---
_id: '7159'
abstract:
- lang: eng
text: 'Cyber-physical systems (CPS) and the Internet-of-Things (IoT) result in a
tremendous amount of generated, measured and recorded time-series data. Extracting
temporal segments that encode patterns with useful information out of these huge
amounts of data is an extremely difficult problem. We propose shape expressions
as a declarative formalism for specifying, querying and extracting sophisticated
temporal patterns from possibly noisy data. Shape expressions are regular expressions
with arbitrary (linear, exponential, sinusoidal, etc.) shapes with parameters
as atomic predicates and additional constraints on these parameters. We equip
shape expressions with a novel noisy semantics that combines regular expression
matching semantics with statistical regression. We characterize essential properties
of the formalism and propose an efficient approximate shape expression matching
procedure. We demonstrate the wide applicability of this technique on two case
studies. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Dejan
full_name: Ničković, Dejan
last_name: Ničković
- first_name: Xin
full_name: Qin, Xin
last_name: Qin
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Cristinel
full_name: Mateis, Cristinel
last_name: Mateis
- first_name: Jyotirmoy
full_name: Deshmukh, Jyotirmoy
last_name: Deshmukh
citation:
ama: 'Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. Shape expressions for
specifying and extracting signal features. In: 19th International Conference
on Runtime Verification. Vol 11757. Springer Nature; 2019:292-309. doi:10.1007/978-3-030-32079-9_17'
apa: 'Ničković, D., Qin, X., Ferrere, T., Mateis, C., & Deshmukh, J. (2019).
Shape expressions for specifying and extracting signal features. In 19th International
Conference on Runtime Verification (Vol. 11757, pp. 292–309). Porto, Portugal:
Springer Nature. https://doi.org/10.1007/978-3-030-32079-9_17'
chicago: Ničković, Dejan, Xin Qin, Thomas Ferrere, Cristinel Mateis, and Jyotirmoy
Deshmukh. “Shape Expressions for Specifying and Extracting Signal Features.” In
19th International Conference on Runtime Verification, 11757:292–309. Springer
Nature, 2019. https://doi.org/10.1007/978-3-030-32079-9_17.
ieee: D. Ničković, X. Qin, T. Ferrere, C. Mateis, and J. Deshmukh, “Shape expressions
for specifying and extracting signal features,” in 19th International Conference
on Runtime Verification, Porto, Portugal, 2019, vol. 11757, pp. 292–309.
ista: 'Ničković D, Qin X, Ferrere T, Mateis C, Deshmukh J. 2019. Shape expressions
for specifying and extracting signal features. 19th International Conference on
Runtime Verification. RV: Runtime Verification, LNCS, vol. 11757, 292–309.'
mla: Ničković, Dejan, et al. “Shape Expressions for Specifying and Extracting Signal
Features.” 19th International Conference on Runtime Verification, vol.
11757, Springer Nature, 2019, pp. 292–309, doi:10.1007/978-3-030-32079-9_17.
short: D. Ničković, X. Qin, T. Ferrere, C. Mateis, J. Deshmukh, in:, 19th International
Conference on Runtime Verification, Springer Nature, 2019, pp. 292–309.
conference:
end_date: 2019-10-11
location: Porto, Portugal
name: 'RV: Runtime Verification'
start_date: 2019-10-08
date_created: 2019-12-09T08:47:55Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2023-09-06T11:24:10Z
day: '01'
department:
- _id: ToHe
doi: 10.1007/978-3-030-32079-9_17
external_id:
isi:
- '000570006300017'
intvolume: ' 11757'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 292-309
project:
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25F2ACDE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11402-N23
name: Rigorous Systems Engineering
publication: 19th International Conference on Runtime Verification
publication_identifier:
isbn:
- '9783030320782'
- '9783030320799'
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Shape expressions for specifying and extracting signal features
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11757
year: '2019'
...
---
_id: '7183'
abstract:
- lang: eng
text: 'A probabilistic vector addition system with states (pVASS) is a finite state
Markov process augmented with non-negative integer counters that can be incremented
or decremented during each state transition, blocking any behaviour that would
cause a counter to decrease below zero. The pVASS can be used as abstractions
of probabilistic programs with many decidable properties. The use of pVASS as
abstractions requires the presence of nondeterminism in the model. In this paper,
we develop techniques for checking fast termination of pVASS with nondeterminism.
That is, for every initial configuration of size n, we consider the worst expected
number of transitions needed to reach a configuration with some counter negative
(the expected termination time). We show that the problem whether the asymptotic
expected termination time is linear is decidable in polynomial time for a certain
natural class of pVASS with nondeterminism. Furthermore, we show the following
dichotomy: if the asymptotic expected termination time is not linear, then it
is at least quadratic, i.e., in Ω(n2).'
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Tomás
full_name: Brázdil, Tomás
last_name: Brázdil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Antonín
full_name: Kucera, Antonín
last_name: Kucera
- first_name: Petr
full_name: Novotný, Petr
id: 3CC3B868-F248-11E8-B48F-1D18A9856A87
last_name: Novotný
- first_name: Dominik
full_name: Velan, Dominik
last_name: Velan
citation:
ama: 'Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. Deciding fast termination
for probabilistic VASS with nondeterminism. In: International Symposium on
Automated Technology for Verification and Analysis. Vol 11781. Springer Nature;
2019:462-478. doi:10.1007/978-3-030-31784-3_27'
apa: 'Brázdil, T., Chatterjee, K., Kucera, A., Novotný, P., & Velan, D. (2019).
Deciding fast termination for probabilistic VASS with nondeterminism. In International
Symposium on Automated Technology for Verification and Analysis (Vol. 11781,
pp. 462–478). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-030-31784-3_27'
chicago: Brázdil, Tomás, Krishnendu Chatterjee, Antonín Kucera, Petr Novotný, and
Dominik Velan. “Deciding Fast Termination for Probabilistic VASS with Nondeterminism.”
In International Symposium on Automated Technology for Verification and Analysis,
11781:462–78. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31784-3_27.
ieee: T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, and D. Velan, “Deciding
fast termination for probabilistic VASS with nondeterminism,” in International
Symposium on Automated Technology for Verification and Analysis, Taipei, Taiwan,
2019, vol. 11781, pp. 462–478.
ista: 'Brázdil T, Chatterjee K, Kucera A, Novotný P, Velan D. 2019. Deciding fast
termination for probabilistic VASS with nondeterminism. International Symposium
on Automated Technology for Verification and Analysis. ATVA: Automated TEchnology
for Verification and Analysis, LNCS, vol. 11781, 462–478.'
mla: Brázdil, Tomás, et al. “Deciding Fast Termination for Probabilistic VASS with
Nondeterminism.” International Symposium on Automated Technology for Verification
and Analysis, vol. 11781, Springer Nature, 2019, pp. 462–78, doi:10.1007/978-3-030-31784-3_27.
short: T. Brázdil, K. Chatterjee, A. Kucera, P. Novotný, D. Velan, in:, International
Symposium on Automated Technology for Verification and Analysis, Springer Nature,
2019, pp. 462–478.
conference:
end_date: 2019-10-31
location: Taipei, Taiwan
name: 'ATVA: Automated TEchnology for Verification and Analysis'
start_date: 2019-10-28
date_created: 2019-12-15T23:00:44Z
date_published: 2019-10-21T00:00:00Z
date_updated: 2023-09-06T12:40:58Z
day: '21'
department:
- _id: KrCh
doi: 10.1007/978-3-030-31784-3_27
external_id:
arxiv:
- '1907.11010'
isi:
- '000723515700027'
intvolume: ' 11781'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.11010
month: '10'
oa: 1
oa_version: Preprint
page: 462-478
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
publication: International Symposium on Automated Technology for Verification and
Analysis
publication_identifier:
eissn:
- '16113349'
isbn:
- '9783030317836'
issn:
- '03029743'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deciding fast termination for probabilistic VASS with nondeterminism
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11781
year: '2019'
...
---
_id: '7182'
abstract:
- lang: eng
text: During infection pathogens secrete small molecules, termed effectors, to manipulate
and control the interaction with their specific hosts. Both the pathogen and the
plant are under high selective pressure to rapidly adapt and co-evolve in what
is usually referred to as molecular arms race. Components of the host’s immune
system form a network that processes information about molecules with a foreign
origin and damage-associated signals, integrating them with developmental and
abiotic cues to adapt the plant’s responses. Both in the case of nucleotide-binding
leucine-rich repeat receptors and leucine-rich repeat receptor kinases interaction
networks have been extensively characterized. However, little is known on whether
pathogenic effectors form complexes to overcome plant immunity and promote disease.
Ustilago maydis, a biotrophic fungal pathogen that infects maize plants, produces
effectors that target hubs in the immune network of the host cell. Here we assess
the capability of U. maydis effector candidates to interact with each other, which
may play a crucial role during the infection process. Using a systematic yeast-two-hybrid
approach and based on a preliminary pooled screen, we selected 63 putative effectors
for one-on-one matings with a library of nearly 300 effector candidates. We found
that 126 of these effector candidates interacted either with themselves or other
predicted effectors. Although the functional relevance of the observed interactions
remains elusive, we propose that the observed abundance in complex formation between
effectors adds an additional level of complexity to effector research and should
be taken into consideration when studying effector evolution and function. Based
on this fundamental finding, we suggest various scenarios which could evolutionarily
drive the formation and stabilization of an effector interactome.
article_number: '1437'
article_processing_charge: No
article_type: original
author:
- first_name: André
full_name: Alcântara, André
last_name: Alcântara
- first_name: Jason
full_name: Bosch, Jason
last_name: Bosch
- first_name: Fahimeh
full_name: Nazari, Fahimeh
last_name: Nazari
- first_name: Gesa
full_name: Hoffmann, Gesa
last_name: Hoffmann
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: Simon
full_name: Uhse, Simon
last_name: Uhse
- first_name: Martin A.
full_name: Darino, Martin A.
last_name: Darino
- first_name: Toluwase
full_name: Olukayode, Toluwase
last_name: Olukayode
- first_name: Daniel
full_name: Reumann, Daniel
last_name: Reumann
- first_name: Laura
full_name: Baggaley, Laura
last_name: Baggaley
- first_name: Armin
full_name: Djamei, Armin
last_name: Djamei
citation:
ama: Alcântara A, Bosch J, Nazari F, et al. Systematic Y2H screening reveals extensive
effector-complex formation. Frontiers in Plant Science. 2019;10(11). doi:10.3389/fpls.2019.01437
apa: Alcântara, A., Bosch, J., Nazari, F., Hoffmann, G., Gallei, M. C., Uhse, S.,
… Djamei, A. (2019). Systematic Y2H screening reveals extensive effector-complex
formation. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2019.01437
chicago: Alcântara, André, Jason Bosch, Fahimeh Nazari, Gesa Hoffmann, Michelle
C Gallei, Simon Uhse, Martin A. Darino, et al. “Systematic Y2H Screening Reveals
Extensive Effector-Complex Formation.” Frontiers in Plant Science. Frontiers,
2019. https://doi.org/10.3389/fpls.2019.01437.
ieee: A. Alcântara et al., “Systematic Y2H screening reveals extensive effector-complex
formation,” Frontiers in Plant Science, vol. 10, no. 11. Frontiers, 2019.
ista: Alcântara A, Bosch J, Nazari F, Hoffmann G, Gallei MC, Uhse S, Darino MA,
Olukayode T, Reumann D, Baggaley L, Djamei A. 2019. Systematic Y2H screening reveals
extensive effector-complex formation. Frontiers in Plant Science. 10(11), 1437.
mla: Alcântara, André, et al. “Systematic Y2H Screening Reveals Extensive Effector-Complex
Formation.” Frontiers in Plant Science, vol. 10, no. 11, 1437, Frontiers,
2019, doi:10.3389/fpls.2019.01437.
short: A. Alcântara, J. Bosch, F. Nazari, G. Hoffmann, M.C. Gallei, S. Uhse, M.A.
Darino, T. Olukayode, D. Reumann, L. Baggaley, A. Djamei, Frontiers in Plant Science
10 (2019).
date_created: 2019-12-15T23:00:43Z
date_published: 2019-11-14T00:00:00Z
date_updated: 2023-09-06T14:33:46Z
day: '14'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.3389/fpls.2019.01437
external_id:
isi:
- '000499821700001'
pmid:
- '31803201'
file:
- access_level: open_access
checksum: 995aa838aec2064d93550de82b40bbd1
content_type: application/pdf
creator: dernst
date_created: 2019-12-16T07:58:43Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7185'
file_name: 2019_FrontiersPlant_Alcantara.pdf
file_size: 1532505
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Plant Science
publication_identifier:
eissn:
- 1664462X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Systematic Y2H screening reveals extensive effector-complex formation
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10
year: '2019'
...
---
_id: '7180'
abstract:
- lang: eng
text: Arabidopsis PIN2 protein directs transport of the phytohormone auxin from
the root tip into the root elongation zone. Variation in hormone transport, which
depends on a delicate interplay between PIN2 sorting to and from polar plasma
membrane domains, determines root growth. By employing a constitutively degraded
version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis.
This response does not require de novo protein synthesis, but involves early events
in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2
sorting and intracellular distribution governs formation of a lateral PIN2 gradient
in gravistimulated roots, coinciding with adjustments in auxin signaling and directional
root growth. Strikingly, simulations indicate that PIN2 gradient formation is
no prerequisite for root bending but rather dampens asymmetric auxin flow and
signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting,
thus, appears essential for determining the rate of gravity-induced root curvature
via attenuation of differential cell elongation.
article_number: '5516'
article_processing_charge: No
article_type: original
author:
- first_name: Katarzyna
full_name: Retzer, Katarzyna
last_name: Retzer
- first_name: Maria
full_name: Akhmanova, Maria
id: 3425EC26-F248-11E8-B48F-1D18A9856A87
last_name: Akhmanova
orcid: 0000-0003-1522-3162
- first_name: Nataliia
full_name: Konstantinova, Nataliia
last_name: Konstantinova
- first_name: Kateřina
full_name: Malínská, Kateřina
last_name: Malínská
- first_name: Johannes
full_name: Leitner, Johannes
last_name: Leitner
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Christian
full_name: Luschnig, Christian
last_name: Luschnig
citation:
ama: Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits
root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature
Communications. 2019;10. doi:10.1038/s41467-019-13543-1
apa: Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek,
J., & Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism
via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-019-13543-1
chicago: Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská,
Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling
Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.”
Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13543-1.
ieee: K. Retzer et al., “Brassinosteroid signaling delimits root gravitropism
via sorting of the Arabidopsis PIN2 auxin transporter,” Nature Communications,
vol. 10. Springer Nature, 2019.
ista: Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J,
Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting
of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.
mla: Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism
via Sorting of the Arabidopsis PIN2 Auxin Transporter.” Nature Communications,
vol. 10, 5516, Springer Nature, 2019, doi:10.1038/s41467-019-13543-1.
short: K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek,
C. Luschnig, Nature Communications 10 (2019).
date_created: 2019-12-15T23:00:43Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T14:08:21Z
day: '01'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.1038/s41467-019-13543-1
external_id:
isi:
- '000500508100001'
pmid:
- '31797871'
file:
- access_level: open_access
checksum: 77e8720a8e0f3091b98159f85be40893
content_type: application/pdf
creator: dernst
date_created: 2019-12-16T07:37:50Z
date_updated: 2020-07-14T12:47:52Z
file_id: '7184'
file_name: 2019_NatureComm_Retzer.pdf
file_size: 5156533
relation: main_file
file_date_updated: 2020-07-14T12:47:52Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 264CBBAC-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02379
name: Modeling epithelial tissue mechanics during cell invasion
publication: Nature Communications
publication_identifier:
eissn:
- '20411723'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis
PIN2 auxin transporter
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 10
year: '2019'
...
---
_id: '7181'
abstract:
- lang: eng
text: Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary
predictions1,2, but the complexity of aligning large datasets requires the use
of approximate solutions3, including the progressive algorithm4. Progressive MSA
methods start by aligning the most similar sequences and subsequently incorporate
the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy
declines substantially as the number of sequences is scaled up5. We introduce
a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard
workstation and substantially improves accuracy on datasets larger than 10,000
sequences. Our regressive algorithm works the other way around to the progressive
algorithm and begins by aligning the most dissimilar sequences. It uses an efficient
divide-and-conquer strategy to run third-party alignment methods in linear time,
regardless of their original complexity. Our approach will enable analyses of
extremely large genomic datasets such as the recently announced Earth BioGenome
Project, which comprises 1.5 million eukaryotic genomes6.
article_processing_charge: No
article_type: original
author:
- first_name: Edgar
full_name: Garriga, Edgar
last_name: Garriga
- first_name: Paolo
full_name: Di Tommaso, Paolo
last_name: Di Tommaso
- first_name: Cedrik
full_name: Magis, Cedrik
last_name: Magis
- first_name: Ionas
full_name: Erb, Ionas
last_name: Erb
- first_name: Leila
full_name: Mansouri, Leila
last_name: Mansouri
- first_name: Athanasios
full_name: Baltzis, Athanasios
last_name: Baltzis
- first_name: Hafid
full_name: Laayouni, Hafid
last_name: Laayouni
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Evan
full_name: Floden, Evan
last_name: Floden
- first_name: Cedric
full_name: Notredame, Cedric
last_name: Notredame
citation:
ama: Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470.
doi:10.1038/s41587-019-0333-6
apa: Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,
… Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf
regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6
chicago: Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri,
Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric
Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive
Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.
ieee: E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf
regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature,
pp. 1466–1470, 2019.
ista: Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H,
Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.
mla: Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf
Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature,
2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.
short: E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H.
Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019)
1466–1470.
date_created: 2019-12-15T23:00:43Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T14:32:52Z
day: '01'
department:
- _id: FyKo
doi: 10.1038/s41587-019-0333-6
ec_funded: 1
external_id:
isi:
- '000500748900021'
pmid:
- '31792410'
intvolume: ' 37'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1466-1470
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Biotechnology
publication_identifier:
eissn:
- '15461696'
issn:
- '10870156'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13059'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Large multiple sequence alignments with a root-to-leaf regressive method
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2019'
...
---
_id: '7202'
abstract:
- lang: eng
text: The cerebral cortex contains multiple areas with distinctive cytoarchitectonical
patterns, but the cellular mechanisms underlying the emergence of this diversity
remain unclear. Here, we have investigated the neuronal output of individual progenitor
cells in the developing mouse neocortex using a combination of methods that together
circumvent the biases and limitations of individual approaches. Our experimental
results indicate that progenitor cells generate pyramidal cell lineages with a
wide range of sizes and laminar configurations. Mathematical modelling indicates
that these outcomes are compatible with a stochastic model of cortical neurogenesis
in which progenitor cells undergo a series of probabilistic decisions that lead
to the specification of very heterogeneous progenies. Our findings support a mechanism
for cortical neurogenesis whose flexibility would make it capable to generate
the diverse cytoarchitectures that characterize distinct neocortical areas.
article_number: e51381
article_processing_charge: No
article_type: original
author:
- first_name: Alfredo
full_name: Llorca, Alfredo
last_name: Llorca
- first_name: Gabriele
full_name: Ciceri, Gabriele
last_name: Ciceri
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Fong Kuan
full_name: Wong, Fong Kuan
last_name: Wong
- first_name: Giovanni
full_name: Diana, Giovanni
last_name: Diana
- first_name: Eleni
full_name: Serafeimidou-Pouliou, Eleni
last_name: Serafeimidou-Pouliou
- first_name: Marian
full_name: Fernández-Otero, Marian
last_name: Fernández-Otero
- first_name: Carmen
full_name: Streicher, Carmen
id: 36BCB99C-F248-11E8-B48F-1D18A9856A87
last_name: Streicher
- first_name: Sebastian J.
full_name: Arnold, Sebastian J.
last_name: Arnold
- first_name: Martin
full_name: Meyer, Martin
last_name: Meyer
- first_name: Simon
full_name: Hippenmeyer, Simon
id: 37B36620-F248-11E8-B48F-1D18A9856A87
last_name: Hippenmeyer
orcid: 0000-0003-2279-1061
- first_name: Miguel
full_name: Maravall, Miguel
last_name: Maravall
- first_name: Oscar
full_name: Marín, Oscar
last_name: Marín
citation:
ama: Llorca A, Ciceri G, Beattie RJ, et al. A stochastic framework of neurogenesis
underlies the assembly of neocortical cytoarchitecture. eLife. 2019;8.
doi:10.7554/eLife.51381
apa: Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou-Pouliou,
E., … Marín, O. (2019). A stochastic framework of neurogenesis underlies the assembly
of neocortical cytoarchitecture. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.51381
chicago: Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong Kuan Wong, Giovanni
Diana, Eleni Serafeimidou-Pouliou, Marian Fernández-Otero, et al. “A Stochastic
Framework of Neurogenesis Underlies the Assembly of Neocortical Cytoarchitecture.”
ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.51381.
ieee: A. Llorca et al., “A stochastic framework of neurogenesis underlies
the assembly of neocortical cytoarchitecture,” eLife, vol. 8. eLife Sciences
Publications, 2019.
ista: Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou-Pouliou E,
Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M,
Marín O. 2019. A stochastic framework of neurogenesis underlies the assembly of
neocortical cytoarchitecture. eLife. 8, e51381.
mla: Llorca, Alfredo, et al. “A Stochastic Framework of Neurogenesis Underlies the
Assembly of Neocortical Cytoarchitecture.” ELife, vol. 8, e51381, eLife
Sciences Publications, 2019, doi:10.7554/eLife.51381.
short: A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou-Pouliou,
M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall,
O. Marín, ELife 8 (2019).
date_created: 2019-12-22T23:00:42Z
date_published: 2019-11-18T00:00:00Z
date_updated: 2023-09-06T14:38:39Z
day: '18'
ddc:
- '570'
department:
- _id: SiHi
doi: 10.7554/eLife.51381
ec_funded: 1
external_id:
isi:
- '000508156800001'
pmid:
- '31736464'
file:
- access_level: open_access
checksum: b460ecc33e1a68265e7adea775021f3a
content_type: application/pdf
creator: dernst
date_created: 2020-02-18T15:19:26Z
date_updated: 2020-07-14T12:47:53Z
file_id: '7503'
file_name: 2019_eLife_Llorca.pdf
file_size: 2960543
relation: main_file
file_date_updated: 2020-07-14T12:47:53Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260018B0-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '725780'
name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development
- _id: 264E56E2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02416
name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: A stochastic framework of neurogenesis underlies the assembly of neocortical
cytoarchitecture
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2019'
...
---
_id: '7179'
abstract:
- lang: eng
text: Glutamate is the major excitatory neurotransmitter in the CNS binding to a
variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8)
can act excitatory or inhibitory, depending on associated signal cascades. Expression
and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the
cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4,
mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to
the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3,
and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants.
Using receptor-specific antibodies in cochlear wholemounts, we found expression
of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution
and confocal microscopy in combination with 3-dimensional reconstructions indicated
a postsynaptic localization of mGluR2 that overlaps with postsynaptic density
protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast,
mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary,
we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament
for new therapeutical strategies that could protect the cochlea against noxious
stimuli and excitotoxicity.
article_processing_charge: No
article_type: original
author:
- first_name: Lisa
full_name: Klotz, Lisa
last_name: Klotz
- first_name: Olaf
full_name: Wendler, Olaf
last_name: Wendler
- first_name: Renato
full_name: Frischknecht, Renato
last_name: Frischknecht
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Holger
full_name: Schulze, Holger
last_name: Schulze
- first_name: Ralf
full_name: Enz, Ralf
last_name: Enz
citation:
ama: Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization
of group II and III metabotropic glutamate receptors at pre- and postsynaptic
sites of inner hair cell ribbon synapses. FASEB Journal. 2019;33(12):13734-13746.
doi:10.1096/fj.201901543R
apa: Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., &
Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors
at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal.
FASEB. https://doi.org/10.1096/fj.201901543R
chicago: Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger
Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate
Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.”
FASEB Journal. FASEB, 2019. https://doi.org/10.1096/fj.201901543R.
ieee: L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz,
“Localization of group II and III metabotropic glutamate receptors at pre- and
postsynaptic sites of inner hair cell ribbon synapses,” FASEB Journal,
vol. 33, no. 12. FASEB, pp. 13734–13746, 2019.
ista: Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization
of group II and III metabotropic glutamate receptors at pre- and postsynaptic
sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.
mla: Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate
Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.”
FASEB Journal, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:10.1096/fj.201901543R.
short: L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz,
FASEB Journal 33 (2019) 13734–13746.
date_created: 2019-12-15T23:00:42Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T14:34:36Z
day: '01'
ddc:
- '571'
- '599'
department:
- _id: RySh
doi: 10.1096/fj.201901543R
external_id:
isi:
- '000507466100054'
pmid:
- '31585509'
file:
- access_level: open_access
checksum: 79e3b72481dc32489911121cf3b7d8d0
content_type: application/pdf
creator: shigemot
date_created: 2020-12-06T17:30:09Z
date_updated: 2020-12-06T17:30:09Z
file_id: '8922'
file_name: Klotz et al 2019 EMBO Reports.pdf
file_size: 4766789
relation: main_file
success: 1
file_date_updated: 2020-12-06T17:30:09Z
has_accepted_license: '1'
intvolume: ' 33'
isi: 1
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Submitted Version
page: 13734-13746
pmid: 1
publication: FASEB Journal
publication_identifier:
eissn:
- '15306860'
publication_status: published
publisher: FASEB
quality_controlled: '1'
scopus_import: '1'
status: public
title: Localization of group II and III metabotropic glutamate receptors at pre- and
postsynaptic sites of inner hair cell ribbon synapses
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 33
year: '2019'
...
---
_id: '7201'
abstract:
- lang: eng
text: Applying machine learning techniques to the quickly growing data in science
and industry requires highly-scalable algorithms. Large datasets are most commonly
processed "data parallel" distributed across many nodes. Each node's contribution
to the overall gradient is summed using a global allreduce. This allreduce is
the single communication and thus scalability bottleneck for most machine learning
workloads. We observe that frequently, many gradient values are (close to) zero,
leading to sparse of sparsifyable communications. To exploit this insight, we
analyze, design, and implement a set of communication-efficient protocols for
sparse input data, in conjunction with efficient machine learning algorithms which
can leverage these primitives. Our communication protocols generalize standard
collective operations, by allowing processes to contribute arbitrary sparse input
data vectors. Our generic communication library, SparCML1, extends MPI to support
additional features, such as non-blocking (asynchronous) operations and low-precision
data representations. As such, SparCML and its techniques will form the basis
of future highly-scalable machine learning frameworks.
article_number: a11
article_processing_charge: No
author:
- first_name: Cedric
full_name: Renggli, Cedric
last_name: Renggli
- first_name: Saleh
full_name: Ashkboos, Saleh
id: 0D0A9058-257B-11EA-A937-9341C3D8BC8A
last_name: Ashkboos
- first_name: Mehdi
full_name: Aghagolzadeh, Mehdi
last_name: Aghagolzadeh
- 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: Torsten
full_name: Hoefler, Torsten
last_name: Hoefler
citation:
ama: 'Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. SparCML: High-performance
sparse communication for machine learning. In: International Conference for
High Performance Computing, Networking, Storage and Analysis, SC. ACM; 2019.
doi:10.1145/3295500.3356222'
apa: 'Renggli, C., Ashkboos, S., Aghagolzadeh, M., Alistarh, D.-A., & Hoefler,
T. (2019). SparCML: High-performance sparse communication for machine learning.
In International Conference for High Performance Computing, Networking, Storage
and Analysis, SC. Denver, CO, Unites States: ACM. https://doi.org/10.1145/3295500.3356222'
chicago: 'Renggli, Cedric, Saleh Ashkboos, Mehdi Aghagolzadeh, Dan-Adrian Alistarh,
and Torsten Hoefler. “SparCML: High-Performance Sparse Communication for Machine
Learning.” In International Conference for High Performance Computing, Networking,
Storage and Analysis, SC. ACM, 2019. https://doi.org/10.1145/3295500.3356222.'
ieee: 'C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, and T. Hoefler,
“SparCML: High-performance sparse communication for machine learning,” in International
Conference for High Performance Computing, Networking, Storage and Analysis, SC,
Denver, CO, Unites States, 2019.'
ista: 'Renggli C, Ashkboos S, Aghagolzadeh M, Alistarh D-A, Hoefler T. 2019. SparCML:
High-performance sparse communication for machine learning. International Conference
for High Performance Computing, Networking, Storage and Analysis, SC. SC: Conference
for High Performance Computing, Networking, Storage and Analysis, a11.'
mla: 'Renggli, Cedric, et al. “SparCML: High-Performance Sparse Communication for
Machine Learning.” International Conference for High Performance Computing,
Networking, Storage and Analysis, SC, a11, ACM, 2019, doi:10.1145/3295500.3356222.'
short: C. Renggli, S. Ashkboos, M. Aghagolzadeh, D.-A. Alistarh, T. Hoefler, in:,
International Conference for High Performance Computing, Networking, Storage and
Analysis, SC, ACM, 2019.
conference:
end_date: 2019-11-19
location: Denver, CO, Unites States
name: 'SC: Conference for High Performance Computing, Networking, Storage and Analysis'
start_date: 2019-11-17
date_created: 2019-12-22T23:00:42Z
date_published: 2019-11-17T00:00:00Z
date_updated: 2023-09-06T14:37:55Z
day: '17'
department:
- _id: DaAl
doi: 10.1145/3295500.3356222
ec_funded: 1
external_id:
arxiv:
- '1802.08021'
isi:
- '000545976800011'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1802.08021
month: '11'
oa: 1
oa_version: Preprint
project:
- _id: 268A44D6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '805223'
name: Elastic Coordination for Scalable Machine Learning
publication: International Conference for High Performance Computing, Networking,
Storage and Analysis, SC
publication_identifier:
eissn:
- '21674337'
isbn:
- '9781450362290'
issn:
- '21674329'
publication_status: published
publisher: ACM
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'SparCML: High-performance sparse communication for machine learning'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '13067'
abstract:
- lang: eng
text: Genetic incompatibilities contribute to reproductive isolation between many
diverging populations, but it is still unclear to what extent they play a role
if divergence happens with gene flow. In contact zones between the "Crab" and
"Wave" ecotypes of the snail Littorina saxatilis divergent selection forms strong
barriers to gene flow, while the role of postzygotic barriers due to selection
against hybrids remains unclear. High embryo abortion rates in this species could
indicate the presence of such barriers. Postzygotic barriers might include genetic
incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation,
both expected to be most pronounced in contact zones. In addition, embryo abortion
might reflect physiological stress on females and embryos independent of any genetic
stress. We examined all embryos of >500 females sampled outside and inside
contact zones of three populations in Sweden. Females' clutch size ranged from
0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean
12%). We described female genotypes by using a hybrid index based on hundreds
of SNPs differentiated between ecotypes with which we characterised female genotypes.
We also calculated female SNP heterozygosity and inversion karyotype. Clutch size
did not vary with female hybrid index and abortion rates were only weakly related
to hybrid index in two sites but not at all in a third site. No additional variation
in abortion rate was explained by female SNP heterozygosity, but increased female
inversion heterozygosity added slightly to increased abortion. Our results show
only weak and probably biologically insignificant postzygotic barriers contributing
to ecotype divergence and the high and variable abortion rates were marginally,
if at all, explained by hybrid index of females.
article_processing_charge: No
author:
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Zuzanna
full_name: Zagrodzka, Zuzanna
last_name: Zagrodzka
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo
abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019.
doi:10.5061/DRYAD.TB2RBNZWK'
apa: 'Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R.
(2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between
Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK'
chicago: 'Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and
Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow
between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.'
ieee: 'K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data
from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?” Dryad, 2019.'
ista: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from:
Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?,
Dryad, 10.5061/DRYAD.TB2RBNZWK.'
mla: 'Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic
Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.'
short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).
date_created: 2023-05-23T16:36:27Z
date_published: 2019-12-02T00:00:00Z
date_updated: 2023-09-06T14:48:57Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.TB2RBNZWK
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.tb2rbnzwk
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '7205'
relation: used_in_publication
status: public
status: public
title: 'Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?'
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_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7214'
abstract:
- lang: eng
text: "Background: Many cancer genomes are extensively rearranged with highly aberrant
chromosomal karyotypes. Structural and copy number variations in cancer genomes
can be determined via abnormal mapping of sequenced reads to the reference genome.
Recently it became possible to reconcile both of these types of large-scale variations
into a karyotype graph representation of the rearranged cancer genomes. Such a
representation, however, does not directly describe the linear and/or circular
structure of the underlying rearranged cancer chromosomes, thus limiting possible
analysis of cancer genomes somatic evolutionary process as well as functional
genomic changes brought by the large-scale genome rearrangements.\r\n\r\nResults:
Here we address the aforementioned limitation by introducing a novel methodological
framework for recovering rearranged cancer chromosomes from karyotype graphs.
For a cancer karyotype graph we formulate an Eulerian Decomposition Problem (EDP)
of finding a collection of linear and/or circular rearranged cancer chromosomes
that are determined by the graph. We derive and prove computational complexities
for several variations of the EDP. We then demonstrate that Eulerian decomposition
of the cancer karyotype graphs is not always unique and present the Consistent
Contig Covering Problem (CCCP) of recovering unambiguous cancer contigs from the
cancer karyotype graph, and describe a novel algorithm CCR capable of solving
CCCP in polynomial time. We apply CCR on a prostate cancer dataset and demonstrate
that it is capable of consistently recovering large cancer contigs even when underlying
cancer genomes are highly rearranged.\r\n\r\nConclusions: CCR can recover rearranged
cancer contigs from karyotype graphs thereby addressing existing limitation in
inferring chromosomal structures of rearranged cancer genomes and advancing our
understanding of both patient/cancer-specific as well as the overall genetic instability
in cancer."
article_number: '641'
article_processing_charge: No
article_type: original
author:
- first_name: Sergey
full_name: Aganezov, Sergey
last_name: Aganezov
- first_name: Ilya
full_name: Zban, Ilya
last_name: Zban
- first_name: Vitalii
full_name: Aksenov, Vitalii
id: 2980135A-F248-11E8-B48F-1D18A9856A87
last_name: Aksenov
- first_name: Nikita
full_name: Alexeev, Nikita
last_name: Alexeev
- first_name: Michael C.
full_name: Schatz, Michael C.
last_name: Schatz
citation:
ama: Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. Recovering rearranged
cancer chromosomes from karyotype graphs. BMC Bioinformatics. 2019;20.
doi:10.1186/s12859-019-3208-4
apa: Aganezov, S., Zban, I., Aksenov, V., Alexeev, N., & Schatz, M. C. (2019).
Recovering rearranged cancer chromosomes from karyotype graphs. BMC Bioinformatics.
BMC. https://doi.org/10.1186/s12859-019-3208-4
chicago: Aganezov, Sergey, Ilya Zban, Vitalii Aksenov, Nikita Alexeev, and Michael
C. Schatz. “Recovering Rearranged Cancer Chromosomes from Karyotype Graphs.” BMC
Bioinformatics. BMC, 2019. https://doi.org/10.1186/s12859-019-3208-4.
ieee: S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, and M. C. Schatz, “Recovering
rearranged cancer chromosomes from karyotype graphs,” BMC Bioinformatics,
vol. 20. BMC, 2019.
ista: Aganezov S, Zban I, Aksenov V, Alexeev N, Schatz MC. 2019. Recovering rearranged
cancer chromosomes from karyotype graphs. BMC Bioinformatics. 20, 641.
mla: Aganezov, Sergey, et al. “Recovering Rearranged Cancer Chromosomes from Karyotype
Graphs.” BMC Bioinformatics, vol. 20, 641, BMC, 2019, doi:10.1186/s12859-019-3208-4.
short: S. Aganezov, I. Zban, V. Aksenov, N. Alexeev, M.C. Schatz, BMC Bioinformatics
20 (2019).
date_created: 2019-12-29T23:00:46Z
date_published: 2019-12-17T00:00:00Z
date_updated: 2023-09-06T14:51:06Z
day: '17'
ddc:
- '570'
department:
- _id: DaAl
doi: 10.1186/s12859-019-3208-4
external_id:
isi:
- '000511618800007'
file:
- access_level: open_access
checksum: 7a30357efdcf8f66587ed495c0927724
content_type: application/pdf
creator: dernst
date_created: 2020-01-02T16:10:58Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7221'
file_name: 2019_BMCBioinfo_Aganezov.pdf
file_size: 1917374
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: BMC Bioinformatics
publication_identifier:
eissn:
- '14712105'
publication_status: published
publisher: BMC
quality_controlled: '1'
scopus_import: '1'
status: public
title: Recovering rearranged cancer chromosomes from karyotype graphs
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 20
year: '2019'
...
---
_id: '7225'
abstract:
- lang: eng
text: "This is a literature teaching resource review for biologically inspired microfluidics
courses\r\nor exploring the diverse applications of microfluidics. The structure
is around key papers and model\r\norganisms. While courses gradually change over
time, a focus remains on understanding how\r\nmicrofluidics has developed as well
as what it can and cannot do for researchers. As a primary\r\nstarting point,
we cover micro-fluid mechanics principles and microfabrication of devices. A variety\r\nof
applications are discussed using model prokaryotic and eukaryotic organisms from
the set\r\nof bacteria (Escherichia coli), trypanosomes (Trypanosoma brucei),
yeast (Saccharomyces cerevisiae),\r\nslime molds (Physarum polycephalum), worms
(Caenorhabditis elegans), flies (Drosophila melangoster),\r\nplants (Arabidopsis
thaliana), and mouse immune cells (Mus musculus). Other engineering and\r\nbiochemical
methods discussed include biomimetics, organ on a chip, inkjet, droplet microfluidics,\r\nbiotic
games, and diagnostics. While we have not yet reached the end-all lab on a chip,\r\nmicrofluidics
can still be used effectively for specific applications."
article_number: '109'
article_processing_charge: Yes
article_type: review
author:
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
citation:
ama: Merrin J. Frontiers in microfluidics, a teaching resource review. Bioengineering.
2019;6(4). doi:10.3390/bioengineering6040109
apa: Merrin, J. (2019). Frontiers in microfluidics, a teaching resource review.
Bioengineering. MDPI. https://doi.org/10.3390/bioengineering6040109
chicago: Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.”
Bioengineering. MDPI, 2019. https://doi.org/10.3390/bioengineering6040109.
ieee: J. Merrin, “Frontiers in microfluidics, a teaching resource review,” Bioengineering,
vol. 6, no. 4. MDPI, 2019.
ista: Merrin J. 2019. Frontiers in microfluidics, a teaching resource review. Bioengineering.
6(4), 109.
mla: Merrin, Jack. “Frontiers in Microfluidics, a Teaching Resource Review.” Bioengineering,
vol. 6, no. 4, 109, MDPI, 2019, doi:10.3390/bioengineering6040109.
short: J. Merrin, Bioengineering 6 (2019).
date_created: 2020-01-05T23:00:45Z
date_published: 2019-12-03T00:00:00Z
date_updated: 2023-09-06T14:52:49Z
day: '03'
ddc:
- '620'
department:
- _id: NanoFab
doi: 10.3390/bioengineering6040109
external_id:
isi:
- '000505590000024'
pmid:
- '31816954'
file:
- access_level: open_access
checksum: 80f1499e2a4caccdf3aa54b137fd99a0
content_type: application/pdf
creator: dernst
date_created: 2020-01-07T14:49:59Z
date_updated: 2020-07-14T12:47:54Z
file_id: '7243'
file_name: 2019_Bioengineering_Merrin.pdf
file_size: 2660780
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Bioengineering
publication_identifier:
eissn:
- '23065354'
publication_status: published
publisher: MDPI
quality_controlled: '1'
scopus_import: '1'
status: public
title: Frontiers in microfluidics, a teaching resource review
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2019'
...
---
_id: '7228'
abstract:
- lang: eng
text: "Traditional concurrent programming involves manipulating shared mutable state.
Alternatives to this programming style are communicating sequential processes
(CSP) and actor models, which share data via explicit communication. These models
have been known for almost half a century, and have recently had started to gain
significant traction among modern programming languages. The common abstraction
for communication between several processes is the channel. Although channels
are similar to producer-consumer data structures, they have different semantics
and support additional operations, such as the select expression. Despite their
growing popularity, most known implementations of channels use lock-based data
structures and can be rather inefficient.\r\n\r\nIn this paper, we present the
first efficient lock-free algorithm for implementing a communication channel for
CSP programming. We provide implementations and experimental results in the Kotlin
and Go programming languages. Our new algorithm outperforms existing implementations
on many workloads, while providing non-blocking progress guarantee. Our design
can serve as an example of how to construct general communication data structures
for CSP and actor models. "
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Nikita
full_name: Koval, Nikita
id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87
last_name: Koval
- 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: Roman
full_name: Elizarov, Roman
last_name: Elizarov
citation:
ama: 'Koval N, Alistarh D-A, Elizarov R. Scalable FIFO channels for programming
via communicating sequential processes. In: 25th Anniversary of Euro-Par.
Vol 11725. Springer Nature; 2019:317-333. doi:10.1007/978-3-030-29400-7_23'
apa: 'Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Scalable FIFO channels
for programming via communicating sequential processes. In 25th Anniversary
of Euro-Par (Vol. 11725, pp. 317–333). Göttingen, Germany: Springer Nature.
https://doi.org/10.1007/978-3-030-29400-7_23'
chicago: Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Scalable FIFO
Channels for Programming via Communicating Sequential Processes.” In 25th Anniversary
of Euro-Par, 11725:317–33. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29400-7_23.
ieee: N. Koval, D.-A. Alistarh, and R. Elizarov, “Scalable FIFO channels for programming
via communicating sequential processes,” in 25th Anniversary of Euro-Par,
Göttingen, Germany, 2019, vol. 11725, pp. 317–333.
ista: 'Koval N, Alistarh D-A, Elizarov R. 2019. Scalable FIFO channels for programming
via communicating sequential processes. 25th Anniversary of Euro-Par. Euro-Par:
European Conference on Parallel Processing, LNCS, vol. 11725, 317–333.'
mla: Koval, Nikita, et al. “Scalable FIFO Channels for Programming via Communicating
Sequential Processes.” 25th Anniversary of Euro-Par, vol. 11725, Springer
Nature, 2019, pp. 317–33, doi:10.1007/978-3-030-29400-7_23.
short: N. Koval, D.-A. Alistarh, R. Elizarov, in:, 25th Anniversary of Euro-Par,
Springer Nature, 2019, pp. 317–333.
conference:
end_date: 2019-08-30
location: Göttingen, Germany
name: 'Euro-Par: European Conference on Parallel Processing'
start_date: 2019-08-26
date_created: 2020-01-05T23:00:46Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:53:59Z
day: '13'
department:
- _id: DaAl
doi: 10.1007/978-3-030-29400-7_23
external_id:
isi:
- '000851061400023'
intvolume: ' 11725'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 317-333
publication: 25th Anniversary of Euro-Par
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9399-4
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Scalable FIFO channels for programming via communicating sequential processes
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11725
year: '2019'
...
---
_id: '7216'
abstract:
- lang: eng
text: 'We present LiveTraVeL (Live Transit Vehicle Labeling), a real-time system
to label a stream of noisy observations of transit vehicle trajectories with the
transit routes they are serving (e.g., northbound bus #5). In order to scale efficiently
to large transit networks, our system first retrieves a small set of candidate
routes from a geometrically indexed data structure, then applies a fine-grained
scoring step to choose the best match. Given that real-time data remains unavailable
for the majority of the world’s transit agencies, these inferences can help feed
a real-time map of a transit system’s trips, infer transit trip delays in real
time, or measure and correct noisy transit tracking data. This system can run
on vehicle observations from a variety of sources that don’t attach route information
to vehicle observations, such as public imagery streams or user-contributed transit
vehicle sightings.We abstract away the specifics of the sensing system and demonstrate
the effectiveness of our system on a "semisynthetic" dataset of all New York City
buses, where we simulate sensed trajectories by starting with fully labeled vehicle
trajectories reported via the GTFS-Realtime protocol, removing the transit route
IDs, and perturbing locations with synthetic noise. Using just the geometric shapes
of the trajectories, we demonstrate that our system converges on the correct route
ID within a few minutes, even after a vehicle switches from serving one trip to
the next.'
article_number: '8917514'
article_processing_charge: No
author:
- first_name: Georg F
full_name: Osang, Georg F
id: 464B40D6-F248-11E8-B48F-1D18A9856A87
last_name: Osang
orcid: 0000-0002-8882-5116
- first_name: James
full_name: Cook, James
last_name: Cook
- first_name: Alex
full_name: Fabrikant, Alex
last_name: Fabrikant
- first_name: Marco
full_name: Gruteser, Marco
last_name: Gruteser
citation:
ama: 'Osang GF, Cook J, Fabrikant A, Gruteser M. LiveTraVeL: Real-time matching
of transit vehicle trajectories to transit routes at scale. In: 2019 IEEE Intelligent
Transportation Systems Conference. IEEE; 2019. doi:10.1109/ITSC.2019.8917514'
apa: 'Osang, G. F., Cook, J., Fabrikant, A., & Gruteser, M. (2019). LiveTraVeL:
Real-time matching of transit vehicle trajectories to transit routes at scale.
In 2019 IEEE Intelligent Transportation Systems Conference. Auckland, New
Zealand: IEEE. https://doi.org/10.1109/ITSC.2019.8917514'
chicago: 'Osang, Georg F, James Cook, Alex Fabrikant, and Marco Gruteser. “LiveTraVeL:
Real-Time Matching of Transit Vehicle Trajectories to Transit Routes at Scale.”
In 2019 IEEE Intelligent Transportation Systems Conference. IEEE, 2019.
https://doi.org/10.1109/ITSC.2019.8917514.'
ieee: 'G. F. Osang, J. Cook, A. Fabrikant, and M. Gruteser, “LiveTraVeL: Real-time
matching of transit vehicle trajectories to transit routes at scale,” in 2019
IEEE Intelligent Transportation Systems Conference, Auckland, New Zealand,
2019.'
ista: 'Osang GF, Cook J, Fabrikant A, Gruteser M. 2019. LiveTraVeL: Real-time matching
of transit vehicle trajectories to transit routes at scale. 2019 IEEE Intelligent
Transportation Systems Conference. ITSC: Intelligent Transportation Systems Conference,
8917514.'
mla: 'Osang, Georg F., et al. “LiveTraVeL: Real-Time Matching of Transit Vehicle
Trajectories to Transit Routes at Scale.” 2019 IEEE Intelligent Transportation
Systems Conference, 8917514, IEEE, 2019, doi:10.1109/ITSC.2019.8917514.'
short: G.F. Osang, J. Cook, A. Fabrikant, M. Gruteser, in:, 2019 IEEE Intelligent
Transportation Systems Conference, IEEE, 2019.
conference:
end_date: 2019-10-30
location: Auckland, New Zealand
name: 'ITSC: Intelligent Transportation Systems Conference'
start_date: 2019-10-27
date_created: 2019-12-29T23:00:47Z
date_published: 2019-11-28T00:00:00Z
date_updated: 2023-09-06T14:50:28Z
day: '28'
department:
- _id: HeEd
doi: 10.1109/ITSC.2019.8917514
external_id:
isi:
- '000521238102050'
isi: 1
language:
- iso: eng
month: '11'
oa_version: None
publication: 2019 IEEE Intelligent Transportation Systems Conference
publication_identifier:
isbn:
- '9781538670248'
publication_status: published
publisher: IEEE
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'LiveTraVeL: Real-time matching of transit vehicle trajectories to transit
routes at scale'
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7231'
abstract:
- lang: eng
text: Piecewise Barrier Tubes (PBT) is a new technique for flowpipe overapproximation
for nonlinear systems with polynomial dynamics, which leverages a combination
of barrier certificates. PBT has advantages over traditional time-step based methods
in dealing with those nonlinear dynamical systems in which there is a large difference
in speed between trajectories, producing an overapproximation that is time independent.
However, the existing approach for PBT is not efficient due to the application
of interval methods for enclosure-box computation, and it can only deal with continuous
dynamical systems without uncertainty. In this paper, we extend the approach with
the ability to handle both continuous and hybrid dynamical systems with uncertainty
that can reside in parameters and/or noise. We also improve the efficiency of
the method significantly, by avoiding the use of interval-based methods for the
enclosure-box computation without loosing soundness. We have developed a C++ prototype
implementing the proposed approach and we evaluate it on several benchmarks. The
experiments show that our approach is more efficient and precise than other methods
in the literature.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Hui
full_name: Kong, Hui
id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87
last_name: Kong
orcid: 0000-0002-3066-6941
- first_name: Ezio
full_name: Bartocci, Ezio
last_name: Bartocci
- first_name: Yu
full_name: Jiang, Yu
last_name: Jiang
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. Piecewise robust barrier tubes
for nonlinear hybrid systems with uncertainty. In: 17th International Conference
on Formal Modeling and Analysis of Timed Systems. Vol 11750. Springer Nature;
2019:123-141. doi:10.1007/978-3-030-29662-9_8'
apa: 'Kong, H., Bartocci, E., Jiang, Y., & Henzinger, T. A. (2019). Piecewise
robust barrier tubes for nonlinear hybrid systems with uncertainty. In 17th
International Conference on Formal Modeling and Analysis of Timed Systems
(Vol. 11750, pp. 123–141). Amsterdam, The Netherlands: Springer Nature. https://doi.org/10.1007/978-3-030-29662-9_8'
chicago: Kong, Hui, Ezio Bartocci, Yu Jiang, and Thomas A Henzinger. “Piecewise
Robust Barrier Tubes for Nonlinear Hybrid Systems with Uncertainty.” In 17th
International Conference on Formal Modeling and Analysis of Timed Systems,
11750:123–41. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_8.
ieee: H. Kong, E. Bartocci, Y. Jiang, and T. A. Henzinger, “Piecewise robust barrier
tubes for nonlinear hybrid systems with uncertainty,” in 17th International
Conference on Formal Modeling and Analysis of Timed Systems, Amsterdam, The
Netherlands, 2019, vol. 11750, pp. 123–141.
ista: 'Kong H, Bartocci E, Jiang Y, Henzinger TA. 2019. Piecewise robust barrier
tubes for nonlinear hybrid systems with uncertainty. 17th International Conference
on Formal Modeling and Analysis of Timed Systems. FORMATS: Formal Modeling and
Analysis of Timed Systems, LNCS, vol. 11750, 123–141.'
mla: Kong, Hui, et al. “Piecewise Robust Barrier Tubes for Nonlinear Hybrid Systems
with Uncertainty.” 17th International Conference on Formal Modeling and Analysis
of Timed Systems, vol. 11750, Springer Nature, 2019, pp. 123–41, doi:10.1007/978-3-030-29662-9_8.
short: H. Kong, E. Bartocci, Y. Jiang, T.A. Henzinger, in:, 17th International Conference
on Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 123–141.
conference:
end_date: 2019-08-29
location: Amsterdam, The Netherlands
name: 'FORMATS: Formal Modeling and Analysis of Timed Systems'
start_date: 2019-08-27
date_created: 2020-01-05T23:00:47Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:55:15Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-030-29662-9_8
external_id:
arxiv:
- '1907.11514'
isi:
- '000611677700008'
intvolume: ' 11750'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1907.11514
month: '08'
oa: 1
oa_version: Preprint
page: 123-141
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 17th International Conference on Formal Modeling and Analysis of Timed
Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9661-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Piecewise robust barrier tubes for nonlinear hybrid systems with uncertainty
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11750
year: '2019'
...
---
_id: '7340'
abstract:
- lang: eng
text: Coupling of endoplasmic reticulum stress to dimerisation‑dependent activation
of the UPR transducer IRE1 is incompletely understood. Whilst the luminal co-chaperone
ERdj4 promotes a complex between the Hsp70 BiP and IRE1's stress-sensing luminal
domain (IRE1LD) that favours the latter's monomeric inactive state and loss of
ERdj4 de-represses IRE1, evidence linking these cellular and in vitro observations
is presently lacking. We report that enforced loading of endogenous BiP onto endogenous
IRE1α repressed UPR signalling in CHO cells and deletions in the IRE1α locus that
de-repressed the UPR in cells, encode flexible regions of IRE1LD that mediated
BiP‑induced monomerisation in vitro. Changes in the hydrogen exchange mass spectrometry
profile of IRE1LD induced by ERdj4 and BiP confirmed monomerisation and were consistent
with active destabilisation of the IRE1LD dimer. Together, these observations
support a competition model whereby waning ER stress passively partitions ERdj4
and BiP to IRE1LD to initiate active repression of UPR signalling.
acknowledgement: We thank the CIMR flow cytometry core facility team (Reiner Schulte,
Chiara Cossetti and Gabriela Grondys-Kotarba) for assistance with FACS, the Huntington
lab for access to the Octet machine, Steffen Preissler for advice on data interpretation,
Roman Kityk and Nicole Luebbehusen for help and advice with HX-MS experiments.
article_number: e50793
article_processing_charge: No
article_type: original
author:
- first_name: Niko Paresh
full_name: Amin-Wetzel, Niko Paresh
id: E95D3014-9D8C-11E9-9C80-D2F8E5697425
last_name: Amin-Wetzel
- first_name: Lisa
full_name: Neidhardt, Lisa
last_name: Neidhardt
- first_name: Yahui
full_name: Yan, Yahui
last_name: Yan
- first_name: Matthias P.
full_name: Mayer, Matthias P.
last_name: Mayer
- first_name: David
full_name: Ron, David
last_name: Ron
citation:
ama: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. Unstructured regions in
IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and repression
of the UPR. eLife. 2019;8. doi:10.7554/eLife.50793
apa: Amin-Wetzel, N. P., Neidhardt, L., Yan, Y., Mayer, M. P., & Ron, D. (2019).
Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal
domain dimer and repression of the UPR. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.50793
chicago: Amin-Wetzel, Niko Paresh, Lisa Neidhardt, Yahui Yan, Matthias P. Mayer,
and David Ron. “Unstructured Regions in IRE1α Specify BiP-Mediated Destabilisation
of the Luminal Domain Dimer and Repression of the UPR.” ELife. eLife Sciences
Publications, 2019. https://doi.org/10.7554/eLife.50793.
ieee: N. P. Amin-Wetzel, L. Neidhardt, Y. Yan, M. P. Mayer, and D. Ron, “Unstructured
regions in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer
and repression of the UPR,” eLife, vol. 8. eLife Sciences Publications,
2019.
ista: Amin-Wetzel NP, Neidhardt L, Yan Y, Mayer MP, Ron D. 2019. Unstructured regions
in IRE1α specify BiP-mediated destabilisation of the luminal domain dimer and
repression of the UPR. eLife. 8, e50793.
mla: Amin-Wetzel, Niko Paresh, et al. “Unstructured Regions in IRE1α Specify BiP-Mediated
Destabilisation of the Luminal Domain Dimer and Repression of the UPR.” ELife,
vol. 8, e50793, eLife Sciences Publications, 2019, doi:10.7554/eLife.50793.
short: N.P. Amin-Wetzel, L. Neidhardt, Y. Yan, M.P. Mayer, D. Ron, ELife 8 (2019).
date_created: 2020-01-19T23:00:39Z
date_published: 2019-12-24T00:00:00Z
date_updated: 2023-09-06T14:58:02Z
day: '24'
ddc:
- '570'
department:
- _id: MaDe
doi: 10.7554/eLife.50793
external_id:
isi:
- '000512303700001'
pmid:
- '31873072'
file:
- access_level: open_access
checksum: 29fcbcd8c1fc7f11a596ed7f14ea1c82
content_type: application/pdf
creator: dernst
date_created: 2020-11-19T11:37:41Z
date_updated: 2020-11-19T11:37:41Z
file_id: '8777'
file_name: 2019_eLife_AminWetzel.pdf
file_size: 4817384
relation: main_file
success: 1
file_date_updated: 2020-11-19T11:37:41Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
eissn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unstructured regions in IRE1α specify BiP-mediated destabilisation of the luminal
domain dimer and repression of the UPR
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2019'
...
---
_id: '7422'
abstract:
- lang: eng
text: Biochemical reactions often occur at low copy numbers but at once in crowded
and diverse environments. Space and stochasticity therefore play an essential
role in biochemical networks. Spatial-stochastic simulations have become a prominent
tool for understanding how stochasticity at the microscopic level influences the
macroscopic behavior of such systems. While particle-based models guarantee the
level of detail necessary to accurately describe the microscopic dynamics at very
low copy numbers, the algorithms used to simulate them typically imply trade-offs
between computational efficiency and biochemical accuracy. eGFRD (enhanced Green’s
Function Reaction Dynamics) is an exact algorithm that evades such trade-offs
by partitioning the N-particle system into M ≤ N analytically tractable one- and
two-particle systems; the analytical solutions (Green’s functions) then are used
to implement an event-driven particle-based scheme that allows particles to make
large jumps in time and space while retaining access to their state variables
at arbitrary simulation times. Here we present “eGFRD2,” a new eGFRD version that
implements the principle of eGFRD in all dimensions, thus enabling efficient particle-based
simulation of biochemical reaction-diffusion processes in the 3D cytoplasm, on
2D planes representing membranes, and on 1D elongated cylinders representative
of, e.g., cytoskeletal tracks or DNA; in 1D, it also incorporates convective motion
used to model active transport. We find that, for low particle densities, eGFRD2
is up to 6 orders of magnitude faster than conventional Brownian dynamics. We
exemplify the capabilities of eGFRD2 by simulating an idealized model of Pom1
gradient formation, which involves 3D diffusion, active transport on microtubules,
and autophosphorylation on the membrane, confirming recent experimental and theoretical
results on this system to hold under genuinely stochastic conditions.
article_number: '054108'
article_processing_charge: No
article_type: original
author:
- first_name: Thomas R
full_name: Sokolowski, Thomas R
id: 3E999752-F248-11E8-B48F-1D18A9856A87
last_name: Sokolowski
orcid: 0000-0002-1287-3779
- first_name: Joris
full_name: Paijmans, Joris
last_name: Paijmans
- first_name: Laurens
full_name: Bossen, Laurens
last_name: Bossen
- first_name: Thomas
full_name: Miedema, Thomas
last_name: Miedema
- first_name: Martijn
full_name: Wehrens, Martijn
last_name: Wehrens
- first_name: Nils B.
full_name: Becker, Nils B.
last_name: Becker
- first_name: Kazunari
full_name: Kaizu, Kazunari
last_name: Kaizu
- first_name: Koichi
full_name: Takahashi, Koichi
last_name: Takahashi
- first_name: Marileen
full_name: Dogterom, Marileen
last_name: Dogterom
- first_name: Pieter Rein
full_name: ten Wolde, Pieter Rein
last_name: ten Wolde
citation:
ama: Sokolowski TR, Paijmans J, Bossen L, et al. eGFRD in all dimensions. The
Journal of Chemical Physics. 2019;150(5). doi:10.1063/1.5064867
apa: Sokolowski, T. R., Paijmans, J., Bossen, L., Miedema, T., Wehrens, M., Becker,
N. B., … ten Wolde, P. R. (2019). eGFRD in all dimensions. The Journal of Chemical
Physics. AIP Publishing. https://doi.org/10.1063/1.5064867
chicago: Sokolowski, Thomas R, Joris Paijmans, Laurens Bossen, Thomas Miedema, Martijn
Wehrens, Nils B. Becker, Kazunari Kaizu, Koichi Takahashi, Marileen Dogterom,
and Pieter Rein ten Wolde. “EGFRD in All Dimensions.” The Journal of Chemical
Physics. AIP Publishing, 2019. https://doi.org/10.1063/1.5064867.
ieee: T. R. Sokolowski et al., “eGFRD in all dimensions,” The Journal
of Chemical Physics, vol. 150, no. 5. AIP Publishing, 2019.
ista: Sokolowski TR, Paijmans J, Bossen L, Miedema T, Wehrens M, Becker NB, Kaizu
K, Takahashi K, Dogterom M, ten Wolde PR. 2019. eGFRD in all dimensions. The Journal
of Chemical Physics. 150(5), 054108.
mla: Sokolowski, Thomas R., et al. “EGFRD in All Dimensions.” The Journal of
Chemical Physics, vol. 150, no. 5, 054108, AIP Publishing, 2019, doi:10.1063/1.5064867.
short: T.R. Sokolowski, J. Paijmans, L. Bossen, T. Miedema, M. Wehrens, N.B. Becker,
K. Kaizu, K. Takahashi, M. Dogterom, P.R. ten Wolde, The Journal of Chemical Physics
150 (2019).
date_created: 2020-01-30T10:34:36Z
date_published: 2019-02-07T00:00:00Z
date_updated: 2023-09-06T14:59:28Z
day: '07'
department:
- _id: GaTk
doi: 10.1063/1.5064867
external_id:
arxiv:
- '1708.09364'
isi:
- '000458109300009'
intvolume: ' 150'
isi: 1
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1708.09364
month: '02'
oa: 1
oa_version: Preprint
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: eGFRD in all dimensions
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 150
year: '2019'
...
---
_id: '7230'
abstract:
- lang: eng
text: Simple drawings of graphs are those in which each pair of edges share at most
one point, either a common endpoint or a proper crossing. In this paper we study
the problem of extending a simple drawing D(G) of a graph G by inserting a set
of edges from the complement of G into D(G) such that the result is a simple drawing.
In the context of rectilinear drawings, the problem is trivial. For pseudolinear
drawings, the existence of such an extension follows from Levi’s enlargement lemma.
In contrast, we prove that deciding if a given set of edges can be inserted into
a simple drawing is NP-complete. Moreover, we show that the maximization version
of the problem is APX-hard. We also present a polynomial-time algorithm for deciding
whether one edge uv can be inserted into D(G) when {u,v} is a dominating set for
the graph G.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Alan M
full_name: Arroyo Guevara, Alan M
id: 3207FDC6-F248-11E8-B48F-1D18A9856A87
last_name: Arroyo Guevara
orcid: 0000-0003-2401-8670
- first_name: Martin
full_name: Derka, Martin
last_name: Derka
- first_name: Irene
full_name: Parada, Irene
last_name: Parada
citation:
ama: 'Arroyo Guevara AM, Derka M, Parada I. Extending simple drawings. In: 27th
International Symposium on Graph Drawing and Network Visualization. Vol 11904.
Springer Nature; 2019:230-243. doi:10.1007/978-3-030-35802-0_18'
apa: 'Arroyo Guevara, A. M., Derka, M., & Parada, I. (2019). Extending simple
drawings. In 27th International Symposium on Graph Drawing and Network Visualization
(Vol. 11904, pp. 230–243). Prague, Czech Republic: Springer Nature. https://doi.org/10.1007/978-3-030-35802-0_18'
chicago: Arroyo Guevara, Alan M, Martin Derka, and Irene Parada. “Extending Simple
Drawings.” In 27th International Symposium on Graph Drawing and Network Visualization,
11904:230–43. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-35802-0_18.
ieee: A. M. Arroyo Guevara, M. Derka, and I. Parada, “Extending simple drawings,”
in 27th International Symposium on Graph Drawing and Network Visualization,
Prague, Czech Republic, 2019, vol. 11904, pp. 230–243.
ista: 'Arroyo Guevara AM, Derka M, Parada I. 2019. Extending simple drawings. 27th
International Symposium on Graph Drawing and Network Visualization. GD: Graph
Drawing and Network Visualization, LNCS, vol. 11904, 230–243.'
mla: Arroyo Guevara, Alan M., et al. “Extending Simple Drawings.” 27th International
Symposium on Graph Drawing and Network Visualization, vol. 11904, Springer
Nature, 2019, pp. 230–43, doi:10.1007/978-3-030-35802-0_18.
short: A.M. Arroyo Guevara, M. Derka, I. Parada, in:, 27th International Symposium
on Graph Drawing and Network Visualization, Springer Nature, 2019, pp. 230–243.
conference:
end_date: 2019-09-20
location: Prague, Czech Republic
name: 'GD: Graph Drawing and Network Visualization'
start_date: 2019-09-17
date_created: 2020-01-05T23:00:47Z
date_published: 2019-11-28T00:00:00Z
date_updated: 2023-09-06T14:56:00Z
day: '28'
department:
- _id: UlWa
doi: 10.1007/978-3-030-35802-0_18
ec_funded: 1
external_id:
arxiv:
- '1908.08129'
isi:
- '000612918800018'
intvolume: ' 11904'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1908.08129
month: '11'
oa: 1
oa_version: Preprint
page: 230-243
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: 27th International Symposium on Graph Drawing and Network Visualization
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0303-5801-3
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extending simple drawings
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11904
year: '2019'
...
---
_id: '7232'
abstract:
- lang: eng
text: 'We present Mixed-time Signal Temporal Logic (STL−MX), a specification formalism
which extends STL by capturing the discrete/ continuous time duality found in
many cyber-physical systems (CPS), as well as mixed-signal electronic designs.
In STL−MX, properties of components with continuous dynamics are expressed in
STL, while specifications of components with discrete dynamics are written in
LTL. To combine the two layers, we evaluate formulas on two traces, discrete-
and continuous-time, and introduce two interface operators that map signals, properties
and their satisfaction signals across the two time domains. We show that STL-mx
has the expressive power of STL supplemented with an implicit T-periodic clock
signal. We develop and implement an algorithm for monitoring STL-mx formulas and
illustrate the approach using a mixed-signal example. '
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ferrere, Thomas
id: 40960E6E-F248-11E8-B48F-1D18A9856A87
last_name: Ferrere
orcid: 0000-0001-5199-3143
- first_name: Oded
full_name: Maler, Oded
last_name: Maler
- first_name: Dejan
full_name: Nickovic, Dejan
id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87
last_name: Nickovic
citation:
ama: 'Ferrere T, Maler O, Nickovic D. Mixed-time signal temporal logic. In: 17th
International Conference on Formal Modeling and Analysis of Timed Systems.
Vol 11750. Springer Nature; 2019:59-75. doi:10.1007/978-3-030-29662-9_4'
apa: 'Ferrere, T., Maler, O., & Nickovic, D. (2019). Mixed-time signal temporal
logic. In 17th International Conference on Formal Modeling and Analysis of
Timed Systems (Vol. 11750, pp. 59–75). Amsterdam, The Netherlands: Springer
Nature. https://doi.org/10.1007/978-3-030-29662-9_4'
chicago: Ferrere, Thomas, Oded Maler, and Dejan Nickovic. “Mixed-Time Signal Temporal
Logic.” In 17th International Conference on Formal Modeling and Analysis of
Timed Systems, 11750:59–75. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-29662-9_4.
ieee: T. Ferrere, O. Maler, and D. Nickovic, “Mixed-time signal temporal logic,”
in 17th International Conference on Formal Modeling and Analysis of Timed Systems,
Amsterdam, The Netherlands, 2019, vol. 11750, pp. 59–75.
ista: 'Ferrere T, Maler O, Nickovic D. 2019. Mixed-time signal temporal logic. 17th
International Conference on Formal Modeling and Analysis of Timed Systems. FORMATS:
Formal Modeling and Anaysis of Timed Systems, LNCS, vol. 11750, 59–75.'
mla: Ferrere, Thomas, et al. “Mixed-Time Signal Temporal Logic.” 17th International
Conference on Formal Modeling and Analysis of Timed Systems, vol. 11750, Springer
Nature, 2019, pp. 59–75, doi:10.1007/978-3-030-29662-9_4.
short: T. Ferrere, O. Maler, D. Nickovic, in:, 17th International Conference on
Formal Modeling and Analysis of Timed Systems, Springer Nature, 2019, pp. 59–75.
conference:
end_date: 2019-08-29
location: Amsterdam, The Netherlands
name: 'FORMATS: Formal Modeling and Anaysis of Timed Systems'
start_date: 2019-08-27
date_created: 2020-01-05T23:00:48Z
date_published: 2019-08-13T00:00:00Z
date_updated: 2023-09-06T14:57:17Z
day: '13'
department:
- _id: ToHe
doi: 10.1007/978-3-030-29662-9_4
external_id:
isi:
- '000611677700004'
intvolume: ' 11750'
isi: 1
language:
- iso: eng
month: '08'
oa_version: None
page: 59-75
project:
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
publication: 17th International Conference on Formal Modeling and Analysis of Timed
Systems
publication_identifier:
eissn:
- 1611-3349
isbn:
- 978-3-0302-9661-2
issn:
- 0302-9743
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixed-time signal temporal logic
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 11750
year: '2019'
...
---
_id: '7420'
abstract:
- lang: eng
text: β1-integrins mediate cell–matrix interactions and their trafficking is important
in the dynamic regulation of cell adhesion, migration and malignant processes,
including cancer cell invasion. Here, we employ an RNAi screen to characterize
regulators of integrin traffic and identify the association of Golgi-localized
gamma ear-containing Arf-binding protein 2 (GGA2) with β1-integrin, and its role
in recycling of active but not inactive β1-integrin receptors. Silencing of GGA2
limits active β1-integrin levels in focal adhesions and decreases cancer cell
migration and invasion, which is in agreement with its ability to regulate the
dynamics of active integrins. By using the proximity-dependent biotin identification
(BioID) method, we identified two RAB family small GTPases, i.e. RAB13 and RAB10,
as novel interactors of GGA2. Functionally, RAB13 silencing triggers the intracellular
accumulation of active β1-integrin, and reduces integrin activity in focal adhesions
and cell migration similarly to GGA2 depletion, indicating that both facilitate
active β1-integrin recycling to the plasma membrane. Thus, GGA2 and RAB13 are
important specificity determinants for integrin activity-dependent traffic.
article_number: jcs233387
article_processing_charge: No
article_type: original
author:
- first_name: Pranshu
full_name: Sahgal, Pranshu
last_name: Sahgal
- first_name: Jonna H
full_name: Alanko, Jonna H
id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87
last_name: Alanko
orcid: 0000-0002-7698-3061
- first_name: Jaroslav
full_name: Icha, Jaroslav
last_name: Icha
- first_name: Ilkka
full_name: Paatero, Ilkka
last_name: Paatero
- first_name: Hellyeh
full_name: Hamidi, Hellyeh
last_name: Hamidi
- first_name: Antti
full_name: Arjonen, Antti
last_name: Arjonen
- first_name: Mika
full_name: Pietilä, Mika
last_name: Pietilä
- first_name: Anne
full_name: Rokka, Anne
last_name: Rokka
- first_name: Johanna
full_name: Ivaska, Johanna
last_name: Ivaska
citation:
ama: Sahgal P, Alanko JH, Icha J, et al. GGA2 and RAB13 promote activity-dependent
β1-integrin recycling. Journal of Cell Science. 2019;132(11). doi:10.1242/jcs.233387
apa: Sahgal, P., Alanko, J. H., Icha, J., Paatero, I., Hamidi, H., Arjonen, A.,
… Ivaska, J. (2019). GGA2 and RAB13 promote activity-dependent β1-integrin recycling.
Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.233387
chicago: Sahgal, Pranshu, Jonna H Alanko, Jaroslav Icha, Ilkka Paatero, Hellyeh
Hamidi, Antti Arjonen, Mika Pietilä, Anne Rokka, and Johanna Ivaska. “GGA2 and
RAB13 Promote Activity-Dependent Β1-Integrin Recycling.” Journal of Cell Science.
The Company of Biologists, 2019. https://doi.org/10.1242/jcs.233387.
ieee: P. Sahgal et al., “GGA2 and RAB13 promote activity-dependent β1-integrin
recycling,” Journal of Cell Science, vol. 132, no. 11. The Company of Biologists,
2019.
ista: Sahgal P, Alanko JH, Icha J, Paatero I, Hamidi H, Arjonen A, Pietilä M, Rokka
A, Ivaska J. 2019. GGA2 and RAB13 promote activity-dependent β1-integrin recycling.
Journal of Cell Science. 132(11), jcs233387.
mla: Sahgal, Pranshu, et al. “GGA2 and RAB13 Promote Activity-Dependent Β1-Integrin
Recycling.” Journal of Cell Science, vol. 132, no. 11, jcs233387, The Company
of Biologists, 2019, doi:10.1242/jcs.233387.
short: P. Sahgal, J.H. Alanko, J. Icha, I. Paatero, H. Hamidi, A. Arjonen, M. Pietilä,
A. Rokka, J. Ivaska, Journal of Cell Science 132 (2019).
date_created: 2020-01-30T10:31:42Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-09-06T15:01:00Z
day: '07'
department:
- _id: MiSi
doi: 10.1242/jcs.233387
external_id:
isi:
- '000473327900017'
pmid:
- '31076515'
intvolume: ' 132'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/jcs.233387
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Science
publication_identifier:
eissn:
- 1477-9137
issn:
- 0021-9533
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
status: public
title: GGA2 and RAB13 promote activity-dependent β1-integrin recycling
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 132
year: '2019'
...
---
_id: '7423'
abstract:
- lang: eng
text: 'We compare finite rank perturbations of the following three ensembles of
complex rectangular random matrices: First, a generalised Wishart ensemble with
one random and two fixed correlation matrices introduced by Borodin and Péché,
second, the product of two independent random matrices where one has correlated
entries, and third, the case when the two random matrices become also coupled
through a fixed matrix. The singular value statistics of all three ensembles is
shown to be determinantal and we derive double contour integral representations
for their respective kernels. Three different kernels are found in the limit of
infinite matrix dimension at the origin of the spectrum. They depend on finite
rank perturbations of the correlation and coupling matrices and are shown to be
integrable. The first kernel (I) is found for two independent matrices from the
second, and two weakly coupled matrices from the third ensemble. It generalises
the Meijer G-kernel for two independent and uncorrelated matrices. The third kernel
(III) is obtained for the generalised Wishart ensemble and for two strongly coupled
matrices. It further generalises the perturbed Bessel kernel of Desrosiers and
Forrester. Finally, kernel (II), found for the ensemble of two coupled matrices,
provides an interpolation between the kernels (I) and (III), generalising previous
findings of part of the authors.'
article_processing_charge: No
article_type: original
author:
- first_name: Gernot
full_name: Akemann, Gernot
last_name: Akemann
- first_name: Tomasz
full_name: Checinski, Tomasz
last_name: Checinski
- first_name: Dangzheng
full_name: Liu, Dangzheng
id: 2F947E34-F248-11E8-B48F-1D18A9856A87
last_name: Liu
- first_name: Eugene
full_name: Strahov, Eugene
last_name: Strahov
citation:
ama: 'Akemann G, Checinski T, Liu D, Strahov E. Finite rank perturbations in products
of coupled random matrices: From one correlated to two Wishart ensembles. Annales
de l’Institut Henri Poincaré, Probabilités et Statistiques. 2019;55(1):441-479.
doi:10.1214/18-aihp888'
apa: 'Akemann, G., Checinski, T., Liu, D., & Strahov, E. (2019). Finite rank
perturbations in products of coupled random matrices: From one correlated to two
Wishart ensembles. Annales de l’Institut Henri Poincaré, Probabilités et Statistiques.
Institute of Mathematical Statistics. https://doi.org/10.1214/18-aihp888'
chicago: 'Akemann, Gernot, Tomasz Checinski, Dangzheng Liu, and Eugene Strahov.
“Finite Rank Perturbations in Products of Coupled Random Matrices: From One Correlated
to Two Wishart Ensembles.” Annales de l’Institut Henri Poincaré, Probabilités
et Statistiques. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-aihp888.'
ieee: 'G. Akemann, T. Checinski, D. Liu, and E. Strahov, “Finite rank perturbations
in products of coupled random matrices: From one correlated to two Wishart ensembles,”
Annales de l’Institut Henri Poincaré, Probabilités et Statistiques, vol.
55, no. 1. Institute of Mathematical Statistics, pp. 441–479, 2019.'
ista: 'Akemann G, Checinski T, Liu D, Strahov E. 2019. Finite rank perturbations
in products of coupled random matrices: From one correlated to two Wishart ensembles.
Annales de l’Institut Henri Poincaré, Probabilités et Statistiques. 55(1), 441–479.'
mla: 'Akemann, Gernot, et al. “Finite Rank Perturbations in Products of Coupled
Random Matrices: From One Correlated to Two Wishart Ensembles.” Annales de
l’Institut Henri Poincaré, Probabilités et Statistiques, vol. 55, no. 1, Institute
of Mathematical Statistics, 2019, pp. 441–79, doi:10.1214/18-aihp888.'
short: G. Akemann, T. Checinski, D. Liu, E. Strahov, Annales de l’Institut Henri
Poincaré, Probabilités et Statistiques 55 (2019) 441–479.
date_created: 2020-01-30T10:36:50Z
date_published: 2019-02-01T00:00:00Z
date_updated: 2023-09-06T14:58:39Z
day: '01'
department:
- _id: LaEr
doi: 10.1214/18-aihp888
external_id:
arxiv:
- '1704.05224'
isi:
- '000456070200013'
intvolume: ' 55'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.05224
month: '02'
oa: 1
oa_version: Preprint
page: 441-479
publication: Annales de l'Institut Henri Poincaré, Probabilités et Statistiques
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: 'Finite rank perturbations in products of coupled random matrices: From one
correlated to two Wishart ensembles'
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 55
year: '2019'
...