---
_id: '4527'
abstract:
- lang: eng
text: |-
We introduce bounded asynchrony, a notion of concurrency tailored to the modeling of biological cell-cell interactions. Bounded asynchrony is the result of a scheduler that bounds the number of steps that one process gets ahead of other processes; this allows the components of a system to move independently while keeping them coupled. Bounded asynchrony accurately reproduces the experimental observations made about certain cell-cell interactions: its constrained nondeterminism captures the variability observed in cells that, although equally potent, assume distinct fates. Real-life cells are not “scheduled”, but we show that distributed real-time behavior can lead to component interactions that are observationally equivalent to bounded asynchrony; this provides a possible mechanistic explanation for the phenomena observed during cell fate specification.
We use model checking to determine cell fates. The nondeterminism of bounded asynchrony causes state explosion during model checking, but partial-order methods are not directly applicable. We present a new algorithm that reduces the number of states that need to be explored: our optimization takes advantage of the bounded-asynchronous progress and the spatially local interactions of components that model cells. We compare our own communication-based reduction with partial-order reduction (on a restricted form of bounded asynchrony) and experiments illustrate that our algorithm leads to significant savings.
acknowledgement: Supported in part by the Swiss National Science Foundation (grant
205321-111840).
alternative_title:
- LNCS
author:
- first_name: Jasmin
full_name: Fisher, Jasmin
last_name: Fisher
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Maria
full_name: Maria Mateescu
id: 3B43276C-F248-11E8-B48F-1D18A9856A87
last_name: Mateescu
- first_name: Nir
full_name: Piterman, Nir
last_name: Piterman
citation:
ama: 'Fisher J, Henzinger TA, Mateescu M, Piterman N. Bounded asynchrony: Concurrency
for modeling cell-cell interactions. In: Vol 5054. Springer; 2008:17-32. doi:10.1007/978-3-540-68413-8_2'
apa: 'Fisher, J., Henzinger, T. A., Mateescu, M., & Piterman, N. (2008). Bounded
asynchrony: Concurrency for modeling cell-cell interactions (Vol. 5054, pp. 17–32).
Presented at the FMSB: Formal Methods in Systems Biology, Springer. https://doi.org/10.1007/978-3-540-68413-8_2'
chicago: 'Fisher, Jasmin, Thomas A Henzinger, Maria Mateescu, and Nir Piterman.
“Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions,” 5054:17–32.
Springer, 2008. https://doi.org/10.1007/978-3-540-68413-8_2.'
ieee: 'J. Fisher, T. A. Henzinger, M. Mateescu, and N. Piterman, “Bounded asynchrony:
Concurrency for modeling cell-cell interactions,” presented at the FMSB: Formal
Methods in Systems Biology, 2008, vol. 5054, pp. 17–32.'
ista: 'Fisher J, Henzinger TA, Mateescu M, Piterman N. 2008. Bounded asynchrony:
Concurrency for modeling cell-cell interactions. FMSB: Formal Methods in Systems
Biology, LNCS, vol. 5054, 17–32.'
mla: 'Fisher, Jasmin, et al. Bounded Asynchrony: Concurrency for Modeling Cell-Cell
Interactions. Vol. 5054, Springer, 2008, pp. 17–32, doi:10.1007/978-3-540-68413-8_2.'
short: J. Fisher, T.A. Henzinger, M. Mateescu, N. Piterman, in:, Springer, 2008,
pp. 17–32.
conference:
name: 'FMSB: Formal Methods in Systems Biology'
date_created: 2018-12-11T12:09:19Z
date_published: 2008-05-26T00:00:00Z
date_updated: 2021-01-12T07:59:27Z
day: '26'
doi: 10.1007/978-3-540-68413-8_2
extern: 1
intvolume: ' 5054'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/bounded_asynchrony.pdf
month: '05'
page: 17 - 32
publication_status: published
publisher: Springer
publist_id: '196'
quality_controlled: 0
status: public
title: 'Bounded asynchrony: Concurrency for modeling cell-cell interactions'
type: conference
volume: 5054
year: '2008'
...
---
_id: '4532'
abstract:
- lang: eng
text: We consider the equivalence problem for labeled Markov chains (LMCs), where
each state is labeled with an observation. Two LMCs are equivalent if every finite
sequence of observations has the same probability of occurrence in the two LMCs.
We show that equivalence can be decided in polynomial time, using a reduction
to the equivalence problem for probabilistic automata, which is known to be solvable
in polynomial time. We provide an alternative algorithm to solve the equivalence
problem, which is based on a new definition of bisimulation for probabilistic
automata. We also extend the technique to decide the equivalence of weighted probabilistic
automata.
author:
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jean
full_name: Raskin, Jean-François
last_name: Raskin
citation:
ama: Doyen L, Henzinger TA, Raskin J. Equivalence of labeled Markov chains. International
Journal of Foundations of Computer Science. 2008;19(3):549-563. doi:10.1142/S0129054108005814
apa: Doyen, L., Henzinger, T. A., & Raskin, J. (2008). Equivalence of labeled
Markov chains. International Journal of Foundations of Computer Science.
World Scientific Publishing. https://doi.org/10.1142/S0129054108005814
chicago: Doyen, Laurent, Thomas A Henzinger, and Jean Raskin. “Equivalence of Labeled
Markov Chains.” International Journal of Foundations of Computer Science.
World Scientific Publishing, 2008. https://doi.org/10.1142/S0129054108005814 .
ieee: L. Doyen, T. A. Henzinger, and J. Raskin, “Equivalence of labeled Markov chains,”
International Journal of Foundations of Computer Science, vol. 19, no.
3. World Scientific Publishing, pp. 549–563, 2008.
ista: Doyen L, Henzinger TA, Raskin J. 2008. Equivalence of labeled Markov chains.
International Journal of Foundations of Computer Science. 19(3), 549–563.
mla: Doyen, Laurent, et al. “Equivalence of Labeled Markov Chains.” International
Journal of Foundations of Computer Science, vol. 19, no. 3, World Scientific
Publishing, 2008, pp. 549–63, doi:10.1142/S0129054108005814 .
short: L. Doyen, T.A. Henzinger, J. Raskin, International Journal of Foundations
of Computer Science 19 (2008) 549–563.
date_created: 2018-12-11T12:09:20Z
date_published: 2008-06-01T00:00:00Z
date_updated: 2021-01-12T07:59:30Z
day: '01'
doi: '10.1142/S0129054108005814 '
extern: 1
intvolume: ' 19'
issue: '3'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/equivalence_of_labeled_markov_chains.pdf
month: '06'
page: 549 - 563
publication: International Journal of Foundations of Computer Science
publication_status: published
publisher: World Scientific Publishing
publist_id: '192'
quality_controlled: 0
status: public
title: Equivalence of labeled Markov chains
type: journal_article
volume: 19
year: '2008'
...
---
_id: '4533'
abstract:
- lang: eng
text: Interface theories have been proposed to support incremental design and independent
implementability. Incremental design means that the compatibility checking of
interfaces can proceed for partial system descriptions, without knowing the interfaces
of all components. Independent implementability means that compatible interfaces
can be refined separately, maintaining compatibility. We show that these interface
theories provide no formal support for component reuse, meaning that the same
component cannot be used to implement several different interfaces in a design.
We add a new operation to interface theories in order to support such reuse. For
example, different interfaces for the same component may refer to different aspects
such as functionality, timing, and power consumption. We give both stateless and
stateful examples for interface theories with component reuse. To illustrate component
reuse in interface-based design, we show how the stateful theory provides a natural
framework for specifying and refining PCI bus clients.
author:
- first_name: Laurent
full_name: Doyen, Laurent
last_name: Doyen
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Barbara
full_name: Jobstmann, Barbara
last_name: Jobstmann
- first_name: Tatjana
full_name: Tatjana Petrov
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: 'Doyen L, Henzinger TA, Jobstmann B, Petrov T. Interface theories with component
reuse. In: ACM; 2008:79-88. doi:10.1145/1450058.1450070'
apa: 'Doyen, L., Henzinger, T. A., Jobstmann, B., & Petrov, T. (2008). Interface
theories with component reuse (pp. 79–88). Presented at the EMSOFT: Embedded Software
, ACM. https://doi.org/10.1145/1450058.1450070'
chicago: Doyen, Laurent, Thomas A Henzinger, Barbara Jobstmann, and Tatjana Petrov.
“Interface Theories with Component Reuse,” 79–88. ACM, 2008. https://doi.org/10.1145/1450058.1450070.
ieee: 'L. Doyen, T. A. Henzinger, B. Jobstmann, and T. Petrov, “Interface theories
with component reuse,” presented at the EMSOFT: Embedded Software , 2008, pp.
79–88.'
ista: 'Doyen L, Henzinger TA, Jobstmann B, Petrov T. 2008. Interface theories with
component reuse. EMSOFT: Embedded Software , 79–88.'
mla: Doyen, Laurent, et al. Interface Theories with Component Reuse. ACM,
2008, pp. 79–88, doi:10.1145/1450058.1450070.
short: L. Doyen, T.A. Henzinger, B. Jobstmann, T. Petrov, in:, ACM, 2008, pp. 79–88.
conference:
name: 'EMSOFT: Embedded Software '
date_created: 2018-12-11T12:09:21Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-01-12T07:59:30Z
day: '01'
doi: 10.1145/1450058.1450070
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/interface_theories_with_component_reuse.pdf
month: '10'
page: 79 - 88
publication_status: published
publisher: ACM
publist_id: '193'
quality_controlled: 0
status: public
title: Interface theories with component reuse
type: conference
year: '2008'
...
---
_id: '4534'
abstract:
- lang: eng
text: A stochastic graph game is played by two players on a game graph with probabilistic
transitions. We consider stochastic graph games with ω-regular winning conditions
specified as parity objectives, and mean-payoff (or limit-average) objectives.
These games lie in NP ∩ coNP. We present a polynomial-time Turing reduction of
stochastic parity games to stochastic mean-payoff games.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, Henzinger TA. Reduction of stochastic parity to stochastic mean-payoff
games. Information Processing Letters. 2008;106(1):1-7. doi:10.1016/j.ipl.2007.08.035
apa: Chatterjee, K., & Henzinger, T. A. (2008). Reduction of stochastic parity
to stochastic mean-payoff games. Information Processing Letters. Elsevier.
https://doi.org/10.1016/j.ipl.2007.08.035
chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Reduction of Stochastic
Parity to Stochastic Mean-Payoff Games.” Information Processing Letters.
Elsevier, 2008. https://doi.org/10.1016/j.ipl.2007.08.035.
ieee: K. Chatterjee and T. A. Henzinger, “Reduction of stochastic parity to stochastic
mean-payoff games,” Information Processing Letters, vol. 106, no. 1. Elsevier,
pp. 1–7, 2008.
ista: Chatterjee K, Henzinger TA. 2008. Reduction of stochastic parity to stochastic
mean-payoff games. Information Processing Letters. 106(1), 1–7.
mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “Reduction of Stochastic Parity
to Stochastic Mean-Payoff Games.” Information Processing Letters, vol.
106, no. 1, Elsevier, 2008, pp. 1–7, doi:10.1016/j.ipl.2007.08.035.
short: K. Chatterjee, T.A. Henzinger, Information Processing Letters 106 (2008)
1–7.
date_created: 2018-12-11T12:09:21Z
date_published: 2008-03-31T00:00:00Z
date_updated: 2021-01-12T07:59:30Z
day: '31'
doi: 10.1016/j.ipl.2007.08.035
extern: 1
intvolume: ' 106'
issue: '1'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/reduction_of_stochastic_parity_to_stochastic_mean-payoff_games.pdf
month: '03'
page: 1 - 7
publication: Information Processing Letters
publication_status: published
publisher: Elsevier
publist_id: '188'
quality_controlled: 0
status: public
title: Reduction of stochastic parity to stochastic mean-payoff games
type: journal_article
volume: 106
year: '2008'
...
---
_id: '4546'
abstract:
- lang: eng
text: We propose the notion of logical reliability for real-time program tasks that
interact through periodically updated program variables. We describe a reliability
analysis that checks if the given short-term (e.g., single-period) reliability
of a program variable update in an implementation is sufficient to meet the logical
reliability requirement (of the program variable) in the long run. We then present
a notion of design by refinement where a task can be refined by another task that
writes to program variables with less logical reliability. The resulting analysis
can be combined with an incremental schedulability analysis for interacting real-time
tasks proposed earlier for the Hierarchical Timing Language (HTL), a coordination
language for distributed real-time systems. We implemented a logical-reliability-enhanced
prototype of the compiler and runtime infrastructure for HTL.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Arkadeb
full_name: Ghosal, Arkadeb
last_name: Ghosal
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Daniel
full_name: Iercan, Daniel
last_name: Iercan
- first_name: Christoph
full_name: Kirsch, Christoph M
last_name: Kirsch
- first_name: Claudio
full_name: Pinello, Claudio
last_name: Pinello
- first_name: Alberto
full_name: Sangiovanni-Vincentelli, Alberto
last_name: Sangiovanni Vincentelli
citation:
ama: 'Chatterjee K, Ghosal A, Henzinger TA, et al. Logical reliability of interacting
real-time tasks. In: IEEE; 2008:909-914. doi:10.1145/1403375.1403595'
apa: 'Chatterjee, K., Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., Pinello,
C., & Sangiovanni Vincentelli, A. (2008). Logical reliability of interacting
real-time tasks (pp. 909–914). Presented at the DATE: Design, Automation and Test
in Europe, IEEE. https://doi.org/10.1145/1403375.1403595'
chicago: Chatterjee, Krishnendu, Arkadeb Ghosal, Thomas A Henzinger, Daniel Iercan,
Christoph Kirsch, Claudio Pinello, and Alberto Sangiovanni Vincentelli. “Logical
Reliability of Interacting Real-Time Tasks,” 909–14. IEEE, 2008. https://doi.org/10.1145/1403375.1403595.
ieee: 'K. Chatterjee et al., “Logical reliability of interacting real-time
tasks,” presented at the DATE: Design, Automation and Test in Europe, 2008, pp.
909–914.'
ista: 'Chatterjee K, Ghosal A, Henzinger TA, Iercan D, Kirsch C, Pinello C, Sangiovanni
Vincentelli A. 2008. Logical reliability of interacting real-time tasks. DATE:
Design, Automation and Test in Europe, 909–914.'
mla: Chatterjee, Krishnendu, et al. Logical Reliability of Interacting Real-Time
Tasks. IEEE, 2008, pp. 909–14, doi:10.1145/1403375.1403595.
short: K. Chatterjee, A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, C. Pinello,
A. Sangiovanni Vincentelli, in:, IEEE, 2008, pp. 909–914.
conference:
name: 'DATE: Design, Automation and Test in Europe'
date_created: 2018-12-11T12:09:25Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:36Z
day: '01'
doi: 10.1145/1403375.1403595
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/logical_reliability_of_interacting_real-time_tasks.pdf
month: '01'
page: 909 - 914
publication_status: published
publisher: IEEE
publist_id: '171'
quality_controlled: 0
status: public
title: Logical reliability of interacting real-time tasks
type: conference
year: '2008'
...
---
_id: '4548'
abstract:
- lang: eng
text: The value of a finite-state two-player zero-sum stochastic game with limit-average
payoff can be approximated to within ε in time exponential in a polynomial in
the size of the game times polynomial in logarithmic in 1/ε, for all ε > 0.
author:
- first_name: Krishnendu
full_name: Krishnendu Chatterjee
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
citation:
ama: Chatterjee K, Majumdar R, Henzinger TA. Stochastic limit-average games are
in EXPTIME. International Journal of Game Theory. 2008;37(2):219-234. doi:10.1007/s00182-007-0110-5
apa: Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2008). Stochastic limit-average
games are in EXPTIME. International Journal of Game Theory. Springer. https://doi.org/10.1007/s00182-007-0110-5
chicago: Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Stochastic
Limit-Average Games Are in EXPTIME.” International Journal of Game Theory.
Springer, 2008. https://doi.org/10.1007/s00182-007-0110-5.
ieee: K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Stochastic limit-average
games are in EXPTIME,” International Journal of Game Theory, vol. 37, no.
2. Springer, pp. 219–234, 2008.
ista: Chatterjee K, Majumdar R, Henzinger TA. 2008. Stochastic limit-average games
are in EXPTIME. International Journal of Game Theory. 37(2), 219–234.
mla: Chatterjee, Krishnendu, et al. “Stochastic Limit-Average Games Are in EXPTIME.”
International Journal of Game Theory, vol. 37, no. 2, Springer, 2008, pp.
219–34, doi:10.1007/s00182-007-0110-5.
short: K. Chatterjee, R. Majumdar, T.A. Henzinger, International Journal of Game
Theory 37 (2008) 219–234.
date_created: 2018-12-11T12:09:25Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T07:59:37Z
day: '01'
doi: 10.1007/s00182-007-0110-5
extern: 1
intvolume: ' 37'
issue: '2'
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/stochastic_limit-average_games_are_in_exptime.pdf
month: '01'
page: 219 - 234
publication: International Journal of Game Theory
publication_status: published
publisher: Springer
publist_id: '168'
quality_controlled: 0
status: public
title: Stochastic limit-average games are in EXPTIME
type: journal_article
volume: 37
year: '2008'
...
---
_id: '4568'
abstract:
- lang: eng
text: We present and evaluate a framework and tool for combining multiple program
analyses which allows the dynamic (on-line) adjustment of the precision of each
analysis depending on the accumulated results. For example, the explicit tracking
of the values of a variable may be switched off in favor of a predicate abstraction
when and where the number of different variable values that have been encountered
has exceeded a specified threshold. The method is evaluated on verifying the SSH
client/server software and shows significant gains compared with predicate abstraction-based
model checking.
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Grégory
full_name: Théoduloz, Grégory
last_name: Théoduloz
citation:
ama: 'Beyer D, Henzinger TA, Théoduloz G. Program analysis with dynamic change of
precision. In: ACM; 2008:29-38. doi:10.1109/ASE.2008.13'
apa: 'Beyer, D., Henzinger, T. A., & Théoduloz, G. (2008). Program analysis
with dynamic change of precision (pp. 29–38). Presented at the ASE: Automated
Software Engineering, ACM. https://doi.org/10.1109/ASE.2008.13'
chicago: Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Program Analysis
with Dynamic Change of Precision,” 29–38. ACM, 2008. https://doi.org/10.1109/ASE.2008.13.
ieee: 'D. Beyer, T. A. Henzinger, and G. Théoduloz, “Program analysis with dynamic
change of precision,” presented at the ASE: Automated Software Engineering, 2008,
pp. 29–38.'
ista: 'Beyer D, Henzinger TA, Théoduloz G. 2008. Program analysis with dynamic change
of precision. ASE: Automated Software Engineering, 29–38.'
mla: Beyer, Dirk, et al. Program Analysis with Dynamic Change of Precision.
ACM, 2008, pp. 29–38, doi:10.1109/ASE.2008.13.
short: D. Beyer, T.A. Henzinger, G. Théoduloz, in:, ACM, 2008, pp. 29–38.
conference:
name: 'ASE: Automated Software Engineering'
date_created: 2018-12-11T12:09:31Z
date_published: 2008-10-07T00:00:00Z
date_updated: 2021-01-12T07:59:46Z
day: '07'
doi: 10.1109/ASE.2008.13
extern: 1
main_file_link:
- open_access: '0'
url: http://pub.ist.ac.at/%7Etah/Publications/program_analysis_with_dynamic_change_of_precision.pdf
month: '10'
page: 29 - 38
publication_status: published
publisher: ACM
publist_id: '140'
quality_controlled: 0
status: public
title: Program analysis with dynamic change of precision
type: conference
year: '2008'
...
---
_id: '517'
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Identity and coalescence in structured populations: A commentary
on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. Genetics
Research. 2008;89(5-6):475-477. doi:10.1017/S0016672308009683'
apa: 'Barton, N. H. (2008). Identity and coalescence in structured populations:
A commentary on “Inbreeding coefficients and coalescence times” by Montgomery
Slatkin. Genetics Research. Cambridge University Press. https://doi.org/10.1017/S0016672308009683'
chicago: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations:
A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery
Slatkin.” Genetics Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672308009683.'
ieee: 'N. H. Barton, “Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” Genetics
Research, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.'
ista: 'Barton NH. 2008. Identity and coalescence in structured populations: A commentary
on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics
Research. 89(5–6), 475–477.'
mla: 'Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A
Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.”
Genetics Research, vol. 89, no. 5–6, Cambridge University Press, 2008,
pp. 475–77, doi:10.1017/S0016672308009683.'
short: N.H. Barton, Genetics Research 89 (2008) 475–477.
date_created: 2018-12-11T11:46:55Z
date_published: 2008-10-29T00:00:00Z
date_updated: 2024-02-14T09:51:09Z
day: '29'
department:
- _id: NiBa
doi: 10.1017/S0016672308009683
intvolume: ' 89'
issue: 5-6
language:
- iso: eng
month: '10'
oa_version: None
page: 475 - 477
publication: Genetics Research
publication_status: published
publisher: Cambridge University Press
publist_id: '7302'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Identity and coalescence in structured populations: A commentary on ''Inbreeding
coefficients and coalescence times'' by Montgomery Slatkin'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2008'
...
---
_id: '12201'
abstract:
- lang: eng
text: The development of plant lateral organs is interesting because, although many
of the same genes seem to be involved in the early growth of primordia, completely
different gene combinations are required for the complete development of organs
such as leaves and stamens. Thus, the genes common to the development of most
organs, which generally form and polarize the primordial ‘envelope’, must at some
stage interact with those that ‘install’ the functional content of the organ –
in the case of the stamen, the four microsporangia. Although distinct genetic
pathways of organ initiation, polarity establishment and setting up the reproductive
cell line can readily be recognized, they do not occur sequentially. Rather, they
are activated early and run in parallel. There is evidence for continuing crosstalk
between these pathways.
acknowledgement: X.F. holds a Clarendon Scholarship from the University of Oxford.
We thank Angela Hay and Jill Harrison for helpful advice and discussion.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Packaging the male germline in plants. Trends in Genetics.
2007;23(10):503-510. doi:10.1016/j.tig.2007.08.005
apa: Feng, X., & Dickinson, H. G. (2007). Packaging the male germline in plants.
Trends in Genetics. Elsevier BV. https://doi.org/10.1016/j.tig.2007.08.005
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”
Trends in Genetics. Elsevier BV, 2007. https://doi.org/10.1016/j.tig.2007.08.005.
ieee: X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” Trends
in Genetics, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007.
ista: Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends
in Genetics. 23(10), 503–510.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”
Trends in Genetics, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:10.1016/j.tig.2007.08.005.
short: X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.
date_created: 2023-01-16T09:22:44Z
date_published: 2007-10-01T00:00:00Z
date_updated: 2023-05-08T10:58:47Z
department:
- _id: XiFe
doi: 10.1016/j.tig.2007.08.005
extern: '1'
external_id:
pmid:
- '17825943'
intvolume: ' 23'
issue: '10'
keyword:
- Genetics
language:
- iso: eng
month: '10'
oa_version: None
page: 503-510
pmid: 1
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9525
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
scopus_import: '1'
status: public
title: Packaging the male germline in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2007'
...
---
_id: '128'
abstract:
- lang: eng
text: 'A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described.
This long tuning range is achieved by simultaneously ramping the external cavity
length with the laser injection current. The laser output pointing remains fixed,
independent of its frequency because of the cover slip cavity design. This system
is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate
with lithium vapor and lithium atom beam experiments. '
acknowledgement: "National Science Foundation\r\nThis work was supported with NSF
Grant No. PHY-0653623. We thank Dr. W. Bickel and Dr. J. Jones for diagnostic equipment,
K. Guerin for assistance with mechanical drawings, and M. Parker of Rincon Research
Inc. for optics components."
article_number: '106108'
arxiv: 1
author:
- first_name: Adra
full_name: Carr, Adra
last_name: Carr
- first_name: Yancey
full_name: Serchest, Yancey
last_name: Serchest
- first_name: Scott R
full_name: Waitukaitis, Scott R
id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87
last_name: Waitukaitis
orcid: 0000-0002-2299-3176
- first_name: John
full_name: Perreault, John
last_name: Perreault
- first_name: Vincent
full_name: Lonij, Vincent
last_name: Lonij
- first_name: Alexander
full_name: Cronin, Alexander
last_name: Cronin
citation:
ama: Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. Cover slip
external cavity diode laser. Review of Scientific Instruments. 2007;78(10).
doi:10.1063/1.2801006
apa: Carr, A., Serchest, Y., Waitukaitis, S. R., Perreault, J., Lonij, V., &
Cronin, A. (2007). Cover slip external cavity diode laser. Review of Scientific
Instruments. American Institute of Physics. https://doi.org/10.1063/1.2801006
chicago: Carr, Adra, Yancey Serchest, Scott R Waitukaitis, John Perreault, Vincent
Lonij, and Alexander Cronin. “Cover Slip External Cavity Diode Laser.” Review
of Scientific Instruments. American Institute of Physics, 2007. https://doi.org/10.1063/1.2801006.
ieee: A. Carr, Y. Serchest, S. R. Waitukaitis, J. Perreault, V. Lonij, and A. Cronin,
“Cover slip external cavity diode laser,” Review of Scientific Instruments,
vol. 78, no. 10. American Institute of Physics, 2007.
ista: Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. 2007.
Cover slip external cavity diode laser. Review of Scientific Instruments. 78(10),
106108.
mla: Carr, Adra, et al. “Cover Slip External Cavity Diode Laser.” Review of Scientific
Instruments, vol. 78, no. 10, 106108, American Institute of Physics, 2007,
doi:10.1063/1.2801006.
short: A. Carr, Y. Serchest, S.R. Waitukaitis, J. Perreault, V. Lonij, A. Cronin,
Review of Scientific Instruments 78 (2007).
date_created: 2018-12-11T11:44:46Z
date_published: 2007-10-29T00:00:00Z
date_updated: 2021-01-12T06:49:35Z
day: '29'
doi: 10.1063/1.2801006
extern: '1'
external_id:
arxiv:
- '0708.0014'
intvolume: ' 78'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/0708.0014
month: '10'
oa: 1
oa_version: Preprint
publication: Review of Scientific Instruments
publication_status: published
publisher: American Institute of Physics
publist_id: '7925'
quality_controlled: '1'
status: public
title: Cover slip external cavity diode laser
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2007'
...
---
_id: '1297'
abstract:
- lang: eng
text: In flies, the large tangential cells of the lobula plate represent an important
processing center for visual navigation based on optic flow. Although the visual
response properties of these cells have been well studied in blowflies, information
on their synaptic organization is mostly lacking. Here we study the distribution
of presynaptic release and postsynaptic inhibitory sites in the same set of cells
in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry,
our results suggest that HS and VS cells of Drosophila express γ-aminobutyric
acid (GABA) receptors in their dendritic region within the lobula plate, thus
being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum,
both cell types express synaptobrevin, suggesting the presence of presynaptic
specializations there. HS- and VS-cell terminals additionally show evidence for
postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings
are in line with the general circuit for visual motion detection and receptive
field properties as postulated from electrophysiological and optical recordings
in blowflies, suggesting a similar functional organization of lobula plate tangential
cells in the two species.
author:
- first_name: Shamprasad
full_name: Raghu, Shamprasad V
last_name: Raghu
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
- first_name: Dierk
full_name: Reiff, Dierk F
last_name: Reiff
citation:
ama: 'Raghu S, Jösch MA, Borst A, Reiff D. Synaptic organization of lobula plate
tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release
sites. Journal of Comparative Neurology. 2007;502(4):598-610. doi:10.1002/cne.21319'
apa: 'Raghu, S., Jösch, M. A., Borst, A., & Reiff, D. (2007). Synaptic organization
of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors
and chemical release sites. Journal of Comparative Neurology. Wiley-Blackwell.
https://doi.org/10.1002/cne.21319'
chicago: 'Raghu, Shamprasad, Maximilian A Jösch, Alexander Borst, and Dierk Reiff.
“Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric
Acid Receptors and Chemical Release Sites.” Journal of Comparative Neurology.
Wiley-Blackwell, 2007. https://doi.org/10.1002/cne.21319.'
ieee: 'S. Raghu, M. A. Jösch, A. Borst, and D. Reiff, “Synaptic organization of
lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and
chemical release sites,” Journal of Comparative Neurology, vol. 502, no.
4. Wiley-Blackwell, pp. 598–610, 2007.'
ista: 'Raghu S, Jösch MA, Borst A, Reiff D. 2007. Synaptic organization of lobula
plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical
release sites. Journal of Comparative Neurology. 502(4), 598–610.'
mla: 'Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential
Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.”
Journal of Comparative Neurology, vol. 502, no. 4, Wiley-Blackwell, 2007,
pp. 598–610, doi:10.1002/cne.21319.'
short: S. Raghu, M.A. Jösch, A. Borst, D. Reiff, Journal of Comparative Neurology
502 (2007) 598–610.
date_created: 2018-12-11T11:51:13Z
date_published: 2007-06-01T00:00:00Z
date_updated: 2021-01-12T06:49:42Z
day: '01'
doi: 10.1002/cne.21319
extern: 1
intvolume: ' 502'
issue: '4'
month: '06'
page: 598 - 610
publication: Journal of Comparative Neurology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5974'
quality_controlled: 0
status: public
title: 'Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric
acid receptors and chemical release sites'
type: journal_article
volume: 502
year: '2007'
...
---
_id: '8483'
abstract:
- lang: eng
text: Atom-resolved real-time studies of kinetic processes in proteins have been
hampered in the past by the lack of experimental techniques that yield sufficient
temporal and atomic resolution. Here we present band-selective optimized flip-angle
short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous
observation of reaction kinetics for a large number of nuclear sites along the
polypeptide chain of a protein with an unprecedented time resolution of a few
seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition
techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic
event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational
transition of α-lactalbumin from a molten globular to the native state for a large
number of amide sites along the polypeptide chain. The kinetic behavior observed
for the disappearance of the molten globule and the appearance of the native state
is monoexponential and uniform along the polypeptide chain. This observation confirms
previous findings that a single transition state ensemble controls folding of
α-lactalbumin from the molten globule to the native state. In a second application,
the spontaneous unfolding of native ubiquitin under nondenaturing conditions is
characterized by amide hydrogen exchange rate constants measured at high pH by
using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual
manner with distinct unfolding regimes.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: V.
full_name: Forge, V.
last_name: Forge
- first_name: B.
full_name: Brutscher, B.
last_name: Brutscher
citation:
ama: Schanda P, Forge V, Brutscher B. Protein folding and unfolding studied at atomic
resolution by fast two-dimensional NMR spectroscopy. Proceedings of the National
Academy of Sciences. 2007;104(27):11257-11262. doi:10.1073/pnas.0702069104
apa: Schanda, P., Forge, V., & Brutscher, B. (2007). Protein folding and unfolding
studied at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.0702069104
chicago: Schanda, Paul, V. Forge, and B. Brutscher. “Protein Folding and Unfolding
Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” Proceedings
of the National Academy of Sciences. National Academy of Sciences, 2007. https://doi.org/10.1073/pnas.0702069104.
ieee: P. Schanda, V. Forge, and B. Brutscher, “Protein folding and unfolding studied
at atomic resolution by fast two-dimensional NMR spectroscopy,” Proceedings
of the National Academy of Sciences, vol. 104, no. 27. National Academy of
Sciences, pp. 11257–11262, 2007.
ista: Schanda P, Forge V, Brutscher B. 2007. Protein folding and unfolding studied
at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings of
the National Academy of Sciences. 104(27), 11257–11262.
mla: Schanda, Paul, et al. “Protein Folding and Unfolding Studied at Atomic Resolution
by Fast Two-Dimensional NMR Spectroscopy.” Proceedings of the National Academy
of Sciences, vol. 104, no. 27, National Academy of Sciences, 2007, pp. 11257–62,
doi:10.1073/pnas.0702069104.
short: P. Schanda, V. Forge, B. Brutscher, Proceedings of the National Academy of
Sciences 104 (2007) 11257–11262.
date_created: 2020-09-18T10:12:54Z
date_published: 2007-07-03T00:00:00Z
date_updated: 2021-01-12T08:19:35Z
day: '03'
doi: 10.1073/pnas.0702069104
extern: '1'
intvolume: ' 104'
issue: '27'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
page: 11257-11262
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
status: public
title: Protein folding and unfolding studied at atomic resolution by fast two-dimensional
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 104
year: '2007'
...
---
_id: '8484'
abstract:
- lang: eng
text: A series of sequential, intra-residue, and bi-directional BEST H–N–CA, H–N–CO,
and H–N–CB pulse sequences is presented that extends the BEST concept introduced
recently for fast multidimensional protein NMR [Schanda et al., J. Am. Chem. Soc.
128 (2006) 9042] to the complete set of experiments required for sequential resonance
assignment. We demonstrate for the protein ubiquitin that 3D BEST H–N–C correlation
spectra can be recorded on a 600 MHz NMR spectrometer equipped with a cryogenic
probe in only a few minutes of acquisition time with sufficient sensitivity to
detect all expected cross peaks.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Ewen
full_name: Lescop, Ewen
last_name: Lescop
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Lescop E, Schanda P, Brutscher B. A set of BEST triple-resonance experiments
for time-optimized protein resonance assignment. Journal of Magnetic Resonance.
2007;187(1):163-169. doi:10.1016/j.jmr.2007.04.002
apa: Lescop, E., Schanda, P., & Brutscher, B. (2007). A set of BEST triple-resonance
experiments for time-optimized protein resonance assignment. Journal of Magnetic
Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2007.04.002
chicago: Lescop, Ewen, Paul Schanda, and Bernhard Brutscher. “A Set of BEST Triple-Resonance
Experiments for Time-Optimized Protein Resonance Assignment.” Journal of Magnetic
Resonance. Elsevier, 2007. https://doi.org/10.1016/j.jmr.2007.04.002.
ieee: E. Lescop, P. Schanda, and B. Brutscher, “A set of BEST triple-resonance experiments
for time-optimized protein resonance assignment,” Journal of Magnetic Resonance,
vol. 187, no. 1. Elsevier, pp. 163–169, 2007.
ista: Lescop E, Schanda P, Brutscher B. 2007. A set of BEST triple-resonance experiments
for time-optimized protein resonance assignment. Journal of Magnetic Resonance.
187(1), 163–169.
mla: Lescop, Ewen, et al. “A Set of BEST Triple-Resonance Experiments for Time-Optimized
Protein Resonance Assignment.” Journal of Magnetic Resonance, vol. 187,
no. 1, Elsevier, 2007, pp. 163–69, doi:10.1016/j.jmr.2007.04.002.
short: E. Lescop, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 187 (2007)
163–169.
date_created: 2020-09-18T10:13:02Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:35Z
day: '01'
doi: 10.1016/j.jmr.2007.04.002
extern: '1'
intvolume: ' 187'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 163-169
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A set of BEST triple-resonance experiments for time-optimized protein resonance
assignment
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 187
year: '2007'
...
---
_id: '8485'
abstract:
- lang: eng
text: High signal to noise is a necessity for the quantification of NMR spectral
parameters to be translated into accurate and precise restraints on protein structure
and dynamics. An important source of long-range structural information is obtained
from 1H–1H residual dipolar couplings (RDCs) measured for weakly aligned molecules.
For sensitivity reasons, such measurements are generally performed on highly deuterated
protein samples. Here we show that high sensitivity is also obtained for protonated
protein samples if the pulse schemes are optimized in terms of longitudinal relaxation
efficiency and J-mismatch compensated coherence transfer. The new sensitivity-optimized
quantitative J-correlation experiment yields important signal gains reaching factors
of 1.5 to 8 for individual correlation peaks when compared to previously proposed
pulse schemes.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Ewen
full_name: Lescop, Ewen
last_name: Lescop
- first_name: Mirjam
full_name: Falge, Mirjam
last_name: Falge
- first_name: Rémy
full_name: Sounier, Rémy
last_name: Sounier
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. Sensitivity-optimized
experiment for the measurement of residual dipolar couplings between amide protons.
Journal of Biomolecular NMR. 2007;38:47-55. doi:10.1007/s10858-006-9138-2
apa: Schanda, P., Lescop, E., Falge, M., Sounier, R., Boisbouvier, J., & Brutscher,
B. (2007). Sensitivity-optimized experiment for the measurement of residual dipolar
couplings between amide protons. Journal of Biomolecular NMR. Springer
Nature. https://doi.org/10.1007/s10858-006-9138-2
chicago: Schanda, Paul, Ewen Lescop, Mirjam Falge, Rémy Sounier, Jérôme Boisbouvier,
and Bernhard Brutscher. “Sensitivity-Optimized Experiment for the Measurement
of Residual Dipolar Couplings between Amide Protons.” Journal of Biomolecular
NMR. Springer Nature, 2007. https://doi.org/10.1007/s10858-006-9138-2.
ieee: P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, and B. Brutscher,
“Sensitivity-optimized experiment for the measurement of residual dipolar couplings
between amide protons,” Journal of Biomolecular NMR, vol. 38. Springer
Nature, pp. 47–55, 2007.
ista: Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. 2007.
Sensitivity-optimized experiment for the measurement of residual dipolar couplings
between amide protons. Journal of Biomolecular NMR. 38, 47–55.
mla: Schanda, Paul, et al. “Sensitivity-Optimized Experiment for the Measurement
of Residual Dipolar Couplings between Amide Protons.” Journal of Biomolecular
NMR, vol. 38, Springer Nature, 2007, pp. 47–55, doi:10.1007/s10858-006-9138-2.
short: P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, B. Brutscher,
Journal of Biomolecular NMR 38 (2007) 47–55.
date_created: 2020-09-18T10:13:12Z
date_published: 2007-03-08T00:00:00Z
date_updated: 2021-01-12T08:19:36Z
day: '08'
doi: 10.1007/s10858-006-9138-2
extern: '1'
intvolume: ' 38'
keyword:
- Spectroscopy
- Biochemistry
language:
- iso: eng
month: '03'
oa_version: None
page: 47-55
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Sensitivity-optimized experiment for the measurement of residual dipolar couplings
between amide protons
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2007'
...
---
_id: '8486'
abstract:
- lang: eng
text: A technique is described that allows reducing acquisition times of multidimensional
NMR experiments by extensive spectral folding. The method is simple and has many
interesting applications for NMR studies of molecular structure, dynamics, and
kinetics.
article_processing_charge: No
article_type: original
author:
- first_name: Ewen
full_name: Lescop, Ewen
last_name: Lescop
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Rodolfo
full_name: Rasia, Rodolfo
last_name: Rasia
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Lescop E, Schanda P, Rasia R, Brutscher B. Automated spectral compression for
fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy.
Journal of the American Chemical Society. 2007;129(10):2756-2757. doi:10.1021/ja068949u
apa: Lescop, E., Schanda, P., Rasia, R., & Brutscher, B. (2007). Automated spectral
compression for fast multidimensional NMR and increased time resolution in real-time
NMR spectroscopy. Journal of the American Chemical Society. American Chemical
Society. https://doi.org/10.1021/ja068949u
chicago: Lescop, Ewen, Paul Schanda, Rodolfo Rasia, and Bernhard Brutscher. “Automated
Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution
in Real-Time NMR Spectroscopy.” Journal of the American Chemical Society.
American Chemical Society, 2007. https://doi.org/10.1021/ja068949u.
ieee: E. Lescop, P. Schanda, R. Rasia, and B. Brutscher, “Automated spectral compression
for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy,”
Journal of the American Chemical Society, vol. 129, no. 10. American Chemical
Society, pp. 2756–2757, 2007.
ista: Lescop E, Schanda P, Rasia R, Brutscher B. 2007. Automated spectral compression
for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy.
Journal of the American Chemical Society. 129(10), 2756–2757.
mla: Lescop, Ewen, et al. “Automated Spectral Compression for Fast Multidimensional
NMR and Increased Time Resolution in Real-Time NMR Spectroscopy.” Journal of
the American Chemical Society, vol. 129, no. 10, American Chemical Society,
2007, pp. 2756–57, doi:10.1021/ja068949u.
short: E. Lescop, P. Schanda, R. Rasia, B. Brutscher, Journal of the American Chemical
Society 129 (2007) 2756–2757.
date_created: 2020-09-18T10:13:21Z
date_published: 2007-02-17T00:00:00Z
date_updated: 2021-01-12T08:19:36Z
day: '17'
doi: 10.1021/ja068949u
extern: '1'
intvolume: ' 129'
issue: '10'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '02'
oa_version: None
page: 2756-2757
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Automated spectral compression for fast multidimensional NMR and increased
time resolution in real-time NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2007'
...
---
_id: '8487'
abstract:
- lang: eng
text: Following unidirectional biophysical events such as the folding of proteins
or the equilibration of binding interactions, requires experimental methods that
yield information at both atomic-level resolution and at high repetition rates.
Toward this end a number of different approaches enabling the rapid acquisition
of 2D NMR spectra have been recently introduced, including spatially encoded “ultrafast”
2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions
by reducing the number of scans that are necessary for completing arbitrary 2D
NMR experiments, the latter operates by reducing the delay between consecutive
scans while preserving sensitivity. Given the complementarities between these
two approaches it seems natural to combine them into a single tool, enabling the
acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate
here this capability with the introduction of “ultraSOFAST” HMQC NMR, a spatially
encoded and relaxation-optimized approach that can provide 2D protein correlation
spectra at ∼1 s repetition rates for samples in the ∼2 mM concentration range.
The principles, relative advantages, and current limitations of this new approach
are discussed, and its application is exemplified with a study of the fast hydrogen−deuterium
exchange characterizing amide sites in Ubiquitin.
article_processing_charge: No
article_type: original
author:
- first_name: Maayan
full_name: Gal, Maayan
last_name: Gal
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Lucio
full_name: Frydman, Lucio
last_name: Frydman
citation:
ama: Gal M, Schanda P, Brutscher B, Frydman L. UltraSOFAST HMQC NMR and the repetitive
acquisition of 2D protein spectra at Hz rates. Journal of the American Chemical
Society. 2007;129(5):1372-1377. doi:10.1021/ja066915g
apa: Gal, M., Schanda, P., Brutscher, B., & Frydman, L. (2007). UltraSOFAST
HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. Journal
of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja066915g
chicago: Gal, Maayan, Paul Schanda, Bernhard Brutscher, and Lucio Frydman. “UltraSOFAST
HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates.” Journal
of the American Chemical Society. American Chemical Society, 2007. https://doi.org/10.1021/ja066915g.
ieee: M. Gal, P. Schanda, B. Brutscher, and L. Frydman, “UltraSOFAST HMQC NMR and
the repetitive acquisition of 2D protein spectra at Hz rates,” Journal of the
American Chemical Society, vol. 129, no. 5. American Chemical Society, pp.
1372–1377, 2007.
ista: Gal M, Schanda P, Brutscher B, Frydman L. 2007. UltraSOFAST HMQC NMR and the
repetitive acquisition of 2D protein spectra at Hz rates. Journal of the American
Chemical Society. 129(5), 1372–1377.
mla: Gal, Maayan, et al. “UltraSOFAST HMQC NMR and the Repetitive Acquisition of
2D Protein Spectra at Hz Rates.” Journal of the American Chemical Society,
vol. 129, no. 5, American Chemical Society, 2007, pp. 1372–77, doi:10.1021/ja066915g.
short: M. Gal, P. Schanda, B. Brutscher, L. Frydman, Journal of the American Chemical
Society 129 (2007) 1372–1377.
date_created: 2020-09-18T10:13:27Z
date_published: 2007-01-10T00:00:00Z
date_updated: 2021-01-12T08:19:37Z
day: '10'
doi: 10.1021/ja066915g
extern: '1'
intvolume: ' 129'
issue: '5'
keyword:
- Colloid and Surface Chemistry
- Biochemistry
- General Chemistry
- Catalysis
language:
- iso: eng
month: '01'
oa_version: None
page: 1372-1377
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at
Hz rates
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 129
year: '2007'
...
---
_id: '8511'
abstract:
- lang: eng
text: "Here we study an amazing phenomenon discovered by Newhouse [S. Newhouse,
Non-density of Axiom A(a) on S2, in: Proc. Sympos. Pure Math., vol. 14, Amer.
Math. Soc., 1970, pp. 191–202; S. Newhouse,\r\nDiffeomorphisms with infinitely
many sinks, Topology 13 (1974) 9–18; S. Newhouse, The abundance of\r\nwild hyperbolic
sets and nonsmooth stable sets of diffeomorphisms, Publ. Math. Inst. Hautes Études
Sci.\r\n50 (1979) 101–151]. It turns out that in the space of Cr smooth diffeomorphisms
Diffr(M) of a compact\r\nsurface M there is an open set U such that a Baire generic
diffeomorphism f ∈ U has infinitely many coexisting sinks. In this paper we make
a step towards understanding “how often does a surface diffeomorphism\r\nhave
infinitely many sinks.” Our main result roughly says that with probability one
for any positive D a\r\nsurface diffeomorphism has only finitely many localized
sinks either of cyclicity bounded by D or those\r\nwhose period is relatively
large compared to its cyclicity. It verifies a particular case of Palis’ Conjecture\r\nsaying
that even though diffeomorphisms with infinitely many coexisting sinks are Baire
generic, they have\r\nprobability zero.\r\nOne of the key points of the proof
is an application of Newton Interpolation Polynomials to study the dynamics initiated
in [V. Kaloshin, B. Hunt, A stretched exponential bound on the rate of growth
of the number\r\nof periodic points for prevalent diffeomorphisms I, Ann. of Math.,
in press, 92 pp.; V. Kaloshin, A stretched\r\nexponential bound on the rate of
growth of the number of periodic points for prevalent diffeomorphisms II,\r\npreprint,
85 pp.]."
article_processing_charge: No
article_type: original
author:
- first_name: A.
full_name: Gorodetski, A.
last_name: Gorodetski
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Gorodetski A, Kaloshin V. How often surface diffeomorphisms have infinitely
many sinks and hyperbolicity of periodic points near a homoclinic tangency. Advances
in Mathematics. 2007;208(2):710-797. doi:10.1016/j.aim.2006.03.012
apa: Gorodetski, A., & Kaloshin, V. (2007). How often surface diffeomorphisms
have infinitely many sinks and hyperbolicity of periodic points near a homoclinic
tangency. Advances in Mathematics. Elsevier. https://doi.org/10.1016/j.aim.2006.03.012
chicago: Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms
Have Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic
Tangency.” Advances in Mathematics. Elsevier, 2007. https://doi.org/10.1016/j.aim.2006.03.012.
ieee: A. Gorodetski and V. Kaloshin, “How often surface diffeomorphisms have infinitely
many sinks and hyperbolicity of periodic points near a homoclinic tangency,” Advances
in Mathematics, vol. 208, no. 2. Elsevier, pp. 710–797, 2007.
ista: Gorodetski A, Kaloshin V. 2007. How often surface diffeomorphisms have infinitely
many sinks and hyperbolicity of periodic points near a homoclinic tangency. Advances
in Mathematics. 208(2), 710–797.
mla: Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms Have
Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic Tangency.”
Advances in Mathematics, vol. 208, no. 2, Elsevier, 2007, pp. 710–97, doi:10.1016/j.aim.2006.03.012.
short: A. Gorodetski, V. Kaloshin, Advances in Mathematics 208 (2007) 710–797.
date_created: 2020-09-18T10:48:27Z
date_published: 2007-01-30T00:00:00Z
date_updated: 2021-01-12T08:19:47Z
day: '30'
doi: 10.1016/j.aim.2006.03.012
extern: '1'
intvolume: ' 208'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '01'
oa_version: None
page: 710-797
publication: Advances in Mathematics
publication_identifier:
issn:
- 0001-8708
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: How often surface diffeomorphisms have infinitely many sinks and hyperbolicity
of periodic points near a homoclinic tangency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 208
year: '2007'
...
---
_id: '8512'
abstract:
- lang: eng
text: "For diffeomorphisms of smooth compact finite-dimensional manifolds, we consider
the problem of how fast the number of periodic points with period n grows as a
function of n. In many familiar cases (e.g., Anosov systems) the growth is exponential,
but arbitrarily fast growth is possible; in fact, the first author has shown that
arbitrarily fast growth is topologically (Baire) generic for C2 or smoother diffeomorphisms.
In the present work we show that, by contrast, for a measure-theoretic notion
of genericity we call “prevalence”, the growth is not much faster than exponential.
Specifically, we show that for each ρ,δ>0, there is a prevalent set of C1+ρ (or
smoother) diffeomorphisms for which the number of periodic n points is bounded
above by exp(Cn1+δ) for some C independent of n. We also obtain a related bound
on the decay of hyperbolicity of the periodic points as a function of n, and obtain
the same results for 1-dimensional endomorphisms. The contrast between topologically
generic and measure-theoretically generic behavior for the growth of the number
of periodic points and the decay of their hyperbolicity show this to be a subtle
and complex phenomenon, reminiscent of KAM theory. Here in Part I we state our
results and describe the methods we use. We complete most of the proof in the
1-dimensional C2-smooth case and outline the remaining steps, deferred to Part
II, that are needed to establish the general case.\r\n\r\nThe novel feature of
the approach we develop in this paper is the introduction of Newton Interpolation
Polynomials as a tool for perturbing trajectories of iterated maps."
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Brian
full_name: Hunt, Brian
last_name: Hunt
citation:
ama: Kaloshin V, Hunt B. Stretched exponential estimates on growth of the number
of periodic points for prevalent diffeomorphisms I. Annals of Mathematics.
2007;165(1):89-170. doi:10.4007/annals.2007.165.89
apa: Kaloshin, V., & Hunt, B. (2007). Stretched exponential estimates on growth
of the number of periodic points for prevalent diffeomorphisms I. Annals of
Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2007.165.89
chicago: Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth
of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Annals of
Mathematics. Princeton University Press, 2007. https://doi.org/10.4007/annals.2007.165.89.
ieee: V. Kaloshin and B. Hunt, “Stretched exponential estimates on growth of the
number of periodic points for prevalent diffeomorphisms I,” Annals of Mathematics,
vol. 165, no. 1. Princeton University Press, pp. 89–170, 2007.
ista: Kaloshin V, Hunt B. 2007. Stretched exponential estimates on growth of the
number of periodic points for prevalent diffeomorphisms I. Annals of Mathematics.
165(1), 89–170.
mla: Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth
of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Annals of
Mathematics, vol. 165, no. 1, Princeton University Press, 2007, pp. 89–170,
doi:10.4007/annals.2007.165.89.
short: V. Kaloshin, B. Hunt, Annals of Mathematics 165 (2007) 89–170.
date_created: 2020-09-18T10:48:33Z
date_published: 2007-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:48Z
day: '01'
doi: 10.4007/annals.2007.165.89
extern: '1'
intvolume: ' 165'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 89-170
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Princeton University Press
quality_controlled: '1'
status: public
title: Stretched exponential estimates on growth of the number of periodic points
for prevalent diffeomorphisms I
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 165
year: '2007'
...
---
_id: '860'
abstract:
- lang: eng
text: We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene
cluster that is associated with a polymorphic congenital cataract that occurs
with frequency of ∼0.3% in a human population. To gain insight into the molecular
mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary
analysis of the available mammalian and newly obtained primate sequences of the
γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the
ancestral state, since it was found in CRYGD of a lower primate and all the surveyed
nonprimate mammals. Crystallin proteins include two structurally similar domains,
and substitutions in mammalian CRYGD protein at site 23 of the first domain were
always associated with substitutions in the structurally reciprocal sites 109
and 136 of the second domain. These data suggest that the cataractogenic effect
of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly
by amino acid changes in a distal domain. We also found that gene conversion was
a factor in the evolution of the γ-crystallin gene cluster throughout different
mammalian clades. The high rate of gene conversion observed between the functional
CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled
with a surprising finding of apparent negative selection in primate pseudogenes
suggest a deleterious impact of recently derived pseudogenes involved in gene
conversion in the γ-crystallin gene cluster.
acknowledgement: This study was supported by the Biodiversity and Dynamics of Gene
Pools program of the Presidium of the Russian Academy of Sciences (support to E.I.R.).
E.I.R. is also supported in part by the National Institute of Diabetes and Digestive
and Kidney Diseases and National Institute of Neurological Disorders and Stroke
(National Institutes of Health), and F.A.K. is supported by a National Science Foundation
graduate research fellowship.
author:
- first_name: Olga
full_name: Plotnikova, Olga V
last_name: Plotnikova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Evgeny
full_name: Ginter, Evgeny K
last_name: Ginter
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
citation:
ama: Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. Conversion
and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic
mutation that reverses the sequence of the human CRYGD gene to an ancestral state.
American Journal of Human Genetics. 2007;81(1):32-43. doi:10.1086/518616
apa: Plotnikova, O., Kondrashov, F., Vlasov, P., Grigorenko, A., Ginter, E., &
Rogaev, E. (2007). Conversion and compensatory evolution of the γ-crystallin genes
and identification of a cataractogenic mutation that reverses the sequence of
the human CRYGD gene to an ancestral state. American Journal of Human Genetics.
Cell Press. https://doi.org/10.1086/518616
chicago: Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko,
Evgeny Ginter, and Evgeny Rogaev. “Conversion and Compensatory Evolution of the
γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses
the Sequence of the Human CRYGD Gene to an Ancestral State.” American Journal
of Human Genetics. Cell Press, 2007. https://doi.org/10.1086/518616.
ieee: O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E.
Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state,” American Journal of Human Genetics, vol. 81, no.
1. Cell Press, pp. 32–43, 2007.
ista: Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007.
Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state. American Journal of Human Genetics. 81(1), 32–43.
mla: Plotnikova, Olga, et al. “Conversion and Compensatory Evolution of the γ-Crystallin
Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence
of the Human CRYGD Gene to an Ancestral State.” American Journal of Human Genetics,
vol. 81, no. 1, Cell Press, 2007, pp. 32–43, doi:10.1086/518616.
short: O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev,
American Journal of Human Genetics 81 (2007) 32–43.
date_created: 2018-12-11T11:48:53Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T08:20:14Z
day: '01'
doi: 10.1086/518616
extern: 1
intvolume: ' 81'
issue: '1'
month: '07'
page: 32 - 43
publication: American Journal of Human Genetics
publication_status: published
publisher: Cell Press
publist_id: '6788'
quality_controlled: 0
status: public
title: Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state
type: journal_article
volume: 81
year: '2007'
...
---
_id: '861'
abstract:
- lang: eng
text: 'Background: Mitochondrial tRNAs have been the subject of study for structural
biologists interested in their secondary structure characteristics, evolutionary
biologists have researched patterns of compensatory and structural evolution and
medical studies have been directed towards understanding the basis of human disease.
However, an up to date, manually curated database of mitochondrially encoded tRNAs
from higher animals is currently not available. Description: We obtained the complete
mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated
all of the tRNAs based on a multiple alignment of each tRNA gene and secondary
structure prediction made independently for each tRNA. The mitochondrial (mt)
tRNA sequences and the secondary structure based multiple alignments are freely
available as Supplemental Information online. Conclusion: We compiled a manually
curated database of mitochondrially encoded tRNAs from tetrapods with completely
sequenced genomes. In the course of our work, we reannotated more than 10% of
all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060
mitochondrial tRNAs. This carefully constructed database can be utilized to enhance
our knowledge in several different fields including the evolution of mt-tRNA secondary
structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers
reporting novel mitochondrial genome sequences should check their tRNA gene annotations
against our database to ensure a higher level of fidelity of their annotation.'
acknowledgement: KYuP and LAM were supported by the Molecular and Cellular Biology
Program of the Russian Academy of Science. KYuP was supported by the Russian Fund
of Basic Research (grant 04-04-49623). LAM was partially supported by grants from
the Howard Hughes Medical Institute (55005610), INTAS (05-1000008-8028). FAK is
a National Science Foundation Graduate Research Fellow.
author:
- first_name: Konstantin
full_name: Popadin, Konstantin Yu
last_name: Popadin
- first_name: Leila
full_name: Mamirova, Leila A
last_name: Mamirova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Popadin K, Mamirova L, Kondrashov F. A manually curated database of tetrapod
mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics.
2007;8. doi:10.1186/1471-2105-8-441
apa: Popadin, K., Mamirova, L., & Kondrashov, F. (2007). A manually curated
database of tetrapod mitochondrially encoded tRNA sequences and secondary structures.
BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-8-441
chicago: Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually
Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary
Structures.” BMC Bioinformatics. BioMed Central, 2007. https://doi.org/10.1186/1471-2105-8-441.
ieee: K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of
tetrapod mitochondrially encoded tRNA sequences and secondary structures,” BMC
Bioinformatics, vol. 8. BioMed Central, 2007.
ista: Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of
tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC
Bioinformatics. 8.
mla: Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially
Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics, vol.
8, BioMed Central, 2007, doi:10.1186/1471-2105-8-441.
short: K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).
date_created: 2018-12-11T11:48:54Z
date_published: 2007-11-14T00:00:00Z
date_updated: 2021-01-12T08:20:18Z
day: '14'
doi: 10.1186/1471-2105-8-441
extern: 1
intvolume: ' 8'
month: '11'
publication: BMC Bioinformatics
publication_status: published
publisher: BioMed Central
publist_id: '6789'
quality_controlled: 0
status: public
title: A manually curated database of tetrapod mitochondrially encoded tRNA sequences
and secondary structures
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
volume: 8
year: '2007'
...