[{"extern":1,"intvolume":"      5054","_id":"4527","quality_controlled":0,"acknowledgement":"Supported in part by the Swiss National Science Foundation (grant 205321-111840).","publist_id":"196","doi":"10.1007/978-3-540-68413-8_2","publisher":"Springer","alternative_title":["LNCS"],"author":[{"last_name":"Fisher","first_name":"Jasmin","full_name":"Fisher, Jasmin"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"id":"3B43276C-F248-11E8-B48F-1D18A9856A87","full_name":"Maria Mateescu","last_name":"Mateescu","first_name":"Maria"},{"full_name":"Piterman, Nir","first_name":"Nir","last_name":"Piterman"}],"publication_status":"published","citation":{"apa":"Fisher, J., Henzinger, T. A., Mateescu, M., &#38; Piterman, N. (2008). Bounded asynchrony: Concurrency for modeling cell-cell interactions (Vol. 5054, pp. 17–32). Presented at the FMSB: Formal Methods in Systems Biology, Springer. <a href=\"https://doi.org/10.1007/978-3-540-68413-8_2\">https://doi.org/10.1007/978-3-540-68413-8_2</a>","ama":"Fisher J, Henzinger TA, Mateescu M, Piterman N. Bounded asynchrony: Concurrency for modeling cell-cell interactions. In: Vol 5054. Springer; 2008:17-32. doi:<a href=\"https://doi.org/10.1007/978-3-540-68413-8_2\">10.1007/978-3-540-68413-8_2</a>","mla":"Fisher, Jasmin, et al. <i>Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions</i>. Vol. 5054, Springer, 2008, pp. 17–32, doi:<a href=\"https://doi.org/10.1007/978-3-540-68413-8_2\">10.1007/978-3-540-68413-8_2</a>.","ieee":"J. Fisher, T. A. Henzinger, M. Mateescu, and N. Piterman, “Bounded asynchrony: Concurrency for modeling cell-cell interactions,” presented at the FMSB: Formal Methods in Systems Biology, 2008, vol. 5054, pp. 17–32.","short":"J. Fisher, T.A. Henzinger, M. Mateescu, N. Piterman, in:, Springer, 2008, pp. 17–32.","ista":"Fisher J, Henzinger TA, Mateescu M, Piterman N. 2008. Bounded asynchrony: Concurrency for modeling cell-cell interactions. FMSB: Formal Methods in Systems Biology, LNCS, vol. 5054, 17–32.","chicago":"Fisher, Jasmin, Thomas A Henzinger, Maria Mateescu, and Nir Piterman. “Bounded Asynchrony: Concurrency for Modeling Cell-Cell Interactions,” 5054:17–32. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-68413-8_2\">https://doi.org/10.1007/978-3-540-68413-8_2</a>."},"year":"2008","volume":5054,"month":"05","type":"conference","abstract":[{"lang":"eng","text":"We introduce bounded asynchrony, a notion of concurrency tailored to the modeling of biological cell-cell interactions. Bounded asynchrony is the result of a scheduler that bounds the number of steps that one process gets ahead of other processes; this allows the components of a system to move independently while keeping them coupled. Bounded asynchrony accurately reproduces the experimental observations made about certain cell-cell interactions: its constrained nondeterminism captures the variability observed in cells that, although equally potent, assume distinct fates. Real-life cells are not “scheduled”, but we show that distributed real-time behavior can lead to component interactions that are observationally equivalent to bounded asynchrony; this provides a possible mechanistic explanation for the phenomena observed during cell fate specification.\nWe use model checking to determine cell fates. The nondeterminism of bounded asynchrony causes state explosion during model checking, but partial-order methods are not directly applicable. We present a new algorithm that reduces the number of states that need to be explored: our optimization takes advantage of the bounded-asynchronous progress and the spatially local interactions of components that model cells. We compare our own communication-based reduction with partial-order reduction (on a restricted form of bounded asynchrony) and experiments illustrate that our algorithm leads to significant savings."}],"day":"26","page":"17 - 32","conference":{"name":"FMSB: Formal Methods in Systems Biology"},"title":"Bounded asynchrony: Concurrency for modeling cell-cell interactions","date_updated":"2021-01-12T07:59:27Z","status":"public","date_created":"2018-12-11T12:09:19Z","date_published":"2008-05-26T00:00:00Z","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/bounded_asynchrony.pdf","open_access":"0"}]},{"date_published":"2008-06-01T00:00:00Z","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/equivalence_of_labeled_markov_chains.pdf","open_access":"0"}],"date_created":"2018-12-11T12:09:20Z","issue":"3","date_updated":"2021-01-12T07:59:30Z","status":"public","publication":"International Journal of Foundations of Computer Science","title":"Equivalence of labeled Markov chains","page":"549 - 563","day":"01","abstract":[{"lang":"eng","text":"We consider the equivalence problem for labeled Markov chains (LMCs), where each state is labeled with an observation. Two LMCs are equivalent if every finite sequence of observations has the same probability of occurrence in the two LMCs. We show that equivalence can be decided in polynomial time, using a reduction to the equivalence problem for probabilistic automata, which is known to be solvable in polynomial time. We provide an alternative algorithm to solve the equivalence problem, which is based on a new definition of bisimulation for probabilistic automata. We also extend the technique to decide the equivalence of weighted probabilistic automata."}],"type":"journal_article","month":"06","volume":19,"year":"2008","citation":{"ista":"Doyen L, Henzinger TA, Raskin J. 2008. Equivalence of labeled Markov chains. International Journal of Foundations of Computer Science. 19(3), 549–563.","chicago":"Doyen, Laurent, Thomas A Henzinger, and Jean Raskin. “Equivalence of Labeled Markov Chains.” <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing, 2008. <a href=\"https://doi.org/10.1142/S0129054108005814 \">https://doi.org/10.1142/S0129054108005814 </a>.","apa":"Doyen, L., Henzinger, T. A., &#38; Raskin, J. (2008). Equivalence of labeled Markov chains. <i>International Journal of Foundations of Computer Science</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129054108005814 \">https://doi.org/10.1142/S0129054108005814 </a>","ama":"Doyen L, Henzinger TA, Raskin J. Equivalence of labeled Markov chains. <i>International Journal of Foundations of Computer Science</i>. 2008;19(3):549-563. doi:<a href=\"https://doi.org/10.1142/S0129054108005814 \">10.1142/S0129054108005814 </a>","mla":"Doyen, Laurent, et al. “Equivalence of Labeled Markov Chains.” <i>International Journal of Foundations of Computer Science</i>, vol. 19, no. 3, World Scientific Publishing, 2008, pp. 549–63, doi:<a href=\"https://doi.org/10.1142/S0129054108005814 \">10.1142/S0129054108005814 </a>.","ieee":"L. Doyen, T. A. Henzinger, and J. Raskin, “Equivalence of labeled Markov chains,” <i>International Journal of Foundations of Computer Science</i>, vol. 19, no. 3. World Scientific Publishing, pp. 549–563, 2008.","short":"L. Doyen, T.A. Henzinger, J. Raskin, International Journal of Foundations of Computer Science 19 (2008) 549–563."},"author":[{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Raskin","first_name":"Jean","full_name":"Raskin, Jean-François"}],"publication_status":"published","publisher":"World Scientific Publishing","doi":"10.1142/S0129054108005814 ","publist_id":"192","_id":"4532","quality_controlled":0,"intvolume":"        19","extern":1},{"_id":"4533","quality_controlled":0,"extern":1,"publication_status":"published","author":[{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger"},{"last_name":"Jobstmann","first_name":"Barbara","full_name":"Jobstmann, Barbara"},{"first_name":"Tatjana","last_name":"Petrov","orcid":"0000-0002-9041-0905","full_name":"Tatjana Petrov","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"publisher":"ACM","doi":"10.1145/1450058.1450070","publist_id":"193","type":"conference","month":"10","year":"2008","citation":{"apa":"Doyen, L., Henzinger, T. A., Jobstmann, B., &#38; Petrov, T. (2008). Interface theories with component reuse (pp. 79–88). Presented at the EMSOFT: Embedded Software , ACM. <a href=\"https://doi.org/10.1145/1450058.1450070\">https://doi.org/10.1145/1450058.1450070</a>","ama":"Doyen L, Henzinger TA, Jobstmann B, Petrov T. Interface theories with component reuse. In: ACM; 2008:79-88. doi:<a href=\"https://doi.org/10.1145/1450058.1450070\">10.1145/1450058.1450070</a>","short":"L. Doyen, T.A. Henzinger, B. Jobstmann, T. Petrov, in:, ACM, 2008, pp. 79–88.","ieee":"L. Doyen, T. A. Henzinger, B. Jobstmann, and T. Petrov, “Interface theories with component reuse,” presented at the EMSOFT: Embedded Software , 2008, pp. 79–88.","mla":"Doyen, Laurent, et al. <i>Interface Theories with Component Reuse</i>. ACM, 2008, pp. 79–88, doi:<a href=\"https://doi.org/10.1145/1450058.1450070\">10.1145/1450058.1450070</a>.","ista":"Doyen L, Henzinger TA, Jobstmann B, Petrov T. 2008. Interface theories with component reuse. EMSOFT: Embedded Software , 79–88.","chicago":"Doyen, Laurent, Thomas A Henzinger, Barbara Jobstmann, and Tatjana Petrov. “Interface Theories with Component Reuse,” 79–88. ACM, 2008. <a href=\"https://doi.org/10.1145/1450058.1450070\">https://doi.org/10.1145/1450058.1450070</a>."},"main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/interface_theories_with_component_reuse.pdf","open_access":"0"}],"date_published":"2008-10-01T00:00:00Z","date_created":"2018-12-11T12:09:21Z","status":"public","date_updated":"2021-01-12T07:59:30Z","title":"Interface theories with component reuse","conference":{"name":"EMSOFT: Embedded Software "},"page":"79 - 88","day":"01","abstract":[{"text":"Interface theories have been proposed to support incremental design and independent implementability. Incremental design means that the compatibility checking of interfaces can proceed for partial system descriptions, without knowing the interfaces of all components. Independent implementability means that compatible interfaces can be refined separately, maintaining compatibility. We show that these interface theories provide no formal support for component reuse, meaning that the same component cannot be used to implement several different interfaces in a design. We add a new operation to interface theories in order to support such reuse. For example, different interfaces for the same component may refer to different aspects such as functionality, timing, and power consumption. We give both stateless and stateful examples for interface theories with component reuse. To illustrate component reuse in interface-based design, we show how the stateful theory provides a natural framework for specifying and refining PCI bus clients.","lang":"eng"}]},{"day":"31","abstract":[{"lang":"eng","text":"A stochastic graph game is played by two players on a game graph with probabilistic transitions. We consider stochastic graph games with ω-regular winning conditions specified as parity objectives, and mean-payoff (or limit-average) objectives. These games lie in NP ∩ coNP. We present a polynomial-time Turing reduction of stochastic parity games to stochastic mean-payoff games."}],"title":"Reduction of stochastic parity to stochastic mean-payoff games","publication":"Information Processing Letters","page":"1 - 7","status":"public","date_updated":"2021-01-12T07:59:30Z","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/reduction_of_stochastic_parity_to_stochastic_mean-payoff_games.pdf","open_access":"0"}],"date_published":"2008-03-31T00:00:00Z","issue":"1","date_created":"2018-12-11T12:09:21Z","citation":{"ista":"Chatterjee K, Henzinger TA. 2008. Reduction of stochastic parity to stochastic mean-payoff games. Information Processing Letters. 106(1), 1–7.","chicago":"Chatterjee, Krishnendu, and Thomas A Henzinger. “Reduction of Stochastic Parity to Stochastic Mean-Payoff Games.” <i>Information Processing Letters</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.ipl.2007.08.035\">https://doi.org/10.1016/j.ipl.2007.08.035</a>.","apa":"Chatterjee, K., &#38; Henzinger, T. A. (2008). Reduction of stochastic parity to stochastic mean-payoff games. <i>Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2007.08.035\">https://doi.org/10.1016/j.ipl.2007.08.035</a>","ama":"Chatterjee K, Henzinger TA. Reduction of stochastic parity to stochastic mean-payoff games. <i>Information Processing Letters</i>. 2008;106(1):1-7. doi:<a href=\"https://doi.org/10.1016/j.ipl.2007.08.035\">10.1016/j.ipl.2007.08.035</a>","mla":"Chatterjee, Krishnendu, and Thomas A. Henzinger. “Reduction of Stochastic Parity to Stochastic Mean-Payoff Games.” <i>Information Processing Letters</i>, vol. 106, no. 1, Elsevier, 2008, pp. 1–7, doi:<a href=\"https://doi.org/10.1016/j.ipl.2007.08.035\">10.1016/j.ipl.2007.08.035</a>.","ieee":"K. Chatterjee and T. A. Henzinger, “Reduction of stochastic parity to stochastic mean-payoff games,” <i>Information Processing Letters</i>, vol. 106, no. 1. Elsevier, pp. 1–7, 2008.","short":"K. Chatterjee, T.A. Henzinger, Information Processing Letters 106 (2008) 1–7."},"year":"2008","volume":106,"type":"journal_article","month":"03","doi":"10.1016/j.ipl.2007.08.035","publist_id":"188","publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"}],"intvolume":"       106","extern":1,"_id":"4534","quality_controlled":0},{"type":"conference","month":"01","year":"2008","citation":{"chicago":"Chatterjee, Krishnendu, Arkadeb Ghosal, Thomas A Henzinger, Daniel Iercan, Christoph Kirsch, Claudio Pinello, and Alberto Sangiovanni Vincentelli. “Logical Reliability of Interacting Real-Time Tasks,” 909–14. IEEE, 2008. <a href=\"https://doi.org/10.1145/1403375.1403595\">https://doi.org/10.1145/1403375.1403595</a>.","ista":"Chatterjee K, Ghosal A, Henzinger TA, Iercan D, Kirsch C, Pinello C, Sangiovanni Vincentelli A. 2008. Logical reliability of interacting real-time tasks. DATE: Design, Automation and Test in Europe, 909–914.","ieee":"K. Chatterjee <i>et al.</i>, “Logical reliability of interacting real-time tasks,” presented at the DATE: Design, Automation and Test in Europe, 2008, pp. 909–914.","mla":"Chatterjee, Krishnendu, et al. <i>Logical Reliability of Interacting Real-Time Tasks</i>. IEEE, 2008, pp. 909–14, doi:<a href=\"https://doi.org/10.1145/1403375.1403595\">10.1145/1403375.1403595</a>.","short":"K. Chatterjee, A. Ghosal, T.A. Henzinger, D. Iercan, C. Kirsch, C. Pinello, A. Sangiovanni Vincentelli, in:, IEEE, 2008, pp. 909–914.","ama":"Chatterjee K, Ghosal A, Henzinger TA, et al. Logical reliability of interacting real-time tasks. In: IEEE; 2008:909-914. doi:<a href=\"https://doi.org/10.1145/1403375.1403595\">10.1145/1403375.1403595</a>","apa":"Chatterjee, K., Ghosal, A., Henzinger, T. A., Iercan, D., Kirsch, C., Pinello, C., &#38; Sangiovanni Vincentelli, A. (2008). Logical reliability of interacting real-time tasks (pp. 909–914). Presented at the DATE: Design, Automation and Test in Europe, IEEE. <a href=\"https://doi.org/10.1145/1403375.1403595\">https://doi.org/10.1145/1403375.1403595</a>"},"date_published":"2008-01-01T00:00:00Z","main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/%7Etah/Publications/logical_reliability_of_interacting_real-time_tasks.pdf"}],"date_created":"2018-12-11T12:09:25Z","date_updated":"2021-01-12T07:59:36Z","status":"public","title":"Logical reliability of interacting real-time tasks","conference":{"name":"DATE: Design, Automation and Test in Europe"},"page":"909 - 914","day":"01","abstract":[{"text":"We propose the notion of logical reliability for real-time program tasks that interact through periodically updated program variables. We describe a reliability analysis that checks if the given short-term (e.g., single-period) reliability of a program variable update in an implementation is sufficient to meet the logical reliability requirement (of the program variable) in the long run. We then present a notion of design by refinement where a task can be refined by another task that writes to program variables with less logical reliability. The resulting analysis can be combined with an incremental schedulability analysis for interacting real-time tasks proposed earlier for the Hierarchical Timing Language (HTL), a coordination language for distributed real-time systems. We implemented a logical-reliability-enhanced prototype of the compiler and runtime infrastructure for HTL.","lang":"eng"}],"quality_controlled":0,"_id":"4546","extern":1,"author":[{"full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Arkadeb","last_name":"Ghosal","full_name":"Ghosal, Arkadeb"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Daniel","last_name":"Iercan","full_name":"Iercan, Daniel"},{"full_name":"Kirsch, Christoph M","last_name":"Kirsch","first_name":"Christoph"},{"full_name":"Pinello, Claudio","first_name":"Claudio","last_name":"Pinello"},{"last_name":"Sangiovanni Vincentelli","first_name":"Alberto","full_name":"Sangiovanni-Vincentelli, Alberto"}],"publication_status":"published","publisher":"IEEE","doi":"10.1145/1403375.1403595","publist_id":"171"},{"extern":1,"intvolume":"        37","quality_controlled":0,"_id":"4548","publist_id":"168","doi":"10.1007/s00182-007-0110-5","publisher":"Springer","publication_status":"published","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Ritankar","last_name":"Majumdar","full_name":"Majumdar, Ritankar S"},{"orcid":"0000−0002−2985−7724","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"}],"citation":{"apa":"Chatterjee, K., Majumdar, R., &#38; Henzinger, T. A. (2008). Stochastic limit-average games are in EXPTIME. <i>International Journal of Game Theory</i>. Springer. <a href=\"https://doi.org/10.1007/s00182-007-0110-5\">https://doi.org/10.1007/s00182-007-0110-5</a>","ama":"Chatterjee K, Majumdar R, Henzinger TA. Stochastic limit-average games are in EXPTIME. <i>International Journal of Game Theory</i>. 2008;37(2):219-234. doi:<a href=\"https://doi.org/10.1007/s00182-007-0110-5\">10.1007/s00182-007-0110-5</a>","short":"K. Chatterjee, R. Majumdar, T.A. Henzinger, International Journal of Game Theory 37 (2008) 219–234.","mla":"Chatterjee, Krishnendu, et al. “Stochastic Limit-Average Games Are in EXPTIME.” <i>International Journal of Game Theory</i>, vol. 37, no. 2, Springer, 2008, pp. 219–34, doi:<a href=\"https://doi.org/10.1007/s00182-007-0110-5\">10.1007/s00182-007-0110-5</a>.","ieee":"K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Stochastic limit-average games are in EXPTIME,” <i>International Journal of Game Theory</i>, vol. 37, no. 2. Springer, pp. 219–234, 2008.","ista":"Chatterjee K, Majumdar R, Henzinger TA. 2008. Stochastic limit-average games are in EXPTIME. International Journal of Game Theory. 37(2), 219–234.","chicago":"Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Stochastic Limit-Average Games Are in EXPTIME.” <i>International Journal of Game Theory</i>. Springer, 2008. <a href=\"https://doi.org/10.1007/s00182-007-0110-5\">https://doi.org/10.1007/s00182-007-0110-5</a>."},"year":"2008","volume":37,"month":"01","type":"journal_article","abstract":[{"text":"The value of a finite-state two-player zero-sum stochastic game with limit-average payoff can be approximated to within ε in time exponential in a polynomial in the size of the game times polynomial in logarithmic in 1/ε, for all ε &gt; 0.","lang":"eng"}],"day":"01","page":"219 - 234","publication":"International Journal of Game Theory","title":"Stochastic limit-average games are in EXPTIME","date_updated":"2021-01-12T07:59:37Z","status":"public","issue":"2","date_created":"2018-12-11T12:09:25Z","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/stochastic_limit-average_games_are_in_exptime.pdf","open_access":"0"}],"date_published":"2008-01-01T00:00:00Z"},{"abstract":[{"lang":"eng","text":"We present and evaluate a framework and tool for combining multiple program analyses which allows the dynamic (on-line) adjustment of the precision of each analysis depending on the accumulated results. For example, the explicit tracking of the values of a variable may be switched off in favor of a predicate abstraction when and where the number of different variable values that have been encountered has exceeded a specified threshold. The method is evaluated on verifying the SSH client/server software and shows significant gains compared with predicate abstraction-based model checking."}],"day":"07","page":"29 - 38","conference":{"name":"ASE: Automated Software Engineering"},"title":"Program analysis with dynamic change of precision","date_updated":"2021-01-12T07:59:46Z","status":"public","date_created":"2018-12-11T12:09:31Z","main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/%7Etah/Publications/program_analysis_with_dynamic_change_of_precision.pdf"}],"date_published":"2008-10-07T00:00:00Z","citation":{"short":"D. Beyer, T.A. Henzinger, G. Théoduloz, in:, ACM, 2008, pp. 29–38.","ieee":"D. Beyer, T. A. Henzinger, and G. Théoduloz, “Program analysis with dynamic change of precision,” presented at the ASE: Automated Software Engineering, 2008, pp. 29–38.","mla":"Beyer, Dirk, et al. <i>Program Analysis with Dynamic Change of Precision</i>. ACM, 2008, pp. 29–38, doi:<a href=\"https://doi.org/10.1109/ASE.2008.13\">10.1109/ASE.2008.13</a>.","apa":"Beyer, D., Henzinger, T. A., &#38; Théoduloz, G. (2008). Program analysis with dynamic change of precision (pp. 29–38). Presented at the ASE: Automated Software Engineering, ACM. <a href=\"https://doi.org/10.1109/ASE.2008.13\">https://doi.org/10.1109/ASE.2008.13</a>","ama":"Beyer D, Henzinger TA, Théoduloz G. Program analysis with dynamic change of precision. In: ACM; 2008:29-38. doi:<a href=\"https://doi.org/10.1109/ASE.2008.13\">10.1109/ASE.2008.13</a>","chicago":"Beyer, Dirk, Thomas A Henzinger, and Grégory Théoduloz. “Program Analysis with Dynamic Change of Precision,” 29–38. ACM, 2008. <a href=\"https://doi.org/10.1109/ASE.2008.13\">https://doi.org/10.1109/ASE.2008.13</a>.","ista":"Beyer D, Henzinger TA, Théoduloz G. 2008. Program analysis with dynamic change of precision. ASE: Automated Software Engineering, 29–38."},"year":"2008","month":"10","type":"conference","publist_id":"140","doi":"10.1109/ASE.2008.13","publisher":"ACM","author":[{"full_name":"Beyer, Dirk","first_name":"Dirk","last_name":"Beyer"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Théoduloz","first_name":"Grégory","full_name":"Théoduloz, Grégory"}],"publication_status":"published","extern":1,"quality_controlled":0,"_id":"4568"},{"year":"2008","volume":89,"scopus_import":"1","month":"10","type":"journal_article","language":[{"iso":"eng"}],"citation":{"ieee":"N. H. Barton, “Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” <i>Genetics Research</i>, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.","mla":"Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” <i>Genetics Research</i>, vol. 89, no. 5–6, Cambridge University Press, 2008, pp. 475–77, doi:<a href=\"https://doi.org/10.1017/S0016672308009683\">10.1017/S0016672308009683</a>.","short":"N.H. Barton, Genetics Research 89 (2008) 475–477.","ama":"Barton NH. Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. <i>Genetics Research</i>. 2008;89(5-6):475-477. doi:<a href=\"https://doi.org/10.1017/S0016672308009683\">10.1017/S0016672308009683</a>","apa":"Barton, N. H. (2008). Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. <i>Genetics Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672308009683\">https://doi.org/10.1017/S0016672308009683</a>","chicago":"Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” <i>Genetics Research</i>. Cambridge University Press, 2008. <a href=\"https://doi.org/10.1017/S0016672308009683\">https://doi.org/10.1017/S0016672308009683</a>.","ista":"Barton NH. 2008. Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics Research. 89(5–6), 475–477."},"oa_version":"None","date_updated":"2024-02-14T09:51:09Z","status":"public","date_created":"2018-12-11T11:46:55Z","issue":"5-6","date_published":"2008-10-29T00:00:00Z","day":"29","page":"475 - 477","title":"Identity and coalescence in structured populations: A commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin","publication":"Genetics Research","intvolume":"        89","quality_controlled":"1","_id":"517","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"}],"publist_id":"7302","doi":"10.1017/S0016672308009683","publisher":"Cambridge University Press"},{"intvolume":"        23","acknowledgement":"X.F. holds a Clarendon Scholarship from the University of Oxford. We thank Angela Hay and Jill Harrison for helpful advice and discussion.","article_processing_charge":"No","quality_controlled":"1","external_id":{"pmid":["17825943"]},"language":[{"iso":"eng"}],"month":"10","article_type":"original","publication":"Trends in Genetics","page":"503-510","status":"public","date_created":"2023-01-16T09:22:44Z","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12201","pmid":1,"doi":"10.1016/j.tig.2007.08.005","publisher":"Elsevier BV","department":[{"_id":"XiFe"}],"publication_status":"published","author":[{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng"},{"first_name":"Hugh G.","last_name":"Dickinson","full_name":"Dickinson, Hugh G."}],"oa_version":"None","citation":{"ieee":"X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” <i>Trends in Genetics</i>, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007.","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” <i>Trends in Genetics</i>, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:<a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">10.1016/j.tig.2007.08.005</a>.","short":"X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.","apa":"Feng, X., &#38; Dickinson, H. G. (2007). Packaging the male germline in plants. <i>Trends in Genetics</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">https://doi.org/10.1016/j.tig.2007.08.005</a>","ama":"Feng X, Dickinson HG. Packaging the male germline in plants. <i>Trends in Genetics</i>. 2007;23(10):503-510. doi:<a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">10.1016/j.tig.2007.08.005</a>","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” <i>Trends in Genetics</i>. Elsevier BV, 2007. <a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">https://doi.org/10.1016/j.tig.2007.08.005</a>.","ista":"Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends in Genetics. 23(10), 503–510."},"keyword":["Genetics"],"scopus_import":"1","year":"2007","volume":23,"type":"journal_article","publication_identifier":{"issn":["0168-9525"]},"abstract":[{"text":"The development of plant lateral organs is interesting because, although many of the same genes seem to be involved in the early growth of primordia, completely different gene combinations are required for the complete development of organs such as leaves and stamens. Thus, the genes common to the development of most organs, which generally form and polarize the primordial ‘envelope’, must at some stage interact with those that ‘install’ the functional content of the organ – in the case of the stamen, the four microsporangia. Although distinct genetic pathways of organ initiation, polarity establishment and setting up the reproductive cell line can readily be recognized, they do not occur sequentially. Rather, they are activated early and run in parallel. There is evidence for continuing crosstalk between these pathways.","lang":"eng"}],"title":"Packaging the male germline in plants","date_updated":"2023-05-08T10:58:47Z","date_published":"2007-10-01T00:00:00Z","issue":"10"},{"publisher":"American Institute of Physics","arxiv":1,"doi":"10.1063/1.2801006","author":[{"first_name":"Adra","last_name":"Carr","full_name":"Carr, Adra"},{"last_name":"Serchest","first_name":"Yancey","full_name":"Serchest, Yancey"},{"last_name":"Waitukaitis","first_name":"Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"},{"first_name":"John","last_name":"Perreault","full_name":"Perreault, John"},{"full_name":"Lonij, Vincent","last_name":"Lonij","first_name":"Vincent"},{"last_name":"Cronin","first_name":"Alexander","full_name":"Cronin, Alexander"}],"publication_status":"published","_id":"128","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_number":"106108","title":"Cover slip external cavity diode laser","abstract":[{"lang":"eng","text":"A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The laser output pointing remains fixed, independent of its frequency because of the cover slip cavity design. This system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments. "}],"issue":"10","date_published":"2007-10-29T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/0708.0014","open_access":"1"}],"date_updated":"2021-01-12T06:49:35Z","citation":{"ama":"Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. Cover slip external cavity diode laser. <i>Review of Scientific Instruments</i>. 2007;78(10). doi:<a href=\"https://doi.org/10.1063/1.2801006\">10.1063/1.2801006</a>","apa":"Carr, A., Serchest, Y., Waitukaitis, S. R., Perreault, J., Lonij, V., &#38; Cronin, A. (2007). Cover slip external cavity diode laser. <i>Review of Scientific Instruments</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.2801006\">https://doi.org/10.1063/1.2801006</a>","short":"A. Carr, Y. Serchest, S.R. Waitukaitis, J. Perreault, V. Lonij, A. Cronin, Review of Scientific Instruments 78 (2007).","ieee":"A. Carr, Y. Serchest, S. R. Waitukaitis, J. Perreault, V. Lonij, and A. Cronin, “Cover slip external cavity diode laser,” <i>Review of Scientific Instruments</i>, vol. 78, no. 10. American Institute of Physics, 2007.","mla":"Carr, Adra, et al. “Cover Slip External Cavity Diode Laser.” <i>Review of Scientific Instruments</i>, vol. 78, no. 10, 106108, American Institute of Physics, 2007, doi:<a href=\"https://doi.org/10.1063/1.2801006\">10.1063/1.2801006</a>.","ista":"Carr A, Serchest Y, Waitukaitis SR, Perreault J, Lonij V, Cronin A. 2007. Cover slip external cavity diode laser. Review of Scientific Instruments. 78(10), 106108.","chicago":"Carr, Adra, Yancey Serchest, Scott R Waitukaitis, John Perreault, Vincent Lonij, and Alexander Cronin. “Cover Slip External Cavity Diode Laser.” <i>Review of Scientific Instruments</i>. American Institute of Physics, 2007. <a href=\"https://doi.org/10.1063/1.2801006\">https://doi.org/10.1063/1.2801006</a>."},"oa_version":"Preprint","type":"journal_article","year":"2007","volume":78,"external_id":{"arxiv":["0708.0014"]},"publist_id":"7925","oa":1,"quality_controlled":"1","acknowledgement":"National Science Foundation\r\nThis work was supported with NSF Grant No. PHY-0653623. We thank Dr. W. Bickel and Dr. J. Jones for diagnostic equipment, K. Guerin for assistance with mechanical drawings, and M. Parker of Rincon Research Inc. for optics components.","intvolume":"        78","publication":"Review of Scientific Instruments","day":"29","date_created":"2018-12-11T11:44:46Z","status":"public","language":[{"iso":"eng"}],"month":"10"},{"type":"journal_article","month":"06","year":"2007","volume":502,"citation":{"ama":"Raghu S, Jösch MA, Borst A, Reiff D. Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. <i>Journal of Comparative Neurology</i>. 2007;502(4):598-610. doi:<a href=\"https://doi.org/10.1002/cne.21319\">10.1002/cne.21319</a>","apa":"Raghu, S., Jösch, M. A., Borst, A., &#38; Reiff, D. (2007). Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. <i>Journal of Comparative Neurology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cne.21319\">https://doi.org/10.1002/cne.21319</a>","short":"S. Raghu, M.A. Jösch, A. Borst, D. Reiff, Journal of Comparative Neurology 502 (2007) 598–610.","mla":"Raghu, Shamprasad, et al. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.” <i>Journal of Comparative Neurology</i>, vol. 502, no. 4, Wiley-Blackwell, 2007, pp. 598–610, doi:<a href=\"https://doi.org/10.1002/cne.21319\">10.1002/cne.21319</a>.","ieee":"S. Raghu, M. A. Jösch, A. Borst, and D. Reiff, “Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites,” <i>Journal of Comparative Neurology</i>, vol. 502, no. 4. Wiley-Blackwell, pp. 598–610, 2007.","ista":"Raghu S, Jösch MA, Borst A, Reiff D. 2007. Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites. Journal of Comparative Neurology. 502(4), 598–610.","chicago":"Raghu, Shamprasad, Maximilian A Jösch, Alexander Borst, and Dierk Reiff. “Synaptic Organization of Lobula Plate Tangential Cells in Drosophila: γ-Aminobutyric Acid Receptors and Chemical Release Sites.” <i>Journal of Comparative Neurology</i>. Wiley-Blackwell, 2007. <a href=\"https://doi.org/10.1002/cne.21319\">https://doi.org/10.1002/cne.21319</a>."},"date_published":"2007-06-01T00:00:00Z","issue":"4","date_created":"2018-12-11T11:51:13Z","status":"public","date_updated":"2021-01-12T06:49:42Z","title":"Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites","publication":"Journal of Comparative Neurology","page":"598 - 610","day":"01","abstract":[{"text":"In flies, the large tangential cells of the lobula plate represent an important processing center for visual navigation based on optic flow. Although the visual response properties of these cells have been well studied in blowflies, information on their synaptic organization is mostly lacking. Here we study the distribution of presynaptic release and postsynaptic inhibitory sites in the same set of cells in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry, our results suggest that HS and VS cells of Drosophila express γ-aminobutyric acid (GABA) receptors in their dendritic region within the lobula plate, thus being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum, both cell types express synaptobrevin, suggesting the presence of presynaptic specializations there. HS- and VS-cell terminals additionally show evidence for postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings are in line with the general circuit for visual motion detection and receptive field properties as postulated from electrophysiological and optical recordings in blowflies, suggesting a similar functional organization of lobula plate tangential cells in the two species.","lang":"eng"}],"quality_controlled":0,"_id":"1297","intvolume":"       502","extern":1,"author":[{"full_name":"Raghu, Shamprasad V","first_name":"Shamprasad","last_name":"Raghu"},{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Maximilian Jösch","last_name":"Jösch","first_name":"Maximilian A"},{"full_name":"Borst, Alexander","last_name":"Borst","first_name":"Alexander"},{"first_name":"Dierk","last_name":"Reiff","full_name":"Reiff, Dierk F"}],"publication_status":"published","publisher":"Wiley-Blackwell","doi":"10.1002/cne.21319","publist_id":"5974"},{"oa_version":"None","citation":{"ista":"Schanda P, Forge V, Brutscher B. 2007. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. Proceedings of the National Academy of Sciences. 104(27), 11257–11262.","chicago":"Schanda, Paul, V. Forge, and B. Brutscher. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>.","apa":"Schanda, P., Forge, V., &#38; Brutscher, B. (2007). Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0702069104\">https://doi.org/10.1073/pnas.0702069104</a>","ama":"Schanda P, Forge V, Brutscher B. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(27):11257-11262. doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>","short":"P. Schanda, V. Forge, B. Brutscher, Proceedings of the National Academy of Sciences 104 (2007) 11257–11262.","mla":"Schanda, Paul, et al. “Protein Folding and Unfolding Studied at Atomic Resolution by Fast Two-Dimensional NMR Spectroscopy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27, National Academy of Sciences, 2007, pp. 11257–62, doi:<a href=\"https://doi.org/10.1073/pnas.0702069104\">10.1073/pnas.0702069104</a>.","ieee":"P. Schanda, V. Forge, and B. Brutscher, “Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 27. National Academy of Sciences, pp. 11257–11262, 2007."},"keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"type":"journal_article","month":"07","article_type":"original","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2007","volume":104,"publication":"Proceedings of the National Academy of Sciences","title":"Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy","page":"11257-11262","day":"03","abstract":[{"text":"Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.","lang":"eng"}],"date_published":"2007-07-03T00:00:00Z","date_created":"2020-09-18T10:12:54Z","issue":"27","date_updated":"2021-01-12T08:19:35Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8483","article_processing_charge":"No","quality_controlled":"1","intvolume":"       104","extern":"1","publisher":"National Academy of Sciences","doi":"10.1073/pnas.0702069104","publication_status":"published","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"},{"first_name":"V.","last_name":"Forge","full_name":"Forge, V."},{"first_name":"B.","last_name":"Brutscher","full_name":"Brutscher, B."}]},{"page":"163-169","publication":"Journal of Magnetic Resonance","title":"A set of BEST triple-resonance experiments for time-optimized protein resonance assignment","abstract":[{"text":"A series of sequential, intra-residue, and bi-directional BEST H–N–CA, H–N–CO, and H–N–CB pulse sequences is presented that extends the BEST concept introduced recently for fast multidimensional protein NMR [Schanda et al., J. Am. Chem. Soc. 128 (2006) 9042] to the complete set of experiments required for sequential resonance assignment. We demonstrate for the protein ubiquitin that 3D BEST H–N–C correlation spectra can be recorded on a 600 MHz NMR spectrometer equipped with a cryogenic probe in only a few minutes of acquisition time with sufficient sensitivity to detect all expected cross peaks.","lang":"eng"}],"day":"01","issue":"1","date_created":"2020-09-18T10:13:02Z","date_published":"2007-07-01T00:00:00Z","status":"public","date_updated":"2021-01-12T08:19:35Z","citation":{"ista":"Lescop E, Schanda P, Brutscher B. 2007. A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. Journal of Magnetic Resonance. 187(1), 163–169.","chicago":"Lescop, Ewen, Paul Schanda, and Bernhard Brutscher. “A Set of BEST Triple-Resonance Experiments for Time-Optimized Protein Resonance Assignment.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">https://doi.org/10.1016/j.jmr.2007.04.002</a>.","ama":"Lescop E, Schanda P, Brutscher B. A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. <i>Journal of Magnetic Resonance</i>. 2007;187(1):163-169. doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">10.1016/j.jmr.2007.04.002</a>","apa":"Lescop, E., Schanda, P., &#38; Brutscher, B. (2007). A set of BEST triple-resonance experiments for time-optimized protein resonance assignment. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">https://doi.org/10.1016/j.jmr.2007.04.002</a>","ieee":"E. Lescop, P. Schanda, and B. Brutscher, “A set of BEST triple-resonance experiments for time-optimized protein resonance assignment,” <i>Journal of Magnetic Resonance</i>, vol. 187, no. 1. Elsevier, pp. 163–169, 2007.","mla":"Lescop, Ewen, et al. “A Set of BEST Triple-Resonance Experiments for Time-Optimized Protein Resonance Assignment.” <i>Journal of Magnetic Resonance</i>, vol. 187, no. 1, Elsevier, 2007, pp. 163–69, doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.04.002\">10.1016/j.jmr.2007.04.002</a>.","short":"E. Lescop, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 187 (2007) 163–169."},"oa_version":"None","language":[{"iso":"eng"}],"article_type":"letter_note","publication_identifier":{"issn":["1090-7807"]},"month":"07","type":"journal_article","year":"2007","volume":187,"publisher":"Elsevier","doi":"10.1016/j.jmr.2007.04.002","author":[{"full_name":"Lescop, Ewen","first_name":"Ewen","last_name":"Lescop"},{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"}],"publication_status":"published","_id":"8484","article_processing_charge":"No","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","intvolume":"       187"},{"date_created":"2020-09-18T10:13:12Z","date_published":"2007-03-08T00:00:00Z","date_updated":"2021-01-12T08:19:36Z","status":"public","page":"47-55","publication":"Journal of Biomolecular NMR","title":"Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons","abstract":[{"text":"High signal to noise is a necessity for the quantification of NMR spectral parameters to be translated into accurate and precise restraints on protein structure and dynamics. An important source of long-range structural information is obtained from 1H–1H residual dipolar couplings (RDCs) measured for weakly aligned molecules. For sensitivity reasons, such measurements are generally performed on highly deuterated protein samples. Here we show that high sensitivity is also obtained for protonated protein samples if the pulse schemes are optimized in terms of longitudinal relaxation efficiency and J-mismatch compensated coherence transfer. The new sensitivity-optimized quantitative J-correlation experiment yields important signal gains reaching factors of 1.5 to 8 for individual correlation peaks when compared to previously proposed pulse schemes.","lang":"eng"}],"day":"08","publication_identifier":{"issn":["0925-2738","1573-5001"]},"article_type":"original","month":"03","type":"journal_article","volume":38,"year":"2007","citation":{"short":"P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, B. Brutscher, Journal of Biomolecular NMR 38 (2007) 47–55.","mla":"Schanda, Paul, et al. “Sensitivity-Optimized Experiment for the Measurement of Residual Dipolar Couplings between Amide Protons.” <i>Journal of Biomolecular NMR</i>, vol. 38, Springer Nature, 2007, pp. 47–55, doi:<a href=\"https://doi.org/10.1007/s10858-006-9138-2\">10.1007/s10858-006-9138-2</a>.","ieee":"P. Schanda, E. Lescop, M. Falge, R. Sounier, J. Boisbouvier, and B. Brutscher, “Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons,” <i>Journal of Biomolecular NMR</i>, vol. 38. Springer Nature, pp. 47–55, 2007.","apa":"Schanda, P., Lescop, E., Falge, M., Sounier, R., Boisbouvier, J., &#38; Brutscher, B. (2007). Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. <i>Journal of Biomolecular NMR</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10858-006-9138-2\">https://doi.org/10.1007/s10858-006-9138-2</a>","ama":"Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. <i>Journal of Biomolecular NMR</i>. 2007;38:47-55. doi:<a href=\"https://doi.org/10.1007/s10858-006-9138-2\">10.1007/s10858-006-9138-2</a>","chicago":"Schanda, Paul, Ewen Lescop, Mirjam Falge, Rémy Sounier, Jérôme Boisbouvier, and Bernhard Brutscher. “Sensitivity-Optimized Experiment for the Measurement of Residual Dipolar Couplings between Amide Protons.” <i>Journal of Biomolecular NMR</i>. Springer Nature, 2007. <a href=\"https://doi.org/10.1007/s10858-006-9138-2\">https://doi.org/10.1007/s10858-006-9138-2</a>.","ista":"Schanda P, Lescop E, Falge M, Sounier R, Boisbouvier J, Brutscher B. 2007. Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons. Journal of Biomolecular NMR. 38, 47–55."},"oa_version":"None","keyword":["Spectroscopy","Biochemistry"],"language":[{"iso":"eng"}],"publication_status":"published","author":[{"last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"first_name":"Ewen","last_name":"Lescop","full_name":"Lescop, Ewen"},{"full_name":"Falge, Mirjam","first_name":"Mirjam","last_name":"Falge"},{"full_name":"Sounier, Rémy","last_name":"Sounier","first_name":"Rémy"},{"full_name":"Boisbouvier, Jérôme","first_name":"Jérôme","last_name":"Boisbouvier"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}],"publisher":"Springer Nature","doi":"10.1007/s10858-006-9138-2","_id":"8485","quality_controlled":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","intvolume":"        38"},{"doi":"10.1021/ja068949u","publisher":"American Chemical Society","publication_status":"published","author":[{"full_name":"Lescop, Ewen","last_name":"Lescop","first_name":"Ewen"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda"},{"full_name":"Rasia, Rodolfo","last_name":"Rasia","first_name":"Rodolfo"},{"first_name":"Bernhard","last_name":"Brutscher","full_name":"Brutscher, Bernhard"}],"intvolume":"       129","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8486","article_processing_charge":"No","quality_controlled":"1","day":"17","abstract":[{"text":"A technique is described that allows reducing acquisition times of multidimensional NMR experiments by extensive spectral folding. The method is simple and has many interesting applications for NMR studies of molecular structure, dynamics, and kinetics.","lang":"eng"}],"title":"Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy","publication":"Journal of the American Chemical Society","page":"2756-2757","date_updated":"2021-01-12T08:19:36Z","status":"public","date_published":"2007-02-17T00:00:00Z","date_created":"2020-09-18T10:13:21Z","issue":"10","language":[{"iso":"eng"}],"oa_version":"None","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"citation":{"mla":"Lescop, Ewen, et al. “Automated Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution in Real-Time NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>, vol. 129, no. 10, American Chemical Society, 2007, pp. 2756–57, doi:<a href=\"https://doi.org/10.1021/ja068949u\">10.1021/ja068949u</a>.","ieee":"E. Lescop, P. Schanda, R. Rasia, and B. Brutscher, “Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy,” <i>Journal of the American Chemical Society</i>, vol. 129, no. 10. American Chemical Society, pp. 2756–2757, 2007.","short":"E. Lescop, P. Schanda, R. Rasia, B. Brutscher, Journal of the American Chemical Society 129 (2007) 2756–2757.","apa":"Lescop, E., Schanda, P., Rasia, R., &#38; Brutscher, B. (2007). Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja068949u\">https://doi.org/10.1021/ja068949u</a>","ama":"Lescop E, Schanda P, Rasia R, Brutscher B. Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. <i>Journal of the American Chemical Society</i>. 2007;129(10):2756-2757. doi:<a href=\"https://doi.org/10.1021/ja068949u\">10.1021/ja068949u</a>","chicago":"Lescop, Ewen, Paul Schanda, Rodolfo Rasia, and Bernhard Brutscher. “Automated Spectral Compression for Fast Multidimensional NMR and Increased Time Resolution in Real-Time NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/ja068949u\">https://doi.org/10.1021/ja068949u</a>.","ista":"Lescop E, Schanda P, Rasia R, Brutscher B. 2007. Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy. Journal of the American Chemical Society. 129(10), 2756–2757."},"volume":129,"year":"2007","type":"journal_article","month":"02","publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_type":"original"},{"intvolume":"       129","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","_id":"8487","quality_controlled":"1","author":[{"full_name":"Gal, Maayan","first_name":"Maayan","last_name":"Gal"},{"first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"},{"full_name":"Frydman, Lucio","first_name":"Lucio","last_name":"Frydman"}],"publication_status":"published","doi":"10.1021/ja066915g","publisher":"American Chemical Society","volume":129,"year":"2007","type":"journal_article","article_type":"original","month":"01","publication_identifier":{"issn":["0002-7863","1520-5126"]},"language":[{"iso":"eng"}],"citation":{"ama":"Gal M, Schanda P, Brutscher B, Frydman L. UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. <i>Journal of the American Chemical Society</i>. 2007;129(5):1372-1377. doi:<a href=\"https://doi.org/10.1021/ja066915g\">10.1021/ja066915g</a>","apa":"Gal, M., Schanda, P., Brutscher, B., &#38; Frydman, L. (2007). UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja066915g\">https://doi.org/10.1021/ja066915g</a>","ieee":"M. Gal, P. Schanda, B. Brutscher, and L. Frydman, “UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates,” <i>Journal of the American Chemical Society</i>, vol. 129, no. 5. American Chemical Society, pp. 1372–1377, 2007.","mla":"Gal, Maayan, et al. “UltraSOFAST HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates.” <i>Journal of the American Chemical Society</i>, vol. 129, no. 5, American Chemical Society, 2007, pp. 1372–77, doi:<a href=\"https://doi.org/10.1021/ja066915g\">10.1021/ja066915g</a>.","short":"M. Gal, P. Schanda, B. Brutscher, L. Frydman, Journal of the American Chemical Society 129 (2007) 1372–1377.","ista":"Gal M, Schanda P, Brutscher B, Frydman L. 2007. UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates. Journal of the American Chemical Society. 129(5), 1372–1377.","chicago":"Gal, Maayan, Paul Schanda, Bernhard Brutscher, and Lucio Frydman. “UltraSOFAST HMQC NMR and the Repetitive Acquisition of 2D Protein Spectra at Hz Rates.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2007. <a href=\"https://doi.org/10.1021/ja066915g\">https://doi.org/10.1021/ja066915g</a>."},"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"oa_version":"None","status":"public","date_updated":"2021-01-12T08:19:37Z","date_published":"2007-01-10T00:00:00Z","issue":"5","date_created":"2020-09-18T10:13:27Z","day":"10","abstract":[{"lang":"eng","text":"Following unidirectional biophysical events such as the folding of proteins or the equilibration of binding interactions, requires experimental methods that yield information at both atomic-level resolution and at high repetition rates. Toward this end a number of different approaches enabling the rapid acquisition of 2D NMR spectra have been recently introduced, including spatially encoded “ultrafast” 2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions by reducing the number of scans that are necessary for completing arbitrary 2D NMR experiments, the latter operates by reducing the delay between consecutive scans while preserving sensitivity. Given the complementarities between these two approaches it seems natural to combine them into a single tool, enabling the acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate here this capability with the introduction of “ultraSOFAST” HMQC NMR, a spatially encoded and relaxation-optimized approach that can provide 2D protein correlation spectra at ∼1 s repetition rates for samples in the ∼2 mM concentration range. The principles, relative advantages, and current limitations of this new approach are discussed, and its application is exemplified with a study of the fast hydrogen−deuterium exchange characterizing amide sites in Ubiquitin."}],"publication":"Journal of the American Chemical Society","title":"UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates","page":"1372-1377"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8511","article_processing_charge":"No","quality_controlled":"1","intvolume":"       208","extern":"1","author":[{"full_name":"Gorodetski, A.","first_name":"A.","last_name":"Gorodetski"},{"first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"}],"publication_status":"published","publisher":"Elsevier","doi":"10.1016/j.aim.2006.03.012","type":"journal_article","article_type":"original","publication_identifier":{"issn":["0001-8708"]},"month":"01","year":"2007","volume":208,"citation":{"chicago":"Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms Have Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic Tangency.” <i>Advances in Mathematics</i>. Elsevier, 2007. <a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">https://doi.org/10.1016/j.aim.2006.03.012</a>.","ista":"Gorodetski A, Kaloshin V. 2007. How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. Advances in Mathematics. 208(2), 710–797.","short":"A. Gorodetski, V. Kaloshin, Advances in Mathematics 208 (2007) 710–797.","ieee":"A. Gorodetski and V. Kaloshin, “How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency,” <i>Advances in Mathematics</i>, vol. 208, no. 2. Elsevier, pp. 710–797, 2007.","mla":"Gorodetski, A., and Vadim Kaloshin. “How Often Surface Diffeomorphisms Have Infinitely Many Sinks and Hyperbolicity of Periodic Points near a Homoclinic Tangency.” <i>Advances in Mathematics</i>, vol. 208, no. 2, Elsevier, 2007, pp. 710–97, doi:<a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">10.1016/j.aim.2006.03.012</a>.","ama":"Gorodetski A, Kaloshin V. How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. <i>Advances in Mathematics</i>. 2007;208(2):710-797. doi:<a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">10.1016/j.aim.2006.03.012</a>","apa":"Gorodetski, A., &#38; Kaloshin, V. (2007). How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency. <i>Advances in Mathematics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.aim.2006.03.012\">https://doi.org/10.1016/j.aim.2006.03.012</a>"},"oa_version":"None","keyword":["General Mathematics"],"language":[{"iso":"eng"}],"date_published":"2007-01-30T00:00:00Z","issue":"2","date_created":"2020-09-18T10:48:27Z","date_updated":"2021-01-12T08:19:47Z","status":"public","title":"How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency","publication":"Advances in Mathematics","page":"710-797","day":"30","abstract":[{"lang":"eng","text":"Here we study an amazing phenomenon discovered by Newhouse [S. Newhouse, Non-density of Axiom A(a) on S2, in: Proc. Sympos. Pure Math., vol. 14, Amer. Math. Soc., 1970, pp. 191–202; S. Newhouse,\r\nDiffeomorphisms with infinitely many sinks, Topology 13 (1974) 9–18; S. Newhouse, The abundance of\r\nwild hyperbolic sets and nonsmooth stable sets of diffeomorphisms, Publ. Math. Inst. Hautes Études Sci.\r\n50 (1979) 101–151]. It turns out that in the space of Cr smooth diffeomorphisms Diffr(M) of a compact\r\nsurface M there is an open set U such that a Baire generic diffeomorphism f ∈ U has infinitely many coexisting sinks. In this paper we make a step towards understanding “how often does a surface diffeomorphism\r\nhave infinitely many sinks.” Our main result roughly says that with probability one for any positive D a\r\nsurface diffeomorphism has only finitely many localized sinks either of cyclicity bounded by D or those\r\nwhose period is relatively large compared to its cyclicity. It verifies a particular case of Palis’ Conjecture\r\nsaying that even though diffeomorphisms with infinitely many coexisting sinks are Baire generic, they have\r\nprobability zero.\r\nOne of the key points of the proof is an application of Newton Interpolation Polynomials to study the dynamics initiated in [V. Kaloshin, B. Hunt, A stretched exponential bound on the rate of growth of the number\r\nof periodic points for prevalent diffeomorphisms I, Ann. of Math., in press, 92 pp.; V. Kaloshin, A stretched\r\nexponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II,\r\npreprint, 85 pp.]."}]},{"title":"Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I","publication":"Annals of Mathematics","page":"89-170","day":"01","abstract":[{"lang":"eng","text":"For diffeomorphisms of smooth compact finite-dimensional manifolds, we consider the problem of how fast the number of periodic points with period n grows as a function of n. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for C2 or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call “prevalence”, the growth is not much faster than exponential. Specifically, we show that for each ρ,δ>0, there is a prevalent set of C1+ρ (or smoother) diffeomorphisms for which the number of periodic n points is bounded above by exp(Cn1+δ) for some C independent of n. We also obtain a related bound on the decay of hyperbolicity of the periodic points as a function of n, and obtain the same results for 1-dimensional endomorphisms. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity show this to be a subtle and complex phenomenon, reminiscent of KAM theory. Here in Part I we state our results and describe the methods we use. We complete most of the proof in the 1-dimensional C2-smooth case and outline the remaining steps, deferred to Part II, that are needed to establish the general case.\r\n\r\nThe novel feature of the approach we develop in this paper is the introduction of Newton Interpolation Polynomials as a tool for perturbing trajectories of iterated maps."}],"date_published":"2007-01-01T00:00:00Z","issue":"1","date_created":"2020-09-18T10:48:33Z","status":"public","date_updated":"2021-01-12T08:19:48Z","oa_version":"None","citation":{"ama":"Kaloshin V, Hunt B. Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. <i>Annals of Mathematics</i>. 2007;165(1):89-170. doi:<a href=\"https://doi.org/10.4007/annals.2007.165.89\">10.4007/annals.2007.165.89</a>","apa":"Kaloshin, V., &#38; Hunt, B. (2007). Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. <i>Annals of Mathematics</i>. Princeton University Press. <a href=\"https://doi.org/10.4007/annals.2007.165.89\">https://doi.org/10.4007/annals.2007.165.89</a>","ieee":"V. Kaloshin and B. Hunt, “Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I,” <i>Annals of Mathematics</i>, vol. 165, no. 1. Princeton University Press, pp. 89–170, 2007.","mla":"Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” <i>Annals of Mathematics</i>, vol. 165, no. 1, Princeton University Press, 2007, pp. 89–170, doi:<a href=\"https://doi.org/10.4007/annals.2007.165.89\">10.4007/annals.2007.165.89</a>.","short":"V. Kaloshin, B. Hunt, Annals of Mathematics 165 (2007) 89–170.","ista":"Kaloshin V, Hunt B. 2007. Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I. Annals of Mathematics. 165(1), 89–170.","chicago":"Kaloshin, Vadim, and Brian Hunt. “Stretched Exponential Estimates on Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” <i>Annals of Mathematics</i>. Princeton University Press, 2007. <a href=\"https://doi.org/10.4007/annals.2007.165.89\">https://doi.org/10.4007/annals.2007.165.89</a>."},"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","month":"01","publication_identifier":{"issn":["0003-486X"]},"year":"2007","volume":165,"publisher":"Princeton University Press","doi":"10.4007/annals.2007.165.89","publication_status":"published","author":[{"first_name":"Vadim","last_name":"Kaloshin","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425"},{"last_name":"Hunt","first_name":"Brian","full_name":"Hunt, Brian"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","_id":"8512","article_processing_charge":"No","intvolume":"       165","extern":"1"},{"status":"public","date_updated":"2021-01-12T08:20:14Z","date_published":"2007-07-01T00:00:00Z","date_created":"2018-12-11T11:48:53Z","issue":"1","day":"01","abstract":[{"text":"We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene cluster that is associated with a polymorphic congenital cataract that occurs with frequency of ∼0.3% in a human population. To gain insight into the molecular mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary analysis of the available mammalian and newly obtained primate sequences of the γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the ancestral state, since it was found in CRYGD of a lower primate and all the surveyed nonprimate mammals. Crystallin proteins include two structurally similar domains, and substitutions in mammalian CRYGD protein at site 23 of the first domain were always associated with substitutions in the structurally reciprocal sites 109 and 136 of the second domain. These data suggest that the cataractogenic effect of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly by amino acid changes in a distal domain. We also found that gene conversion was a factor in the evolution of the γ-crystallin gene cluster throughout different mammalian clades. The high rate of gene conversion observed between the functional CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled with a surprising finding of apparent negative selection in primate pseudogenes suggest a deleterious impact of recently derived pseudogenes involved in gene conversion in the γ-crystallin gene cluster.","lang":"eng"}],"publication":"American Journal of Human Genetics","title":"Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state","page":"32 - 43","volume":81,"year":"2007","type":"journal_article","month":"07","citation":{"apa":"Plotnikova, O., Kondrashov, F., Vlasov, P., Grigorenko, A., Ginter, E., &#38; Rogaev, E. (2007). Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. <i>American Journal of Human Genetics</i>. Cell Press. <a href=\"https://doi.org/10.1086/518616\">https://doi.org/10.1086/518616</a>","ama":"Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. <i>American Journal of Human Genetics</i>. 2007;81(1):32-43. doi:<a href=\"https://doi.org/10.1086/518616\">10.1086/518616</a>","short":"O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev, American Journal of Human Genetics 81 (2007) 32–43.","ieee":"O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E. Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state,” <i>American Journal of Human Genetics</i>, vol. 81, no. 1. Cell Press, pp. 32–43, 2007.","mla":"Plotnikova, Olga, et al. “Conversion and Compensatory Evolution of the γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence of the Human CRYGD Gene to an Ancestral State.” <i>American Journal of Human Genetics</i>, vol. 81, no. 1, Cell Press, 2007, pp. 32–43, doi:<a href=\"https://doi.org/10.1086/518616\">10.1086/518616</a>.","ista":"Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007. Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state. American Journal of Human Genetics. 81(1), 32–43.","chicago":"Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko, Evgeny Ginter, and Evgeny Rogaev. “Conversion and Compensatory Evolution of the γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence of the Human CRYGD Gene to an Ancestral State.” <i>American Journal of Human Genetics</i>. Cell Press, 2007. <a href=\"https://doi.org/10.1086/518616\">https://doi.org/10.1086/518616</a>."},"author":[{"first_name":"Olga","last_name":"Plotnikova","full_name":"Plotnikova, Olga V"},{"orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Vlasov, Peter K","first_name":"Peter","last_name":"Vlasov"},{"full_name":"Grigorenko, Anastasia P","first_name":"Anastasia","last_name":"Grigorenko"},{"full_name":"Ginter, Evgeny K","last_name":"Ginter","first_name":"Evgeny"},{"last_name":"Rogaev","first_name":"Evgeny","full_name":"Rogaev, Evgeny I"}],"publication_status":"published","doi":"10.1086/518616","publist_id":"6788","publisher":"Cell Press","intvolume":"        81","extern":1,"acknowledgement":"This study was supported by the Biodiversity and Dynamics of Gene Pools program of the Presidium of the Russian Academy of Sciences (support to E.I.R.). E.I.R. is also supported in part by the National Institute of Diabetes and Digestive and Kidney Diseases and National Institute of Neurological Disorders and Stroke (National Institutes of Health), and F.A.K. is supported by a National Science Foundation graduate research fellowship.","_id":"860","quality_controlled":0},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).","ieee":"K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures,” <i>BMC Bioinformatics</i>, vol. 8. BioMed Central, 2007.","mla":"Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” <i>BMC Bioinformatics</i>, vol. 8, BioMed Central, 2007, doi:<a href=\"https://doi.org/10.1186/1471-2105-8-441\">10.1186/1471-2105-8-441</a>.","ama":"Popadin K, Mamirova L, Kondrashov F. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. <i>BMC Bioinformatics</i>. 2007;8. doi:<a href=\"https://doi.org/10.1186/1471-2105-8-441\">10.1186/1471-2105-8-441</a>","apa":"Popadin, K., Mamirova, L., &#38; Kondrashov, F. (2007). A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. <i>BMC Bioinformatics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2105-8-441\">https://doi.org/10.1186/1471-2105-8-441</a>","chicago":"Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary Structures.” <i>BMC Bioinformatics</i>. BioMed Central, 2007. <a href=\"https://doi.org/10.1186/1471-2105-8-441\">https://doi.org/10.1186/1471-2105-8-441</a>.","ista":"Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics. 8."},"month":"11","type":"journal_article","volume":8,"year":"2007","license":"https://creativecommons.org/licenses/by/4.0/","publication":"BMC Bioinformatics","title":"A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures","abstract":[{"text":"Background: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description: We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.","lang":"eng"}],"day":"14","date_created":"2018-12-11T11:48:54Z","date_published":"2007-11-14T00:00:00Z","date_updated":"2021-01-12T08:20:18Z","status":"public","_id":"861","quality_controlled":0,"acknowledgement":"KYuP and LAM were supported by the Molecular and Cellular Biology Program of the Russian Academy of Science. KYuP was supported by the Russian Fund of Basic Research (grant 04-04-49623). LAM was partially supported by grants from the Howard Hughes Medical Institute (55005610), INTAS (05-1000008-8028). FAK is a National Science Foundation Graduate Research Fellow.","extern":1,"intvolume":"         8","publisher":"BioMed Central","publist_id":"6789","doi":"10.1186/1471-2105-8-441","author":[{"full_name":"Popadin, Konstantin Yu","last_name":"Popadin","first_name":"Konstantin"},{"last_name":"Mamirova","first_name":"Leila","full_name":"Mamirova, Leila A"},{"full_name":"Fyodor Kondrashov","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov"}],"publication_status":"published"}]