---
_id: '6071'
abstract:
- lang: eng
text: 'Transcription factors, by binding to specific sequences on the DNA, control
the precise spatio-temporal expression of genes inside a cell. However, this specificity
is limited, leading to frequent incorrect binding of transcription factors that
might have deleterious consequences on the cell. By constructing a biophysical
model of TF-DNA binding in the context of gene regulation, I will first explore
how regulatory constraints can strongly shape the distribution of a population
in sequence space. Then, by directly linking this to a picture of multiple types
of transcription factors performing their functions simultaneously inside the
cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions
between transcription factors and binding sites that lead to erroneous regulatory
states -- and understand the constraints this places on the design of regulatory
systems. I will then develop a generic theoretical framework to investigate the
coevolution of multiple transcription factors and multiple binding sites, in the
context of a gene regulatory network that performs a certain function. As a particular
tractable version of this problem, I will consider the evolution of two transcription
factors when they transmit upstream signals to downstream target genes. Specifically,
I will describe the evolutionary steady states and the evolutionary pathways involved,
along with their timescales, of a system that initially undergoes a transcription
factor duplication event. To connect this important theoretical model to the prominent
biological event of transcription factor duplication giving rise to paralogous
families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription
factors, a major family in humans, and focus on the patterns of evolution that
paralogs have undergone in their various protein domains in the recent past. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
citation:
ama: Prizak R. Coevolution of transcription factors and their binding sites in sequence
space. 2019. doi:10.15479/at:ista:th6071
apa: Prizak, R. (2019). Coevolution of transcription factors and their binding
sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071
chicago: Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding
Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.
ieee: R. Prizak, “Coevolution of transcription factors and their binding sites in
sequence space,” Institute of Science and Technology Austria, 2019.
ista: Prizak R. 2019. Coevolution of transcription factors and their binding sites
in sequence space. Institute of Science and Technology Austria.
mla: Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites
in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.
short: R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in
Sequence Space, Institute of Science and Technology Austria, 2019.
date_created: 2019-03-06T16:16:10Z
date_published: 2019-03-11T00:00:00Z
date_updated: 2023-09-22T10:00:48Z
day: '11'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GaTk
- _id: NiBa
doi: 10.15479/at:ista:th6071
file:
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checksum: e60a72de35d270b31f1a23d50f224ec0
content_type: application/pdf
creator: rprizak
date_created: 2019-03-06T16:05:07Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6072'
file_name: Thesis_final_PDFA_RoshanPrizak.pdf
file_size: 20995465
relation: main_file
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checksum: 67c2630333d05ebafef5f018863a8465
content_type: application/zip
creator: rprizak
date_created: 2019-03-06T16:09:39Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6073'
file_name: thesis_v2_merge.zip
file_size: 85705272
relation: source_file
title: Latex files
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '189'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1358'
relation: part_of_dissertation
status: public
- id: '955'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Coevolution of transcription factors and their binding sites in sequence space
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '7436'
abstract:
- lang: eng
text: 'For an ordinary K3 surface over an algebraically closed field of positive
characteristic we show that every automorphism lifts to characteristic zero. Moreover,
we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one
correspondence with the Fourier-Mukai partners of the geometric generic fiber
of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai
partners of the K3 surfaces with Picard rank two and with discriminant equal to
minus of a prime number, in terms of the class number of the prime, holds over
a field of positive characteristic as well. We show that the image of the derived
autoequivalence group of a K3 surface of finite height in the group of isometries
of its crystalline cohomology has index at least two. Moreover, we provide a conditional
upper bound on the kernel of this natural cohomological descent map. Further,
we give an extended remark in the appendix on the possibility of an F-crystal
structure on the crystalline cohomology of a K3 surface over an algebraically
closed field of positive characteristic and show that the naive F-crystal structure
fails in being compatible with inner product. '
article_processing_charge: No
article_type: original
author:
- first_name: Tanya K
full_name: Srivastava, Tanya K
id: 4D046628-F248-11E8-B48F-1D18A9856A87
last_name: Srivastava
citation:
ama: Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic.
Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177
apa: Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive
characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177
chicago: Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive
Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177.
ieee: T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,”
Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019.
ista: Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic.
Documenta Mathematica. 24, 1135–1177.
mla: Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.”
Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177.
short: T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.
date_created: 2020-02-02T23:01:06Z
date_published: 2019-05-20T00:00:00Z
date_updated: 2023-10-17T07:42:21Z
day: '20'
ddc:
- '510'
department:
- _id: TaHa
doi: 10.25537/dm.2019v24.1135-1177
external_id:
arxiv:
- '1809.08970'
isi:
- '000517806400019'
file:
- access_level: open_access
checksum: 9a1a64bd49ab03fa4f738fb250fc4f90
content_type: application/pdf
creator: dernst
date_created: 2020-02-03T06:26:12Z
date_updated: 2020-07-14T12:47:58Z
file_id: '7438'
file_name: 2019_DocumMath_Srivastava.pdf
file_size: 469730
relation: main_file
file_date_updated: 2020-07-14T12:47:58Z
has_accepted_license: '1'
intvolume: ' 24'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1135-1177
publication: Documenta Mathematica
publication_identifier:
eissn:
- 1431-0643
issn:
- 1431-0635
publication_status: published
publisher: EMS Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: On derived equivalences of k3 surfaces in positive characteristic
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2019'
...
---
_id: '72'
abstract:
- lang: eng
text: We consider the totally asymmetric simple exclusion process (TASEP) with non-random
initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle
initially at the origin. For ρ<λ, there is a shock and the second class particle
moves with speed 1−λ−ρ. For large time t, we show that the position of the second
class particle fluctuates on a t1/3 scale and determine its limiting law. We also
obtain the limiting distribution of the number of steps made by the second class
particle until time t.
article_processing_charge: No
article_type: original
author:
- first_name: Patrick
full_name: Ferrari, Patrick
last_name: Ferrari
- first_name: Promit
full_name: Ghosal, Promit
last_name: Ghosal
- first_name: Peter
full_name: Nejjar, Peter
id: 4BF426E2-F248-11E8-B48F-1D18A9856A87
last_name: Nejjar
citation:
ama: Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP
with non-random initial condition. Annales de l’institut Henri Poincare (B)
Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916
apa: Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class
particle in TASEP with non-random initial condition. Annales de l’institut
Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics.
https://doi.org/10.1214/18-AIHP916
chicago: Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second
Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut
Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics,
2019. https://doi.org/10.1214/18-AIHP916.
ieee: P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle
in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare
(B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical
Statistics, pp. 1203–1225, 2019.
ista: Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle
in TASEP with non-random initial condition. Annales de l’institut Henri Poincare
(B) Probability and Statistics. 55(3), 1203–1225.
mla: Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with
Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability
and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019,
pp. 1203–25, doi:10.1214/18-AIHP916.
short: P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B)
Probability and Statistics 55 (2019) 1203–1225.
date_created: 2018-12-11T11:44:29Z
date_published: 2019-09-25T00:00:00Z
date_updated: 2023-10-17T08:53:45Z
day: '25'
department:
- _id: LaEr
- _id: JaMa
doi: 10.1214/18-AIHP916
ec_funded: 1
external_id:
arxiv:
- '1710.02323'
isi:
- '000487763200001'
intvolume: ' 55'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.02323
month: '09'
oa: 1
oa_version: Preprint
page: 1203-1225
project:
- _id: 258DCDE6-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '338804'
name: Random matrices, universality and disordered quantum systems
- _id: 256E75B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '716117'
name: Optimal Transport and Stochastic Dynamics
publication: Annales de l'institut Henri Poincare (B) Probability and Statistics
publication_identifier:
issn:
- 0246-0203
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Limit law of a second class particle in TASEP with non-random initial condition
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 55
year: '2019'
...
---
_id: '6657'
abstract:
- lang: eng
text: 'In this article a model is described how Open Access definitions can be formed
on the basis of objective criteria. The common Open Access definitions such as
"gold" and "green" are not exactly defined. This becomes a problem as soon as
one begins to measure Open Access, for example if the development of the Open
Access share should be monitored. This was discussed in the working group on Open
Access Monitoring of the AT2OA project and the present model was developed,
which is based on 5 critics with 4 characteristics: location, licence, version,
embargo and conditions of the Open Access publication are taken into account.
In the meantime, the model has also been tested in practice using R scripts, and
the initial results are quite promising.'
article_processing_charge: No
article_type: original
author:
- first_name: Patrick
full_name: Danowski, Patrick
id: 2EBD1598-F248-11E8-B48F-1D18A9856A87
last_name: Danowski
orcid: 0000-0002-6026-4409
citation:
ama: Danowski P. An Austrian proposal for the classification of Open Access Tuples
(COAT) - distinguish different open access types beyond colors. Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 2019;72(1):59-65.
doi:10.31263/voebm.v72i1.2276
apa: Danowski, P. (2019). An Austrian proposal for the classification of Open Access
Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v72i1.2276
chicago: Danowski, Patrick. “An Austrian Proposal for the Classification of Open
Access Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.”
Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare.
Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019. https://doi.org/10.31263/voebm.v72i1.2276.
ieee: P. Danowski, “An Austrian proposal for the classification of Open Access Tuples
(COAT) - distinguish different open access types beyond colors,” Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, vol.
72, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp.
59–65, 2019.
ista: Danowski P. 2019. An Austrian proposal for the classification of Open Access
Tuples (COAT) - distinguish different open access types beyond colors. Mitteilungen
der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 72(1), 59–65.
mla: Danowski, Patrick. “An Austrian Proposal for the Classification of Open Access
Tuples (COAT) - Distinguish Different Open Access Types beyond Colors.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol.
72, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2019,
pp. 59–65, doi:10.31263/voebm.v72i1.2276.
short: P. Danowski, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
Und Bibliothekare 72 (2019) 59–65.
date_created: 2019-07-21T21:59:15Z
date_published: 2019-05-17T00:00:00Z
date_updated: 2023-10-17T11:33:58Z
day: '17'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v72i1.2276
file:
- access_level: open_access
checksum: c0d2695d6d0d34e62ba06fb3f0ebaaed
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-22T08:45:03Z
date_updated: 2020-07-14T12:47:35Z
file_id: '6661'
file_name: 2019_MitteilungenDerVOEB_Danowski.pdf
file_size: 468558
relation: main_file
file_date_updated: 2020-07-14T12:47:35Z
has_accepted_license: '1'
intvolume: ' 72'
issue: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 59-65
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
eissn:
- 1022-2588
publication_status: published
publisher: Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
quality_controlled: '1'
related_material:
record:
- id: '5686'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: An Austrian proposal for the classification of Open Access Tuples (COAT) -
distinguish different open access types beyond colors
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 72
year: '2019'
...
---
_id: '6646'
abstract:
- lang: eng
text: We demonstrate robust retention of valley coherence and its control via polariton
pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity
exciton polaritons at room temperature.
article_number: paper JTu2A.52
article_processing_charge: No
author:
- first_name: Mandeep
full_name: Khatoniar, Mandeep
last_name: Khatoniar
- first_name: Nicholas
full_name: Yama, Nicholas
last_name: Yama
- first_name: Areg
full_name: Ghazaryan, Areg
id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87
last_name: Ghazaryan
orcid: 0000-0001-9666-3543
- first_name: Sriram
full_name: Guddala, Sriram
last_name: Guddala
- first_name: Pouyan
full_name: Ghaemi, Pouyan
last_name: Ghaemi
- first_name: Vinod
full_name: Menon, Vinod
last_name: Menon
citation:
ama: 'Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. Room temperature
control of valley coherence in bilayer WS2 exciton polaritons. In: CLEO: Applications
and Technology. Optica Publishing Group; 2019. doi:10.1364/cleo_at.2019.jtu2a.52'
apa: 'Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., & Menon,
V. (2019). Room temperature control of valley coherence in bilayer WS2 exciton
polaritons. In CLEO: Applications and Technology. San Jose, CA, United
States: Optica Publishing Group. https://doi.org/10.1364/cleo_at.2019.jtu2a.52'
chicago: 'Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan
Ghaemi, and Vinod Menon. “Room Temperature Control of Valley Coherence in Bilayer
WS2 Exciton Polaritons.” In CLEO: Applications and Technology. Optica
Publishing Group, 2019. https://doi.org/10.1364/cleo_at.2019.jtu2a.52.'
ieee: 'M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, and V. Menon,
“Room temperature control of valley coherence in bilayer WS2 exciton polaritons,”
in CLEO: Applications and Technology, San Jose, CA, United States, 2019.'
ista: 'Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. 2019. Room
temperature control of valley coherence in bilayer WS2 exciton polaritons. CLEO:
Applications and Technology. CLEO: Conference on Lasers and Electro-Optics, paper
JTu2A.52.'
mla: 'Khatoniar, Mandeep, et al. “Room Temperature Control of Valley Coherence in
Bilayer WS2 Exciton Polaritons.” CLEO: Applications and Technology, paper
JTu2A.52, Optica Publishing Group, 2019, doi:10.1364/cleo_at.2019.jtu2a.52.'
short: 'M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:,
CLEO: Applications and Technology, Optica Publishing Group, 2019.'
conference:
end_date: 2019-05-10
location: San Jose, CA, United States
name: 'CLEO: Conference on Lasers and Electro-Optics'
start_date: 2019-05-05
date_created: 2019-07-17T09:40:44Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2023-10-17T12:14:29Z
day: '01'
department:
- _id: MiLe
doi: 10.1364/cleo_at.2019.jtu2a.52
language:
- iso: eng
month: '05'
oa_version: None
publication: 'CLEO: Applications and Technology'
publication_identifier:
isbn:
- '9781943580576'
publication_status: published
publisher: Optica Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Room temperature control of valley coherence in bilayer WS2 exciton polaritons
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...