[{"extern":1,"date_created":"2018-12-11T12:05:44Z","publication_status":"published","month":"09","year":"2005","day":"19","quality_controlled":0,"acknowledgement":"This research was supported in part by the ONR grant N00014-02-1-0671, the AFOSR MURI grant F49620-00-1-0327, and the NSF grant CCR-0225610.\nThis is an extended version of the paper “Games with Secure Equilibria” that appeared in the proceedings of Logic in Computer Science (LICS), 2004.","abstract":[{"lang":"eng","text":"In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent's payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it often suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of omega-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium."}],"type":"conference","publist_id":"2269","volume":3657,"date_updated":"2021-01-12T07:53:00Z","publisher":"Springer","date_published":"2005-09-19T00:00:00Z","page":"141 - 161","conference":{"name":"FMCO: Formal Methods for Components and Objects"},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Krishnendu Chatterjee","first_name":"Krishnendu"},{"full_name":"Thomas Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"last_name":"Jurdziński","first_name":"Marcin","full_name":"Jurdziński, Marcin"}],"intvolume":"      3657","title":"Games with secure equilibria","alternative_title":["LNCS"],"status":"public","_id":"3892","doi":"10.1007/11561163_7","citation":{"short":"K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, Springer, 2005, pp. 141–161.","ieee":"K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,” presented at the FMCO: Formal Methods for Components and Objects, 2005, vol. 3657, pp. 141–161.","ama":"Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. In: Vol 3657. Springer; 2005:141-161. doi:<a href=\"https://doi.org/10.1007/11561163_7\">10.1007/11561163_7</a>","ista":"Chatterjee K, Henzinger TA, Jurdziński M. 2005. Games with secure equilibria. FMCO: Formal Methods for Components and Objects, LNCS, vol. 3657, 141–161.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Jurdziński, M. (2005). Games with secure equilibria (Vol. 3657, pp. 141–161). Presented at the FMCO: Formal Methods for Components and Objects, Springer. <a href=\"https://doi.org/10.1007/11561163_7\">https://doi.org/10.1007/11561163_7</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games with Secure Equilibria,” 3657:141–61. Springer, 2005. <a href=\"https://doi.org/10.1007/11561163_7\">https://doi.org/10.1007/11561163_7</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Games with Secure Equilibria</i>. Vol. 3657, Springer, 2005, pp. 141–61, doi:<a href=\"https://doi.org/10.1007/11561163_7\">10.1007/11561163_7</a>."}},{"quality_controlled":0,"day":"05","type":"conference","abstract":[{"lang":"eng","text":"We study infinite stochastic games played by two-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players' goals are not necessarily conflicting), and undiscounted. We show that if each player has an W-regular objective expressed as a paxity objective, then there exists an epsilon-Nash equilibrium, for every epsilon &gt; 0. However, exact Nash equilibria need not exist. We study the complexity of finding values (payoff profile) of an epsilon-Nash equilibrium. We show that the values of an epsilon-Nash equilibrium in nonzero-sum concurrent parity games can be computed by solving the following two simpler problems: computing the values of zero-sum (the goals of the players axe strictly conflicting) concurrent parity games and computing epsilon-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives. As a consequence we establish that values of an epsilon-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME."}],"year":"2005","month":"09","publication_status":"published","date_created":"2018-12-11T12:05:44Z","extern":1,"doi":"10.1007/11539452_32","citation":{"apa":"Chatterjee, K. (2005). Two-player nonzero-sum ω-regular games (Vol. 3653, pp. 413–427). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/11539452_32\">https://doi.org/10.1007/11539452_32</a>","mla":"Chatterjee, Krishnendu. <i>Two-Player Nonzero-Sum ω-Regular Games</i>. Vol. 3653, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 413–27, doi:<a href=\"https://doi.org/10.1007/11539452_32\">10.1007/11539452_32</a>.","chicago":"Chatterjee, Krishnendu. “Two-Player Nonzero-Sum ω-Regular Games,” 3653:413–27. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005. <a href=\"https://doi.org/10.1007/11539452_32\">https://doi.org/10.1007/11539452_32</a>.","ama":"Chatterjee K. Two-player nonzero-sum ω-regular games. In: Vol 3653. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2005:413-427. doi:<a href=\"https://doi.org/10.1007/11539452_32\">10.1007/11539452_32</a>","ista":"Chatterjee K. 2005. Two-player nonzero-sum ω-regular games. CONCUR: Concurrency Theory, LNCS , vol. 3653, 413–427.","short":"K. Chatterjee, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 413–427.","ieee":"K. Chatterjee, “Two-player nonzero-sum ω-regular games,” presented at the CONCUR: Concurrency Theory, 2005, vol. 3653, pp. 413–427."},"_id":"3893","alternative_title":["LNCS "],"status":"public","title":"Two-player nonzero-sum ω-regular games","author":[{"full_name":"Krishnendu Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"}],"page":"413 - 427","conference":{"name":"CONCUR: Concurrency Theory"},"date_published":"2005-09-05T00:00:00Z","intvolume":"      3653","date_updated":"2021-01-12T07:53:00Z","publist_id":"2267","volume":3653,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"extern":1,"date_created":"2018-12-11T12:05:45Z","year":"2005","month":"02","publication_status":"published","quality_controlled":0,"day":"14","type":"conference","abstract":[{"text":"Temporal Logic Model Checking is one of the most potent tools for the verification of finite state systems. Computation Tree Logic (CTL) has gained popularity because unlike most other logics, CTL model checking of a single transition system can be achieved in polynomial time. However, in most real-life problems, specially in distributed and parallel systems, the system consist of a set of concurrent processes and the verification problem translates to model check the composition of the component processes. Since explicit composition leads to state explosion, verifying the system without actually composing the components is attractive, even for possibly restrictive class of systems. We show that the problem of compositional CTL model checking is PSPACE complete for the class of systems composed of components that are tree-like transition structure and do not interact among themselves. For the simplest forms of existential and universal CTL formulas model checking turns out to be NP complete and coNP complete, respectively. The results hold for both synchronous and asynchronous composition.","lang":"eng"}],"acknowledgement":"Pallab Dasgupta and P.P.Chakrabarti thank the Dept. of Science & Tech., Govt. of India, for partial support of this work","date_updated":"2021-01-12T07:53:02Z","publist_id":"2261","volume":3326,"publisher":"Springer","conference":{"name":"IWDC: International Workshop on Distributed Computing "},"author":[{"first_name":"Krishnendu","full_name":"Krishnendu Chatterjee","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Dasgupta","first_name":"Pallab","full_name":"Dasgupta, Pallab"},{"last_name":"Chakrabarti","full_name":"Chakrabarti, Partha P","first_name":"Partha"}],"page":"89 - 102","date_published":"2005-02-14T00:00:00Z","intvolume":"      3326","alternative_title":["LNCS"],"status":"public","title":"Complexity of compositional model checking of computation tree logic on simple structures","citation":{"ieee":"K. Chatterjee, P. Dasgupta, and P. Chakrabarti, “Complexity of compositional model checking of computation tree logic on simple structures,” presented at the IWDC: International Workshop on Distributed Computing , 2005, vol. 3326, pp. 89–102.","short":"K. Chatterjee, P. Dasgupta, P. Chakrabarti, in:, Springer, 2005, pp. 89–102.","ista":"Chatterjee K, Dasgupta P, Chakrabarti P. 2005. Complexity of compositional model checking of computation tree logic on simple structures. IWDC: International Workshop on Distributed Computing , LNCS, vol. 3326, 89–102.","ama":"Chatterjee K, Dasgupta P, Chakrabarti P. Complexity of compositional model checking of computation tree logic on simple structures. In: Vol 3326. Springer; 2005:89-102. doi:<a href=\"https://doi.org/10.1007/978-3-540-30536-1_13\">10.1007/978-3-540-30536-1_13</a>","chicago":"Chatterjee, Krishnendu, Pallab Dasgupta, and Partha Chakrabarti. “Complexity of Compositional Model Checking of Computation Tree Logic on Simple Structures,” 3326:89–102. Springer, 2005. <a href=\"https://doi.org/10.1007/978-3-540-30536-1_13\">https://doi.org/10.1007/978-3-540-30536-1_13</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Complexity of Compositional Model Checking of Computation Tree Logic on Simple Structures</i>. Vol. 3326, Springer, 2005, pp. 89–102, doi:<a href=\"https://doi.org/10.1007/978-3-540-30536-1_13\">10.1007/978-3-540-30536-1_13</a>.","apa":"Chatterjee, K., Dasgupta, P., &#38; Chakrabarti, P. (2005). Complexity of compositional model checking of computation tree logic on simple structures (Vol. 3326, pp. 89–102). Presented at the IWDC: International Workshop on Distributed Computing , Springer. <a href=\"https://doi.org/10.1007/978-3-540-30536-1_13\">https://doi.org/10.1007/978-3-540-30536-1_13</a>"},"doi":"10.1007/978-3-540-30536-1_13","_id":"3896"},{"extern":"1","oa_version":"None","date_created":"2018-12-11T12:05:47Z","year":"2005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","publication_status":"published","main_file_link":[{"url":"http://www.docstoc.com/docs/15327566/1-The-drawback-of-mobility-invasive-species-in-a-globalised-world"}],"type":"conference","day":"01","language":[{"iso":"eng"}],"publisher":"Elsevier","date_updated":"2021-01-12T07:53:05Z","publist_id":"2252","conference":{"name":"Marie Curie Conference"},"author":[{"full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","last_name":"Cremer"},{"last_name":"Boomsma","first_name":"Jacobus","full_name":"Boomsma, Jacobus"}],"date_published":"2005-09-01T00:00:00Z","status":"public","title":"The drawback of mobility: invasive species in a globalised world","citation":{"apa":"Cremer, S., &#38; Boomsma, J. (2005). The drawback of mobility: invasive species in a globalised world. Presented at the Marie Curie Conference, Elsevier.","chicago":"Cremer, Sylvia, and Jacobus Boomsma. “The Drawback of Mobility: Invasive Species in a Globalised World.” Elsevier, 2005.","mla":"Cremer, Sylvia, and Jacobus Boomsma. <i>The Drawback of Mobility: Invasive Species in a Globalised World</i>. Elsevier, 2005.","ama":"Cremer S, Boomsma J. The drawback of mobility: invasive species in a globalised world. In: Elsevier; 2005.","ista":"Cremer S, Boomsma J. 2005. The drawback of mobility: invasive species in a globalised world. Marie Curie Conference.","short":"S. Cremer, J. Boomsma, in:, Elsevier, 2005.","ieee":"S. Cremer and J. Boomsma, “The drawback of mobility: invasive species in a globalised world,” presented at the Marie Curie Conference, 2005."},"_id":"3902"},{"date_created":"2018-12-11T12:05:52Z","extern":"1","issue":"5","oa_version":"None","abstract":[{"text":"In the ant Cardiocondyla obscurior, wingless males compete with nestmate males for access to female mating\r\npartners, leading to local mate competition (LMC). Queen number varies between colonies, resulting in\r\nvariation in the strength of LMC. Cremer &amp; Heinze (2002, Proceedings of the Royal Society of London, Series B,\r\n269, 417–422) showed that colonies responded to increasing queen number by producing a less femalebiased\r\nsex ratio, as predicted by LMC theory. However, the proximate mechanisms responsible for this\r\nvariation in the sex ratio could not be determined because the study was restricted to adult sex ratios.With\r\nLMC, the primary sex ratio (proportion of haploid eggs laid by the queen) is expected to be female biased,\r\nwhich lowers the conflict between queens and workers over sex allocation. We compared the primary sex\r\nratios laid by queens in monogynous and in polygynous experimental colonies of C. obscurior. The\r\nproportion of haploid eggs laid by queens was significantly lower in single-queen than in multiple-queen\r\ncolonies. Furthermore, queens rapidly adjusted their primary sex ratios to changes in colony queen\r\nnumber. This is the first report of an adaptive adjustment of the primary sex ratio in response to LMC by\r\nant queens.","lang":"eng"}],"type":"journal_article","day":"01","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2005","month":"05","intvolume":"        69","date_published":"2005-05-01T00:00:00Z","page":"1031 - 1035","author":[{"full_name":"De Menten, Ludivine","first_name":"Ludivine","last_name":"De Menten"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","last_name":"Cremer"},{"full_name":"Heinze, Jürgen","first_name":"Jürgen","last_name":"Heinze"},{"first_name":"Serge","full_name":"Aron, Serge","last_name":"Aron"}],"publisher":"Elsevier","language":[{"iso":"eng"}],"volume":69,"publist_id":"2237","date_updated":"2021-01-12T07:53:10Z","_id":"3915","publication":"Animal Behaviour","doi":"10.1016/j.anbehav.2004.09.005","citation":{"ama":"De Menten L, Cremer S, Heinze J, Aron S. Primary sex ratio adjustment by ant queens in response to local mate competition. <i>Animal Behaviour</i>. 2005;69(5):1031-1035. doi:<a href=\"https://doi.org/10.1016/j.anbehav.2004.09.005\">10.1016/j.anbehav.2004.09.005</a>","ista":"De Menten L, Cremer S, Heinze J, Aron S. 2005. Primary sex ratio adjustment by ant queens in response to local mate competition. Animal Behaviour. 69(5), 1031–1035.","short":"L. De Menten, S. Cremer, J. Heinze, S. Aron, Animal Behaviour 69 (2005) 1031–1035.","ieee":"L. De Menten, S. Cremer, J. Heinze, and S. Aron, “Primary sex ratio adjustment by ant queens in response to local mate competition,” <i>Animal Behaviour</i>, vol. 69, no. 5. Elsevier, pp. 1031–1035, 2005.","apa":"De Menten, L., Cremer, S., Heinze, J., &#38; Aron, S. (2005). Primary sex ratio adjustment by ant queens in response to local mate competition. <i>Animal Behaviour</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.anbehav.2004.09.005\">https://doi.org/10.1016/j.anbehav.2004.09.005</a>","chicago":"De Menten, Ludivine, Sylvia Cremer, Jürgen Heinze, and Serge Aron. “Primary Sex Ratio Adjustment by Ant Queens in Response to Local Mate Competition.” <i>Animal Behaviour</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.anbehav.2004.09.005\">https://doi.org/10.1016/j.anbehav.2004.09.005</a>.","mla":"De Menten, Ludivine, et al. “Primary Sex Ratio Adjustment by Ant Queens in Response to Local Mate Competition.” <i>Animal Behaviour</i>, vol. 69, no. 5, Elsevier, 2005, pp. 1031–35, doi:<a href=\"https://doi.org/10.1016/j.anbehav.2004.09.005\">10.1016/j.anbehav.2004.09.005</a>."},"title":"Primary sex ratio adjustment by ant queens in response to local mate competition","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","year":"2005","publication_status":"published","type":"journal_article","abstract":[{"lang":"eng","text":"Divergent reproductive interests of males and females often cause sexual conflict [1] and [2]. Males of many species manipulate females by transferring seminal fluids that boost female short-term fecundity while decreasing their life expectancy and future reproductivity [3] and [4]. The life history of ants, however, is expected to reduce sexual conflict; whereas most insect females show repeated phases of mating and reproduction, antqueens mate only during a short period early in life and undergo a lifelong commitment to their mates by storing sperm [5]. Furthermore, sexual offspring can only be reared after a sterile worker force has been built up [5]. Therefore, the males should also profit from a long female lifespan. In the antCardiocondyla obscurior, mating indeed has a positive effect on the lifetime reproductive success of queens. Queens that mated to either one fertile or one sterilized male lived considerably longer and started laying eggs earlier than virgin queens. Only queens that received viable sperm from fertile males showed increased fecundity. The lack of a trade-off between fecundity and longevity is unexpected, given evolutionary theories of aging [6]. Our data instead reveal the existence of sexual cooperation in ants."}],"day":"08","extern":"1","issue":"3","oa_version":"None","date_created":"2018-12-11T12:05:52Z","status":"public","title":"Sexual cooperation: mating increases longevity in ant queens","citation":{"chicago":"Schrempf, Alexandra, Jürgen Heinze, and Sylvia Cremer. “Sexual Cooperation: Mating Increases Longevity in Ant Queens.” <i>Current Biology</i>. Cell Press, 2005. <a href=\"https://doi.org/10.1016/j.cub.2005.01.036\">https://doi.org/10.1016/j.cub.2005.01.036</a>.","mla":"Schrempf, Alexandra, et al. “Sexual Cooperation: Mating Increases Longevity in Ant Queens.” <i>Current Biology</i>, vol. 15, no. 3, Cell Press, 2005, pp. 267–70, doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.036\">10.1016/j.cub.2005.01.036</a>.","apa":"Schrempf, A., Heinze, J., &#38; Cremer, S. (2005). Sexual cooperation: mating increases longevity in ant queens. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2005.01.036\">https://doi.org/10.1016/j.cub.2005.01.036</a>","ieee":"A. Schrempf, J. Heinze, and S. Cremer, “Sexual cooperation: mating increases longevity in ant queens,” <i>Current Biology</i>, vol. 15, no. 3. Cell Press, pp. 267–270, 2005.","short":"A. Schrempf, J. Heinze, S. Cremer, Current Biology 15 (2005) 267–270.","ista":"Schrempf A, Heinze J, Cremer S. 2005. Sexual cooperation: mating increases longevity in ant queens. Current Biology. 15(3), 267–270.","ama":"Schrempf A, Heinze J, Cremer S. Sexual cooperation: mating increases longevity in ant queens. <i>Current Biology</i>. 2005;15(3):267-270. doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.036\">10.1016/j.cub.2005.01.036</a>"},"doi":"10.1016/j.cub.2005.01.036","_id":"3916","publication":"Current Biology","language":[{"iso":"eng"}],"publisher":"Cell Press","date_updated":"2021-01-12T07:53:10Z","publist_id":"2238","volume":15,"intvolume":"        15","author":[{"last_name":"Schrempf","full_name":"Schrempf, Alexandra","first_name":"Alexandra"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"},{"first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"page":"267 - 270","date_published":"2005-02-08T00:00:00Z"},{"language":[{"iso":"eng"}],"publisher":"Cell Press","date_updated":"2021-01-12T07:53:18Z","volume":22,"publist_id":"2195","intvolume":"        22","author":[{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"},{"first_name":"Nobuo","full_name":"Kanazawa, Nobuo","last_name":"Kanazawa"},{"last_name":"Selg","first_name":"Manuel","full_name":"Selg, Manuel"},{"last_name":"Samson","first_name":"Thomas","full_name":"Samson, Thomas"},{"last_name":"Roos","first_name":"Gunnel","full_name":"Roos, Gunnel"},{"last_name":"Reinhardt","full_name":"Reinhardt, Dieter","first_name":"Dieter"},{"last_name":"Pabst","full_name":"Pabst, Reinhard","first_name":"Reinhard"},{"full_name":"Lutz, Manfred","first_name":"Manfred","last_name":"Lutz"},{"full_name":"Sorokin, Lydia","first_name":"Lydia","last_name":"Sorokin"}],"page":"19 - 29","date_published":"2005-01-25T00:00:00Z","status":"public","title":"The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node","citation":{"chicago":"Sixt, Michael K, Nobuo Kanazawa, Manuel Selg, Thomas Samson, Gunnel Roos, Dieter Reinhardt, Reinhard Pabst, Manfred Lutz, and Lydia Sorokin. “The Conduit System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph Node.” <i>Immunity</i>. Cell Press, 2005. <a href=\"https://doi.org/10.1016/j.immuni.2004.11.013\">https://doi.org/10.1016/j.immuni.2004.11.013</a>.","mla":"Sixt, Michael K., et al. “The Conduit System Transports Soluble Antigens from the Afferent Lymph to Resident Dendritic Cells in the T Cell Area of the Lymph Node.” <i>Immunity</i>, vol. 22, no. 1, Cell Press, 2005, pp. 19–29, doi:<a href=\"https://doi.org/10.1016/j.immuni.2004.11.013\">10.1016/j.immuni.2004.11.013</a>.","apa":"Sixt, M. K., Kanazawa, N., Selg, M., Samson, T., Roos, G., Reinhardt, D., … Sorokin, L. (2005). The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. <i>Immunity</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.immuni.2004.11.013\">https://doi.org/10.1016/j.immuni.2004.11.013</a>","ieee":"M. K. Sixt <i>et al.</i>, “The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node,” <i>Immunity</i>, vol. 22, no. 1. Cell Press, pp. 19–29, 2005.","short":"M.K. Sixt, N. Kanazawa, M. Selg, T. Samson, G. Roos, D. Reinhardt, R. Pabst, M. Lutz, L. Sorokin, Immunity 22 (2005) 19–29.","ista":"Sixt MK, Kanazawa N, Selg M, Samson T, Roos G, Reinhardt D, Pabst R, Lutz M, Sorokin L. 2005. The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. Immunity. 22(1), 19–29.","ama":"Sixt MK, Kanazawa N, Selg M, et al. The conduit system transports soluble antigens from the afferent lymph to resident dendritic cells in the T cell area of the lymph node. <i>Immunity</i>. 2005;22(1):19-29. doi:<a href=\"https://doi.org/10.1016/j.immuni.2004.11.013\">10.1016/j.immuni.2004.11.013</a>"},"doi":"10.1016/j.immuni.2004.11.013","_id":"3933","publication":"Immunity","extern":"1","oa_version":"None","issue":"1","date_created":"2018-12-11T12:05:58Z","year":"2005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","publication_status":"published","type":"journal_article","abstract":[{"lang":"eng","text":"Resident dendritic cells (DC) within the T cell area of the lymph node take up soluble antigens that enter via the afferent lymphatics before antigen carrying DC arrive from the periphery. The reticular network within the lymph node is a conduit system forming the infrastructure for the fast delivery of soluble substances from the afferent lymph to the lumen of high endothelial venules (HEVs). Using high-resolution light microscopy and 3D reconstruction, we show here that these conduits are unique basement membrane-like structures ensheathed by fibroblastic reticular cells with occasional resident DC embedded within this cell layer. Conduit-associated DC are capable of taking up and processing soluble antigens transported within the conduits, whereas immigrated mature DC occur remote from the reticular fibers. The conduit system is, therefore, not a closed compartment that shuttles substances through the lymph node but represents the morphological equivalent to the filtering function of the lymph node."}],"day":"25"},{"date_created":"2018-12-11T12:06:16Z","extern":1,"type":"conference","abstract":[{"lang":"eng","text":"We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems."}],"quality_controlled":0,"day":"01","year":"2005","month":"01","publication_status":"published","page":"64 - 75","author":[{"last_name":"Wang","first_name":"Yusu","full_name":"Wang, Yusu"},{"last_name":"Agarwal","first_name":"Pankaj","full_name":"Agarwal, Pankaj K"},{"full_name":"Brown, Paul","first_name":"Paul","last_name":"Brown"},{"full_name":"Herbert Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Rudolph, Johannes","first_name":"Johannes","last_name":"Rudolph"}],"conference":{"name":"PSB: Pacific Symposium on Biocomputing"},"date_published":"2005-01-01T00:00:00Z","publisher":"World Scientific Publishing","date_updated":"2021-01-12T07:53:38Z","publist_id":"2143","doi":"10.1142/9789812702456_0007","citation":{"short":"Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, J. Rudolph, in:, World Scientific Publishing, 2005, pp. 64–75.","ieee":"Y. Wang, P. Agarwal, P. Brown, H. Edelsbrunner, and J. Rudolph, “Coarse and reliable geometric alignment for protein docking,” presented at the PSB: Pacific Symposium on Biocomputing, 2005, pp. 64–75.","ama":"Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. Coarse and reliable geometric alignment for protein docking. In: World Scientific Publishing; 2005:64-75. doi:<a href=\"https://doi.org/10.1142/9789812702456_0007\">10.1142/9789812702456_0007</a>","ista":"Wang Y, Agarwal P, Brown P, Edelsbrunner H, Rudolph J. 2005. Coarse and reliable geometric alignment for protein docking. PSB: Pacific Symposium on Biocomputing, 64–75.","apa":"Wang, Y., Agarwal, P., Brown, P., Edelsbrunner, H., &#38; Rudolph, J. (2005). Coarse and reliable geometric alignment for protein docking (pp. 64–75). Presented at the PSB: Pacific Symposium on Biocomputing, World Scientific Publishing. <a href=\"https://doi.org/10.1142/9789812702456_0007\">https://doi.org/10.1142/9789812702456_0007</a>","mla":"Wang, Yusu, et al. <i>Coarse and Reliable Geometric Alignment for Protein Docking</i>. World Scientific Publishing, 2005, pp. 64–75, doi:<a href=\"https://doi.org/10.1142/9789812702456_0007\">10.1142/9789812702456_0007</a>.","chicago":"Wang, Yusu, Pankaj Agarwal, Paul Brown, Herbert Edelsbrunner, and Johannes Rudolph. “Coarse and Reliable Geometric Alignment for Protein Docking,” 64–75. World Scientific Publishing, 2005. <a href=\"https://doi.org/10.1142/9789812702456_0007\">https://doi.org/10.1142/9789812702456_0007</a>."},"_id":"3982","status":"public","title":"Coarse and reliable geometric alignment for protein docking"},{"publisher":"ACS","publist_id":"2144","volume":44,"date_updated":"2021-01-12T07:53:39Z","intvolume":"        44","date_published":"2005-11-24T00:00:00Z","page":"16563 - 16573","author":[{"full_name":"Sohn, Jungsan","first_name":"Jungsan","last_name":"Sohn"},{"full_name":"Parks, Jerry M","first_name":"Jerry","last_name":"Parks"},{"full_name":"Buhrman, Gregory","first_name":"Gregory","last_name":"Buhrman"},{"first_name":"Paul","full_name":"Brown, Paul","last_name":"Brown"},{"full_name":"Kristjánsdóttir, Kolbrun","first_name":"Kolbrun","last_name":"Kristjánsdóttir"},{"full_name":"Safi, Alexias","first_name":"Alexias","last_name":"Safi"},{"first_name":"Herbert","full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yang","full_name":"Yang, Weitao T","first_name":"Weitao"},{"last_name":"Rudolph","full_name":"Rudolph, Johannes","first_name":"Johannes"}],"title":"Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate","status":"public","_id":"3983","publication":"Biochemistry","doi":"10.1021/bi0516879","citation":{"apa":"Sohn, J., Parks, J., Buhrman, G., Brown, P., Kristjánsdóttir, K., Safi, A., … Rudolph, J. (2005). Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. <i>Biochemistry</i>. ACS. <a href=\"https://doi.org/10.1021/bi0516879\">https://doi.org/10.1021/bi0516879</a>","chicago":"Sohn, Jungsan, Jerry Parks, Gregory Buhrman, Paul Brown, Kolbrun Kristjánsdóttir, Alexias Safi, Herbert Edelsbrunner, Weitao Yang, and Johannes Rudolph. “Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.” <i>Biochemistry</i>. ACS, 2005. <a href=\"https://doi.org/10.1021/bi0516879\">https://doi.org/10.1021/bi0516879</a>.","mla":"Sohn, Jungsan, et al. “Experimental Validation of the Docking Orientation of Cdc25 with Its Cdk2-CycA Protein Substrate.” <i>Biochemistry</i>, vol. 44, no. 50, ACS, 2005, pp. 16563–73, doi:<a href=\"https://doi.org/10.1021/bi0516879\">10.1021/bi0516879</a>.","ama":"Sohn J, Parks J, Buhrman G, et al. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. <i>Biochemistry</i>. 2005;44(50):16563-16573. doi:<a href=\"https://doi.org/10.1021/bi0516879\">10.1021/bi0516879</a>","ista":"Sohn J, Parks J, Buhrman G, Brown P, Kristjánsdóttir K, Safi A, Edelsbrunner H, Yang W, Rudolph J. 2005. Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate. Biochemistry. 44(50), 16563–16573.","short":"J. Sohn, J. Parks, G. Buhrman, P. Brown, K. Kristjánsdóttir, A. Safi, H. Edelsbrunner, W. Yang, J. Rudolph, Biochemistry 44 (2005) 16563–16573.","ieee":"J. Sohn <i>et al.</i>, “Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate,” <i>Biochemistry</i>, vol. 44, no. 50. ACS, pp. 16563–16573, 2005."},"extern":1,"issue":"50","date_created":"2018-12-11T12:06:16Z","publication_status":"published","month":"11","year":"2005","abstract":[{"text":"Cdc25 phosphatases are key activators of the eukaryotic cell cycle and compelling anticancer targets because their overexpression has been associated with numerous cancers. However, drug discovery targeting these phosphatases has been hampered by the lack of structural information about how Cdc25s interact with their native protein substrates, the cyclin-dependent kinases. Herein, we predict a docked orientation for Cdc25B with its Cdk2-pTpY-CycA protein substrate by a rigid-body docking method and refine the docked models with full-scale molecular dynamics simulations and minimization. We validate the stable ensemble structure experimentally by a variety of in vitro and in vivo techniques. Specifically, we compare our model with a crystal structure of the substrate-trapping mutant of Cdc25B. We identify and validate in vivo a novel hot-spot residue on Cdc25B (Arg492) that plays a central role in protein substrate recognition. We identify a hot-spot residue on the Substrate Cdk2 (Asp206) and confirm its interaction with hot-spot residues on Cdc25 using hot-spot swapping and double mutant cycles to derive interaction energies. Our experimentally validated model is consistent with previous studies of Cdk2 and its interaction partners and initiates the opportunity for drug discovery of inhibitors that target the remote binding sites of this protein-protein interaction.","lang":"eng"}],"type":"journal_article","day":"24","quality_controlled":0},{"volume":18,"publist_id":"1982","date_updated":"2021-01-12T07:54:47Z","publisher":"Wiley-Blackwell","date_published":"2005-09-01T00:00:00Z","author":[{"first_name":"Nicholas H","full_name":"Nicholas Barton","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jitka","full_name":"Jitka Polechova","last_name":"Polechova","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"}],"page":"1186 - 1190","intvolume":"        18","title":"The limitations of adaptive dynamics as a model of evolution","status":"public","publication":"Journal of Evolutionary Biology","_id":"4138","doi":"10.1111/j.1420-9101.2005.00943.x","citation":{"ieee":"N. H. Barton and J. Polechova, “The limitations of adaptive dynamics as a model of evolution,” <i>Journal of Evolutionary Biology</i>, vol. 18, no. 5. Wiley-Blackwell, pp. 1186–1190, 2005.","short":"N.H. Barton, J. Polechova, Journal of Evolutionary Biology 18 (2005) 1186–1190.","ista":"Barton NH, Polechova J. 2005. The limitations of adaptive dynamics as a model of evolution. Journal of Evolutionary Biology. 18(5), 1186–1190.","ama":"Barton NH, Polechova J. The limitations of adaptive dynamics as a model of evolution. <i>Journal of Evolutionary Biology</i>. 2005;18(5):1186-1190. doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2005.00943.x\">10.1111/j.1420-9101.2005.00943.x</a>","chicago":"Barton, Nicholas H, and Jitka Polechova. “The Limitations of Adaptive Dynamics as a Model of Evolution.” <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1111/j.1420-9101.2005.00943.x\">https://doi.org/10.1111/j.1420-9101.2005.00943.x</a>.","mla":"Barton, Nicholas H., and Jitka Polechova. “The Limitations of Adaptive Dynamics as a Model of Evolution.” <i>Journal of Evolutionary Biology</i>, vol. 18, no. 5, Wiley-Blackwell, 2005, pp. 1186–90, doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2005.00943.x\">10.1111/j.1420-9101.2005.00943.x</a>.","apa":"Barton, N. H., &#38; Polechova, J. (2005). The limitations of adaptive dynamics as a model of evolution. <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1420-9101.2005.00943.x\">https://doi.org/10.1111/j.1420-9101.2005.00943.x</a>"},"issue":"5","extern":1,"date_created":"2018-12-11T12:07:10Z","publication_status":"published","month":"09","year":"2005","day":"01","quality_controlled":0,"abstract":[{"text":"Adaptive dynamics describes the evolution of an asexual population through the successive substitution of mutations of small effect. Waxman &amp; Gavrilets (2005) give an excellent overview of the method and its applications. In this note, we focus on the plausibility of the key assumption that mutations have small effects, and the consequences of relaxing that assumption. We argue that: (i) successful mutations often have large effects; (ii) such mutations generate a qualitatively different evolutionary pattern, which is inherently stochastic; and (iii) in models of competition for a continuous resource, selection becomes very weak once several phenotypes are established. This makes the effects of introducing new mutations unpredictable using the methods of adaptive dynamics.\n\nWe should make clear at the outset that our criticism is of methods that rely on local analysis of fitness gradients (eqn 2 of Waxman &amp; Gavrilets, 2005), and not of the broader idea that evolution can be understood by examining the invasion of successive mutations. We use the term ‘adaptive dynamics’ to refer to the former technique, and contrast it with a more general population genetic analysis of probabilities of invasion.","lang":"eng"}],"type":"journal_article"},{"date_created":"2018-12-11T12:07:12Z","extern":"1","issue":"4","oa_version":"None","abstract":[{"text":"Wnt11 plays a central role in tissue morphogenesis during vertebrate gastrulation, but the molecular and cellular mechanisms by which Wnt11 exerts its effects remain poorly understood. Here, we show that Wnt11 functions during zebrafish gastrulation by regulating the cohesion of mesodermal and endodermal (mesendodermal) progenitor cells. Importantly, we demonstrate that Wnt11 activity in this process is mediated by the GTPase Rab5, a key regulator of early endocytosis, as blocking Rab5c activity in wild-type embryos phenocopies slb/wnt11 mutants, and enhancing Rab5c activity in slb/wnt11 mutant embryos rescues the mutant phenotype. In addition, we find that Wnt11 and Rab5c control the endocytosis of E-cadherin and are required in mesendodermal cells for E-cadherin-mediated cell cohesion. Together, our results suggest that Wnt11 controls tissue morphogenesis by modulating E-cadherin-mediated cell cohesion through Rab5c, a novel mechanism of Wnt signaling in gastrulation.","lang":"eng"}],"type":"journal_article","day":"01","publication_status":"published","month":"10","year":"2005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         9","date_published":"2005-10-01T00:00:00Z","author":[{"last_name":"Ulrich","full_name":"Ulrich, Florian","first_name":"Florian"},{"full_name":"Krieg, Michael","first_name":"Michael","last_name":"Krieg"},{"full_name":"Schötz, Eva","first_name":"Eva","last_name":"Schötz"},{"last_name":"Link","first_name":"Vinzenz","full_name":"Link, Vinzenz"},{"last_name":"Castanon","full_name":"Castanon, Irinka","first_name":"Irinka"},{"first_name":"Viktor","full_name":"Schnabel, Viktor","last_name":"Schnabel"},{"last_name":"Taubenberger","full_name":"Taubenberger, Anna","first_name":"Anna"},{"full_name":"Müller, Daniel","first_name":"Daniel","last_name":"Müller"},{"last_name":"Puech","first_name":"Pierre","full_name":"Puech, Pierre"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"page":"555 - 564","publisher":"Cell Press","article_processing_charge":"No","language":[{"iso":"eng"}],"volume":9,"publist_id":"1977","date_updated":"2021-01-12T07:54:50Z","_id":"4144","publication":"Developmental Cell","doi":"10.1016/j.devcel.2005.08.011","citation":{"short":"F. Ulrich, M. Krieg, E. Schötz, V. Link, I. Castanon, V. Schnabel, A. Taubenberger, D. Müller, P. Puech, C.-P.J. Heisenberg, Developmental Cell 9 (2005) 555–564.","ieee":"F. Ulrich <i>et al.</i>, “Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin,” <i>Developmental Cell</i>, vol. 9, no. 4. Cell Press, pp. 555–564, 2005.","ama":"Ulrich F, Krieg M, Schötz E, et al. Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. <i>Developmental Cell</i>. 2005;9(4):555-564. doi:<a href=\"https://doi.org/10.1016/j.devcel.2005.08.011\">10.1016/j.devcel.2005.08.011</a>","ista":"Ulrich F, Krieg M, Schötz E, Link V, Castanon I, Schnabel V, Taubenberger A, Müller D, Puech P, Heisenberg C-PJ. 2005. Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. Developmental Cell. 9(4), 555–564.","apa":"Ulrich, F., Krieg, M., Schötz, E., Link, V., Castanon, I., Schnabel, V., … Heisenberg, C.-P. J. (2005). Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2005.08.011\">https://doi.org/10.1016/j.devcel.2005.08.011</a>","mla":"Ulrich, Florian, et al. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin.” <i>Developmental Cell</i>, vol. 9, no. 4, Cell Press, 2005, pp. 555–64, doi:<a href=\"https://doi.org/10.1016/j.devcel.2005.08.011\">10.1016/j.devcel.2005.08.011</a>.","chicago":"Ulrich, Florian, Michael Krieg, Eva Schötz, Vinzenz Link, Irinka Castanon, Viktor Schnabel, Anna Taubenberger, Daniel Müller, Pierre Puech, and Carl-Philipp J Heisenberg. “Wnt11 Functions in Gastrulation by Controlling Cell Cohesion through Rab5c and E-Cadherin.” <i>Developmental Cell</i>. Cell Press, 2005. <a href=\"https://doi.org/10.1016/j.devcel.2005.08.011\">https://doi.org/10.1016/j.devcel.2005.08.011</a>."},"title":"Wnt11 functions in gastrulation by controlling cell cohesion through Rab5c and E-cadherin","status":"public"},{"publication":"Journal of Cell Science","_id":"4155","doi":"10.1242/​jcs.02547","citation":{"short":"P. Puech, A. Taubenberger, F. Ulrich, M. Krieg, D. Mueller, C.-P.J. Heisenberg, Journal of Cell Science 118 (2005) 4199–4206.","ieee":"P. Puech, A. Taubenberger, F. Ulrich, M. Krieg, D. Mueller, and C.-P. J. Heisenberg, “Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy,” <i>Journal of Cell Science</i>, vol. 118, no. 18. Company of Biologists, pp. 4199–4206, 2005.","ama":"Puech P, Taubenberger A, Ulrich F, Krieg M, Mueller D, Heisenberg C-PJ. Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. <i>Journal of Cell Science</i>. 2005;118(18):4199-4206. doi:<a href=\"https://doi.org/10.1242/​jcs.02547\">10.1242/​jcs.02547</a>","ista":"Puech P, Taubenberger A, Ulrich F, Krieg M, Mueller D, Heisenberg C-PJ. 2005. Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. Journal of Cell Science. 118(18), 4199–4206.","apa":"Puech, P., Taubenberger, A., Ulrich, F., Krieg, M., Mueller, D., &#38; Heisenberg, C.-P. J. (2005). Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/​jcs.02547\">https://doi.org/10.1242/​jcs.02547</a>","chicago":"Puech, Pierre, Anna Taubenberger, Florian Ulrich, Michael Krieg, Daniel Mueller, and Carl-Philipp J Heisenberg. “Measuring Cell Adhesion Forces of Primary Gastrulating Cells from Zebrafish Using Atomic Force Microscopy.” <i>Journal of Cell Science</i>. Company of Biologists, 2005. <a href=\"https://doi.org/10.1242/​jcs.02547\">https://doi.org/10.1242/​jcs.02547</a>.","mla":"Puech, Pierre, et al. “Measuring Cell Adhesion Forces of Primary Gastrulating Cells from Zebrafish Using Atomic Force Microscopy.” <i>Journal of Cell Science</i>, vol. 118, no. 18, Company of Biologists, 2005, pp. 4199–206, doi:<a href=\"https://doi.org/10.1242/​jcs.02547\">10.1242/​jcs.02547</a>."},"title":"Measuring cell adhesion forces of primary gastrulating cells from zebrafish using atomic force microscopy","status":"public","intvolume":"       118","date_published":"2005-01-01T00:00:00Z","page":"4199 - 4206","author":[{"first_name":"Pierre","full_name":"Puech, Pierre","last_name":"Puech"},{"last_name":"Taubenberger","full_name":"Taubenberger, Anna","first_name":"Anna"},{"first_name":"Florian","full_name":"Ulrich, Florian","last_name":"Ulrich"},{"last_name":"Krieg","full_name":"Krieg, Michael","first_name":"Michael"},{"last_name":"Mueller","full_name":"Mueller, Daniel","first_name":"Daniel"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Company of Biologists","language":[{"iso":"eng"}],"article_processing_charge":"No","publist_id":"1964","volume":118,"date_updated":"2021-01-12T07:54:54Z","abstract":[{"lang":"eng","text":"During vertebrate gastrulation, progenitor cells of different germ layers acquire specific adhesive properties that contribute to germ layer formation and separation. Wnt signals have been suggested to function in this process by modulating the different levels of adhesion between the germ layers, however, direct evidence for this is still lacking. Here we show that Wnt11, a key signal regulating gastrulation movements, is needed for the adhesion of zebrafish mesendodermal progenitor cells to fibronectin, an abundant extracellular matrix component during gastrulation. To measure this effect, we developed an assay to quantify the adhesion of single zebrafish primary mesendodermal progenitors using atomic-force microscopy (AFM). We observed significant differences in detachment force and work between cultured mesendodermal progenitors from wild-type embryos and from slb/wit11 mutant embryos, which carry a loss-of-function mutation in the wnt11 gene, when tested on fibronectin-coated substrates. These differences were probably due to reduced adhesion to the fibronectin substrate as neither the overall cell morphology nor the cell elasticity grossly differed between wild-type and mutant cells. Furthermore, in the presence of inhibitors of fibronectin-integrin binding, such as RGD peptides, the adhesion force and work were strongly decreased, indicating that integrins are involved in the binding of mesendodermal progenitors in our assay. These findings demonstrate that AFM can be used to quantitatively determine the substrate-adhesion of cultured primary gastrulating cells and provide insight into the role of Wnt11 signalling in modulating cell adhesion at the single cell scale."}],"type":"journal_article","day":"01","publication_status":"published","month":"01","year":"2005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:07:16Z","extern":"1","oa_version":"None","issue":"18"},{"date_created":"2018-12-11T12:07:21Z","extern":"1","issue":"4","oa_version":"None","abstract":[{"text":"In this study, we elucidate the roles of the winged-helix transcription factor Foxa2 in ventral CNS development in zebrafish. Through cloning of monorail (mol), which we find encodes the transcription factor Foxa2, and phenotypic analysis of mol(-/-) embryos, we show that floorplate is induced in the absence of Foxa2 function but fails to further differentiate. In mol(-/-) mutants, expression of Foxa and Hh family genes is not maintained in floorplate cells and lateral expansion of the floorplate fails to occur. Our results suggest that this is due to defects both in the regulation of Hh activity in medial floorplate cells as well as cell-autonomous requirements for Foxa2 in the prospective laterally positioned floorplate cells themselves. Foxa2 is also required for induction and/or patterning of several distinct cell types in the ventral CNS. Serotonergic neurones of the raphe nucleus and the trochlear motor nucleus are absent in mol(-/-) embryos, and oculomotor and facial motoneurones ectopically occupy ventral CNS midline positions in the midbrain and hindbrain. There is also a severe reduction of prospective oligodendrocytes in the midbrain and hindbrain. Finally, in the absence of Foxa2, at least two likely Hh pathway target genes are ectopically expressed in more dorsal regions of the midbrain and hindbrain ventricular neuroepithelium, raising the possibility that Foxa2 activity may normally be required to limit the range of action of secreted Hh proteins.","lang":"eng"}],"type":"journal_article","day":"15","publication_status":"published","year":"2005","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","intvolume":"       132","date_published":"2005-02-15T00:00:00Z","page":"645 - 658","author":[{"full_name":"Norton, Will","first_name":"Will","last_name":"Norton"},{"full_name":"Mangoli, Maryam","first_name":"Maryam","last_name":"Mangoli"},{"last_name":"Lele","full_name":"Lele, Zsolt","first_name":"Zsolt"},{"last_name":"Pogoda","full_name":"Pogoda, Hans","first_name":"Hans"},{"last_name":"Diamond","first_name":"Brianne","full_name":"Diamond, Brianne"},{"last_name":"Mercurio","full_name":"Mercurio, Sara","first_name":"Sara"},{"last_name":"Russell","full_name":"Russell, Claire","first_name":"Claire"},{"first_name":"Hiroki","full_name":"Teraoka, Hiroki","last_name":"Teraoka"},{"last_name":"Stickney","full_name":"Stickney, Heather","first_name":"Heather"},{"last_name":"Rauch","first_name":"Gerd","full_name":"Rauch, Gerd"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Houart","first_name":"Corinne","full_name":"Houart, Corinne"},{"last_name":"Schilling","full_name":"Schilling, Thomas","first_name":"Thomas"},{"first_name":"Hans","full_name":"Frohnhoefer, Hans","last_name":"Frohnhoefer"},{"first_name":"Sepand","full_name":"Rastegar, Sepand","last_name":"Rastegar"},{"last_name":"Neumann","full_name":"Neumann, Carl","first_name":"Carl"},{"full_name":"Gardiner, R Mark","first_name":"R Mark","last_name":"Gardiner"},{"first_name":"Uwe","full_name":"Strähle, Uwe","last_name":"Strähle"},{"last_name":"Geisler","first_name":"Robert","full_name":"Geisler, Robert"},{"last_name":"Rees","full_name":"Rees, Michelle","first_name":"Michelle"},{"last_name":"Talbot","full_name":"Talbot, William","first_name":"William"},{"full_name":"Wilson, Stephen","first_name":"Stephen","last_name":"Wilson"}],"publisher":"Company of Biologists","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":132,"publist_id":"1952","date_updated":"2021-01-12T07:55:00Z","publication":"Development","_id":"4167","doi":"10.1242/dev.01611","citation":{"ama":"Norton W, Mangoli M, Lele Z, et al. Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. <i>Development</i>. 2005;132(4):645-658. doi:<a href=\"https://doi.org/10.1242/dev.01611\">10.1242/dev.01611</a>","ista":"Norton W, Mangoli M, Lele Z, Pogoda H, Diamond B, Mercurio S, Russell C, Teraoka H, Stickney H, Rauch G, Heisenberg C-PJ, Houart C, Schilling T, Frohnhoefer H, Rastegar S, Neumann C, Gardiner RM, Strähle U, Geisler R, Rees M, Talbot W, Wilson S. 2005. Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. Development. 132(4), 645–658.","short":"W. Norton, M. Mangoli, Z. Lele, H. Pogoda, B. Diamond, S. Mercurio, C. Russell, H. Teraoka, H. Stickney, G. Rauch, C.-P.J. Heisenberg, C. Houart, T. Schilling, H. Frohnhoefer, S. Rastegar, C. Neumann, R.M. Gardiner, U. Strähle, R. Geisler, M. Rees, W. Talbot, S. Wilson, Development 132 (2005) 645–658.","ieee":"W. Norton <i>et al.</i>, “Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones,” <i>Development</i>, vol. 132, no. 4. Company of Biologists, pp. 645–658, 2005.","apa":"Norton, W., Mangoli, M., Lele, Z., Pogoda, H., Diamond, B., Mercurio, S., … Wilson, S. (2005). Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.01611\">https://doi.org/10.1242/dev.01611</a>","chicago":"Norton, Will, Maryam Mangoli, Zsolt Lele, Hans Pogoda, Brianne Diamond, Sara Mercurio, Claire Russell, et al. “Monorail/Foxa2 Regulates Floorplate Differentiation and Specification of Oligodendrocytes, Serotonergic Raphe Neurones and Cranial Motoneurones.” <i>Development</i>. Company of Biologists, 2005. <a href=\"https://doi.org/10.1242/dev.01611\">https://doi.org/10.1242/dev.01611</a>.","mla":"Norton, Will, et al. “Monorail/Foxa2 Regulates Floorplate Differentiation and Specification of Oligodendrocytes, Serotonergic Raphe Neurones and Cranial Motoneurones.” <i>Development</i>, vol. 132, no. 4, Company of Biologists, 2005, pp. 645–58, doi:<a href=\"https://doi.org/10.1242/dev.01611\">10.1242/dev.01611</a>."},"title":"Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones","status":"public"},{"date_updated":"2021-01-12T07:55:02Z","publist_id":"1947","volume":132,"language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Company of Biologists","page":"1187 - 1198","author":[{"full_name":"Montero, Juan","first_name":"Juan","last_name":"Montero"},{"full_name":"Carvalho, Lara","first_name":"Lara","last_name":"Carvalho"},{"last_name":"Wilsch Bräuninger","full_name":"Wilsch Bräuninger, Michaela","first_name":"Michaela"},{"full_name":"Kilian, Beate","first_name":"Beate","last_name":"Kilian"},{"last_name":"Mustafa","first_name":"Chigdem","full_name":"Mustafa, Chigdem"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"date_published":"2005-03-15T00:00:00Z","intvolume":"       132","status":"public","title":"Shield formation at the onset of zebrafish gastrulation","citation":{"apa":"Montero, J., Carvalho, L., Wilsch Bräuninger, M., Kilian, B., Mustafa, C., &#38; Heisenberg, C.-P. J. (2005). Shield formation at the onset of zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.01667\">https://doi.org/10.1242/dev.01667</a>","mla":"Montero, Juan, et al. “Shield Formation at the Onset of Zebrafish Gastrulation.” <i>Development</i>, vol. 132, no. 6, Company of Biologists, 2005, pp. 1187–98, doi:<a href=\"https://doi.org/10.1242/dev.01667\">10.1242/dev.01667</a>.","chicago":"Montero, Juan, Lara Carvalho, Michaela Wilsch Bräuninger, Beate Kilian, Chigdem Mustafa, and Carl-Philipp J Heisenberg. “Shield Formation at the Onset of Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2005. <a href=\"https://doi.org/10.1242/dev.01667\">https://doi.org/10.1242/dev.01667</a>.","short":"J. Montero, L. Carvalho, M. Wilsch Bräuninger, B. Kilian, C. Mustafa, C.-P.J. Heisenberg, Development 132 (2005) 1187–1198.","ieee":"J. Montero, L. Carvalho, M. Wilsch Bräuninger, B. Kilian, C. Mustafa, and C.-P. J. Heisenberg, “Shield formation at the onset of zebrafish gastrulation,” <i>Development</i>, vol. 132, no. 6. Company of Biologists, pp. 1187–1198, 2005.","ama":"Montero J, Carvalho L, Wilsch Bräuninger M, Kilian B, Mustafa C, Heisenberg C-PJ. Shield formation at the onset of zebrafish gastrulation. <i>Development</i>. 2005;132(6):1187-1198. doi:<a href=\"https://doi.org/10.1242/dev.01667\">10.1242/dev.01667</a>","ista":"Montero J, Carvalho L, Wilsch Bräuninger M, Kilian B, Mustafa C, Heisenberg C-PJ. 2005. Shield formation at the onset of zebrafish gastrulation. Development. 132(6), 1187–1198."},"doi":"10.1242/dev.01667","_id":"4171","publication":"Development","issue":"6","oa_version":"None","extern":"1","date_created":"2018-12-11T12:07:22Z","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2005","publication_status":"published","day":"15","type":"journal_article","abstract":[{"text":"During vertebrate gastrulation, the three germ layers, ectoderm, mesoderm and endoderm are formed, and the resulting progenitor cells are brought into the positions from which they will later contribute more complex tissues and organs. A core element in this process is the internalization of mesodermal and endodermal progenitors at the onset of gastrulation. Although many of the molecules that induce mesendoderm have been identified, much less is known about the cellular mechanisms underlying mesendodermal cell internalization and germ layer formation. Here we show that at the onset of zebrafish gastrulation, mesendodermal progenitors in dorsal/axial regions of the germ ring internalize by single cell delamination. Once internalized, mesendodermal progenitors upregulate ECadherin (Cadherin 1) expression, become increasingly motile and eventually migrate along the overlying epiblast (ectodermal) cell layer towards the animal pole of the gastrula. When E-Cadherin function is compromised, mesendodermal progenitors still internalize, but, with gastrulation proceeding, fail to elongate and efficiently migrate along the epiblast, whereas epiblast cells themselves exhibit reduced radial cell intercalation movements. This indicates that cadherin-mediated cell-cell adhesion is needed within the forming shield for both epiblast cell intercalation, and mesendodermal progenitor cell elongation and migration during zebrafish gastrulation. Our data provide insight into the cellular mechanisms underlying mesendodermal progenitor cell internalization and subsequent migration during zebrafish gastrulation, and the role of cadherin-mediated cell-cell adhesion in these processes.","lang":"eng"}]},{"title":"Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure","status":"public","publication":"Mechanisms of Development","_id":"4183","doi":"10.1016/j.mod.2005.06.010","citation":{"ista":"Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2005. Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. Mechanisms of Development. 122(Supplement 1), S112–S113.","ama":"Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. <i>Mechanisms of Development</i>. 2005;122(Supplement 1):S112-S113. doi:<a href=\"https://doi.org/10.1016/j.mod.2005.06.010\">10.1016/j.mod.2005.06.010</a>","ieee":"M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg, “Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure,” <i>Mechanisms of Development</i>, vol. 122, no. Supplement 1. Elsevier, pp. S112–S113, 2005.","short":"M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Mechanisms of Development 122 (2005) S112–S113.","mla":"Köppen, Mathias, et al. “Misshapen Mediates Actin-Based Cell Contraction during Zebrafish Epiboly and Drosophila Dorsal Closure.” <i>Mechanisms of Development</i>, vol. 122, no. Supplement 1, Elsevier, 2005, pp. S112–13, doi:<a href=\"https://doi.org/10.1016/j.mod.2005.06.010\">10.1016/j.mod.2005.06.010</a>.","chicago":"Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and Carl-Philipp J Heisenberg. “Misshapen Mediates Actin-Based Cell Contraction during Zebrafish Epiboly and Drosophila Dorsal Closure.” <i>Mechanisms of Development</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.mod.2005.06.010\">https://doi.org/10.1016/j.mod.2005.06.010</a>.","apa":"Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., &#38; Heisenberg, C.-P. J. (2005). Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. <i>Mechanisms of Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mod.2005.06.010\">https://doi.org/10.1016/j.mod.2005.06.010</a>"},"publisher":"Elsevier","article_processing_charge":"No","language":[{"iso":"eng"}],"publist_id":"1936","volume":122,"date_updated":"2021-01-12T07:55:07Z","intvolume":"       122","date_published":"2005-01-01T00:00:00Z","author":[{"last_name":"Köppen","full_name":"Köppen, Mathias","first_name":"Mathias"},{"full_name":"Fernández, Beatriz","first_name":"Beatriz","last_name":"Fernández"},{"last_name":"Carvalho","full_name":"Carvalho, Lara","first_name":"Lara"},{"last_name":"Jacinto","full_name":"Jacinto, António","first_name":"António"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"page":"S112 - S113","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2005","month":"01","abstract":[{"text":"The spreading of an epithelial cell sheet over a substrate is a common process during embryogenesis. Typical examples include epiboly during zebrafish gastrulation and Drosophila dorsal closure. We provide evidence that in both cases, actin-based contraction of the leading edge of the epithelium is of critical importance.","lang":"eng"}],"acknowledgement":"Poster Abstract","type":"journal_article","day":"01","extern":"1","issue":"Supplement 1","oa_version":"None","date_created":"2018-12-11T12:07:27Z"},{"type":"journal_article","abstract":[{"text":"We examined causes of speciation in asexual populations in both sympatry and parapatry, providing an alternative explanation for the speciation patterns reported by Dieckmann and Doebeli (1999) and Doebeli and Dieckmann (2003). Both in sympatry and parapatry, they find that speciation occurs relatively easily. We reveal that in the sympatric clonal model, the equilibrium distribution is continuous and the disruptive selection driving evolution of discrete clusters is only transient. Hence, if discrete phenotypes are to remain stable in the sympatric sexual model, there should be some source of nontransient disruptive selection that will drive evolution of assortment. We analyze sexually reproducing populations using the Bulmer’s infinitesimal model and show that cost-free assortment alone leads to speciation and disruptive selection only arises when the optimal distribution cannot be matched—in this example, because the phenotypic range is limited. In addition, Doebeli and Dieckmann’s analyses assumed a high genetic variance and a high mutation rate. Thus, these theoretical models do not support the conclusion that sympatric speciation is a likely outcome of competition for resources. In their parapatric model (Doebeli and Dieckmann 2003), clustering into distinct phenotypes is driven by edge effects, rather than by frequency-dependent competition.","lang":"eng"}],"quality_controlled":0,"day":"01","year":"2005","month":"06","publication_status":"published","date_created":"2018-12-11T12:07:50Z","extern":1,"issue":"6","doi":"10.1111/j.0014-3820.2005.tb01771.x","citation":{"short":"J. Polechova, N.H. Barton, Evolution; International Journal of Organic Evolution 59 (2005) 1194–1210.","ieee":"J. Polechova and N. H. Barton, “Speciation through competition: A critical review,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 59, no. 6. Wiley-Blackwell, pp. 1194–1210, 2005.","ama":"Polechova J, Barton NH. Speciation through competition: A critical review. <i>Evolution; International Journal of Organic Evolution</i>. 2005;59(6):1194-1210. doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">10.1111/j.0014-3820.2005.tb01771.x</a>","ista":"Polechova J, Barton NH. 2005. Speciation through competition: A critical review. Evolution; International Journal of Organic Evolution. 59(6), 1194–1210.","apa":"Polechova, J., &#38; Barton, N. H. (2005). Speciation through competition: A critical review. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">https://doi.org/10.1111/j.0014-3820.2005.tb01771.x</a>","mla":"Polechova, Jitka, and Nicholas H. Barton. “Speciation through Competition: A Critical Review.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 59, no. 6, Wiley-Blackwell, 2005, pp. 1194–210, doi:<a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">10.1111/j.0014-3820.2005.tb01771.x</a>.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Speciation through Competition: A Critical Review.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2005. <a href=\"https://doi.org/10.1111/j.0014-3820.2005.tb01771.x\">https://doi.org/10.1111/j.0014-3820.2005.tb01771.x</a>."},"_id":"4249","publication":"Evolution; International Journal of Organic Evolution","status":"public","title":"Speciation through competition: A critical review","intvolume":"        59","page":"1194 - 1210","author":[{"full_name":"Jitka Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","orcid":"0000-0003-0951-3112"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Nicholas Barton"}],"date_published":"2005-06-01T00:00:00Z","publisher":"Wiley-Blackwell","date_updated":"2021-01-12T07:55:36Z","publist_id":"1849","volume":59},{"intvolume":"       169","date_published":"2005-03-01T00:00:00Z","page":"2353 - 2370","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Nicholas Barton","first_name":"Nicholas H"},{"last_name":"Otto","first_name":"Sarah","full_name":"Otto, Sarah P"}],"publisher":"Genetics Society of America","publist_id":"1846","volume":169,"date_updated":"2021-01-12T07:55:37Z","publication":"Genetics","_id":"4251","citation":{"ieee":"N. H. Barton and S. Otto, “Evolution of recombination due to random drift,” <i>Genetics</i>, vol. 169, no. 4. Genetics Society of America, pp. 2353–2370, 2005.","short":"N.H. Barton, S. Otto, Genetics 169 (2005) 2353–2370.","ista":"Barton NH, Otto S. 2005. Evolution of recombination due to random drift. Genetics. 169(4), 2353–2370.","ama":"Barton NH, Otto S. Evolution of recombination due to random drift. <i>Genetics</i>. 2005;169(4):2353-2370. doi:<a href=\"https://doi.org/10.1534/genetics.104.032821\">10.1534/genetics.104.032821</a>","mla":"Barton, Nicholas H., and Sarah Otto. “Evolution of Recombination Due to Random Drift.” <i>Genetics</i>, vol. 169, no. 4, Genetics Society of America, 2005, pp. 2353–70, doi:<a href=\"https://doi.org/10.1534/genetics.104.032821\">10.1534/genetics.104.032821</a>.","chicago":"Barton, Nicholas H, and Sarah Otto. “Evolution of Recombination Due to Random Drift.” <i>Genetics</i>. Genetics Society of America, 2005. <a href=\"https://doi.org/10.1534/genetics.104.032821\">https://doi.org/10.1534/genetics.104.032821</a>.","apa":"Barton, N. H., &#38; Otto, S. (2005). Evolution of recombination due to random drift. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.104.032821\">https://doi.org/10.1534/genetics.104.032821</a>"},"doi":"10.1534/genetics.104.032821","title":"Evolution of recombination due to random drift","status":"public","date_created":"2018-12-11T12:07:51Z","extern":1,"issue":"4","abstract":[{"lang":"eng","text":"In finite populations subject to selection, genetic drift generates negative linkage disequilibrium, on average, even if selection acts independently (i.e. multiplicatively) upon all loci. Negative disequilibrium reduces the variance in fitness and hence, by FISHER's Fundamental Theorem (1930), slows the rate of increase in mean fitness. Modifiers that increase recombination eliminate the negative disequilibria that impede selection and consequently increase in frequency by 'hitch-hiking'. In addition, recombinant progeny are more fit on average than non-recombinant progeny when there is negative linkage disequilibrium and loci interact multiplicatively. For both these reasons, stochastic fluctuations in linkage disequilibrium in finite populations favor the evolution of increased rates of recombination, even in the absence of epistatic interactions among loci and even when disequilibrium is initially absent. The method developed within this paper quantifies the strength of selection on a modifier allele that increases recombination due to stochastically generated linkage disequilibria. The analysis indicates that, in a population subject to multiplicative selection, genetic associations generated by drift do select for increased recombination, a result that is confirmed by Monte Carlo simulations. Selection for a modifier that increases recombination is highest when linkage among all loci is tight, when beneficial alleles rise from low to high frequency, and when the population size is small."}],"type":"journal_article","day":"01","quality_controlled":0,"publication_status":"published","year":"2005","month":"03"},{"date_created":"2018-12-11T12:07:51Z","extern":1,"issue":"1459","type":"journal_article","abstract":[{"lang":"eng","text":"Empirical studies of quantitative genetic variation have revealed robust patterns that are observed both across traits and across species. However, these patterns have no compelling explanation, and some of the observations even appear to be mutually incompatible. We review and extend a major class of theoretical models, ‘mutation–selection models’, that have been proposed to explain quantitative genetic variation. We also briefly review an alternative class of ‘balancing selection models’. We consider to what extent the models are compatible with the general observations, and argue that a key issue is understanding and modelling pleiotropy. We discuss some"}],"quality_controlled":0,"day":"29","month":"07","year":"2005","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569515/"}],"intvolume":"       360","author":[{"last_name":"Johnson","first_name":"Toby","full_name":"Johnson, Toby"},{"full_name":"Nicholas Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"page":"1411 - 1425","date_published":"2005-07-29T00:00:00Z","publisher":"Royal Society, The","date_updated":"2021-01-12T07:55:38Z","oa":1,"publist_id":"1847","volume":360,"doi":"10.1098/rstb.2005.1667","citation":{"apa":"Johnson, T., &#38; Barton, N. H. (2005). Theoretical models of selection and mutationon quantitative traits. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2005.1667\">https://doi.org/10.1098/rstb.2005.1667</a>","mla":"Johnson, Toby, and Nicholas H. Barton. “Theoretical Models of Selection and Mutationon Quantitative Traits.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 360, no. 1459, Royal Society, The, 2005, pp. 1411–25, doi:<a href=\"https://doi.org/10.1098/rstb.2005.1667\">10.1098/rstb.2005.1667</a>.","chicago":"Johnson, Toby, and Nicholas H Barton. “Theoretical Models of Selection and Mutationon Quantitative Traits.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2005. <a href=\"https://doi.org/10.1098/rstb.2005.1667\">https://doi.org/10.1098/rstb.2005.1667</a>.","ama":"Johnson T, Barton NH. Theoretical models of selection and mutationon quantitative traits. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2005;360(1459):1411-1425. doi:<a href=\"https://doi.org/10.1098/rstb.2005.1667\">10.1098/rstb.2005.1667</a>","ista":"Johnson T, Barton NH. 2005. Theoretical models of selection and mutationon quantitative traits. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 360(1459), 1411–1425.","short":"T. Johnson, N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 360 (2005) 1411–1425.","ieee":"T. Johnson and N. H. Barton, “Theoretical models of selection and mutationon quantitative traits,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 360, no. 1459. Royal Society, The, pp. 1411–1425, 2005."},"_id":"4252","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","status":"public","title":"Theoretical models of selection and mutationon quantitative traits"},{"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","year":"2005","day":"01","quality_controlled":"1","abstract":[{"text":"We show that the idea of predicates on heap objects can be cast in the framework of predicate abstraction. This leads to an alternative view on the underlying concepts of three-valued shape analysis by Sagiv, Reps and Wilhelm. Our construction of the abstract post operator is analogous to the corresponding construction for classical predicate abstraction, except that predicates over objects on the heap take the place of state predicates, and boolean heaps (sets of bitvectors) take the place of boolean states (bitvectors). A program is abstracted to a program over boolean heaps. For each command of the program, the corresponding abstract command is effectively constructed by deductive reasoning, namely by the application of the weakest precondition operator and an entailment test. We thus obtain a symbolic framework for shape analysis.","lang":"eng"}],"type":"conference","oa_version":"None","title":"Boolean Heaps","status":"public","publication":"12th International Symposium on Static Analysis","doi":"10.1007/11547662_19","citation":{"ieee":"A. Podelski and T. Wies, “Boolean Heaps,” in <i>12th International Symposium on Static Analysis</i>, London, United Kingdom, 2005, vol. 3672, pp. 268–283.","short":"A. Podelski, T. Wies, in:, 12th International Symposium on Static Analysis, Springer, 2005, pp. 268–283.","ista":"Podelski A, Wies T. 2005. Boolean Heaps. 12th International Symposium on Static Analysis. SAS: Static Analysis Symposium, LNCS, vol. 3672, 268–283.","ama":"Podelski A, Wies T. Boolean Heaps. In: <i>12th International Symposium on Static Analysis</i>. Vol 3672. Springer; 2005:268-283. doi:<a href=\"https://doi.org/10.1007/11547662_19\">10.1007/11547662_19</a>","chicago":"Podelski, Andreas, and Thomas Wies. “Boolean Heaps.” In <i>12th International Symposium on Static Analysis</i>, 3672:268–83. Springer, 2005. <a href=\"https://doi.org/10.1007/11547662_19\">https://doi.org/10.1007/11547662_19</a>.","mla":"Podelski, Andreas, and Thomas Wies. “Boolean Heaps.” <i>12th International Symposium on Static Analysis</i>, vol. 3672, Springer, 2005, pp. 268–83, doi:<a href=\"https://doi.org/10.1007/11547662_19\">10.1007/11547662_19</a>.","apa":"Podelski, A., &#38; Wies, T. (2005). Boolean Heaps. In <i>12th International Symposium on Static Analysis</i> (Vol. 3672, pp. 268–283). London, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/11547662_19\">https://doi.org/10.1007/11547662_19</a>"},"publist_id":"1092","volume":3672,"date_updated":"2025-07-01T12:10:29Z","intvolume":"      3672","publication_identifier":{"isbn":["978-3-540-28584-7"]},"extern":"1","date_created":"2018-12-11T12:08:29Z","scopus_import":"1","alternative_title":["LNCS"],"_id":"4367","publisher":"Springer","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2005-01-01T00:00:00Z","author":[{"full_name":"Podelski, Andreas","first_name":"Andreas","last_name":"Podelski"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies","full_name":"Wies, Thomas","first_name":"Thomas"}],"conference":{"name":"SAS: Static Analysis Symposium","location":"London, United Kingdom","start_date":"2005-09-07","end_date":"2005-09-09"},"page":"268-283"},{"date_created":"2018-12-11T12:08:41Z","oa_version":"None","extern":"1","quality_controlled":"1","day":"12","type":"conference","abstract":[{"lang":"eng","text":"While a typical software component has a clearly specified (static) interface in terms of the methods and the input/output types they support, information about the correct sequencing of method calls the client must invoke is usually undocumented. In this paper, we propose a novel solution for automatically extracting such temporal specifications for Java classes. Given a Java class, and a safety property such as \"the exception E should not be raised\", the corresponding (dynamic) interface is the most general way of invoking the methods in the class so that the safety property is not violated. Our synthesis method first constructs a symbolic representation of the finite state-transition system obtained from the class using predicate abstraction. Constructing the interface then corresponds to solving a partial-information two-player game on this symbolic graph. We present a sound approach to solve this computationally-hard problem approximately using algorithms for learning finite automata and symbolic model checking for branching-time logics. We describe an implementation of the proposed techniques in the tool JIST--- Java Interface Synthesis Tool---and demonstrate that the tool can construct interfaces accurately and efficiently for sample Java2SDK library classes."}],"year":"2005","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","page":"98 - 109","author":[{"full_name":"Alur, Rajeev","first_name":"Rajeev","last_name":"Alur"},{"full_name":"Cerny, Pavol","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"},{"last_name":"Madhusudan","first_name":"P.","full_name":"Madhusudan, P."},{"full_name":"Nam, Wonhong","first_name":"Wonhong","last_name":"Nam"}],"conference":{"location":"Long Beach, CA, United States","start_date":"2005-01-12","end_date":"2005-01-14","name":"POPL: Principles of Programming Languages"},"date_published":"2005-01-12T00:00:00Z","date_updated":"2025-07-01T12:07:02Z","publist_id":"1053","language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"ACM","doi":"10.1145/1040305.1040314","citation":{"ama":"Alur R, Cerny P, Madhusudan P, Nam W. Synthesis of interface specifications for Java classes. In: <i>Proceedings of the 32nd ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages</i>. ACM; 2005:98-109. doi:<a href=\"https://doi.org/10.1145/1040305.1040314\">10.1145/1040305.1040314</a>","ista":"Alur R, Cerny P, Madhusudan P, Nam W. 2005. Synthesis of interface specifications for Java classes. Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages. POPL: Principles of Programming Languages, 98–109.","short":"R. Alur, P. Cerny, P. Madhusudan, W. Nam, in:, Proceedings of the 32nd ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, ACM, 2005, pp. 98–109.","ieee":"R. Alur, P. Cerny, P. Madhusudan, and W. Nam, “Synthesis of interface specifications for Java classes,” in <i>Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages</i>, Long Beach, CA, United States, 2005, pp. 98–109.","apa":"Alur, R., Cerny, P., Madhusudan, P., &#38; Nam, W. (2005). Synthesis of interface specifications for Java classes. In <i>Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages</i> (pp. 98–109). Long Beach, CA, United States: ACM. <a href=\"https://doi.org/10.1145/1040305.1040314\">https://doi.org/10.1145/1040305.1040314</a>","chicago":"Alur, Rajeev, Pavol Cerny, P. Madhusudan, and Wonhong Nam. “Synthesis of Interface Specifications for Java Classes.” In <i>Proceedings of the 32nd ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages</i>, 98–109. ACM, 2005. <a href=\"https://doi.org/10.1145/1040305.1040314\">https://doi.org/10.1145/1040305.1040314</a>.","mla":"Alur, Rajeev, et al. “Synthesis of Interface Specifications for Java Classes.” <i>Proceedings of the 32nd ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages</i>, ACM, 2005, pp. 98–109, doi:<a href=\"https://doi.org/10.1145/1040305.1040314\">10.1145/1040305.1040314</a>."},"publication":"Proceedings of the 32nd ACM SIGPLAN-SIGACT symposium on Principles of programming languages","_id":"4404","status":"public","title":"Synthesis of interface specifications for Java classes"}]