[{"publist_id":"159","author":[{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger"},{"first_name":"Marcin","last_name":"Jurdziński","full_name":"Jurdziński, Marcin"}],"title":"Mean-payoff parity games","citation":{"ista":"Chatterjee K, Henzinger TA, Jurdziński M. 2005. Mean-payoff parity games. LICS: Logic in Computer Science, 178–187.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Mean-Payoff Parity Games,” 178–87. IEEE, 2005. https://doi.org/10.1109/LICS.2005.26.","ama":"Chatterjee K, Henzinger TA, Jurdziński M. Mean-payoff parity games. In: IEEE; 2005:178-187. doi:10.1109/LICS.2005.26","apa":"Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2005). Mean-payoff parity games (pp. 178–187). Presented at the LICS: Logic in Computer Science, IEEE. https://doi.org/10.1109/LICS.2005.26","short":"K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, IEEE, 2005, pp. 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.","mla":"Chatterjee, Krishnendu, et al. Mean-Payoff Parity Games. IEEE, 2005, pp. 178–87, doi:10.1109/LICS.2005.26."},"date_updated":"2021-01-12T07:59:39Z","extern":1,"type":"conference","conference":{"name":"LICS: Logic in Computer Science"},"status":"public","_id":"4554","page":"178 - 187","date_published":"2005-09-19T00:00:00Z","doi":"10.1109/LICS.2005.26","date_created":"2018-12-11T12:09:27Z","year":"2005","publication_status":"published","day":"19","quality_controlled":0,"publisher":"IEEE","month":"09","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"}]},{"extern":1,"date_updated":"2021-01-12T07:59:42Z","citation":{"apa":"Chakrabarti, A., Chatterjee, K., Henzinger, T. A., Kupferman, O., & 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. https://doi.org/10.1007/11560548_7","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:10.1007/11560548_7","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.","short":"A. Chakrabarti, K. Chatterjee, T.A. Henzinger, O. Kupferman, R. Majumdar, in:, Springer, 2005, pp. 50–64.","mla":"Chakrabarti, Arindam, et al. Verifying Quantitative Properties Using Bound Functions. Vol. 3725, Springer, 2005, pp. 50–64, doi:10.1007/11560548_7.","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.","chicago":"Chakrabarti, Arindam, Krishnendu Chatterjee, Thomas A Henzinger, Orna Kupferman, and Ritankar Majumdar. “Verifying Quantitative Properties Using Bound Functions,” 3725:50–64. Springer, 2005. https://doi.org/10.1007/11560548_7."},"title":"Verifying quantitative properties using bound functions","author":[{"first_name":"Arindam","full_name":"Chakrabarti, Arindam","last_name":"Chakrabarti"},{"orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"},{"last_name":"Majumdar","full_name":"Majumdar, Ritankar S","first_name":"Ritankar"}],"publist_id":"149","_id":"4560","status":"public","conference":{"name":"CHARME: Correct Hardware Design and Verification Methods"},"type":"conference","day":"19","year":"2005","publication_status":"published","date_created":"2018-12-11T12:09:29Z","doi":"10.1007/11560548_7","date_published":"2005-09-19T00:00:00Z","volume":3725,"page":"50 - 64","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"}],"intvolume":" 3725","month":"09","quality_controlled":0,"alternative_title":["LNCS"],"publisher":"Springer"},{"status":"public","conference":{"name":"UAI: Uncertainty in Artificial Intelligence"},"type":"conference","_id":"4557","title":"Counterexample-guided planning","publist_id":"157","author":[{"orcid":"0000-0002-4561-241X","full_name":"Krishnendu Chatterjee","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Henzinger","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Jhala","full_name":"Jhala, Ranjit","first_name":"Ranjit"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar S"}],"extern":1,"date_updated":"2021-01-12T07:59:41Z","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Counterexample-Guided Planning,” 104–11. AUAI Press, 2005.","ista":"Chatterjee K, Henzinger TA, Jhala R, Majumdar R. 2005. Counterexample-guided planning. UAI: Uncertainty in Artificial Intelligence, 104–111.","mla":"Chatterjee, Krishnendu, et al. Counterexample-Guided Planning. AUAI Press, 2005, pp. 104–11.","short":"K. Chatterjee, T.A. Henzinger, R. Jhala, R. Majumdar, in:, AUAI Press, 2005, pp. 104–111.","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.","ama":"Chatterjee K, Henzinger TA, Jhala R, Majumdar R. Counterexample-guided planning. In: AUAI Press; 2005:104-111.","apa":"Chatterjee, K., Henzinger, T. A., Jhala, R., & Majumdar, R. (2005). Counterexample-guided planning (pp. 104–111). Presented at the UAI: Uncertainty in Artificial Intelligence, AUAI Press."},"month":"01","main_file_link":[{"url":"http://uai.sis.pitt.edu/papers/05/p104-chatterjee.pdf","open_access":"0"}],"publisher":"AUAI Press","quality_controlled":0,"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"}],"date_created":"2018-12-11T12:09:28Z","date_published":"2005-01-01T00:00:00Z","page":"104 - 111","day":"01","publication_status":"published","year":"2005"},{"status":"public","conference":{"name":"FASE: Fundamental Approaches To Software Engineering"},"type":"conference","_id":"4579","title":"Checking memory safety with BLAST","publist_id":"131","author":[{"first_name":"Dirk","last_name":"Beyer","full_name":"Beyer, Dirk"},{"last_name":"Henzinger","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ranjit","full_name":"Jhala, Ranjit","last_name":"Jhala"},{"last_name":"Majumdar","full_name":"Majumdar, Ritankar S","first_name":"Ritankar"}],"extern":1,"date_updated":"2021-01-12T07:59:51Z","citation":{"mla":"Beyer, Dirk, et al. Checking Memory Safety with BLAST. Vol. 3442, Springer, 2005, pp. 2–18, doi:10.1007/978-3-540-31984-9_2.","ama":"Beyer D, Henzinger TA, Jhala R, Majumdar R. Checking memory safety with BLAST. In: Vol 3442. Springer; 2005:2-18. doi:10.1007/978-3-540-31984-9_2","apa":"Beyer, D., Henzinger, T. A., Jhala, R., & Majumdar, R. (2005). Checking memory safety with BLAST (Vol. 3442, pp. 2–18). Presented at the FASE: Fundamental Approaches To Software Engineering, Springer. https://doi.org/10.1007/978-3-540-31984-9_2","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.","short":"D. Beyer, T.A. Henzinger, R. Jhala, R. Majumdar, in:, Springer, 2005, pp. 2–18.","chicago":"Beyer, Dirk, Thomas A Henzinger, Ranjit Jhala, and Ritankar Majumdar. “Checking Memory Safety with BLAST,” 3442:2–18. Springer, 2005. https://doi.org/10.1007/978-3-540-31984-9_2.","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."},"intvolume":" 3442","month":"03","publisher":"Springer","alternative_title":["LNCS"],"quality_controlled":0,"acknowledgement":"This research was supported in part by the NSF grants CCR-0234690, CCR-0225610, and ITR-0326577.","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T12:09:34Z","doi":"10.1007/978-3-540-31984-9_2","volume":3442,"date_published":"2005-03-24T00:00:00Z","page":"2 - 18","day":"24","publication_status":"published","year":"2005"},{"conference":{"name":"WWW: World Wide Web Conference"},"type":"conference","status":"public","_id":"4576","author":[{"last_name":"Beyer","full_name":"Beyer, Dirk","first_name":"Dirk"},{"last_name":"Chakrabarti","full_name":"Chakrabarti, Arindam","first_name":"Arindam"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"132","title":"Web service interfaces","citation":{"mla":"Beyer, Dirk, et al. Web Service Interfaces. ACM, 2005, pp. 148–59, doi:10.1145/1060745.1060770.","ama":"Beyer D, Chakrabarti A, Henzinger TA. Web service interfaces. In: ACM; 2005:148-159. doi:10.1145/1060745.1060770","apa":"Beyer, D., Chakrabarti, A., & Henzinger, T. A. (2005). Web service interfaces (pp. 148–159). Presented at the WWW: World Wide Web Conference, ACM. https://doi.org/10.1145/1060745.1060770","short":"D. Beyer, A. Chakrabarti, T.A. Henzinger, in:, ACM, 2005, pp. 148–159.","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. https://doi.org/10.1145/1060745.1060770.","ista":"Beyer D, Chakrabarti A, Henzinger TA. 2005. Web service interfaces. WWW: World Wide Web Conference, 148–159."},"date_updated":"2021-01-12T07:59:50Z","extern":1,"quality_controlled":0,"publisher":"ACM","month":"05","abstract":[{"lang":"eng","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."}],"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.","page":"148 - 159","date_created":"2018-12-11T12:09:33Z","date_published":"2005-05-01T00:00:00Z","doi":"10.1145/1060745.1060770","publication_status":"published","year":"2005","day":"01"},{"page":"139 - 170","date_published":"2005-11-21T00:00:00Z","volume":345,"issue":"1","doi":"10.1016/j.tcs.2005.07.033","date_created":"2018-12-11T12:09:49Z","year":"2005","publication_status":"published","day":"21","publication":"Theoretical Computer Science","quality_controlled":0,"publisher":"Elsevier","month":"11","intvolume":" 345","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"}],"publist_id":"80","author":[{"last_name":"De Alfaro","full_name":"de Alfaro, Luca","first_name":"Luca"},{"last_name":"Faella","full_name":"Faella, Marco","first_name":"Marco"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger"},{"last_name":"Majumdar","full_name":"Majumdar, Ritankar S","first_name":"Ritankar"},{"first_name":"Mariëlle","last_name":"Stoelinga","full_name":"Stoelinga, Mariëlle"}],"title":"Model checking discounted temporal properties","citation":{"chicago":"De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties.” Theoretical Computer Science. Elsevier, 2005. https://doi.org/10.1016/j.tcs.2005.07.033.","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.","mla":"De Alfaro, Luca, et al. “Model Checking Discounted Temporal Properties.” Theoretical Computer Science, vol. 345, no. 1, Elsevier, 2005, pp. 139–70, doi:10.1016/j.tcs.2005.07.033.","short":"L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, Theoretical Computer Science 345 (2005) 139–170.","ieee":"L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Model checking discounted temporal properties,” Theoretical Computer Science, vol. 345, no. 1. Elsevier, pp. 139–170, 2005.","ama":"De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Model checking discounted temporal properties. Theoretical Computer Science. 2005;345(1):139-170. doi:10.1016/j.tcs.2005.07.033","apa":"De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., & Stoelinga, M. (2005). Model checking discounted temporal properties. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2005.07.033"},"date_updated":"2021-01-12T08:00:37Z","extern":1,"type":"journal_article","status":"public","_id":"4625"},{"day":"15","publication_status":"published","year":"2005","date_created":"2018-12-11T12:09:49Z","volume":195,"date_published":"2005-07-15T00:00:00Z","doi":"10.1007/1-4020-3532-2_3","page":"83 - 104","abstract":[{"lang":"eng","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."}],"intvolume":" 195","month":"07","alternative_title":["NATO Science Series: Mathematics, Physics, and Chemistry"],"publisher":"Springer","quality_controlled":0,"extern":1,"date_updated":"2021-01-12T08:00:36Z","citation":{"chicago":"De Alfaro, Luca, and Thomas A Henzinger. “Interface-Based Design,” 195:83–104. Springer, 2005. https://doi.org/10.1007/1-4020-3532-2_3.","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.","mla":"De Alfaro, Luca, and Thomas A. Henzinger. Interface-Based Design. Vol. 195, Springer, 2005, pp. 83–104, doi:10.1007/1-4020-3532-2_3.","short":"L. De Alfaro, T.A. Henzinger, in:, Springer, 2005, pp. 83–104.","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.","apa":"De Alfaro, L., & Henzinger, T. A. (2005). Interface-based design (Vol. 195, pp. 83–104). Presented at the Engineering Theories of Software Intensive Systems, Springer. https://doi.org/10.1007/1-4020-3532-2_3","ama":"De Alfaro L, Henzinger TA. Interface-based design. In: Vol 195. Springer; 2005:83-104. doi:10.1007/1-4020-3532-2_3"},"title":"Interface-based design","publist_id":"85","author":[{"full_name":"de Alfaro, Luca","last_name":"De Alfaro","first_name":"Luca"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"_id":"4624","status":"public","conference":{"name":"Engineering Theories of Software Intensive Systems"},"type":"conference"},{"_id":"575","status":"public","type":"conference","conference":{"name":"QELS: Quantum Electronics and Laser Science"},"extern":1,"citation":{"mla":"Hosten, Onur, et al. Counterfactual Quantum Computation. Vol. 1, IEEE, 2005, pp. 365–67, doi: 10.1109/QELS.2005.1548783.","apa":"Hosten, O., Rakher, M., Barreiro, J., Peters, N., & Kwiat, P. (2005). Counterfactual quantum computation (Vol. 1, pp. 365–367). Presented at the QELS: Quantum Electronics and Laser Science, IEEE. https://doi.org/ 10.1109/QELS.2005.1548783","ama":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual quantum computation. In: Vol 1. IEEE; 2005:365-367. doi: 10.1109/QELS.2005.1548783","short":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, in:, IEEE, 2005, pp. 365–367.","ieee":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual quantum computation,” presented at the QELS: Quantum Electronics and Laser Science, 2005, vol. 1, pp. 365–367.","chicago":"Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Quantum Computation,” 1:365–67. IEEE, 2005. https://doi.org/ 10.1109/QELS.2005.1548783.","ista":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2005. Counterfactual quantum computation. QELS: Quantum Electronics and Laser Science, QELS, vol. 1, 365–367."},"date_updated":"2021-01-12T08:03:18Z","title":"Counterfactual quantum computation","publist_id":"7237","author":[{"orcid":"0000-0002-2031-204X","full_name":"Onur Hosten","last_name":"Hosten","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur"},{"first_name":"Matthew","full_name":"Rakher, Matthew T","last_name":"Rakher"},{"last_name":"Barreiro","full_name":"Barreiro, Julio T","first_name":"Julio"},{"last_name":"Peters","full_name":"Peters, Nicholas A","first_name":"Nicholas"},{"full_name":"Kwiat, Paul G","last_name":"Kwiat","first_name":"Paul"}],"abstract":[{"text":"We present the first demonstration of Jozsa's "counterfactual computation", using an optical Grover's search algorithm. We put the algorithm in a superposition of 'running' and 'not-running', obtaining information even though the algorithm does not run.","lang":"eng"}],"month":"01","intvolume":" 1","quality_controlled":0,"publisher":"IEEE","alternative_title":["QELS"],"day":"01","publication_status":"published","year":"2005","date_published":"2005-01-01T00:00:00Z","doi":" 10.1109/QELS.2005.1548783","volume":1,"date_created":"2018-12-11T11:47:16Z","page":"365 - 367"},{"publication_status":"published","year":"2005","publication_identifier":{"issn":["0147-006X","1545-4126"]},"language":[{"iso":"eng"}],"publication":"Annual Review of Neuroscience","day":"21","page":"451-501","date_created":"2019-03-21T09:31:29Z","volume":28,"date_published":"2005-07-21T00:00:00Z","doi":"10.1146/annurev.neuro.27.070203.144259","abstract":[{"text":"A current challenge in neuroscience is to bridge the gaps between genes, proteins, neurons, neural circuits, and behavior in a single animal model. The nematode Caenorhabditis elegans has unique features that facilitate this synthesis. Its nervous system includes exactly 302 neurons, and their pattern of synaptic connectivity is known. With only five olfactory neurons, C. elegans can dynamically respond to dozens of attractive and repellant odors. Thermosensory neurons enable the nematode to remember its cultivation temperature and to track narrow isotherms. Polymodal sensory neurons detect a wide range of nociceptive cues and signal robust escape responses. Pairing of sensory stimuli leads to long-lived changes in behavior consistent with associative learning. Worms exhibit social behaviors and complex ultradian rhythms driven by Ca2+ oscillators with clock-like properties. Genetic analysis has identified gene products required for nervous system function and elucidated the molecular and neural bases of behaviors.","lang":"eng"}],"oa_version":"None","pmid":1,"publisher":"Annual Reviews","quality_controlled":"1","intvolume":" 28","month":"07","citation":{"ieee":"M. de Bono and A. Villu Maricq, “Neuronal substrates of complex behaviors in C. elegans,” Annual Review of Neuroscience, vol. 28. Annual Reviews, pp. 451–501, 2005.","short":"M. de Bono, A. Villu Maricq, Annual Review of Neuroscience 28 (2005) 451–501.","apa":"de Bono, M., & Villu Maricq, A. (2005). Neuronal substrates of complex behaviors in C. elegans. Annual Review of Neuroscience. Annual Reviews. https://doi.org/10.1146/annurev.neuro.27.070203.144259","ama":"de Bono M, Villu Maricq A. Neuronal substrates of complex behaviors in C. elegans. Annual Review of Neuroscience. 2005;28:451-501. doi:10.1146/annurev.neuro.27.070203.144259","mla":"de Bono, Mario, and Andres Villu Maricq. “Neuronal Substrates of Complex Behaviors in C. Elegans.” Annual Review of Neuroscience, vol. 28, Annual Reviews, 2005, pp. 451–501, doi:10.1146/annurev.neuro.27.070203.144259.","ista":"de Bono M, Villu Maricq A. 2005. Neuronal substrates of complex behaviors in C. elegans. Annual Review of Neuroscience. 28, 451–501.","chicago":"Bono, Mario de, and Andres Villu Maricq. “Neuronal Substrates of Complex Behaviors in C. Elegans.” Annual Review of Neuroscience. Annual Reviews, 2005. https://doi.org/10.1146/annurev.neuro.27.070203.144259."},"date_updated":"2021-01-12T08:06:24Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","extern":"1","article_processing_charge":"No","external_id":{"pmid":["16022603"]},"author":[{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono"},{"first_name":"Andres","full_name":"Villu Maricq, Andres","last_name":"Villu Maricq"}],"title":"Neuronal substrates of complex behaviors in C. elegans","_id":"6153","article_type":"original","type":"journal_article","status":"public"},{"intvolume":" 15","month":"05","quality_controlled":"1","publisher":"Elsevier","oa_version":"None","pmid":1,"date_created":"2019-03-21T09:37:48Z","doi":"10.1016/j.cub.2005.04.017","date_published":"2005-05-24T00:00:00Z","volume":15,"issue":"10","page":"905-917","language":[{"iso":"eng"}],"publication":"Current Biology","day":"24","year":"2005","publication_status":"published","publication_identifier":{"issn":["0960-9822"]},"status":"public","type":"journal_article","_id":"6154","title":"Experience-dependent modulation of C. elegans behavior by ambient oxygen","external_id":{"pmid":["15916947"]},"author":[{"first_name":"Benny H.H.","last_name":"Cheung","full_name":"Cheung, Benny H.H."},{"last_name":"Cohen","full_name":"Cohen, Merav","first_name":"Merav"},{"first_name":"Candida","full_name":"Rogers, Candida","last_name":"Rogers"},{"first_name":"Onder","full_name":"Albayram, Onder","last_name":"Albayram"},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","extern":"1","date_updated":"2021-01-12T08:06:24Z","citation":{"ista":"Cheung BHH, Cohen M, Rogers C, Albayram O, de Bono M. 2005. Experience-dependent modulation of C. elegans behavior by ambient oxygen. Current Biology. 15(10), 905–917.","chicago":"Cheung, Benny H.H., Merav Cohen, Candida Rogers, Onder Albayram, and Mario de Bono. “Experience-Dependent Modulation of C. Elegans Behavior by Ambient Oxygen.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.04.017.","short":"B.H.H. Cheung, M. Cohen, C. Rogers, O. Albayram, M. de Bono, Current Biology 15 (2005) 905–917.","ieee":"B. H. H. Cheung, M. Cohen, C. Rogers, O. Albayram, and M. de Bono, “Experience-dependent modulation of C. elegans behavior by ambient oxygen,” Current Biology, vol. 15, no. 10. Elsevier, pp. 905–917, 2005.","apa":"Cheung, B. H. H., Cohen, M., Rogers, C., Albayram, O., & de Bono, M. (2005). Experience-dependent modulation of C. elegans behavior by ambient oxygen. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2005.04.017","ama":"Cheung BHH, Cohen M, Rogers C, Albayram O, de Bono M. Experience-dependent modulation of C. elegans behavior by ambient oxygen. Current Biology. 2005;15(10):905-917. doi:10.1016/j.cub.2005.04.017","mla":"Cheung, Benny H. H., et al. “Experience-Dependent Modulation of C. Elegans Behavior by Ambient Oxygen.” Current Biology, vol. 15, no. 10, Elsevier, 2005, pp. 905–17, doi:10.1016/j.cub.2005.04.017."}},{"author":[{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","last_name":"Vogels","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"},{"full_name":"Abbott, L. F.","last_name":"Abbott","first_name":"L. F."}],"article_processing_charge":"No","external_id":{"pmid":["16291952"]},"title":"Signal propagation and logic gating in networks of integrate-and-fire neurons","citation":{"chicago":"Vogels, Tim P, and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” Journal of Neuroscience. Society for Neuroscience, 2005. https://doi.org/10.1523/jneurosci.3508-05.2005.","ista":"Vogels TP, Abbott LF. 2005. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 25(46), 10786–10795.","mla":"Vogels, Tim P., and L. F. Abbott. “Signal Propagation and Logic Gating in Networks of Integrate-and-Fire Neurons.” Journal of Neuroscience, vol. 25, no. 46, Society for Neuroscience, 2005, pp. 10786–95, doi:10.1523/jneurosci.3508-05.2005.","apa":"Vogels, T. P., & Abbott, L. F. (2005). Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/jneurosci.3508-05.2005","ama":"Vogels TP, Abbott LF. Signal propagation and logic gating in networks of integrate-and-fire neurons. Journal of Neuroscience. 2005;25(46):10786-10795. doi:10.1523/jneurosci.3508-05.2005","short":"T.P. Vogels, L.F. Abbott, Journal of Neuroscience 25 (2005) 10786–10795.","ieee":"T. P. Vogels and L. F. Abbott, “Signal propagation and logic gating in networks of integrate-and-fire neurons,” Journal of Neuroscience, vol. 25, no. 46. Society for Neuroscience, pp. 10786–10795, 2005."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publisher":"Society for Neuroscience","quality_controlled":"1","oa":1,"page":"10786-10795","date_published":"2005-11-16T00:00:00Z","doi":"10.1523/jneurosci.3508-05.2005","date_created":"2020-06-25T13:12:33Z","year":"2005","day":"16","publication":"Journal of Neuroscience","type":"journal_article","article_type":"original","status":"public","_id":"8028","date_updated":"2021-01-12T08:16:37Z","extern":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6725859/","open_access":"1"}],"month":"11","intvolume":" 25","abstract":[{"text":"Transmission of signals within the brain is essential for cognitive function, but it is not clear how neural circuits support reliable and accurate signal propagation over a sufficiently large dynamic range. Two modes of propagation have been studied: synfire chains, in which synchronous activity travels through feedforward layers of a neuronal network, and the propagation of fluctuations in firing rate across these layers. In both cases, a sufficient amount of noise, which was added to previous models from an external source, had to be included to support stable propagation. Sparse, randomly connected networks of spiking model neurons can generate chaotic patterns of activity. We investigate whether this activity, which is a more realistic noise source, is sufficient to allow for signal transmission. We find that, for rate-coded signals but not for synfire chains, such networks support robust and accurate signal reproduction through up to six layers if appropriate adjustments are made in synaptic strengths. We investigate the factors affecting transmission and show that multiple signals can propagate simultaneously along different pathways. Using this feature, we show how different types of logic gates can arise within the architecture of the random network through the strengthening of specific synapses.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":25,"issue":"46","publication_identifier":{"issn":["0270-6474","1529-2401"]},"publication_status":"published","language":[{"iso":"eng"}]},{"month":"07","intvolume":" 28","abstract":[{"lang":"eng","text":"Neural network modeling is often concerned with stimulus-driven responses, but most of the activity in the brain is internally generated. Here, we review network models of internally generated activity, focusing on three types of network dynamics: (a) sustained responses to transient stimuli, which provide a model of working memory; (b) oscillatory network activity; and (c) chaotic activity, which models complex patterns of background spiking in cortical and other circuits. We also review propagation of stimulus-driven activity through spontaneously active networks. Exploring these aspects of neural network dynamics is critical for understanding how neural circuits produce cognitive function."}],"pmid":1,"oa_version":"None","issue":"1","volume":28,"publication_identifier":{"issn":["0147-006X","1545-4126"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"review","type":"journal_article","status":"public","_id":"8029","date_updated":"2021-01-12T08:16:37Z","extern":"1","publisher":"Annual Reviews","quality_controlled":"1","page":"357-376","doi":"10.1146/annurev.neuro.28.061604.135637","date_published":"2005-07-21T00:00:00Z","date_created":"2020-06-25T13:13:11Z","year":"2005","day":"21","publication":"Annual Review of Neuroscience","author":[{"id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181","last_name":"Vogels"},{"full_name":"Rajan, Kanaka","last_name":"Rajan","first_name":"Kanaka"},{"first_name":"L.F.","last_name":"Abbott","full_name":"Abbott, L.F."}],"article_processing_charge":"No","external_id":{"pmid":["16022600"]},"title":"Neural network dynamics","citation":{"mla":"Vogels, Tim P., et al. “Neural Network Dynamics.” Annual Review of Neuroscience, vol. 28, no. 1, Annual Reviews, 2005, pp. 357–76, doi:10.1146/annurev.neuro.28.061604.135637.","ieee":"T. P. Vogels, K. Rajan, and L. F. Abbott, “Neural network dynamics,” Annual Review of Neuroscience, vol. 28, no. 1. Annual Reviews, pp. 357–376, 2005.","short":"T.P. Vogels, K. Rajan, L.F. Abbott, Annual Review of Neuroscience 28 (2005) 357–376.","apa":"Vogels, T. P., Rajan, K., & Abbott, L. F. (2005). Neural network dynamics. Annual Review of Neuroscience. Annual Reviews. https://doi.org/10.1146/annurev.neuro.28.061604.135637","ama":"Vogels TP, Rajan K, Abbott LF. Neural network dynamics. Annual Review of Neuroscience. 2005;28(1):357-376. doi:10.1146/annurev.neuro.28.061604.135637","chicago":"Vogels, Tim P, Kanaka Rajan, and L.F. Abbott. “Neural Network Dynamics.” Annual Review of Neuroscience. Annual Reviews, 2005. https://doi.org/10.1146/annurev.neuro.28.061604.135637.","ista":"Vogels TP, Rajan K, Abbott LF. 2005. Neural network dynamics. Annual Review of Neuroscience. 28(1), 357–376."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425"},{"abstract":[{"lang":"eng","text":"Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5′ end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2005.01.008"}],"month":"01","intvolume":" 15","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":15,"issue":"2","_id":"9491","type":"journal_article","article_type":"original","status":"public","date_updated":"2021-12-14T09:12:26Z","extern":"1","department":[{"_id":"DaZi"}],"quality_controlled":"1","publisher":"Elsevier","oa":1,"year":"2005","day":"26","publication":"Current Biology","page":"154-159","date_published":"2005-01-26T00:00:00Z","doi":"10.1016/j.cub.2005.01.008","date_created":"2021-06-07T10:24:30Z","citation":{"ista":"Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 15(2), 154–159.","chicago":"Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.01.008.","ama":"Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 2005;15(2):154-159. doi:10.1016/j.cub.2005.01.008","apa":"Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E., & Henikoff, S. (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2005.01.008","ieee":"R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes,” Current Biology, vol. 15, no. 2. Elsevier, pp. 154–159, 2005.","short":"R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff, Current Biology 15 (2005) 154–159.","mla":"Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” Current Biology, vol. 15, no. 2, Elsevier, 2005, pp. 154–59, doi:10.1016/j.cub.2005.01.008."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","author":[{"first_name":"Robert K.","last_name":"Tran","full_name":"Tran, Robert K."},{"last_name":"Henikoff","full_name":"Henikoff, Jorja G.","first_name":"Jorja G."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Ditt, Renata F.","last_name":"Ditt","first_name":"Renata F."},{"full_name":"Jacobsen, Steven E.","last_name":"Jacobsen","first_name":"Steven E."},{"first_name":"Steven","last_name":"Henikoff","full_name":"Henikoff, Steven"}],"article_processing_charge":"No","external_id":{"pmid":["15668172 "]},"title":"DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes"},{"date_created":"2021-06-07T13:12:41Z","date_published":"2005-10-19T00:00:00Z","doi":"10.1186/gb-2005-6-11-r90","publication":"Genome Biology","day":"19","year":"2005","oa":1,"quality_controlled":"1","publisher":"Springer Nature","title":"Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis","article_processing_charge":"No","external_id":{"pmid":["16277745"]},"author":[{"full_name":"Tran, Robert K.","last_name":"Tran","first_name":"Robert K."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman"},{"full_name":"de Bustos, Cecilia","last_name":"de Bustos","first_name":"Cecilia"},{"first_name":"Renata F.","last_name":"Ditt","full_name":"Ditt, Renata F."},{"first_name":"Jorja G.","last_name":"Henikoff","full_name":"Henikoff, Jorja G."},{"first_name":"Anders M.","full_name":"Lindroth, Anders M.","last_name":"Lindroth"},{"first_name":"Jeffrey","last_name":"Delrow","full_name":"Delrow, Jeffrey"},{"first_name":"Tom","full_name":"Boyle, Tom","last_name":"Boyle"},{"last_name":"Kwong","full_name":"Kwong, Samson","first_name":"Samson"},{"first_name":"Terri D.","full_name":"Bryson, Terri D.","last_name":"Bryson"},{"last_name":"Jacobsen","full_name":"Jacobsen, Steven E.","first_name":"Steven E."},{"first_name":"Steven","last_name":"Henikoff","full_name":"Henikoff, Steven"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"mla":"Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology, vol. 6, no. 11, R90, Springer Nature, 2005, doi:10.1186/gb-2005-6-11-r90.","ieee":"R. K. Tran et al., “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis,” Genome Biology, vol. 6, no. 11. Springer Nature, 2005.","short":"R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth, J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome Biology 6 (2005).","apa":"Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth, A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. Springer Nature. https://doi.org/10.1186/gb-2005-6-11-r90","ama":"Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 2005;6(11). doi:10.1186/gb-2005-6-11-r90","chicago":"Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology. Springer Nature, 2005. https://doi.org/10.1186/gb-2005-6-11-r90.","ista":"Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 6(11), R90."},"article_number":"R90","issue":"11","volume":6,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1465-6906"],"issn":["1474-760X"]},"intvolume":" 6","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/gb-2005-6-11-r90"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.","lang":"eng"}],"department":[{"_id":"DaZi"}],"extern":"1","date_updated":"2021-12-14T09:09:41Z","status":"public","article_type":"original","type":"journal_article","_id":"9514"},{"page":"3191 - 3201","date_published":"2005-11-01T00:00:00Z","volume":14,"issue":"21","doi":"10.1093/hmg/ddi350","date_created":"2018-12-11T11:48:48Z","year":"2005","publication_status":"published","day":"01","publication":"Human Molecular Genetics","quality_controlled":0,"publisher":"Oxford University Press","month":"11","intvolume":" 14","abstract":[{"lang":"eng","text":"The impact of an amino acid replacement on the organism's fitness can vary from lethal to selectively neutral and even, in rare cases, beneficial. Substantial data are available on either pathogenic or acceptable replacements. However, the whole distribution of coefficients of selection against individual replacements is not known for any organism. To ascertain this distribution for human proteins, we combined data on pathogenic missense mutations, on human non-synonymous SNPs and on human-chimpanzee divergence of orthologous proteins. Fractions of amino acid replacements which reduce fitness by >10-2, 10-2-10-4, 10-4-10-5 and <10-5 are 25, 49, 14 and 12%, respectively. On average, the strength of selection against a replacement is substantially higher when chemically dissimilar amino acids are involved, and the Grantham's index of a replacement explains 35% of variance in the average logarithm of selection coefficients associated with different replacements. Still, the impact of a replacement depends on its context within the protein more than on its own nature. Reciprocal replacements are often associated with rather different selection coefficients, in particular, replacements of non-polar amino acids with polar ones are typically much more deleterious than replacements in the opposite direction. However, differences between evolutionary fluxes of reciprocal replacements are only weakly correlated with the differences between the corresponding selection coefficients."}],"publist_id":"6807","author":[{"full_name":"Yampolsky, Lev Y","last_name":"Yampolsky","first_name":"Lev"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"full_name":"Kondrashov, Alexey S","last_name":"Kondrashov","first_name":"Alexey"}],"title":"Distribution of the strength of selection against amino acid replacements in human proteins","citation":{"chicago":"Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi350.","ista":"Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 14(21), 3191–3201.","mla":"Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino Acid Replacements in Human Proteins.” Human Molecular Genetics, vol. 14, no. 21, Oxford University Press, 2005, pp. 3191–201, doi:10.1093/hmg/ddi350.","ama":"Yampolsky L, Kondrashov F, Kondrashov A. Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. 2005;14(21):3191-3201. doi:10.1093/hmg/ddi350","apa":"Yampolsky, L., Kondrashov, F., & Kondrashov, A. (2005). Distribution of the strength of selection against amino acid replacements in human proteins. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi350","short":"L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005) 3191–3201.","ieee":"L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength of selection against amino acid replacements in human proteins,” Human Molecular Genetics, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005."},"date_updated":"2021-01-12T08:19:13Z","extern":1,"type":"journal_article","status":"public","_id":"843"},{"title":"SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds","author":[{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"},{"first_name":"Ēriks","last_name":"Kupče","full_name":"Kupče, Ēriks"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:38Z","citation":{"chicago":"Schanda, Paul, Ēriks Kupče, and Bernhard Brutscher. “SOFAST-HMQC Experiments for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” Journal of Biomolecular NMR. Springer Nature, 2005. https://doi.org/10.1007/s10858-005-4425-x.","ista":"Schanda P, Kupče Ē, Brutscher B. 2005. SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. Journal of Biomolecular NMR. 33(4), 199–211.","mla":"Schanda, Paul, et al. “SOFAST-HMQC Experiments for Recording Two-Dimensional Deteronuclear Correlation Spectra of Proteins within a Few Seconds.” Journal of Biomolecular NMR, vol. 33, no. 4, Springer Nature, 2005, pp. 199–211, doi:10.1007/s10858-005-4425-x.","ama":"Schanda P, Kupče Ē, Brutscher B. SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. Journal of Biomolecular NMR. 2005;33(4):199-211. doi:10.1007/s10858-005-4425-x","apa":"Schanda, P., Kupče, Ē., & Brutscher, B. (2005). SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds. Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-005-4425-x","ieee":"P. Schanda, Ē. Kupče, and B. Brutscher, “SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds,” Journal of Biomolecular NMR, vol. 33, no. 4. Springer Nature, pp. 199–211, 2005.","short":"P. Schanda, Ē. Kupče, B. Brutscher, Journal of Biomolecular NMR 33 (2005) 199–211."},"status":"public","keyword":["Spectroscopy","Biochemistry"],"type":"journal_article","article_type":"original","_id":"8491","volume":33,"date_published":"2005-12-01T00:00:00Z","issue":"4","doi":"10.1007/s10858-005-4425-x","date_created":"2020-09-18T10:13:59Z","page":"199-211","day":"01","publication":"Journal of Biomolecular NMR","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0925-2738","1573-5001"]},"publication_status":"published","year":"2005","month":"12","intvolume":" 33","quality_controlled":"1","publisher":"Springer Nature","oa_version":"None","abstract":[{"text":"Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H–15N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record 1H–15N and 1H−13C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard 1H–15N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme, IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement of one-bond 1H–13C and 1H–15N scalar and residual dipolar coupling constants.","lang":"eng"}]},{"_id":"8492","article_type":"original","type":"journal_article","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"status":"public","date_updated":"2021-01-12T08:19:39Z","citation":{"ama":"Schanda P, Brutscher B. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. Journal of the American Chemical Society. 2005;127(22):8014-8015. doi:10.1021/ja051306e","apa":"Schanda, P., & Brutscher, B. (2005). Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja051306e","ieee":"P. Schanda and B. Brutscher, “Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds,” Journal of the American Chemical Society, vol. 127, no. 22. American Chemical Society, pp. 8014–8015, 2005.","short":"P. Schanda, B. Brutscher, Journal of the American Chemical Society 127 (2005) 8014–8015.","mla":"Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds.” Journal of the American Chemical Society, vol. 127, no. 22, American Chemical Society, 2005, pp. 8014–15, doi:10.1021/ja051306e.","ista":"Schanda P, Brutscher B. 2005. Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds. Journal of the American Chemical Society. 127(22), 8014–8015.","chicago":"Schanda, Paul, and Bernhard Brutscher. “Very Fast Two-Dimensional NMR Spectroscopy for Real-Time Investigation of Dynamic Events in Proteins on the Time Scale of Seconds.” Journal of the American Chemical Society. American Chemical Society, 2005. https://doi.org/10.1021/ja051306e."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_processing_charge":"No","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"}],"title":"Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds","abstract":[{"lang":"eng","text":"We demonstrate for different protein samples that 2D 1H−15N correlation NMR spectra can be recorded in a few seconds of acquisition time using a new band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence experiment. This has enabled us to measure fast hydrogen−deuterium exchange rate constants along the backbone of a small globular protein fragment by real-time 2D NMR."}],"oa_version":"None","quality_controlled":"1","publisher":"American Chemical Society","intvolume":" 127","month":"05","publication_status":"published","year":"2005","publication_identifier":{"issn":["0002-7863","1520-5126"]},"language":[{"iso":"eng"}],"publication":"Journal of the American Chemical Society","day":"14","page":"8014-8015","date_created":"2020-09-18T10:14:05Z","volume":127,"issue":"22","date_published":"2005-05-14T00:00:00Z","doi":"10.1021/ja051306e"},{"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:19:49Z","citation":{"ieee":"J. Bourgain and V. Kaloshin, “On diffusion in high-dimensional Hamiltonian systems,” Journal of Functional Analysis, vol. 229, no. 1. Elsevier, pp. 1–61, 2005.","short":"J. Bourgain, V. Kaloshin, Journal of Functional Analysis 229 (2005) 1–61.","ama":"Bourgain J, Kaloshin V. On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. 2005;229(1):1-61. doi:10.1016/j.jfa.2004.09.006","apa":"Bourgain, J., & Kaloshin, V. (2005). On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2004.09.006","mla":"Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” Journal of Functional Analysis, vol. 229, no. 1, Elsevier, 2005, pp. 1–61, doi:10.1016/j.jfa.2004.09.006.","ista":"Bourgain J, Kaloshin V. 2005. On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. 229(1), 1–61.","chicago":"Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” Journal of Functional Analysis. Elsevier, 2005. https://doi.org/10.1016/j.jfa.2004.09.006."},"title":"On diffusion in high-dimensional Hamiltonian systems","author":[{"first_name":"Jean","full_name":"Bourgain, Jean","last_name":"Bourgain"},{"last_name":"Kaloshin","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"article_processing_charge":"No","_id":"8516","status":"public","keyword":["Analysis"],"article_type":"original","type":"journal_article","day":"01","language":[{"iso":"eng"}],"publication":"Journal of Functional Analysis","publication_identifier":{"issn":["0022-1236"]},"year":"2005","publication_status":"published","date_published":"2005-12-01T00:00:00Z","volume":229,"doi":"10.1016/j.jfa.2004.09.006","issue":"1","date_created":"2020-09-18T10:49:06Z","page":"1-61","oa_version":"None","abstract":[{"lang":"eng","text":"The purpose of this paper is to construct examples of diffusion for E-Hamiltonian perturbations\r\nof completely integrable Hamiltonian systems in 2d-dimensional phase space, with d large.\r\nIn the first part of the paper, simple and explicit examples are constructed illustrating absence\r\nof ‘long-time’ stability for size E Hamiltonian perturbations of quasi-convex integrable systems\r\nalready when the dimension 2d of phase space becomes as large as log 1/E . We first produce\r\nthe example in Gevrey class and then a real analytic one, with some additional work.\r\nIn the second part, we consider again E-Hamiltonian perturbations of completely integrable\r\nHamiltonian system in 2d-dimensional space with E-small but not too small, |E| > exp(−d), with\r\nd the number of degrees of freedom assumed large. It is shown that for a class of analytic\r\ntime-periodic perturbations, there exist linearly diffusing trajectories. The underlying idea for\r\nboth examples is similar and consists in coupling a fixed degree of freedom with a large\r\nnumber of them. The procedure and analytical details are however significantly different. As\r\nmentioned, the construction in Part I is totally elementary while Part II is more involved, relying\r\nin particular on the theory of normally hyperbolic invariant manifolds, methods of generating\r\nfunctions, Aubry–Mather theory, and Mather’s variational methods."}],"month":"12","intvolume":" 229","publisher":"Elsevier","quality_controlled":"1"},{"volume":50,"issue":"3","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf"}],"month":"05","intvolume":" 50","abstract":[{"lang":"eng","text":"Sequence analysis of protein and mitochondrially encoded tRNA genes shows that substitutions\r\nproducing pathogenic effects in humans are often found in normal, healthy individuals from other species.\r\nAnalysis of stability of protein and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations can be neutralized by other, compensatory substitutions that restore the structural stability of the\r\nmolecule. Further study of such substitutions will, hopefully, lead to new methods for curing genetic dis-\r\neases that may be based on the correction of molecule stability as a whole instead of reversing an individual\r\npathogenic mutation."}],"oa_version":"None","pmid":1,"date_updated":"2021-01-12T08:21:01Z","extern":"1","article_type":"original","type":"journal_article","status":"public","_id":"877","page":"389 - 395","date_published":"2005-05-01T00:00:00Z","date_created":"2018-12-11T11:48:58Z","year":"2005","day":"01","publication":"Biofizika","quality_controlled":"1","publisher":"Pleiades Publishing","author":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"}],"publist_id":"6769","external_id":{"pmid":["15977826"]},"article_processing_charge":"No","title":"The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution","citation":{"ista":"Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 50(3), 389–395.","chicago":"Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” Biofizika. Pleiades Publishing, 2005.","apa":"Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. Pleiades Publishing.","ama":"Kondrashov F. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 2005;50(3):389-395.","short":"F. Kondrashov, Biofizika 50 (2005) 389–395.","ieee":"F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005.","mla":"Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publist_id":"6770","author":[{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"title":"In search of the limits of evolution","citation":{"mla":"Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics, vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:10.1038/ng0105-9.","ama":"Kondrashov F. In search of the limits of evolution. Nature Genetics. 2005;37(1):9-10. doi:10.1038/ng0105-9","apa":"Kondrashov, F. (2005). In search of the limits of evolution. Nature Genetics. Nature Publishing Group. https://doi.org/10.1038/ng0105-9","ieee":"F. Kondrashov, “In search of the limits of evolution,” Nature Genetics, vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005.","short":"F. Kondrashov, Nature Genetics 37 (2005) 9–10.","chicago":"Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics. Nature Publishing Group, 2005. https://doi.org/10.1038/ng0105-9.","ista":"Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics. 37(1), 9–10."},"date_updated":"2021-01-12T08:21:02Z","extern":1,"type":"journal_article","status":"public","_id":"878","page":"9 - 10","date_created":"2018-12-11T11:48:59Z","date_published":"2005-01-01T00:00:00Z","volume":37,"issue":"1","doi":"10.1038/ng0105-9","publication_status":"published","year":"2005","publication":"Nature Genetics","day":"01","quality_controlled":0,"publisher":"Nature Publishing Group","intvolume":" 37","month":"01","abstract":[{"lang":"eng","text":"Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions.\n"}]},{"year":"2005","publication_status":"published","publication":"Human Molecular Genetics","day":"15","page":"2415 - 2419","date_created":"2018-12-11T11:49:00Z","volume":14,"date_published":"2005-08-15T00:00:00Z","issue":"16","doi":"10.1093/hmg/ddi243","abstract":[{"text":"Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify ∼90% of all known pathogenic mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively.","lang":"eng"}],"acknowledgement":"The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS.\n","quality_controlled":0,"publisher":"Oxford University Press","intvolume":" 14","month":"08","citation":{"chicago":"Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi243.","ista":"Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.","mla":"Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” Human Molecular Genetics, vol. 14, no. 16, Oxford University Press, 2005, pp. 2415–19, doi:10.1093/hmg/ddi243.","ama":"Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 2005;14(16):2415-2419. doi:10.1093/hmg/ddi243","apa":"Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi243","ieee":"F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” Human Molecular Genetics, vol. 14, no. 16. Oxford University Press, pp. 2415–2419, 2005.","short":"F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419."},"date_updated":"2021-01-12T08:21:10Z","extern":1,"author":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov"}],"publist_id":"6767","title":"Prediction of pathogenic mutations in mitochondrially encoded human tRNAs","_id":"882","type":"journal_article","status":"public"},{"day":"01","publication":"Biofizika","language":[{"iso":"eng"}],"publication_status":"published","year":"2005","date_published":"2005-05-01T00:00:00Z","issue":"3","volume":50,"date_created":"2018-12-11T11:48:59Z","page":"396 - 403","pmid":1,"oa_version":"None","abstract":[{"text":"Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY). Such evolution sheds light on the relationship between structure and function of tRNA molecules and its impact on the patterns of molecular evolution.","lang":"eng"}],"month":"05","intvolume":" 50","publisher":"Pleiades Publishing","quality_controlled":"1","main_file_link":[{"url":"http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf"}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” Biofizika. Pleiades Publishing, 2005.","ista":"Kondrashov F. 2005. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 50(3), 396–403.","mla":"Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403.","apa":"Kondrashov, F. (2005). The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. Pleiades Publishing.","ama":"Kondrashov F. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 2005;50(3):396-403.","short":"F. Kondrashov, Biofizika 50 (2005) 396–403.","ieee":"F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005."},"date_updated":"2021-01-12T08:21:07Z","title":"The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus","author":[{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"}],"publist_id":"6768","article_processing_charge":"No","external_id":{"pmid":["15977827"]},"_id":"880","status":"public","type":"journal_article"},{"date_published":"2005-02-10T00:00:00Z","issue":"7026","volume":433,"doi":"10.1038/nature03306","date_created":"2018-12-11T11:49:03Z","page":"633 - 638","day":"10","publication":"Nature","year":"2005","publication_status":"published","month":"02","intvolume":" 433","quality_controlled":0,"publisher":"Nature Publishing Group","acknowledgement":"S.S. and I.A.A. were supported by the Genome Canada Foundation.","abstract":[{"lang":"eng","text":"Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day."}],"title":"A universal trend of amino acid gain and loss in protein evolution","publist_id":"6757","author":[{"full_name":"Jordan, Ingo K","last_name":"Jordan","first_name":"Ingo"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"last_name":"Adzhubeǐ","full_name":"Adzhubeǐ, Ivan A","first_name":"Ivan"},{"first_name":"Yuri","full_name":"Wolf, Yuri I","last_name":"Wolf"},{"first_name":"Eugene","full_name":"Koonin, Eugene V","last_name":"Koonin"},{"first_name":"Alexey","last_name":"Kondrashov","full_name":"Kondrashov, Alexey S"},{"first_name":"Shamil","last_name":"Sunyaev","full_name":"Sunyaev, Shamil R"}],"extern":1,"citation":{"chicago":"Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin, Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature. Nature Publishing Group, 2005. https://doi.org/10.1038/nature03306.","ista":"Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature. 433(7026), 633–638.","mla":"Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” Nature, vol. 433, no. 7026, Nature Publishing Group, 2005, pp. 633–38, doi:10.1038/nature03306.","short":"I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov, S. Sunyaev, Nature 433 (2005) 633–638.","ieee":"I. Jordan et al., “A universal trend of amino acid gain and loss in protein evolution,” Nature, vol. 433, no. 7026. Nature Publishing Group, pp. 633–638, 2005.","ama":"Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid gain and loss in protein evolution. Nature. 2005;433(7026):633-638. doi:10.1038/nature03306","apa":"Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov, A., & Sunyaev, S. (2005). A universal trend of amino acid gain and loss in protein evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature03306"},"date_updated":"2021-01-12T08:21:23Z","status":"public","type":"journal_article","_id":"893"},{"_id":"9529","status":"public","type":"journal_article","article_type":"review","extern":"1","date_updated":"2021-12-14T09:13:13Z","department":[{"_id":"DaZi"}],"pmid":1,"oa_version":"None","abstract":[{"lang":"eng","text":"Eukaryotic organisms have the remarkable ability to inherit states of gene activity without altering the underlying DNA sequence. This epigenetic inheritance can persist over thousands of years, providing an alternative to genetic mutations as a substrate for natural selection. Epigenetic inheritance might be propagated by differences in DNA methylation, post-translational histone modifications, and deposition of histone variants. Mounting evidence also indicates that small interfering RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining states of gene activity. Much of the epigenetic machinery of many organisms, including Arabidopsis, appears to be directed at silencing viruses and transposable elements, with epigenetic regulation of endogenous genes being mostly derived from such processes."}],"intvolume":" 15","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0959-437X"]},"volume":15,"issue":"5","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Zilberman, D., & Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2005.07.002","ama":"Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 2005;15(5):557-562. doi:10.1016/j.gde.2005.07.002","short":"D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15 (2005) 557–562.","ieee":"D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective silence,” Current Opinion in Genetics and Development, vol. 15, no. 5. Elsevier, pp. 557–562, 2005.","mla":"Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” Current Opinion in Genetics and Development, vol. 15, no. 5, Elsevier, 2005, pp. 557–62, doi:10.1016/j.gde.2005.07.002.","ista":"Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 15(5), 557–562.","chicago":"Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” Current Opinion in Genetics and Development. Elsevier, 2005. https://doi.org/10.1016/j.gde.2005.07.002."},"title":"Epigenetic inheritance in Arabidopsis: Selective silence","external_id":{"pmid":["16085410"]},"article_processing_charge":"No","author":[{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"}],"quality_controlled":"1","publisher":"Elsevier","publication":"Current Opinion in Genetics and Development","year":"2005","date_created":"2021-06-08T09:05:56Z","date_published":"2005-10-01T00:00:00Z","doi":"10.1016/j.gde.2005.07.002","page":"557-562"},{"publisher":"Wiley","quality_controlled":"1","date_created":"2023-08-01T10:38:01Z","date_published":"2005-06-24T00:00:00Z","doi":"10.1002/adma.200402086","page":"1361-1365","publication":"Advanced Materials","day":"24","year":"2005","title":"Cutting into solids with micropatterned gels","external_id":{"pmid":["34412440"]},"article_processing_charge":"No","author":[{"first_name":"S. K.","full_name":"Smoukov, S. K.","last_name":"Smoukov"},{"full_name":"Bishop, K. J. M.","last_name":"Bishop","first_name":"K. J. M."},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"},{"first_name":"C. J.","last_name":"Campbell","full_name":"Campbell, C. J."},{"full_name":"Grzybowski, B. A.","last_name":"Grzybowski","first_name":"B. A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Smoukov SK, Bishop KJM, Klajn R, Campbell CJ, Grzybowski BA. 2005. Cutting into solids with micropatterned gels. Advanced Materials. 17(11), 1361–1365.","chicago":"Smoukov, S. K., K. J. M. Bishop, Rafal Klajn, C. J. Campbell, and B. A. Grzybowski. “Cutting into Solids with Micropatterned Gels.” Advanced Materials. Wiley, 2005. https://doi.org/10.1002/adma.200402086.","ama":"Smoukov SK, Bishop KJM, Klajn R, Campbell CJ, Grzybowski BA. Cutting into solids with micropatterned gels. Advanced Materials. 2005;17(11):1361-1365. doi:10.1002/adma.200402086","apa":"Smoukov, S. K., Bishop, K. J. M., Klajn, R., Campbell, C. J., & Grzybowski, B. A. (2005). Cutting into solids with micropatterned gels. Advanced Materials. Wiley. https://doi.org/10.1002/adma.200402086","ieee":"S. K. Smoukov, K. J. M. Bishop, R. Klajn, C. J. Campbell, and B. A. Grzybowski, “Cutting into solids with micropatterned gels,” Advanced Materials, vol. 17, no. 11. Wiley, pp. 1361–1365, 2005.","short":"S.K. Smoukov, K.J.M. Bishop, R. Klajn, C.J. Campbell, B.A. Grzybowski, Advanced Materials 17 (2005) 1361–1365.","mla":"Smoukov, S. K., et al. “Cutting into Solids with Micropatterned Gels.” Advanced Materials, vol. 17, no. 11, Wiley, 2005, pp. 1361–65, doi:10.1002/adma.200402086."},"intvolume":" 17","month":"06","scopus_import":"1","oa_version":"None","pmid":1,"abstract":[{"text":"Hydrogel stamps can microstructure solid surfaces, i.e., modify the surface topology of metals, glasses, and crystals. It is demonstrated that stamps soaked in an appropriate etchant can remove material with micrometer-scale precision. The Figure shows an array of concentric circles etched in glass using the immersion wet stamping process described (scale bar: 500 μm).","lang":"eng"}],"volume":17,"issue":"11","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0935-9648"],"eissn":["1521-4095"]},"keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"status":"public","article_type":"original","type":"journal_article","_id":"13431","extern":"1","date_updated":"2023-08-08T11:53:16Z"},{"extern":"1","date_updated":"2023-08-08T12:39:52Z","_id":"13433","status":"public","keyword":["Organic Chemistry"],"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1385-2728"],"eissn":["1875-5348"]},"publication_status":"published","issue":"18","volume":8,"oa_version":"None","abstract":[{"lang":"eng","text":"Self-assembled monolayers (SAMs) of alkane thiols on gold and other metals are versatile constructs with which to study interfacial phenomena and reactions at surfaces. Surface properties of SAMs - e.g., wettability, stability in diverse environments, propensity to interact with or to resist adsorption of macromolecules -- depend on and can be controlled flexibly by the properties of the functional (head) groups in the w position of the alkyl chain. SAMs provide a basis for many important scientific and technological applications, ranging from micropatterning methods, through sensing, to biological recognition. Despite their importance, the literature on SAMs and the synthesis of molecules that constitute them remains scattered and often conflicting. The purpose of this Review is (i) to summarize the applications and physical properties of SAMs and (ii) to systematize the strategies of synthesis of ω-functionalized alkane thiols. Generic retrosynthetic scheme is developed that allows efficient synthetic planning. Issues related to the selection of appropriate protecting groups and the ways of introduction of the thiol functionality are discussed in detail, and illustrated with examples of syntheses of several complex alkane thiols."}],"month":"12","intvolume":" 8","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Witt, Dariusz, Rafal Klajn, Piotr Barski, and Bartosz Grzybowski. “Applications, Properties and Synthesis of w-Functionalized n-Alkanethiols and Disulfides - the Building Blocks of Self-Assembled Monolayers.” Current Organic Chemistry. Bentham Science, 2005. https://doi.org/10.2174/1385272043369421.","ista":"Witt D, Klajn R, Barski P, Grzybowski B. 2005. Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers. Current Organic Chemistry. 8(18), 1763–1797.","mla":"Witt, Dariusz, et al. “Applications, Properties and Synthesis of w-Functionalized n-Alkanethiols and Disulfides - the Building Blocks of Self-Assembled Monolayers.” Current Organic Chemistry, vol. 8, no. 18, Bentham Science, 2005, pp. 1763–97, doi:10.2174/1385272043369421.","ieee":"D. Witt, R. Klajn, P. Barski, and B. Grzybowski, “Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers,” Current Organic Chemistry, vol. 8, no. 18. Bentham Science, pp. 1763–1797, 2005.","short":"D. Witt, R. Klajn, P. Barski, B. Grzybowski, Current Organic Chemistry 8 (2005) 1763–1797.","apa":"Witt, D., Klajn, R., Barski, P., & Grzybowski, B. (2005). Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers. Current Organic Chemistry. Bentham Science. https://doi.org/10.2174/1385272043369421","ama":"Witt D, Klajn R, Barski P, Grzybowski B. Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers. Current Organic Chemistry. 2005;8(18):1763-1797. doi:10.2174/1385272043369421"},"title":"Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers","author":[{"last_name":"Witt","full_name":"Witt, Dariusz","first_name":"Dariusz"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","last_name":"Klajn","full_name":"Klajn, Rafal"},{"full_name":"Barski, Piotr","last_name":"Barski","first_name":"Piotr"},{"first_name":"Bartosz","last_name":"Grzybowski","full_name":"Grzybowski, Bartosz"}],"article_processing_charge":"No","day":"01","publication":"Current Organic Chemistry","year":"2005","doi":"10.2174/1385272043369421","date_published":"2005-12-01T00:00:00Z","date_created":"2023-08-01T10:38:58Z","page":"1763-1797","publisher":"Bentham Science","quality_controlled":"1"},{"keyword":["Electrochemistry","Spectroscopy","Surfaces and Interfaces","Condensed Matter Physics","General Materials Science"],"status":"public","article_type":"original","type":"journal_article","_id":"13432","extern":"1","date_updated":"2023-08-08T12:15:48Z","intvolume":" 21","month":"01","scopus_import":"1","pmid":1,"oa_version":"None","abstract":[{"text":"A new experimental technique is described that uses reaction−diffusion phenomena as a means of one-step microfabrication of complex, multilevel surface reliefs. Thin films of dry gelatin doped with potassium hexacyanoferrate are chemically micropatterned with a solution of silver nitrate delivered from an agarose stamp. Precipitation reaction between the two salts causes the surface to deform. The mechanism of surface deformation is shown to involve a sequence of reactions, diffusion, and gel swelling/contraction. This mechanism is established experimentally and provides a basis of a theoretical lattice-gas model that allows prediction surface topographies emerging from arbitrary geometries of the stamped features. The usefulness of the technique is demonstrated by using it to rapidly prepare two types of mold for passive microfluidic mixers.","lang":"eng"}],"issue":"1","volume":21,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1520-5827"],"issn":["0743-7463"]},"title":"One-step multilevel microfabrication by reaction−diffusion","article_processing_charge":"No","external_id":{"pmid":["15620333"]},"author":[{"full_name":"Campbell, Christopher J.","last_name":"Campbell","first_name":"Christopher J."},{"last_name":"Klajn","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"},{"last_name":"Fialkowski","full_name":"Fialkowski, Marcin","first_name":"Marcin"},{"last_name":"Grzybowski","full_name":"Grzybowski, Bartosz A.","first_name":"Bartosz A."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Campbell, C. J., Klajn, R., Fialkowski, M., & Grzybowski, B. A. (2005). One-step multilevel microfabrication by reaction−diffusion. Langmuir. American Chemical Society. https://doi.org/10.1021/la0487747","ama":"Campbell CJ, Klajn R, Fialkowski M, Grzybowski BA. One-step multilevel microfabrication by reaction−diffusion. Langmuir. 2005;21(1):418-423. doi:10.1021/la0487747","short":"C.J. Campbell, R. Klajn, M. Fialkowski, B.A. Grzybowski, Langmuir 21 (2005) 418–423.","ieee":"C. J. Campbell, R. Klajn, M. Fialkowski, and B. A. Grzybowski, “One-step multilevel microfabrication by reaction−diffusion,” Langmuir, vol. 21, no. 1. American Chemical Society, pp. 418–423, 2005.","mla":"Campbell, Christopher J., et al. “One-Step Multilevel Microfabrication by Reaction−diffusion.” Langmuir, vol. 21, no. 1, American Chemical Society, 2005, pp. 418–23, doi:10.1021/la0487747.","ista":"Campbell CJ, Klajn R, Fialkowski M, Grzybowski BA. 2005. One-step multilevel microfabrication by reaction−diffusion. Langmuir. 21(1), 418–423.","chicago":"Campbell, Christopher J., Rafal Klajn, Marcin Fialkowski, and Bartosz A. Grzybowski. “One-Step Multilevel Microfabrication by Reaction−diffusion.” Langmuir. American Chemical Society, 2005. https://doi.org/10.1021/la0487747."},"quality_controlled":"1","publisher":"American Chemical Society","date_created":"2023-08-01T10:38:29Z","date_published":"2005-01-21T00:00:00Z","doi":"10.1021/la0487747","page":"418-423","publication":"Langmuir","day":"21","year":"2005"}]