---
_id: '9221'
abstract:
- lang: eng
text: "Recent works have shown that gradient descent can find a global minimum for
over-parameterized neural networks where the widths of all the hidden layers scale
polynomially with N (N being the number of training samples). In this paper, we
prove that, for deep networks, a single layer of width N following the input layer
suffices to ensure a similar guarantee. In particular, all the remaining layers
are allowed to have constant widths, and form a pyramidal topology. We show an
application of our result to the widely used LeCun’s initialization and obtain
an over-parameterization requirement for the single wide layer of order N2.\r\n"
acknowledgement: The authors would like to thank Jan Maas, Mahdi Soltanolkotabi, and
Daniel Soudry for the helpful discussions, Marius Kloft, Matthias Hein and Quoc
Dinh Tran for proofreading portions of a prior version of this paper, and James
Martens for a clarification concerning LeCun’s initialization. M. Mondelli was partially
supported by the 2019 Lopez-Loreta Prize. Q. Nguyen was partially supported by the
German Research Foundation (DFG) award KL 2698/2-1.
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Quynh
full_name: Nguyen, Quynh
last_name: Nguyen
- first_name: Marco
full_name: Mondelli, Marco
id: 27EB676C-8706-11E9-9510-7717E6697425
last_name: Mondelli
orcid: 0000-0002-3242-7020
citation:
ama: 'Nguyen Q, Mondelli M. Global convergence of deep networks with one wide layer
followed by pyramidal topology. In: 34th Conference on Neural Information Processing
Systems. Vol 33. Neural Information Processing Systems Foundation; 2020:11961–11972.'
apa: 'Nguyen, Q., & Mondelli, M. (2020). Global convergence of deep networks
with one wide layer followed by pyramidal topology. In 34th Conference on Neural
Information Processing Systems (Vol. 33, pp. 11961–11972). Vancouver, Canada:
Neural Information Processing Systems Foundation.'
chicago: Nguyen, Quynh, and Marco Mondelli. “Global Convergence of Deep Networks
with One Wide Layer Followed by Pyramidal Topology.” In 34th Conference on
Neural Information Processing Systems, 33:11961–11972. Neural Information
Processing Systems Foundation, 2020.
ieee: Q. Nguyen and M. Mondelli, “Global convergence of deep networks with one wide
layer followed by pyramidal topology,” in 34th Conference on Neural Information
Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 11961–11972.
ista: 'Nguyen Q, Mondelli M. 2020. Global convergence of deep networks with one
wide layer followed by pyramidal topology. 34th Conference on Neural Information
Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in
Neural Information Processing Systems, vol. 33, 11961–11972.'
mla: Nguyen, Quynh, and Marco Mondelli. “Global Convergence of Deep Networks with
One Wide Layer Followed by Pyramidal Topology.” 34th Conference on Neural Information
Processing Systems, vol. 33, Neural Information Processing Systems Foundation,
2020, pp. 11961–11972.
short: Q. Nguyen, M. Mondelli, in:, 34th Conference on Neural Information Processing
Systems, Neural Information Processing Systems Foundation, 2020, pp. 11961–11972.
conference:
end_date: 2020-12-12
location: Vancouver, Canada
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2020-12-06
date_created: 2021-03-03T12:06:02Z
date_published: 2020-07-07T00:00:00Z
date_updated: 2025-05-14T11:27:13Z
day: '07'
department:
- _id: MaMo
external_id:
arxiv:
- '2002.07867'
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2002.07867
month: '07'
oa: 1
oa_version: Preprint
page: 11961–11972
project:
- _id: 059876FA-7A3F-11EA-A408-12923DDC885E
name: Prix Lopez-Loretta 2019 - Marco Mondelli
publication: 34th Conference on Neural Information Processing Systems
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Global convergence of deep networks with one wide layer followed by pyramidal
topology
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2020'
...
---
_id: '9222'
article_processing_charge: No
author:
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: 'Katsaros G. Transport data for: Site‐controlled uniform Ge/Si Hut wires with
electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222'
apa: 'Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut
wires with electrically tunable spin–orbit coupling. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:9222'
chicago: 'Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si
Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science
and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.'
ieee: 'G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires
with electrically tunable spin–orbit coupling.” Institute of Science and Technology
Austria, 2020.'
ista: 'Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires
with electrically tunable spin–orbit coupling, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:9222.'
mla: 'Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut
Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science
and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.'
short: G. Katsaros, (2020).
contributor:
- contributor_type: research_group
first_name: Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
corr_author: '1'
date_created: 2021-03-05T18:00:47Z
date_published: 2020-03-16T00:00:00Z
date_updated: 2025-06-12T07:16:21Z
day: '16'
ddc:
- '530'
department:
- _id: GeKa
doi: 10.15479/AT:ISTA:9222
file:
- access_level: open_access
checksum: 41b66e195ed3dbd73077feee77b05652
content_type: application/x-zip-compressed
creator: gkatsaro
date_created: 2021-03-05T17:50:45Z
date_updated: 2021-03-05T17:50:45Z
file_id: '9223'
file_name: DOI_SiteControlledHWs.zip
file_size: 13317557
relation: main_file
- access_level: open_access
checksum: a1dc5f710ba4b3bb7f248195ba754ab2
content_type: text/plain
creator: dernst
date_created: 2021-03-10T07:31:50Z
date_updated: 2021-03-10T07:31:50Z
file_id: '9233'
file_name: Readme.txt
file_size: 3515
relation: main_file
success: 1
file_date_updated: 2021-03-10T07:31:50Z
fulldoi: https://doi.org/10.15479/AT:ISTA:9222
has_accepted_license: '1'
month: '03'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '7541'
relation: used_in_publication
status: public
status: public
title: 'Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically
tunable spin–orbit coupling'
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: '2020'
...
---
_id: '9249'
abstract:
- lang: eng
text: Rhombic dodecahedron is a space filling polyhedron which represents the close
packing of spheres in 3D space and the Voronoi structures of the face centered
cubic (FCC) lattice. In this paper, we describe a new coordinate system where
every 3-integer coordinates grid point corresponds to a rhombic dodecahedron centroid.
In order to illustrate the interest of the new coordinate system, we propose the
characterization of 3D digital plane with its topological features, such as the
interrelation between the thickness of the digital plane and the separability
constraint we aim to obtain. We also present the characterization of 3D digital
lines and study it as the intersection of multiple digital planes. Characterization
of 3D digital sphere with relevant topological features is proposed as well along
with the 48-symmetry appearing in the new coordinate system.
acknowledgement: "This work has been partially supported by the European Research
Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation
programme, grant no. 788183, and the DFG Collaborative Research Center TRR 109,
‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no.
I 02979-N35. "
article_processing_charge: No
article_type: original
author:
- first_name: Ranita
full_name: Biswas, Ranita
id: 3C2B033E-F248-11E8-B48F-1D18A9856A87
last_name: Biswas
orcid: 0000-0002-5372-7890
- first_name: Gaëlle
full_name: Largeteau-Skapin, Gaëlle
last_name: Largeteau-Skapin
- first_name: Rita
full_name: Zrour, Rita
last_name: Zrour
- first_name: Eric
full_name: Andres, Eric
last_name: Andres
citation:
ama: Biswas R, Largeteau-Skapin G, Zrour R, Andres E. Digital objects in rhombic
dodecahedron grid. Mathematical Morphology - Theory and Applications. 2020;4(1):143-158.
doi:10.1515/mathm-2020-0106
apa: Biswas, R., Largeteau-Skapin, G., Zrour, R., & Andres, E. (2020). Digital
objects in rhombic dodecahedron grid. Mathematical Morphology - Theory and
Applications. De Gruyter. https://doi.org/10.1515/mathm-2020-0106
chicago: Biswas, Ranita, Gaëlle Largeteau-Skapin, Rita Zrour, and Eric Andres. “Digital
Objects in Rhombic Dodecahedron Grid.” Mathematical Morphology - Theory and
Applications. De Gruyter, 2020. https://doi.org/10.1515/mathm-2020-0106.
ieee: R. Biswas, G. Largeteau-Skapin, R. Zrour, and E. Andres, “Digital objects
in rhombic dodecahedron grid,” Mathematical Morphology - Theory and Applications,
vol. 4, no. 1. De Gruyter, pp. 143–158, 2020.
ista: Biswas R, Largeteau-Skapin G, Zrour R, Andres E. 2020. Digital objects in
rhombic dodecahedron grid. Mathematical Morphology - Theory and Applications.
4(1), 143–158.
mla: Biswas, Ranita, et al. “Digital Objects in Rhombic Dodecahedron Grid.” Mathematical
Morphology - Theory and Applications, vol. 4, no. 1, De Gruyter, 2020, pp.
143–58, doi:10.1515/mathm-2020-0106.
short: R. Biswas, G. Largeteau-Skapin, R. Zrour, E. Andres, Mathematical Morphology
- Theory and Applications 4 (2020) 143–158.
corr_author: '1'
date_created: 2021-03-16T08:55:19Z
date_published: 2020-11-17T00:00:00Z
date_updated: 2025-04-14T07:48:35Z
day: '17'
ddc:
- '510'
department:
- _id: HeEd
doi: 10.1515/mathm-2020-0106
ec_funded: 1
file:
- access_level: open_access
checksum: 4a1043fa0548a725d464017fe2483ce0
content_type: application/pdf
creator: dernst
date_created: 2021-03-22T08:56:37Z
date_updated: 2021-03-22T08:56:37Z
file_id: '9272'
file_name: 2020_MathMorpholTheoryAppl_Biswas.pdf
file_size: 3668725
relation: main_file
success: 1
file_date_updated: 2021-03-22T08:56:37Z
fulldoi: https://doi.org/10.1515/mathm-2020-0106
has_accepted_license: '1'
intvolume: ' 4'
issue: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 143-158
project:
- _id: 266A2E9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '788183'
name: Alpha Shape Theory Extended
- _id: 2561EBF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I02979-N35
name: Persistence and stability of geometric complexes
publication: Mathematical Morphology - Theory and Applications
publication_identifier:
issn:
- 2353-3390
publication_status: published
publisher: De Gruyter
quality_controlled: '1'
status: public
title: Digital objects in rhombic dodecahedron grid
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: 4
year: '2020'
...
---
_id: '9299'
abstract:
- lang: eng
text: We call a multigraph non-homotopic if it can be drawn in the plane in such
a way that no two edges connecting the same pair of vertices can be continuously
transformed into each other without passing through a vertex, and no loop can
be shrunk to its end-vertex in the same way. It is easy to see that a non-homotopic
multigraph on n>1 vertices can have arbitrarily many edges. We prove that the
number of crossings between the edges of a non-homotopic multigraph with n vertices
and m>4n edges is larger than cm2n for some constant c>0 , and that this
bound is tight up to a polylogarithmic factor. We also show that the lower bound
is not asymptotically sharp as n is fixed and m⟶∞ .
acknowledgement: Supported by the National Research, Development and Innovation Office,
NKFIH, KKP-133864, K-131529, K-116769, K-132696, by the Higher Educational Institutional
Excellence Program 2019 NKFIH-1158-6/2019, the Austrian Science Fund (FWF), grant
Z 342-N31, by the Ministry of Education and Science of the Russian Federation MegaGrant
No. 075-15-2019-1926, and by the ERC Synergy Grant “Dynasnet” No. 810115. A full
version can be found at https://arxiv.org/abs/2006.14908.
article_processing_charge: No
arxiv: 1
author:
- first_name: János
full_name: Pach, János
id: E62E3130-B088-11EA-B919-BF823C25FEA4
last_name: Pach
- first_name: Gábor
full_name: Tardos, Gábor
last_name: Tardos
- first_name: Géza
full_name: Tóth, Géza
last_name: Tóth
citation:
ama: 'Pach J, Tardos G, Tóth G. Crossings between non-homotopic edges. In: 28th
International Symposium on Graph Drawing and Network Visualization. Vol 12590.
LNCS. Springer Nature; 2020:359-371. doi:10.1007/978-3-030-68766-3_28'
apa: 'Pach, J., Tardos, G., & Tóth, G. (2020). Crossings between non-homotopic
edges. In 28th International Symposium on Graph Drawing and Network Visualization
(Vol. 12590, pp. 359–371). Virtual, Online: Springer Nature. https://doi.org/10.1007/978-3-030-68766-3_28'
chicago: Pach, János, Gábor Tardos, and Géza Tóth. “Crossings between Non-Homotopic
Edges.” In 28th International Symposium on Graph Drawing and Network Visualization,
12590:359–71. LNCS. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-68766-3_28.
ieee: J. Pach, G. Tardos, and G. Tóth, “Crossings between non-homotopic edges,”
in 28th International Symposium on Graph Drawing and Network Visualization,
Virtual, Online, 2020, vol. 12590, pp. 359–371.
ista: 'Pach J, Tardos G, Tóth G. 2020. Crossings between non-homotopic edges. 28th
International Symposium on Graph Drawing and Network Visualization. GD: Graph
Drawing and Network VisualizationLNCS vol. 12590, 359–371.'
mla: Pach, János, et al. “Crossings between Non-Homotopic Edges.” 28th International
Symposium on Graph Drawing and Network Visualization, vol. 12590, Springer
Nature, 2020, pp. 359–71, doi:10.1007/978-3-030-68766-3_28.
short: J. Pach, G. Tardos, G. Tóth, in:, 28th International Symposium on Graph Drawing
and Network Visualization, Springer Nature, 2020, pp. 359–371.
conference:
end_date: 2020-09-18
location: Virtual, Online
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2020-09-16
date_created: 2021-03-28T22:01:44Z
date_published: 2020-09-20T00:00:00Z
date_updated: 2025-04-15T07:16:52Z
day: '20'
department:
- _id: HeEd
doi: 10.1007/978-3-030-68766-3_28
external_id:
arxiv:
- '2006.14908'
fulldoi: https://doi.org/10.1007/978-3-030-68766-3_28
intvolume: ' 12590'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/2006.14908
month: '09'
oa: 1
oa_version: Preprint
page: 359-371
project:
- _id: 268116B8-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00342
name: Mathematics, Computer Science
publication: 28th International Symposium on Graph Drawing and Network Visualization
publication_identifier:
eissn:
- 1611-3349
isbn:
- '9783030687656'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
series_title: LNCS
status: public
title: Crossings between non-homotopic edges
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12590
year: '2020'
...
---
_id: '9308'
acknowledgement: This research was carried out with the support of the Russian Foundation
for Basic Research(grant no. 19-01-00169)
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
orcid: 0000-0002-7840-5062
- first_name: Uli
full_name: Wagner, Uli
id: 36690CA2-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0000-0002-1494-0568
- first_name: Isaac
full_name: Mabillard, Isaac
id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87
last_name: Mabillard
- first_name: A. B.
full_name: Skopenkov, A. B.
last_name: Skopenkov
citation:
ama: Avvakumov S, Wagner U, Mabillard I, Skopenkov AB. Eliminating higher-multiplicity
intersections, III. Codimension 2. Russian Mathematical Surveys. 2020;75(6):1156-1158.
doi:10.1070/RM9943
apa: Avvakumov, S., Wagner, U., Mabillard, I., & Skopenkov, A. B. (2020). Eliminating
higher-multiplicity intersections, III. Codimension 2. Russian Mathematical
Surveys. IOP Publishing. https://doi.org/10.1070/RM9943
chicago: Avvakumov, Sergey, Uli Wagner, Isaac Mabillard, and A. B. Skopenkov. “Eliminating
Higher-Multiplicity Intersections, III. Codimension 2.” Russian Mathematical
Surveys. IOP Publishing, 2020. https://doi.org/10.1070/RM9943.
ieee: S. Avvakumov, U. Wagner, I. Mabillard, and A. B. Skopenkov, “Eliminating higher-multiplicity
intersections, III. Codimension 2,” Russian Mathematical Surveys, vol.
75, no. 6. IOP Publishing, pp. 1156–1158, 2020.
ista: Avvakumov S, Wagner U, Mabillard I, Skopenkov AB. 2020. Eliminating higher-multiplicity
intersections, III. Codimension 2. Russian Mathematical Surveys. 75(6), 1156–1158.
mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III.
Codimension 2.” Russian Mathematical Surveys, vol. 75, no. 6, IOP Publishing,
2020, pp. 1156–58, doi:10.1070/RM9943.
short: S. Avvakumov, U. Wagner, I. Mabillard, A.B. Skopenkov, Russian Mathematical
Surveys 75 (2020) 1156–1158.
date_created: 2021-04-04T22:01:22Z
date_published: 2020-12-01T00:00:00Z
date_updated: 2025-07-02T10:54:51Z
day: '01'
department:
- _id: UlWa
doi: 10.1070/RM9943
external_id:
arxiv:
- '1511.03501'
isi:
- '000625983100001'
fulldoi: https://doi.org/10.1070/RM9943
intvolume: ' 75'
isi: 1
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1511.03501
month: '12'
oa: 1
oa_version: Preprint
page: 1156-1158
publication: Russian Mathematical Surveys
publication_identifier:
issn:
- 0036-0279
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
related_material:
record:
- id: '10220'
relation: later_version
status: public
- id: '8183'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Eliminating higher-multiplicity intersections, III. Codimension 2
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 75
year: '2020'
...
---
_id: '9326'
abstract:
- lang: eng
text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes
energy from catabolic processes to synthesize ATP. Complex I, the first and the
largest protein complex of the chain, harvests electrons from NADH to reduce quinone,
while pumping protons across the mitochondrial membrane. Detailed knowledge of
the working principle of such coupled charge-transfer processes remains, however,
fragmentary due to bottlenecks in understanding redox-driven conformational transitions
and their interplay with the hydrated proton pathways. Complex I from Thermus
thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons
from NADH. Here, employing the latest crystal structure of T. thermophilus complex
I, we have used microsecond-scale molecular dynamics simulations to study the
chemo-mechanical coupling between redox changes of the iron–sulfur clusters and
conformational transitions across complex I. First, we identify the redox switches
within complex I, which allosterically couple the dynamics of the quinone binding
pocket to the site of NADH reduction. Second, our free-energy calculations reveal
that the affinity of the quinone, specifically menaquinone, for the binding-site
is higher than that of its reduced, menaquinol forma design essential for menaquinol
release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser
than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup
of the former furnishes stronger binding interactions with the pocket, favoring
menaquinone for charge transport in T. thermophilus. Our computations are consistent
with experimentally validated mutations and hierarchize the key residues into
three functional classes, identifying new mutation targets. Third, long-range
hydrogen-bond networks connecting the quinone-binding site to the transmembrane
subunits are found to be responsible for proton pumping. Put together, the simulations
reveal the molecular design principles linking redox reactions to quinone turnover
to proton translocation in complex I.
article_processing_charge: No
author:
- first_name: Chitrak
full_name: Gupta, Chitrak
last_name: Gupta
- first_name: Umesh
full_name: Khaniya, Umesh
last_name: Khaniya
- first_name: Chun
full_name: Chan, Chun
last_name: Chan
- first_name: Francois
full_name: Dehez, Francois
last_name: Dehez
- first_name: Mrinal
full_name: Shekhar, Mrinal
last_name: Shekhar
- first_name: M. R.
full_name: Gunner, M. R.
last_name: Gunner
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: Abhishek
full_name: Singharoy, Abhishek
last_name: Singharoy
citation:
ama: Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling
in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002
apa: Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., …
Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory
complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002
chicago: Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar,
M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge
Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical
Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002.
ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in
respiratory complex I.” American Chemical Society, 2020.
ista: Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot
C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory
complex I, American Chemical Society, 10.1021/jacs.9b13450.s002.
mla: Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in
Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002.
short: C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov,
C. Chipot, A. Singharoy, (2020).
date_created: 2021-04-14T12:05:20Z
date_published: 2020-05-20T00:00:00Z
date_updated: 2025-07-10T11:55:01Z
day: '20'
department:
- _id: LeSa
doi: 10.1021/jacs.9b13450.s002
fulldoi: https://doi.org/10.1021/jacs.9b13450.s002
month: '05'
oa_version: Published Version
publisher: American Chemical Society
related_material:
record:
- id: '8040'
relation: used_in_publication
status: public
status: public
title: Charge transfer and chemo-mechanical coupling in respiratory complex I
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
OA_place: publisher
OA_type: hybrid
_id: '9526'
abstract:
- lang: eng
text: DNA methylation and histone H1 mediate transcriptional silencing of genes
and transposable elements, but how they interact is unclear. In plants and animals
with mosaic genomic methylation, functionally mysterious methylation is also common
within constitutively active housekeeping genes. Here, we show that H1 is enriched
in methylated sequences, including genes, of Arabidopsis thaliana, yet this enrichment
is independent of DNA methylation. Loss of H1 disperses heterochromatin, globally
alters nucleosome organization, and activates H1-bound genes, but only weakly
de-represses transposable elements. However, H1 loss strongly activates transposable
elements hypomethylated through mutation of DNA methyltransferase MET1. Hypomethylation
of genes also activates antisense transcription, which is modestly enhanced by
H1 loss. Our results demonstrate that H1 and DNA methylation jointly maintain
transcriptional homeostasis by silencing transposable elements and aberrant intragenic
transcripts. Such functionality plausibly explains why DNA methylation, a well-known
mutagen, has been maintained within coding sequences of crucial plant and animal
genes.
article_processing_charge: No
article_type: original
author:
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Jonathan D.
full_name: Moore, Jonathan D.
last_name: Moore
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. DNA methylation and histone
H1 jointly repress transposable elements and aberrant intragenic transcripts.
Molecular Cell. 2020;77(2):310-323.e7. doi:10.1016/j.molcel.2019.10.011
apa: Choi, J., Lyons, D. B., Kim, M. Y., Moore, J. D., & Zilberman, D. (2020).
DNA methylation and histone H1 jointly repress transposable elements and aberrant
intragenic transcripts. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2019.10.011
chicago: Choi, Jaemyung, David B. Lyons, M. Yvonne Kim, Jonathan D. Moore, and Daniel
Zilberman. “DNA Methylation and Histone H1 Jointly Repress Transposable Elements
and Aberrant Intragenic Transcripts.” Molecular Cell. Elsevier, 2020. https://doi.org/10.1016/j.molcel.2019.10.011.
ieee: J. Choi, D. B. Lyons, M. Y. Kim, J. D. Moore, and D. Zilberman, “DNA methylation
and histone H1 jointly repress transposable elements and aberrant intragenic transcripts,”
Molecular Cell, vol. 77, no. 2. Elsevier, p. 310–323.e7, 2020.
ista: Choi J, Lyons DB, Kim MY, Moore JD, Zilberman D. 2020. DNA methylation and
histone H1 jointly repress transposable elements and aberrant intragenic transcripts.
Molecular Cell. 77(2), 310–323.e7.
mla: Choi, Jaemyung, et al. “DNA Methylation and Histone H1 Jointly Repress Transposable
Elements and Aberrant Intragenic Transcripts.” Molecular Cell, vol. 77,
no. 2, Elsevier, 2020, p. 310–323.e7, doi:10.1016/j.molcel.2019.10.011.
short: J. Choi, D.B. Lyons, M.Y. Kim, J.D. Moore, D. Zilberman, Molecular Cell 77
(2020) 310–323.e7.
date_created: 2021-06-08T06:37:09Z
date_published: 2020-01-16T00:00:00Z
date_updated: 2024-10-16T12:14:37Z
day: '16'
department:
- _id: DaZi
doi: 10.1016/j.molcel.2019.10.011
extern: '1'
external_id:
pmid:
- '31732458'
fulldoi: https://doi.org/10.1016/j.molcel.2019.10.011
intvolume: ' 77'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2019.10.011
month: '01'
oa: 1
oa_version: Published Version
page: 310-323.e7
pmid: 1
publication: Molecular Cell
publication_identifier:
eissn:
- 1097-4164
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation and histone H1 jointly repress transposable elements and aberrant
intragenic transcripts
type: journal_article
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
volume: 77
year: '2020'
...
---
_id: '9630'
abstract:
- lang: eng
text: Various kinds of data are routinely represented as discrete probability distributions.
Examples include text documents summarized by histograms of word occurrences and
images represented as histograms of oriented gradients. Viewing a discrete probability
distribution as a point in the standard simplex of the appropriate dimension,
we can understand collections of such objects in geometric and topological terms. Importantly,
instead of using the standard Euclidean distance, we look into dissimilarity measures
with information-theoretic justification, and we develop the theory needed for
applying topological data analysis in this setting. In doing so, we emphasize
constructions that enable the usage of existing computational topology software
in this context.
acknowledgement: This research is partially supported by the Office of Naval Research,
through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR
109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of
the Austrian Science Fund (FWF).
article_processing_charge: Yes
article_type: original
author:
- first_name: Herbert
full_name: Edelsbrunner, Herbert
id: 3FB178DA-F248-11E8-B48F-1D18A9856A87
last_name: Edelsbrunner
orcid: 0000-0002-9823-6833
- first_name: Ziga
full_name: Virk, Ziga
id: 2E36B656-F248-11E8-B48F-1D18A9856A87
last_name: Virk
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0009-0009-9111-8429
citation:
ama: Edelsbrunner H, Virk Z, Wagner H. Topological data analysis in information
space. Journal of Computational Geometry. 2020;11(2):162-182. doi:10.20382/jocg.v11i2a7
apa: Edelsbrunner, H., Virk, Z., & Wagner, H. (2020). Topological data analysis
in information space. Journal of Computational Geometry. Carleton University.
https://doi.org/10.20382/jocg.v11i2a7
chicago: Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Topological Data
Analysis in Information Space.” Journal of Computational Geometry. Carleton
University, 2020. https://doi.org/10.20382/jocg.v11i2a7.
ieee: H. Edelsbrunner, Z. Virk, and H. Wagner, “Topological data analysis in information
space,” Journal of Computational Geometry, vol. 11, no. 2. Carleton University,
pp. 162–182, 2020.
ista: Edelsbrunner H, Virk Z, Wagner H. 2020. Topological data analysis in information
space. Journal of Computational Geometry. 11(2), 162–182.
mla: Edelsbrunner, Herbert, et al. “Topological Data Analysis in Information Space.”
Journal of Computational Geometry, vol. 11, no. 2, Carleton University,
2020, pp. 162–82, doi:10.20382/jocg.v11i2a7.
short: H. Edelsbrunner, Z. Virk, H. Wagner, Journal of Computational Geometry 11
(2020) 162–182.
corr_author: '1'
date_created: 2021-07-04T22:01:26Z
date_published: 2020-12-14T00:00:00Z
date_updated: 2026-04-02T14:35:31Z
day: '14'
ddc:
- '510'
- '000'
department:
- _id: HeEd
doi: 10.20382/jocg.v11i2a7
file:
- access_level: open_access
checksum: f02d0b2b3838e7891a6c417fc34ffdcd
content_type: application/pdf
creator: asandaue
date_created: 2021-08-11T11:55:11Z
date_updated: 2021-08-11T11:55:11Z
file_id: '9882'
file_name: 2020_JournalOfComputationalGeometry_Edelsbrunner.pdf
file_size: 1449234
relation: main_file
success: 1
file_date_updated: 2021-08-11T11:55:11Z
fulldoi: https://doi.org/10.20382/jocg.v11i2a7
has_accepted_license: '1'
intvolume: ' 11'
issue: '2'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/3.0/
month: '12'
oa: 1
oa_version: Published Version
page: 162-182
project:
- _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316
grant_number: I4887
name: Persistent Homology, Algorithms and Stochastic Geometry
publication: Journal of Computational Geometry
publication_identifier:
eissn:
- 1920-180X
publication_status: published
publisher: Carleton University
quality_controlled: '1'
scopus_import: '1'
status: public
title: Topological data analysis in information space
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 11
year: '2020'
...
---
_id: '9631'
abstract:
- lang: eng
text: The ability to leverage large-scale hardware parallelism has been one of the
key enablers of the accelerated recent progress in machine learning. Consequently,
there has been considerable effort invested into developing efficient parallel
variants of classic machine learning algorithms. However, despite the wealth of
knowledge on parallelization, some classic machine learning algorithms often prove
hard to parallelize efficiently while maintaining convergence. In this paper,
we focus on efficient parallel algorithms for the key machine learning task of
inference on graphical models, in particular on the fundamental belief propagation
algorithm. We address the challenge of efficiently parallelizing this classic
paradigm by showing how to leverage scalable relaxed schedulers in this context.
We present an extensive empirical study, showing that our approach outperforms
previous parallel belief propagation implementations both in terms of scalability
and in terms of wall-clock convergence time, on a range of practical applications.
acknowledgement: "We thank Marco Mondelli for discussions related to LDPC decoding,
and Giorgi Nadiradze for discussions on analysis of relaxed schedulers. This project
has received funding from the European Research Council (ERC) under the European\r\nUnion’s
Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML)."
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Vitaly
full_name: Aksenov, Vitaly
last_name: Aksenov
- 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: Janne
full_name: Korhonen, Janne
id: C5402D42-15BC-11E9-A202-CA2BE6697425
last_name: Korhonen
citation:
ama: 'Aksenov V, Alistarh D-A, Korhonen J. Scalable belief propagation via relaxed
scheduling. In: Vol 33. Neural Information Processing Systems Foundation; 2020:22361-22372.'
apa: 'Aksenov, V., Alistarh, D.-A., & Korhonen, J. (2020). Scalable belief propagation
via relaxed scheduling (Vol. 33, pp. 22361–22372). Presented at the NeurIPS: Conference
on Neural Information Processing Systems, Vancouver, Canada: Neural Information
Processing Systems Foundation.'
chicago: Aksenov, Vitaly, Dan-Adrian Alistarh, and Janne Korhonen. “Scalable Belief
Propagation via Relaxed Scheduling,” 33:22361–72. Neural Information Processing
Systems Foundation, 2020.
ieee: 'V. Aksenov, D.-A. Alistarh, and J. Korhonen, “Scalable belief propagation
via relaxed scheduling,” presented at the NeurIPS: Conference on Neural Information
Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 22361–22372.'
ista: 'Aksenov V, Alistarh D-A, Korhonen J. 2020. Scalable belief propagation via
relaxed scheduling. NeurIPS: Conference on Neural Information Processing Systems,
Advances in Neural Information Processing Systems, vol. 33, 22361–22372.'
mla: Aksenov, Vitaly, et al. Scalable Belief Propagation via Relaxed Scheduling.
Vol. 33, Neural Information Processing Systems Foundation, 2020, pp. 22361–72.
short: V. Aksenov, D.-A. Alistarh, J. Korhonen, in:, Neural Information Processing
Systems Foundation, 2020, pp. 22361–22372.
conference:
end_date: 2020-12-12
location: Vancouver, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2020-12-06
corr_author: '1'
date_created: 2021-07-04T22:01:26Z
date_published: 2020-12-06T00:00:00Z
date_updated: 2026-06-18T19:54:53Z
day: '06'
ddc:
- '000'
department:
- _id: DaAl
ec_funded: 1
external_id:
arxiv:
- '2002.11505'
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2020/hash/fdb2c3bab9d0701c4a050a4d8d782c7f-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
page: 22361-22372
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
isbn:
- '9781713829546'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scalable belief propagation via relaxed scheduling
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2020'
...
---
_id: '9632'
abstract:
- lang: eng
text: "Second-order information, in the form of Hessian- or Inverse-Hessian-vector
products, is a fundamental tool for solving optimization problems. Recently, there
has been significant interest in utilizing this information in the context of
deep\r\nneural networks; however, relatively little is known about the quality
of existing approximations in this context. Our work examines this question, identifies
issues with existing approaches, and proposes a method called WoodFisher to compute
a faithful and efficient estimate of the inverse Hessian. Our main application
is to neural network compression, where we build on the classic Optimal Brain
Damage/Surgeon framework. We demonstrate that WoodFisher significantly outperforms
popular state-of-the-art methods for oneshot pruning. Further, even when iterative,
gradual pruning is allowed, our method results in a gain in test accuracy over
the state-of-the-art approaches, for standard image classification datasets such
as ImageNet ILSVRC. We examine how our method can be extended to take into account
first-order information, as well as\r\nillustrate its ability to automatically
set layer-wise pruning thresholds and perform compression in the limited-data
regime. The code is available at the following link, https://github.com/IST-DASLab/WoodFisher."
acknowledgement: This project has received funding from the European Research Council
(ERC) under the European Union’s Horizon 2020 research and innovation programme
(grant agreement No 805223 ScaleML). Also, we would like to thank Alexander Shevchenko,
Alexandra Peste, and other members of the group for fruitful discussions.
alternative_title:
- Advances in Neural Information Processing Systems
article_processing_charge: No
arxiv: 1
author:
- first_name: Sidak Pal
full_name: Singh, Sidak Pal
id: DD138E24-D89D-11E9-9DC0-DEF6E5697425
last_name: Singh
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Singh SP, Alistarh D-A. WoodFisher: Efficient second-order approximation for
neural network compression. In: Vol 33. Neural Information Processing Systems
Foundation; 2020:18098-18109.'
apa: 'Singh, S. P., & Alistarh, D.-A. (2020). WoodFisher: Efficient second-order
approximation for neural network compression (Vol. 33, pp. 18098–18109). Presented
at the NeurIPS: Conference on Neural Information Processing Systems, Vancouver,
Canada: Neural Information Processing Systems Foundation.'
chicago: 'Singh, Sidak Pal, and Dan-Adrian Alistarh. “WoodFisher: Efficient Second-Order
Approximation for Neural Network Compression,” 33:18098–109. Neural Information
Processing Systems Foundation, 2020.'
ieee: 'S. P. Singh and D.-A. Alistarh, “WoodFisher: Efficient second-order approximation
for neural network compression,” presented at the NeurIPS: Conference on Neural
Information Processing Systems, Vancouver, Canada, 2020, vol. 33, pp. 18098–18109.'
ista: 'Singh SP, Alistarh D-A. 2020. WoodFisher: Efficient second-order approximation
for neural network compression. NeurIPS: Conference on Neural Information Processing
Systems, Advances in Neural Information Processing Systems, vol. 33, 18098–18109.'
mla: 'Singh, Sidak Pal, and Dan-Adrian Alistarh. WoodFisher: Efficient Second-Order
Approximation for Neural Network Compression. Vol. 33, Neural Information
Processing Systems Foundation, 2020, pp. 18098–109.'
short: S.P. Singh, D.-A. Alistarh, in:, Neural Information Processing Systems Foundation,
2020, pp. 18098–18109.
conference:
end_date: 2020-12-12
location: Vancouver, Canada
name: 'NeurIPS: Conference on Neural Information Processing Systems'
start_date: 2020-12-06
corr_author: '1'
date_created: 2021-07-04T22:01:26Z
date_published: 2020-12-06T00:00:00Z
date_updated: 2026-06-18T19:55:12Z
day: '06'
ddc:
- '000'
department:
- _id: DaAl
- _id: ToHe
ec_funded: 1
external_id:
arxiv:
- '2004.14340'
intvolume: ' 33'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://proceedings.neurips.cc/paper/2020/hash/d1ff1ec86b62cd5f3903ff19c3a326b2-Abstract.html
month: '12'
oa: 1
oa_version: Published Version
page: 18098-18109
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication_identifier:
isbn:
- '9781713829546'
issn:
- 1049-5258
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'WoodFisher: Efficient second-order approximation for neural network compression'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2020'
...
---
_id: '9706'
abstract:
- lang: eng
text: 'Additional file 2: Supplementary Tables. The association of pre-adjusted
protein levels with biological and technical covariates. Protein levels were adjusted
for age, sex, array plate and four genetic principal components (population structure)
prior to analyses. Significant associations are emboldened. (Table S1). pQTLs
associated with inflammatory biomarker levels from Bayesian penalised regression
model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated
with inflammatory biomarker levels from ordinary least squares regression model
(P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary
least squares GWAS and EWAS performed on inflammatory protein levels (n = 70)
in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs
associated with inflammatory biomarker levels from ordinary least squares regression
model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary
least squares and Bayesian penalised regression models for concordantly identified
SNPs. (Table S6). Estimate of heritability for blood protein levels as well as
proportion of variance explained attributable to different prior mixtures. (Table
S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood)
and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant
SNPs identified by linear model and Bayesian penalised regression and whether
they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation
for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression
are putatively associated with circulating inflammatory proteins that harbour
pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified
by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table
S12). CpGs associated with inflammatory protein biomarkers as identified by linear
model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory
protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10.
(Table S14). Estimate of variance explained for blood protein levels by DNA methylation
as well as proportion of explained attributable to different prior mixtures -
BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide
DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression
model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker
levels explained by common genetic and methylation data (joint and conditional
estimates from BayesR+). Ordered by combined variance explained by genetic and
epigenetic data - smallest to largest. Significant results from t-tests comparing
distributions for variance explained by methylation or genetics alone versus combined
estimate are emboldened. (Table S17). Genetic and epigenetic factors identified
by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian
Randomisation analyses to assess whether proteins with concordantly identified
genetic signals are causally associated with Alzheimer’s disease risk. (Table
S19).'
article_processing_charge: No
author:
- first_name: Robert F.
full_name: Hillary, Robert F.
last_name: Hillary
- first_name: Daniel
full_name: Trejo-Banos, Daniel
last_name: Trejo-Banos
- first_name: Athanasios
full_name: Kousathanas, Athanasios
last_name: Kousathanas
- first_name: Daniel L.
full_name: McCartney, Daniel L.
last_name: McCartney
- first_name: Sarah E.
full_name: Harris, Sarah E.
last_name: Harris
- first_name: Anna J.
full_name: Stevenson, Anna J.
last_name: Stevenson
- first_name: Marion
full_name: Patxot, Marion
last_name: Patxot
- first_name: Sven Erik
full_name: Ojavee, Sven Erik
last_name: Ojavee
- first_name: Qian
full_name: Zhang, Qian
last_name: Zhang
- first_name: David C.
full_name: Liewald, David C.
last_name: Liewald
- first_name: Craig W.
full_name: Ritchie, Craig W.
last_name: Ritchie
- first_name: Kathryn L.
full_name: Evans, Kathryn L.
last_name: Evans
- first_name: Elliot M.
full_name: Tucker-Drob, Elliot M.
last_name: Tucker-Drob
- first_name: Naomi R.
full_name: Wray, Naomi R.
last_name: Wray
- first_name: 'Allan F. '
full_name: 'McRae, Allan F. '
last_name: McRae
- first_name: Peter M.
full_name: Visscher, Peter M.
last_name: Visscher
- first_name: Ian J.
full_name: Deary, Ian J.
last_name: Deary
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: 'Riccardo E. '
full_name: 'Marioni, Riccardo E. '
last_name: Marioni
citation:
ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. 2020. doi:10.6084/m9.figshare.12629697.v1
apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris,
S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method
genome- and epigenome-wide studies of inflammatory protein levels in healthy older
adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1
chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel
L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional
File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein
Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1.
ieee: R. F. Hillary et al., “Additional file 2 of multi-method genome- and
epigenome-wide studies of inflammatory protein levels in healthy older adults.”
Springer Nature, 2020.
ista: Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson
AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob
EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional
file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein
levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1.
mla: Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and
Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.
Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1.
short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris,
A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie,
K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary,
M.R. Robinson, R.E. Marioni, (2020).
date_created: 2021-07-23T08:59:15Z
date_published: 2020-07-09T00:00:00Z
date_updated: 2026-04-02T14:28:32Z
day: '09'
department:
- _id: MaRo
doi: 10.6084/m9.figshare.12629697.v1
fulldoi: https://doi.org/10.6084/m9.figshare.12629697.v1
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.12629697.v1
month: '07'
oa: 1
oa_version: Published Version
other_data_license: CC0 + CC BY (4.0)
publisher: Springer Nature
related_material:
record:
- id: '8133'
relation: used_in_publication
status: public
status: public
title: Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory
protein levels in healthy older adults
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_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9708'
abstract:
- lang: eng
text: This research data supports 'Hard antinodal gap revealed by quantum oscillations
in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file
for plotting each figure is provided.
article_processing_charge: No
author:
- first_name: Mate
full_name: Hartstein, Mate
last_name: Hartstein
- first_name: Yu-Te
full_name: Hsu, Yu-Te
last_name: Hsu
- first_name: Kimberly A
full_name: Modic, Kimberly A
id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425
last_name: Modic
orcid: 0000-0001-9760-3147
- first_name: Juan
full_name: Porras, Juan
last_name: Porras
- first_name: Toshinao
full_name: Loew, Toshinao
last_name: Loew
- first_name: Matthieu
full_name: Le Tacon, Matthieu
last_name: Le Tacon
- first_name: Huakun
full_name: Zuo, Huakun
last_name: Zuo
- first_name: Jinhua
full_name: Wang, Jinhua
last_name: Wang
- first_name: Zengwei
full_name: Zhu, Zengwei
last_name: Zhu
- first_name: Mun
full_name: Chan, Mun
last_name: Chan
- first_name: Ross
full_name: McDonald, Ross
last_name: McDonald
- first_name: Gilbert
full_name: Lonzarich, Gilbert
last_name: Lonzarich
- first_name: Bernhard
full_name: Keimer, Bernhard
last_name: Keimer
- first_name: Suchitra
full_name: Sebastian, Suchitra
last_name: Sebastian
- first_name: Neil
full_name: Harrison, Neil
last_name: Harrison
citation:
ama: Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal
gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc
superconductors.” 2020. doi:10.17863/cam.50169
apa: Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M.,
… Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by
quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.”
Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169
chicago: Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew,
Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal
Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc
Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169.
ieee: M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap
revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc
superconductors.’” Apollo - University of Cambridge, 2020.
ista: Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang
J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N.
2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations
in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University
of Cambridge, 10.17863/cam.50169.
mla: Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed
by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.”
Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169.
short: M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H.
Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian,
N. Harrison, (2020).
date_created: 2021-07-23T10:00:35Z
date_published: 2020-05-29T00:00:00Z
date_updated: 2025-07-10T11:54:51Z
day: '29'
department:
- _id: KiMo
doi: 10.17863/cam.50169
fulldoi: https://doi.org/10.17863/cam.50169
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.17863/CAM.50169
month: '05'
oa: 1
oa_version: Published Version
publisher: Apollo - University of Cambridge
related_material:
record:
- id: '7942'
relation: used_in_publication
status: public
status: public
title: Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations
in the pseudogap regime of underdoped high-Tc superconductors'
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_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9776'
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001
apa: Grah, R., & Friedlander, T. (2020). Supporting information. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001
chicago: Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001.
ieee: R. Grah and T. Friedlander, “Supporting information.” Public Library of Science,
2020.
ista: Grah R, Friedlander T. 2020. Supporting information, Public Library of Science,
10.1371/journal.pcbi.1007642.s001.
mla: Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library
of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001.
short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:15:04Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2025-06-12T06:58:06Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s001
fulldoi: https://doi.org/10.1371/journal.pcbi.1007642.s001
month: '02'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '7569'
relation: used_in_publication
status: public
status: public
title: Supporting information
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9777'
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002
apa: Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library
of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002
chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library
of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002.
ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science,
2020.
ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science,
10.1371/journal.pcbi.1007642.s002.
mla: Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library
of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002.
short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:21:51Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2025-06-12T06:58:06Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s002
fulldoi: https://doi.org/10.1371/journal.pcbi.1007642.s002
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pcbi.1007642.s002
month: '02'
oa: 1
oa_version: None
publisher: Public Library of Science
related_material:
record:
- id: '7569'
relation: used_in_publication
status: public
status: public
title: Maximizing crosstalk
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '9779'
article_processing_charge: No
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Tamar
full_name: Friedlander, Tamar
last_name: Friedlander
citation:
ama: Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003
apa: Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public
Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003
chicago: Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public
Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003.
ieee: R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library
of Science, 2020.
ista: Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library
of Science, 10.1371/journal.pcbi.1007642.s003.
mla: Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values.
Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003.
short: R. Grah, T. Friedlander, (2020).
date_created: 2021-08-06T07:24:37Z
date_published: 2020-02-25T00:00:00Z
date_updated: 2025-06-12T06:58:06Z
day: '25'
department:
- _id: GaTk
doi: 10.1371/journal.pcbi.1007642.s003
fulldoi: https://doi.org/10.1371/journal.pcbi.1007642.s003
month: '02'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '7569'
relation: used_in_publication
status: public
status: public
title: Distribution of crosstalk values
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
_id: '9780'
abstract:
- lang: eng
text: "PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C
2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°"
article_processing_charge: No
author:
- first_name: Werner
full_name: Schlemmer, Werner
last_name: Schlemmer
- first_name: Philipp
full_name: Nothdurft, Philipp
last_name: Nothdurft
- first_name: Alina
full_name: Petzold, Alina
last_name: Petzold
- first_name: Gisbert
full_name: Riess, Gisbert
last_name: Riess
- first_name: Philipp
full_name: Frühwirt, Philipp
last_name: Frühwirt
- first_name: Max
full_name: Schmallegger, Max
last_name: Schmallegger
- first_name: Georg
full_name: Gescheidt-Demner, Georg
last_name: Gescheidt-Demner
- first_name: Roland
full_name: Fischer, Roland
last_name: Fischer
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Wolfgang
full_name: Kern, Wolfgang
last_name: Kern
- first_name: Stefan
full_name: Spirk, Stefan
last_name: Spirk
citation:
ama: 'Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal
Structure Determination. 2020. doi:10.5517/ccdc.csd.cc24vsrk'
apa: 'Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger,
M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination.
CCDC. https://doi.org/10.5517/ccdc.csd.cc24vsrk'
chicago: 'Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp
Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental
Crystal Structure Determination.” CCDC, 2020. https://doi.org/10.5517/ccdc.csd.cc24vsrk.'
ieee: 'W. Schlemmer et al., “CCDC 1991959: Experimental Crystal Structure
Determination.” CCDC, 2020.'
ista: 'Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M,
Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959:
Experimental Crystal Structure Determination, CCDC, 10.5517/ccdc.csd.cc24vsrk.'
mla: 'Schlemmer, Werner, et al. CCDC 1991959: Experimental Crystal Structure
Determination. CCDC, 2020, doi:10.5517/ccdc.csd.cc24vsrk.'
short: W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger,
G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020).
date_created: 2021-08-06T07:41:07Z
date_published: 2020-03-22T00:00:00Z
date_updated: 2026-06-18T19:32:35Z
day: '22'
department:
- _id: StFr
doi: 10.5517/ccdc.csd.cc24vsrk
fulldoi: https://doi.org/10.5517/ccdc.csd.cc24vsrk
main_file_link:
- open_access: '1'
url: https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk
month: '03'
oa: 1
oa_version: Published Version
publisher: CCDC
related_material:
record:
- id: '8329'
relation: used_in_publication
status: public
status: public
title: 'CCDC 1991959: Experimental Crystal Structure Determination'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2020'
...
---
OA_place: publisher
OA_type: hybrid
_id: '9798'
abstract:
- lang: eng
text: Fitness interactions between mutations can influence a population’s evolution
in many different ways. While epistatic effects are difficult to measure precisely,
important information is captured by the mean and variance of log fitnesses for
individuals carrying different numbers of mutations. We derive predictions for
these quantities from a class of simple fitness landscapes, based on models of
optimizing selection on quantitative traits. We also explore extensions to the
models, including modular pleiotropy, variable effect sizes, mutational bias and
maladaptation of the wild type. We illustrate our approach by reanalysing a large
dataset of mutant effects in a yeast snoRNA. Though characterized by some large
epistatic effects, these data give a good overall fit to the non-epistatic null
model, suggesting that epistasis might have limited influence on the evolutionary
dynamics in this system. We also show how the amount of epistasis depends on both
the underlying fitness landscape and the distribution of mutations, and so is
expected to vary in consistent ways between new mutations, standing variation
and fixed mutations.
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: John J.
full_name: Welch, John J.
last_name: Welch
citation:
ama: Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis
on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957472.v1
apa: Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S2 from the
distribution of epistasis on simple fitness landscapes. Royal Society of London.
https://doi.org/10.6084/m9.figshare.7957472.v1
chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from
the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of
London, 2020. https://doi.org/10.6084/m9.figshare.7957472.v1.
ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution
of epistasis on simple fitness landscapes.” Royal Society of London, 2020.
ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution
of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957472.v1.
mla: Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S2 from
the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society
of London, 2020, doi:10.6084/m9.figshare.7957472.v1.
short: C. Fraisse, J.J. Welch, (2020).
date_created: 2021-08-06T11:18:15Z
date_published: 2020-10-15T00:00:00Z
date_updated: 2026-06-18T19:05:02Z
day: '15'
department:
- _id: BeVi
- _id: NiBa
doi: 10.6084/m9.figshare.7957472.v1
fulldoi: https://doi.org/10.6084/m9.figshare.7957472.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7957472.v1
month: '10'
oa: 1
oa_version: Published Version
publisher: Royal Society of London
related_material:
record:
- id: '6467'
relation: used_in_publication
status: public
status: public
title: Simulation code for Fig S2 from the distribution of epistasis on simple fitness
landscapes
type: research_data_reference
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
year: '2020'
...
---
OA_place: publisher
OA_type: hybrid
_id: '9799'
abstract:
- lang: eng
text: Fitness interactions between mutations can influence a population’s evolution
in many different ways. While epistatic effects are difficult to measure precisely,
important information is captured by the mean and variance of log fitnesses for
individuals carrying different numbers of mutations. We derive predictions for
these quantities from a class of simple fitness landscapes, based on models of
optimizing selection on quantitative traits. We also explore extensions to the
models, including modular pleiotropy, variable effect sizes, mutational bias and
maladaptation of the wild type. We illustrate our approach by reanalysing a large
dataset of mutant effects in a yeast snoRNA. Though characterized by some large
epistatic effects, these data give a good overall fit to the non-epistatic null
model, suggesting that epistasis might have limited influence on the evolutionary
dynamics in this system. We also show how the amount of epistasis depends on both
the underlying fitness landscape and the distribution of mutations, and so is
expected to vary in consistent ways between new mutations, standing variation
and fixed mutations.
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: John J.
full_name: Welch, John J.
last_name: Welch
citation:
ama: Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis
on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957469.v1
apa: Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S1 from the
distribution of epistasis on simple fitness landscapes. Royal Society of London.
https://doi.org/10.6084/m9.figshare.7957469.v1
chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from
the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of
London, 2020. https://doi.org/10.6084/m9.figshare.7957469.v1.
ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution
of epistasis on simple fitness landscapes.” Royal Society of London, 2020.
ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution
of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957469.v1.
mla: Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from
the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society
of London, 2020, doi:10.6084/m9.figshare.7957469.v1.
short: C. Fraisse, J.J. Welch, (2020).
date_created: 2021-08-06T11:26:57Z
date_published: 2020-10-15T00:00:00Z
date_updated: 2026-06-18T19:05:02Z
day: '15'
department:
- _id: BeVi
- _id: NiBa
doi: 10.6084/m9.figshare.7957469.v1
fulldoi: https://doi.org/10.6084/m9.figshare.7957469.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.7957469.v1
month: '10'
oa: 1
oa_version: Published Version
publisher: Royal Society of London
related_material:
record:
- id: '6467'
relation: used_in_publication
status: public
status: public
title: Simulation code for Fig S1 from the distribution of epistasis on simple fitness
landscapes
type: research_data_reference
user_id: 0043cee0-e5fc-11ee-9736-f83bc23afbf0
year: '2020'
...
---
_id: '6488'
abstract:
- lang: eng
text: We prove a central limit theorem for the difference of linear eigenvalue statistics
of a sample covariance matrix W˜ and its minor W. We find that the fluctuation
of this difference is much smaller than those of the individual linear statistics,
as a consequence of the strong correlation between the eigenvalues of W˜ and W.
Our result identifies the fluctuation of the spatial derivative of the approximate
Gaussian field in the recent paper by Dumitru and Paquette. Unlike in a similar
result for Wigner matrices, for sample covariance matrices, the fluctuation may
entirely vanish.
article_number: '2050006'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Giorgio
full_name: Cipolloni, Giorgio
id: 42198EFA-F248-11E8-B48F-1D18A9856A87
last_name: Cipolloni
orcid: 0000-0002-4901-7992
- first_name: László
full_name: Erdös, László
id: 4DBD5372-F248-11E8-B48F-1D18A9856A87
last_name: Erdös
orcid: 0000-0001-5366-9603
citation:
ama: 'Cipolloni G, Erdös L. Fluctuations for differences of linear eigenvalue statistics
for sample covariance matrices. Random Matrices: Theory and Application.
2020;9(3). doi:10.1142/S2010326320500069'
apa: 'Cipolloni, G., & Erdös, L. (2020). Fluctuations for differences of linear
eigenvalue statistics for sample covariance matrices. Random Matrices: Theory
and Application. World Scientific Publishing. https://doi.org/10.1142/S2010326320500069'
chicago: 'Cipolloni, Giorgio, and László Erdös. “Fluctuations for Differences of
Linear Eigenvalue Statistics for Sample Covariance Matrices.” Random Matrices:
Theory and Application. World Scientific Publishing, 2020. https://doi.org/10.1142/S2010326320500069.'
ieee: 'G. Cipolloni and L. Erdös, “Fluctuations for differences of linear eigenvalue
statistics for sample covariance matrices,” Random Matrices: Theory and Application,
vol. 9, no. 3. World Scientific Publishing, 2020.'
ista: 'Cipolloni G, Erdös L. 2020. Fluctuations for differences of linear eigenvalue
statistics for sample covariance matrices. Random Matrices: Theory and Application.
9(3), 2050006.'
mla: 'Cipolloni, Giorgio, and László Erdös. “Fluctuations for Differences of Linear
Eigenvalue Statistics for Sample Covariance Matrices.” Random Matrices: Theory
and Application, vol. 9, no. 3, 2050006, World Scientific Publishing, 2020,
doi:10.1142/S2010326320500069.'
short: 'G. Cipolloni, L. Erdös, Random Matrices: Theory and Application 9 (2020).'
date_created: 2019-05-26T21:59:14Z
date_published: 2020-07-01T00:00:00Z
date_updated: 2025-07-10T11:53:26Z
day: '01'
department:
- _id: LaEr
doi: 10.1142/S2010326320500069
ec_funded: 1
external_id:
arxiv:
- '1806.08751'
isi:
- '000547464400001'
fulldoi: https://doi.org/10.1142/S2010326320500069
intvolume: ' 9'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1806.08751
month: '07'
oa: 1
oa_version: Preprint
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: 'Random Matrices: Theory and Application'
publication_identifier:
eissn:
- 2010-3271
issn:
- 2010-3263
publication_status: published
publisher: World Scientific Publishing
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fluctuations for differences of linear eigenvalue statistics for sample covariance
matrices
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2020'
...
---
_id: '6563'
abstract:
- lang: eng
text: "This paper presents two algorithms. The first decides the existence of a
pointed homotopy between given simplicial maps \U0001D453,\U0001D454:\U0001D44B→\U0001D44C,
and the second computes the group [\U0001D6F4\U0001D44B,\U0001D44C]∗ of pointed
homotopy classes of maps from a suspension; in both cases, the target Y is assumed
simply connected. More generally, these algorithms work relative to \U0001D434⊆\U0001D44B."
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Marek
full_name: Filakovský, Marek
id: 3E8AF77E-F248-11E8-B48F-1D18A9856A87
last_name: Filakovský
- first_name: Lukas
full_name: Vokřínek, Lukas
last_name: Vokřínek
citation:
ama: Filakovský M, Vokřínek L. Are two given maps homotopic? An algorithmic viewpoint.
Foundations of Computational Mathematics. 2020;20:311-330. doi:10.1007/s10208-019-09419-x
apa: Filakovský, M., & Vokřínek, L. (2020). Are two given maps homotopic? An
algorithmic viewpoint. Foundations of Computational Mathematics. Springer
Nature. https://doi.org/10.1007/s10208-019-09419-x
chicago: Filakovský, Marek, and Lukas Vokřínek. “Are Two given Maps Homotopic? An
Algorithmic Viewpoint.” Foundations of Computational Mathematics. Springer
Nature, 2020. https://doi.org/10.1007/s10208-019-09419-x.
ieee: M. Filakovský and L. Vokřínek, “Are two given maps homotopic? An algorithmic
viewpoint,” Foundations of Computational Mathematics, vol. 20. Springer
Nature, pp. 311–330, 2020.
ista: Filakovský M, Vokřínek L. 2020. Are two given maps homotopic? An algorithmic
viewpoint. Foundations of Computational Mathematics. 20, 311–330.
mla: Filakovský, Marek, and Lukas Vokřínek. “Are Two given Maps Homotopic? An Algorithmic
Viewpoint.” Foundations of Computational Mathematics, vol. 20, Springer
Nature, 2020, pp. 311–30, doi:10.1007/s10208-019-09419-x.
short: M. Filakovský, L. Vokřínek, Foundations of Computational Mathematics 20 (2020)
311–330.
date_created: 2019-06-16T21:59:14Z
date_published: 2020-04-01T00:00:00Z
date_updated: 2025-07-10T11:53:32Z
day: '01'
department:
- _id: UlWa
doi: 10.1007/s10208-019-09419-x
external_id:
arxiv:
- '1312.2337'
isi:
- '000522437400004'
fulldoi: https://doi.org/10.1007/s10208-019-09419-x
intvolume: ' 20'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1312.2337
month: '04'
oa: 1
oa_version: Preprint
page: 311-330
project:
- _id: 26611F5C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P31312
name: Algorithms for Embeddings and Homotopy Theory
publication: Foundations of Computational Mathematics
publication_identifier:
eissn:
- 1615-3383
issn:
- 1615-3375
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Are two given maps homotopic? An algorithmic viewpoint
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2020'
...