[{"month":"12","publisher":"Elsevier","year":"2015","publication":"Information and Computation","_id":"1731","volume":245,"article_processing_charge":"No","citation":{"short":"K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, Information and Computation 245 (2015) 3–16.","apa":"Chatterjee, K., Doyen, L., Gimbert, H., &#38; Henzinger, T. A. (2015). Randomness for free. <i>Information and Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ic.2015.06.003\">https://doi.org/10.1016/j.ic.2015.06.003</a>","ama":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. Randomness for free. <i>Information and Computation</i>. 2015;245(12):3-16. doi:<a href=\"https://doi.org/10.1016/j.ic.2015.06.003\">10.1016/j.ic.2015.06.003</a>","ista":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2015. Randomness for free. Information and Computation. 245(12), 3–16.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Hugo Gimbert, and Thomas A Henzinger. “Randomness for Free.” <i>Information and Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ic.2015.06.003\">https://doi.org/10.1016/j.ic.2015.06.003</a>.","mla":"Chatterjee, Krishnendu, et al. “Randomness for Free.” <i>Information and Computation</i>, vol. 245, no. 12, Elsevier, 2015, pp. 3–16, doi:<a href=\"https://doi.org/10.1016/j.ic.2015.06.003\">10.1016/j.ic.2015.06.003</a>.","ieee":"K. Chatterjee, L. Doyen, H. Gimbert, and T. A. Henzinger, “Randomness for free,” <i>Information and Computation</i>, vol. 245, no. 12. Elsevier, pp. 3–16, 2015."},"oa":1,"arxiv":1,"external_id":{"arxiv":["1006.0673"],"isi":["000368899100002"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1016/j.ic.2015.06.003","date_published":"2015-12-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","publist_id":"5395","ec_funded":1,"date_updated":"2025-09-23T10:32:00Z","publication_status":"published","status":"public","issue":"12","page":"3 - 16","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1006.0673"}],"corr_author":"1","day":"01","related_material":{"record":[{"id":"3856","status":"public","relation":"earlier_version"}]},"date_created":"2018-12-11T11:53:42Z","isi":1,"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"first_name":"Hugo","full_name":"Gimbert, Hugo","last_name":"Gimbert"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"}],"type":"journal_article","intvolume":"       245","doi":"10.1016/j.ic.2015.06.003","oa_version":"Preprint","abstract":[{"text":"We consider two-player zero-sum games on graphs. These games can be classified on the basis of the information of the players and on the mode of interaction between them. On the basis of information the classification is as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided complete-observation (one player has complete observation); and (c) complete-observation (both players have complete view of the game). On the basis of mode of interaction we have the following classification: (a) concurrent (both players interact simultaneously); and (b) turn-based (both players interact in turn). The two sources of randomness in these games are randomness in transition function and randomness in strategies. In general, randomized strategies are more powerful than deterministic strategies, and randomness in transitions gives more general classes of games. In this work we present a complete characterization for the classes of games where randomness is not helpful in: (a) the transition function probabilistic transition can be simulated by deterministic transition); and (b) strategies (pure strategies are as powerful as randomized strategies). As consequence of our characterization we obtain new undecidability results for these games. ","lang":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"Randomness for free","quality_controlled":"1"},{"oa_version":"Preprint","doi":"10.1109/ICRA.2015.7139019","quality_controlled":"1","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs), that are a standard framework for robotics applications to model uncertainties present in the real world, with temporal logic specifications. All temporal logic specifications in linear-time temporal logic (LTL) can be expressed as parity objectives. We study the qualitative analysis problem for POMDPs with parity objectives that asks whether there is a controller (policy) to ensure that the objective holds with probability 1 (almost-surely). While the qualitative analysis of POMDPs with parity objectives is undecidable, recent results show that when restricted to finite-memory policies the problem is EXPTIME-complete. While the problem is intractable in theory, we present a practical approach to solve the qualitative analysis problem. We designed several heuristics to deal with the exponential complexity, and have used our implementation on a number of well-known POMDP examples for robotics applications. Our results provide the first practical approach to solve the qualitative analysis of robot motion planning with LTL properties in the presence of uncertainty.","lang":"eng"}],"title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","department":[{"_id":"KrCh"}],"related_material":{"record":[{"relation":"earlier_version","id":"5424","status":"public"},{"id":"5426","status":"public","relation":"earlier_version"}]},"day":"01","page":"325 - 330","main_file_link":[{"url":"http://arxiv.org/abs/1409.3360","open_access":"1"}],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chmelik","first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gupta, Raghav","first_name":"Raghav","last_name":"Gupta"},{"last_name":"Kanodia","first_name":"Ayush","full_name":"Kanodia, Ayush"}],"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"type":"conference","date_created":"2018-12-11T11:53:43Z","date_updated":"2023-02-23T12:25:52Z","publist_id":"5394","ec_funded":1,"publication_status":"published","status":"public","_id":"1732","publisher":"IEEE","month":"01","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1109/ICRA.2015.7139019","date_published":"2015-01-01T00:00:00Z","scopus_import":1,"language":[{"iso":"eng"}],"citation":{"ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. In: IEEE; 2015:325-330. doi:<a href=\"https://doi.org/10.1109/ICRA.2015.7139019\">10.1109/ICRA.2015.7139019</a>","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Qualitative analysis of POMDPs with temporal logic specifications for robotics applications. ICRA: International Conference on Robotics and Automation, 325–330.","apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2015). Qualitative analysis of POMDPs with temporal logic specifications for robotics applications (pp. 325–330). Presented at the ICRA: International Conference on Robotics and Automation, Seattle, WA, United States: IEEE. <a href=\"https://doi.org/10.1109/ICRA.2015.7139019\">https://doi.org/10.1109/ICRA.2015.7139019</a>","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, IEEE, 2015, pp. 325–330.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Qualitative analysis of POMDPs with temporal logic specifications for robotics applications,” presented at the ICRA: International Conference on Robotics and Automation, Seattle, WA, United States, 2015, pp. 325–330.","mla":"Chatterjee, Krishnendu, et al. <i>Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications</i>. IEEE, 2015, pp. 325–30, doi:<a href=\"https://doi.org/10.1109/ICRA.2015.7139019\">10.1109/ICRA.2015.7139019</a>.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Qualitative Analysis of POMDPs with Temporal Logic Specifications for Robotics Applications,” 325–30. IEEE, 2015. <a href=\"https://doi.org/10.1109/ICRA.2015.7139019\">https://doi.org/10.1109/ICRA.2015.7139019</a>."},"external_id":{"arxiv":["1409.3360"]},"conference":{"name":"ICRA: International Conference on Robotics and Automation","end_date":"2015-05-30","location":"Seattle, WA, United States","start_date":"2015-05-26"},"arxiv":1,"oa":1},{"oa_version":"None","doi":"10.1111/cgf.12594","quality_controlled":"1","abstract":[{"lang":"eng","text":"Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. &quot;Image-based methods&quot; try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. &quot;Parametric methods&quot; instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture."}],"department":[{"_id":"BeBi"}],"title":"Recent advances in facial appearance capture","day":"01","page":"709 - 733","main_file_link":[{"url":"https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf"}],"author":[{"last_name":"Klehm","full_name":"Klehm, Oliver","first_name":"Oliver"},{"last_name":"Rousselle","full_name":"Rousselle, Fabrice","first_name":"Fabrice"},{"last_name":"Papas","first_name":"Marios","full_name":"Papas, Marios"},{"last_name":"Bradley","full_name":"Bradley, Derek","first_name":"Derek"},{"first_name":"Christophe","full_name":"Hery, Christophe","last_name":"Hery"},{"first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385"},{"last_name":"Jarosz","full_name":"Jarosz, Wojciech","first_name":"Wojciech"},{"last_name":"Beeler","full_name":"Beeler, Thabo","first_name":"Thabo"}],"intvolume":"        34","type":"journal_article","date_created":"2018-12-11T11:53:43Z","isi":1,"date_updated":"2025-09-23T10:32:38Z","publist_id":"5391","issue":"2","publication_status":"published","status":"public","publication":"Computer Graphics Forum","_id":"1734","month":"05","publisher":"Wiley-Blackwell","year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-05-01T00:00:00Z","fulldoi":"https://doi.org/10.1111/cgf.12594","scopus_import":"1","language":[{"iso":"eng"}],"volume":34,"article_processing_charge":"No","citation":{"ista":"Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum. 34(2), 709–733.","ama":"Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance capture. <i>Computer Graphics Forum</i>. 2015;34(2):709-733. doi:<a href=\"https://doi.org/10.1111/cgf.12594\">10.1111/cgf.12594</a>","short":"O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733.","apa":"Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler, T. (2015). Recent advances in facial appearance capture. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/cgf.12594\">https://doi.org/10.1111/cgf.12594</a>","ieee":"O. Klehm <i>et al.</i>, “Recent advances in facial appearance capture,” <i>Computer Graphics Forum</i>, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015.","chicago":"Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial Appearance Capture.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1111/cgf.12594\">https://doi.org/10.1111/cgf.12594</a>.","mla":"Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” <i>Computer Graphics Forum</i>, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:<a href=\"https://doi.org/10.1111/cgf.12594\">10.1111/cgf.12594</a>."},"external_id":{"isi":["000358326600063"]}},{"day":"01","page":"473 - 480","intvolume":"        34","type":"journal_article","author":[{"first_name":"Ryoichi","full_name":"Ando, Ryoichi","last_name":"Ando"},{"last_name":"Thürey","full_name":"Thürey, Nils","first_name":"Nils"},{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"date_created":"2018-12-11T11:53:44Z","oa_version":"Submitted Version","ddc":["000"],"doi":"10.1111/cgf.12576","quality_controlled":"1","title":"A dimension-reduced pressure solver for liquid simulations","department":[{"_id":"ChWo"}],"abstract":[{"text":"This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations.","lang":"eng"}],"_id":"1735","publication":"Computer Graphics Forum","year":"2015","publisher":"Wiley","month":"05","date_published":"2015-05-01T00:00:00Z","fulldoi":"https://doi.org/10.1111/cgf.12576","language":[{"iso":"eng"}],"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"creator":"system","file_name":"IST-2016-607-v1+1_coarsegrid.pdf","file_size":6312352,"date_updated":"2020-07-14T12:45:15Z","file_id":"5218","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"590752bf977855b337a80f78a9bc2404","date_created":"2018-12-12T10:16:30Z"}],"external_id":{"isi":["000358326600045"]},"file_date_updated":"2020-07-14T12:45:15Z","oa":1,"has_accepted_license":"1","article_processing_charge":"No","volume":34,"citation":{"apa":"Ando, R., Thürey, N., &#38; Wojtan, C. (2015). A dimension-reduced pressure solver for liquid simulations. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.12576\">https://doi.org/10.1111/cgf.12576</a>","short":"R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480.","ama":"Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid simulations. <i>Computer Graphics Forum</i>. 2015;34(2):473-480. doi:<a href=\"https://doi.org/10.1111/cgf.12576\">10.1111/cgf.12576</a>","ista":"Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480.","mla":"Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” <i>Computer Graphics Forum</i>, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:<a href=\"https://doi.org/10.1111/cgf.12576\">10.1111/cgf.12576</a>.","chicago":"Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” <i>Computer Graphics Forum</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/cgf.12576\">https://doi.org/10.1111/cgf.12576</a>.","ieee":"R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for liquid simulations,” <i>Computer Graphics Forum</i>, vol. 34, no. 2. Wiley, pp. 473–480, 2015."},"acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad","date_updated":"2025-09-22T14:29:19Z","publist_id":"5389","issue":"2","pubrep_id":"607","status":"public","publication_status":"published"},{"pmid":1,"publist_id":"5324","date_updated":"2025-09-23T09:30:27Z","status":"public","publication_status":"published","issue":"6","year":"2015","publisher":"Nature Publishing Group","month":"06","_id":"1789","publication":"European Journal of Human Genetics","external_id":{"isi":["000354474600013"],"pmid":["25138099"]},"oa":1,"volume":23,"article_processing_charge":"No","citation":{"mla":"Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” <i>European Journal of Human Genetics</i>, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:<a href=\"https://doi.org/10.1038/ejhg.2014.165\">10.1038/ejhg.2014.165</a>.","chicago":"Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” <i>European Journal of Human Genetics</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ejhg.2014.165\">https://doi.org/10.1038/ejhg.2014.165</a>.","ieee":"A. Kuechler <i>et al.</i>, “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” <i>European Journal of Human Genetics</i>, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015.","apa":"Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. <i>European Journal of Human Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ejhg.2014.165\">https://doi.org/10.1038/ejhg.2014.165</a>","short":"A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760.","ama":"Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. <i>European Journal of Human Genetics</i>. 2015;23(6):753-760. doi:<a href=\"https://doi.org/10.1038/ejhg.2014.165\">10.1038/ejhg.2014.165</a>","ista":"Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760."},"fulldoi":"https://doi.org/10.1038/ejhg.2014.165","date_published":"2015-06-15T00:00:00Z","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1038/ejhg.2014.165","oa_version":"Submitted Version","department":[{"_id":"GaNo"}],"title":"Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome","abstract":[{"text":"Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID.","lang":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/","open_access":"1"}],"page":"753 - 760","day":"15","isi":1,"date_created":"2018-12-11T11:54:01Z","type":"journal_article","intvolume":"        23","author":[{"last_name":"Kuechler","full_name":"Kuechler, Alma","first_name":"Alma"},{"last_name":"Zink","full_name":"Zink, Alexander","first_name":"Alexander"},{"last_name":"Wieland","first_name":"Thomas","full_name":"Wieland, Thomas"},{"full_name":"Lüdecke, Hermann","first_name":"Hermann","last_name":"Lüdecke"},{"last_name":"Cremer","first_name":"Kirsten","full_name":"Cremer, Kirsten"},{"last_name":"Salviati","full_name":"Salviati, Leonardo","first_name":"Leonardo"},{"first_name":"Pamela","full_name":"Magini, Pamela","last_name":"Magini"},{"last_name":"Najafi","first_name":"Kimia","full_name":"Najafi, Kimia"},{"last_name":"Zweier","full_name":"Zweier, Christiane","first_name":"Christiane"},{"first_name":"Johanna","full_name":"Czeschik, Johanna","last_name":"Czeschik"},{"full_name":"Aretz, Stefan","first_name":"Stefan","last_name":"Aretz"},{"last_name":"Endele","full_name":"Endele, Sabine","first_name":"Sabine"},{"full_name":"Tamburrino, Federica","first_name":"Federica","last_name":"Tamburrino"},{"first_name":"Claudia","full_name":"Pinato, Claudia","last_name":"Pinato"},{"last_name":"Clementi","full_name":"Clementi, Maurizio","first_name":"Maurizio"},{"last_name":"Gundlach","first_name":"Jasmin","full_name":"Gundlach, Jasmin"},{"last_name":"Maylahn","full_name":"Maylahn, Carina","first_name":"Carina"},{"last_name":"Mazzanti","first_name":"Laura","full_name":"Mazzanti, Laura"},{"last_name":"Wohlleber","first_name":"Eva","full_name":"Wohlleber, Eva"},{"last_name":"Schwarzmayr","full_name":"Schwarzmayr, Thomas","first_name":"Thomas"},{"first_name":"Roxana","full_name":"Kariminejad, Roxana","last_name":"Kariminejad"},{"last_name":"Schlessinger","full_name":"Schlessinger, Avner","first_name":"Avner"},{"last_name":"Wieczorek","full_name":"Wieczorek, Dagmar","first_name":"Dagmar"},{"last_name":"Strom","full_name":"Strom, Tim","first_name":"Tim"},{"first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","orcid":"0000-0002-7673-7178"},{"full_name":"Engels, Hartmut","first_name":"Hartmut","last_name":"Engels"}]},{"publist_id":"5318","date_updated":"2025-09-23T08:30:43Z","pubrep_id":"454","status":"public","publication_status":"published","article_number":"e0127657","issue":"6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"year":"2015","publisher":"Public Library of Science","month":"06","_id":"1793","publication":"PLoS One","external_id":{"isi":["000356630900069"]},"file_date_updated":"2020-07-14T12:45:16Z","oa":1,"has_accepted_license":"1","citation":{"ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots,” <i>PLoS One</i>, vol. 10, no. 6. Public Library of Science, 2015.","mla":"Symonova, Olga, et al. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” <i>PLoS One</i>, vol. 10, no. 6, e0127657, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657\">10.1371/journal.pone.0127657</a>.","chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0127657\">https://doi.org/10.1371/journal.pone.0127657</a>.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. PLoS One. 10(6), e0127657.","ama":"Symonova O, Topp C, Edelsbrunner H. DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. <i>PLoS One</i>. 2015;10(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0127657\">10.1371/journal.pone.0127657</a>","apa":"Symonova, O., Topp, C., &#38; Edelsbrunner, H. (2015). DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0127657\">https://doi.org/10.1371/journal.pone.0127657</a>","short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (2015)."},"article_processing_charge":"No","volume":10,"fulldoi":"https://doi.org/10.1371/journal.pone.0127657","scopus_import":"1","date_published":"2015-06-01T00:00:00Z","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"file_id":"5150","date_updated":"2020-07-14T12:45:16Z","file_size":1850825,"file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"d20f26461ca575276ad3ed9ce4bfc787","relation":"main_file","date_created":"2018-12-12T10:15:30Z"}],"doi":"10.1371/journal.pone.0127657","ddc":["000"],"oa_version":"Published Version","title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"abstract":[{"text":"We present a software platform for reconstructing and analyzing the growth of a plant root system from a time-series of 3D voxelized shapes. It aligns the shapes with each other, constructs a geometric graph representation together with the function that records the time of growth, and organizes the branches into a hierarchy that reflects the order of creation. The software includes the automatic computation of structural and dynamic traits for each root in the system enabling the quantification of growth on fine-scale. These are important advances in plant phenotyping with applications to the study of genetic and environmental influences on growth.","lang":"eng"}],"quality_controlled":"1","related_material":{"record":[{"relation":"research_data","id":"9737","status":"public"}]},"day":"01","corr_author":"1","isi":1,"date_created":"2018-12-11T11:54:02Z","type":"journal_article","intvolume":"        10","author":[{"orcid":"0000-0003-2012-9947","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga","first_name":"Olga"},{"last_name":"Topp","first_name":"Christopher","full_name":"Topp, Christopher"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"}],"license":"https://creativecommons.org/licenses/by/4.0/"},{"date_created":"2018-12-11T11:54:06Z","isi":1,"author":[{"orcid":"0000-0001-5964-0203","last_name":"Altmeyer","first_name":"Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","full_name":"Altmeyer, Sebastian"},{"first_name":"Younghae","full_name":"Do, Younghae","last_name":"Do"},{"last_name":"Lai","full_name":"Lai, Ying","first_name":"Ying"}],"type":"journal_article","intvolume":"         5","corr_author":"1","day":"12","abstract":[{"text":"It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control.","lang":"eng"}],"department":[{"_id":"BjHo"}],"title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","quality_controlled":"1","doi":"10.1038/srep10781","ddc":["530"],"oa_version":"Published Version","citation":{"ista":"Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781.","ama":"Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. 2015;5. doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>","apa":"Altmeyer, S., Do, Y., &#38; Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. <i>Scientific Reports</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>","short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015).","ieee":"S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” <i>Scientific Reports</i>, vol. 5. Nature Publishing Group, 2015.","mla":"Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>, vol. 5, 10781, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/srep10781\">10.1038/srep10781</a>.","chicago":"Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” <i>Scientific Reports</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/srep10781\">https://doi.org/10.1038/srep10781</a>."},"article_processing_charge":"No","volume":5,"has_accepted_license":"1","oa":1,"external_id":{"isi":["000356150200001"]},"file_date_updated":"2020-07-14T12:45:16Z","file":[{"file_name":"IST-2016-450-v1+1_srep10781.pdf","file_size":2449723,"creator":"system","file_id":"5280","date_updated":"2020-07-14T12:45:16Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7716f582f8c9d82d8f2bf80bf896b440","date_created":"2018-12-12T10:17:26Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-06-12T00:00:00Z","fulldoi":"https://doi.org/10.1038/srep10781","language":[{"iso":"eng"}],"scopus_import":"1","month":"06","publisher":"Nature Publishing Group","year":"2015","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"Scientific Reports","_id":"1804","article_number":"10781","publication_status":"published","pubrep_id":"450","status":"public","publist_id":"5306","date_updated":"2025-09-29T10:58:13Z"},{"abstract":[{"lang":"eng","text":"We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard."}],"title":"Homological reconstruction and simplification in R3","department":[{"_id":"HeEd"}],"quality_controlled":"1","OA_type":"free access","doi":"10.1016/j.comgeo.2014.08.010","article_type":"original","ddc":["500"],"oa_version":"Published Version","isi":1,"date_created":"2018-12-11T11:54:06Z","OA_place":"publisher","author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"last_name":"Bauer","orcid":"0000-0002-9683-0724","first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich"},{"first_name":"Olivier","full_name":"Devillers, Olivier","last_name":"Devillers"},{"full_name":"Glisse, Marc","first_name":"Marc","last_name":"Glisse"},{"last_name":"Lieutier","full_name":"Lieutier, André","first_name":"André"}],"project":[{"call_identifier":"FP7","name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"intvolume":"        48","type":"journal_article","page":"606 - 621","main_file_link":[{"url":"https://doi.org/10.1016/j.comgeo.2014.08.010","open_access":"1"}],"corr_author":"1","related_material":{"record":[{"status":"public","id":"2812","relation":"earlier_version"}]},"day":"03","publication_status":"published","status":"public","issue":"8","publist_id":"5305","ec_funded":1,"date_updated":"2026-06-18T17:57:28Z","citation":{"ama":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. 2015;48(8):606-621. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>","ista":"Attali D, Bauer U, Devillers O, Glisse M, Lieutier A. 2015. Homological reconstruction and simplification in R3. Computational Geometry: Theory and Applications. 48(8), 606–621.","apa":"Attali, D., Bauer, U., Devillers, O., Glisse, M., &#38; Lieutier, A. (2015). Homological reconstruction and simplification in R3. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>","short":"D. Attali, U. Bauer, O. Devillers, M. Glisse, A. Lieutier, Computational Geometry: Theory and Applications 48 (2015) 606–621.","ieee":"D. Attali, U. Bauer, O. Devillers, M. Glisse, and A. Lieutier, “Homological reconstruction and simplification in R3,” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8. Elsevier, pp. 606–621, 2015.","mla":"Attali, Dominique, et al. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 8, Elsevier, 2015, pp. 606–21, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">10.1016/j.comgeo.2014.08.010</a>.","chicago":"Attali, Dominique, Ulrich Bauer, Olivier Devillers, Marc Glisse, and André Lieutier. “Homological Reconstruction and Simplification in R3.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.010\">https://doi.org/10.1016/j.comgeo.2014.08.010</a>."},"volume":48,"article_processing_charge":"No","external_id":{"isi":["000357353200006"]},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.comgeo.2014.08.010","date_published":"2015-06-03T00:00:00Z","scopus_import":"1","publisher":"Elsevier","month":"06","year":"2015","publication":"Computational Geometry: Theory and Applications","_id":"1805"},{"day":"01","corr_author":"1","main_file_link":[{"url":"http://arxiv.org/abs/1401.1727","open_access":"1"}],"page":"603 - 624","intvolume":"        21","type":"journal_article","author":[{"last_name":"Goldman","first_name":"Michael","full_name":"Goldman, Michael"},{"last_name":"Royo-Letelier","first_name":"Jimena","full_name":"Royo-Letelier, Jimena","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"date_created":"2018-12-11T11:54:07Z","oa_version":"Preprint","doi":"10.1051/cocv/2014040","quality_controlled":"1","title":"Sharp interface limit for two components Bose-Einstein condensates","department":[{"_id":"RoSe"}],"abstract":[{"text":"We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.","lang":"eng"}],"_id":"1807","publication":"ESAIM - Control, Optimisation and Calculus of Variations","year":"2015","publisher":"EDP Sciences","month":"05","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1051/cocv/2014040","scopus_import":"1","date_published":"2015-05-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["1401.1727"],"isi":["000356012000001"]},"arxiv":1,"oa":1,"article_processing_charge":"No","volume":21,"citation":{"mla":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3, EDP Sciences, 2015, pp. 603–24, doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>.","chicago":"Goldman, Michael, and Jimena Royo-Letelier. “Sharp Interface Limit for Two Components Bose-Einstein Condensates.” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences, 2015. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>.","ieee":"M. Goldman and J. Royo-Letelier, “Sharp interface limit for two components Bose-Einstein condensates,” <i>ESAIM - Control, Optimisation and Calculus of Variations</i>, vol. 21, no. 3. EDP Sciences, pp. 603–624, 2015.","apa":"Goldman, M., &#38; Royo-Letelier, J. (2015). Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/cocv/2014040\">https://doi.org/10.1051/cocv/2014040</a>","short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","ama":"Goldman M, Royo-Letelier J. Sharp interface limit for two components Bose-Einstein condensates. <i>ESAIM - Control, Optimisation and Calculus of Variations</i>. 2015;21(3):603-624. doi:<a href=\"https://doi.org/10.1051/cocv/2014040\">10.1051/cocv/2014040</a>","ista":"Goldman M, Royo-Letelier J. 2015. Sharp interface limit for two components Bose-Einstein condensates. ESAIM - Control, Optimisation and Calculus of Variations. 21(3), 603–624."},"date_updated":"2025-09-23T10:45:09Z","publist_id":"5303","issue":"3","status":"public","publication_status":"published"},{"day":"01","author":[{"last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"}],"type":"journal_article","intvolume":"        25","isi":1,"date_created":"2018-12-11T11:54:07Z","oa_version":"None","doi":"10.1145/2745799","quality_controlled":"1","department":[{"_id":"ToHe"}],"title":"Guest editors' introduction to special issue on computational methods in systems biology","publication":"ACM Transactions on Modeling and Computer Simulation","_id":"1808","publisher":"ACM","month":"05","year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1145/2745799","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2015-05-01T00:00:00Z","citation":{"apa":"Gupta, A., &#38; Henzinger, T. A. (2015). Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>","short":"A. Gupta, T.A. Henzinger, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ista":"Gupta A, Henzinger TA. 2015. Guest editors’ introduction to special issue on computational methods in systems biology. ACM Transactions on Modeling and Computer Simulation. 25(2), 7.","ama":"Gupta A, Henzinger TA. Guest editors’ introduction to special issue on computational methods in systems biology. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>","mla":"Gupta, Ashutosh, and Thomas A. Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 7, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2745799\">10.1145/2745799</a>.","chicago":"Gupta, Ashutosh, and Thomas A Henzinger. “Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2745799\">https://doi.org/10.1145/2745799</a>.","ieee":"A. Gupta and T. A. Henzinger, “Guest editors’ introduction to special issue on computational methods in systems biology,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015."},"article_processing_charge":"No","volume":25,"external_id":{"isi":["000354789200001"]},"date_updated":"2025-09-23T09:11:51Z","publist_id":"5302","issue":"2","article_number":"7","publication_status":"published","status":"public"},{"publication":"PLoS One","_id":"1809","publisher":"Public Library of Science","month":"05","year":"2015","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"content_type":"application/pdf","access_level":"open_access","creator":"system","file_size":2748982,"file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf","date_updated":"2020-07-14T12:45:17Z","file_id":"4730","date_created":"2018-12-12T10:09:07Z","relation":"main_file","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743"}],"date_published":"2015-05-18T00:00:00Z","fulldoi":"https://doi.org/10.1371/journal.pone.0126907","scopus_import":"1","language":[{"iso":"eng"}],"article_processing_charge":"No","citation":{"ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” <i>PLoS One</i>, vol. 10, no. 5. Public Library of Science, 2015.","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” <i>PLoS One</i>, vol. 10, no. 5, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>.","ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. 2015;10(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0126907\">10.1371/journal.pone.0126907</a>","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","apa":"Trubenova, B., Novak, S., &#38; Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0126907\">https://doi.org/10.1371/journal.pone.0126907</a>"},"volume":10,"external_id":{"isi":["000354917300064"]},"file_date_updated":"2020-07-14T12:45:17Z","oa":1,"has_accepted_license":"1","date_updated":"2025-09-23T09:21:54Z","publist_id":"5299","issue":"5","publication_status":"published","status":"public","pubrep_id":"453","corr_author":"1","related_material":{"record":[{"relation":"research_data","id":"9715","status":"public"},{"relation":"research_data","id":"9772","status":"public"}]},"day":"18","author":[{"first_name":"Barbora","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","orcid":"0000-0002-6873-2967"},{"orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian","full_name":"Novak, Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Reinmar","full_name":"Hager, Reinmar","last_name":"Hager"}],"type":"journal_article","intvolume":"        10","isi":1,"date_created":"2018-12-11T11:54:07Z","ddc":["570","576"],"oa_version":"Published Version","doi":"10.1371/journal.pone.0126907","quality_controlled":"1","abstract":[{"lang":"eng","text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations."}],"title":"Indirect genetic effects and the dynamics of social interactions","department":[{"_id":"NiBa"}]},{"quality_controlled":"1","title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","department":[{"_id":"ToBo"}],"abstract":[{"lang":"eng","text":"Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing."}],"oa_version":"Published Version","ddc":["570"],"doi":"10.1016/j.mib.2015.05.008","type":"journal_article","intvolume":"        27","project":[{"name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","call_identifier":"FWF"},{"name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507","call_identifier":"FP7"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"author":[{"orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias"}],"date_created":"2018-12-11T11:54:08Z","isi":1,"day":"01","corr_author":"1","page":"1 - 9","status":"public","pubrep_id":"493","publication_status":"published","date_updated":"2025-09-23T07:55:38Z","publist_id":"5298","ec_funded":1,"fulldoi":"https://doi.org/10.1016/j.mib.2015.05.008","date_published":"2015-06-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","file":[{"checksum":"1683bb0f42ef892a5b3b71a050d65d25","relation":"main_file","date_created":"2018-12-12T10:17:23Z","date_updated":"2020-07-14T12:45:17Z","file_id":"5277","file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","file_size":1047255,"creator":"system","access_level":"open_access","content_type":"application/pdf"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","oa":1,"external_id":{"isi":["000365065400003"]},"file_date_updated":"2020-07-14T12:45:17Z","article_processing_charge":"No","volume":27,"citation":{"ieee":"M. T. Bollenbach, “Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution,” <i>Current Opinion in Microbiology</i>, vol. 27. Elsevier, pp. 1–9, 2015.","mla":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>, vol. 27, Elsevier, 2015, pp. 1–9, doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>.","chicago":"Bollenbach, Mark Tobias. “Antimicrobial Interactions: Mechanisms and Implications for Drug Discovery and Resistance Evolution.” <i>Current Opinion in Microbiology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>.","ama":"Bollenbach MT. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. 2015;27:1-9. doi:<a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">10.1016/j.mib.2015.05.008</a>","ista":"Bollenbach MT. 2015. Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. Current Opinion in Microbiology. 27, 1–9.","apa":"Bollenbach, M. T. (2015). Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution. <i>Current Opinion in Microbiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.mib.2015.05.008\">https://doi.org/10.1016/j.mib.2015.05.008</a>","short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9."},"_id":"1810","publication":"Current Opinion in Microbiology","year":"2015","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"month":"06","publisher":"Elsevier"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"creator":"system","file_name":"IST-2016-446-v1+1_document.pdf","file_size":1900925,"file_id":"5184","date_updated":"2020-07-14T12:45:17Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"551f751a75b39b89a1db2f7f498f9a49","date_created":"2018-12-12T10:15:59Z"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1088/1367-2630/17/4/045005","date_published":"2015-04-01T00:00:00Z","scopus_import":"1","volume":17,"citation":{"mla":"Lahrz, Martin, et al. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>, vol. 17, no. 4, 045005, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>.","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>.","ieee":"M. Lahrz, M. Lemeshko, and L. Mathey, “Exotic roton excitations in quadrupolar Bose–Einstein condensates ,” <i>New Journal of Physics</i>, vol. 17, no. 4. IOP Publishing, 2015.","apa":"Lahrz, M., Lemeshko, M., &#38; Mathey, L. (2015). Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>","short":"M. Lahrz, M. Lemeshko, L. Mathey, New Journal of Physics 17 (2015).","ista":"Lahrz M, Lemeshko M, Mathey L. 2015. Exotic roton excitations in quadrupolar Bose–Einstein condensates . New Journal of Physics. 17(4), 045005.","ama":"Lahrz M, Lemeshko M, Mathey L. Exotic roton excitations in quadrupolar Bose–Einstein condensates . <i>New Journal of Physics</i>. 2015;17(4). doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>"},"article_processing_charge":"No","file_date_updated":"2020-07-14T12:45:17Z","external_id":{"isi":["000354022400001"]},"has_accepted_license":"1","oa":1,"publication":"New Journal of Physics","_id":"1812","publisher":"IOP Publishing","month":"04","year":"2015","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"issue":"4","article_number":"045005","publication_status":"published","status":"public","pubrep_id":"446","date_updated":"2025-09-23T08:45:19Z","publist_id":"5294","author":[{"last_name":"Lahrz","full_name":"Lahrz, Martin","first_name":"Martin"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"},{"last_name":"Mathey","first_name":"Ludwig","full_name":"Mathey, Ludwig"}],"intvolume":"        17","type":"journal_article","isi":1,"date_created":"2018-12-11T11:54:09Z","day":"01","quality_controlled":"1","abstract":[{"text":"We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules.\r\n","lang":"eng"}],"department":[{"_id":"MiLe"}],"title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","ddc":["530"],"oa_version":"Published Version","doi":"10.1088/1367-2630/17/4/045005"},{"corr_author":"1","day":"18","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.03447"}],"author":[{"first_name":"Richard","full_name":"Schmidt, Richard","last_name":"Schmidt"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko"}],"type":"journal_article","intvolume":"       114","isi":1,"date_created":"2018-12-11T11:54:09Z","oa_version":"Preprint","doi":"10.1103/PhysRevLett.114.203001","quality_controlled":"1","abstract":[{"lang":"eng","text":"We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system."}],"department":[{"_id":"MiLe"}],"title":"Rotation of quantum impurities in the presence of a many-body environment","publication":"Physical Review Letters","_id":"1813","publisher":"American Physical Society","month":"05","year":"2015","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1103/PhysRevLett.114.203001","scopus_import":"1","date_published":"2015-05-18T00:00:00Z","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":114,"citation":{"short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","apa":"Schmidt, R., &#38; Lemeshko, M. (2015). Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>","ama":"Schmidt R, Lemeshko M. Rotation of quantum impurities in the presence of a many-body environment. <i>Physical Review Letters</i>. 2015;114(20). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>","ista":"Schmidt R, Lemeshko M. 2015. Rotation of quantum impurities in the presence of a many-body environment. Physical Review Letters. 114(20), 203001.","chicago":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">https://doi.org/10.1103/PhysRevLett.114.203001</a>.","mla":"Schmidt, Richard, and Mikhail Lemeshko. “Rotation of Quantum Impurities in the Presence of a Many-Body Environment.” <i>Physical Review Letters</i>, vol. 114, no. 20, 203001, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.114.203001\">10.1103/PhysRevLett.114.203001</a>.","ieee":"R. Schmidt and M. Lemeshko, “Rotation of quantum impurities in the presence of a many-body environment,” <i>Physical Review Letters</i>, vol. 114, no. 20. American Physical Society, 2015."},"external_id":{"arxiv":["1502.03447"],"isi":["000354969900003"]},"arxiv":1,"oa":1,"date_updated":"2025-09-23T10:40:28Z","publist_id":"5293","issue":"20","publication_status":"published","article_number":"203001","status":"public"},{"abstract":[{"text":"We present an efficient wavefront tracking algorithm for animating bodies of water that interact with their environment. Our contributions include: a novel wavefront tracking technique that enables dispersion, refraction, reflection, and diffraction in the same simulation; a unique multivalued function interpolation method that enables our simulations to elegantly sidestep the Nyquist limit; a dispersion approximation for efficiently amplifying the number of simulated waves by several orders of magnitude; and additional extensions that allow for time-dependent effects and interactive artistic editing of the resulting animation. Our contributions combine to give us multitudes more wave details than similar algorithms, while maintaining high frame rates and allowing close camera zooms.","lang":"eng"}],"title":"Water wave animation via wavefront parameter interpolation","department":[{"_id":"ChWo"}],"quality_controlled":"1","doi":"10.1145/2714572","ddc":["000"],"oa_version":"Submitted Version","date_created":"2018-12-11T11:54:09Z","isi":1,"project":[{"call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23"},{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan","first_name":"Stefan","last_name":"Jeschke"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        34","type":"journal_article","corr_author":"1","day":"01","article_number":"27","publication_status":"published","pubrep_id":"575","status":"public","issue":"3","ec_funded":1,"publist_id":"5292","date_updated":"2025-09-29T11:05:55Z","article_processing_charge":"No","citation":{"ieee":"S. Jeschke and C. Wojtan, “Water wave animation via wavefront parameter interpolation,” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3. ACM, 2015.","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>.","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Animation via Wavefront Parameter Interpolation.” <i>ACM Transactions on Graphics</i>, vol. 34, no. 3, 27, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>.","ista":"Jeschke S, Wojtan C. 2015. Water wave animation via wavefront parameter interpolation. ACM Transactions on Graphics. 34(3), 27.","ama":"Jeschke S, Wojtan C. Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. 2015;34(3). doi:<a href=\"https://doi.org/10.1145/2714572\">10.1145/2714572</a>","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","apa":"Jeschke, S., &#38; Wojtan, C. (2015). Water wave animation via wavefront parameter interpolation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2714572\">https://doi.org/10.1145/2714572</a>"},"volume":34,"has_accepted_license":"1","oa":1,"external_id":{"isi":["000354800700004"]},"file_date_updated":"2020-07-14T12:45:17Z","file":[{"file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf","file_size":23712153,"creator":"system","date_updated":"2020-07-14T12:45:17Z","file_id":"4933","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"67c9f4fa370def68cdf31299e48bc91f","date_created":"2018-12-12T10:12:15Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-04-01T00:00:00Z","fulldoi":"https://doi.org/10.1145/2714572","scopus_import":"1","language":[{"iso":"eng"}],"month":"04","publisher":"ACM","year":"2015","publication":"ACM Transactions on Graphics","_id":"1814"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","fulldoi":"https://doi.org/10.1038/nature14215","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2015-03-16T00:00:00Z","article_processing_charge":"No","citation":{"ieee":"S. Porazinski <i>et al.</i>, “YAP is essential for tissue tension to ensure vertebrate 3D body shape,” <i>Nature</i>, vol. 521, no. 7551. Nature Publishing Group, pp. 217–221, 2015.","mla":"Porazinski, Sean, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>, vol. 521, no. 7551, Nature Publishing Group, 2015, pp. 217–21, doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>.","chicago":"Porazinski, Sean, Huijia Wang, Yoichi Asaoka, Martin Behrndt, Tatsuo Miyamoto, Hitoshi Morita, Shoji Hata, et al. “YAP Is Essential for Tissue Tension to Ensure Vertebrate 3D Body Shape.” <i>Nature</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>.","ama":"Porazinski S, Wang H, Asaoka Y, et al. YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. 2015;521(7551):217-221. doi:<a href=\"https://doi.org/10.1038/nature14215\">10.1038/nature14215</a>","ista":"Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens G, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld J, Link B, Senga T, Castillo Morales A, Urrutia A, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg C-PJ, Furutani Seiki M. 2015. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature. 521(7551), 217–221.","apa":"Porazinski, S., Wang, H., Asaoka, Y., Behrndt, M., Miyamoto, T., Morita, H., … Furutani Seiki, M. (2015). YAP is essential for tissue tension to ensure vertebrate 3D body shape. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature14215\">https://doi.org/10.1038/nature14215</a>","short":"S. Porazinski, H. Wang, Y. Asaoka, M. Behrndt, T. Miyamoto, H. Morita, S. Hata, T. Sasaki, G. Krens, Y. Osada, S. Asaka, A. Momoi, S. Linton, J. Miesfeld, B. Link, T. Senga, A. Castillo Morales, A. Urrutia, N. Shimizu, H. Nagase, S. Matsuura, S. Bagby, H. Kondoh, H. Nishina, C.-P.J. Heisenberg, M. Furutani Seiki, Nature 521 (2015) 217–221."},"volume":521,"oa":1,"external_id":{"pmid":["25778702"],"isi":["000354377800058"]},"publication":"Nature","_id":"1817","month":"03","publisher":"Nature Publishing Group","year":"2015","issue":"7551","publication_status":"published","status":"public","date_updated":"2025-09-29T11:07:11Z","publist_id":"5289","pmid":1,"author":[{"first_name":"Sean","full_name":"Porazinski, Sean","last_name":"Porazinski"},{"last_name":"Wang","first_name":"Huijia","full_name":"Wang, Huijia"},{"last_name":"Asaoka","first_name":"Yoichi","full_name":"Asaoka, Yoichi"},{"first_name":"Martin","full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt"},{"last_name":"Miyamoto","full_name":"Miyamoto, Tatsuo","first_name":"Tatsuo"},{"last_name":"Morita","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi"},{"last_name":"Hata","first_name":"Shoji","full_name":"Hata, Shoji"},{"full_name":"Sasaki, Takashi","first_name":"Takashi","last_name":"Sasaki"},{"orcid":"0000-0003-4761-5996","last_name":"Krens","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","first_name":"Gabriel"},{"last_name":"Osada","first_name":"Yumi","full_name":"Osada, Yumi"},{"first_name":"Satoshi","full_name":"Asaka, Satoshi","last_name":"Asaka"},{"last_name":"Momoi","first_name":"Akihiro","full_name":"Momoi, Akihiro"},{"last_name":"Linton","full_name":"Linton, Sarah","first_name":"Sarah"},{"last_name":"Miesfeld","full_name":"Miesfeld, Joel","first_name":"Joel"},{"last_name":"Link","first_name":"Brian","full_name":"Link, Brian"},{"last_name":"Senga","full_name":"Senga, Takeshi","first_name":"Takeshi"},{"full_name":"Castillo Morales, Atahualpa","first_name":"Atahualpa","last_name":"Castillo Morales"},{"last_name":"Urrutia","full_name":"Urrutia, Araxi","first_name":"Araxi"},{"last_name":"Shimizu","full_name":"Shimizu, Nobuyoshi","first_name":"Nobuyoshi"},{"full_name":"Nagase, Hideaki","first_name":"Hideaki","last_name":"Nagase"},{"last_name":"Matsuura","first_name":"Shinya","full_name":"Matsuura, Shinya"},{"full_name":"Bagby, Stefan","first_name":"Stefan","last_name":"Bagby"},{"last_name":"Kondoh","full_name":"Kondoh, Hisato","first_name":"Hisato"},{"last_name":"Nishina","first_name":"Hiroshi","full_name":"Nishina, Hiroshi"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"},{"last_name":"Furutani Seiki","full_name":"Furutani Seiki, Makoto","first_name":"Makoto"}],"type":"journal_article","intvolume":"       521","date_created":"2018-12-11T11:54:10Z","isi":1,"corr_author":"1","day":"16","page":"217 - 221","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues. "}],"title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","department":[{"_id":"CaHe"}],"oa_version":"Submitted Version","doi":"10.1038/nature14215"},{"quality_controlled":"1","department":[{"_id":"NiBa"}],"title":"Limits to adaptation along environmental gradients","abstract":[{"text":"Why do species not adapt to ever-wider ranges of conditions, gradually expanding their ecological niche and geographic range? Gene flow across environments has two conflicting effects: although it increases genetic variation, which is a prerequisite for adaptation, gene flow may swamp adaptation to local conditions. In 1956, Haldane proposed that, when the environment varies across space, &quot;swamping&quot; by gene flow creates a positive feedback between low population size and maladaptation, leading to a sharp range margin. However, current deterministic theory shows that, when variance can evolve, there is no such limit. Using simple analytical tools and simulations, we show that genetic drift can generate a sharp margin to a species' range, by reducing genetic variance below the level needed for adaptation to spatially variable conditions. Aided by separation of ecological and evolutionary timescales, the identified effective dimensionless parameters reveal a simple threshold that predicts when adaptation at the range margin fails. Two observable parameters determine the threshold: (i) the effective environmental gradient, which can be measured by the loss of fitness due to dispersal to a different environment; and (ii) the efficacy of selection relative to genetic drift. The theory predicts sharp range margins even in the absence of abrupt changes in the environment. Furthermore, it implies that gradual worsening of conditions across a species' habitat may lead to a sudden range fragmentation, when adaptation to a wide span of conditions within a single species becomes impossible.","lang":"eng"}],"oa_version":"Submitted Version","doi":"10.1073/pnas.1421515112","type":"journal_article","intvolume":"       112","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0003-0951-3112","last_name":"Polechova","full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","first_name":"Jitka"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:54:11Z","isi":1,"day":"19","corr_author":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/","open_access":"1"}],"page":"6401 - 6406","issue":"20","status":"public","publication_status":"published","date_updated":"2025-09-23T09:27:16Z","publist_id":"5288","ec_funded":1,"pmid":1,"date_published":"2015-05-19T00:00:00Z","fulldoi":"https://doi.org/10.1073/pnas.1421515112","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"external_id":{"isi":["000354729500058"],"pmid":["25941385"]},"article_processing_charge":"No","citation":{"mla":"Polechova, Jitka, and Nicholas H. Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>, vol. 112, no. 20, National Academy of Sciences, 2015, pp. 6401–06, doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>.","chicago":"Polechova, Jitka, and Nicholas H Barton. “Limits to Adaptation along Environmental Gradients.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>.","ieee":"J. Polechova and N. H. Barton, “Limits to adaptation along environmental gradients,” <i>PNAS</i>, vol. 112, no. 20. National Academy of Sciences, pp. 6401–6406, 2015.","apa":"Polechova, J., &#38; Barton, N. H. (2015). Limits to adaptation along environmental gradients. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1421515112\">https://doi.org/10.1073/pnas.1421515112</a>","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","ama":"Polechova J, Barton NH. Limits to adaptation along environmental gradients. <i>PNAS</i>. 2015;112(20):6401-6406. doi:<a href=\"https://doi.org/10.1073/pnas.1421515112\">10.1073/pnas.1421515112</a>"},"volume":112,"_id":"1818","publication":"PNAS","year":"2015","month":"05","publisher":"National Academy of Sciences"},{"page":"1175 - 1187","corr_author":"1","day":"03","isi":1,"date_created":"2018-12-11T11:54:11Z","author":[{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Stéphanie","full_name":"Robert, Stéphanie","last_name":"Robert"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiřĺ","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiřĺ"}],"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"type":"journal_article","intvolume":"         8","doi":"10.1016/j.molp.2015.03.007","oa_version":"None","abstract":[{"lang":"eng","text":"The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity."}],"title":"Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana","department":[{"_id":"JiFr"}],"quality_controlled":"1","publisher":"Elsevier","month":"08","year":"2015","publication":"Molecular Plant","_id":"1819","volume":8,"article_processing_charge":"No","citation":{"ista":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. 2015. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. Molecular Plant. 8(8), 1175–1187.","ama":"Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. 2015;8(8):1175-1187. doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>","apa":"Zwiewka, M., Nodzyński, T., Robert, S., Vanneste, S., &#38; Friml, J. (2015). Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>","short":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, J. Friml, Molecular Plant 8 (2015) 1175–1187.","ieee":"M. Zwiewka, T. Nodzyński, S. Robert, S. Vanneste, and J. Friml, “Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana,” <i>Molecular Plant</i>, vol. 8, no. 8. Elsevier, pp. 1175–1187, 2015.","mla":"Zwiewka, Marta, et al. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>, vol. 8, no. 8, Elsevier, 2015, pp. 1175–87, doi:<a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">10.1016/j.molp.2015.03.007</a>.","chicago":"Zwiewka, Marta, Tomasz Nodzyński, Stéphanie Robert, Steffen Vanneste, and Jiří Friml. “Osmotic Stress Modulates the Balance between Exocytosis and Clathrin Mediated Endocytosis in Arabidopsis Thaliana.” <i>Molecular Plant</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.molp.2015.03.007\">https://doi.org/10.1016/j.molp.2015.03.007</a>."},"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); European Social Fund (CZ.1.07/2.3.00/20.0043) and the Czech Science Foundation GAČR (GA13-40637S) to J.F.; project Postdoc I. (CZ.1.07/2.3.00/30.0009) co-financed by the European Social Fund and the state budget of the Czech Republic to M.Z. and T.N..","external_id":{"isi":["000359136100006"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2015-08-03T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.molp.2015.03.007","scopus_import":"1","language":[{"iso":"eng"}],"ec_funded":1,"publist_id":"5287","date_updated":"2025-09-23T09:47:17Z","publication_status":"published","status":"public","issue":"8"},{"quality_controlled":"1","abstract":[{"text":"Abstract Drug combinations are increasingly important in disease treatments, for combating drug resistance, and for elucidating fundamental relationships in cell physiology. When drugs are combined, their individual effects on cells may be amplified or weakened. Such drug interactions are crucial for treatment efficacy, but their underlying mechanisms remain largely unknown. To uncover the causes of drug interactions, we developed a systematic approach based on precise quantification of the individual and joint effects of antibiotics on growth of genome-wide Escherichia coli gene deletion strains. We found that drug interactions between antibiotics representing the main modes of action are highly robust to genetic perturbation. This robustness is encapsulated in a general principle of bacterial growth, which enables the quantitative prediction of mutant growth rates under drug combinations. Rare violations of this principle exposed recurring cellular functions controlling drug interactions. In particular, we found that polysaccharide and ATP synthesis control multiple drug interactions with previously unexplained mechanisms, and small molecule adjuvants targeting these functions synthetically reshape drug interactions in predictable ways. These results provide a new conceptual framework for the design of multidrug combinations and suggest that there are universal mechanisms at the heart of most drug interactions. Synopsis A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways. Drug interactions between antibiotics are highly robust to genetic perturbations. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions. Diverse drug interactions are controlled by recurring cellular functions, including LPS synthesis and ATP synthesis. A general principle of bacterial growth enables the prediction of mutant growth rates under drug combinations. Rare violations of this principle expose cellular functions that control drug interactions and can be targeted by small molecules to alter drug interactions in predictable ways.","lang":"eng"}],"title":"Systematic discovery of drug interaction mechanisms","department":[{"_id":"ToBo"}],"oa_version":"Published Version","ddc":["570"],"doi":"10.15252/msb.20156098","author":[{"first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume","last_name":"Chevereau"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"}],"project":[{"call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"},{"call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","grant_number":"303507","name":"Optimality principles in responses to antibiotics"}],"type":"journal_article","intvolume":"        11","isi":1,"date_created":"2018-12-11T11:54:12Z","corr_author":"1","day":"01","issue":"4","article_number":"807","publication_status":"published","pubrep_id":"395","status":"public","date_updated":"2025-09-23T13:38:00Z","publist_id":"5283","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file":[{"relation":"main_file","checksum":"4289b518fbe2166682fb1a1ef9b405f3","date_created":"2018-12-12T10:14:34Z","creator":"system","file_name":"IST-2015-395-v1+1_807.full.pdf","file_size":1273573,"date_updated":"2020-07-14T12:45:17Z","file_id":"5087","content_type":"application/pdf","access_level":"open_access"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.15252/msb.20156098","scopus_import":"1","date_published":"2015-04-01T00:00:00Z","volume":11,"article_processing_charge":"No","citation":{"ieee":"G. Chevereau and M. T. Bollenbach, “Systematic discovery of drug interaction mechanisms,” <i>Molecular Systems Biology</i>, vol. 11, no. 4. Nature Publishing Group, 2015.","mla":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” <i>Molecular Systems Biology</i>, vol. 11, no. 4, 807, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.15252/msb.20156098\">10.15252/msb.20156098</a>.","chicago":"Chevereau, Guillaume, and Mark Tobias Bollenbach. “Systematic Discovery of Drug Interaction Mechanisms.” <i>Molecular Systems Biology</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.15252/msb.20156098\">https://doi.org/10.15252/msb.20156098</a>.","ama":"Chevereau G, Bollenbach MT. Systematic discovery of drug interaction mechanisms. <i>Molecular Systems Biology</i>. 2015;11(4). doi:<a href=\"https://doi.org/10.15252/msb.20156098\">10.15252/msb.20156098</a>","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807.","apa":"Chevereau, G., &#38; Bollenbach, M. T. (2015). Systematic discovery of drug interaction mechanisms. <i>Molecular Systems Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.15252/msb.20156098\">https://doi.org/10.15252/msb.20156098</a>","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (2015)."},"file_date_updated":"2020-07-14T12:45:17Z","external_id":{"isi":["000354022300005"]},"oa":1,"has_accepted_license":"1","publication":"Molecular Systems Biology","_id":"1823","publisher":"Nature Publishing Group","month":"04","year":"2015","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"}},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"year":"2015","month":"04","publisher":"Nature Publishing Group","_id":"1824","publication":"Nature Communications","has_accepted_license":"1","oa":1,"file_date_updated":"2020-07-14T12:45:17Z","external_id":{"isi":["000353705000003"]},"article_processing_charge":"No","volume":6,"citation":{"ama":"Knebel J, Weber M, Krüger TH, Frey E. Evolutionary games of condensates in coupled birth-death processes. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms7977\">10.1038/ncomms7977</a>","ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977.","apa":"Knebel, J., Weber, M., Krüger, T. H., &#38; Frey, E. (2015). Evolutionary games of condensates in coupled birth-death processes. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms7977\">https://doi.org/10.1038/ncomms7977</a>","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (2015).","ieee":"J. Knebel, M. Weber, T. H. Krüger, and E. Frey, “Evolutionary games of condensates in coupled birth-death processes,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","mla":"Knebel, Johannes, et al. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” <i>Nature Communications</i>, vol. 6, 6977, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms7977\">10.1038/ncomms7977</a>.","chicago":"Knebel, Johannes, Markus Weber, Torben H Krüger, and Erwin Frey. “Evolutionary Games of Condensates in Coupled Birth-Death Processes.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms7977\">https://doi.org/10.1038/ncomms7977</a>."},"fulldoi":"https://doi.org/10.1038/ncomms7977","language":[{"iso":"eng"}],"scopus_import":"1","date_published":"2015-04-24T00:00:00Z","file":[{"date_created":"2018-12-12T10:16:54Z","checksum":"c4cffb5c8b245e658a34eac71a03e7cc","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5245","date_updated":"2020-07-14T12:45:17Z","creator":"system","file_name":"IST-2016-451-v1+1_ncomms7977.pdf","file_size":1151501}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5282","date_updated":"2025-09-23T08:44:01Z","pubrep_id":"451","status":"public","publication_status":"published","article_number":"6977","day":"24","date_created":"2018-12-11T11:54:13Z","isi":1,"intvolume":"         6","type":"journal_article","author":[{"last_name":"Knebel","full_name":"Knebel, Johannes","first_name":"Johannes"},{"last_name":"Weber","full_name":"Weber, Markus","first_name":"Markus"},{"orcid":"0000-0002-4821-3297","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Frey, Erwin","first_name":"Erwin","last_name":"Frey"}],"doi":"10.1038/ncomms7977","ddc":["530"],"oa_version":"Published Version","title":"Evolutionary games of condensates in coupled birth-death processes","department":[{"_id":"LaEr"}],"abstract":[{"text":"Condensation phenomena arise through a collective behaviour of particles. They are observed in both classical and quantum systems, ranging from the formation of traffic jams in mass transport models to the macroscopic occupation of the energetic ground state in ultra-cold bosonic gases (Bose-Einstein condensation). Recently, it has been shown that a driven and dissipative system of bosons may form multiple condensates. Which states become the condensates has, however, remained elusive thus far. The dynamics of this condensation are described by coupled birth-death processes, which also occur in evolutionary game theory. Here we apply concepts from evolutionary game theory to explain the formation of multiple condensates in such driven-dissipative bosonic systems. We show that the vanishing of relative entropy production determines their selection. The condensation proceeds exponentially fast, but the system never comes to rest. Instead, the occupation numbers of condensates may oscillate, as we demonstrate for a rock-paper-scissors game of condensates.","lang":"eng"}],"quality_controlled":"1"}]