
Limitation of time promotes cooperation in structured collaboration systems. IEEE
Transactions on Network Science and Engineering. 12(1), 4–12.
mla: Zhang, Yichao, et al. “Limitation of Time Promotes Cooperation in Structured
Collaboration Systems.” IEEE Transactions on Network Science and Engineering,
vol. 12, no. 1, IEEE, 2025, pp. 4–12, doi:10.1109/TNSE.2024.3481434.
short: Y. Zhang, J. Wang, G. Wen, J. Guan, S. Zhou, G. Chen, K. Chatterjee, M. Perc,
IEEE Transactions on Network Science and Engineering 12 (2025) 4–12.
date_created: 2024-11-10T23:02:00Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-02-27T12:35:48Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/TNSE.2024.3481434
external_id:
isi:
- '001385382200040'
fulldoi: https://doi.org/10.1109/TNSE.2024.3481434
intvolume: ' 12'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 4-12
publication: IEEE Transactions on Network Science and Engineering
publication_identifier:
eissn:
- 2327-4697
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limitation of time promotes cooperation in structured collaboration systems
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18580'
abstract:
- lang: eng
text: Motivated by the study of recurrent orbits and dynamics within a Morse set
of a Morse decomposition we introduce the concept of Morse predecomposition of
an isolated invariant set within the setting of both combinatorial and classical
dynamical systems. While Morse decomposition summarizes solely the gradient part
of a dynamical system, the developed generalization extends to the recurrent component
as well. In particular, a chain recurrent set, which is indecomposable in terms
of Morse decomposition, can be represented more finely in the Morse predecomposition
framework. This generalization is achieved by forgoing the poset structure inherent
to Morse decomposition and relaxing the notion of connection between Morse sets
(elements of Morse decomposition) in favor of what we term ’links’. We prove that
a Morse decomposition is a special case of Morse predecomposition indexed by a
poset. Additionally, we show how a Morse predecomposition may be condensed back
to retrieve a Morse decomposition.
acknowledgement: 'M.L. acknowledge support by the Dioscuri program initiated by the
Max Planck Society, jointly managed with the National Science Centre (Poland), and
mutually funded by the Polish Ministry of Science and Higher Education and the German
Federal Ministry of Education and Research. M.L. also acknowledges that this project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. Research
of M.M. is partially supported by the Polish National Science Center under Opus
Grant No. 2019/35/B/ST1/00874. The work of K.M. was partially supported by the National
Science Foundation under awards DMS-1839294 and HDR TRIPODS award CCF-1934924, DARPA
contract HR0011-16-2-0033, National Institutes of Health award R01 GM126555, Air
Force Office of Scientific Research under award numbers FA9550-23-1-0011, AWD00010853-MOD002
and MURI FA9550-23-1-0400. K.M. was also supported by a grant from the Simons Foundation.
Open access funding provided by Institute of Science and Technology (IST Austria). '
article_number: '5'
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Michał
full_name: Lipiński, Michał
id: dfffb474-4317-11ee-8f5c-fe3fc95a425e
last_name: Lipiński
orcid: 0000-0001-9789-9750
- first_name: Konstantin
full_name: Mischaikow, Konstantin
last_name: Mischaikow
- first_name: Marian
full_name: Mrozek, Marian
last_name: Mrozek
citation:
ama: Lipiński M, Mischaikow K, Mrozek M. Morse predecomposition of an invariant
set. Qualitative Theory of Dynamical Systems. 2025;24(1). doi:10.1007/s12346-024-01144-3
apa: Lipiński, M., Mischaikow, K., & Mrozek, M. (2025). Morse predecomposition
of an invariant set. Qualitative Theory of Dynamical Systems. Springer
Nature. https://doi.org/10.1007/s12346-024-01144-3
chicago: Lipiński, Michał, Konstantin Mischaikow, and Marian Mrozek. “Morse Predecomposition
of an Invariant Set.” Qualitative Theory of Dynamical Systems. Springer
Nature, 2025. https://doi.org/10.1007/s12346-024-01144-3.
ieee: M. Lipiński, K. Mischaikow, and M. Mrozek, “Morse predecomposition of an invariant
set,” Qualitative Theory of Dynamical Systems, vol. 24, no. 1. Springer
Nature, 2025.
ista: Lipiński M, Mischaikow K, Mrozek M. 2025. Morse predecomposition of an invariant
set. Qualitative Theory of Dynamical Systems. 24(1), 5.
mla: Lipiński, Michał, et al. “Morse Predecomposition of an Invariant Set.” Qualitative
Theory of Dynamical Systems, vol. 24, no. 1, 5, Springer Nature, 2025, doi:10.1007/s12346-024-01144-3.
short: M. Lipiński, K. Mischaikow, M. Mrozek, Qualitative Theory of Dynamical Systems
24 (2025).
corr_author: '1'
date_created: 2024-11-24T23:01:47Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-04-14T07:54:56Z
day: '01'
ddc:
- '514'
- '510'
department:
- _id: UlWa
doi: 10.1007/s12346-024-01144-3
ec_funded: 1
external_id:
arxiv:
- '2312.08013'
isi:
- '001356000500005'
file:
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checksum: 73309a57cc798d696caa57b6aa1467d8
content_type: application/pdf
creator: mlipinsk
date_created: 2024-11-28T06:52:38Z
date_updated: 2024-11-28T06:52:38Z
file_id: '18595'
file_name: 2025_predecomposition.pdf
file_size: 1483668
relation: main_file
success: 1
file_date_updated: 2024-11-28T06:52:38Z
fulldoi: https://doi.org/10.1007/s12346-024-01144-3
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
issue: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
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call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Qualitative Theory of Dynamical Systems
publication_identifier:
eissn:
- 1662-3592
issn:
- 1575-5460
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Morse predecomposition of an invariant set
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: 24
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '18626'
abstract:
- lang: eng
text: "The local angle property of the (order-1) Delaunay triangulations of a generic
set in R2\r\n asserts that the sum of two angles opposite a common edge is less
than π. This paper extends this property to higher order and uses it to generalize
two classic properties from order-1 to order-2: (1) among the complete level-2
hypertriangulations of a generic point set in R2, the order-2 Delaunay triangulation
lexicographically maximizes the sorted angle vector; (2) among the maximal level-2
hypertriangulations of a generic point set in R2, the order-2 Delaunay triangulation
is the only one that has the local angle property. We also use our method of establishing
(2) to give a new short proof of the angle vector optimality for the (order-1)
Delaunay triangulation. For order-1, both properties have been instrumental in
numerous applications of Delaunay triangulations, and we expect that their generalization
will make order-2 Delaunay triangulations more attractive to applications as well."
acknowledgement: Work by the first and third authors is partially supported by the
European Research Council (ERC), grant no. 788183, by the Wittgenstein Prize, Austrian
Science Fund (FWF), grant no. Z 342-N31, and by the DFG Collaborative Research Center
TRR 109, Austrian Science Fund (FWF), grant no. I 02979-N35. Work by the second
author is partially supported by the Alexander von Humboldt Foundation.
article_number: '110055'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Alexey
full_name: Garber, Alexey
last_name: Garber
- first_name: Morteza
full_name: Saghafian, Morteza
id: f86f7148-b140-11ec-9577-95435b8df824
last_name: Saghafian
citation:
ama: Edelsbrunner H, Garber A, Saghafian M. Order-2 Delaunay triangulations optimize
angles. Advances in Mathematics. 2025;461. doi:10.1016/j.aim.2024.110055
apa: Edelsbrunner, H., Garber, A., & Saghafian, M. (2025). Order-2 Delaunay
triangulations optimize angles. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2024.110055
chicago: Edelsbrunner, Herbert, Alexey Garber, and Morteza Saghafian. “Order-2 Delaunay
Triangulations Optimize Angles.” Advances in Mathematics. Elsevier, 2025.
https://doi.org/10.1016/j.aim.2024.110055.
ieee: H. Edelsbrunner, A. Garber, and M. Saghafian, “Order-2 Delaunay triangulations
optimize angles,” Advances in Mathematics, vol. 461. Elsevier, 2025.
ista: Edelsbrunner H, Garber A, Saghafian M. 2025. Order-2 Delaunay triangulations
optimize angles. Advances in Mathematics. 461, 110055.
mla: Edelsbrunner, Herbert, et al. “Order-2 Delaunay Triangulations Optimize Angles.”
Advances in Mathematics, vol. 461, 110055, Elsevier, 2025, doi:10.1016/j.aim.2024.110055.
short: H. Edelsbrunner, A. Garber, M. Saghafian, Advances in Mathematics 461 (2025).
corr_author: '1'
date_created: 2024-12-08T23:01:54Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-04-15T07:16:53Z
day: '01'
department:
- _id: HeEd
doi: 10.1016/j.aim.2024.110055
ec_funded: 1
external_id:
arxiv:
- '2310.18238'
isi:
- '001370682500001'
fulldoi: https://doi.org/10.1016/j.aim.2024.110055
intvolume: ' 461'
isi: 1
language:
- iso: eng
main_file_link:
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url: https://doi.org/10.48550/arXiv.2310.18238
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Advances in Mathematics
publication_identifier:
eissn:
- 1090-2082
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Order-2 Delaunay triangulations optimize angles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 461
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18632'
abstract:
- lang: eng
text: 'For an arbitrary dimension (Formula presented.), we study: the polyharmonic
Gaussian field (Formula presented.) on the discrete torus (Formula presented.),
that is the random field whose law on (Formula presented.) given by (Formula presented.)
where (Formula presented.) is the Lebesgue measure and (Formula presented.) is
the discrete Laplacian; the associated discrete Liouville quantum gravity (LQG)
measure associated with it, that is, the random measure on (Formula presented.)
(Formula presented.) where (Formula presented.) is a regularity parameter. As
(Formula presented.), we prove convergence of the fields (Formula presented.)
to the polyharmonic Gaussian field (Formula presented.) on the continuous torus
(Formula presented.), as well as convergence of the random measures (Formula presented.)
to the LQG measure (Formula presented.) on (Formula presented.), for all (Formula
presented.). '
acknowledgement: "KTS is grateful to Christoph Thiele for valuable discussions and
helpful references. LDS is grateful to Nathanaël Berestycki for valuable discussions
on Gaussian Multiplicative Chaoses. The authors are grateful to an anonymous reviewer
for suggestions which improved the presentation.\r\nThe authors gratefully acknowledge
funding by the Deutsche Forschungsgemeinschaft through the project ‘Random Riemannian
Geometry’ within the SPP 2265 ‘Random Geometric Systems.'\r\nLDS gratefully acknowledges
financial support from the European Research Council (grant agreement No. 716117,
awarded to J. Maas) and from the Austrian Science Fund (FWF). His research was funded
by the Austrian Science Fund (FWF) project 10.55776/F65 and project 10.55776/ESP208.\r\nRH,
EK, and KTS gratefully acknowledge funding by the Hausdorff Center for Mathematics
(project ID 390685813), and through project B03 within the CRC 1060 (project ID
211504053). RH and KTS also gratefully acknowledges financial support from the European
Research Council through the ERC AdG ‘RicciBounds’ (grant agreement 694405).\r\nOpen
access funding enabled and organized by Projekt DEAL."
article_processing_charge: Yes (via OA deal)
article_type: original
arxiv: 1
author:
- first_name: Lorenzo
full_name: Dello Schiavo, Lorenzo
id: ECEBF480-9E4F-11EA-B557-B0823DDC885E
last_name: Dello Schiavo
orcid: 0000-0002-9881-6870
- first_name: Ronan
full_name: Herry, Ronan
last_name: Herry
- first_name: Eva
full_name: Kopfer, Eva
last_name: Kopfer
- first_name: Karl Theodor
full_name: Sturm, Karl Theodor
last_name: Sturm
citation:
ama: 'Dello Schiavo L, Herry R, Kopfer E, Sturm KT. Polyharmonic fields and Liouville
quantum gravity measures on tori of arbitrary dimension: From discrete to continuous.
Mathematische Nachrichten. 2025;298(1):244-281. doi:10.1002/mana.202400169'
apa: 'Dello Schiavo, L., Herry, R., Kopfer, E., & Sturm, K. T. (2025). Polyharmonic
fields and Liouville quantum gravity measures on tori of arbitrary dimension:
From discrete to continuous. Mathematische Nachrichten. Wiley. https://doi.org/10.1002/mana.202400169'
chicago: 'Dello Schiavo, Lorenzo, Ronan Herry, Eva Kopfer, and Karl Theodor Sturm.
“Polyharmonic Fields and Liouville Quantum Gravity Measures on Tori of Arbitrary
Dimension: From Discrete to Continuous.” Mathematische Nachrichten. Wiley,
2025. https://doi.org/10.1002/mana.202400169.'
ieee: 'L. Dello Schiavo, R. Herry, E. Kopfer, and K. T. Sturm, “Polyharmonic fields
and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete
to continuous,” Mathematische Nachrichten, vol. 298, no. 1. Wiley, pp.
244–281, 2025.'
ista: 'Dello Schiavo L, Herry R, Kopfer E, Sturm KT. 2025. Polyharmonic fields and
Liouville quantum gravity measures on tori of arbitrary dimension: From discrete
to continuous. Mathematische Nachrichten. 298(1), 244–281.'
mla: 'Dello Schiavo, Lorenzo, et al. “Polyharmonic Fields and Liouville Quantum
Gravity Measures on Tori of Arbitrary Dimension: From Discrete to Continuous.”
Mathematische Nachrichten, vol. 298, no. 1, Wiley, 2025, pp. 244–81, doi:10.1002/mana.202400169.'
short: L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Mathematische Nachrichten
298 (2025) 244–281.
date_created: 2024-12-08T23:01:56Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-04-14T07:27:49Z
day: '01'
ddc:
- '510'
department:
- _id: JaMa
doi: 10.1002/mana.202400169
ec_funded: 1
external_id:
arxiv:
- '2302.02963'
isi:
- '001366948500001'
file:
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checksum: 1dc50d156feb777c86d779fb1c9ac875
content_type: application/pdf
creator: dernst
date_created: 2025-01-13T10:34:42Z
date_updated: 2025-01-13T10:34:42Z
file_id: '18838'
file_name: 2025_MathNachrichten_DelloSchiavo.pdf
file_size: 1734511
relation: main_file
success: 1
file_date_updated: 2025-01-13T10:34:42Z
fulldoi: https://doi.org/10.1002/mana.202400169
has_accepted_license: '1'
intvolume: ' 298'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: 244-281
project:
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
- _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2
grant_number: F6504
name: Taming Complexity in Partial Differential Systems
- _id: 34dbf174-11ca-11ed-8bc3-afe9d43d4b9c
grant_number: E208
name: Configuration Spaces over Non-Smooth Spaces
publication: Mathematische Nachrichten
publication_identifier:
eissn:
- 1522-2616
issn:
- 0025-584X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary
dimension: From discrete to continuous'
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: 298
year: '2025'
...
---
OA_place: repository
OA_type: gold
_id: '18697'
abstract:
- lang: eng
text: The information-processing capability of the brain’s cellular network depends
on the physical wiring pattern between neurons and their molecular and functional
characteristics. Mapping neurons and resolving their individual synaptic connections
can be achieved by volumetric imaging at nanoscale resolution with dense cellular
labelling. Light microscopy is uniquely positioned to visualize specific molecules
but dense, synapse-level circuit reconstruction by light microscopy has been out
of reach due to limitations in resolution, contrast, and volumetric imaging capability.
Here we developed light-microscopy based connectomics (LICONN). We integrated
specifically engineered hydrogel embedding and expansion with comprehensive deep-learning
based segmentation and analysis of connectivity, thus directly incorporating molecular
information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level
brain tissue phenotyping in biological experiments in a readily adoptable manner.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
- _id: ScienComp
- _id: PreCl
- _id: M-Shop
- _id: E-Lib
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Julia
full_name: Lyudchik, Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
citation:
ama: Danzl JG, Lyudchik J, Kreuzinger C. Light-microscopy based connectomic reconstruction
of mammalian brain tissue. 2025. doi:10.15479/AT:ISTA:18697
apa: Danzl, J. G., Lyudchik, J., & Kreuzinger, C. (2025). Light-microscopy based
connectomic reconstruction of mammalian brain tissue. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:18697
chicago: Danzl, Johann G, Julia Lyudchik, and Caroline Kreuzinger. “Light-Microscopy
Based Connectomic Reconstruction of Mammalian Brain Tissue.” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18697.
ieee: J. G. Danzl, J. Lyudchik, and C. Kreuzinger, “Light-microscopy based connectomic
reconstruction of mammalian brain tissue.” Institute of Science and Technology
Austria, 2025.
ista: Danzl JG, Lyudchik J, Kreuzinger C. 2025. Light-microscopy based connectomic
reconstruction of mammalian brain tissue, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:18697.
mla: Danzl, Johann G., et al. Light-Microscopy Based Connectomic Reconstruction
of Mammalian Brain Tissue. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT:ISTA:18697.
short: J.G. Danzl, J. Lyudchik, C. Kreuzinger, (2025).
contributor:
- contributor_type: researcher
first_name: Mojtaba
id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87
last_name: Tavakoli
orcid: 0000-0002-7667-6854
- contributor_type: researcher
first_name: Julia
id: 46E28B80-F248-11E8-B48F-1D18A9856A87
last_name: Lyudchik
- contributor_type: researcher
first_name: Michal
last_name: Januszewski
- contributor_type: researcher
first_name: Vitali
id: 7e146587-8972-11ed-ae7b-d7a32ea86a81
last_name: Vistunou
- contributor_type: researcher
first_name: Nathalie
id: 40E7F008-F248-11E8-B48F-1D18A9856A87
last_name: Agudelo Duenas
- contributor_type: researcher
first_name: Jakob
id: 937696FA-C996-11E9-8C7C-CF13E6697425
last_name: Vorlaufer
- contributor_type: researcher
first_name: Christoph M
id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87
last_name: Sommer
orcid: 0000-0003-1216-9105
- contributor_type: researcher
first_name: Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
- contributor_type: researcher
first_name: Bárbara
id: 3B03AA1A-F248-11E8-B48F-1D18A9856A87
last_name: Oliveira
- contributor_type: researcher
first_name: Alban
last_name: Cenameri
- contributor_type: researcher
first_name: Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- contributor_type: researcher
first_name: Viren
last_name: Jain
- contributor_type: researcher
first_name: Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
corr_author: '1'
date_created: 2024-12-20T09:22:20Z
date_published: 2025-03-03T00:00:00Z
date_updated: 2026-04-28T13:33:34Z
day: '03'
ddc:
- '570'
department:
- _id: JoDa
doi: 10.15479/AT:ISTA:18697
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month: '03'
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title: Light-microscopy based connectomic reconstruction of mammalian brain tissue
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legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
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...
---
_id: '18712'
abstract:
- lang: eng
text: 'This file contains the code associated with the manuscript ''Effect of assortative
mating and sexual selection on polygenic barriers to gene flow''. '
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
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last_name: Sachdeva
citation:
ama: Surendranadh P, Sachdeva H. Mathematica notebook and Fortran code for “Effect
of assortative mating and sexual selection on polygenic barriers to gene flow.”
2025. doi:10.15479/AT:ISTA:17344
apa: Surendranadh, P., & Sachdeva, H. (2025). Mathematica notebook and Fortran
code for “Effect of assortative mating and sexual selection on polygenic barriers
to gene flow.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17344
chicago: Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook and
Fortran Code for ‘Effect of Assortative Mating and Sexual Selection on Polygenic
Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:17344.
ieee: P. Surendranadh and H. Sachdeva, “Mathematica notebook and Fortran code for
‘Effect of assortative mating and sexual selection on polygenic barriers to gene
flow.’” Institute of Science and Technology Austria, 2025.
ista: Surendranadh P, Sachdeva H. 2025. Mathematica notebook and Fortran code for
‘Effect of assortative mating and sexual selection on polygenic barriers to gene
flow’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17344.
mla: Surendranadh, Parvathy, and Himani Sachdeva. Mathematica Notebook and Fortran
Code for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers
to Gene Flow.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:17344.
short: P. Surendranadh, H. Sachdeva, (2025).
corr_author: '1'
date_created: 2025-01-01T15:28:27Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2025-12-30T08:44:12Z
day: '07'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT:ISTA:17344
file:
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checksum: 9c5f91876014706990a0728c3675cd2a
content_type: application/zip
creator: psurendr
date_created: 2025-01-02T12:30:27Z
date_updated: 2025-01-02T12:30:27Z
file_id: '18722'
file_name: Codes.zip
file_size: 326835
relation: main_file
success: 1
- access_level: open_access
checksum: 47fe98b7cc526e634e42de58f5eae288
content_type: text/plain
creator: psurendr
date_created: 2025-01-02T12:30:39Z
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file_size: 620
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fulldoi: https://doi.org/10.15479/AT:ISTA:17344
has_accepted_license: '1'
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19876'
relation: used_in_publication
status: public
status: public
title: Mathematica notebook and Fortran code for 'Effect of assortative mating and
sexual selection on polygenic barriers to gene flow'
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: research_data
user_id: 9947682f-b9fa-11ee-9c4a-b3ffaafe6614
year: '2025'
...
---
OA_type: closed access
_id: '18765'
abstract:
- lang: eng
text: Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach
coupling differential fluorescent labeling to genetic manipulations in dividing
cells and their lineages. MADM uniquely enables the generation and visualization
of individual control or homozygous mutant cells in a heterozygous genetic environment.
Among its diverse applications, MADM has been used to dissect cell-autonomous
gene functions important for cortical development and neural development in general.
The high cellular resolution offered by MADM also permits the analysis of transcriptomic
changes of individual cells upon genetic manipulations. In this chapter, we describe
an experimental protocol combining the generation and isolation of MADM-labeled
cells with downstream single-cell RNA-sequencing technologies to probe cell-type
specific phenotypes due to genetic mutations at single-cell resolution.
acknowledged_ssus:
- _id: Bio
acknowledgement: 'We thank all Hippenmeyer lab members for support and discussions.
Experimental steps described were optimized with support provided by the Imaging
& Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter
Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine
(CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship).
This work was supported by ISTA institutional funds: The Austrian Science Fund Special
Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.'
alternative_title:
- Methods in Molecular Biology
article_processing_charge: No
author:
- first_name: Giselle T
full_name: Cheung, Giselle T
id: 471195F6-F248-11E8-B48F-1D18A9856A87
last_name: Cheung
orcid: 0000-0001-8457-2572
- first_name: Florian
full_name: Pauler, Florian
id: 48EA0138-F248-11E8-B48F-1D18A9856A87
last_name: Pauler
orcid: 0000-0002-7462-0048
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
citation:
ama: 'Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant
Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).
In: Garcia-Marques J, Lee T, eds. Lineage Tracing. Vol 2886. MIMB. New
York, NY: Springer Nature; 2025:139-151. doi:10.1007/978-1-0716-4310-5_7'
apa: 'Cheung, G. T., Pauler, F., & Hippenmeyer, S. (2025). Probing Cell-Type
Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis
with Double Markers (MADM). In J. Garcia-Marques & T. Lee (Eds.), Lineage
Tracing (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-4310-5_7'
chicago: 'Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type
Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis
with Double Markers (MADM).” In Lineage Tracing, edited by Jorge Garcia-Marques
and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. https://doi.org/10.1007/978-1-0716-4310-5_7.'
ieee: 'G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity
of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double
Markers (MADM),” in Lineage Tracing, vol. 2886, J. Garcia-Marques and T.
Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.'
ista: 'Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of
Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers
(MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.'
mla: Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype
at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” Lineage
Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer
Nature, 2025, pp. 139–51, doi:10.1007/978-1-0716-4310-5_7.
short: G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.),
Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151.
corr_author: '1'
date_created: 2025-01-07T08:36:47Z
date_published: 2025-01-03T00:00:00Z
date_updated: 2025-04-14T07:43:46Z
day: '03'
department:
- _id: SiHi
doi: 10.1007/978-1-0716-4310-5_7
ec_funded: 1
editor:
- first_name: Jorge
full_name: Garcia-Marques, Jorge
last_name: Garcia-Marques
- first_name: Tzumin
full_name: Lee, Tzumin
last_name: Lee
external_id:
pmid:
- '39745639'
fulldoi: https://doi.org/10.1007/978-1-0716-4310-5_7
intvolume: ' 2886'
language:
- iso: eng
month: '01'
oa_version: None
page: 139-151
place: New York, NY
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Lineage Tracing
publication_identifier:
eisbn:
- '9781071643105'
eissn:
- 1940-6029
isbn:
- '9781071643099'
issn:
- 1064-3745
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: MIMB
status: public
title: Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using
Mosaic Analysis with Double Markers (MADM)
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2886
year: '2025'
...
---
APC_amount: 12348 EUR
OA_place: publisher
OA_type: hybrid
_id: '18778'
abstract:
- lang: eng
text: Transcription by RNA polymerase II (Pol II) can be repressed by noncoding
RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs
repress transcription remains unclear. Here we present cryogenic-electron microscopy
structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA
and RNA bind to Pol II during transcription elongation. Further, we show how distinct
domains of the general transcription factor TFIIF control repressive activity.
Together, we reveal how a noncoding RNA can regulate mammalian gene expression.
acknowledged_ssus:
- _id: LifeSc
- _id: EM-Fac
- _id: ScienComp
- _id: PreCl
acknowledgement: We thank the members of the Bernecky laboratory for helpful discussions
and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding
assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU
data collection. We thank D. Slade (Max Perutz Laboratories and Medical University
of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank
N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of
Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank
C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported
by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The
funders had no role in study design, data collection and analysis, decision to publish
or preparation of the manuscript. This research was further supported by the Scientific
Service Units of ISTA through resources provided by the Laboratory Support Facility,
Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Katarina
full_name: Tluckova, Katarina
id: 4AC7D980-F248-11E8-B48F-1D18A9856A87
last_name: Tluckova
- first_name: Beata M
full_name: Kaczmarek, Beata M
id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87
last_name: Kaczmarek
- first_name: Anita P
full_name: Testa Salmazo, Anita P
id: 41F1F098-F248-11E8-B48F-1D18A9856A87
last_name: Testa Salmazo
- first_name: Carrie A
full_name: Bernecky, Carrie A
id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87
last_name: Bernecky
orcid: 0000-0003-0893-7036
citation:
ama: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian
transcriptional repression by noncoding RNA. Nature Structural & Molecular
Biology. 2025;32:607-612. doi:10.1038/s41594-024-01448-7
apa: Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., & Bernecky, C. (2025).
Mechanism of mammalian transcriptional repression by noncoding RNA. Nature
Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01448-7
chicago: Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie
Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.”
Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01448-7.
ieee: K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism
of mammalian transcriptional repression by noncoding RNA,” Nature Structural
& Molecular Biology, vol. 32. Springer Nature, pp. 607–612, 2025.
ista: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of
mammalian transcriptional repression by noncoding RNA. Nature Structural &
Molecular Biology. 32, 607–612.
mla: Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression
by Noncoding RNA.” Nature Structural & Molecular Biology, vol. 32,
Springer Nature, 2025, pp. 607–12, doi:10.1038/s41594-024-01448-7.
short: K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural
& Molecular Biology 32 (2025) 607–612.
corr_author: '1'
date_created: 2025-01-08T11:20:20Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-11-20T10:28:36Z
day: '01'
ddc:
- '570'
department:
- _id: CaBe
doi: 10.1038/s41594-024-01448-7
external_id:
isi:
- '001390268000001'
pmid:
- '39762629'
file:
- access_level: open_access
checksum: 2919b30b271f395888e880076a680d73
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T08:17:27Z
date_updated: 2025-04-16T08:17:27Z
file_id: '19573'
file_name: 2025_NatureStrucMolBiol_Tluckova.pdf
file_size: 9306639
relation: main_file
success: 1
file_date_updated: 2025-04-16T08:17:27Z
fulldoi: https://doi.org/10.1038/s41594-024-01448-7
has_accepted_license: '1'
intvolume: ' 32'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 607-612
pmid: 1
project:
- _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30
grant_number: P34185
name: Regulation of mammalian transcription by noncoding RNA
publication: Nature Structural & Molecular Biology
publication_identifier:
eissn:
- 1545-9985
issn:
- 1545-9993
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '14644'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Mechanism of mammalian transcriptional repression by noncoding RNA
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: 32
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '18821'
abstract:
- lang: eng
text: 'Even though the one-dimensional contact interaction requires no regularization,
renormalization methods have been shown to improve the convergence of numerical
calculations considerably. In this work, we compare and contrast these methods:
“the running coupling constant” where the two-body ground-state energy is used
as a renormalization condition, and two effective interaction approaches that
include information about the ground as well as excited states. In particular,
we calculate the energies and densities of few-fermion systems in a harmonic oscillator
with the configuration-interaction method and compare the results based upon renormalized
and bare interactions. We find that the use of the running coupling constant instead
of the bare interaction improves convergence significantly. A comparison with
an effective interaction, which is designed to reproduce the relative part of
the energy spectrum of two particles, showed a similar improvement. The effective
interaction provides an additional improvement if the center-of-mass excitations
are included in the construction. Finally, we discuss the transformation of observables
alongside the renormalization of the potential, and demonstrate that this might
be an essential ingredient for accurate numerical calculations.'
acknowledgement: We thank J. Cremon and J. Bjerlin for earlier contributions to the
configuration-interaction calculations used in this work (see Refs. [49,50]). F.B.
and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter,
and Lila Chergui. We further want to thank Lila Chergui for helpful comments on
the paper. This research was financially supported by the Knut and Alice Wallenberg
Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No.
2022-03654 VR).
article_number: '013303'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Fabian
full_name: Brauneis, Fabian
last_name: Brauneis
- first_name: Hans Werner
full_name: Hammer, Hans Werner
last_name: Hammer
- first_name: Stephanie M.
full_name: Reimann, Stephanie M.
last_name: Reimann
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized
interactions using one-dimensional few-body systems as a testbed. Physical
Review A. 2025;111(1). doi:10.1103/PhysRevA.111.013303
apa: Brauneis, F., Hammer, H. W., Reimann, S. M., & Volosniev, A. (2025). Comparison
of renormalized interactions using one-dimensional few-body systems as a testbed.
Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.111.013303
chicago: Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev.
“Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems
as a Testbed.” Physical Review A. American Physical Society, 2025. https://doi.org/10.1103/PhysRevA.111.013303.
ieee: F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of
renormalized interactions using one-dimensional few-body systems as a testbed,”
Physical Review A, vol. 111, no. 1. American Physical Society, 2025.
ista: Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized
interactions using one-dimensional few-body systems as a testbed. Physical Review
A. 111(1), 013303.
mla: Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional
Few-Body Systems as a Testbed.” Physical Review A, vol. 111, no. 1, 013303,
American Physical Society, 2025, doi:10.1103/PhysRevA.111.013303.
short: F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111
(2025).
date_created: 2025-01-12T23:04:00Z
date_published: 2025-01-03T00:00:00Z
date_updated: 2025-02-27T12:41:58Z
day: '03'
department:
- _id: MiLe
doi: 10.1103/PhysRevA.111.013303
external_id:
arxiv:
- '2408.10052'
isi:
- '001398791400004'
fulldoi: https://doi.org/10.1103/PhysRevA.111.013303
intvolume: ' 111'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2408.10052'
month: '01'
oa: 1
oa_version: Preprint
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Comparison of renormalized interactions using one-dimensional few-body systems
as a testbed
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 111
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18823'
article_number: kiae651
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Dechang
full_name: Cao, Dechang
last_name: Cao
- first_name: Joke G
full_name: De Jaeger-Braet, Joke G
id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5
last_name: De Jaeger-Braet
citation:
ama: 'Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation
alterations across generations. Plant Physiology. 2025;197(1). doi:10.1093/plphys/kiae651'
apa: 'Cao, D., & De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures:
DNA methylation alterations across generations. Plant Physiology. Oxford
University Press. https://doi.org/10.1093/plphys/kiae651'
chicago: 'Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures:
DNA Methylation Alterations across Generations.” Plant Physiology. Oxford
University Press, 2025. https://doi.org/10.1093/plphys/kiae651.'
ieee: 'D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation
alterations across generations,” Plant Physiology, vol. 197, no. 1. Oxford
University Press, 2025.'
ista: 'Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation
alterations across generations. Plant Physiology. 197(1), kiae651.'
mla: 'Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures:
DNA Methylation Alterations across Generations.” Plant Physiology, vol.
197, no. 1, kiae651, Oxford University Press, 2025, doi:10.1093/plphys/kiae651.'
short: D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).
corr_author: '1'
date_created: 2025-01-12T23:04:02Z
date_published: 2025-01-01T00:00:00Z
date_updated: 2025-07-15T08:18:19Z
day: '01'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1093/plphys/kiae651
external_id:
isi:
- '001382979900001'
pmid:
- '39691053'
file:
- access_level: open_access
checksum: a9b2a12d7bc6174f27e28413e9c77a9c
content_type: application/pdf
creator: dernst
date_created: 2025-07-15T08:17:25Z
date_updated: 2025-07-15T08:17:25Z
file_id: '20023'
file_name: 2025_PlantPhysiology_Cao.pdf
file_size: 1214018
relation: main_file
success: 1
file_date_updated: 2025-07-15T08:17:25Z
fulldoi: https://doi.org/10.1093/plphys/kiae651
has_accepted_license: '1'
intvolume: ' 197'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Memory of maternal temperatures: DNA methylation alterations across generations'
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: 197
year: '2025'
...
---
_id: '18837'
abstract:
- lang: eng
text: Super-resolution methods provide far better spatial resolution than the optical
diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless,
they have yet to attain widespread use in plants, largely due to plants’ challenging
optical properties. Expansion microscopy improves effective resolution by isotropically
increasing the physical distances between sample structures while preserving relative
spatial arrangements and clearing the sample. However, its application to plants
has been hindered by the rigid, mechanically cohesive structure of plant tissues.
Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis
thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over
conventional microscopy. Our results highlight the microtubule cytoskeleton organization
and interaction between molecularly defined cellular constituents. Combining PlantEx
with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution
and visualize the complex organization of subcellular organelles from intact tissues
by example of the densely packed COPI-coated vesicles associated with the Golgi
apparatus and put these into a cellular structural context. Our results show that
expansion microscopy can be applied to increase effective imaging resolution in
Arabidopsis root specimens.
article_processing_charge: No
author:
- first_name: Johann G
full_name: Danzl, Johann G
id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87
last_name: Danzl
orcid: 0000-0001-8559-3973
- first_name: Caroline
full_name: Kreuzinger, Caroline
id: 382077BA-F248-11E8-B48F-1D18A9856A87
last_name: Kreuzinger
citation:
ama: Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution
expansion microscopy in plant roots.” 2025. doi:10.15479/AT:ISTA:18837
apa: Danzl, J. G., & Kreuzinger, C. (2025). Research Data for the publication
“Super-resolution expansion microscopy in plant roots.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:18837
chicago: Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication
‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18837.
ieee: J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution
expansion microscopy in plant roots.’” Institute of Science and Technology Austria,
2025.
ista: Danzl JG, Kreuzinger C. 2025. Research Data for the publication ‘Super-resolution
expansion microscopy in plant roots’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:18837.
mla: Danzl, Johann G., and Caroline Kreuzinger. Research Data for the Publication
“Super-Resolution Expansion Microscopy in Plant Roots.” Institute of Science
and Technology Austria, 2025, doi:10.15479/AT:ISTA:18837.
short: J.G. Danzl, C. Kreuzinger, (2025).
contributor:
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first_name: Michelle C
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status: public
status: public
title: Research Data for the publication "Super-resolution expansion microscopy in
plant roots"
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name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data
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year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '18848'
abstract:
- lang: eng
text: Type II CRISPR endonucleases are widely used programmable genome editing tools.
Recently, CRISPR-Cas systems with highly compact nucleases have been discovered,
including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures
of a Cas9d nuclease (747 amino acids in length) in multiple functional states,
revealing a stepwise process of DNA targeting involving a conformational switch
in a REC2 domain insertion. Our structures provide insights into the intricately
folded guide RNA which acts as a structural scaffold to anchor small, flexible
protein domains for DNA recognition. The sgRNA can be truncated by up to ~25%
yet still retain activity in vivo. Using ancestral sequence reconstruction, we
generated compact nucleases capable of efficient genome editing in mammalian cells.
Collectively, our results provide mechanistic insights into the evolution and
DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for
future re-engineering of minimal RNA-guided DNA endonucleases.
acknowledgement: We would like to thank M. Ocampo Camacho and M.F. Canedo Ocampo for
assistance with the figures. We thank M. Hooper for assistance developing the GFP
assay and operating the CE machine for in vitro cleavage analysis. We thank E. Schwartz
and A. Brilot for expert cryo-EM support in the Sauer Structural Biology Laboratory
at UT Austin. This work was funded, in part, by a sponsored research agreement with
Metagenomi, Inc. (to D.W.T), a Welch Foundation Research Grant F-1938 (to D.W.T),
and the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research
Grant (to D.W.T), and a grant from the National Institute of Allergy and Infectious
Diseases (NIAID 1R01AI110577 to K.A.J.).
article_number: '457'
article_processing_charge: Yes
article_type: original
author:
- first_name: Rodrigo Fregoso
full_name: Ocampo, Rodrigo Fregoso
last_name: Ocampo
- first_name: Jack Peter Kelly
full_name: Bravo, Jack Peter Kelly
id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e
last_name: Bravo
orcid: 0000-0003-0456-0753
- first_name: Tyler L.
full_name: Dangerfield, Tyler L.
last_name: Dangerfield
- first_name: Isabel
full_name: Nocedal, Isabel
last_name: Nocedal
- first_name: Samatar A.
full_name: Jirde, Samatar A.
last_name: Jirde
- first_name: Lisa M.
full_name: Alexander, Lisa M.
last_name: Alexander
- first_name: Nicole C.
full_name: Thomas, Nicole C.
last_name: Thomas
- first_name: Anjali
full_name: Das, Anjali
last_name: Das
- first_name: Sarah
full_name: Nielson, Sarah
last_name: Nielson
- first_name: Kenneth A.
full_name: Johnson, Kenneth A.
last_name: Johnson
- first_name: Christopher T.
full_name: Brown, Christopher T.
last_name: Brown
- first_name: Cristina N.
full_name: Butterfield, Cristina N.
last_name: Butterfield
- first_name: Daniela S.A.
full_name: Goltsman, Daniela S.A.
last_name: Goltsman
- first_name: David W.
full_name: Taylor, David W.
last_name: Taylor
citation:
ama: Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d
and its resurrected ancestor. Nature Communications. 2025;16. doi:10.1038/s41467-024-55573-4
apa: Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S.
A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and
its resurrected ancestor. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-55573-4
chicago: Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield,
Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al.
“DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” Nature Communications.
Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55573-4.
ieee: R. F. Ocampo et al., “DNA targeting by compact Cas9d and its resurrected
ancestor,” Nature Communications, vol. 16. Springer Nature, 2025.
ista: Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas
NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor
DW. 2025. DNA targeting by compact Cas9d and its resurrected ancestor. Nature
Communications. 16, 457.
mla: Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected
Ancestor.” Nature Communications, vol. 16, 457, Springer Nature, 2025,
doi:10.1038/s41467-024-55573-4.
short: R.F. Ocampo, J.P.K. Bravo, T.L. Dangerfield, I. Nocedal, S.A. Jirde, L.M.
Alexander, N.C. Thomas, A. Das, S. Nielson, K.A. Johnson, C.T. Brown, C.N. Butterfield,
D.S.A. Goltsman, D.W. Taylor, Nature Communications 16 (2025).
date_created: 2025-01-19T23:01:50Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2025-07-03T11:58:22Z
day: '07'
ddc:
- '570'
department:
- _id: JaBr
doi: 10.1038/s41467-024-55573-4
external_id:
pmid:
- '39774105'
file:
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checksum: 885e96690620790d5c9f188a1587b4cd
content_type: application/pdf
creator: dernst
date_created: 2025-01-22T14:35:22Z
date_updated: 2025-01-22T14:35:22Z
file_id: '18869'
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intvolume: ' 16'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA targeting by compact Cas9d and its resurrected ancestor
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: 16
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18849'
abstract:
- lang: eng
text: Many biological systems operate near the physical limits to their performance,
suggesting that aspects of their behavior and underlying mechanisms could be derived
from optimization principles. However, such principles have often been applied
only in simplified models. Here, we explore a detailed mechanistic model of the
gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize
the information that gene expression levels provide about nuclear positions. This
optimization is conducted under realistic constraints, such as limits on the number
of available molecules. Remarkably, the optimal networks we derive closely match
the architecture and spatial gene expression profiles observed in the real organism.
Our framework quantifies the tradeoffs involved in maximizing functional performance
and allows for the exploration of alternative network configurations, addressing
the question of which features are necessary and which are contingent. Our results
suggest that multiple solutions to the optimization problem might exist across
closely related organisms, offering insights into the evolution of gene regulatory
networks.
acknowledgement: We thank Nicholas H. Barton for his comments on the manuscript, Benjamin
Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early
collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many
persistently inspiring conversations. This work was supported in part by the Human
Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European
Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for
the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730,
and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE
priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored
by the Hessian Ministry for Science and Research, Arts and Culture (HMWK).
article_number: e2402925121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Thomas
full_name: Gregor, Thomas
last_name: Gregor
- first_name: William
full_name: Bialek, William
last_name: Bialek
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory
network from an optimization principle. Proceedings of the National Academy
of Sciences. 2025;122(1). doi:10.1073/pnas.2402925121
apa: Sokolowski, T. R., Gregor, T., Bialek, W., & Tkačik, G. (2025). Deriving
a genetic regulatory network from an optimization principle. Proceedings of
the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2402925121
chicago: Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik.
“Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2402925121.
ieee: T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic
regulatory network from an optimization principle,” Proceedings of the National
Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025.
ista: Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory
network from an optimization principle. Proceedings of the National Academy of
Sciences. 122(1), e2402925121.
mla: Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an
Optimization Principle.” Proceedings of the National Academy of Sciences,
vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:10.1073/pnas.2402925121.
short: T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National
Academy of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:50Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-02-16T12:26:51Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2402925121
external_id:
isi:
- '001392772400001'
pmid:
- '39752518'
file:
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checksum: 8dbfc7d495413340225ebfae69b0cf9a
content_type: application/pdf
creator: dernst
date_created: 2025-01-20T10:10:04Z
date_updated: 2025-01-20T10:10:04Z
file_id: '18862'
file_name: 2025_PNAS_Sokolowski.pdf
file_size: 19073585
relation: main_file
success: 1
file_date_updated: 2025-01-20T10:10:04Z
fulldoi: https://doi.org/10.1073/pnas.2402925121
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
- _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9
grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
- _id: 2665AAFE-B435-11E9-9278-68D0E5697425
grant_number: RGP0034/2018
name: Can evolution minimize spurious signaling crosstalk to reach optimal performance?
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deriving a genetic regulatory network from an optimization principle
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: 122
year: '2025'
...
---
APC_amount: 3261,23 EUR
OA_place: publisher
OA_type: hybrid
_id: '18850'
abstract:
- lang: eng
text: 'Biophysical constraints limit the specificity with which transcription factors
(TFs) can target regulatory DNA. While individual nontarget binding events may
be low affinity, the sheer number of such interactions could present a challenge
for gene regulation by degrading its precision or possibly leading to an erroneous
induction state. Chromatin can prevent nontarget binding by rendering DNA physically
inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by
pioneer factors (PFs). Under what conditions and by how much can chromatin reduce
regulatory errors on a global scale? We use a theoretical approach to compare
two scenarios for gene regulation: one that relies on TF binding to free DNA alone
and one that uses a combination of TFs and chromatin-regulating PFs to achieve
desired gene expression patterns. We find, first, that chromatin effectively silences
groups of genes that should be simultaneously OFF, thereby allowing more accurate
graded control of expression for the remaining ON genes. Second, chromatin buffers
the deleterious consequences of nontarget binding as the number of OFF genes grows,
permitting a substantial expansion in regulatory complexity. Third, chromatin-based
regulation productively co-opts nontarget TF binding for ON genes in order to
establish a “leaky” baseline expression level, which targeted activator or repressor
binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin
simultaneously alleviates pressure for high specificity of regulatory interactions
and enables an increase in genome size with minimal impact on global expression
error.'
acknowledgement: M.L.P. was supported by the European Molecular Biology Laboratory
(EMBL) Interdisciplinary Postdoc Programme (EIPOD4 fellowships), cofunded by Marie
Skłodowska-Curie Actions (Grant Agreement No. 847543). J.C. and M.L.P. were supported
by EMBL Core Funding and Theory@EMBL. This work is supported by European Research
Council Grant DynaTrans (101118866) to G.T. We would like to thank the members of
the J.C. and G.T. groups, especially Natalia Misunou, Michal Hledík, and Réka Borbély,
for helpful feedback and discussion. We also thank EMBL IT Services for the use
of high performance computing resources.
article_number: e2411887121
article_processing_charge: No
article_type: original
author:
- first_name: Mindy Liu
full_name: Perkins, Mindy Liu
last_name: Perkins
- first_name: Justin
full_name: Crocker, Justin
last_name: Crocker
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene
regulation with factors of limited specificity. Proceedings of the National
Academy of Sciences. 2025;122(1). doi:10.1073/pnas.2411887121
apa: Perkins, M. L., Crocker, J., & Tkačik, G. (2025). Chromatin enables precise
and scalable gene regulation with factors of limited specificity. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2411887121
chicago: Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables
Precise and Scalable Gene Regulation with Factors of Limited Specificity.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2411887121.
ieee: M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable
gene regulation with factors of limited specificity,” Proceedings of the National
Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025.
ista: Perkins ML, Crocker J, Tkačik G. 2025. Chromatin enables precise and scalable
gene regulation with factors of limited specificity. Proceedings of the National
Academy of Sciences. 122(1), e2411887121.
mla: Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation
with Factors of Limited Specificity.” Proceedings of the National Academy of
Sciences, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025,
doi:10.1073/pnas.2411887121.
short: M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy
of Sciences 122 (2025).
corr_author: '1'
date_created: 2025-01-19T23:01:51Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2026-05-06T12:43:59Z
day: '07'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1073/pnas.2411887121
external_id:
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pmid:
- '39793086'
file:
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checksum: 86a8d25a6e282aeb4128f1d0b86ff911
content_type: application/pdf
creator: dernst
date_created: 2025-01-20T09:38:32Z
date_updated: 2025-01-20T09:38:32Z
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file_date_updated: 2025-01-20T09:38:32Z
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has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9
grant_number: '101118866'
name: 'Transcription in 4D: the dynamic interplay between chromatin architecture
and gene expression in developing pseudo-embryos'
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/officerredshirt/network_crosstalk
scopus_import: '1'
status: public
title: Chromatin enables precise and scalable gene regulation with factors of limited
specificity
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: 122
year: '2025'
...