[{"title":"Time-varying Reeb graphs for continuous space-time data","author":[{"full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Harer","full_name":"Harer, John","first_name":"John"},{"first_name":"Ajith","full_name":"Mascarenhas, Ajith","last_name":"Mascarenhas"},{"first_name":"Valerio","last_name":"Pascucci","full_name":"Pascucci, Valerio"},{"first_name":"Jack","full_name":"Snoeyink, Jack","last_name":"Snoeyink"}],"page":"149 - 166","date_updated":"2021-01-12T07:53:34Z","status":"public","volume":41,"publist_id":"2158","month":"11","year":"2008","type":"journal_article","publication_status":"published","citation":{"ama":"Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying Reeb graphs for continuous space-time data. <i>Computational Geometry: Theory and Applications</i>. 2008;41(3):149-166. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2007.11.001\">10.1016/j.comgeo.2007.11.001</a>","ieee":"H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink, “Time-varying Reeb graphs for continuous space-time data,” <i>Computational Geometry: Theory and Applications</i>, vol. 41, no. 3. Elsevier, pp. 149–166, 2008.","apa":"Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., &#38; Snoeyink, J. (2008). Time-varying Reeb graphs for continuous space-time data. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2007.11.001\">https://doi.org/10.1016/j.comgeo.2007.11.001</a>","chicago":"Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci, and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.comgeo.2007.11.001\">https://doi.org/10.1016/j.comgeo.2007.11.001</a>.","ista":"Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 41(3), 149–166.","short":"H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational Geometry: Theory and Applications 41 (2008) 149–166.","mla":"Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” <i>Computational Geometry: Theory and Applications</i>, vol. 41, no. 3, Elsevier, 2008, pp. 149–66, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2007.11.001\">10.1016/j.comgeo.2007.11.001</a>."},"day":"01","publication":"Computational Geometry: Theory and Applications","_id":"3971","date_published":"2008-11-01T00:00:00Z","extern":1,"abstract":[{"lang":"eng","text":"The Reeb graph is a useful tool in visualizing real-valued data obtained from computational simulations of physical processes. We characterize the evolution of the Reeb graph of a time-varying continuous function defined in three-dimensional space. We show how to maintain the Reeb graph over time and compress the entire sequence of Reeb graphs into a single, partially persistent data structure, and augment this data structure with Betti numbers to describe the topology of level sets and with path seeds to assist in the fast extraction of level sets for visualization."}],"issue":"3","quality_controlled":0,"intvolume":"        41","publisher":"Elsevier","date_created":"2018-12-11T12:06:12Z","doi":"10.1016/j.comgeo.2007.11.001"},{"publisher":"ACM","date_created":"2018-12-11T12:06:13Z","doi":"10.1145/1377676.1377720","quality_controlled":0,"date_published":"2008-01-01T00:00:00Z","extern":1,"abstract":[{"lang":"eng","text":"Generalizing the concept of a Reeb graph, the Reeb space of a multivariate continuous mapping identifies points of the domain that belong to a common component of the preimage of a point in the range. We study the local and global structure of this space for generic, piecewise linear mappings on a combinatorial manifold."}],"day":"01","_id":"3974","conference":{"name":"SCG: Symposium on Computational Geometry"},"year":"2008","type":"conference","publication_status":"published","citation":{"ieee":"H. Edelsbrunner, J. Harer, and A. Patel, “Reeb spaces of piecewise linear mappings,” presented at the SCG: Symposium on Computational Geometry, 2008, pp. 242–250.","ama":"Edelsbrunner H, Harer J, Patel A. Reeb spaces of piecewise linear mappings. In: ACM; 2008:242-250. doi:<a href=\"https://doi.org/10.1145/1377676.1377720\">10.1145/1377676.1377720</a>","apa":"Edelsbrunner, H., Harer, J., &#38; Patel, A. (2008). Reeb spaces of piecewise linear mappings (pp. 242–250). Presented at the SCG: Symposium on Computational Geometry, ACM. <a href=\"https://doi.org/10.1145/1377676.1377720\">https://doi.org/10.1145/1377676.1377720</a>","mla":"Edelsbrunner, Herbert, et al. <i>Reeb Spaces of Piecewise Linear Mappings</i>. ACM, 2008, pp. 242–50, doi:<a href=\"https://doi.org/10.1145/1377676.1377720\">10.1145/1377676.1377720</a>.","ista":"Edelsbrunner H, Harer J, Patel A. 2008. Reeb spaces of piecewise linear mappings. SCG: Symposium on Computational Geometry, 242–250.","chicago":"Edelsbrunner, Herbert, John Harer, and Amit Patel. “Reeb Spaces of Piecewise Linear Mappings,” 242–50. ACM, 2008. <a href=\"https://doi.org/10.1145/1377676.1377720\">https://doi.org/10.1145/1377676.1377720</a>.","short":"H. Edelsbrunner, J. Harer, A. Patel, in:, ACM, 2008, pp. 242–250."},"publist_id":"2155","month":"01","date_updated":"2021-01-12T07:53:35Z","status":"public","author":[{"full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Harer, John","last_name":"Harer","first_name":"John"},{"first_name":"Amit","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","full_name":"Amit Patel","last_name":"Patel"}],"title":"Reeb spaces of piecewise linear mappings","page":"242 - 250"},{"date_updated":"2025-07-02T05:52:43Z","status":"public","title":"The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Storch, D.","last_name":"Storch","first_name":"D."},{"full_name":"Šizling, A.","last_name":"Šizling","first_name":"A."},{"full_name":"Reif, J.","last_name":"Reif","first_name":"J."},{"last_name":"Polechova","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka","orcid":"0000-0003-0951-3112"},{"last_name":"Šizlingová","full_name":"Šizlingová, E.","first_name":"E."},{"first_name":"K.","full_name":"Gaston, K.","last_name":"Gaston"}],"page":"771 - 784","year":"2008","publication_status":"published","type":"journal_article","citation":{"mla":"Storch, D., et al. “The Quest for a Null Model for Macroecological Patterns: Geometry of Species Distributions at Multiple Spatial Scales.” <i>Ecology Letters</i>, vol. 11, no. 8, Wiley, 2008, pp. 771–84, doi:<a href=\"https://doi.org/10.1111/j.1461-0248.2008.01206.x\">10.1111/j.1461-0248.2008.01206.x</a>.","chicago":"Storch, D., A. Šizling, J. Reif, Jitka Polechova, E. Šizlingová, and K. Gaston. “The Quest for a Null Model for Macroecological Patterns: Geometry of Species Distributions at Multiple Spatial Scales.” <i>Ecology Letters</i>. Wiley, 2008. <a href=\"https://doi.org/10.1111/j.1461-0248.2008.01206.x\">https://doi.org/10.1111/j.1461-0248.2008.01206.x</a>.","short":"D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, K. Gaston, Ecology Letters 11 (2008) 771–784.","ista":"Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. 2008. The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales. Ecology Letters. 11(8), 771–784.","apa":"Storch, D., Šizling, A., Reif, J., Polechova, J., Šizlingová, E., &#38; Gaston, K. (2008). The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales. <i>Ecology Letters</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1461-0248.2008.01206.x\">https://doi.org/10.1111/j.1461-0248.2008.01206.x</a>","ieee":"D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, and K. Gaston, “The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales,” <i>Ecology Letters</i>, vol. 11, no. 8. Wiley, pp. 771–784, 2008.","ama":"Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales. <i>Ecology Letters</i>. 2008;11(8):771-784. doi:<a href=\"https://doi.org/10.1111/j.1461-0248.2008.01206.x\">10.1111/j.1461-0248.2008.01206.x</a>"},"language":[{"iso":"eng"}],"volume":11,"publist_id":"1985","article_processing_charge":"No","month":"08","oa_version":"None","date_published":"2008-08-01T00:00:00Z","extern":"1","abstract":[{"text":"There have been several attempts to build a unified framework for macroecological patterns. However, these have mostly been based either on questionable assumptions or have had to be parameterized to obtain realistic predictions. Here, we propose a new model explicitly considering patterns of aggregated species distributions on multiple spatial scales, the property which lies behind all spatial macroecological patterns, using the idea we term ‘generalized fractals’. Species’ spatial distributions were modelled by a random hierarchical process in which the original ‘habitat’ patches were randomly replaced by sets of smaller patches nested within them, and the statistical properties of modelled species assemblages were compared with macroecological patterns in observed bird data. Without parameterization based on observed patterns, this simple model predicts realistic patterns of species abundance, distribution and diversity, including fractal-like spatial distributions, the frequency distribution of species occupancies/abundances and the species–area relationship. Although observed macroecological patterns may differ in some quantitative properties, our concept of random hierarchical aggregation can be considered as an appropriate null model of fundamental macroecological patterns which can potentially be modified to accommodate ecologically important variables.","lang":"eng"}],"day":"01","publication":"Ecology Letters","_id":"4135","intvolume":"        11","date_created":"2018-12-11T12:07:09Z","publisher":"Wiley","doi":"10.1111/j.1461-0248.2008.01206.x","issue":"8","scopus_import":"1","quality_controlled":"1"},{"doi":"10.1016/j.ydbio.2008.05.529","intvolume":"       320","date_created":"2018-12-11T12:07:11Z","publisher":"Elsevier","issue":"1","abstract":[{"lang":"eng","text":"The zyxin-related LPP protein is localized at focal adhesions and cell-cell contacts and is involved in the regulation of smooth muscle cell migration. A known interaction partner of LPP in human is the tumor suppressor protein SCRIB. Knocking down scrib expression c uring zebrafish embryonic development results in defects of convergence and extension (C&amp;amp;E) movements, which occur during gastrulation and mediate elongation of the anterior-posterior body axis. Mediolateral cell polarization underlying C&amp;amp;E is regulated by a noncanonical Writ signaling pathway constituting the vertebrate planar cell polarity (PCP) pathway. Here, we investigated the role of Lpp during early zebrafish development. We show that morpholino knockdown of Ipp results in defects of C&amp;amp;E, phenocopying noncanonical Wnt signaling mutants. Time-lapse analysis associates the defective dorsal convergence movements with a reduced ability to migrate along straight paths. In addition, expression of Lpp is significantly reduced in Wnt11 morphants and in embryos overexpressing Wnt11 or a dominant-negative form of Rho kinase 2, which is a downstream effector of Wnt11, Suggesting that Lpp expression is dependent on noncanonical Wnt signaling. Finally, we demonstrate that Lpp interacts with the PCP protein Scrib in zebrafish, and that Lpp and Scrib cooperate for the mediation of C&amp;amp;E. (C) 2008 Elsevier Inc. All rights reserved."}],"oa_version":"None","date_published":"2008-08-01T00:00:00Z","extern":"1","_id":"4141","publication":"Developmental Biology","day":"01","publication_status":"published","citation":{"apa":"Vervenne, H., Crombez, K., Lambaerts, K., Carvalho, L., Köppen, M., Heisenberg, C.-P. J., … Petit, M. (2008). Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2008.05.529\">https://doi.org/10.1016/j.ydbio.2008.05.529</a>","mla":"Vervenne, Hilke, et al. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” <i>Developmental Biology</i>, vol. 320, no. 1, Elsevier, 2008, pp. 267–77, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2008.05.529\">10.1016/j.ydbio.2008.05.529</a>.","chicago":"Vervenne, Hilke, Koen Crombez, Kathleen Lambaerts, Lara Carvalho, Mathias Köppen, Carl-Philipp J Heisenberg, Wim Van De Ven, and Marleen Petit. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” <i>Developmental Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.ydbio.2008.05.529\">https://doi.org/10.1016/j.ydbio.2008.05.529</a>.","ista":"Vervenne H, Crombez K, Lambaerts K, Carvalho L, Köppen M, Heisenberg C-PJ, Van De Ven W, Petit M. 2008. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 320(1), 267–277.","short":"H. Vervenne, K. Crombez, K. Lambaerts, L. Carvalho, M. Köppen, C.-P.J. Heisenberg, W. Van De Ven, M. Petit, Developmental Biology 320 (2008) 267–277.","ieee":"H. Vervenne <i>et al.</i>, “Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation,” <i>Developmental Biology</i>, vol. 320, no. 1. Elsevier, pp. 267–277, 2008.","ama":"Vervenne H, Crombez K, Lambaerts K, et al. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. <i>Developmental Biology</i>. 2008;320(1):267-277. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2008.05.529\">10.1016/j.ydbio.2008.05.529</a>"},"type":"journal_article","year":"2008","article_processing_charge":"No","month":"08","language":[{"iso":"eng"}],"volume":320,"publist_id":"1978","status":"public","date_updated":"2021-01-12T07:54:48Z","page":"267 - 277","author":[{"full_name":"Vervenne, Hilke","last_name":"Vervenne","first_name":"Hilke"},{"first_name":"Koen","last_name":"Crombez","full_name":"Crombez, Koen"},{"first_name":"Kathleen","last_name":"Lambaerts","full_name":"Lambaerts, Kathleen"},{"first_name":"Lara","last_name":"Carvalho","full_name":"Carvalho, Lara"},{"last_name":"Köppen","full_name":"Köppen, Mathias","first_name":"Mathias"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"full_name":"Van De Ven, Wim","last_name":"Van De Ven","first_name":"Wim"},{"first_name":"Marleen","last_name":"Petit","full_name":"Petit, Marleen"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation"},{"issue":"1","doi":"10.2976/1.2834817","publisher":"HFSP Publishing","date_created":"2018-12-11T12:07:14Z","intvolume":"         2","_id":"4150","day":"01","publication":"HFSP Journal","abstract":[{"lang":"eng","text":"This study provides direct functional evidence that differential adhesion, measurable as quantitative differences in tissue surface tension, influences spatial positioning between zebrafish germ layer tissues. We show that embryonic ectodermal and mesendodermal tissues generated by mRNA-overexpression behave on long-time scales like immiscible fluids. When mixed in hanging drop culture, their cells segregate into discrete phases with ectoderm adopting an internal position relative to the mesendoderm. The position adopted directly correlates with differences in tissue surface tension. We also show that germ layer tissues from untreated embryos, when extirpated and placed in culture, adopt a configuration similar to those of their mRNA-overexpressing counterparts. Down-regulating E-cadherin expression in the ectoderm leads to reduced surface tension and results in phase reversal with E-cadherin-depleted ectoderm cells now adopting an external position relative to the mesendoderm. These results show that in vitro cell sorting of zebrafish mesendoderm and ectoderm tissues is specified by tissue interfacial tensions. We perform a mathematical analysis indicating that tissue interfacial tension between actively motile cells contributes to the spatial organization and dynamics of these zebrafish germ layers in vivo."}],"extern":"1","oa_version":"None","date_published":"2008-02-01T00:00:00Z","month":"02","article_processing_charge":"No","publist_id":"1969","language":[{"iso":"eng"}],"volume":2,"citation":{"ama":"Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. <i>HFSP Journal</i>. 2008;2(1):42-56. doi:<a href=\"https://doi.org/10.2976/1.2834817\">10.2976/1.2834817</a>","ieee":"E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P. J. Heisenberg, and R. Foty, “Quantitative differences in tissue surface tension influence zebrafish germ layer positioning,” <i>HFSP Journal</i>, vol. 2, no. 1. HFSP Publishing, pp. 42–56, 2008.","apa":"Schötz, E., Burdine, R., Julicher, F., Steinberg, M., Heisenberg, C.-P. J., &#38; Foty, R. (2008). Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. <i>HFSP Journal</i>. HFSP Publishing. <a href=\"https://doi.org/10.2976/1.2834817\">https://doi.org/10.2976/1.2834817</a>","ista":"Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. 2008. Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. HFSP Journal. 2(1), 42–56.","chicago":"Schötz, Eva, Rebecca Burdine, Frank Julicher, Malcolm Steinberg, Carl-Philipp J Heisenberg, and Ramsey Foty. “Quantitative Differences in Tissue Surface Tension Influence Zebrafish Germ Layer Positioning.” <i>HFSP Journal</i>. HFSP Publishing, 2008. <a href=\"https://doi.org/10.2976/1.2834817\">https://doi.org/10.2976/1.2834817</a>.","short":"E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P.J. Heisenberg, R. Foty, HFSP Journal 2 (2008) 42–56.","mla":"Schötz, Eva, et al. “Quantitative Differences in Tissue Surface Tension Influence Zebrafish Germ Layer Positioning.” <i>HFSP Journal</i>, vol. 2, no. 1, HFSP Publishing, 2008, pp. 42–56, doi:<a href=\"https://doi.org/10.2976/1.2834817\">10.2976/1.2834817</a>."},"type":"journal_article","publication_status":"published","year":"2008","page":"42 - 56","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Quantitative differences in tissue surface tension influence zebrafish germ layer positioning","author":[{"first_name":"Eva","last_name":"Schötz","full_name":"Schötz, Eva"},{"first_name":"Rebecca","full_name":"Burdine, Rebecca","last_name":"Burdine"},{"last_name":"Julicher","full_name":"Julicher, Frank","first_name":"Frank"},{"first_name":"Malcolm","full_name":"Steinberg, Malcolm","last_name":"Steinberg"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Foty","full_name":"Foty, Ramsey","first_name":"Ramsey"}],"status":"public","date_updated":"2021-01-12T07:54:52Z"},{"issue":"16","intvolume":"       135","date_created":"2018-12-11T12:07:19Z","publisher":"Company of Biologists","doi":"10.1242/dev.022228","day":"15","publication":"Development","_id":"4161","date_published":"2008-08-15T00:00:00Z","oa_version":"None","extern":"1","abstract":[{"lang":"eng","text":"Handedness of the vertebrate body plan critically depends on transient embryonic structures/ organs that generate cilia-dependent leftward fluid flow within constrained extracellular environments. Although the function of ciliated organs in laterality determination has been extensively studied, how they are formed during embryogenesis is still poorly understood. Here we show that Kupffer's vesicle (KV), the zebrafish organ of laterality, arises from a surface epithelium previously thought to adopt exclusively extra-embryonic fates. Live multi-photon confocal imaging reveals that surface epithelial cells undergo Nodal/TGF beta signalling-dependent ingression at the dorsal germ ring margin prior to gastrulation, to give rise to dorsal forerunner cells (DFCs), the precursors of KV. DFCs then migrate attached to the overlying surface epithelium and rearrange into rosette-like epithelial structures at the end of gastrulation. During early somitogenesis, these epithelial rosettes coalesce into a single rosette that differentiates into the KV with a ciliated lumen at its apical centre. Our results provide novel insights into the morphogenetic transformations that shape the laterality organ in zebrafish and suggest a conserved progenitor role of the surface epithelium during laterality organ formation in vertebrates."}],"volume":135,"language":[{"iso":"eng"}],"publist_id":"1956","article_processing_charge":"No","month":"08","year":"2008","type":"journal_article","citation":{"ama":"Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. Origin and shaping of the laterality organ in zebrafish. <i>Development</i>. 2008;135(16):2807-2813. doi:<a href=\"https://doi.org/10.1242/dev.022228\">10.1242/dev.022228</a>","ieee":"P. Oteíza, M. Köppen, M. Concha, and C.-P. J. Heisenberg, “Origin and shaping of the laterality organ in zebrafish,” <i>Development</i>, vol. 135, no. 16. Company of Biologists, pp. 2807–2813, 2008.","chicago":"Oteíza, Pablo, Mathias Köppen, Miguel Concha, and Carl-Philipp J Heisenberg. “Origin and Shaping of the Laterality Organ in Zebrafish.” <i>Development</i>. Company of Biologists, 2008. <a href=\"https://doi.org/10.1242/dev.022228\">https://doi.org/10.1242/dev.022228</a>.","ista":"Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. 2008. Origin and shaping of the laterality organ in zebrafish. Development. 135(16), 2807–2813.","short":"P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008) 2807–2813.","mla":"Oteíza, Pablo, et al. “Origin and Shaping of the Laterality Organ in Zebrafish.” <i>Development</i>, vol. 135, no. 16, Company of Biologists, 2008, pp. 2807–13, doi:<a href=\"https://doi.org/10.1242/dev.022228\">10.1242/dev.022228</a>.","apa":"Oteíza, P., Köppen, M., Concha, M., &#38; Heisenberg, C.-P. J. (2008). Origin and shaping of the laterality organ in zebrafish. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.022228\">https://doi.org/10.1242/dev.022228</a>"},"publication_status":"published","title":"Origin and shaping of the laterality organ in zebrafish","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Oteíza","full_name":"Oteíza, Pablo","first_name":"Pablo"},{"last_name":"Köppen","full_name":"Köppen, Mathias","first_name":"Mathias"},{"last_name":"Concha","full_name":"Concha, Miguel","first_name":"Miguel"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"page":"2807 - 2813","date_updated":"2021-01-12T07:54:57Z","status":"public"},{"intvolume":"        47","date_created":"2018-12-11T12:07:26Z","publisher":"Wiley-Blackwell","doi":"10.1002/anie.200803552","issue":"50","oa_version":"None","date_published":"2008-12-01T00:00:00Z","extern":"1","abstract":[{"text":"(Figure Presented) The name's Bond: Separated cells form membranous nanotubes whose tips are tethered by adhesive bonds (see picture). The lifetime of receptor-ligand interactions can be measured by using membrane nanotubes of living cells as constant force actuators. Because the nanotubes are extruded from living cells at conditions approaching the physiological, cellular processes can be both studied and utilized. ","lang":"eng"}],"day":"01","publication":"Angewandte Chemie - International Edition","_id":"4180","year":"2008","citation":{"apa":"Krieg, M., Helenius, J., Heisenberg, C.-P. J., &#38; Mueller, D. (2008). A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/anie.200803552\">https://doi.org/10.1002/anie.200803552</a>","short":"M. Krieg, J. Helenius, C.-P.J. Heisenberg, D. Mueller, Angewandte Chemie - International Edition 47 (2008) 9775–9777.","ista":"Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. 2008. A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. 47(50), 9775–9777.","chicago":"Krieg, Michael, Jonne Helenius, Carl-Philipp J Heisenberg, and Daniel Mueller. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.” <i>Angewandte Chemie - International Edition</i>. Wiley-Blackwell, 2008. <a href=\"https://doi.org/10.1002/anie.200803552\">https://doi.org/10.1002/anie.200803552</a>.","mla":"Krieg, Michael, et al. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.” <i>Angewandte Chemie - International Edition</i>, vol. 47, no. 50, Wiley-Blackwell, 2008, pp. 9775–77, doi:<a href=\"https://doi.org/10.1002/anie.200803552\">10.1002/anie.200803552</a>.","ama":"Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. <i>Angewandte Chemie - International Edition</i>. 2008;47(50):9775-9777. doi:<a href=\"https://doi.org/10.1002/anie.200803552\">10.1002/anie.200803552</a>","ieee":"M. Krieg, J. Helenius, C.-P. J. Heisenberg, and D. Mueller, “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics,” <i>Angewandte Chemie - International Edition</i>, vol. 47, no. 50. Wiley-Blackwell, pp. 9775–9777, 2008."},"type":"journal_article","publication_status":"published","volume":47,"language":[{"iso":"eng"}],"publist_id":"1939","article_processing_charge":"No","month":"12","date_updated":"2021-01-12T07:55:06Z","status":"public","author":[{"first_name":"Michael","full_name":"Krieg, Michael","last_name":"Krieg"},{"first_name":"Jonne","last_name":"Helenius","full_name":"Helenius, Jonne"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Daniel","last_name":"Mueller","full_name":"Mueller, Daniel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics","page":"9775 - 9777"},{"citation":{"short":"M. Krieg, Y. Arboleda Estudillo, P. Puech, J. Käfer, F. Graner, D. Mueller, C.-P.J. Heisenberg, Nature Cell Biology 10 (2008) 429–436.","chicago":"Krieg, Michael, Yohanna Arboleda Estudillo, Pierre Puech, Jos Käfer, François Graner, Daniel Mueller, and Carl-Philipp J Heisenberg. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2008. <a href=\"https://doi.org/10.1038/ncb1705\">https://doi.org/10.1038/ncb1705</a>.","ista":"Krieg M, Arboleda Estudillo Y, Puech P, Käfer J, Graner F, Mueller D, Heisenberg C-PJ. 2008. Tensile forces govern germ-layer organization in zebrafish. Nature Cell Biology. 10(4), 429–436.","mla":"Krieg, Michael, et al. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.” <i>Nature Cell Biology</i>, vol. 10, no. 4, Nature Publishing Group, 2008, pp. 429–36, doi:<a href=\"https://doi.org/10.1038/ncb1705\">10.1038/ncb1705</a>.","apa":"Krieg, M., Arboleda Estudillo, Y., Puech, P., Käfer, J., Graner, F., Mueller, D., &#38; Heisenberg, C.-P. J. (2008). Tensile forces govern germ-layer organization in zebrafish. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb1705\">https://doi.org/10.1038/ncb1705</a>","ama":"Krieg M, Arboleda Estudillo Y, Puech P, et al. Tensile forces govern germ-layer organization in zebrafish. <i>Nature Cell Biology</i>. 2008;10(4):429-436. doi:<a href=\"https://doi.org/10.1038/ncb1705\">10.1038/ncb1705</a>","ieee":"M. Krieg <i>et al.</i>, “Tensile forces govern germ-layer organization in zebrafish,” <i>Nature Cell Biology</i>, vol. 10, no. 4. Nature Publishing Group, pp. 429–436, 2008."},"type":"journal_article","publication_status":"published","year":"2008","month":"03","article_processing_charge":"No","publist_id":"1938","volume":10,"language":[{"iso":"eng"}],"status":"public","date_updated":"2021-01-12T07:55:07Z","page":"429 - 436","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Tensile forces govern germ-layer organization in zebrafish","author":[{"full_name":"Krieg, Michael","last_name":"Krieg","first_name":"Michael"},{"first_name":"Yohanna","last_name":"Arboleda Estudillo","full_name":"Arboleda Estudillo, Yohanna"},{"first_name":"Pierre","full_name":"Puech, Pierre","last_name":"Puech"},{"first_name":"Jos","full_name":"Käfer, Jos","last_name":"Käfer"},{"first_name":"François","full_name":"Graner, François","last_name":"Graner"},{"first_name":"Daniel","last_name":"Mueller","full_name":"Mueller, Daniel"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"doi":"10.1038/ncb1705","date_created":"2018-12-11T12:07:26Z","publisher":"Nature Publishing Group","intvolume":"        10","issue":"4","abstract":[{"lang":"eng","text":"Understanding the factors that direct tissue organization during development is one of the most fundamental goals in developmental biology. Various hypotheses explain cell sorting and tissue organization on the basis of the adhesive and mechanical properties of the constituent cells(1). However, validating these hypotheses has been difficult due to the lack of appropriate tools to measure these parameters. Here we use atomic force microscopy ( AFM) to quantify the adhesive and mechanical properties of individual ectoderm, mesoderm and endoderm progenitor cells from gastrulating zebrafish embryos. Combining these data with tissue self-assembly in vitro and the sorting behaviour of progenitors in vivo, we have shown that differential actomyosin-dependent cell-cortex tension, regulated by Nodal/ TGF beta-signalling ( transforming growth factor beta), constitutes a key factor that directs progenitor-cell sorting. These results demonstrate a previously unrecognized role for Nodal-controlled cell-cortex tension in germ-layer organization during gastrulation."}],"extern":"1","oa_version":"None","date_published":"2008-03-23T00:00:00Z","_id":"4181","day":"23","publication":"Nature Cell Biology"},{"article_processing_charge":"No","month":"09","volume":135,"language":[{"iso":"eng"}],"publist_id":"1928","citation":{"ama":"Kai M, Heisenberg C-PJ, Tada M. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. <i>Development</i>. 2008;135(18):3043-3051. doi:<a href=\"https://doi.org/10.1242/dev.020396\">10.1242/dev.020396</a>","ieee":"M. Kai, C.-P. J. Heisenberg, and M. Tada, “Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation,” <i>Development</i>, vol. 135, no. 18. Company of Biologists, pp. 3043–3051, 2008.","apa":"Kai, M., Heisenberg, C.-P. J., &#38; Tada, M. (2008). Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.020396\">https://doi.org/10.1242/dev.020396</a>","chicago":"Kai, Masatake, Carl-Philipp J Heisenberg, and Masazumi Tada. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” <i>Development</i>. Company of Biologists, 2008. <a href=\"https://doi.org/10.1242/dev.020396\">https://doi.org/10.1242/dev.020396</a>.","short":"M. Kai, C.-P.J. Heisenberg, M. Tada, Development 135 (2008) 3043–3051.","ista":"Kai M, Heisenberg C-PJ, Tada M. 2008. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 135(18), 3043–3051.","mla":"Kai, Masatake, et al. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” <i>Development</i>, vol. 135, no. 18, Company of Biologists, 2008, pp. 3043–51, doi:<a href=\"https://doi.org/10.1242/dev.020396\">10.1242/dev.020396</a>."},"type":"journal_article","publication_status":"published","year":"2008","page":"3043 - 3051","title":"Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kai","full_name":"Kai, Masatake","first_name":"Masatake"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tada","full_name":"Tada, Masazumi","first_name":"Masazumi"}],"status":"public","date_updated":"2021-01-12T07:55:11Z","issue":"18","doi":"10.1242/dev.020396","intvolume":"       135","date_created":"2018-12-11T12:07:29Z","publisher":"Company of Biologists","_id":"4190","publication":"Development","day":"15","abstract":[{"lang":"eng","text":"During vertebrate gastrulation, cells forming the prechordal plate undergo directed migration as a cohesive cluster. Recent studies revealed that E-cadherin-mediated coherence between these cells plays an important role in effective anterior migration, and that platelet-derived growth factor (Pdgf) appears to act as a guidance cue in this process. However, the mechanisms underlying this process at the individual cell level remain poorly understood. We have identified miles apart (mil) as a suppressor of defective anterior migration of the prospective prechordal plate in silberblick (slb)/wnt11 mutant embryos, in which E-cadherin-mediated coherence of cell movement is reduced. mil encodes Edg5, a sphingosine-1-phosphate (S1P) receptor belonging to a family of five G-protein-coupled receptors (S1PRs). S1P is a lipid signalling molecule that has been implicated in regulating cytoskeletal rearrangements, cell motility and cell adhesion in a variety of cell types. We examined the roles of Mil in anterior migration of prechordal plate progenitor cells and found that, in slb embryos injected with mil-MO, cells migrate with increased motility but decreased directionality, without restoring the coherence of cell migration. This indicates that prechordal plate progenitor cells can migrate effectively as individuals, as well as in a coherent cluster of cells. Moreover, we demonstrate that Mil regulates cell motility and polarisation through Pdgf and its intracellular effecter PI3K, but modulates cell coherence independently of the Pdgf/PI3K pathway, thus co-ordinating cell motility and coherence. These results suggest that the net migration of prechordal plate progenitors is determined by different parameters, including motility, persistence and coherence."}],"date_published":"2008-09-15T00:00:00Z","oa_version":"None","extern":"1"},{"_id":"4193","publication":"Journal of Cell Science","day":"01","abstract":[{"text":"The controlled adhesion of cells to each other and to the extracellular matrix is crucial for tissue development and maintenance. Numerous assays have been developed to quantify cell adhesion. Among these, the use of atomic force microscopy (AFM) for single-cell force spectroscopy (SCFS) has recently been established. This assay permits the adhesion of living cells to be studied in near-physiological conditions. This implementation of AFM allows unrivaled spatial and temporal control of cells, as well as highly quantitative force actuation and force measurement that is sufficiently sensitive to characterize the interaction of single molecules. Therefore, not only overall cell adhesion but also the properties of single adhesion-receptor-ligand interactions can be studied. Here we describe current implementations and applications of SCFS, as well as potential pitfalls, and outline how developments will provide insight into the forces, energetics and kinetics of cell-adhesion processes.","lang":"eng"}],"extern":"1","oa_version":"None","date_published":"2008-06-01T00:00:00Z","issue":"11","doi":"10.1242/​jcs.030999","publisher":"Company of Biologists","date_created":"2018-12-11T12:07:30Z","intvolume":"       121","page":"1785 - 1791","title":"Single-cell force spectroscopy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Jonne","last_name":"Helenius","full_name":"Helenius, Jonne"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Hermann","last_name":"Gaub","full_name":"Gaub, Hermann"},{"last_name":"Mueller","full_name":"Mueller, Daniel","first_name":"Daniel"}],"status":"public","date_updated":"2021-01-12T07:55:12Z","month":"06","article_processing_charge":"No","publist_id":"1924","volume":121,"language":[{"iso":"eng"}],"type":"journal_article","publication_status":"published","citation":{"ama":"Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. Single-cell force spectroscopy. <i>Journal of Cell Science</i>. 2008;121(11):1785-1791. doi:<a href=\"https://doi.org/10.1242/​jcs.030999\">10.1242/​jcs.030999</a>","ieee":"J. Helenius, C.-P. J. Heisenberg, H. Gaub, and D. Mueller, “Single-cell force spectroscopy,” <i>Journal of Cell Science</i>, vol. 121, no. 11. Company of Biologists, pp. 1785–1791, 2008.","short":"J. Helenius, C.-P.J. Heisenberg, H. Gaub, D. Mueller, Journal of Cell Science 121 (2008) 1785–1791.","chicago":"Helenius, Jonne, Carl-Philipp J Heisenberg, Hermann Gaub, and Daniel Mueller. “Single-Cell Force Spectroscopy.” <i>Journal of Cell Science</i>. Company of Biologists, 2008. <a href=\"https://doi.org/10.1242/​jcs.030999\">https://doi.org/10.1242/​jcs.030999</a>.","ista":"Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. 2008. Single-cell force spectroscopy. Journal of Cell Science. 121(11), 1785–1791.","mla":"Helenius, Jonne, et al. “Single-Cell Force Spectroscopy.” <i>Journal of Cell Science</i>, vol. 121, no. 11, Company of Biologists, 2008, pp. 1785–91, doi:<a href=\"https://doi.org/10.1242/​jcs.030999\">10.1242/​jcs.030999</a>.","apa":"Helenius, J., Heisenberg, C.-P. J., Gaub, H., &#38; Mueller, D. (2008). Single-cell force spectroscopy. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/​jcs.030999\">https://doi.org/10.1242/​jcs.030999</a>"},"year":"2008"},{"issue":"4","doi":"10.1016/j.gde.2008.07.011","publisher":"Elsevier","date_created":"2018-12-11T12:07:32Z","intvolume":"        18","_id":"4198","day":"01","publication":"Current Opinion in Genetics & Development","abstract":[{"text":"Animal body plan arises during gastrulation and organogenesis by the coordination of inductive events and cell movements. Several signaling pathways, such as BMP, FGF, Hedgehog, Nodal, and Wnt have well-recognized instructive roles in cell fate specification during vertebrate embryogenesis. Growing evidence indicates that BMP, Nodal, and FGF signaling also regulate cell movements, and that they do so through mechanisms distinct from those that specify cell fates. Moreover, pathways controlling cell movements can also indirectly influence cell fate specification by regulating dimensions and relative positions of interacting tissues. The current challenge is to delineate the molecular mechanisms via which the major signaling pathways regulate cell fate specification and movements, and how these two processes are coordinated to ensure normal development.","lang":"eng"}],"extern":"1","oa_version":"None","date_published":"2008-01-01T00:00:00Z","month":"01","article_processing_charge":"No","publist_id":"1918","language":[{"iso":"eng"}],"volume":18,"citation":{"mla":"Heisenberg, Carl-Philipp J., and Lilianna Solnica Krezel. “Back and Forth between Cell Fate Specification and Movement during Vertebrate Gastrulation.” <i>Current Opinion in Genetics &#38; Development</i>, vol. 18, no. 4, Elsevier, 2008, pp. 311–16, doi:<a href=\"https://doi.org/10.1016/j.gde.2008.07.011\">10.1016/j.gde.2008.07.011</a>.","short":"C.-P.J. Heisenberg, L. Solnica Krezel, Current Opinion in Genetics &#38; Development 18 (2008) 311–316.","ista":"Heisenberg C-PJ, Solnica Krezel L. 2008. Back and forth between cell fate specification and movement during vertebrate gastrulation. Current Opinion in Genetics &#38; Development. 18(4), 311–316.","chicago":"Heisenberg, Carl-Philipp J, and Lilianna Solnica Krezel. “Back and Forth between Cell Fate Specification and Movement during Vertebrate Gastrulation.” <i>Current Opinion in Genetics &#38; Development</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.gde.2008.07.011\">https://doi.org/10.1016/j.gde.2008.07.011</a>.","apa":"Heisenberg, C.-P. J., &#38; Solnica Krezel, L. (2008). Back and forth between cell fate specification and movement during vertebrate gastrulation. <i>Current Opinion in Genetics &#38; Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2008.07.011\">https://doi.org/10.1016/j.gde.2008.07.011</a>","ieee":"C.-P. J. Heisenberg and L. Solnica Krezel, “Back and forth between cell fate specification and movement during vertebrate gastrulation,” <i>Current Opinion in Genetics &#38; Development</i>, vol. 18, no. 4. Elsevier, pp. 311–316, 2008.","ama":"Heisenberg C-PJ, Solnica Krezel L. Back and forth between cell fate specification and movement during vertebrate gastrulation. <i>Current Opinion in Genetics &#38; Development</i>. 2008;18(4):311-316. doi:<a href=\"https://doi.org/10.1016/j.gde.2008.07.011\">10.1016/j.gde.2008.07.011</a>"},"type":"journal_article","publication_status":"published","year":"2008","page":"311 - 316","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"first_name":"Lilianna","last_name":"Solnica Krezel","full_name":"Solnica Krezel, Lilianna"}],"title":"Back and forth between cell fate specification and movement during vertebrate gastrulation","status":"public","date_updated":"2021-01-12T07:55:14Z"},{"citation":{"ieee":"T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, and F. Julicher, “Precision of the Dpp gradient,” <i>Development</i>, vol. 135, no. 6. Company of Biologists, pp. 1137–1146, 2008.","ama":"Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F. Precision of the Dpp gradient. <i>Development</i>. 2008;135(6):1137-1146. doi:<a href=\"https://doi.org/10.1242/dev.012062\">10.1242/dev.012062</a>","apa":"Bollenbach, T., Pantazis, P., Kicheva, A., Bokel, C., González Gaitán, M., &#38; Julicher, F. (2008). Precision of the Dpp gradient. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.012062\">https://doi.org/10.1242/dev.012062</a>","mla":"Bollenbach, Tobias, et al. “Precision of the Dpp Gradient.” <i>Development</i>, vol. 135, no. 6, Company of Biologists, 2008, pp. 1137–46, doi:<a href=\"https://doi.org/10.1242/dev.012062\">10.1242/dev.012062</a>.","chicago":"Bollenbach, Tobias, Periklis Pantazis, Anna Kicheva, Christian Bokel, Marcos González Gaitán, and Frank Julicher. “Precision of the Dpp Gradient.” <i>Development</i>. Company of Biologists, 2008. <a href=\"https://doi.org/10.1242/dev.012062\">https://doi.org/10.1242/dev.012062</a>.","short":"T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, F. Julicher, Development 135 (2008) 1137–1146.","ista":"Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F. 2008. Precision of the Dpp gradient. Development. 135(6), 1137–1146."},"publication_status":"published","type":"journal_article","year":"2008","month":"03","volume":135,"publist_id":"1889","status":"public","date_updated":"2021-01-12T07:55:27Z","page":"1137 - 1146","author":[{"first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"},{"first_name":"Periklis","full_name":"Pantazis, Periklis","last_name":"Pantazis"},{"last_name":"Kicheva","full_name":"Anna Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna"},{"full_name":"Bokel,  Christian","last_name":"Bokel","first_name":"Christian"},{"first_name":"Marcos","full_name":"González-Gaitán, Marcos","last_name":"González Gaitán"},{"first_name":"Frank","full_name":"Julicher, Frank","last_name":"Julicher"}],"title":"Precision of the Dpp gradient","doi":"10.1242/dev.012062","intvolume":"       135","publisher":"Company of Biologists","date_created":"2018-12-11T12:07:42Z","quality_controlled":0,"issue":"6","abstract":[{"lang":"eng","text":"Morphogen concentration gradients provide positional information by activating target genes in a concentration-dependent manner. Recent reports show that the gradient of the syncytial morphogen Bicoid seems to provide precise positional information to determine target gene domains. For secreted morphogenetic ligands, the precision of the gradients, the signal transduction and the reliability of target gene expression domains have not been studied. Here we investigate these issues for the TGF-beta-type morphogen Dpp. We first studied theoretically how cell-to-cell variability in the source, the target tissue, or both, contribute to the variations of the gradient. Fluctuations in the source and target generate a local maximum of precision at a finite distance to the source. We then determined experimentally in the wing epithelium: (1) the precision of the Dpp concentration gradient; (2) the precision of the Dpp signaling activity profile; and (3) the precision of activation of the Dpp target gene spalt. As captured by our theoretical description, the Dpp gradient provides positional information with a maximal precision a few cells away from the source. This maximal precision corresponds to a positional uncertainly of about a single cell diameter. The precision of the Dpp gradient accounts for the precision of the spalt expression range, implying that Dpp can act as a morphogen to coarsely determine the expression pattern of target genes."}],"date_published":"2008-03-15T00:00:00Z","extern":1,"_id":"4227","publication":"Development","day":"15"},{"day":"23","_id":"4244","conference":{"name":"WCCI: IEEE World Congress on Computational Intelligence"},"extern":1,"date_published":"2008-09-23T00:00:00Z","abstract":[{"text":"This paper presents a new approach to optimization of an energy-constrained modulation scheme for wireless sensor networks by taking advantage of a novel bio-inspired optimization algorithm. The algorithm is inspired by Wrightpsilas shifting balance theory (SBT) of evolution in population genetics. The total energy consumption of an energy-constrained modulation scheme is minimized by using the new SBT-based optimization algorithm. The results obtained by this new algorithm are compared with other popular optimization algorithms. Numerical experiments are performed to demonstrate that the SBT-based algorithm could be used as an efficient optimizer for solving the optimization problems arising from currently emerging energy-efficient wireless sensor networks.","lang":"eng"}],"quality_controlled":0,"date_created":"2018-12-11T12:07:49Z","publisher":"IEEE","doi":"10.1109/CEC.2008.4631167","title":"A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks","author":[{"first_name":"Erfu","full_name":"Yang, Erfu","last_name":"Yang"},{"full_name":"Nicholas Barton","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arslan","full_name":"Arslan, Tughrul","first_name":"Tughrul"},{"full_name":"Erdogan, Ahmet T","last_name":"Erdogan","first_name":"Ahmet"}],"page":"2749 - 2756","date_updated":"2021-01-12T07:55:34Z","status":"public","publist_id":"1861","month":"09","year":"2008","citation":{"mla":"Yang, Erfu, et al. <i>A Novel Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks</i>. IEEE, 2008, pp. 2749–56, doi:<a href=\"https://doi.org/10.1109/CEC.2008.4631167\">10.1109/CEC.2008.4631167</a>.","ista":"Yang E, Barton NH, Arslan T, Erdogan A. 2008. A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks. WCCI: IEEE World Congress on Computational Intelligence, 2749–2756.","chicago":"Yang, Erfu, Nicholas H Barton, Tughrul Arslan, and Ahmet Erdogan. “A Novel Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks,” 2749–56. IEEE, 2008. <a href=\"https://doi.org/10.1109/CEC.2008.4631167\">https://doi.org/10.1109/CEC.2008.4631167</a>.","short":"E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, IEEE, 2008, pp. 2749–2756.","apa":"Yang, E., Barton, N. H., Arslan, T., &#38; Erdogan, A. (2008). A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks (pp. 2749–2756). Presented at the WCCI: IEEE World Congress on Computational Intelligence, IEEE. <a href=\"https://doi.org/10.1109/CEC.2008.4631167\">https://doi.org/10.1109/CEC.2008.4631167</a>","ieee":"E. Yang, N. H. Barton, T. Arslan, and A. Erdogan, “A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks,” presented at the WCCI: IEEE World Congress on Computational Intelligence, 2008, pp. 2749–2756.","ama":"Yang E, Barton NH, Arslan T, Erdogan A. A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks. In: IEEE; 2008:2749-2756. doi:<a href=\"https://doi.org/10.1109/CEC.2008.4631167\">10.1109/CEC.2008.4631167</a>"},"publication_status":"published","type":"conference"},{"page":"1921 - 1935","author":[{"first_name":"Bart","full_name":"Pannebakker, Bart A","last_name":"Pannebakker"},{"full_name":"Halligan, Daniel","last_name":"Halligan","first_name":"Daniel"},{"first_name":"K Tracy","last_name":"Reynolds","full_name":"Reynolds, K Tracy"},{"full_name":"Ballantyne, Gavin A","last_name":"Ballantyne","first_name":"Gavin"},{"full_name":"Shuker, David M","last_name":"Shuker","first_name":"David"},{"last_name":"Barton","full_name":"Nicholas Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Stuart","last_name":"West","full_name":"West, Stuart A"}],"title":"Effects of spontaneous mutation accumulation on sex ratio traits","status":"public","date_updated":"2021-01-12T07:55:34Z","month":"08","publist_id":"1860","volume":62,"publication_status":"published","type":"journal_article","citation":{"ista":"Pannebakker B, Halligan D, Reynolds KT, Ballantyne G, Shuker D, Barton NH, West S. 2008. Effects of spontaneous mutation accumulation on sex ratio traits. Evolution; International Journal of Organic Evolution. 62(8), 1921–1935.","chicago":"Pannebakker, Bart, Daniel Halligan, K Tracy Reynolds, Gavin Ballantyne, David Shuker, Nicholas H Barton, and Stuart West. “Effects of Spontaneous Mutation Accumulation on Sex Ratio Traits.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell, 2008. <a href=\"https://doi.org/10.1111/j.1558-5646.2008.00434.x\">https://doi.org/10.1111/j.1558-5646.2008.00434.x</a>.","short":"B. Pannebakker, D. Halligan, K.T. Reynolds, G. Ballantyne, D. Shuker, N.H. Barton, S. West, Evolution; International Journal of Organic Evolution 62 (2008) 1921–1935.","mla":"Pannebakker, Bart, et al. “Effects of Spontaneous Mutation Accumulation on Sex Ratio Traits.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 62, no. 8, Wiley-Blackwell, 2008, pp. 1921–35, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2008.00434.x\">10.1111/j.1558-5646.2008.00434.x</a>.","apa":"Pannebakker, B., Halligan, D., Reynolds, K. T., Ballantyne, G., Shuker, D., Barton, N. H., &#38; West, S. (2008). Effects of spontaneous mutation accumulation on sex ratio traits. <i>Evolution; International Journal of Organic Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2008.00434.x\">https://doi.org/10.1111/j.1558-5646.2008.00434.x</a>","ama":"Pannebakker B, Halligan D, Reynolds KT, et al. Effects of spontaneous mutation accumulation on sex ratio traits. <i>Evolution; International Journal of Organic Evolution</i>. 2008;62(8):1921-1935. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2008.00434.x\">10.1111/j.1558-5646.2008.00434.x</a>","ieee":"B. Pannebakker <i>et al.</i>, “Effects of spontaneous mutation accumulation on sex ratio traits,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 62, no. 8. Wiley-Blackwell, pp. 1921–1935, 2008."},"year":"2008","_id":"4245","publication":"Evolution; International Journal of Organic Evolution","day":"01","abstract":[{"lang":"eng","text":"Sex allocation theory has proved extremely successful at predicting when individuals should adjust the sex of their offspring in response to environmental conditions. However, we know rather little about the underlying genetics of sex ratio or how genetic architecture might constrain adaptive sex-ratio behavior. We examined how mutation influenced genetic variation in the sex ratios produced by the parasitoid wasp Nasonia vitripennis. In a mutation accumulation experiment, we determined the mutability of sex ratio, and compared this with the amount of genetic variation observed in natural populations. We found that the mutability (h2m) ranges from 0.001 to 0.002, similar to estimates for life-history traits in other organisms. These estimates suggest one mutation every 5–60 generations, which shift the sex ratio by approximately 0.01 (proportion males). In this and other studies, the genetic variation in N. vitripennis sex ratio ranged from 0.02 to 0.17 (broad-sense heritability, H2). If sex ratio is maintained by mutation–selection balance, a higher genetic variance would be expected given our mutational parameters. Instead, the observed genetic variance perhaps suggests additional selection against sex-ratio mutations with deleterious effects on other fitness traits as well as sex ratio (i.e., pleiotropy), as has been argued to be the case more generally."}],"extern":1,"date_published":"2008-08-01T00:00:00Z","quality_controlled":0,"issue":"8","doi":"10.1111/j.1558-5646.2008.00434.x","date_created":"2018-12-11T12:07:49Z","publisher":"Wiley-Blackwell","intvolume":"        62"},{"alternative_title":["LNCS"],"day":"01","_id":"4366","conference":{"name":"CAV: Computer Aided Verification"},"extern":1,"date_published":"2008-01-01T00:00:00Z","abstract":[{"text":"Termination of a heap-manipulating program generally depends on preconditions that express heap assumptions (i.e., assertions describing reachability, aliasing, separation and sharing in the heap). We present an algorithm for the inference of such preconditions. The algorithm exploits a unique interplay between counterexample-producing abstract termination checker and shape analysis. The shape analysis produces heap assumptions on demand to eliminate counterexamples, i.e., non-terminating abstract computations. The experiments with our prototype implementation indicate its practical potential.","lang":"eng"}],"quality_controlled":0,"date_created":"2018-12-11T12:08:29Z","publisher":"Springer","intvolume":"      5123","doi":"10.1007/978-3-540-70545-1_31","author":[{"first_name":"Andreas","last_name":"Podelski","full_name":"Podelski,Andreas"},{"first_name":"Andrey","full_name":"Rybalchenko, Andrey","last_name":"Rybalchenko"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies","full_name":"Thomas Wies"}],"title":"Heap Assumptions on Demand","page":"314 - 327","date_updated":"2021-01-12T07:56:26Z","status":"public","publist_id":"1091","volume":5123,"month":"01","year":"2008","type":"conference","citation":{"mla":"Podelski, Andreas, et al. <i>Heap Assumptions on Demand</i>. Vol. 5123, Springer, 2008, pp. 314–27, doi:<a href=\"https://doi.org/10.1007/978-3-540-70545-1_31\">10.1007/978-3-540-70545-1_31</a>.","ista":"Podelski A, Rybalchenko A, Wies T. 2008. Heap Assumptions on Demand. CAV: Computer Aided Verification, LNCS, vol. 5123, 314–327.","chicago":"Podelski, Andreas, Andrey Rybalchenko, and Thomas Wies. “Heap Assumptions on Demand,” 5123:314–27. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-70545-1_31\">https://doi.org/10.1007/978-3-540-70545-1_31</a>.","short":"A. Podelski, A. Rybalchenko, T. Wies, in:, Springer, 2008, pp. 314–327.","apa":"Podelski, A., Rybalchenko, A., &#38; Wies, T. (2008). Heap Assumptions on Demand (Vol. 5123, pp. 314–327). Presented at the CAV: Computer Aided Verification, Springer. <a href=\"https://doi.org/10.1007/978-3-540-70545-1_31\">https://doi.org/10.1007/978-3-540-70545-1_31</a>","ieee":"A. Podelski, A. Rybalchenko, and T. Wies, “Heap Assumptions on Demand,” presented at the CAV: Computer Aided Verification, 2008, vol. 5123, pp. 314–327.","ama":"Podelski A, Rybalchenko A, Wies T. Heap Assumptions on Demand. In: Vol 5123. Springer; 2008:314-327. doi:<a href=\"https://doi.org/10.1007/978-3-540-70545-1_31\">10.1007/978-3-540-70545-1_31</a>"},"publication_status":"published"},{"oa_version":"None","date_published":"2008-03-11T00:00:00Z","extern":"1","abstract":[{"lang":"eng","text":"We survey some of the problems associated with checking whether a given behavior (a sequence, a Boolean signal or a continuous signal) satisfies a property specified in an appropriate temporal logic and describe two such monitoring algorithms for the real-time logic MITL."}],"day":"11","publication":"Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday","alternative_title":["LNCS"],"_id":"4371","date_created":"2018-12-11T12:08:30Z","publisher":"Springer","doi":"10.1007/978-3-540-78127-1_26","scopus_import":"1","quality_controlled":"1","date_updated":"2023-02-14T10:42:38Z","status":"public","author":[{"last_name":"Maler","full_name":"Maler, Oded","first_name":"Oded"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"last_name":"Pnueli","full_name":"Pnueli, Amir","first_name":"Amir"}],"title":"Checking Temporal Properties of Discrete, Timed and Continuous Behaviors","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"475 - 505","year":"2008","citation":{"ama":"Maler O, Nickovic D, Pnueli A. Checking Temporal Properties of Discrete, Timed and Continuous Behaviors. In: <i>Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday</i>. Springer; 2008:475-505. doi:<a href=\"https://doi.org/10.1007/978-3-540-78127-1_26\">10.1007/978-3-540-78127-1_26</a>","ieee":"O. Maler, D. Nickovic, and A. Pnueli, “Checking Temporal Properties of Discrete, Timed and Continuous Behaviors,” in <i>Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday</i>, Springer, 2008, pp. 475–505.","apa":"Maler, O., Nickovic, D., &#38; Pnueli, A. (2008). Checking Temporal Properties of Discrete, Timed and Continuous Behaviors. In <i>Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday</i> (pp. 475–505). Springer. <a href=\"https://doi.org/10.1007/978-3-540-78127-1_26\">https://doi.org/10.1007/978-3-540-78127-1_26</a>","short":"O. Maler, D. Nickovic, A. Pnueli, in:, Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday, Springer, 2008, pp. 475–505.","ista":"Maler O, Nickovic D, Pnueli A. 2008.Checking Temporal Properties of Discrete, Timed and Continuous Behaviors. In: Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday. LNCS, , 475–505.","chicago":"Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Checking Temporal Properties of Discrete, Timed and Continuous Behaviors.” In <i>Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday</i>, 475–505. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-78127-1_26\">https://doi.org/10.1007/978-3-540-78127-1_26</a>.","mla":"Maler, Oded, et al. “Checking Temporal Properties of Discrete, Timed and Continuous Behaviors.” <i>Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday</i>, Springer, 2008, pp. 475–505, doi:<a href=\"https://doi.org/10.1007/978-3-540-78127-1_26\">10.1007/978-3-540-78127-1_26</a>."},"publication_status":"published","type":"book_chapter","language":[{"iso":"eng"}],"publist_id":"1087","publication_identifier":{"isbn":["9783540781264"]},"article_processing_charge":"No","month":"03"},{"page":"372 - 382","author":[{"first_name":"Rachid","last_name":"Guerraoui","full_name":"Guerraoui, Rachid"},{"last_name":"Henzinger","full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"last_name":"Jobstmann","full_name":"Jobstmann, Barbara","first_name":"Barbara"},{"last_name":"Singh","full_name":"Vasu Singh","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu"}],"title":"Model checking transactional memories","oa":1,"status":"public","date_updated":"2021-01-12T07:56:34Z","file":[{"creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:46:28Z","access_level":"open_access","relation":"main_file","checksum":"1238258a27f212fc1a2050a9a246da20","file_size":201583,"date_created":"2018-12-12T10:14:05Z","file_name":"IST-2012-74-v1+1_Model_checking_transactional_memories.pdf","file_id":"5054"}],"month":"01","publist_id":"1073","type":"conference","citation":{"ieee":"R. Guerraoui, T. A. Henzinger, B. Jobstmann, and V. Singh, “Model checking transactional memories,” presented at the PLDI: Programming Languages Design and Implementation, 2008, pp. 372–382.","ama":"Guerraoui R, Henzinger TA, Jobstmann B, Singh V. Model checking transactional memories. In: ACM; 2008:372-382. doi:<a href=\"https://doi.org/10.1145/1375581.1375626\">10.1145/1375581.1375626</a>","mla":"Guerraoui, Rachid, et al. <i>Model Checking Transactional Memories</i>. ACM, 2008, pp. 372–82, doi:<a href=\"https://doi.org/10.1145/1375581.1375626\">10.1145/1375581.1375626</a>.","ista":"Guerraoui R, Henzinger TA, Jobstmann B, Singh V. 2008. Model checking transactional memories. PLDI: Programming Languages Design and Implementation, 372–382.","short":"R. Guerraoui, T.A. Henzinger, B. Jobstmann, V. Singh, in:, ACM, 2008, pp. 372–382.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, Barbara Jobstmann, and Vasu Singh. “Model Checking Transactional Memories,” 372–82. ACM, 2008. <a href=\"https://doi.org/10.1145/1375581.1375626\">https://doi.org/10.1145/1375581.1375626</a>.","apa":"Guerraoui, R., Henzinger, T. A., Jobstmann, B., &#38; Singh, V. (2008). Model checking transactional memories (pp. 372–382). Presented at the PLDI: Programming Languages Design and Implementation, ACM. <a href=\"https://doi.org/10.1145/1375581.1375626\">https://doi.org/10.1145/1375581.1375626</a>"},"publication_status":"published","year":"2008","conference":{"name":"PLDI: Programming Languages Design and Implementation"},"_id":"4384","day":"01","abstract":[{"lang":"eng","text":"Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom.\n\nOur main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system."}],"date_published":"2008-01-01T00:00:00Z","extern":1,"quality_controlled":0,"file_date_updated":"2020-07-14T12:46:28Z","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/model_checking_transactional_memories.pdf","open_access":"0"}],"doi":"10.1145/1375581.1375626","publisher":"ACM","date_created":"2018-12-11T12:08:34Z"},{"doi":"10.1007/978-3-540-87779-0_21","main_file_link":[{"open_access":"0","url":"http://pub.ist.ac.at/%7Etah/Publications/permissiveness_in_transactional_memories.pdf"}],"publisher":"Springer","date_created":"2018-12-11T12:08:35Z","intvolume":"      5218","quality_controlled":0,"abstract":[{"text":"We introduce the notion of permissiveness in transactional memories (TM). Intuitively, a TM is permissive if it never aborts a transaction when it need not. More specifically, a TM is permissive with respect to a safety property p if the TM accepts every history that satisfies p. Permissiveness, like safety and liveness, can be used as a metric to compare TMs. We illustrate that it is impractical to achieve permissiveness deterministically, and then show how randomization can be used to achieve permissiveness efficiently. We introduce Adaptive Validation STM (AVSTM), which is probabilistically permissive with respect to opacity; that is, every opaque history is accepted by AVSTM with positive probability. Moreover, AVSTM guarantees lock freedom. Owing to its permissiveness, AVSTM outperforms other STMs by up to 40% in read dominated workloads in high contention scenarios. But, in low contention scenarios, the book-keeping done by AVSTM to achieve permissiveness makes AVSTM, on average, 20-30% worse than existing STMs.","lang":"eng"}],"extern":1,"date_published":"2008-09-10T00:00:00Z","conference":{"name":"DISC: Distributed Computing"},"_id":"4386","alternative_title":["LNCS"],"day":"10","type":"conference","publication_status":"published","citation":{"apa":"Guerraoui, R., Henzinger, T. A., &#38; Singh, V. (2008). Permissiveness in transactional memories (Vol. 5218, pp. 305–319). Presented at the DISC: Distributed Computing, Springer. <a href=\"https://doi.org/10.1007/978-3-540-87779-0_21\">https://doi.org/10.1007/978-3-540-87779-0_21</a>","mla":"Guerraoui, Rachid, et al. <i>Permissiveness in Transactional Memories</i>. Vol. 5218, Springer, 2008, pp. 305–19, doi:<a href=\"https://doi.org/10.1007/978-3-540-87779-0_21\">10.1007/978-3-540-87779-0_21</a>.","ista":"Guerraoui R, Henzinger TA, Singh V. 2008. Permissiveness in transactional memories. DISC: Distributed Computing, LNCS, vol. 5218, 305–319.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Permissiveness in Transactional Memories,” 5218:305–19. Springer, 2008. <a href=\"https://doi.org/10.1007/978-3-540-87779-0_21\">https://doi.org/10.1007/978-3-540-87779-0_21</a>.","short":"R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2008, pp. 305–319.","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Permissiveness in transactional memories,” presented at the DISC: Distributed Computing, 2008, vol. 5218, pp. 305–319.","ama":"Guerraoui R, Henzinger TA, Singh V. Permissiveness in transactional memories. In: Vol 5218. Springer; 2008:305-319. doi:<a href=\"https://doi.org/10.1007/978-3-540-87779-0_21\">10.1007/978-3-540-87779-0_21</a>"},"year":"2008","month":"09","publist_id":"1072","volume":5218,"status":"public","date_updated":"2021-01-12T07:56:35Z","page":"305 - 319","title":"Permissiveness in transactional memories","author":[{"last_name":"Guerraoui","full_name":"Guerraoui, Rachid","first_name":"Rachid"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Thomas Henzinger"},{"last_name":"Singh","full_name":"Vasu Singh","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu"}],"acknowledgement":"This research was supported by the Swiss National Science Foundation."},{"quality_controlled":0,"doi":"10.1007/978-3-540-85361-9_6","main_file_link":[{"url":"http://pub.ist.ac.at/%7Etah/Publications/completeness_and_nondeterminism_in_model_checking_transactional_memories.pdf","open_access":"0"}],"intvolume":"      5201","date_created":"2018-12-11T12:08:35Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"name":"CONCUR: Concurrency Theory"},"_id":"4387","day":"30","alternative_title":["LNCS"],"abstract":[{"text":"Software transactional memory (STM) offers a disciplined concurrent programming model for exploiting the parallelism of modern processor architectures. This paper presents the first deterministic specification automata for strict serializability and opacity in STMs. Using an antichain-based tool, we show our deterministic specifications to be equivalent to more intuitive, nondeterministic specification automata (which are too large to be determinized automatically). Using deterministic specification automata, we obtain a complete verification tool for STMs. We also show how to model and verify contention management within STMs. We automatically check the opacity of popular STM algorithms, such as TL2 and DSTM, with a universal contention manager. The universal contention manager is nondeterministic and establishes correctness for all possible contention management schemes.","lang":"eng"}],"date_published":"2008-07-30T00:00:00Z","extern":1,"month":"07","volume":5201,"publist_id":"1071","citation":{"ama":"Guerraoui R, Henzinger TA, Singh V. Completeness and nondeterminism in model checking transactional memories. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:21-35. doi:<a href=\"https://doi.org/10.1007/978-3-540-85361-9_6\">10.1007/978-3-540-85361-9_6</a>","ieee":"R. Guerraoui, T. A. Henzinger, and V. Singh, “Completeness and nondeterminism in model checking transactional memories,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201, pp. 21–35.","apa":"Guerraoui, R., Henzinger, T. A., &#38; Singh, V. (2008). Completeness and nondeterminism in model checking transactional memories (Vol. 5201, pp. 21–35). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-540-85361-9_6\">https://doi.org/10.1007/978-3-540-85361-9_6</a>","short":"R. Guerraoui, T.A. Henzinger, V. Singh, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 21–35.","chicago":"Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Completeness and Nondeterminism in Model Checking Transactional Memories,” 5201:21–35. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. <a href=\"https://doi.org/10.1007/978-3-540-85361-9_6\">https://doi.org/10.1007/978-3-540-85361-9_6</a>.","ista":"Guerraoui R, Henzinger TA, Singh V. 2008. Completeness and nondeterminism in model checking transactional memories. CONCUR: Concurrency Theory, LNCS, vol. 5201, 21–35.","mla":"Guerraoui, Rachid, et al. <i>Completeness and Nondeterminism in Model Checking Transactional Memories</i>. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 21–35, doi:<a href=\"https://doi.org/10.1007/978-3-540-85361-9_6\">10.1007/978-3-540-85361-9_6</a>."},"publication_status":"published","type":"conference","year":"2008","page":"21 - 35","author":[{"first_name":"Rachid","full_name":"Guerraoui, Rachid","last_name":"Guerraoui"},{"full_name":"Thomas Henzinger","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Singh","full_name":"Vasu Singh","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","first_name":"Vasu"}],"title":"Completeness and nondeterminism in model checking transactional memories","acknowledgement":"This research was supported by the Swiss National Science Foundation.","status":"public","date_updated":"2021-01-12T07:56:35Z"},{"date_created":"2018-12-11T12:08:38Z","publisher":"Springer","quality_controlled":0,"date_published":"2008-01-01T00:00:00Z","extern":1,"_id":"4397","conference":{"name":"CAV: Computer Aided Verification"},"day":"01","alternative_title":["LNCS 5123"],"publication_status":"published","citation":{"ieee":"D. Beyer, D. Zufferey, and R. Majumdar, “CSIsat: Interpolation for LA+EUF,” presented at the CAV: Computer Aided Verification, 2008, pp. 304–308.","ama":"Beyer D, Zufferey D, Majumdar R. CSIsat: Interpolation for LA+EUF. In: Springer; 2008:304-308.","apa":"Beyer, D., Zufferey, D., &#38; Majumdar, R. (2008). CSIsat: Interpolation for LA+EUF (pp. 304–308). Presented at the CAV: Computer Aided Verification, Springer.","mla":"Beyer, Dirk, et al. <i>CSIsat: Interpolation for LA+EUF</i>. Springer, 2008, pp. 304–08.","short":"D. Beyer, D. Zufferey, R. Majumdar, in:, Springer, 2008, pp. 304–308.","chicago":"Beyer, Dirk, Damien Zufferey, and Ritankar Majumdar. “CSIsat: Interpolation for LA+EUF,” 304–8. Springer, 2008.","ista":"Beyer D, Zufferey D, Majumdar R. 2008. CSIsat: Interpolation for LA+EUF. CAV: Computer Aided Verification, LNCS 5123, , 304–308."},"type":"conference","year":"2008","month":"01","publist_id":"1060","status":"public","date_updated":"2021-01-12T07:56:40Z","page":"304 - 308","title":"CSIsat: Interpolation for LA+EUF","author":[{"full_name":"Beyer, Dirk","last_name":"Beyer","first_name":"Dirk"},{"full_name":"Damien Zufferey","last_name":"Zufferey","first_name":"Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Majumdar, Ritankar S","last_name":"Majumdar","first_name":"Ritankar"}]}]