[{"title":"Time-varying Reeb graphs for continuous space-time data","publist_id":"2158","day":"01","month":"11","OA_type":"free access","_id":"3971","author":[{"last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"John","full_name":"Harer, John","last_name":"Harer"},{"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"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","oa_version":"None","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>","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>","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.","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.","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>.","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>.","short":"H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational Geometry: Theory and Applications 41 (2008) 149–166."},"intvolume":"        41","date_updated":"2026-05-29T09:15:13Z","abstract":[{"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.","lang":"eng"}],"volume":41,"type":"journal_article","date_created":"2018-12-11T12:06:12Z","status":"public","date_published":"2008-11-01T00:00:00Z","doi":"10.1016/j.comgeo.2007.11.001","publisher":"Elsevier","language":[{"iso":"eng"}],"issue":"3","article_type":"original","extern":"1","article_processing_charge":"No","page":"149 - 166","publication_identifier":{"issn":["0925-7721"],"eissn":["1879-081X"]},"year":"2008","publication":"Computational Geometry: Theory and Applications"},{"month":"06","day":"09","title":"Reeb spaces of piecewise linear mappings","publist_id":"2155","_id":"3974","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"first_name":"John","last_name":"Harer","full_name":"Harer, John"},{"full_name":"Patel, Amit","last_name":"Patel","id":"34A254A0-F248-11E8-B48F-1D18A9856A87","first_name":"Amit"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","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."}],"publication_status":"published","oa_version":"None","date_updated":"2026-05-29T09:01:13Z","citation":{"ista":"Edelsbrunner H, Harer J, Patel A. 2008. Reeb spaces of piecewise linear mappings. Proceedings of the twenty-fourth annual symposium on Computational geometry. SCG: Symposium on Computational Geometry, 242–250.","mla":"Edelsbrunner, Herbert, et al. “Reeb Spaces of Piecewise Linear Mappings.” <i>Proceedings of the Twenty-Fourth Annual Symposium on Computational Geometry</i>, Association for Computing Machinery, 2008, pp. 242–50, doi:<a href=\"https://doi.org/10.1145/1377676.1377720\">10.1145/1377676.1377720</a>.","chicago":"Edelsbrunner, Herbert, John Harer, and Amit Patel. “Reeb Spaces of Piecewise Linear Mappings.” In <i>Proceedings of the Twenty-Fourth Annual Symposium on Computational Geometry</i>, 242–50. Association for Computing Machinery, 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:, Proceedings of the Twenty-Fourth Annual Symposium on Computational Geometry, Association for Computing Machinery, 2008, pp. 242–250.","ieee":"H. Edelsbrunner, J. Harer, and A. Patel, “Reeb spaces of piecewise linear mappings,” in <i>Proceedings of the twenty-fourth annual symposium on Computational geometry</i>, College Park, MD, United States, 2008, pp. 242–250.","ama":"Edelsbrunner H, Harer J, Patel A. Reeb spaces of piecewise linear mappings. In: <i>Proceedings of the Twenty-Fourth Annual Symposium on Computational Geometry</i>. Association for Computing Machinery; 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. In <i>Proceedings of the twenty-fourth annual symposium on Computational geometry</i> (pp. 242–250). College Park, MD, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/1377676.1377720\">https://doi.org/10.1145/1377676.1377720</a>"},"language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","doi":"10.1145/1377676.1377720","date_published":"2008-06-09T00:00:00Z","date_created":"2018-12-11T12:06:13Z","status":"public","article_processing_charge":"No","extern":"1","page":"242 - 250","publication_identifier":{"isbn":["9781605580715"]},"conference":{"end_date":"2008-06-11","name":"SCG: Symposium on Computational Geometry","location":"College Park, MD, United States","start_date":"2008-06-09"},"publication":"Proceedings of the twenty-fourth annual symposium on Computational geometry","year":"2008"},{"publist_id":"1985","title":"The quest for a null model for macroecological patterns: Geometry of species distributions at multiple spatial scales","scopus_import":"1","month":"08","day":"01","_id":"4135","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Storch, D.","last_name":"Storch","first_name":"D."},{"first_name":"A.","last_name":"Šizling","full_name":"Šizling, A."},{"full_name":"Reif, J.","last_name":"Reif","first_name":"J."},{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","last_name":"Polechova","full_name":"Polechova, Jitka"},{"first_name":"E.","full_name":"Šizlingová, E.","last_name":"Šizlingová"},{"first_name":"K.","last_name":"Gaston","full_name":"Gaston, K."}],"intvolume":"        11","date_updated":"2025-07-02T05:52:43Z","citation":{"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>","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.","short":"D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, K. Gaston, Ecology Letters 11 (2008) 771–784.","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>.","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."},"oa_version":"None","publication_status":"published","volume":11,"type":"journal_article","abstract":[{"lang":"eng","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."}],"status":"public","date_created":"2018-12-11T12:07:09Z","issue":"8","publisher":"Wiley","doi":"10.1111/j.1461-0248.2008.01206.x","date_published":"2008-08-01T00:00:00Z","language":[{"iso":"eng"}],"extern":"1","article_processing_charge":"No","page":"771 - 784","year":"2008","quality_controlled":"1","publication":"Ecology Letters"},{"day":"01","title":"Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation","OA_type":"free access","author":[{"last_name":"Vervenne","full_name":"Vervenne, Hilke","first_name":"Hilke"},{"first_name":"Koen","last_name":"Crombez","full_name":"Crombez, Koen"},{"first_name":"Kathleen","full_name":"Lambaerts, Kathleen","last_name":"Lambaerts"},{"first_name":"Lara","last_name":"Carvalho","full_name":"Carvalho, Lara"},{"first_name":"Mathias","full_name":"Köppen, Mathias","last_name":"Köppen"},{"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":"Wim","full_name":"Van De Ven, Wim","last_name":"Van De Ven"},{"last_name":"Petit","full_name":"Petit, Marleen","first_name":"Marleen"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"None","date_updated":"2026-05-29T08:31:06Z","intvolume":"       320","date_created":"2018-12-11T12:07:11Z","status":"public","article_processing_charge":"No","publication_identifier":{"issn":["0012-1606"]},"publication":"Developmental Biology","pmid":1,"month":"08","publist_id":"1978","_id":"4141","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":320,"type":"journal_article","publication_status":"published","citation":{"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>.","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.","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>.","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.","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>","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>","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."},"doi":"10.1016/j.ydbio.2008.05.529","date_published":"2008-08-01T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Elsevier","issue":"1","article_type":"original","extern":"1","page":"267 - 277","external_id":{"pmid":["18582857"]},"year":"2008"},{"_id":"4150","month":"02","pmid":1,"publist_id":"1969","volume":2,"type":"journal_article","citation":{"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>.","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>.","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.","short":"E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P.J. Heisenberg, R. Foty, HFSP Journal 2 (2008) 42–56.","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>","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>"},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","extern":"1","article_type":"original","issue":"1","date_published":"2008-02-01T00:00:00Z","publisher":"HFSP Publishing","doi":"10.2976/1.2834817","language":[{"iso":"eng"}],"oa":1,"year":"2008","page":"42 - 56","external_id":{"pmid":["19404452"]},"OA_type":"free access","day":"01","title":"Quantitative differences in tissue surface tension influence zebrafish germ layer positioning","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."}],"date_updated":"2026-06-02T09:01:41Z","intvolume":"         2","oa_version":"Published Version","author":[{"full_name":"Schötz, Eva","last_name":"Schötz","first_name":"Eva"},{"full_name":"Burdine, Rebecca","last_name":"Burdine","first_name":"Rebecca"},{"first_name":"Frank","full_name":"Julicher, Frank","last_name":"Julicher"},{"first_name":"Malcolm","last_name":"Steinberg","full_name":"Steinberg, Malcolm"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"first_name":"Ramsey","full_name":"Foty, Ramsey","last_name":"Foty"}],"article_processing_charge":"No","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.2976/1.2834817"}],"date_created":"2018-12-11T12:07:14Z","publication":"HFSP Journal"},{"article_processing_charge":"No","status":"public","date_created":"2018-12-11T12:07:19Z","publication":"Development","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"OA_type":"closed access","day":"15","title":"Origin and shaping of the laterality organ in zebrafish","abstract":[{"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.","lang":"eng"}],"date_updated":"2026-05-29T07:25:53Z","intvolume":"       135","oa_version":"None","author":[{"first_name":"Pablo","last_name":"Oteíza","full_name":"Oteíza, Pablo"},{"first_name":"Mathias","full_name":"Köppen, Mathias","last_name":"Köppen"},{"full_name":"Concha, Miguel","last_name":"Concha","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"}],"extern":"1","article_type":"original","issue":"16","doi":"10.1242/dev.022228","date_published":"2008-08-15T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Company of Biologists","year":"2008","page":"2807 - 2813","external_id":{"pmid":["18635607"]},"_id":"4161","month":"08","pmid":1,"publist_id":"1956","type":"journal_article","volume":135,"citation":{"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.","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>.","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>.","short":"P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008) 2807–2813.","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.","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>","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","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"publication":"Angewandte Chemie - International Edition","publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"article_processing_charge":"No","date_created":"2018-12-11T12:07:26Z","status":"public","oa_version":"None","intvolume":"        47","date_updated":"2026-05-29T07:20:40Z","abstract":[{"lang":"eng","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. "}],"author":[{"full_name":"Krieg, Michael","last_name":"Krieg","first_name":"Michael"},{"full_name":"Helenius, Jonne","last_name":"Helenius","first_name":"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":"Daniel","full_name":"Mueller, Daniel","last_name":"Mueller"}],"OA_type":"closed access","title":"A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics","day":"26","year":"2008","external_id":{"pmid":["19035533"]},"page":"9775 - 9777","article_type":"original","extern":"1","publisher":"Wiley-Blackwell","doi":"10.1002/anie.200803552","language":[{"iso":"eng"}],"date_published":"2008-11-26T00:00:00Z","issue":"50","publication_status":"published","citation":{"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>.","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>.","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.","short":"M. Krieg, J. Helenius, C.-P.J. Heisenberg, D. Mueller, Angewandte Chemie - International Edition 47 (2008) 9775–9777.","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.","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>","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>"},"type":"journal_article","volume":47,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"4180","publist_id":"1939","pmid":1,"month":"11"},{"_id":"4181","publist_id":"1938","pmid":1,"month":"03","publication_status":"published","citation":{"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>","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>","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.","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>.","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>.","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.","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."},"type":"journal_article","volume":10,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"letter_note","extern":"1","doi":"10.1038/ncb1705","language":[{"iso":"eng"}],"date_published":"2008-03-23T00:00:00Z","publisher":"Nature Publishing Group","issue":"4","year":"2008","external_id":{"pmid":["18364700 "]},"page":"429 - 436","OA_type":"closed access","title":"Tensile forces govern germ-layer organization in zebrafish","day":"23","oa_version":"None","date_updated":"2026-05-29T07:13:59Z","intvolume":"        10","abstract":[{"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.","lang":"eng"}],"author":[{"first_name":"Michael","last_name":"Krieg","full_name":"Krieg, Michael"},{"full_name":"Arboleda Estudillo, Yohanna","last_name":"Arboleda Estudillo","first_name":"Yohanna"},{"first_name":"Pierre","last_name":"Puech","full_name":"Puech, Pierre"},{"last_name":"Käfer","full_name":"Käfer, Jos","first_name":"Jos"},{"full_name":"Graner, François","last_name":"Graner","first_name":"François"},{"first_name":"Daniel","full_name":"Mueller, Daniel","last_name":"Mueller"},{"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"}],"article_processing_charge":"No","date_created":"2018-12-11T12:07:26Z","status":"public","publication":"Nature Cell Biology","publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]}},{"OA_place":"repository","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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>.","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.","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.","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.","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>","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>"},"publication_status":"published","volume":135,"type":"journal_article","publist_id":"1928","month":"09","pmid":1,"_id":"4190","external_id":{"pmid":["18701549"]},"page":"3043 - 3051","year":"2008","issue":"18","publisher":"Company of Biologists","date_published":"2008-09-15T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1242/dev.020396","extern":"1","article_type":"original","author":[{"last_name":"Kai","full_name":"Kai, Masatake","first_name":"Masatake"},{"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"},{"first_name":"Masazumi","full_name":"Tada, Masazumi","last_name":"Tada"}],"intvolume":"       135","date_updated":"2026-05-21T08:53:00Z","oa_version":"None","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."}],"title":"Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation","day":"15","OA_type":"green","publication":"Development","status":"public","date_created":"2018-12-11T12:07:29Z","article_processing_charge":"No"},{"publication":"Journal of Cell Science","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"article_processing_charge":"No","date_created":"2018-12-11T12:07:30Z","status":"public","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"}],"oa_version":"None","intvolume":"       121","date_updated":"2026-05-28T14:11:54Z","author":[{"last_name":"Helenius","full_name":"Helenius, Jonne","first_name":"Jonne"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"first_name":"Hermann","full_name":"Gaub, Hermann","last_name":"Gaub"},{"full_name":"Mueller, Daniel","last_name":"Mueller","first_name":"Daniel"}],"OA_type":"green","day":"01","title":"Single-cell force spectroscopy","year":"2008","page":"1785 - 1791","external_id":{"pmid":["18492792"]},"article_type":"comment","extern":"1","publisher":"Company of Biologists","doi":"10.1242/jcs.030999","language":[{"iso":"eng"}],"date_published":"2008-06-01T00:00:00Z","issue":"11","type":"journal_article","volume":121,"publication_status":"published","citation":{"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.","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>","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>","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>.","ista":"Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. 2008. Single-cell force spectroscopy. Journal of Cell Science. 121(11), 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>.","short":"J. Helenius, C.-P.J. Heisenberg, H. Gaub, D. Mueller, Journal of Cell Science 121 (2008) 1785–1791."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","_id":"4193","pmid":1,"month":"06","publist_id":"1924"},{"_id":"4198","publist_id":"1918","pmid":1,"month":"01","publication_status":"published","citation":{"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>.","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.","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.","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.","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>","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","volume":18,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"review","extern":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"date_published":"2008-01-01T00:00:00Z","doi":"10.1016/j.gde.2008.07.011","issue":"4","year":"2008","external_id":{"pmid":["18721878"]},"page":"311 - 316","OA_type":"closed access","title":"Back and forth between cell fate specification and movement during vertebrate gastrulation","day":"01","oa_version":"None","date_updated":"2026-05-28T14:03:47Z","intvolume":"        18","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"}],"author":[{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"},{"last_name":"Solnica Krezel","full_name":"Solnica Krezel, Lilianna","first_name":"Lilianna"}],"article_processing_charge":"No","date_created":"2018-12-11T12:07:32Z","status":"public","publication":"Current Opinion in Genetics & Development","publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]}},{"publication":"Development","article_processing_charge":"No","status":"public","date_created":"2018-12-11T12:07:42Z","intvolume":"       135","date_updated":"2026-05-28T13:59:30Z","oa_version":"None","abstract":[{"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.","lang":"eng"}],"author":[{"first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"},{"full_name":"Pantazis, Periklis","last_name":"Pantazis","first_name":"Periklis"},{"last_name":"Kicheva","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","orcid":"0000-0003-4509-4998"},{"last_name":"Bokel","full_name":"Bokel, Christian","first_name":"Christian"},{"first_name":"Marcos","full_name":"González Gaitán, Marcos","last_name":"González Gaitán"},{"full_name":"Julicher, Frank","last_name":"Julicher","first_name":"Frank"}],"OA_type":"closed access","title":"Precision of the Dpp gradient","day":"15","year":"2008","external_id":{"pmid":["18296653"]},"page":"1137 - 1146","extern":"1","article_type":"original","issue":"6","doi":"10.1242/dev.012062","language":[{"iso":"eng"}],"date_published":"2008-03-15T00:00:00Z","publisher":"Company of Biologists","citation":{"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>","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>","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.","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>.","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>.","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.","short":"T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, F. Julicher, Development 135 (2008) 1137–1146."},"publication_status":"published","volume":135,"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"4227","publist_id":"1889","month":"03","pmid":1},{"page":"2749 - 2756","publication_identifier":{"isbn":["9781424418237"]},"conference":{"name":"WCCI: IEEE World Congress on Computational Intelligence","end_date":"2008-06-06","location":"Hong Kong","start_date":"2008-06-01"},"year":"2008","publisher":"IEEE","doi":"10.1109/CEC.2008.4631167","date_published":"2008-09-23T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:07:49Z","status":"public","article_processing_charge":"No","extern":"1","author":[{"last_name":"Yang","full_name":"Yang, Erfu","first_name":"Erfu"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Arslan, Tughrul","last_name":"Arslan","first_name":"Tughrul"},{"first_name":"Ahmet","full_name":"Erdogan, Ahmet","last_name":"Erdogan"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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"}],"type":"conference","oa_version":"None","publication_status":"published","citation":{"short":"E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, IEEE, 2008, pp. 2749–2756.","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>.","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>.","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.","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, Hong Kong: IEEE. <a href=\"https://doi.org/10.1109/CEC.2008.4631167\">https://doi.org/10.1109/CEC.2008.4631167</a>","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>","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, Hong Kong, 2008, pp. 2749–2756."},"date_updated":"2026-05-28T13:57:07Z","month":"09","day":"23","title":"A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks","publist_id":"1861","OA_type":"closed access","_id":"4244"},{"title":"Effects of spontaneous mutation accumulation on sex ratio traits","day":"01","OA_type":"closed access","author":[{"first_name":"Bart","last_name":"Pannebakker","full_name":"Pannebakker, Bart"},{"first_name":"Daniel","last_name":"Halligan","full_name":"Halligan, Daniel"},{"first_name":"K Tracy","last_name":"Reynolds","full_name":"Reynolds, K Tracy"},{"last_name":"Ballantyne","full_name":"Ballantyne, Gavin","first_name":"Gavin"},{"first_name":"David","last_name":"Shuker","full_name":"Shuker, David"},{"last_name":"Barton","full_name":"Barton, Nicholas H","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"}],"intvolume":"        62","date_updated":"2026-05-28T13:46:48Z","oa_version":"None","abstract":[{"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.","lang":"eng"}],"status":"public","date_created":"2018-12-11T12:07:49Z","article_processing_charge":"No","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication":"Evolution; International Journal of Organic Evolution","publist_id":"1860","month":"08","pmid":1,"_id":"4245","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"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. Oxford Academic, pp. 1921–1935, 2008.","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>. Oxford Academic. <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>","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, Oxford Academic, 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>.","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>. Oxford Academic, 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>."},"publication_status":"published","volume":62,"type":"journal_article","issue":"8","publisher":"Oxford Academic","doi":"10.1111/j.1558-5646.2008.00434.x","language":[{"iso":"eng"}],"date_published":"2008-08-01T00:00:00Z","extern":"1","article_type":"original","external_id":{"pmid":["18522711"]},"page":"1921 - 1935","year":"2008"},{"author":[{"first_name":"Armando","last_name":"Rastelli","full_name":"Rastelli, Armando"},{"first_name":"Mathieu","full_name":"Stoffel, Mathieu","last_name":"Stoffel"},{"first_name":"Ângelo","full_name":"Malachias, Ângelo S","last_name":"Malachias"},{"full_name":"Merdzhanova, Tsvetelina","last_name":"Merdzhanova","first_name":"Tsvetelina"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Georgios Katsaros","last_name":"Katsaros"},{"full_name":"Kern, Klaus","last_name":"Kern","first_name":"Klaus"},{"first_name":"Till","last_name":"Metzger","full_name":"Metzger, Till H"},{"last_name":"Schmidt","full_name":"Schmidt, Oliver G","first_name":"Oliver"}],"volume":8,"type":"journal_article","abstract":[{"text":"Scanning probe microscopy; Semiconductor quantum dots; Composition gradients; Composition profiles; Nanotomography; Single quantum dots; Strained sige/si; Three-dimensional (3D); Wet-chemical etchings; X-ray scattering measurements; quantum dot; methodology; nanotechnology; optical tomography; scanning probe microscopy; three dimensional imaging; Imaging, Three-Dimensional; Materials Testing; Microscopy, Scanning Probe; Nanotechnology; Quantum Dots; Tomography,","lang":"eng"}],"publication_status":"published","citation":{"short":"A. Rastelli, M. Stoffel, Â. Malachias, T. Merdzhanova, G. Katsaros, K. Kern, T. Metzger, O. Schmidt, Nano Letters 8 (2008) 1404–1409.","ista":"Rastelli A, Stoffel M, Malachias Â, Merdzhanova T, Katsaros G, Kern K, Metzger T, Schmidt O. 2008. Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography. Nano Letters. 8(5), 1404–1409.","chicago":"Rastelli, Armando, Mathieu Stoffel, Ângelo Malachias, Tsvetelina Merdzhanova, Georgios Katsaros, Klaus Kern, Till Metzger, and Oliver Schmidt. “Three-Dimensional Composition Profiles of Single Quantum Dots Determined by Scanning-Probe-Microscopy-Based Nanotomography.” <i>Nano Letters</i>. American Chemical Society, 2008. <a href=\"https://doi.org/10.1021/nl080290y\">https://doi.org/10.1021/nl080290y</a>.","mla":"Rastelli, Armando, et al. “Three-Dimensional Composition Profiles of Single Quantum Dots Determined by Scanning-Probe-Microscopy-Based Nanotomography.” <i>Nano Letters</i>, vol. 8, no. 5, American Chemical Society, 2008, pp. 1404–09, doi:<a href=\"https://doi.org/10.1021/nl080290y\">10.1021/nl080290y</a>.","apa":"Rastelli, A., Stoffel, M., Malachias, Â., Merdzhanova, T., Katsaros, G., Kern, K., … Schmidt, O. (2008). Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/nl080290y\">https://doi.org/10.1021/nl080290y</a>","ama":"Rastelli A, Stoffel M, Malachias Â, et al. Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography. <i>Nano Letters</i>. 2008;8(5):1404-1409. doi:<a href=\"https://doi.org/10.1021/nl080290y\">10.1021/nl080290y</a>","ieee":"A. Rastelli <i>et al.</i>, “Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography,” <i>Nano Letters</i>, vol. 8, no. 5. American Chemical Society, pp. 1404–1409, 2008."},"date_updated":"2021-01-12T06:52:57Z","intvolume":"         8","day":"01","month":"05","title":"Three-dimensional composition profiles of single quantum dots determined by scanning-probe-microscopy-based nanotomography","publist_id":"5374","_id":"1749","page":"1404 - 1409","publication":"Nano Letters","quality_controlled":0,"year":"2008","date_published":"2008-05-01T00:00:00Z","publisher":"American Chemical Society","doi":"10.1021/nl080290y","issue":"5","acknowledgement":"This work was supported by the BMBF (No. 03N8711) and the EU project D-DotFET (No. 012150)","date_created":"2018-12-11T11:53:48Z","status":"public","extern":1},{"day":"29","month":"08","title":"Positioning of strained islands by interaction with surface nanogrooves","publist_id":"5373","_id":"1751","author":[{"full_name":"Georgios Katsaros","last_name":"Katsaros","first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tersoff, Jerry","last_name":"Tersoff","first_name":"Jerry"},{"first_name":"Mathieu","last_name":"Stoffel","full_name":"Stoffel, Mathieu"},{"last_name":"Rastelli","full_name":"Rastelli, Armando","first_name":"Armando"},{"first_name":"P","last_name":"Acosta Diaz","full_name":"Acosta-Diaz, P"},{"first_name":"Gouranga","full_name":"Kar, Gouranga S","last_name":"Kar"},{"last_name":"Costantini","full_name":"Costantini, Giovanni","first_name":"Giovanni"},{"full_name":"Schmidt, Oliver G","last_name":"Schmidt","first_name":"Oliver"},{"first_name":"Klaus","full_name":"Kern, Klaus","last_name":"Kern"}],"type":"journal_article","volume":101,"abstract":[{"lang":"eng","text":"When strained Stranski-Krastanow islands are used as &quot;self-assembled quantum dots,&quot; a key goal is to control the island position. Here we show that nanoscale grooves can control the nucleation of epitaxial Ge islands on Si(001), and can drive lateral motion of existing islands onto the grooves, even when the grooves are very narrow and shallow compared to the islands. A position centered on the groove minimizes energy. We use as prototype grooves the trenches which form naturally around islands. During coarsening, the shrinking islands move laterally to sit directly astride that trench. In subsequent growth, we demonstrate that islands nucleate on the &quot;empty trenches&quot; which remain on the surface after complete dissolution of the original islands."}],"publication_status":"published","intvolume":"       101","citation":{"mla":"Katsaros, Georgios, et al. “Positioning of Strained Islands by Interaction with Surface Nanogrooves.” <i>Physical Review Letters</i>, vol. 101, no. 9, American Physical Society, 2008, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.101.096103\">10.1103/PhysRevLett.101.096103</a>.","ista":"Katsaros G, Tersoff J, Stoffel M, Rastelli A, Acosta Diaz P, Kar G, Costantini G, Schmidt O, Kern K. 2008. Positioning of strained islands by interaction with surface nanogrooves. Physical Review Letters. 101(9).","chicago":"Katsaros, Georgios, Jerry Tersoff, Mathieu Stoffel, Armando Rastelli, P Acosta Diaz, Gouranga Kar, Giovanni Costantini, Oliver Schmidt, and Klaus Kern. “Positioning of Strained Islands by Interaction with Surface Nanogrooves.” <i>Physical Review Letters</i>. American Physical Society, 2008. <a href=\"https://doi.org/10.1103/PhysRevLett.101.096103\">https://doi.org/10.1103/PhysRevLett.101.096103</a>.","short":"G. Katsaros, J. Tersoff, M. Stoffel, A. Rastelli, P. Acosta Diaz, G. Kar, G. Costantini, O. Schmidt, K. Kern, Physical Review Letters 101 (2008).","ieee":"G. Katsaros <i>et al.</i>, “Positioning of strained islands by interaction with surface nanogrooves,” <i>Physical Review Letters</i>, vol. 101, no. 9. American Physical Society, 2008.","ama":"Katsaros G, Tersoff J, Stoffel M, et al. Positioning of strained islands by interaction with surface nanogrooves. <i>Physical Review Letters</i>. 2008;101(9). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.101.096103\">10.1103/PhysRevLett.101.096103</a>","apa":"Katsaros, G., Tersoff, J., Stoffel, M., Rastelli, A., Acosta Diaz, P., Kar, G., … Kern, K. (2008). Positioning of strained islands by interaction with surface nanogrooves. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.101.096103\">https://doi.org/10.1103/PhysRevLett.101.096103</a>"},"date_updated":"2021-01-12T06:52:58Z","date_published":"2008-08-29T00:00:00Z","publisher":"American Physical Society","doi":"10.1103/PhysRevLett.101.096103","issue":"9","date_created":"2018-12-11T11:53:49Z","status":"public","extern":1,"publication":"Physical Review Letters","quality_controlled":0,"year":"2008"},{"extern":1,"status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0902.1827"}],"date_created":"2018-12-11T11:53:53Z","issue":"7202","acknowledgement":"This work was supported by SNF and ETHZ. P.J.L. was supported by the EU with an MC-EIF. A.B. was supported by NSERC, CIFAR and FQRNT","doi":"10.1038/nature07112","publisher":"Nature Publishing Group","date_published":"2008-07-17T00:00:00Z","year":"2008","quality_controlled":0,"publication":"Nature","page":"315 - 318","_id":"1763","publist_id":"5358","title":"Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system","day":"17","month":"07","citation":{"mla":"Fink, Johannes M., et al. “Climbing the Jaynes-Cummings Ladder and Observing Its √n Nonlinearity in a Cavity QED System.” <i>Nature</i>, vol. 454, no. 7202, Nature Publishing Group, 2008, pp. 315–18, doi:<a href=\"https://doi.org/10.1038/nature07112\">10.1038/nature07112</a>.","ista":"Fink JM, Göppl M, Baur M, Bianchetti R, Leek P, Blais A, Wallraff A. 2008. Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. Nature. 454(7202), 315–318.","chicago":"Fink, Johannes M, M Göppl, Matthias Baur, R Bianchetti, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Climbing the Jaynes-Cummings Ladder and Observing Its √n Nonlinearity in a Cavity QED System.” <i>Nature</i>. Nature Publishing Group, 2008. <a href=\"https://doi.org/10.1038/nature07112\">https://doi.org/10.1038/nature07112</a>.","short":"J.M. Fink, M. Göppl, M. Baur, R. Bianchetti, P. Leek, A. Blais, A. Wallraff, Nature 454 (2008) 315–318.","ama":"Fink JM, Göppl M, Baur M, et al. Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. <i>Nature</i>. 2008;454(7202):315-318. doi:<a href=\"https://doi.org/10.1038/nature07112\">10.1038/nature07112</a>","apa":"Fink, J. M., Göppl, M., Baur, M., Bianchetti, R., Leek, P., Blais, A., &#38; Wallraff, A. (2008). Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature07112\">https://doi.org/10.1038/nature07112</a>","ieee":"J. M. Fink <i>et al.</i>, “Climbing the Jaynes-Cummings ladder and observing its √n nonlinearity in a cavity QED system,” <i>Nature</i>, vol. 454, no. 7202. Nature Publishing Group, pp. 315–318, 2008."},"intvolume":"       454","date_updated":"2021-01-12T06:53:03Z","publication_status":"published","abstract":[{"text":"The field of cavity quantum electrodynamics (QED), traditionally studied in atomic systems, has gained new momentum by recent reports of quantum optical experiments with solid-state semiconducting and superconducting systems. In cavity QED, the observation of the vacuum Rabi mode splitting is used to investigate the nature of matter-light interaction at a quantum-mechanical level. However, this effect can, at least in principle, be explained classically as the normal mode splitting of two coupled linear oscillators. It has been suggested that an observation of the scaling of the resonant atom-photon coupling strength in the Jaynes-Cummings energy ladder with the square root of photon number n is sufficient to prove that the system is quantum mechanical in nature. Here we report a direct spectroscopic observation of this characteristic quantum nonlinearity. Measuring the photonic degree of freedom of the coupled system, our measurements provide unambiguous spectroscopic evidence for the quantum nature of the resonant atom-field interaction in cavity QED. We explore atom-photon superposition states involving up to two photons, using a spectroscopic pump and probe technique. The experiments have been performed in a circuit QED set-up, in which very strong coupling is realized by the large dipole coupling strength and the long coherence time of a superconducting qubit embedded in a high-quality on-chip microwave cavity. Circuit QED systems also provide a natural quantum interface between flying qubits (photons) and stationary qubits for applications in quantum information processing and communication.","lang":"eng"}],"volume":454,"type":"journal_article","author":[{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Johannes Fink"},{"full_name":"Göppl, M","last_name":"Göppl","first_name":"M"},{"first_name":"Matthias","full_name":"Baur, Matthias P","last_name":"Baur"},{"full_name":"Bianchetti, R","last_name":"Bianchetti","first_name":"R"},{"first_name":"Peter","last_name":"Leek","full_name":"Leek, Peter J"},{"first_name":"Alexandre","last_name":"Blais","full_name":"Blais, Alexandre"},{"full_name":"Wallraff, Andreas","last_name":"Wallraff","first_name":"Andreas"}]},{"_id":"1764","publist_id":"5357","title":"Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift","day":"28","month":"11","intvolume":"       322","citation":{"ieee":"A. Fragner <i>et al.</i>, “Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift,” <i>Science</i>, vol. 322, no. 5906. American Association for the Advancement of Science, pp. 1357–1360, 2008.","apa":"Fragner, A., Göppl, M., Fink, J. M., Baur, M., Bianchetti, R., Leek, P., … Wallraff, A. (2008). Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1164482\">https://doi.org/10.1126/science.1164482</a>","ama":"Fragner A, Göppl M, Fink JM, et al. Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift. <i>Science</i>. 2008;322(5906):1357-1360. doi:<a href=\"https://doi.org/10.1126/science.1164482\">10.1126/science.1164482</a>","ista":"Fragner A, Göppl M, Fink JM, Baur M, Bianchetti R, Leek P, Blais A, Wallraff A. 2008. Resolving vacuum fluctuations in an electrical circuit by measuring the lamb shift. Science. 322(5906), 1357–1360.","chicago":"Fragner, A, M Göppl, Johannes M Fink, Matthias Baur, R Bianchetti, Peter Leek, Alexandre Blais, and Andreas Wallraff. “Resolving Vacuum Fluctuations in an Electrical Circuit by Measuring the Lamb Shift.” <i>Science</i>. American Association for the Advancement of Science, 2008. <a href=\"https://doi.org/10.1126/science.1164482\">https://doi.org/10.1126/science.1164482</a>.","mla":"Fragner, A., et al. “Resolving Vacuum Fluctuations in an Electrical Circuit by Measuring the Lamb Shift.” <i>Science</i>, vol. 322, no. 5906, American Association for the Advancement of Science, 2008, pp. 1357–60, doi:<a href=\"https://doi.org/10.1126/science.1164482\">10.1126/science.1164482</a>.","short":"A. Fragner, M. Göppl, J.M. Fink, M. Baur, R. Bianchetti, P. Leek, A. Blais, A. Wallraff, Science 322 (2008) 1357–1360."},"date_updated":"2021-01-12T06:53:03Z","publication_status":"published","abstract":[{"text":"Quantum theory predicts that empty space is not truly empty. Even in the absence of any particles or radiation, in pure vacuum, virtual particles are constantly created and annihilated. In an electromagnetic field, the presence of virtual photons manifests itself as a small renormalization of the energy of a quantum system, known as the Lamb shift. We present an experimental observation of the Lamb shift in a solid-state system. The strong dispersive coupling of a superconducting electronic circuit acting as a quantum bit (qubit) to the vacuum field in a transmission-line resonator leads to measurable Lamb shifts of up to 1.4% of the qubit transition frequency. The qubit is also observed to couple more strongly to the vacuum field than to a single photon inside the cavity, an effect that is explained by taking into account the limited anharmonicity of the higher excited qubit states.","lang":"eng"}],"volume":322,"type":"journal_article","author":[{"first_name":"A","last_name":"Fragner","full_name":"Fragner, A"},{"last_name":"Göppl","full_name":"Göppl, M","first_name":"M"},{"last_name":"Fink","full_name":"Johannes Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","orcid":"0000-0001-8112-028X"},{"last_name":"Baur","full_name":"Baur, Matthias P","first_name":"Matthias"},{"first_name":"R","last_name":"Bianchetti","full_name":"Bianchetti, R"},{"first_name":"Peter","full_name":"Leek, Peter J","last_name":"Leek"},{"first_name":"Alexandre","last_name":"Blais","full_name":"Blais, Alexandre"},{"first_name":"Andreas","last_name":"Wallraff","full_name":"Wallraff, Andreas"}],"extern":1,"status":"public","date_created":"2018-12-11T11:53:53Z","issue":"5906","acknowledgement":"This work was supported by the Swiss National Science Foundation and ETHZ. P.J.L. was supported by the European Commission with a Marie Curie Intra-European Fellowship. A.B. was supported by the Natural Sciences and Engineering Research Council of Canada, Canadian Institute for Advanced Research, and Fonds Québécois de la Recherche sur la Nature et les Technologies","publisher":"American Association for the Advancement of Science","date_published":"2008-11-28T00:00:00Z","doi":"10.1126/science.1164482","year":"2008","quality_controlled":0,"publication":"Science","page":"1357 - 1360"},{"type":"journal_article","abstract":[{"lang":"eng","text":"High quality on-chip microwave resonators have recently found prominent new applications in quantum optics and quantum information processing experiments with superconducting electronic circuits, a field now known as circuit quantum electrodynamics (QED). They are also used as single photon detectors and parametric amplifiers. Here we analyze the physical properties of coplanar waveguide resonators and their relation to the materials properties for use in circuit QED. We have designed and fabricated resonators with fundamental frequencies from 2 to 9 GHz and quality factors ranging from a few hundreds to a several hundred thousands controlled by appropriately designed input and output coupling capacitors. The microwave transmission spectra measured at temperatures of 20 mK are shown to be in good agreement with theoretical lumped element and distributed element transmission matrix models. In particular, the experimentally determined resonance frequencies, quality factors, and insertion losses are fully and consistently explained by the two models for all measured devices. The high level of control and flexibility in design renders these resonators ideal for storing and manipulating quantum electromagnetic fields in integrated superconducting electronic circuits."}],"volume":104,"publication_status":"published","date_updated":"2021-01-12T06:53:03Z","intvolume":"       104","citation":{"apa":"Göppl, M., Fragner, A., Baur, M., Bianchetti, R., Filipp, S., Fink, J. M., … Wallraff, A. (2008). Coplanar waveguide resonators for circuit quantum electrodynamics. <i>Journal of Applied Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.3010859\">https://doi.org/10.1063/1.3010859</a>","ama":"Göppl M, Fragner A, Baur M, et al. Coplanar waveguide resonators for circuit quantum electrodynamics. <i>Journal of Applied Physics</i>. 2008;104(11). doi:<a href=\"https://doi.org/10.1063/1.3010859\">10.1063/1.3010859</a>","ieee":"M. Göppl <i>et al.</i>, “Coplanar waveguide resonators for circuit quantum electrodynamics,” <i>Journal of Applied Physics</i>, vol. 104, no. 11. American Institute of Physics, 2008.","short":"M. Göppl, A. Fragner, M. Baur, R. Bianchetti, S. Filipp, J.M. Fink, P. Leek, G. Puebla, L. Steffen, A. Wallraff, Journal of Applied Physics 104 (2008).","mla":"Göppl, M., et al. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.” <i>Journal of Applied Physics</i>, vol. 104, no. 11, American Institute of Physics, 2008, doi:<a href=\"https://doi.org/10.1063/1.3010859\">10.1063/1.3010859</a>.","chicago":"Göppl, M, A Fragner, Matthias Baur, R Bianchetti, Stefan Filipp, Johannes M Fink, Peter Leek, G Puebla, L. Steffen, and Andreas Wallraff. “Coplanar Waveguide Resonators for Circuit Quantum Electrodynamics.” <i>Journal of Applied Physics</i>. American Institute of Physics, 2008. <a href=\"https://doi.org/10.1063/1.3010859\">https://doi.org/10.1063/1.3010859</a>.","ista":"Göppl M, Fragner A, Baur M, Bianchetti R, Filipp S, Fink JM, Leek P, Puebla G, Steffen L, Wallraff A. 2008. Coplanar waveguide resonators for circuit quantum electrodynamics. Journal of Applied Physics. 104(11)."},"author":[{"last_name":"Göppl","full_name":"Göppl, M","first_name":"M"},{"first_name":"A","full_name":"Fragner, A","last_name":"Fragner"},{"first_name":"Matthias","full_name":"Baur, Matthias P","last_name":"Baur"},{"first_name":"R","last_name":"Bianchetti","full_name":"Bianchetti, R"},{"first_name":"Stefan","last_name":"Filipp","full_name":"Filipp, Stefan"},{"last_name":"Fink","full_name":"Johannes Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"},{"last_name":"Leek","full_name":"Leek, Peter J","first_name":"Peter"},{"full_name":"Puebla, G","last_name":"Puebla","first_name":"G"},{"first_name":"L.","last_name":"Steffen","full_name":"Steffen, L. Kraig"},{"full_name":"Wallraff, Andreas","last_name":"Wallraff","first_name":"Andreas"}],"_id":"1765","day":"01","month":"01","title":"Coplanar waveguide resonators for circuit quantum electrodynamics","publist_id":"5355","publication":"Journal of Applied Physics","quality_controlled":0,"year":"2008","extern":1,"date_published":"2008-01-01T00:00:00Z","doi":"10.1063/1.3010859","publisher":"American Institute of Physics","acknowledgement":"This work was supported by Swiss National Fund (SNF) and ETH Zürich. P.J.L. was supported by the EC with a MC-EIF","issue":"11","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0807.4094"}],"date_created":"2018-12-11T11:53:53Z","oa":1,"status":"public"},{"publication":"Monthly Notices of the Royal Astronomical Society","publication_identifier":{"issn":["0035-8711","1365-2966"]},"article_processing_charge":"No","status":"public","main_file_link":[{"url":"https://doi.org/10.1111/j.1365-2966.2008.12945.x","open_access":"1"}],"date_created":"2024-09-06T09:09:01Z","abstract":[{"lang":"eng","text":"High-redshift quasars (z >~ 6) drive ionization fronts into the intergalactic medium (IGM). If the thickness of the front can be measured, it can provide a novel constraint on the ionizing spectral energy distribution (SED). Here we follow the propagation of an I-front into a uniform IGM, and compute its thickness for a range of possible quasar spectra and ages. We also explore the effects of uniform and non-uniform ionizing backgrounds. We find that even for hard spectra, the fronts are initially thin, with a thickness much smaller than the mean free path of ionizing photons, but the thickness increases as the front approaches equilibrium in 10^8 - 10^9 years, and can eventually significantly exceed simple estimates based on the mean free path. With a high intrinsic hydrogen column density obscuring the source (log(N_H/cm^-2) >~ 19.2) or a hard power-law spectrum combined with some obscuration (e.g. dlog(F_\\nu)/dlog(\\nu) >~ -1.2 at log(N_H/cm^-2) >~ 18.0), the thickness of the front exceeds ~1 physical Mpc and may be measurable from the morphology of its redshifted 21cm signal. We find that the highly ionized inner part of the front, which may be probed by Lyman line absorption spectra, remains sharp for bright quasars unless a large obscuring column (log(N_H/cm^-2) >~ 19.2) removes most of their ionizing photons up to ~40 eV. For obscured sources with log(N_H/cm^-2) >~ 19.8, embedded in a significantly neutral IGM, the black Lyman-alpha trough (where the neutral fraction is ~10^-3) underestimates the size of the HII region by a factor of >~4."}],"date_updated":"2024-09-25T13:54:14Z","intvolume":"       385","oa_version":"Published Version","author":[{"first_name":"R. H.","last_name":"Kramer","full_name":"Kramer, R. H."},{"last_name":"Haiman","full_name":"Haiman, Zoltán","first_name":"Zoltán","id":"7c006e8c-cc0d-11ee-8322-cb904ef76f36"}],"day":"13","title":"The thickness of high-redshift quasar ionization fronts as a constraint on the ionizing spectral energy distribution","year":"2008","quality_controlled":"1","page":"1561-1575","extern":"1","article_type":"original","issue":"3","doi":"10.1111/j.1365-2966.2008.12945.x","date_published":"2008-03-13T00:00:00Z","publisher":"Oxford University Press","language":[{"iso":"eng"}],"oa":1,"type":"journal_article","volume":385,"citation":{"apa":"Kramer, R. H., &#38; Haiman, Z. (2008). The thickness of high-redshift quasar ionization fronts as a constraint on the ionizing spectral energy distribution. <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/j.1365-2966.2008.12945.x\">https://doi.org/10.1111/j.1365-2966.2008.12945.x</a>","ama":"Kramer RH, Haiman Z. The thickness of high-redshift quasar ionization fronts as a constraint on the ionizing spectral energy distribution. <i>Monthly Notices of the Royal Astronomical Society</i>. 2008;385(3):1561-1575. doi:<a href=\"https://doi.org/10.1111/j.1365-2966.2008.12945.x\">10.1111/j.1365-2966.2008.12945.x</a>","ieee":"R. H. Kramer and Z. Haiman, “The thickness of high-redshift quasar ionization fronts as a constraint on the ionizing spectral energy distribution,” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 385, no. 3. Oxford University Press, pp. 1561–1575, 2008.","short":"R.H. Kramer, Z. Haiman, Monthly Notices of the Royal Astronomical Society 385 (2008) 1561–1575.","ista":"Kramer RH, Haiman Z. 2008. The thickness of high-redshift quasar ionization fronts as a constraint on the ionizing spectral energy distribution. Monthly Notices of the Royal Astronomical Society. 385(3), 1561–1575.","mla":"Kramer, R. H., and Zoltán Haiman. “The Thickness of High-Redshift Quasar Ionization Fronts as a Constraint on the Ionizing Spectral Energy Distribution.” <i>Monthly Notices of the Royal Astronomical Society</i>, vol. 385, no. 3, Oxford University Press, 2008, pp. 1561–75, doi:<a href=\"https://doi.org/10.1111/j.1365-2966.2008.12945.x\">10.1111/j.1365-2966.2008.12945.x</a>.","chicago":"Kramer, R. H., and Zoltán Haiman. “The Thickness of High-Redshift Quasar Ionization Fronts as a Constraint on the Ionizing Spectral Energy Distribution.” <i>Monthly Notices of the Royal Astronomical Society</i>. Oxford University Press, 2008. <a href=\"https://doi.org/10.1111/j.1365-2966.2008.12945.x\">https://doi.org/10.1111/j.1365-2966.2008.12945.x</a>."},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17721","scopus_import":"1","month":"03"}]