---
_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'
...