---
_id: '6621'
abstract:
- lang: eng
text: We read with great interest the recent work in PNAS by Bergero et al. (1)
describing differences in male and female recombination patterns on the guppy
(Poecilia reticulata) sex chromosome. We fully agree that recombination in males
is largely confined to the ends of the sex chromosome. Bergero et al. interpret
these results to suggest that our previous findings of population-level variation
in the degree of sex chromosome differentiation in this species (2) are incorrect.
However, we suggest that their results are entirely consistent with our previous
report, and that their interpretation presents a false controversy.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Alison E.
full_name: Wright, Alison E.
last_name: Wright
- first_name: Iulia
full_name: Darolti, Iulia
last_name: Darolti
- first_name: Natasha I.
full_name: Bloch, Natasha I.
last_name: Bloch
- first_name: Vicencio
full_name: Oostra, Vicencio
last_name: Oostra
- first_name: Benjamin A.
full_name: Sandkam, Benjamin A.
last_name: Sandkam
- first_name: Séverine D.
full_name: Buechel, Séverine D.
last_name: Buechel
- first_name: Niclas
full_name: Kolm, Niclas
last_name: Kolm
- first_name: Felix
full_name: Breden, Felix
last_name: Breden
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Judith E.
full_name: Mank, Judith E.
last_name: Mank
citation:
ama: Wright AE, Darolti I, Bloch NI, et al. On the power to detect rare recombination
events. Proceedings of the National Academy of Sciences of the United States
of America. 2019;116(26):12607-12608. doi:10.1073/pnas.1905555116
apa: Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel,
S. D., … Mank, J. E. (2019). On the power to detect rare recombination events.
Proceedings of the National Academy of Sciences of the United States of America.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1905555116
chicago: Wright, Alison E., Iulia Darolti, Natasha I. Bloch, Vicencio Oostra, Benjamin
A. Sandkam, Séverine D. Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and
Judith E. Mank. “On the Power to Detect Rare Recombination Events.” Proceedings
of the National Academy of Sciences of the United States of America. Proceedings
of the National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1905555116.
ieee: A. E. Wright et al., “On the power to detect rare recombination events,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 116, no. 26. Proceedings of the National Academy of Sciences, pp. 12607–12608,
2019.
ista: Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N,
Breden F, Vicoso B, Mank JE. 2019. On the power to detect rare recombination events.
Proceedings of the National Academy of Sciences of the United States of America.
116(26), 12607–12608.
mla: Wright, Alison E., et al. “On the Power to Detect Rare Recombination Events.”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 116, no. 26, Proceedings of the National Academy of Sciences, 2019, pp. 12607–08,
doi:10.1073/pnas.1905555116.
short: A.E. Wright, I. Darolti, N.I. Bloch, V. Oostra, B.A. Sandkam, S.D. Buechel,
N. Kolm, F. Breden, B. Vicoso, J.E. Mank, Proceedings of the National Academy
of Sciences of the United States of America 116 (2019) 12607–12608.
date_created: 2019-07-07T21:59:25Z
date_published: 2019-06-25T00:00:00Z
date_updated: 2023-10-17T12:44:15Z
day: '25'
department:
- _id: BeVi
doi: 10.1073/pnas.1905555116
external_id:
isi:
- '000472719100010'
pmid:
- '31213531'
intvolume: ' 116'
isi: 1
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1905555116
month: '06'
oa: 1
oa_version: Published Version
page: 12607-12608
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the power to detect rare recombination events
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 116
year: '2019'
...
---
_id: '6856'
abstract:
- lang: eng
text: 'Plant mating systems play a key role in structuring genetic variation both
within and between species. In hybrid zones, the outcomes and dynamics of hybridization
are usually interpreted as the balance between gene flow and selection against
hybrids. Yet, mating systems can introduce selective forces that alter these expectations;
with diverse outcomes for the level and direction of gene flow depending on variation
in outcrossing and whether the mating systems of the species pair are the same
or divergent. We present a survey of hybridization in 133 species pairs from 41
plant families and examine how patterns of hybridization vary with mating system.
We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and
the frequency of reproductive isolating barriers vary in relation to mating system/s
of the species pair. We combine these results with a simulation model and examples
from the literature to address two general themes: (i) the two‐way interaction
between introgression and the evolution of reproductive systems, and (ii) how
mating system can facilitate or restrict interspecific gene flow. We conclude
that examining mating system with hybridization provides unique opportunities
to understand divergence and the processes underlying reproductive isolation.'
article_processing_charge: No
article_type: original
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Yaniv
full_name: Brandvain, Yaniv
last_name: Brandvain
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Sarah
full_name: Yakimowski, Sarah
last_name: Yakimowski
- first_name: Tanmay
full_name: Dixit, Tanmay
last_name: Dixit
- first_name: Christian
full_name: Lexer, Christian
last_name: Lexer
- first_name: Eva
full_name: Cereghetti, Eva
id: 71AA91B4-05ED-11EA-8BEB-F5833E63BD63
last_name: Cereghetti
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: 'Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid
zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist.
2019;224(3):1035-1047. doi:10.1111/nph.16180'
apa: 'Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit,
T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180'
chicago: 'Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse,
Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field.
“Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries
to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.'
ieee: 'M. Pickup et al., “Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no.
3. Wiley, pp. 1035–1047, 2019.'
ista: 'Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer
C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.'
mla: 'Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation,
Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no.
3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.'
short: M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit,
C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.
date_created: 2019-09-07T14:35:40Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-10-18T08:47:08Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/nph.16180
ec_funded: 1
external_id:
pmid:
- '31505037'
file:
- access_level: open_access
checksum: 21e4c95599bbcaf7c483b89954658672
content_type: application/pdf
creator: dernst
date_created: 2019-11-13T08:15:05Z
date_updated: 2020-07-14T12:47:42Z
file_id: '7011'
file_name: 2019_NewPhytologist_Pickup.pdf
file_size: 1511958
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 224'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
oa: 1
oa_version: Published Version
page: 1035-1047
pmid: 1
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Mating system variation in hybrid zones: Facilitation, barriers and asymmetries
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: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 224
year: '2019'
...
---
_id: '6647'
abstract:
- lang: eng
text: The Tverberg theorem is one of the cornerstones of discrete geometry. It states
that, given a set X of at least (d+1)(r-1)+1 points in R^d, one can find a partition
X=X_1 cup ... cup X_r of X, such that the convex hulls of the X_i, i=1,...,r,
all share a common point. In this paper, we prove a strengthening of this theorem
that guarantees a partition which, in addition to the above, has the property
that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections.
Possible generalizations and algorithmic aspects are also discussed. As a concrete
application, we show that any n points in the plane in general position span floor[n/3]
vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries
have pairwise nonempty intersections; this number is clearly best possible. A
previous result of Alvarez-Rebollar et al. guarantees floor[n/6] pairwise crossing
triangles. Our result generalizes to a result about simplices in R^d,d >=2.
alternative_title:
- LIPIcs
author:
- first_name: Radoslav
full_name: Fulek, Radoslav
id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87
last_name: Fulek
orcid: 0000-0001-8485-1774
- first_name: Bernd
full_name: Gärtner, Bernd
last_name: Gärtner
- first_name: Andrey
full_name: Kupavskii, Andrey
last_name: Kupavskii
- first_name: Pavel
full_name: Valtr, Pavel
last_name: Valtr
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
citation:
ama: 'Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg
theorem. In: 35th International Symposium on Computational Geometry. Vol
129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019:38:1-38:13. doi:10.4230/LIPICS.SOCG.2019.38'
apa: 'Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2019).
The crossing Tverberg theorem. In 35th International Symposium on Computational
Geometry (Vol. 129, p. 38:1-38:13). Portland, OR, United States: Schloss Dagstuhl
- Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.38'
chicago: Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli
Wagner. “The Crossing Tverberg Theorem.” In 35th International Symposium on
Computational Geometry, 129:38:1-38:13. Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.38.
ieee: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing
Tverberg theorem,” in 35th International Symposium on Computational Geometry,
Portland, OR, United States, 2019, vol. 129, p. 38:1-38:13.
ista: 'Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2019. The crossing Tverberg
theorem. 35th International Symposium on Computational Geometry. SoCG 2019: Symposium
on Computational Geometry, LIPIcs, vol. 129, 38:1-38:13.'
mla: Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” 35th International
Symposium on Computational Geometry, vol. 129, Schloss Dagstuhl - Leibniz-Zentrum
für Informatik, 2019, p. 38:1-38:13, doi:10.4230/LIPICS.SOCG.2019.38.
short: R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, in:, 35th International
Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik,
2019, p. 38:1-38:13.
conference:
end_date: 2019-06-21
location: Portland, OR, United States
name: 'SoCG 2019: Symposium on Computational Geometry'
start_date: 2019-06-18
date_created: 2019-07-17T10:35:04Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-12-13T12:03:35Z
day: '01'
ddc:
- '000'
- '510'
department:
- _id: UlWa
doi: 10.4230/LIPICS.SOCG.2019.38
external_id:
arxiv:
- '1812.04911'
file:
- access_level: open_access
checksum: d6d017f8b41291b94d102294fa96ae9c
content_type: application/pdf
creator: dernst
date_created: 2019-07-24T06:54:52Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6667'
file_name: 2019_LIPICS_Fulek.pdf
file_size: 559837
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 129'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 38:1-38:13
project:
- _id: 261FA626-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02281
name: Eliminating intersections in drawings of graphs
publication: 35th International Symposium on Computational Geometry
publication_identifier:
isbn:
- '9783959771047'
issn:
- 1868-8969
publication_status: published
publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik
quality_controlled: '1'
related_material:
record:
- id: '13974'
relation: later_version
status: public
scopus_import: 1
status: public
title: The crossing Tverberg theorem
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2019'
...
---
_id: '6676'
abstract:
- lang: eng
text: "It is impossible to deterministically solve wait-free consensus in an asynchronous
system. The classic proof uses a valency argument, which constructs an infinite
execution by repeatedly extending a finite execution. We introduce extension-based
proofs, a class of impossibility proofs that are modelled as an interaction between
a prover and a protocol and that include valency arguments.\r\n\r\nUsing proofs
based on combinatorial topology, it has been shown that it is impossible to deterministically
solve k-set agreement among n > k ≥ 2 processes in a wait-free manner. However,
it was unknown whether proofs based on simpler techniques were possible. We show
that this impossibility result cannot be obtained by an extension-based proof
and, hence, extension-based proofs are limited in power."
article_processing_charge: No
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: James
full_name: Aspnes, James
last_name: Aspnes
- first_name: Faith
full_name: Ellen, Faith
last_name: Ellen
- first_name: Rati
full_name: Gelashvili, Rati
last_name: Gelashvili
- first_name: Leqi
full_name: Zhu, Leqi
last_name: Zhu
citation:
ama: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based
proofs fail. In: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
of Computing. ACM Press; 2019:986-996. doi:10.1145/3313276.3316407'
apa: 'Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2019).
Why extension-based proofs fail. In Proceedings of the 51st Annual ACM SIGACT
Symposium on Theory of Computing (pp. 986–996). Phoenix, AZ, United States:
ACM Press. https://doi.org/10.1145/3313276.3316407'
chicago: Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi
Zhu. “Why Extension-Based Proofs Fail.” In Proceedings of the 51st Annual ACM
SIGACT Symposium on Theory of Computing, 986–96. ACM Press, 2019. https://doi.org/10.1145/3313276.3316407.
ieee: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based
proofs fail,” in Proceedings of the 51st Annual ACM SIGACT Symposium on Theory
of Computing, Phoenix, AZ, United States, 2019, pp. 986–996.
ista: 'Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2019. Why extension-based
proofs fail. Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of
Computing. STOC: Symposium on Theory of Computing, 986–996.'
mla: Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” Proceedings
of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press,
2019, pp. 986–96, doi:10.1145/3313276.3316407.
short: D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, in:, Proceedings
of the 51st Annual ACM SIGACT Symposium on Theory of Computing, ACM Press, 2019,
pp. 986–996.
conference:
end_date: 2019-06-26
location: Phoenix, AZ, United States
name: 'STOC: Symposium on Theory of Computing'
start_date: 2019-06-23
date_created: 2019-07-24T09:13:05Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2023-12-13T12:28:28Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3313276.3316407
external_id:
arxiv:
- '1811.01421'
isi:
- '000523199100089'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1811.01421
month: '06'
oa: 1
oa_version: Preprint
page: 986-996
publication: Proceedings of the 51st Annual ACM SIGACT Symposium on Theory of Computing
publication_identifier:
isbn:
- '9781450367059'
publication_status: published
publisher: ACM Press
quality_controlled: '1'
related_material:
record:
- id: '14364'
relation: later_version
status: public
scopus_import: '1'
status: public
title: Why extension-based proofs fail
type: conference
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
year: '2019'
...
---
_id: '7950'
abstract:
- lang: eng
text: "The input to the token swapping problem is a graph with vertices v1, v2,
. . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The
goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number
of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token
swapping on a tree, also known as “sorting with a transposition tree,” is not
known to be in P nor NP-complete. We present some partial results:\r\n1. An
optimum swap sequence may need to perform a swap on a leaf vertex that has the
correct token (a “happy leaf”), disproving a conjecture of Vaughan.\r\n2. Any
algorithm that fixes happy leaves—as all known approximation algorithms for the
problem do—has approximation factor at least 4/3. Furthermore, the two best-known
2-approximation algorithms have approximation factor exactly 2.\r\n3. A generalized
problem—weighted coloured token swapping—is NP-complete on trees, but solvable
in polynomial time on paths and stars. In this version, tokens and vertices
\ have colours, and colours have weights. The goal is to get every
token to a vertex of the same colour, and the cost of a swap is the sum of the
weights of the two tokens involved."
article_number: '1903.06981'
article_processing_charge: No
author:
- first_name: Ahmad
full_name: Biniaz, Ahmad
last_name: Biniaz
- first_name: Kshitij
full_name: Jain, Kshitij
last_name: Jain
- first_name: Anna
full_name: Lubiw, Anna
last_name: Lubiw
- first_name: Zuzana
full_name: Masárová, Zuzana
id: 45CFE238-F248-11E8-B48F-1D18A9856A87
last_name: Masárová
orcid: 0000-0002-6660-1322
- first_name: Tillmann
full_name: Miltzow, Tillmann
last_name: Miltzow
- first_name: Debajyoti
full_name: Mondal, Debajyoti
last_name: Mondal
- first_name: Anurag Murty
full_name: Naredla, Anurag Murty
last_name: Naredla
- first_name: Josef
full_name: Tkadlec, Josef
id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87
last_name: Tkadlec
orcid: 0000-0002-1097-9684
- first_name: Alexi
full_name: Turcotte, Alexi
last_name: Turcotte
citation:
ama: Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. arXiv.
apa: Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte,
A. (n.d.). Token swapping on trees. arXiv.
chicago: Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow,
Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token
Swapping on Trees.” ArXiv, n.d.
ieee: A. Biniaz et al., “Token swapping on trees,” arXiv. .
ista: Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec
J, Turcotte A. Token swapping on trees. arXiv, 1903.06981.
mla: Biniaz, Ahmad, et al. “Token Swapping on Trees.” ArXiv, 1903.06981.
short: A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla,
J. Tkadlec, A. Turcotte, ArXiv (n.d.).
date_created: 2020-06-08T12:25:25Z
date_published: 2019-03-16T00:00:00Z
date_updated: 2024-01-04T12:42:08Z
day: '16'
department:
- _id: HeEd
- _id: UlWa
- _id: KrCh
external_id:
arxiv:
- '1903.06981'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1903.06981
month: '03'
oa: 1
oa_version: Preprint
publication: arXiv
publication_status: submitted
related_material:
record:
- id: '7944'
relation: dissertation_contains
status: public
- id: '12833'
relation: later_version
status: public
status: public
title: Token swapping on trees
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6418'
abstract:
- lang: eng
text: Males and females of Artemia franciscana, a crustacean commonly used in the
aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes,
but the nature and extent of differentiation of these chromosomes is unknown.
Here, we characterize the Z chromosome by detecting genomic regions that show
lower genomic coverage in female than in male samples, and regions that harbor
an excess of female-specific SNPs. We detect many Z-specific genes, which no longer
have homologs on the W, but also Z-linked genes that appear to have diverged very
recently from their existing W-linked homolog. We assess patterns of male and
female expression in two tissues with extensive morphological dimorphism, gonads,
and heads. In agreement with their morphology, sex-biased expression is common
in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased
genes, and seems to in fact have a mechanism of dosage compensation that leads
to equal expression in males and in females. Both of these patterns are contrary
to most ZW systems studied so far, making A. franciscana an excellent model for
investigating the interplay between the evolution of sexual dimorphism and dosage
compensation, as well as Z chromosome evolution in general.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Ann K
full_name: Huylmans, Ann K
id: 4C0A3874-F248-11E8-B48F-1D18A9856A87
last_name: Huylmans
orcid: 0000-0001-8871-4961
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Ariana
full_name: Macon, Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- first_name: William J
full_name: Gammerdinger, William J
id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87
last_name: Gammerdinger
orcid: 0000-0001-9638-1220
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene
expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome
biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053
apa: Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso,
B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053
chicago: Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger,
and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the
Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford
University Press, 2019. https://doi.org/10.1093/gbe/evz053.
ieee: A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso,
“Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University
Press, pp. 1033–1044, 2019.
ista: Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased
gene expression and dosage compensation on the Artemia franciscana Z-chromosome.
Genome biology and evolution. 11(4), 1033–1044.
mla: Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation
on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution,
vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.
short: A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome
Biology and Evolution 11 (2019) 1033–1044.
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2024-02-21T12:45:41Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evz053
ec_funded: 1
external_id:
isi:
- '000476569800003'
file:
- access_level: open_access
checksum: 7d0ede297b6741f3dc89cd59017c7642
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:29:38Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6446'
file_name: 2019_GBE_Huylmans.pdf
file_size: 1256303
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file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1033-1044
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genome biology and evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '6060'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Sex-biased gene expression and dosage compensation on the Artemia franciscana
Z-chromosome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2019'
...
---
_id: '7016'
abstract:
- lang: eng
text: Organisms cope with change by employing transcriptional regulators. However,
when faced with rare environments, the evolution of transcriptional regulators
and their promoters may be too slow. We ask whether the intrinsic instability
of gene duplication and amplification provides a generic alternative to canonical
gene regulation. By real-time monitoring of gene copy number mutations in E. coli,
we show that gene duplications and amplifications enable adaptation to fluctuating
environments by rapidly generating copy number, and hence expression level, polymorphism.
This ‘amplification-mediated gene expression tuning’ occurs on timescales similar
to canonical gene regulation and can deal with rapid environmental changes. Mathematical
modeling shows that amplifications also tune gene expression in stochastic environments
where transcription factor-based schemes are hard to evolve or maintain. The fleeting
nature of gene amplifications gives rise to a generic population-level mechanism
that relies on genetic heterogeneity to rapidly tune expression of any gene, without
leaving any genomic signature.
article_processing_charge: No
author:
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Tomanek I. Data for the paper “Gene amplification as a form of population-level
gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016
apa: Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level
gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016
chicago: Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of
Population-Level Gene Expression Regulation.’” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.
ieee: I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level
gene expression regulation.’” Institute of Science and Technology Austria, 2019.
ista: Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level
gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.
mla: Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level
Gene Expression Regulation.” Institute of Science and Technology Austria,
2019, doi:10.15479/AT:ISTA:7016.
short: I. Tomanek, (2019).
contributor:
- contributor_type: project_leader
first_name: Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
date_created: 2019-11-13T09:07:31Z
date_published: 2019-11-13T00:00:00Z
date_updated: 2024-02-21T12:45:25Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:7016
file:
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content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:52:21Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - amplified.
file_id: '7017'
file_name: D8_S35_R2_001.fastq
file_size: 2456192500
relation: main_file
title: Locus1_amplified
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checksum: a4ac50bf655d9c751f0305ade5c2ee16
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:52:59Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - ancestral.
file_id: '7018'
file_name: IT028_S11_R2_001.fastq
file_size: 2833452234
relation: main_file
title: Locus1_ancestral
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content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:54:10Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 1 - amplified, after
DOG-selection.
file_id: '7019'
file_name: D8-DOG1_S47_R2_001.fastq
file_size: 2878017264
relation: main_file
title: Locus1_amplified_DOG
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checksum: d9550a4c044116075fa83f8f2ea31d6f
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:54:27Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - amplified.
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file_name: D4_S71_R2_001.fastq
file_size: 2180826995
relation: main_file
title: Locus2_amplified
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checksum: 466ceb302c020ac013007a879fcde69d
content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-13T08:55:58Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - ancestral.
file_id: '7021'
file_name: IT030_S23_R2_001.fastq
file_size: 2108826444
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title: Locus2_ancestral
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content_type: application/octet-stream
creator: itomanek
date_created: 2019-11-21T12:31:01Z
date_updated: 2020-07-14T12:47:47Z
description: Illumina whole genome sequence data for Locus 2 - amplified, after
DOG-selection.
file_id: '7092'
file_name: D4-DOG1_S83_R2_001.fastq
file_size: 3144330494
relation: main_file
title: Locus2_amplified_DOG
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checksum: bf7d4b053f14af4655fb5574209fdb2d
content_type: application/zip
creator: itomanek
date_created: 2020-01-14T11:22:27Z
date_updated: 2020-07-14T12:47:47Z
description: Compressed genbank file format containing the sequence of the chromosomal
reporter gene cassette.
file_id: '7273'
file_name: galK_dual_reporter_cassette.gb.zip
file_size: 4179
relation: main_file
title: DNA sequence of the chromosomal reporter gene cassette
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date_updated: 2020-07-14T12:47:47Z
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file_name: Readme_7016.txt
file_size: 435
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title: Read_me_sequence_data
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content_type: application/zip
creator: itomanek
date_created: 2020-01-22T15:44:16Z
date_updated: 2020-07-14T12:47:47Z
description: FACS data associated with Fig. 2c - see read_me_FACS
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date_updated: 2020-07-14T12:47:47Z
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creator: itomanek
date_created: 2020-01-22T15:44:16Z
date_updated: 2020-07-14T12:47:47Z
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file_size: 868
relation: main_file
- access_level: open_access
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content_type: application/zip
creator: itomanek
date_created: 2020-01-22T15:44:17Z
date_updated: 2020-07-14T12:47:47Z
description: microfluidics time trace data - see read_me_microfluidics
file_id: '7354'
file_name: microfuidics_data.zip
file_size: 8141727
relation: main_file
title: microfluidics data
file_date_updated: 2020-07-14T12:47:47Z
has_accepted_license: '1'
keyword:
- Escherichia coli
- gene amplification
- galactose
- DOG
- experimental evolution
- Illumina sequence data
- FACS data
- microfluidics data
month: '11'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7652'
relation: used_in_publication
status: public
status: public
title: Data for the paper "Gene amplification as a form of population-level gene expression
regulation"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7154'
article_processing_charge: No
author:
- first_name: Ruslan
full_name: Guseinov, Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
citation:
ama: Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated
shells.” 2019. doi:10.15479/AT:ISTA:7154
apa: Guseinov, R. (2019). Supplementary data for “Programming temporal morphing
of self-actuated shells.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7154
chicago: Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing
of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:7154.
ieee: R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated
shells.’” Institute of Science and Technology Austria, 2019.
ista: Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of
self-actuated shells’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7154.
mla: Guseinov, Ruslan. Supplementary Data for “Programming Temporal Morphing
of Self-Actuated Shells.” Institute of Science and Technology Austria, 2019,
doi:10.15479/AT:ISTA:7154.
short: R. Guseinov, (2019).
contributor:
- first_name: Ruslan
id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87
last_name: Guseinov
orcid: 0000-0001-9819-5077
- first_name: Connor
last_name: McMahan
- first_name: Jesus
id: 2DC83906-F248-11E8-B48F-1D18A9856A87
last_name: Perez Rodriguez
- first_name: Chiara
last_name: Daraio
- first_name: Bernd
id: 49876194-F248-11E8-B48F-1D18A9856A87
last_name: Bickel
orcid: 0000-0001-6511-9385
date_created: 2019-12-09T07:52:46Z
date_published: 2019-12-06T00:00:00Z
date_updated: 2024-02-21T12:45:03Z
day: '06'
ddc:
- '000'
department:
- _id: BeBi
doi: 10.15479/AT:ISTA:7154
ec_funded: 1
file:
- access_level: open_access
checksum: 155133e6e188e85b3c0676a5e70b9341
content_type: application/x-zip-compressed
creator: dernst
date_created: 2019-12-09T07:52:17Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7155'
file_name: temporal_morphing_supp_data.zip
file_size: 65307107
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '8433'
relation: used_in_publication
status: deleted
- id: '7262'
relation: used_in_publication
status: public
status: public
title: Supplementary data for "Programming temporal morphing of self-actuated shells"
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6060'
article_processing_charge: No
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation
on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019.
doi:10.15479/AT:ISTA:6060
apa: Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al.,
2019). . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6060
chicago: Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and
Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et
Al., 2019). .” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6060.
ieee: B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al.,
2019). .” Institute of Science and Technology Austria, 2019.
ista: Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage
compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al.,
2019). , Institute of Science and Technology Austria, 10.15479/AT:ISTA:6060.
mla: Vicoso, Beatriz. Supplementary Data for “Sex-Biased Gene Expression and
Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et
Al., 2019). . Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6060.
short: B. Vicoso, (2019).
date_created: 2019-02-28T10:55:15Z
date_published: 2019-02-28T00:00:00Z
date_updated: 2024-02-21T12:45:42Z
day: '28'
department:
- _id: BeVi
doi: 10.15479/AT:ISTA:6060
file:
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content_type: application/zip
creator: bvicoso
date_created: 2019-02-28T10:54:27Z
date_updated: 2020-07-14T12:47:17Z
file_id: '6061'
file_name: SupData.zip
file_size: 36646050
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file_date_updated: 2020-07-14T12:47:17Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6418'
relation: research_paper
status: public
status: public
title: 'Supplementary data for "Sex-biased gene expression and dosage compensation
on the Artemia franciscana Z-chromosome" (Huylman, Toups et al., 2019). '
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6074'
abstract:
- lang: eng
text: "This dataset contains the supplementary data for the research paper \"Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition\".\r\n\r\nThe contained files have the following content:\r\n'Supplementary
Figures.pdf'\r\n\tAdditional figures (as referenced in the paper).\r\n'Supplementary
Table 1. Statistics.xlsx'\r\n\tDetails on statistical tests performed in the paper.\r\n'Supplementary
Table 2. Differentially expressed gene analysis.xlsx'\r\n\tResults for the differential
gene expression analysis for embryonic (E9.5; analysis with edgeR) and in vitro
(ESCs, EBs, NPCs; analysis with DESeq2) samples.\r\n'Supplementary Table 3. Gene
Ontology (GO) term enrichment analysis.xlsx'\r\n\tResults for the GO term enrichment
analysis for differentially expressed genes in embryonic (GO E9.5) and in vitro
(GO ESC, GO EBs, GO NPCs) samples. Differentially expressed genes for in vitro
samples were split into upregulated and downregulated genes (up/down) and the
analysis was performed on each subset (e.g. GO ESC up / GO ESC down).\r\n'Supplementary
Table 4. Differentially expressed gene analysis for CFC samples.xlsx'\r\n\tResults
for the differential gene expression analysis for samples from adult mice before
(HC - Homecage) and 1h and 3h after contextual fear conditioning (1h and 3h, respectively).
Each sheet shows the results for a different comparison. Sheets 1-3 show results
for comparisons between timepoints for wild type (WT) samples only and sheets
4-6 for the same comparisons in mutant (Het) samples. Sheets 7-9 show results
for comparisons between genotypes at each time point and sheet 10 contains the
results for the analysis of differential expression trajectories between wild
type and mutant.\r\n'Supplementary Table 5. Cluster identification.xlsx'\r\n\tResults
for k-means clustering of genes by expression. Sheet 1 shows clustering of just
the genes with significantly different expression trajectories between genotypes.
Sheet 2 shows clustering of all genes that are significantly differentially expressed
in any of the comparisons (includes also genes with same trajectories).\r\n'Supplementary
Table 6. GO term cluster analysis.xlsx'\r\n\tResults for the GO term enrichment
analysis and EWCE analysis for enrichment of cell type specific genes for each
cluster identified by clustering genes with different expression trajectories
(see Table S5, sheet 1).\r\n'Supplementary Table 7. Setd5 mass spectrometry results.xlsx'\r\n\tResults
showing proteins interacting with Setd5 as identified by mass spectrometry. Sheet
1 shows protein protein interaction data generated from these results (combined
with data from the STRING database. Sheet 2 shows the results of the statistical
analysis with limma.\r\n'Supplementary Table 8. PolII ChIP-seq analysis.xlsx'\r\n\tResults
for the Chip-Seq analysis for binding of RNA polymerase II (PolII). Sheet 1 shows
results for differential binding of PolII at the transcription start site (TSS)
between genotypes and sheets 2+3 show the corresponding GO enrichment analysis
for these differentially bound genes. Sheet 4 shows RNAseq counts for genes with
increased binding of PolII at the TSS."
article_processing_charge: No
author:
- first_name: Christoph
full_name: Dotter, Christoph
id: 4C66542E-F248-11E8-B48F-1D18A9856A87
last_name: Dotter
orcid: 0000-0002-9033-9096
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
citation:
ama: Dotter C, Novarino G. Supplementary data for the research paper “Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition.” 2019. doi:10.15479/AT:ISTA:6074
apa: Dotter, C., & Novarino, G. (2019). Supplementary data for the research
paper “Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental
gene expression and cognition.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6074
chicago: Dotter, Christoph, and Gaia Novarino. “Supplementary Data for the Research
Paper ‘Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental
Gene Expression and Cognition.’” Institute of Science and Technology Austria,
2019. https://doi.org/10.15479/AT:ISTA:6074.
ieee: C. Dotter and G. Novarino, “Supplementary data for the research paper ‘Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition.’” Institute of Science and Technology Austria, 2019.
ista: Dotter C, Novarino G. 2019. Supplementary data for the research paper ‘Haploinsufficiency
of the intellectual disability gene SETD5 disturbs developmental gene expression
and cognition’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:6074.
mla: Dotter, Christoph, and Gaia Novarino. Supplementary Data for the Research
Paper “Haploinsufficiency of the Intellectual Disability Gene SETD5 Disturbs Developmental
Gene Expression and Cognition.” Institute of Science and Technology Austria,
2019, doi:10.15479/AT:ISTA:6074.
short: C. Dotter, G. Novarino, (2019).
date_created: 2019-03-07T13:32:35Z
date_published: 2019-01-09T00:00:00Z
date_updated: 2024-02-21T13:41:01Z
day: '09'
ddc:
- '570'
department:
- _id: GaNo
doi: 10.15479/AT:ISTA:6074
file:
- access_level: open_access
checksum: bc1b285edca9e98a2c63d153c79bb75b
content_type: application/zip
creator: dernst
date_created: 2019-03-07T13:37:19Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6084'
file_name: Setd5_paper.zip
file_size: 33202743
relation: supplementary_material
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '3'
relation: research_paper
status: public
status: public
title: Supplementary data for the research paper "Haploinsufficiency of the intellectual
disability gene SETD5 disturbs developmental gene expression and cognition"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6062'
abstract:
- lang: eng
text: Open the files in Jupyter Notebook (reccomended https://www.anaconda.com/distribution/#download-section
with Python 3.7).
article_processing_charge: No
author:
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
citation:
ama: Nardin M. Supplementary Code and Data for the paper “The Entorhinal Cognitive
Map is Attracted to Goals.” 2019. doi:10.15479/AT:ISTA:6062
apa: Nardin, M. (2019). Supplementary Code and Data for the paper “The Entorhinal
Cognitive Map is Attracted to Goals.” Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:6062
chicago: Nardin, Michele. “Supplementary Code and Data for the Paper ‘The Entorhinal
Cognitive Map Is Attracted to Goals.’” Institute of Science and Technology Austria,
2019. https://doi.org/10.15479/AT:ISTA:6062.
ieee: M. Nardin, “Supplementary Code and Data for the paper ‘The Entorhinal Cognitive
Map is Attracted to Goals.’” Institute of Science and Technology Austria, 2019.
ista: Nardin M. 2019. Supplementary Code and Data for the paper ‘The Entorhinal
Cognitive Map is Attracted to Goals’, Institute of Science and Technology Austria,
10.15479/AT:ISTA:6062.
mla: Nardin, Michele. Supplementary Code and Data for the Paper “The Entorhinal
Cognitive Map Is Attracted to Goals.” Institute of Science and Technology
Austria, 2019, doi:10.15479/AT:ISTA:6062.
short: M. Nardin, (2019).
date_created: 2019-03-04T14:20:58Z
date_published: 2019-03-29T00:00:00Z
date_updated: 2024-02-21T12:46:04Z
day: '29'
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6062
file:
- access_level: open_access
checksum: 48e7b9a02939b763417733239522a236
content_type: application/zip
creator: mnardin
date_created: 2019-03-05T09:29:37Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6068'
file_name: Online_data.zip
file_size: 37002186
relation: main_file
title: Data for the paper "The Entorhinal Cognitive Map is Attracted to Goals"
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by-sa/4.0/
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6194'
relation: research_paper
status: public
status: public
title: Supplementary Code and Data for the paper "The Entorhinal Cognitive Map is
Attracted to Goals"
tmp:
image: /images/cc_by_sa.png
legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode
name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC
BY-SA 4.0)
short: CC BY-SA (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6089'
abstract:
- lang: eng
text: Pleiotropy is the well-established idea that a single mutation affects multiple
phenotypes. If a mutation has opposite effects on fitness when expressed in different
contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce
the efficacy of selection by limiting the fixation of beneficial mutations through
adaptation, and the removal of deleterious mutations through purifying selection.
Although this has been widely discussed, in particular in the context of a putative
“gender load,” it has yet to be systematically quantified. In this work, we empirically
estimate to which extent different pleiotropic regimes impede the efficacy of
selection in Drosophila melanogaster. We use whole-genome polymorphism data from
a single African population and divergence data from D. simulans to estimate the
fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction
of selection (DoS). After controlling for confounding covariates, we find that
the different pleiotropic regimes have a relatively small, but significant, effect
on selection efficacy. Specifically, our results suggest that pleiotropic sexual
antagonism may restrict the efficacy of selection, but that this conflict can
be resolved by limiting the expression of genes to the sex where they are beneficial.
Intermediate levels of pleiotropy across tissues and life stages can also lead
to maladaptation in D. melanogaster, due to inefficient purifying selection combined
with low frequency of mutations that confer a selective advantage. Thus, our study
highlights the need to consider the efficacy of selection in the context of antagonistic
pleiotropy, and of genetic conflict in general.
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection
in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515.
doi:10.1093/molbev/msy246
apa: Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates
the efficacy of selection in drosophila melanogaster. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246
chicago: Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy
Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular
Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.
ieee: C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy
of selection in drosophila melanogaster,” Molecular biology and evolution,
vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.
ista: Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy
of selection in drosophila melanogaster. Molecular biology and evolution. 36(3),
500–515.
mla: Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection
in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36,
no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.
short: C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36
(2019) 500–515.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2024-02-21T13:59:17Z
day: '01'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/molbev/msy246
external_id:
isi:
- '000462585100006'
pmid:
- '30590559'
intvolume: ' 36'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30590559
month: '03'
oa: 1
oa_version: Submitted Version
page: 500-515
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular biology and evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '5757'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Pleiotropy modulates the efficacy of selection in drosophila melanogaster
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2019'
...
---
_id: '6179'
abstract:
- lang: eng
text: "In the first part of this thesis we consider large random matrices with arbitrary
expectation and a general slowly decaying correlation among its entries. We prove
universality of the local eigenvalue statistics and optimal local laws for the
resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic
control of a multivariate cumulant expansion.\r\nIn the second part we consider
Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue
distribution the local eigenvalue statistics are uni- versal and form a Pearcey
process. Since the density of states typically exhibits only square root or cubic
root cusp singularities, our work complements previous results on the bulk and
edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta
universality conjecture for the last remaining universality type. Our analysis
holds not only for exact cusps, but approximate cusps as well, where an ex- tended
Pearcey process emerges. As a main technical ingredient we prove an optimal local
law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow-
nian motion to the cusp regime.\r\nIn the third and final part we explore the
entrywise linear statistics of Wigner ma- trices and identify the fluctuations
for a large class of test functions with little regularity. This enables us to
study the rectangular Young diagram obtained from the interlacing eigenvalues
of the random matrix and its minor, and we find that, despite having the same
limit, the fluctuations differ from those of the algebraic Young tableaux equipped
with the Plancharel measure."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dominik J
full_name: Schröder, Dominik J
id: 408ED176-F248-11E8-B48F-1D18A9856A87
last_name: Schröder
orcid: 0000-0002-2904-1856
citation:
ama: 'Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix
theory. 2019. doi:10.15479/AT:ISTA:th6179'
apa: 'Schröder, D. J. (2019). From Dyson to Pearcey: Universal statistics in
random matrix theory. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th6179'
chicago: 'Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random
Matrix Theory.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:th6179.'
ieee: 'D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix
theory,” Institute of Science and Technology Austria, 2019.'
ista: 'Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random
matrix theory. Institute of Science and Technology Austria.'
mla: 'Schröder, Dominik J. From Dyson to Pearcey: Universal Statistics in Random
Matrix Theory. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:th6179.'
short: 'D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix
Theory, Institute of Science and Technology Austria, 2019.'
date_created: 2019-03-28T08:58:59Z
date_published: 2019-03-18T00:00:00Z
date_updated: 2024-02-22T14:34:33Z
day: '18'
ddc:
- '515'
- '519'
degree_awarded: PhD
department:
- _id: LaEr
doi: 10.15479/AT:ISTA:th6179
ec_funded: 1
file:
- access_level: closed
checksum: 6926f66f28079a81c4937e3764be00fc
content_type: application/x-gzip
creator: dernst
date_created: 2019-03-28T08:53:52Z
date_updated: 2020-07-14T12:47:21Z
file_id: '6180'
file_name: 2019_Schroeder_Thesis.tar.gz
file_size: 7104482
relation: source_file
- access_level: open_access
checksum: 7d0ebb8d1207e89768cdd497a5bf80fb
content_type: application/pdf
creator: dernst
date_created: 2019-03-28T08:53:52Z
date_updated: 2020-07-14T12:47:21Z
file_id: '6181'
file_name: 2019_Schroeder_Thesis.pdf
file_size: 4228794
relation: main_file
file_date_updated: 2020-07-14T12:47:21Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '375'
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1144'
relation: part_of_dissertation
status: public
- id: '6186'
relation: part_of_dissertation
status: public
- id: '6185'
relation: part_of_dissertation
status: public
- id: '6182'
relation: part_of_dissertation
status: public
- id: '1012'
relation: part_of_dissertation
status: public
- id: '6184'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
title: 'From Dyson to Pearcey: Universal statistics in random matrix theory'
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6482'
abstract:
- lang: eng
text: 'Computer vision systems for automatic image categorization have become accurate
and reliable enough that they can run continuously for days or even years as components
of real-world commercial applications. A major open problem in this context, however,
is quality control. Good classification performance can only be expected if systems
run under the specific conditions, in particular data distributions, that they
were trained for. Surprisingly, none of the currently used deep network architectures
have a built-in functionality that could detect if a network operates on data
from a distribution it was not trained for, such that potentially a warning to
the human users could be triggered. In this work, we describe KS(conf), a procedure
for detecting such outside of specifications (out-of-specs) operation, based on
statistical testing of the network outputs. We show by extensive experiments using
the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that
KS(conf) reliably detects out-of-specs situations. It furthermore has a number
of properties that make it a promising candidate for practical deployment: it
is easy to implement, adds almost no overhead to the system, works with all networks,
including pretrained ones, and requires no a priori knowledge of how the data
distribution could change. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Rémy
full_name: Sun, Rémy
last_name: Sun
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside
of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:10.1007/978-3-030-12939-2_18'
apa: 'Sun, R., & Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet
operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at
the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature.
https://doi.org/10.1007/978-3-030-12939-2_18'
chicago: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a
ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature,
2019. https://doi.org/10.1007/978-3-030-12939-2_18.'
ieee: 'R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates
outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition,
Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.'
ista: 'Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates
outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS,
vol. 11269, 244–259.'
mla: 'Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet
Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019,
pp. 244–59, doi:10.1007/978-3-030-12939-2_18.'
short: R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.
conference:
end_date: 2018-10-12
location: Stuttgart, Germany
name: 'GCPR: Conference on Pattern Recognition'
start_date: 2018-10-09
date_created: 2019-05-24T09:48:36Z
date_published: 2019-02-14T00:00:00Z
date_updated: 2024-02-22T14:57:29Z
day: '14'
department:
- _id: ChLa
doi: 10.1007/978-3-030-12939-2_18
ec_funded: 1
external_id:
arxiv:
- '1804.04171'
intvolume: ' 11269'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1804.04171
month: '02'
oa: 1
oa_version: Preprint
page: 244-259
project:
- _id: 2532554C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '308036'
name: Lifelong Learning of Visual Scene Understanding
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030129385'
- '9783030129392'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '6944'
relation: later_version
status: public
scopus_import: '1'
status: public
title: 'KS(conf): A light-weight test if a ConvNet operates outside of Its specifications'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11269
year: '2019'
...
---
_id: '6642'
abstract:
- lang: eng
text: We present a thermodynamically based approach to the design of models for
viscoelastic fluids with stress diffusion effect. In particular, we show how to
add a stress diffusion term to some standard viscoelastic rate-type models (Giesekus,
FENE-P, Johnson–Segalman, Phan-Thien–Tanner and Bautista–Manero–Puig) so that
the resulting models with the added stress diffusion term are thermodynamically
consistent in the sense that they obey the first and the second law of thermodynamics.
We point out the potential applications of the provided thermodynamical background
in the study of flows of fluids described by the proposed models.
article_number: '020002'
article_processing_charge: No
author:
- first_name: Mark
full_name: Dostalík, Mark
last_name: Dostalík
- first_name: Vít
full_name: Pruša, Vít
last_name: Pruša
- first_name: Tomas
full_name: Skrivan, Tomas
id: 486A5A46-F248-11E8-B48F-1D18A9856A87
last_name: Skrivan
citation:
ama: 'Dostalík M, Pruša V, Skrivan T. On diffusive variants of some classical viscoelastic
rate-type models. In: AIP Conference Proceedings. Vol 2107. AIP Publishing;
2019. doi:10.1063/1.5109493'
apa: 'Dostalík, M., Pruša, V., & Skrivan, T. (2019). On diffusive variants of
some classical viscoelastic rate-type models. In AIP Conference Proceedings
(Vol. 2107). Zlin, Czech Republic: AIP Publishing. https://doi.org/10.1063/1.5109493'
chicago: Dostalík, Mark, Vít Pruša, and Tomas Skrivan. “On Diffusive Variants of
Some Classical Viscoelastic Rate-Type Models.” In AIP Conference Proceedings,
Vol. 2107. AIP Publishing, 2019. https://doi.org/10.1063/1.5109493.
ieee: M. Dostalík, V. Pruša, and T. Skrivan, “On diffusive variants of some classical
viscoelastic rate-type models,” in AIP Conference Proceedings, Zlin, Czech
Republic, 2019, vol. 2107.
ista: Dostalík M, Pruša V, Skrivan T. 2019. On diffusive variants of some classical
viscoelastic rate-type models. AIP Conference Proceedings. 8th International Conference
on Novel Trends in Rheology vol. 2107, 020002.
mla: Dostalík, Mark, et al. “On Diffusive Variants of Some Classical Viscoelastic
Rate-Type Models.” AIP Conference Proceedings, vol. 2107, 020002, AIP Publishing,
2019, doi:10.1063/1.5109493.
short: M. Dostalík, V. Pruša, T. Skrivan, in:, AIP Conference Proceedings, AIP Publishing,
2019.
conference:
end_date: 2019-07-31
location: Zlin, Czech Republic
name: 8th International Conference on Novel Trends in Rheology
start_date: 2019-07-30
date_created: 2019-07-15T10:07:09Z
date_published: 2019-05-21T00:00:00Z
date_updated: 2024-02-28T13:01:28Z
day: '21'
department:
- _id: ChWo
doi: 10.1063/1.5109493
external_id:
arxiv:
- '1902.07983'
isi:
- '000479303100002'
intvolume: ' 2107'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07983
month: '05'
oa: 1
oa_version: Preprint
publication: AIP Conference Proceedings
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: On diffusive variants of some classical viscoelastic rate-type models
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2107
year: '2019'
...
---
_id: '7226'
article_number: '123504'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Vojkan
full_name: Jaksic, Vojkan
last_name: Jaksic
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Jaksic V, Seiringer R. Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics.
2019;60(12). doi:10.1063/1.5138135'
apa: 'Jaksic, V., & Seiringer, R. (2019). Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical
Physics. AIP Publishing. https://doi.org/10.1063/1.5138135'
chicago: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5138135.'
ieee: 'V. Jaksic and R. Seiringer, “Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018,” Journal of Mathematical Physics,
vol. 60, no. 12. AIP Publishing, 2019.'
ista: 'Jaksic V, Seiringer R. 2019. Introduction to the Special Collection: International
Congress on Mathematical Physics (ICMP) 2018. Journal of Mathematical Physics.
60(12), 123504.'
mla: 'Jaksic, Vojkan, and Robert Seiringer. “Introduction to the Special Collection:
International Congress on Mathematical Physics (ICMP) 2018.” Journal of Mathematical
Physics, vol. 60, no. 12, 123504, AIP Publishing, 2019, doi:10.1063/1.5138135.'
short: V. Jaksic, R. Seiringer, Journal of Mathematical Physics 60 (2019).
date_created: 2020-01-05T23:00:46Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2024-02-28T13:01:45Z
day: '01'
ddc:
- '500'
department:
- _id: RoSe
doi: 10.1063/1.5138135
external_id:
isi:
- '000505529800002'
file:
- access_level: open_access
checksum: bbd12ad1999a9ad7ba4d3c6f2e579c22
content_type: application/pdf
creator: dernst
date_created: 2020-01-07T14:59:13Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7244'
file_name: 2019_JournalMathPhysics_Jaksic.pdf
file_size: 1025015
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 60'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Journal of Mathematical Physics
publication_identifier:
issn:
- '00222488'
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Introduction to the Special Collection: International Congress on Mathematical
Physics (ICMP) 2018'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2019'
...
---
_id: '7190'
abstract:
- lang: eng
text: We investigate the ground-state energy of a one-dimensional Fermi gas with
two bosonic impurities. We consider spinless fermions with no fermion-fermion
interactions. The fermion-impurity and impurity-impurity interactions are modeled
with Dirac delta functions. First, we study the case where impurity and fermion
have equal masses, and the impurity-impurity two-body interaction is identical
to the fermion-impurity interaction, such that the system is solvable with the
Bethe ansatz. For attractive interactions, we find that the energy of the impurity-impurity
subsystem is below the energy of the bound state that exists without the Fermi
gas. We interpret this as a manifestation of attractive boson-boson interactions
induced by the fermionic medium, and refer to the impurity-impurity subsystem
as an in-medium bound state. For repulsive interactions, we find no in-medium
bound states. Second, we construct an effective model to describe these interactions,
and compare its predictions to the exact solution. We use this effective model
to study nonintegrable systems with unequal masses and/or potentials. We discuss
parameter regimes for which impurity-impurity attraction induced by the Fermi
gas can lead to the formation of in-medium bound states made of bosons that repel
each other in the absence of the Fermi gas.
article_number: '033177'
article_processing_charge: No
article_type: original
author:
- first_name: D.
full_name: Huber, D.
last_name: Huber
- first_name: H.-W.
full_name: Hammer, H.-W.
last_name: Hammer
- first_name: Artem
full_name: Volosniev, Artem
id: 37D278BC-F248-11E8-B48F-1D18A9856A87
last_name: Volosniev
orcid: 0000-0003-0393-5525
citation:
ama: Huber D, Hammer H-W, Volosniev A. In-medium bound states of two bosonic impurities
in a one-dimensional Fermi gas. Physical Review Research. 2019;1(3). doi:10.1103/physrevresearch.1.033177
apa: Huber, D., Hammer, H.-W., & Volosniev, A. (2019). In-medium bound states
of two bosonic impurities in a one-dimensional Fermi gas. Physical Review Research.
American Physical Society. https://doi.org/10.1103/physrevresearch.1.033177
chicago: Huber, D., H.-W. Hammer, and Artem Volosniev. “In-Medium Bound States of
Two Bosonic Impurities in a One-Dimensional Fermi Gas.” Physical Review Research.
American Physical Society, 2019. https://doi.org/10.1103/physrevresearch.1.033177.
ieee: D. Huber, H.-W. Hammer, and A. Volosniev, “In-medium bound states of two bosonic
impurities in a one-dimensional Fermi gas,” Physical Review Research, vol.
1, no. 3. American Physical Society, 2019.
ista: Huber D, Hammer H-W, Volosniev A. 2019. In-medium bound states of two bosonic
impurities in a one-dimensional Fermi gas. Physical Review Research. 1(3), 033177.
mla: Huber, D., et al. “In-Medium Bound States of Two Bosonic Impurities in a One-Dimensional
Fermi Gas.” Physical Review Research, vol. 1, no. 3, 033177, American Physical
Society, 2019, doi:10.1103/physrevresearch.1.033177.
short: D. Huber, H.-W. Hammer, A. Volosniev, Physical Review Research 1 (2019).
date_created: 2019-12-17T13:03:41Z
date_published: 2019-12-16T00:00:00Z
date_updated: 2024-02-28T13:11:40Z
day: '16'
ddc:
- '530'
department:
- _id: MiLe
doi: 10.1103/physrevresearch.1.033177
ec_funded: 1
external_id:
arxiv:
- '1908.02483'
file:
- access_level: open_access
checksum: 382eb67e62a77052a23887332d363f96
content_type: application/pdf
creator: dernst
date_created: 2019-12-18T07:13:14Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7193'
file_name: 2019_PhysRevResearch_Huber.pdf
file_size: 1370022
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
intvolume: ' 1'
issue: '3'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Physical Review Research
publication_identifier:
issn:
- 2643-1564
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: In-medium bound states of two bosonic impurities in a one-dimensional Fermi
gas
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: 1
year: '2019'
...
---
_id: '6575'
abstract:
- lang: eng
text: Motivated by recent experimental observations of coherent many-body revivals
in a constrained Rydbergatom chain, we construct a weak quasilocal deformation
of the Rydberg-blockaded Hamiltonian, whichmakes the revivals virtually perfect.
Our analysis suggests the existence of an underlying nonintegrableHamiltonian
which supports an emergent SU(2)-spin dynamics within a small subspace of the
many-bodyHilbert space. We show that such perfect dynamics necessitates the existence
of atypical, nonergodicenergy eigenstates—quantum many-body scars. Furthermore,
using these insights, we construct a toymodel that hosts exact quantum many-body
scars, providing an intuitive explanation of their origin. Ourresults offer specific
routes to enhancing coherent many-body revivals and provide a step towardestablishing
the stability of quantum many-body scars in the thermodynamic limit.
article_number: '220603'
article_processing_charge: No
article_type: original
author:
- first_name: Soonwon
full_name: Choi, Soonwon
last_name: Choi
- first_name: Christopher J.
full_name: Turner, Christopher J.
last_name: Turner
- first_name: Hannes
full_name: Pichler, Hannes
last_name: Pichler
- first_name: Wen Wei
full_name: Ho, Wen Wei
last_name: Ho
- first_name: Alexios
full_name: Michailidis, Alexios
id: 36EBAD38-F248-11E8-B48F-1D18A9856A87
last_name: Michailidis
orcid: 0000-0002-8443-1064
- first_name: Zlatko
full_name: Papić, Zlatko
last_name: Papić
- first_name: Maksym
full_name: Serbyn, Maksym
id: 47809E7E-F248-11E8-B48F-1D18A9856A87
last_name: Serbyn
orcid: 0000-0002-2399-5827
- first_name: Mikhail D.
full_name: Lukin, Mikhail D.
last_name: Lukin
- first_name: Dmitry A.
full_name: Abanin, Dmitry A.
last_name: Abanin
citation:
ama: Choi S, Turner CJ, Pichler H, et al. Emergent SU(2) dynamics and perfect quantum
many-body scars. Physical Review Letters. 2019;122(22). doi:10.1103/PhysRevLett.122.220603
apa: Choi, S., Turner, C. J., Pichler, H., Ho, W. W., Michailidis, A., Papić, Z.,
… Abanin, D. A. (2019). Emergent SU(2) dynamics and perfect quantum many-body
scars. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.220603
chicago: Choi, Soonwon, Christopher J. Turner, Hannes Pichler, Wen Wei Ho, Alexios
Michailidis, Zlatko Papić, Maksym Serbyn, Mikhail D. Lukin, and Dmitry A. Abanin.
“Emergent SU(2) Dynamics and Perfect Quantum Many-Body Scars.” Physical Review
Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.220603.
ieee: S. Choi et al., “Emergent SU(2) dynamics and perfect quantum many-body
scars,” Physical Review Letters, vol. 122, no. 22. American Physical Society,
2019.
ista: Choi S, Turner CJ, Pichler H, Ho WW, Michailidis A, Papić Z, Serbyn M, Lukin
MD, Abanin DA. 2019. Emergent SU(2) dynamics and perfect quantum many-body scars.
Physical Review Letters. 122(22), 220603.
mla: Choi, Soonwon, et al. “Emergent SU(2) Dynamics and Perfect Quantum Many-Body
Scars.” Physical Review Letters, vol. 122, no. 22, 220603, American Physical
Society, 2019, doi:10.1103/PhysRevLett.122.220603.
short: S. Choi, C.J. Turner, H. Pichler, W.W. Ho, A. Michailidis, Z. Papić, M. Serbyn,
M.D. Lukin, D.A. Abanin, Physical Review Letters 122 (2019).
date_created: 2019-06-23T21:59:13Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2024-02-28T13:12:22Z
day: '07'
department:
- _id: MaSe
doi: 10.1103/PhysRevLett.122.220603
external_id:
arxiv:
- '1812.05561'
isi:
- '000470885800005'
intvolume: ' 122'
isi: 1
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1812.05561
month: '06'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Emergent SU(2) dynamics and perfect quantum many-body scars
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2019'
...
---
_id: '6092'
abstract:
- lang: eng
text: In 1915, Einstein and de Haas and Barnett demonstrated that changing the magnetization
of a magnetic material results in mechanical rotation and vice versa. At the microscopic
level, this effect governs the transfer between electron spin and orbital angular
momentum, and lattice degrees of freedom, understanding which is key for molecular
magnets, nano-magneto-mechanics, spintronics, and ultrafast magnetism. Until now,
the timescales of electron-to-lattice angular momentum transfer remain unclear,
since modeling this process on a microscopic level requires the addition of an
infinite amount of quantum angular momenta. We show that this problem can be solved
by reformulating it in terms of the recently discovered angulon quasiparticles,
which results in a rotationally invariant quantum many-body theory. In particular,
we demonstrate that nonperturbative effects take place even if the electron-phonon
coupling is weak and give rise to angular momentum transfer on femtosecond timescales.
article_number: '064428'
article_processing_charge: No
author:
- first_name: Johann H
full_name: Mentink, Johann H
last_name: Mentink
- first_name: Mikhail
full_name: Katsnelson, Mikhail
last_name: Katsnelson
- first_name: Mikhail
full_name: Lemeshko, Mikhail
id: 37CB05FA-F248-11E8-B48F-1D18A9856A87
last_name: Lemeshko
orcid: 0000-0002-6990-7802
citation:
ama: Mentink JH, Katsnelson M, Lemeshko M. Quantum many-body dynamics of the Einstein-de
Haas effect. Physical Review B. 2019;99(6). doi:10.1103/PhysRevB.99.064428
apa: Mentink, J. H., Katsnelson, M., & Lemeshko, M. (2019). Quantum many-body
dynamics of the Einstein-de Haas effect. Physical Review B. American Physical
Society. https://doi.org/10.1103/PhysRevB.99.064428
chicago: Mentink, Johann H, Mikhail Katsnelson, and Mikhail Lemeshko. “Quantum Many-Body
Dynamics of the Einstein-de Haas Effect.” Physical Review B. American Physical
Society, 2019. https://doi.org/10.1103/PhysRevB.99.064428.
ieee: J. H. Mentink, M. Katsnelson, and M. Lemeshko, “Quantum many-body dynamics
of the Einstein-de Haas effect,” Physical Review B, vol. 99, no. 6. American
Physical Society, 2019.
ista: Mentink JH, Katsnelson M, Lemeshko M. 2019. Quantum many-body dynamics of
the Einstein-de Haas effect. Physical Review B. 99(6), 064428.
mla: Mentink, Johann H., et al. “Quantum Many-Body Dynamics of the Einstein-de Haas
Effect.” Physical Review B, vol. 99, no. 6, 064428, American Physical Society,
2019, doi:10.1103/PhysRevB.99.064428.
short: J.H. Mentink, M. Katsnelson, M. Lemeshko, Physical Review B 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2024-02-28T13:11:54Z
day: '01'
department:
- _id: MiLe
doi: 10.1103/PhysRevB.99.064428
external_id:
arxiv:
- '1802.01638'
isi:
- '000459223400004'
intvolume: ' 99'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.01638
month: '02'
oa: 1
oa_version: Preprint
project:
- _id: 26031614-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29902
name: Quantum rotations in the presence of a many-body environment
publication: Physical Review B
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Quantum many-body dynamics of the Einstein-de Haas effect
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '6090'
abstract:
- lang: eng
text: Cells need to reliably sense external ligand concentrations to achieve various
biological functions such as chemotaxis or signaling. The molecular recognition
of ligands by surface receptors is degenerate in many systems, leading to crosstalk
between ligand-receptor pairs. Crosstalk is often thought of as a deviation from
optimal specific recognition, as the binding of noncognate ligands can interfere
with the detection of the receptor's cognate ligand, possibly leading to a false
triggering of a downstream signaling pathway. Here we quantify the optimal precision
of sensing the concentrations of multiple ligands by a collection of promiscuous
receptors. We demonstrate that crosstalk can improve precision in concentration
sensing and discrimination tasks. To achieve superior precision, the additional
information about ligand concentrations contained in short binding events of the
noncognate ligand should be exploited. We present a proofreading scheme to realize
an approximate estimation of multiple ligand concentrations that reaches a precision
close to the derived optimal bounds. Our results help rationalize the observed
ubiquity of receptor crosstalk in molecular sensing.
article_number: '022423'
article_processing_charge: No
author:
- first_name: Martín
full_name: Carballo-Pacheco, Martín
last_name: Carballo-Pacheco
- first_name: Jonathan
full_name: Desponds, Jonathan
last_name: Desponds
- first_name: Tatyana
full_name: Gavrilchenko, Tatyana
last_name: Gavrilchenko
- first_name: Andreas
full_name: Mayer, Andreas
last_name: Mayer
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Gautam
full_name: Reddy, Gautam
last_name: Reddy
- first_name: Ilya
full_name: Nemenman, Ilya
last_name: Nemenman
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves
concentration sensing of multiple ligands. Physical Review E. 2019;99(2).
doi:10.1103/PhysRevE.99.022423
apa: Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R.,
Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing
of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423
chicago: Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas
Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor
Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review
E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.
ieee: M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration
sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American
Physical Society, 2019.
ista: Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G,
Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of
multiple ligands. Physical Review E. 99(2), 022423.
mla: Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration
Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423,
American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.
short: M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G.
Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-26T00:00:00Z
date_updated: 2024-02-28T13:12:06Z
day: '26'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.99.022423
external_id:
isi:
- '000459916500007'
intvolume: ' 99'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/448118v1.abstract
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Receptor crosstalk improves concentration sensing of multiple ligands
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...