[{"year":"2005","conference":{"name":"LCTES: Languages, Compilers, and Tools for Embedded Systems"},"type":"conference","quality_controlled":0,"title":"Composable code generation for distributed Giotto","doi":"10.1145/1065910.1065914","publisher":"ACM","date_updated":"2021-01-12T07:57:06Z","publication_status":"published","day":"01","status":"public","date_published":"2005-06-01T00:00:00Z","publist_id":"275","abstract":[{"text":"We present a compositional approach to the implementation of hard real-time software running on a distributed platform. We explain how several code suppliers, coordinated by a system integrator, can independently generate different parts of the distributed software. The task structure, interaction, and timing is specified as a Giotto program. Each supplier is given a part of the Giotto program and a timing interface, from which the supplier generates task and scheduling code. The integrator then checks, individually for each supplier, in pseudo-polynomial time, if the supplied code meets its timing specification. If all checks succeed, then the supplied software parts are guaranteed to work together and implement the original Giotto program. The feasibility of the approach is demonstrated by a prototype implementation.","lang":"eng"}],"page":"21 - 30","_id":"4457","month":"06","author":[{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kirsch, Christoph M","first_name":"Christoph","last_name":"Kirsch"},{"first_name":"Slobodan","last_name":"Matic","full_name":"Matic, Slobodan"}],"date_created":"2018-12-11T12:08:57Z","citation":{"ama":"Henzinger TA, Kirsch C, Matic S. Composable code generation for distributed Giotto. In: ACM; 2005:21-30. doi:<a href=\"https://doi.org/10.1145/1065910.1065914\">10.1145/1065910.1065914</a>","ista":"Henzinger TA, Kirsch C, Matic S. 2005. Composable code generation for distributed Giotto. LCTES: Languages, Compilers, and Tools for Embedded Systems, 21–30.","apa":"Henzinger, T. A., Kirsch, C., &#38; Matic, S. (2005). Composable code generation for distributed Giotto (pp. 21–30). Presented at the LCTES: Languages, Compilers, and Tools for Embedded Systems, ACM. <a href=\"https://doi.org/10.1145/1065910.1065914\">https://doi.org/10.1145/1065910.1065914</a>","chicago":"Henzinger, Thomas A, Christoph Kirsch, and Slobodan Matic. “Composable Code Generation for Distributed Giotto,” 21–30. ACM, 2005. <a href=\"https://doi.org/10.1145/1065910.1065914\">https://doi.org/10.1145/1065910.1065914</a>.","ieee":"T. A. Henzinger, C. Kirsch, and S. Matic, “Composable code generation for distributed Giotto,” presented at the LCTES: Languages, Compilers, and Tools for Embedded Systems, 2005, pp. 21–30.","mla":"Henzinger, Thomas A., et al. <i>Composable Code Generation for Distributed Giotto</i>. ACM, 2005, pp. 21–30, doi:<a href=\"https://doi.org/10.1145/1065910.1065914\">10.1145/1065910.1065914</a>.","short":"T.A. Henzinger, C. Kirsch, S. Matic, in:, ACM, 2005, pp. 21–30."},"extern":1},{"intvolume":"      3829","_id":"4536","acknowledgement":"Supported in part by the AFOSR MURI grant F49620-00-1-0327 and the NSF grants CCR-0208875 and CCR-0225610.","page":"144 - 161","abstract":[{"text":"We show how to automatically construct and refine rectangular abstractions of systems of linear differential equations. From a hybrid automaton whose dynamics are given by a system of linear differential equations, our method computes automatically a sequence of rectangular hybrid automata that are increasingly precise overapproximations of the original hybrid automaton. We prove an optimality criterion for successive refinements. We also show that this method can take into account a safety property to be verified, refining only relevant parts of the state space. The practicability of the method is illustrated on a benchmark case study. ","lang":"eng"}],"publist_id":"190","date_published":"2005-12-13T00:00:00Z","status":"public","extern":1,"alternative_title":["LNCS"],"date_created":"2018-12-11T12:09:22Z","citation":{"mla":"Doyen, Laurent, et al. <i>Automatic Rectangular Refinement of Affine Hybrid Systems</i>. Vol. 3829, Springer, 2005, pp. 144–61, doi:<a href=\"https://doi.org/DOI: 10.1007/11603009_13\">DOI: 10.1007/11603009_13</a>.","short":"L. Doyen, T.A. Henzinger, J. Raskin, in:, Springer, 2005, pp. 144–161.","ieee":"L. Doyen, T. A. Henzinger, and J. Raskin, “Automatic rectangular refinement of affine hybrid systems,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2005, vol. 3829, pp. 144–161.","chicago":"Doyen, Laurent, Thomas A Henzinger, and Jean Raskin. “Automatic Rectangular Refinement of Affine Hybrid Systems,” 3829:144–61. Springer, 2005. <a href=\"https://doi.org/DOI: 10.1007/11603009_13\">https://doi.org/DOI: 10.1007/11603009_13</a>.","apa":"Doyen, L., Henzinger, T. A., &#38; Raskin, J. (2005). Automatic rectangular refinement of affine hybrid systems (Vol. 3829, pp. 144–161). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. <a href=\"https://doi.org/DOI: 10.1007/11603009_13\">https://doi.org/DOI: 10.1007/11603009_13</a>","ista":"Doyen L, Henzinger TA, Raskin J. 2005. Automatic rectangular refinement of affine hybrid systems. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 3829, 144–161.","ama":"Doyen L, Henzinger TA, Raskin J. Automatic rectangular refinement of affine hybrid systems. In: Vol 3829. Springer; 2005:144-161. doi:<a href=\"https://doi.org/DOI: 10.1007/11603009_13\">DOI: 10.1007/11603009_13</a>"},"author":[{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724"},{"last_name":"Raskin","first_name":"Jean","full_name":"Raskin, Jean-François"}],"month":"12","type":"conference","volume":3829,"conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems"},"year":"2005","day":"13","publication_status":"published","date_updated":"2021-01-12T07:59:31Z","publisher":"Springer","doi":"DOI: 10.1007/11603009_13","title":"Automatic rectangular refinement of affine hybrid systems","quality_controlled":0},{"publication_status":"published","day":"07","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2021-01-12T07:59:34Z","title":"Semiperfect-information games","doi":"10.1007/11590156_1","quality_controlled":0,"volume":3821,"type":"conference","conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"year":"2005","alternative_title":["LNCS"],"extern":1,"date_created":"2018-12-11T12:09:23Z","citation":{"short":"K. Chatterjee, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 1–18.","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger. <i>Semiperfect-Information Games</i>. Vol. 3821, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 1–18, doi:<a href=\"https://doi.org/10.1007/11590156_1\">10.1007/11590156_1</a>.","ieee":"K. Chatterjee and T. A. Henzinger, “Semiperfect-information games,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, 2005, vol. 3821, pp. 1–18.","chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger. “Semiperfect-Information Games,” 3821:1–18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005. <a href=\"https://doi.org/10.1007/11590156_1\">https://doi.org/10.1007/11590156_1</a>.","apa":"Chatterjee, K., &#38; Henzinger, T. A. (2005). Semiperfect-information games (Vol. 3821, pp. 1–18). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/11590156_1\">https://doi.org/10.1007/11590156_1</a>","ista":"Chatterjee K, Henzinger TA. 2005. Semiperfect-information games. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LNCS, vol. 3821, 1–18.","ama":"Chatterjee K, Henzinger TA. Semiperfect-information games. In: Vol 3821. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2005:1-18. doi:<a href=\"https://doi.org/10.1007/11590156_1\">10.1007/11590156_1</a>"},"month":"12","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"_id":"4541","intvolume":"      3821","abstract":[{"text":"Much recent research has focused on the applications of games with ω-regular objectives in the control and verification of reactive systems. However, many of the game-based models are ill-suited for these applications, because they assume that each player has complete information about the state of the system (they are “perfect-information” games). This is because in many situations, a controller does not see the private state of the plant. Such scenarios are naturally modeled by “partial-information” games. On the other hand, these games are intractable; for example, partial-information games with simple reachability objectives are 2EXPTIME-complete.\nWe study the intermediate case of “semiperfect-information” games, where one player has complete knowledge of the state, while the other player has only partial knowledge. This model is appropriate in control situations where a controller must cope with plant behavior that is as adversarial as possible, i.e., the controller has partial information while the plant has perfect information. As is customary, we assume that the controller and plant take turns to make moves. We show that these semiperfect-information turn-based games are equivalent to perfect-information concurrent games, where the two players choose their moves simultaneously and independently. Since the perfect-information concurrent games are well-understood, we obtain several results of how semiperfect-information turn-based games differ from perfect-information turn-based games on one hand, and from partial-information turn-based games on the other hand. In particular, semiperfect-information turn-based games can benefit from randomized strategies while the perfect-information variety cannot, and semiperfect-information turn-based games are in NP ∩ coNP for all parity objectives.\n","lang":"eng"}],"page":"1 - 18","date_published":"2005-12-07T00:00:00Z","status":"public","publist_id":"182"},{"status":"public","date_published":"2005-06-24T00:00:00Z","publist_id":"158","abstract":[{"lang":"eng","text":"The theory of graph games with ω-regular winning conditions is the foundation for modeling and synthesizing reactive processes. In the case of stochastic reactive processes, the corresponding stochastic graph games have three players, two of them (System and Environment) behaving adversarially, and the third (Uncertainty) behaving probabilistically. We consider two problems for stochastic graph games: the qualitative problem asks for the set of states from which a player can win with probability 1 (almost-sure winning); the quantitative problem asks for the maximal probability of winning (optimal winning) from each state. We show that for Rabin winning conditions, both problems are in NP. As these problems were known to be NP-hard, it follows that they are NP-complete for Rabin conditions, and dually, coNP-complete for Streett conditions. The proof proceeds by showing that pure memoryless strategies suffice for qualitatively and quantitatively winning stochastic graph games with Rabin conditions. This insight is of interest in its own right, as it implies that controllers for Rabin objectives have simple implementations. We also prove that for every ω-regular condition, optimal winning strategies are no more complex than almost-sure winning strategies."}],"page":"878 - 890","acknowledgement":"This research was supported in part by the ONR grant N00014-02-1-0671, the AFOSR MURI grant F49620-00-1-0327, and the NSF grant CCR-0225610.","intvolume":"      3580","_id":"4553","month":"06","author":[{"orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"de Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"}],"citation":{"ama":"Chatterjee K, De Alfaro L, Henzinger TA. The complexity of stochastic Rabin and Streett games. In: Vol 3580. Springer; 2005:878-890. doi:<a href=\"https://doi.org/10.1007/11523468_71\">10.1007/11523468_71</a>","apa":"Chatterjee, K., De Alfaro, L., &#38; Henzinger, T. A. (2005). The complexity of stochastic Rabin and Streett games (Vol. 3580, pp. 878–890). Presented at the ICALP: Automata, Languages and Programming, Springer. <a href=\"https://doi.org/10.1007/11523468_71\">https://doi.org/10.1007/11523468_71</a>","ista":"Chatterjee K, De Alfaro L, Henzinger TA. 2005. The complexity of stochastic Rabin and Streett games. ICALP: Automata, Languages and Programming, LNCS, vol. 3580, 878–890.","ieee":"K. Chatterjee, L. De Alfaro, and T. A. Henzinger, “The complexity of stochastic Rabin and Streett games,” presented at the ICALP: Automata, Languages and Programming, 2005, vol. 3580, pp. 878–890.","chicago":"Chatterjee, Krishnendu, Luca De Alfaro, and Thomas A Henzinger. “The Complexity of Stochastic Rabin and Streett Games,” 3580:878–90. Springer, 2005. <a href=\"https://doi.org/10.1007/11523468_71\">https://doi.org/10.1007/11523468_71</a>.","short":"K. Chatterjee, L. De Alfaro, T.A. Henzinger, in:, Springer, 2005, pp. 878–890.","mla":"Chatterjee, Krishnendu, et al. <i>The Complexity of Stochastic Rabin and Streett Games</i>. Vol. 3580, Springer, 2005, pp. 878–90, doi:<a href=\"https://doi.org/10.1007/11523468_71\">10.1007/11523468_71</a>."},"date_created":"2018-12-11T12:09:27Z","alternative_title":["LNCS"],"extern":1,"year":"2005","conference":{"name":"ICALP: Automata, Languages and Programming"},"volume":3580,"type":"conference","quality_controlled":0,"title":"The complexity of stochastic Rabin and Streett games","doi":"10.1007/11523468_71","publisher":"Springer","date_updated":"2021-01-12T07:59:39Z","publication_status":"published","day":"24"},{"type":"conference","year":"2005","conference":{"name":"LICS: Logic in Computer Science"},"publisher":"IEEE","date_updated":"2021-01-12T07:59:39Z","publication_status":"published","day":"19","quality_controlled":0,"title":"Mean-payoff parity games","doi":"10.1109/LICS.2005.26","_id":"4554","date_published":"2005-09-19T00:00:00Z","status":"public","publist_id":"159","abstract":[{"text":"Games played on graphs may have qualitative objectives, such as the satisfaction of an ω-regular property, or quantitative objectives, such as the optimization of a real-valued reward. When games are used to model reactive systems with both fairness assumptions and quantitative (e.g., resource) constraints, then the corresponding objective combines both a qualitative and a quantitative component. In a general case of interest, the qualitative component is a parity condition and the quantitative component is a mean-payoff reward. We study and solve such mean-payoff parity games. We also prove some interesting facts about mean-payoff parity games which distinguish them both from mean-payoff and from parity games. In particular, we show that optimal strategies exist in mean-payoff parity games, but they may require infinite memory.","lang":"eng"}],"page":"178 - 187","citation":{"ama":"Chatterjee K, Henzinger TA, Jurdziński M. Mean-payoff parity games. In: IEEE; 2005:178-187. doi:<a href=\"https://doi.org/10.1109/LICS.2005.26\">10.1109/LICS.2005.26</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Jurdziński, M. (2005). Mean-payoff parity games (pp. 178–187). Presented at the LICS: Logic in Computer Science, IEEE. <a href=\"https://doi.org/10.1109/LICS.2005.26\">https://doi.org/10.1109/LICS.2005.26</a>","ista":"Chatterjee K, Henzinger TA, Jurdziński M. 2005. Mean-payoff parity games. LICS: Logic in Computer Science, 178–187.","ieee":"K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Mean-payoff parity games,” presented at the LICS: Logic in Computer Science, 2005, pp. 178–187.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Mean-Payoff Parity Games,” 178–87. IEEE, 2005. <a href=\"https://doi.org/10.1109/LICS.2005.26\">https://doi.org/10.1109/LICS.2005.26</a>.","short":"K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, IEEE, 2005, pp. 178–187.","mla":"Chatterjee, Krishnendu, et al. <i>Mean-Payoff Parity Games</i>. IEEE, 2005, pp. 178–87, doi:<a href=\"https://doi.org/10.1109/LICS.2005.26\">10.1109/LICS.2005.26</a>."},"date_created":"2018-12-11T12:09:27Z","extern":1,"month":"09","author":[{"orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Jurdziński, Marcin","last_name":"Jurdziński","first_name":"Marcin"}]},{"_id":"4557","publist_id":"157","status":"public","date_published":"2005-01-01T00:00:00Z","page":"104 - 111","abstract":[{"text":"Planning in adversarial and uncertain environments can be modeled as the problem of devising strategies in stochastic perfect information games. These games are generalizations of Markov decision processes (MDPs): there are two (adversarial) players, and a source of randomness. The main practical obstacle to computing winning strategies in such games is the size of the state space. In practice therefore, one typically works with abstractions of the model. The diffculty is to come up with an abstraction that is neither too coarse to remove all winning strategies (plans), nor too fine to be intractable. In verification, the paradigm of counterexample-guided abstraction refinement has been successful to construct useful but parsimonious abstractions automatically. We extend this paradigm to probabilistic models (namely, perfect information games and, as a special case, MDPs). This allows us to apply the counterexample-guided abstraction paradigm to the AI planning problem. As special cases, we get planning algorithms for MDPs and deterministic systems that automatically construct system abstractions.","lang":"eng"}],"citation":{"apa":"Chatterjee, K., Henzinger, T. A., Jhala, R., &#38; Majumdar, R. (2005). Counterexample-guided planning (pp. 104–111). Presented at the UAI: Uncertainty in Artificial Intelligence, AUAI Press.","ista":"Chatterjee K, Henzinger TA, Jhala R, Majumdar R. 2005. Counterexample-guided planning. UAI: Uncertainty in Artificial Intelligence, 104–111.","ama":"Chatterjee K, Henzinger TA, Jhala R, Majumdar R. Counterexample-guided planning. In: AUAI Press; 2005:104-111.","short":"K. Chatterjee, T.A. Henzinger, R. Jhala, R. Majumdar, in:, AUAI Press, 2005, pp. 104–111.","mla":"Chatterjee, Krishnendu, et al. <i>Counterexample-Guided Planning</i>. AUAI Press, 2005, pp. 104–11.","ieee":"K. Chatterjee, T. A. Henzinger, R. Jhala, and R. Majumdar, “Counterexample-guided planning,” presented at the UAI: Uncertainty in Artificial Intelligence, 2005, pp. 104–111.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Counterexample-Guided Planning,” 104–11. AUAI Press, 2005."},"date_created":"2018-12-11T12:09:28Z","extern":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jhala","first_name":"Ranjit","full_name":"Jhala, Ranjit"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar S"}],"month":"01","type":"conference","main_file_link":[{"url":"http://uai.sis.pitt.edu/papers/05/p104-chatterjee.pdf","open_access":"0"}],"year":"2005","conference":{"name":"UAI: Uncertainty in Artificial Intelligence"},"date_updated":"2021-01-12T07:59:41Z","publisher":"AUAI Press","day":"01","publication_status":"published","quality_controlled":0,"title":"Counterexample-guided planning"},{"year":"2005","conference":{"name":"CHARME: Correct Hardware Design and Verification Methods"},"volume":3725,"type":"conference","quality_controlled":0,"title":"Verifying quantitative properties using bound functions","doi":"10.1007/11560548_7","publisher":"Springer","date_updated":"2021-01-12T07:59:42Z","publication_status":"published","day":"19","status":"public","date_published":"2005-09-19T00:00:00Z","publist_id":"149","abstract":[{"text":"We define and study a quantitative generalization of the traditional boolean framework of model-based specification and verification. In our setting, propositions have integer values at states, and properties have integer values on traces. For example, the value of a quantitative proposition at a state may represent power consumed at the state, and the value of a quantitative property on a trace may represent energy used along the trace. The value of a quantitative property at a state, then, is the maximum (or minimum) value achievable over all possible traces from the state. In this framework, model checking can be used to compute, for example, the minimum battery capacity necessary for achieving a given objective, or the maximal achievable lifetime of a system with a given initial battery capacity. In the case of open systems, these problems require the solution of games with integer values.\nQuantitative model checking and game solving is undecidable, except if bounds on the computation can be found. Indeed, many interesting quantitative properties, like minimal necessary battery capacity and maximal achievable lifetime, can be naturally specified by quantitative-bound automata, which are finite automata with integer registers whose analysis is constrained by a bound function f that maps each system K to an integer f(K). Along with the linear-time, automaton-based view of quantitative verification, we present a corresponding branching-time view based on a quantitative-bound μ-calculus, and we study the relationship, expressive power, and complexity of both views.\n","lang":"eng"}],"page":"50 - 64","intvolume":"      3725","_id":"4560","month":"09","author":[{"last_name":"Chakrabarti","first_name":"Arindam","full_name":"Chakrabarti, Arindam"},{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"},{"full_name":"Majumdar, Ritankar S","first_name":"Ritankar","last_name":"Majumdar"}],"date_created":"2018-12-11T12:09:29Z","citation":{"ista":"Chakrabarti A, Chatterjee K, Henzinger TA, Kupferman O, Majumdar R. 2005. Verifying quantitative properties using bound functions. CHARME: Correct Hardware Design and Verification Methods, LNCS, vol. 3725, 50–64.","apa":"Chakrabarti, A., Chatterjee, K., Henzinger, T. A., Kupferman, O., &#38; Majumdar, R. (2005). Verifying quantitative properties using bound functions (Vol. 3725, pp. 50–64). Presented at the CHARME: Correct Hardware Design and Verification Methods, Springer. <a href=\"https://doi.org/10.1007/11560548_7\">https://doi.org/10.1007/11560548_7</a>","ama":"Chakrabarti A, Chatterjee K, Henzinger TA, Kupferman O, Majumdar R. Verifying quantitative properties using bound functions. In: Vol 3725. Springer; 2005:50-64. doi:<a href=\"https://doi.org/10.1007/11560548_7\">10.1007/11560548_7</a>","short":"A. Chakrabarti, K. Chatterjee, T.A. Henzinger, O. Kupferman, R. Majumdar, in:, Springer, 2005, pp. 50–64.","mla":"Chakrabarti, Arindam, et al. <i>Verifying Quantitative Properties Using Bound Functions</i>. Vol. 3725, Springer, 2005, pp. 50–64, doi:<a href=\"https://doi.org/10.1007/11560548_7\">10.1007/11560548_7</a>.","chicago":"Chakrabarti, Arindam, Krishnendu Chatterjee, Thomas A Henzinger, Orna Kupferman, and Ritankar Majumdar. “Verifying Quantitative Properties Using Bound Functions,” 3725:50–64. Springer, 2005. <a href=\"https://doi.org/10.1007/11560548_7\">https://doi.org/10.1007/11560548_7</a>.","ieee":"A. Chakrabarti, K. Chatterjee, T. A. Henzinger, O. Kupferman, and R. Majumdar, “Verifying quantitative properties using bound functions,” presented at the CHARME: Correct Hardware Design and Verification Methods, 2005, vol. 3725, pp. 50–64."},"alternative_title":["LNCS"],"extern":1},{"acknowledgement":"This research was supported in part by the ONR grant N00014-02-1-0671 and by the NSF grants CCR-0234690 and CCR-0225610.","_id":"4576","abstract":[{"text":"We present a language for specifying web service interfaces. A web service interface puts three kinds of constraints on the users of the service. First, the interface specifies the methods that can be called by a client, together with types of input and output parameters; these are called signature constraints. Second, the interface may specify propositional constraints on method calls and output values that may oc- cur in a web service conversation; these are called consis- tency constraints. Third, the interface may specify temporal constraints on the ordering of method calls; these are called protocol constraints. The interfaces can be used to check, first, if two or more web services are compatible, and second, if a web service A can be safely substituted for a web ser- vice B. The algorithm for compatibility checking verifies that two or more interfaces fulfill each others’ constraints. The algorithm for substitutivity checking verifies that service A demands fewer and fulfills more constraints than service B.","lang":"eng"}],"page":"148 - 159","status":"public","date_published":"2005-05-01T00:00:00Z","publist_id":"132","extern":1,"date_created":"2018-12-11T12:09:33Z","citation":{"short":"D. Beyer, A. Chakrabarti, T.A. Henzinger, in:, ACM, 2005, pp. 148–159.","mla":"Beyer, Dirk, et al. <i>Web Service Interfaces</i>. ACM, 2005, pp. 148–59, doi:<a href=\"https://doi.org/10.1145/1060745.1060770\">10.1145/1060745.1060770</a>.","ieee":"D. Beyer, A. Chakrabarti, and T. A. Henzinger, “Web service interfaces,” presented at the WWW: World Wide Web Conference, 2005, pp. 148–159.","chicago":"Beyer, Dirk, Arindam Chakrabarti, and Thomas A Henzinger. “Web Service Interfaces,” 148–59. ACM, 2005. <a href=\"https://doi.org/10.1145/1060745.1060770\">https://doi.org/10.1145/1060745.1060770</a>.","apa":"Beyer, D., Chakrabarti, A., &#38; Henzinger, T. A. (2005). Web service interfaces (pp. 148–159). Presented at the WWW: World Wide Web Conference, ACM. <a href=\"https://doi.org/10.1145/1060745.1060770\">https://doi.org/10.1145/1060745.1060770</a>","ista":"Beyer D, Chakrabarti A, Henzinger TA. 2005. Web service interfaces. WWW: World Wide Web Conference, 148–159.","ama":"Beyer D, Chakrabarti A, Henzinger TA. Web service interfaces. In: ACM; 2005:148-159. doi:<a href=\"https://doi.org/10.1145/1060745.1060770\">10.1145/1060745.1060770</a>"},"month":"05","author":[{"first_name":"Dirk","last_name":"Beyer","full_name":"Beyer, Dirk"},{"last_name":"Chakrabarti","first_name":"Arindam","full_name":"Chakrabarti, Arindam"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724"}],"type":"conference","conference":{"name":"WWW: World Wide Web Conference"},"year":"2005","publication_status":"published","day":"01","publisher":"ACM","date_updated":"2021-01-12T07:59:50Z","title":"Web service interfaces","doi":"10.1145/1060745.1060770","quality_controlled":0},{"author":[{"first_name":"Dirk","last_name":"Beyer","full_name":"Beyer, Dirk"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jhala, Ranjit","last_name":"Jhala","first_name":"Ranjit"},{"full_name":"Majumdar, Ritankar S","last_name":"Majumdar","first_name":"Ritankar"}],"month":"03","extern":1,"alternative_title":["LNCS"],"date_created":"2018-12-11T12:09:34Z","citation":{"apa":"Beyer, D., Henzinger, T. A., Jhala, R., &#38; Majumdar, R. (2005). Checking memory safety with BLAST (Vol. 3442, pp. 2–18). Presented at the FASE: Fundamental Approaches To Software Engineering, Springer. <a href=\"https://doi.org/10.1007/978-3-540-31984-9_2\">https://doi.org/10.1007/978-3-540-31984-9_2</a>","ista":"Beyer D, Henzinger TA, Jhala R, Majumdar R. 2005. Checking memory safety with BLAST. FASE: Fundamental Approaches To Software Engineering, LNCS, vol. 3442, 2–18.","ama":"Beyer D, Henzinger TA, Jhala R, Majumdar R. Checking memory safety with BLAST. In: Vol 3442. Springer; 2005:2-18. doi:<a href=\"https://doi.org/10.1007/978-3-540-31984-9_2\">10.1007/978-3-540-31984-9_2</a>","short":"D. Beyer, T.A. Henzinger, R. Jhala, R. Majumdar, in:, Springer, 2005, pp. 2–18.","mla":"Beyer, Dirk, et al. <i>Checking Memory Safety with BLAST</i>. Vol. 3442, Springer, 2005, pp. 2–18, doi:<a href=\"https://doi.org/10.1007/978-3-540-31984-9_2\">10.1007/978-3-540-31984-9_2</a>.","ieee":"D. Beyer, T. A. Henzinger, R. Jhala, and R. Majumdar, “Checking memory safety with BLAST,” presented at the FASE: Fundamental Approaches To Software Engineering, 2005, vol. 3442, pp. 2–18.","chicago":"Beyer, Dirk, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Checking Memory Safety with BLAST,” 3442:2–18. Springer, 2005. <a href=\"https://doi.org/10.1007/978-3-540-31984-9_2\">https://doi.org/10.1007/978-3-540-31984-9_2</a>."},"page":"2 - 18","abstract":[{"lang":"eng","text":"BLAST is an automatic verification tool for checking temporal safety properties of C programs. Given a C program and a temporal safety property, BLAST statically proves that either the program satisfies the safety property or the program has an execution trace that exhibits a violation of the property. BLAST constructs, explores, and refines abstractions of the program state space based on lazy predicate abstraction and interpolation-based predicate discovery. We show how BLAST can be used to statically prove memory safety for C programs. We take a two-step approach. First, we use Ccured, a type-based memory safety analyzer, to annotate with run-time checks all program points that cannot be proved memory safe by the type system. Second, we use BLAST to remove as many of the run-time checks as possible (by proving that these checks never fail), and to generate for the remaining run-time checks execution traces that witness them fail. Our experience shows that BLAST can remove many of the run-time checks added by Ccured and provide useful information to the programmer about many of the remaining checks."}],"publist_id":"131","status":"public","date_published":"2005-03-24T00:00:00Z","intvolume":"      3442","_id":"4579","acknowledgement":"This research was supported in part by the NSF grants CCR-0234690, CCR-0225610, and ITR-0326577.","doi":"10.1007/978-3-540-31984-9_2","title":"Checking memory safety with BLAST","quality_controlled":0,"day":"24","publication_status":"published","date_updated":"2021-01-12T07:59:51Z","publisher":"Springer","conference":{"name":"FASE: Fundamental Approaches To Software Engineering"},"year":"2005","type":"conference","volume":3442},{"title":"Interface-based design","doi":"10.1007/1-4020-3532-2_3","quality_controlled":0,"publication_status":"published","day":"15","publisher":"Springer","date_updated":"2021-01-12T08:00:36Z","conference":{"name":"Engineering Theories of Software Intensive Systems"},"year":"2005","volume":195,"type":"conference","month":"07","author":[{"first_name":"Luca","last_name":"De Alfaro","full_name":"de Alfaro, Luca"},{"full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["NATO Science Series: Mathematics, Physics, and Chemistry"],"extern":1,"citation":{"short":"L. De Alfaro, T.A. Henzinger, in:, Springer, 2005, pp. 83–104.","mla":"De Alfaro, Luca, and Thomas A. Henzinger. <i>Interface-Based Design</i>. Vol. 195, Springer, 2005, pp. 83–104, doi:<a href=\"https://doi.org/10.1007/1-4020-3532-2_3\">10.1007/1-4020-3532-2_3</a>.","ieee":"L. De Alfaro and T. A. Henzinger, “Interface-based design,” presented at the Engineering Theories of Software Intensive Systems, 2005, vol. 195, pp. 83–104.","chicago":"De Alfaro, Luca, and Thomas A Henzinger. “Interface-Based Design,” 195:83–104. Springer, 2005. <a href=\"https://doi.org/10.1007/1-4020-3532-2_3\">https://doi.org/10.1007/1-4020-3532-2_3</a>.","apa":"De Alfaro, L., &#38; Henzinger, T. A. (2005). Interface-based design (Vol. 195, pp. 83–104). Presented at the Engineering Theories of Software Intensive Systems, Springer. <a href=\"https://doi.org/10.1007/1-4020-3532-2_3\">https://doi.org/10.1007/1-4020-3532-2_3</a>","ista":"De Alfaro L, Henzinger TA. 2005. Interface-based design. Engineering Theories of Software Intensive Systems, NATO Science Series: Mathematics, Physics, and Chemistry, vol. 195, 83–104.","ama":"De Alfaro L, Henzinger TA. Interface-based design. In: Vol 195. Springer; 2005:83-104. doi:<a href=\"https://doi.org/10.1007/1-4020-3532-2_3\">10.1007/1-4020-3532-2_3</a>"},"date_created":"2018-12-11T12:09:49Z","abstract":[{"text":"Surveying results from [5] and [6], we motivate and introduce the theory behind formalizing rich interfaces for software and hardware components. Rich interfaces specify the protocol aspects of component interaction. Their formalization, called interface automata, permits a compiler to check the compatibility of component interaction protocols. Interface automata 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, while still maintaining compatibility.","lang":"eng"}],"page":"83 - 104","status":"public","date_published":"2005-07-15T00:00:00Z","publist_id":"85","intvolume":"       195","_id":"4624"},{"author":[{"full_name":"de Alfaro, Luca","first_name":"Luca","last_name":"De Alfaro"},{"last_name":"Faella","first_name":"Marco","full_name":"Faella, Marco"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar S"},{"full_name":"Stoelinga, Mariëlle","first_name":"Mariëlle","last_name":"Stoelinga"}],"month":"11","date_created":"2018-12-11T12:09:49Z","citation":{"ieee":"L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Model checking discounted temporal properties,” <i>Theoretical Computer Science</i>, vol. 345, no. 1. Elsevier, pp. 139–170, 2005.","chicago":"De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties.” <i>Theoretical Computer Science</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.tcs.2005.07.033\">https://doi.org/10.1016/j.tcs.2005.07.033</a>.","mla":"De Alfaro, Luca, et al. “Model Checking Discounted Temporal Properties.” <i>Theoretical Computer Science</i>, vol. 345, no. 1, Elsevier, 2005, pp. 139–70, doi:<a href=\"https://doi.org/10.1016/j.tcs.2005.07.033\">10.1016/j.tcs.2005.07.033</a>.","short":"L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, Theoretical Computer Science 345 (2005) 139–170.","ama":"De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Model checking discounted temporal properties. <i>Theoretical Computer Science</i>. 2005;345(1):139-170. doi:<a href=\"https://doi.org/10.1016/j.tcs.2005.07.033\">10.1016/j.tcs.2005.07.033</a>","apa":"De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., &#38; Stoelinga, M. (2005). Model checking discounted temporal properties. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2005.07.033\">https://doi.org/10.1016/j.tcs.2005.07.033</a>","ista":"De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2005. Model checking discounted temporal properties. Theoretical Computer Science. 345(1), 139–170."},"extern":1,"publist_id":"80","publication":"Theoretical Computer Science","issue":"1","date_published":"2005-11-21T00:00:00Z","status":"public","page":"139 - 170","abstract":[{"text":"Temporal logic is two-valued: formulas are interpreted as 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.\n\nWe 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.","lang":"eng"}],"_id":"4625","intvolume":"       345","quality_controlled":0,"doi":"10.1016/j.tcs.2005.07.033","title":"Model checking discounted temporal properties","date_updated":"2021-01-12T08:00:37Z","publisher":"Elsevier","day":"21","publication_status":"published","year":"2005","type":"journal_article","volume":345},{"title":"A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides","doi":"10.1080/10425170410001667348","external_id":{"pmid":["15352294"]},"publication_identifier":{"issn":["1042-5179"]},"date_updated":"2023-05-08T10:58:29Z","year":"2004","article_processing_charge":"No","author":[{"full_name":"Liao, Zhihua","last_name":"Liao","first_name":"Zhihua"},{"first_name":"Min","last_name":"Chen","full_name":"Chen, Min"},{"full_name":"Gong, Yifu","first_name":"Yifu","last_name":"Gong"},{"last_name":"Guo","first_name":"Liang","full_name":"Guo, Liang"},{"last_name":"Tan","first_name":"Qiumin","full_name":"Tan, Qiumin"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Sun","first_name":"Xiaofen","full_name":"Sun, Xiaofen"},{"full_name":"Tan, Feng","first_name":"Feng","last_name":"Tan"},{"last_name":"Tang","first_name":"Kexuan","full_name":"Tang, Kexuan"}],"article_type":"original","citation":{"chicago":"Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>. Informa UK Limited, 2004. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>.","ieee":"Z. Liao <i>et al.</i>, “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” <i>DNA Sequence</i>, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.","short":"Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158.","mla":"Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>.","ama":"Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. 2004;15(2):153-158. doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>","ista":"Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.","apa":"Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004). A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>"},"keyword":["Endocrinology","Genetics","Molecular Biology","Biochemistry"],"page":"153-158","issue":"2","acknowledgement":"This study was financially supported by China National High-Tech “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences, Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic tree.","_id":"12203","language":[{"iso":"eng"}],"department":[{"_id":"XiFe"}],"pmid":1,"quality_controlled":"1","publication_status":"published","publisher":"Informa UK Limited","volume":15,"type":"journal_article","oa_version":"None","extern":"1","scopus_import":"1","date_created":"2023-01-16T09:24:50Z","abstract":[{"lang":"eng","text":"Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs."}],"status":"public","date_published":"2004-01-01T00:00:00Z","publication":"DNA Sequence","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        15"},{"date_updated":"2023-02-20T08:40:21Z","day":"16","publication_identifier":{"issn":["0148-0227"]},"doi":"10.1029/2003jd003973","title":"Spatial and temporal variability of meteorological variables at Haut Glacier d'Arolla (Switzerland) during the ablation season 2001: Measurements and simulations","article_processing_charge":"No","year":"2004","keyword":["Paleontology","Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Earth-Surface Processes","Geochemistry and Petrology","Soil Science","Water Science and Technology","Ecology","Aquatic Science","Forestry","Oceanography","Geophysics"],"citation":{"ista":"Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. 2004. Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. Journal of Geophysical Research: Atmospheres. 109(D3), D03103.","apa":"Strasser, U., Corripio, J., Pellicciotti, F., Burlando, P., Brock, B., &#38; Funk, M. (2004). Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2003jd003973\">https://doi.org/10.1029/2003jd003973</a>","ama":"Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations. <i>Journal of Geophysical Research: Atmospheres</i>. 2004;109(D3). doi:<a href=\"https://doi.org/10.1029/2003jd003973\">10.1029/2003jd003973</a>","short":"U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, M. Funk, Journal of Geophysical Research: Atmospheres 109 (2004).","mla":"Strasser, Ulrich, et al. “Spatial and Temporal Variability of Meteorological Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001: Measurements and Simulations.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 109, no. D3, D03103, American Geophysical Union, 2004, doi:<a href=\"https://doi.org/10.1029/2003jd003973\">10.1029/2003jd003973</a>.","chicago":"Strasser, Ulrich, Javier Corripio, Francesca Pellicciotti, Paolo Burlando, Ben Brock, and Martin Funk. “Spatial and Temporal Variability of Meteorological Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001: Measurements and Simulations.” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2004. <a href=\"https://doi.org/10.1029/2003jd003973\">https://doi.org/10.1029/2003jd003973</a>.","ieee":"U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, and M. Funk, “Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 109, no. D3. American Geophysical Union, 2004."},"article_type":"original","author":[{"full_name":"Strasser, Ulrich","last_name":"Strasser","first_name":"Ulrich"},{"full_name":"Corripio, Javier","first_name":"Javier","last_name":"Corripio"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"last_name":"Burlando","first_name":"Paolo","full_name":"Burlando, Paolo"},{"last_name":"Brock","first_name":"Ben","full_name":"Brock, Ben"},{"full_name":"Funk, Martin","last_name":"Funk","first_name":"Martin"}],"article_number":"D03103","month":"02","_id":"12658","language":[{"iso":"eng"}],"issue":"D3","publisher":"American Geophysical Union","publication_status":"published","quality_controlled":"1","type":"journal_article","volume":109,"date_created":"2023-02-20T08:18:57Z","extern":"1","scopus_import":"1","oa_version":"None","intvolume":"       109","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Geophysical Research: Atmospheres","status":"public","date_published":"2004-02-16T00:00:00Z","abstract":[{"lang":"eng","text":"[1] During the ablation period 2001 a glaciometeorological experiment was carried out on Haut Glacier d'Arolla, Switzerland. Five meteorological stations were installed on the glacier, and one permanent automatic weather station in the glacier foreland. The altitudes of the stations ranged between 2500 and 3000 m a.s.l., and they were in operation from end of May to beginning of September 2001. The spatial arrangement of the stations and temporal duration of the measurements generated a unique data set enabling the analysis of the spatial and temporal variability of the meteorological variables across an alpine glacier. All measurements were taken at a nominal height of 2 m, and hourly averages were derived for the analysis. The wind regime was dominated by the glacier wind (mean value 2.8 m s−1) but due to erosion by the synoptic gradient wind, occasionally the wind would blow up the valley. A slight decrease in mean 2 m air temperatures with altitude was found, however the 2 m air temperature gradient varied greatly and frequently changed its sign. Mean relative humidity was 71% and exhibited limited spatial variation. Mean incoming shortwave radiation and albedo both generally increased with elevation. The different components of shortwave radiation are quantified with a parameterization scheme. Resulting spatial variations are mainly due to horizon obstruction and reflections from surrounding slopes, i.e., topography. The effect of clouds accounts for a loss of 30% of the extraterrestrial flux. Albedos derived from a Landsat TM image of 30 July show remarkably constant values, in the range 0.49 to 0.50, across snow covered parts of the glacier, while albedo is highly spatially variable below the zone of continuous snow cover. These results are verified with ground measurements and compared with parameterized albedo. Mean longwave radiative fluxes decreased with elevation due to lower air temperatures and the effect of upper hemisphere slopes. It is shown through parameterization that this effect would even be more pronounced without the effect of clouds. Results are discussed with respect to a similar study which has been carried out on Pasterze Glacier (Austria). The presented algorithms for interpolating, parameterizing and simulating variables and parameters in alpine regions are integrated in the software package AMUNDSEN which is freely available to be adapted and further developed by the community."}]},{"volume":57,"type":"journal_article","article_processing_charge":"No","year":"2004","publication_identifier":{"issn":["0010-3640","1097-0312"]},"publication_status":"published","day":"01","publisher":"Wiley","date_updated":"2021-01-12T08:19:50Z","title":"A limit shape theorem for periodic stochastic dispersion","doi":"10.1002/cpa.20032","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        57","_id":"8517","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider the evolution of a connected set on the plane carried by a space periodic incompressible stochastic flow. While for almost every realization of the stochastic flow at time t most of the particles are at a distance of order equation image away from the origin, there is a measure zero set of points that escape to infinity at the linear rate. We study the set of points visited by the original set by time t and show that such a set, when scaled down by the factor of t, has a limiting nonrandom shape."}],"page":"1127-1158","date_published":"2004-09-01T00:00:00Z","status":"public","issue":"9","publication":"Communications on Pure and Applied Mathematics","article_type":"original","extern":"1","citation":{"ama":"Dolgopyat D, Kaloshin V, Koralov L. A limit shape theorem for periodic stochastic dispersion. <i>Communications on Pure and Applied Mathematics</i>. 2004;57(9):1127-1158. doi:<a href=\"https://doi.org/10.1002/cpa.20032\">10.1002/cpa.20032</a>","apa":"Dolgopyat, D., Kaloshin, V., &#38; Koralov, L. (2004). A limit shape theorem for periodic stochastic dispersion. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.20032\">https://doi.org/10.1002/cpa.20032</a>","ista":"Dolgopyat D, Kaloshin V, Koralov L. 2004. A limit shape theorem for periodic stochastic dispersion. Communications on Pure and Applied Mathematics. 57(9), 1127–1158.","ieee":"D. Dolgopyat, V. Kaloshin, and L. Koralov, “A limit shape theorem for periodic stochastic dispersion,” <i>Communications on Pure and Applied Mathematics</i>, vol. 57, no. 9. Wiley, pp. 1127–1158, 2004.","chicago":"Dolgopyat, Dmitry, Vadim Kaloshin, and Leonid Koralov. “A Limit Shape Theorem for Periodic Stochastic Dispersion.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2004. <a href=\"https://doi.org/10.1002/cpa.20032\">https://doi.org/10.1002/cpa.20032</a>.","short":"D. Dolgopyat, V. Kaloshin, L. Koralov, Communications on Pure and Applied Mathematics 57 (2004) 1127–1158.","mla":"Dolgopyat, Dmitry, et al. “A Limit Shape Theorem for Periodic Stochastic Dispersion.” <i>Communications on Pure and Applied Mathematics</i>, vol. 57, no. 9, Wiley, 2004, pp. 1127–58, doi:<a href=\"https://doi.org/10.1002/cpa.20032\">10.1002/cpa.20032</a>."},"keyword":["Applied Mathematics","General Mathematics"],"date_created":"2020-09-18T10:49:12Z","month":"09","oa_version":"None","author":[{"full_name":"Dolgopyat, Dmitry","last_name":"Dolgopyat","first_name":"Dmitry"},{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628"},{"first_name":"Leonid","last_name":"Koralov","full_name":"Koralov, Leonid"}]},{"year":"2004","article_processing_charge":"No","volume":32,"type":"journal_article","quality_controlled":"1","title":"Sample path properties of the stochastic flows","doi":"10.1214/aop/1078415827","publisher":"Institute of Mathematical Statistics","date_updated":"2021-01-12T08:19:50Z","publication_status":"published","publication_identifier":{"issn":["0091-1798"]},"day":"04","date_published":"2004-03-04T00:00:00Z","status":"public","publication":"The Annals of Probability","issue":"1A","page":"1-27","_id":"8518","intvolume":"        32","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","author":[{"full_name":"Koralov, Leonid","first_name":"Leonid","last_name":"Koralov"},{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim"},{"full_name":"Dolgopyat, Dmitry","first_name":"Dmitry","last_name":"Dolgopyat"}],"oa_version":"None","citation":{"ama":"Koralov L, Kaloshin V, Dolgopyat D. Sample path properties of the stochastic flows. <i>The Annals of Probability</i>. 2004;32(1A):1-27. doi:<a href=\"https://doi.org/10.1214/aop/1078415827\">10.1214/aop/1078415827</a>","apa":"Koralov, L., Kaloshin, V., &#38; Dolgopyat, D. (2004). Sample path properties of the stochastic flows. <i>The Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/aop/1078415827\">https://doi.org/10.1214/aop/1078415827</a>","ista":"Koralov L, Kaloshin V, Dolgopyat D. 2004. Sample path properties of the stochastic flows. The Annals of Probability. 32(1A), 1–27.","ieee":"L. Koralov, V. Kaloshin, and D. Dolgopyat, “Sample path properties of the stochastic flows,” <i>The Annals of Probability</i>, vol. 32, no. 1A. Institute of Mathematical Statistics, pp. 1–27, 2004.","chicago":"Koralov, Leonid, Vadim Kaloshin, and Dmitry Dolgopyat. “Sample Path Properties of the Stochastic Flows.” <i>The Annals of Probability</i>. Institute of Mathematical Statistics, 2004. <a href=\"https://doi.org/10.1214/aop/1078415827\">https://doi.org/10.1214/aop/1078415827</a>.","short":"L. Koralov, V. Kaloshin, D. Dolgopyat, The Annals of Probability 32 (2004) 1–27.","mla":"Koralov, Leonid, et al. “Sample Path Properties of the Stochastic Flows.” <i>The Annals of Probability</i>, vol. 32, no. 1A, Institute of Mathematical Statistics, 2004, pp. 1–27, doi:<a href=\"https://doi.org/10.1214/aop/1078415827\">10.1214/aop/1078415827</a>."},"date_created":"2020-09-18T10:49:19Z","extern":"1","article_type":"original"},{"page":"884 - 892","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."}],"publist_id":"6786","issue":"4","publication":"Protein Science","date_published":"2004-04-01T00:00:00Z","status":"public","_id":"864","intvolume":"        13","acknowledgement":"We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful suggestions, and the NIH Intramural Research Program forsupport.","author":[{"first_name":"Anna","last_name":"Panchenko","full_name":"Panchenko, Anna R"},{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"},{"last_name":"Bryant","first_name":"Stephen","full_name":"Bryant, Stephen H"}],"month":"04","extern":1,"citation":{"mla":"Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” <i>Protein Science</i>, vol. 13, no. 4, Wiley-Blackwell, 2004, pp. 884–92, doi:<a href=\"https://doi.org/10.1110/ps.03465504\">10.1110/ps.03465504</a>.","short":"A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.","chicago":"Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of Functional Sites by Analysis of Sequence and Structure Conservation.” <i>Protein Science</i>. Wiley-Blackwell, 2004. <a href=\"https://doi.org/10.1110/ps.03465504\">https://doi.org/10.1110/ps.03465504</a>.","ieee":"A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites by analysis of sequence and structure conservation,” <i>Protein Science</i>, 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.","apa":"Panchenko, A., Kondrashov, F., &#38; Bryant, S. (2004). Prediction of functional sites by analysis of sequence and structure conservation. <i>Protein Science</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1110/ps.03465504\">https://doi.org/10.1110/ps.03465504</a>","ama":"Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis of sequence and structure conservation. <i>Protein Science</i>. 2004;13(4):884-892. doi:<a href=\"https://doi.org/10.1110/ps.03465504\">10.1110/ps.03465504</a>"},"date_created":"2018-12-11T11:48:55Z","year":"2004","type":"journal_article","volume":13,"doi":"10.1110/ps.03465504","title":"Prediction of functional sites by analysis of sequence and structure conservation","quality_controlled":0,"day":"01","publication_status":"published","date_updated":"2021-01-12T08:20:22Z","publisher":"Wiley-Blackwell"},{"intvolume":"        32","_id":"870","issue":"5","publist_id":"6780","publication":"Nucleic Acids Research","status":"public","date_published":"2004-01-01T00:00:00Z","page":"1731 - 1737","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T11:48:56Z","citation":{"ieee":"F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human gene morbidity,” <i>Nucleic Acids Research</i>, vol. 32, no. 5. Oxford University Press, pp. 1731–1737, 2004.","chicago":"Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical Assay of Human Gene Morbidity.” <i>Nucleic Acids Research</i>. Oxford University Press, 2004. <a href=\"https://doi.org/10.1093/nar/gkh330\">https://doi.org/10.1093/nar/gkh330</a>.","short":"F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004) 1731–1737.","mla":"Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.” <i>Nucleic Acids Research</i>, vol. 32, no. 5, Oxford University Press, 2004, pp. 1731–37, doi:<a href=\"https://doi.org/10.1093/nar/gkh330\">10.1093/nar/gkh330</a>.","ama":"Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene morbidity. <i>Nucleic Acids Research</i>. 2004;32(5):1731-1737. doi:<a href=\"https://doi.org/10.1093/nar/gkh330\">10.1093/nar/gkh330</a>","apa":"Kondrashov, F., Ogurtsov, A., &#38; Kondrashov, A. (2004). Bioinformatical assay of human gene morbidity. <i>Nucleic Acids Research</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/nar/gkh330\">https://doi.org/10.1093/nar/gkh330</a>","ista":"Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human gene morbidity. Nucleic Acids Research. 32(5), 1731–1737."},"extern":1,"author":[{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ogurtsov, Aleksey Yu","first_name":"Aleksey","last_name":"Ogurtsov"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"}],"month":"01","type":"journal_article","volume":32,"year":"2004","date_updated":"2021-01-12T08:20:37Z","publisher":"Oxford University Press","day":"01","publication_status":"published","quality_controlled":0,"doi":"10.1093/nar/gkh330","title":"Bioinformatical assay of human gene morbidity"},{"quality_controlled":0,"title":"A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications","doi":"10.1016/j.tig.2004.05.001","publisher":"Elsevier","date_updated":"2021-01-12T08:20:54Z","publication_status":"published","day":"01","year":"2004","volume":20,"type":"journal_article","month":"07","author":[{"last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"},{"full_name":"Koonin, Eugene V","last_name":"Koonin","first_name":"Eugene"}],"citation":{"apa":"Kondrashov, F., &#38; Koonin, E. (2004). A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">https://doi.org/10.1016/j.tig.2004.05.001</a>","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.","ama":"Kondrashov F, Koonin E. A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications. <i>Trends in Genetics</i>. 2004;20(7):287-291. doi:<a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">10.1016/j.tig.2004.05.001</a>","mla":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” <i>Trends in Genetics</i>, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:<a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">10.1016/j.tig.2004.05.001</a>.","short":"F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.","ieee":"F. Kondrashov and E. Koonin, “A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications,” <i>Trends in Genetics</i>, vol. 20, no. 7. Elsevier, pp. 287–291, 2004.","chicago":"Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.” <i>Trends in Genetics</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.tig.2004.05.001\">https://doi.org/10.1016/j.tig.2004.05.001</a>."},"date_created":"2018-12-11T11:48:58Z","extern":1,"date_published":"2004-07-01T00:00:00Z","status":"public","issue":"7","publist_id":"6775","publication":"Trends in Genetics","abstract":[{"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.","lang":"eng"}],"page":"287 - 291","intvolume":"        20","_id":"875"},{"page":"1207 - 1212","abstract":[{"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.","lang":"eng"}],"publication":"Nature Genetics","publist_id":"6759","issue":"11","status":"public","date_published":"2004-11-01T00:00:00Z","_id":"889","intvolume":"        36","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":[{"full_name":"Kern, Andrew D","first_name":"Andrew","last_name":"Kern"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694"}],"month":"11","extern":1,"citation":{"ista":"Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.","apa":"Kern, A., &#38; Kondrashov, F. (2004). Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng1451\">https://doi.org/10.1038/ng1451</a>","ama":"Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs. <i>Nature Genetics</i>. 2004;36(11):1207-1212. doi:<a href=\"https://doi.org/10.1038/ng1451\">10.1038/ng1451</a>","mla":"Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” <i>Nature Genetics</i>, vol. 36, no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:<a href=\"https://doi.org/10.1038/ng1451\">10.1038/ng1451</a>.","short":"A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.","chicago":"Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory Evolution in Mammalian Mitochondrial TRNAs.” <i>Nature Genetics</i>. Nature Publishing Group, 2004. <a href=\"https://doi.org/10.1038/ng1451\">https://doi.org/10.1038/ng1451</a>.","ieee":"A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs,” <i>Nature Genetics</i>, vol. 36, no. 11. Nature Publishing Group, pp. 1207–1212, 2004."},"date_created":"2018-12-11T11:49:02Z","year":"2004","type":"journal_article","volume":36,"doi":"10.1038/ng1451","title":"Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs","quality_controlled":0,"day":"01","publication_status":"published","date_updated":"2021-01-12T08:21:17Z","publisher":"Nature Publishing Group"},{"citation":{"apa":"Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., &#38; Kondrashov, A. (2004). Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature02601\">https://doi.org/10.1038/nature02601</a>","ista":"Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature. 429(6991), 558–562.","ama":"Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. <i>Nature</i>. 2004;429(6991):558-562. doi:<a href=\"https://doi.org/10.1038/nature02601\">10.1038/nature02601</a>","mla":"Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” <i>Nature</i>, vol. 429, no. 6991, Nature Publishing Group, 2004, pp. 558–62, doi:<a href=\"https://doi.org/10.1038/nature02601\">10.1038/nature02601</a>.","short":"G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature 429 (2004) 558–562.","ieee":"G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive selection at sites of multiple amino acid replacements since rat-mouse divergence,” <i>Nature</i>, vol. 429, no. 6991. Nature Publishing Group, pp. 558–562, 2004.","chicago":"Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev, and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements since Rat-Mouse Divergence.” <i>Nature</i>. Nature Publishing Group, 2004. <a href=\"https://doi.org/10.1038/nature02601\">https://doi.org/10.1038/nature02601</a>."},"date_created":"2018-12-11T11:49:05Z","extern":1,"author":[{"first_name":"Georgii","last_name":"Bazykin","full_name":"Bazykin, Georgii A"},{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aleksey","last_name":"Ogurtsov","full_name":"Ogurtsov, Aleksey Yu"},{"last_name":"Sunyaev","first_name":"Shamil","full_name":"Sunyaev, Shamil R"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"}],"month":"06","intvolume":"       429","_id":"898","acknowledgement":"We thank N. Bierne for a number of suggestions. G.A.B. was supported by a BWF graduate fellowship. S.S. was supported by Genome Canada Foundation.","publication":"Nature","publist_id":"6746","issue":"6991","date_published":"2004-06-03T00:00:00Z","status":"public","page":"558 - 562","abstract":[{"text":"New alleles become fixed owing to random drift of nearly neutral mutations or to positive selection of substantially advantageous mutations. After decades of debate, the fraction of fixations driven by selection remains uncertain. Within 9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each other at two nucleotide sites and 1,982 codons with three differences. At codons where rat-mouse divergence involved two non-synonymous substitutions, both of them occurred in the same lineage, either rat or mouse, in 64% of cases; however, independent substitutions would occur in the same lineage with a probability of only 50%. All three non-synonymous substitutions occurred in the same lineage for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12 pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions in the same lineage. This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement.","lang":"eng"}],"date_updated":"2021-01-12T08:21:37Z","publisher":"Nature Publishing Group","day":"03","publication_status":"published","quality_controlled":0,"doi":"10.1038/nature02601","title":"Positive selection at sites of multiple amino acid replacements since rat-mouse divergence","type":"journal_article","volume":429,"year":"2004"}]