---
_id: '4581'
abstract:
- lang: eng
text: We have extended the software model checker BLAST to automatically generate
test suites that guarantee full coverage with respect to a given predicate. More
precisely, given a C program and a target predicate p, BLAST determines the set
L of program locations which program execution can reach with p true, and automatically
generates a set of test vectors that exhibit the truth of p at all locations in
L. We have used BLAST to generate test suites and to detect dead code in C programs
with up to 30 K lines of code. The analysis and test vector generation is fully
automatic (no user intervention) and exact (no false positives).
author:
- first_name: Dirk
full_name: Beyer, Dirk
last_name: Beyer
- first_name: Adam
full_name: Chlipala, Adam J
last_name: Chlipala
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
citation:
ama: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. Generating tests from
counterexamples. In: IEEE; 2004:326-335. doi:10.1109/ICSE.2004.1317455'
apa: 'Beyer, D., Chlipala, A., Henzinger, T. A., Jhala, R., & Majumdar, R. (2004).
Generating tests from counterexamples (pp. 326–335). Presented at the ICSE: Software
Engineering, IEEE. https://doi.org/10.1109/ICSE.2004.1317455'
chicago: Beyer, Dirk, Adam Chlipala, Thomas A Henzinger, Ranjit Jhala, and Ritankar
Majumdar. “Generating Tests from Counterexamples,” 326–35. IEEE, 2004. https://doi.org/10.1109/ICSE.2004.1317455.
ieee: 'D. Beyer, A. Chlipala, T. A. Henzinger, R. Jhala, and R. Majumdar, “Generating
tests from counterexamples,” presented at the ICSE: Software Engineering, 2004,
pp. 326–335.'
ista: 'Beyer D, Chlipala A, Henzinger TA, Jhala R, Majumdar R. 2004. Generating
tests from counterexamples. ICSE: Software Engineering, 326–335.'
mla: Beyer, Dirk, et al. Generating Tests from Counterexamples. IEEE, 2004,
pp. 326–35, doi:10.1109/ICSE.2004.1317455.
short: D. Beyer, A. Chlipala, T.A. Henzinger, R. Jhala, R. Majumdar, in:, IEEE,
2004, pp. 326–335.
conference:
name: 'ICSE: Software Engineering'
date_created: 2018-12-11T12:09:35Z
date_published: 2004-07-26T00:00:00Z
date_updated: 2021-01-12T07:59:52Z
day: '26'
doi: 10.1109/ICSE.2004.1317455
extern: 1
month: '07'
page: 326 - 335
publication_status: published
publisher: IEEE
publist_id: '128'
quality_controlled: 0
status: public
title: Generating tests from counterexamples
type: conference
year: '2004'
...
---
_id: '4629'
abstract:
- lang: eng
text: 'Temporal logic is two-valued: a property is either true or false. When applied
to the analysis of stochastic systems, or systems with imprecise formal models,
temporal logic is therefore fragile: even small changes in the model can lead
to opposite truth values for a specification. We present a generalization of the
branching-time logic Ctl which achieves robustness with respect to model perturbations
by giving a quantitative interpretation to predicates and logical operators, and
by discounting the importance of events according to how late they occur. In every
state, the value of a formula is a real number in the interval [0,1], where 1
corresponds to truth and 0 to falsehood. The boolean operators and and or are
replaced by min and max, the path quantifiers ∃ and ∀ determine sup and inf over
all paths from a given state, and the temporal operators and □ specify sup and
inf over a given path; a new operator averages all values along a path. Furthermore,
all path operators are discounted by a parameter that can be chosen to give more
weight to states that are closer to the beginning of the path. We interpret the
resulting logic Dctl over transition systems, Markov chains, and Markov decision
processes. We present two semantics for Dctl: a path semantics, inspired by the
standard interpretation of state and path formulas in CTL, and a fixpoint semantics,
inspired by the μ-calculus evaluation of CTL formulas. We show that, while these
semantics coincide for CTL, they differ for Dctl, and we provide model-checking
algorithms for both semantics.'
acknowledgement: This research was supported in part by the AFOSR MURI grant F49620-00-1-0327,
the ONR grant N00014-02-1-0671, and the NSF grants CCR-0132780, CCR-9988172, CCR-0225610,
and CCR-0234690.
alternative_title:
- LNCS
author:
- first_name: Luca
full_name: de Alfaro, Luca
last_name: De Alfaro
- first_name: Marco
full_name: Faella, Marco
last_name: Faella
- first_name: Thomas A
full_name: Thomas Henzinger
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ritankar
full_name: Majumdar, Ritankar S
last_name: Majumdar
- first_name: Mariëlle
full_name: Stoelinga, Mariëlle
last_name: Stoelinga
citation:
ama: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Model checking
discounted temporal properties. In: Vol 2988. Springer; 2004:77-92. doi:10.1007/978-3-540-24730-2_6'
apa: 'De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga,
M. (2004). Model checking discounted temporal properties (Vol. 2988, pp. 77–92).
Presented at the TACAS: Tools and Algorithms for the Construction and Analysis
of Systems, Springer. https://doi.org/10.1007/978-3-540-24730-2_6'
chicago: De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and
Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties,” 2988:77–92.
Springer, 2004. https://doi.org/10.1007/978-3-540-24730-2_6.
ieee: 'L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga,
“Model checking discounted temporal properties,” presented at the TACAS: Tools
and Algorithms for the Construction and Analysis of Systems, 2004, vol. 2988,
pp. 77–92.'
ista: 'De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2004. Model
checking discounted temporal properties. TACAS: Tools and Algorithms for the Construction
and Analysis of Systems, LNCS, vol. 2988, 77–92.'
mla: De Alfaro, Luca, et al. Model Checking Discounted Temporal Properties.
Vol. 2988, Springer, 2004, pp. 77–92, doi:10.1007/978-3-540-24730-2_6.
short: L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, in:,
Springer, 2004, pp. 77–92.
conference:
name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems'
date_created: 2018-12-11T12:09:50Z
date_published: 2004-03-18T00:00:00Z
date_updated: 2021-01-12T08:00:38Z
day: '18'
doi: 10.1007/978-3-540-24730-2_6
extern: 1
intvolume: ' 2988'
month: '03'
page: 77 - 92
publication_status: published
publisher: Springer
publist_id: '79'
quality_controlled: 0
status: public
title: Model checking discounted temporal properties
type: conference
volume: 2988
year: '2004'
...
---
_id: '6155'
abstract:
- lang: eng
text: 'The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate
cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by
gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator
is nitric oxide, which acts through sGCs to regulate diverse cellular events.
In C. elegans the function of sGCs is mysterious: the worm genome does not appear
to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely
related to mammalian β than α subunits [1]. Here, we show that two of the seven
C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36
are expressed in a small number of neurons. These include the body cavity neurons
AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans
and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like
and β-like sGC subunits and that their function in the URX sensory neurons is
sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely
required for C. elegans to aggregate. Instead, these molecules may transduce one
of several pathways that induce C. elegans to aggregate or may modulate aggregation
by responding to cues in C. elegans body fluid.'
author:
- first_name: Benny H.H
full_name: Cheung, Benny H.H
last_name: Cheung
- first_name: Fausto
full_name: Arellano-Carbajal, Fausto
last_name: Arellano-Carbajal
- first_name: Irene
full_name: Rybicki, Irene
last_name: Rybicki
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. Soluble guanylate cyclases
act in neurons exposed to the body fluid to promote C. elegans aggregation behavior.
Current Biology. 2004;14(12):1105-1111. doi:10.1016/j.cub.2004.06.027
apa: Cheung, B. H. ., Arellano-Carbajal, F., Rybicki, I., & de Bono, M. (2004).
Soluble guanylate cyclases act in neurons exposed to the body fluid to promote
C. elegans aggregation behavior. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.027
chicago: Cheung, Benny H.H, Fausto Arellano-Carbajal, Irene Rybicki, and Mario de
Bono. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to
Promote C. Elegans Aggregation Behavior.” Current Biology. Elsevier, 2004.
https://doi.org/10.1016/j.cub.2004.06.027.
ieee: B. H. . Cheung, F. Arellano-Carbajal, I. Rybicki, and M. de Bono, “Soluble
guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans
aggregation behavior,” Current Biology, vol. 14, no. 12. Elsevier, pp.
1105–1111, 2004.
ista: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate
cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation
behavior. Current Biology. 14(12), 1105–1111.
mla: Cheung, Benny H. .., et al. “Soluble Guanylate Cyclases Act in Neurons Exposed
to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology,
vol. 14, no. 12, Elsevier, 2004, pp. 1105–11, doi:10.1016/j.cub.2004.06.027.
short: B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology
14 (2004) 1105–1111.
date_created: 2019-03-21T09:42:01Z
date_published: 2004-06-22T00:00:00Z
date_updated: 2021-01-12T08:06:25Z
day: '22'
doi: 10.1016/j.cub.2004.06.027
extern: '1'
external_id:
pmid:
- '15203005'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 1105-1111
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Soluble guanylate cyclases act in neurons exposed to the body fluid to promote
C. elegans aggregation behavior
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2004'
...
---
_id: '7334'
abstract:
- lang: eng
text: 'Fundamental and phenomenological models for cells, stacks, and complete systems
of PEFC and SOFC are reviewed and their predictive power is assessed by comparing
model simulations against experiments. Computationally efficient models suited
for engineering design include the (1+1) dimensionality approach, which decouples
the membrane in-plane and through-plane processes, and the volume-averaged-method
(VAM) that considers only the lumped effect of pre-selected system components.
The former model was shown to capture the measured lateral current density inhomogeneities
in a PEFC and the latter was used for the optimization of commercial SOFC systems.
State Space Modeling (SSM) was used to identify the main reaction pathways in
SOFC and, in conjunction with the implementation of geometrically well-defined
electrodes, has opened a new direction for the understanding of electrochemical
reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced
anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann
(LB) method for transport in porous media and the full 3-D Computational Fluid
Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all
components of the relevant physics and they can improve the understanding of the
related phenomena, a necessary condition for the development of both appropriate
simplified models as well as reliable technologies. Within the LB framework, a
technique for the characterization and computer-reconstruction of the porous electrode
structure was developed using advanced pattern recognition algorithms. In CFD
modeling, 3-D simulations were used to investigate SOFC with internal methane
steam reforming and have exemplified the significance of porous and novel fractal
channel distributors for the fuel and oxidant delivery, as well as for the cooling
of PEFC. As importantly, the novel concept has been put forth of functionally
designed, fractal-shaped fuel cells, showing promise of significant performance
improvements over the conventional rectangular shaped units. Thermo-economic modeling
for the optimization of PEFC is finally addressed. '
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Mantzaras, John
last_name: Mantzaras
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
- first_name: Markus
full_name: Roos, Markus
last_name: Roos
- first_name: Wilhelm
full_name: Brandstätter, Wilhelm
last_name: Brandstätter
- first_name: Michel
full_name: Prestat, Michel
last_name: Prestat
- first_name: Ludwig J.
full_name: Gauckler, Ludwig J.
last_name: Gauckler
- first_name: Bernhard
full_name: Andreaus, Bernhard
last_name: Andreaus
- first_name: Faegheh
full_name: Hajbolouri, Faegheh
last_name: Hajbolouri
- first_name: Stephan M.
full_name: Senn, Stephan M.
last_name: Senn
- first_name: Dimos
full_name: Poulikakos, Dimos
last_name: Poulikakos
- first_name: Andreas K.
full_name: Chaniotis, Andreas K.
last_name: Chaniotis
- first_name: Diego
full_name: Larrain, Diego
last_name: Larrain
- first_name: Nordahl
full_name: Autissier, Nordahl
last_name: Autissier
- first_name: François
full_name: Maréchal, François
last_name: Maréchal
citation:
ama: Mantzaras J, Freunberger SA, Büchi FN, et al. Fuel cell modeling and simulations.
CHIMIA International Journal for Chemistry. 2004;58(12):857-868. doi:10.2533/000942904777677029
apa: Mantzaras, J., Freunberger, S. A., Büchi, F. N., Roos, M., Brandstätter, W.,
Prestat, M., … Maréchal, F. (2004). Fuel cell modeling and simulations. CHIMIA
International Journal for Chemistry. Swiss Chemical Society. https://doi.org/10.2533/000942904777677029
chicago: Mantzaras, John, Stefan Alexander Freunberger, Felix N. Büchi, Markus Roos,
Wilhelm Brandstätter, Michel Prestat, Ludwig J. Gauckler, et al. “Fuel Cell Modeling
and Simulations.” CHIMIA International Journal for Chemistry. Swiss Chemical
Society, 2004. https://doi.org/10.2533/000942904777677029.
ieee: J. Mantzaras et al., “Fuel cell modeling and simulations,” CHIMIA
International Journal for Chemistry, vol. 58, no. 12. Swiss Chemical Society,
pp. 857–868, 2004.
ista: Mantzaras J, Freunberger SA, Büchi FN, Roos M, Brandstätter W, Prestat M,
Gauckler LJ, Andreaus B, Hajbolouri F, Senn SM, Poulikakos D, Chaniotis AK, Larrain
D, Autissier N, Maréchal F. 2004. Fuel cell modeling and simulations. CHIMIA International
Journal for Chemistry. 58(12), 857–868.
mla: Mantzaras, John, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International
Journal for Chemistry, vol. 58, no. 12, Swiss Chemical Society, 2004, pp.
857–68, doi:10.2533/000942904777677029.
short: J. Mantzaras, S.A. Freunberger, F.N. Büchi, M. Roos, W. Brandstätter, M.
Prestat, L.J. Gauckler, B. Andreaus, F. Hajbolouri, S.M. Senn, D. Poulikakos,
A.K. Chaniotis, D. Larrain, N. Autissier, F. Maréchal, CHIMIA International Journal
for Chemistry 58 (2004) 857–868.
date_created: 2020-01-15T12:24:23Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:09Z
day: '01'
doi: 10.2533/000942904777677029
extern: '1'
intvolume: ' 58'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 857-868
publication: CHIMIA International Journal for Chemistry
publication_identifier:
issn:
- 0009-4293
publication_status: published
publisher: Swiss Chemical Society
quality_controlled: '1'
status: public
title: Fuel cell modeling and simulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2004'
...
---
_id: '7333'
abstract:
- lang: eng
text: The analysis of the complete H2/air polymer electrolyte fuel cell system shows
that process air humidification is one of the biggest obstacles for a high performance
portable system in the kW range. Therefore, a new concept, with passive process
air humidification integrated into the stack, has been developed. Humidification
in each cell makes the process independent from the number of cells and the operation
mode, thus making the concept fully scalable. Without external humidification
the system is simpler, smaller, and cheaper. The humidification of the process
air is achieved by transfer of product water from the exhaust air, through part
of the membrane, to the dry intake air. Tests have shown that cells using the
concept of internal humidification and operated with dry air at 70 ° have almost
the same performance as when operated with external humidification. A 42‐cell
stack with this internal humidification concept was built and integrated into
a portable 1 kW power generator system.
article_processing_charge: No
article_type: original
author:
- first_name: M.
full_name: Santis, M.
last_name: Santis
- first_name: D.
full_name: Schmid, D.
last_name: Schmid
- first_name: M.
full_name: Ruge, M.
last_name: Ruge
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: F.N.
full_name: Büchi, F.N.
last_name: Büchi
citation:
ama: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. Modular stack-internal
air humidification concept-verification in a 1 kW stack. Fuel Cells. 2004;4(3):214-218.
doi:10.1002/fuce.200400028
apa: Santis, M., Schmid, D., Ruge, M., Freunberger, S. A., & Büchi, F. N. (2004).
Modular stack-internal air humidification concept-verification in a 1 kW stack.
Fuel Cells. Wiley. https://doi.org/10.1002/fuce.200400028
chicago: Santis, M., D. Schmid, M. Ruge, Stefan Alexander Freunberger, and F.N.
Büchi. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW
Stack.” Fuel Cells. Wiley, 2004. https://doi.org/10.1002/fuce.200400028.
ieee: M. Santis, D. Schmid, M. Ruge, S. A. Freunberger, and F. N. Büchi, “Modular
stack-internal air humidification concept-verification in a 1 kW stack,” Fuel
Cells, vol. 4, no. 3. Wiley, pp. 214–218, 2004.
ista: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. 2004. Modular stack-internal
air humidification concept-verification in a 1 kW stack. Fuel Cells. 4(3), 214–218.
mla: Santis, M., et al. “Modular Stack-Internal Air Humidification Concept-Verification
in a 1 KW Stack.” Fuel Cells, vol. 4, no. 3, Wiley, 2004, pp. 214–18, doi:10.1002/fuce.200400028.
short: M. Santis, D. Schmid, M. Ruge, S.A. Freunberger, F.N. Büchi, Fuel Cells 4
(2004) 214–218.
date_created: 2020-01-15T12:24:14Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T08:13:08Z
day: '01'
doi: 10.1002/fuce.200400028
extern: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
page: 214-218
publication: Fuel Cells
publication_identifier:
issn:
- 1615-6846
- 1615-6854
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Modular stack-internal air humidification concept-verification in a 1 kW stack
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2004'
...
---
_id: '864'
abstract:
- lang: eng
text: 'We present a method for prediction of functional sites in a set of aligned
protein sequences. The method selects sites which are both well conserved and
clustered together in space, as inferred from the 3D structures of proteins included
in the alignment. We tested the method using 86 alignments from the NCBI CDD database,
where the sites of experimentally determined ligand and/or macromolecular interactions
are annotated. In agreement with earlier investigations, we found that functional
site predictions are most successful when overall background sequence conservation
is low, such that sites under evolutionary constraint become apparent. In addition,
we found that averaging of conservation values across spatially clustered sites
improves predictions under certain conditions: that is, when overall conservation
is relatively high and when the site in question involves a large macromolecular
binding interface. Under these conditions it is better to look for clusters of
conserved sites than to look for particular conserved sites.'
acknowledgement: We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful
suggestions, and the NIH Intramural Research Program forsupport.
author:
- first_name: Anna
full_name: Panchenko, Anna R
last_name: Panchenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephen
full_name: Bryant, Stephen H
last_name: Bryant
citation:
ama: Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis
of sequence and structure conservation. Protein Science. 2004;13(4):884-892.
doi:10.1110/ps.03465504
apa: Panchenko, A., Kondrashov, F., & Bryant, S. (2004). Prediction of functional
sites by analysis of sequence and structure conservation. Protein Science.
Wiley-Blackwell. https://doi.org/10.1110/ps.03465504
chicago: Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of
Functional Sites by Analysis of Sequence and Structure Conservation.” Protein
Science. Wiley-Blackwell, 2004. https://doi.org/10.1110/ps.03465504.
ieee: A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites
by analysis of sequence and structure conservation,” Protein Science, vol.
13, no. 4. Wiley-Blackwell, pp. 884–892, 2004.
ista: Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites
by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892.
mla: Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence
and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell,
2004, pp. 884–92, doi:10.1110/ps.03465504.
short: A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.
date_created: 2018-12-11T11:48:55Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T08:20:22Z
day: '01'
doi: 10.1110/ps.03465504
extern: 1
intvolume: ' 13'
issue: '4'
month: '04'
page: 884 - 892
publication: Protein Science
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6786'
quality_controlled: 0
status: public
title: Prediction of functional sites by analysis of sequence and structure conservation
type: journal_article
volume: 13
year: '2004'
...
---
_id: '870'
abstract:
- lang: eng
text: Only a fraction of eukaryotic genes affect the phenotype drastically. We compared
18 parameters in 1273 human morbid genes, known to cause diseases, and in the
remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have
wider phylogenetic distributions, are more similar to essential genes of Drosophila
melanogaster, code for longer proteins containing more alanine and glycine and
less histidine, lysine and methionine, possess larger numbers of longer introns
with more accurate splicing signals and have higher and broader expressions. These
differences make it possible to classify as non-morbid 34% of human genes with
unknown morbidity, when only 5% of known morbid genes are incorrectly classified
as non-morbid. This classification can help to identify disease-causing genes
among multiple candidates.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey Yu
last_name: Ogurtsov
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene
morbidity. Nucleic Acids Research. 2004;32(5):1731-1737. doi:10.1093/nar/gkh330
apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2004). Bioinformatical
assay of human gene morbidity. Nucleic Acids Research. Oxford University
Press. https://doi.org/10.1093/nar/gkh330
chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical
Assay of Human Gene Morbidity.” Nucleic Acids Research. Oxford University
Press, 2004. https://doi.org/10.1093/nar/gkh330.
ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human
gene morbidity,” Nucleic Acids Research, vol. 32, no. 5. Oxford University
Press, pp. 1731–1737, 2004.
ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human
gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.
mla: Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.”
Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004,
pp. 1731–37, doi:10.1093/nar/gkh330.
short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004)
1731–1737.
date_created: 2018-12-11T11:48:56Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:37Z
day: '01'
doi: 10.1093/nar/gkh330
extern: 1
intvolume: ' 32'
issue: '5'
month: '01'
page: 1731 - 1737
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '6780'
quality_controlled: 0
status: public
title: Bioinformatical assay of human gene morbidity
type: journal_article
volume: 32
year: '2004'
...
---
_id: '875'
abstract:
- lang: eng
text: The dominance of wild-type alleles and the concomitant recessivity of deleterious
mutant alleles might have evolved by natural selection or could be a by-product
of the molecular and physiological mechanisms of gene action. We compared the
properties of human haplosufficient genes, whose wild-type alleles are dominant
over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes,
which produce an abnormal phenotype when heterozygous for a loss-of-function allele.
The fraction of haplosufficient genes is the highest among the genes that encode
enzymes, which is best compatible with the physiological theory. Haploinsufficient
genes, on average, have more paralogs than haplosufficient genes, supporting the
idea that gene dosage could be important for the initial fixation of duplications.
Thus, haplo(in)sufficiency of a gene and its propensity for duplication might
have a common evolutionary basis.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
citation:
ama: Kondrashov F, Koonin E. A common framework for understanding the origin of
genetic dominance and evolutionary fates of gene duplications. Trends in Genetics.
2004;20(7):287-291. doi:10.1016/j.tig.2004.05.001
apa: Kondrashov, F., & Koonin, E. (2004). A common framework for understanding
the origin of genetic dominance and evolutionary fates of gene duplications. Trends
in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2004.05.001
chicago: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding
the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.”
Trends in Genetics. Elsevier, 2004. https://doi.org/10.1016/j.tig.2004.05.001.
ieee: F. Kondrashov and E. Koonin, “A common framework for understanding the origin
of genetic dominance and evolutionary fates of gene duplications,” Trends in
Genetics, vol. 20, no. 7. Elsevier, pp. 287–291, 2004.
ista: Kondrashov F, Koonin E. 2004. A common framework for understanding the origin
of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics.
20(7), 287–291.
mla: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding
the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.”
Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001.
short: F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.
date_created: 2018-12-11T11:48:58Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T08:20:54Z
day: '01'
doi: 10.1016/j.tig.2004.05.001
extern: 1
intvolume: ' 20'
issue: '7'
month: '07'
page: 287 - 291
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6775'
quality_controlled: 0
status: public
title: A common framework for understanding the origin of genetic dominance and evolutionary
fates of gene duplications
type: journal_article
volume: 20
year: '2004'
...
---
_id: '889'
abstract:
- lang: eng
text: 'The function of protein and RNA molecules depends on complex epistatic interactions
between sites. Therefore, the deleterious effect of a mutation can be suppressed
by a compensatory second-site substitution. In relating a list of 86 pathogenic
mutations in human IRNAs encoded by mitochondrial genes to the sequences of their
mammalian orthologs, we noted that 52 pathogenic mutations were present in normal
tRNAs of one or several nonhuman mammals. We found at least five mechanisms of
compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in
one of the four tRNA stems: restoration of the affected Watson-Crick interaction
(25 cases), strengthening of another pair (4 cases), creation of a new pair (8
cases), changes of multiple interactions in the affected stem (11 cases) and changes
involving the interaction between the loop and stem structures (3 cases). A pathogenic
mutation and its compensating substitution are fixed in a lineage in rapid succession,
and often a compensatory interaction evolves convergently in different clades.
At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving
mammalian (RNAs participate in such interactions, indicating that the evolution
of tRNAs proceeds along highly epistatic fitness ridges.'
acknowledgement: We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp,
S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were
supported by a grant from the US National Institutes of Health to S. Nuzhdin, and
A.D.K. is a Howard Hughes
author:
- first_name: Andrew
full_name: Kern, Andrew D
last_name: Kern
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs. Nature Genetics. 2004;36(11):1207-1212.
doi:10.1038/ng1451
apa: Kern, A., & Kondrashov, F. (2004). Mechanisms and convergence of compensatory
evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing
Group. https://doi.org/10.1038/ng1451
chicago: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory
Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics. Nature Publishing
Group, 2004. https://doi.org/10.1038/ng1451.
ieee: A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11. Nature
Publishing Group, pp. 1207–1212, 2004.
ista: Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.
mla: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory
Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36,
no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451.
short: A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.
date_created: 2018-12-11T11:49:02Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T08:21:17Z
day: '01'
doi: 10.1038/ng1451
extern: 1
intvolume: ' 36'
issue: '11'
month: '11'
page: 1207 - 1212
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6759'
quality_controlled: 0
status: public
title: Mechanisms and convergence of compensatory evolution in mammalian mitochondrial
tRNAs
type: journal_article
volume: 36
year: '2004'
...
---
_id: '9493'
abstract:
- lang: eng
text: In a number of organisms, transgenes containing transcribed inverted repeats
(IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated
with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA
silencing also causes extensive cytosine methylation of homologous DNA in both
the transgene "trigger" and any other homologous DNA sequences--"targets". Endogenous
genomic sequences, including transposable elements and repeated elements, are
also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4)
is required for maintenance of DNA methylation at several endogenous loci and
for the establishment of methylation at the FWA gene. Here, we show that mutation
of AGO4 substantially reduces the maintenance of DNA methylation triggered by
IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA
methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences,
while the IR trigger sequences lose methylation in all sequence contexts. Finally,
we find that AGO4 and the DRM methyltransferase genes are required for maintenance
of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the
accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting
that AGO4 may function downstream of siRNA production.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Lisa K.
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: Zhixin
full_name: Xie, Zhixin
last_name: Xie
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of
Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.
Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055
apa: Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &
Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation
triggered by inverted repeats. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.055
chicago: Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C.
Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed
DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier,
2004. https://doi.org/10.1016/j.cub.2004.06.055.
ieee: D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E.
Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered
by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220,
2004.
ista: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004.
Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted
repeats. Current Biology. 14(13), 1214–1220.
mla: Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA
Methylation Triggered by Inverted Repeats.” Current Biology, vol. 14, no.
13, Elsevier, 2004, pp. 1214–20, doi:10.1016/j.cub.2004.06.055.
short: D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen,
Current Biology 14 (2004) 1214–1220.
date_created: 2021-06-07T10:33:00Z
date_published: 2004-07-13T00:00:00Z
date_updated: 2021-12-14T08:52:00Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cub.2004.06.055
extern: '1'
external_id:
pmid:
- '15242620 '
intvolume: ' 14'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2004.06.055
month: '07'
oa: 1
oa_version: Published Version
page: 1214-1220
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by
inverted repeats
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 14
year: '2004'
...