[{"main_file_link":[{"url":"http://arxiv.org/abs/1408.4036","open_access":"1"}],"page":"587 - 620","doi":"10.1007/s00454-015-9679-9","year":"2015","day":"02","status":"public","type":"journal_article","_id":"1730","date_created":"2018-12-11T11:53:42Z","oa":1,"publication":"Discrete & Computational Geometry","publist_id":"5397","intvolume":"        53","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Colin De Verdière, Éric","first_name":"Éric","last_name":"Colin De Verdière"},{"full_name":"Hubard, Alfredo","first_name":"Alfredo","last_name":"Hubard"},{"full_name":"De Mesmay, Arnaud N","id":"3DB2F25C-F248-11E8-B48F-1D18A9856A87","last_name":"De Mesmay","first_name":"Arnaud N"}],"oa_version":"Preprint","citation":{"short":"É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete &#38; Computational Geometry 53 (2015) 587–620.","mla":"Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” <i>Discrete &#38; Computational Geometry</i>, vol. 53, no. 3, Springer, 2015, pp. 587–620, doi:<a href=\"https://doi.org/10.1007/s00454-015-9679-9\">10.1007/s00454-015-9679-9</a>.","apa":"Colin De Verdière, É., Hubard, A., &#38; de Mesmay, A. N. (2015). Discrete systolic inequalities and decompositions of triangulated surfaces. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-015-9679-9\">https://doi.org/10.1007/s00454-015-9679-9</a>","chicago":"Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00454-015-9679-9\">https://doi.org/10.1007/s00454-015-9679-9</a>.","ama":"Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities and decompositions of triangulated surfaces. <i>Discrete &#38; Computational Geometry</i>. 2015;53(3):587-620. doi:<a href=\"https://doi.org/10.1007/s00454-015-9679-9\">10.1007/s00454-015-9679-9</a>","ista":"Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete &#38; Computational Geometry. 53(3), 587–620.","ieee":"É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities and decompositions of triangulated surfaces,” <i>Discrete &#38; Computational Geometry</i>, vol. 53, no. 3. Springer, pp. 587–620, 2015."},"department":[{"_id":"UlWa"}],"quality_controlled":"1","date_updated":"2021-01-12T06:52:49Z","title":"Discrete systolic inequalities and decompositions of triangulated surfaces","volume":53,"date_published":"2015-04-02T00:00:00Z","language":[{"iso":"eng"}],"publisher":"Springer","issue":"3","month":"04","publication_status":"published","abstract":[{"text":"How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations.","lang":"eng"}]},{"oa":1,"day":"01","doi":"10.1016/j.ic.2015.06.003","year":"2015","page":"3 - 16","related_material":{"record":[{"relation":"earlier_version","id":"3856","status":"public"}]},"scopus_import":1,"intvolume":"       245","publist_id":"5395","publication":"Information and Computation","date_updated":"2023-02-23T11:45:42Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"citation":{"short":"K. Chatterjee, L. Doyen, H. Gimbert, T.A. Henzinger, Information and Computation 245 (2015) 3–16.","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.","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>","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>.","ista":"Chatterjee K, Doyen L, Gimbert H, Henzinger TA. 2015. Randomness for free. Information and Computation. 245(12), 3–16."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","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"}],"publication_status":"published","publisher":"Elsevier","date_published":"2015-12-01T00:00:00Z","title":"Randomness for free","date_created":"2018-12-11T11:53:42Z","_id":"1731","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1006.0673"}],"status":"public","ec_funded":1,"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"call_identifier":"FP7","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","oa_version":"Preprint","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Gimbert, Hugo","last_name":"Gimbert","first_name":"Hugo"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724"}],"month":"12","issue":"12","language":[{"iso":"eng"}],"volume":245},{"external_id":{"arxiv":["1409.3360"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T12:25:52Z","citation":{"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.","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>","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>.","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.","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>","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, IEEE, 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>."},"date_published":"2015-01-01T00:00:00Z","publisher":"IEEE","title":"Qualitative analysis of POMDPs with temporal logic specifications for robotics applications","publication_status":"published","abstract":[{"lang":"eng","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."}],"doi":"10.1109/ICRA.2015.7139019","year":"2015","page":"325 - 330","day":"01","oa":1,"arxiv":1,"publist_id":"5394","scopus_import":1,"related_material":{"record":[{"id":"5424","relation":"earlier_version","status":"public"},{"status":"public","relation":"earlier_version","id":"5426"}]},"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Chmelik","first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Raghav","last_name":"Gupta","full_name":"Gupta, Raghav"},{"last_name":"Kanodia","first_name":"Ayush","full_name":"Kanodia, Ayush"}],"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","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","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa_version":"Preprint","language":[{"iso":"eng"}],"month":"01","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.3360"}],"date_created":"2018-12-11T11:53:43Z","type":"conference","_id":"1732","conference":{"end_date":"2015-05-30","start_date":"2015-05-26","name":"ICRA: International Conference on Robotics and Automation","location":"Seattle, WA, United States"},"ec_funded":1},{"scopus_import":1,"intvolume":"        34","publist_id":"5389","publication":"Computer Graphics Forum","oa":1,"acknowledgement":"The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad","year":"2015","page":"473 - 480","doi":"10.1111/cgf.12576","day":"01","abstract":[{"lang":"eng","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."}],"publication_status":"published","ddc":["000"],"date_published":"2015-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:15Z","publisher":"Wiley","title":"A dimension-reduced pressure solver for liquid simulations","date_updated":"2023-02-23T10:12:11Z","department":[{"_id":"ChWo"}],"citation":{"short":"R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 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>.","ista":"Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480.","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>.","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>","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>","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"607","date_created":"2018-12-11T11:53:44Z","type":"journal_article","_id":"1735","status":"public","has_accepted_license":"1","month":"05","issue":"2","file":[{"date_created":"2018-12-12T10:16:30Z","date_updated":"2020-07-14T12:45:15Z","content_type":"application/pdf","file_name":"IST-2016-607-v1+1_coarsegrid.pdf","relation":"main_file","access_level":"open_access","file_size":6312352,"file_id":"5218","checksum":"590752bf977855b337a80f78a9bc2404","creator":"system"}],"language":[{"iso":"eng"}],"volume":34,"quality_controlled":"1","oa_version":"Submitted Version","author":[{"full_name":"Ando, Ryoichi","first_name":"Ryoichi","last_name":"Ando"},{"last_name":"Thürey","first_name":"Nils","full_name":"Thürey, Nils"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan"}]},{"intvolume":"        23","publist_id":"5324","publication":"European Journal of Human Genetics","day":"15","year":"2015","page":"753 - 760","doi":"10.1038/ejhg.2014.165","oa":1,"date_published":"2015-06-15T00:00:00Z","publisher":"Nature Publishing Group","pmid":1,"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"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25138099"]},"date_updated":"2021-01-12T06:53:12Z","department":[{"_id":"GaNo"}],"citation":{"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.","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>.","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>","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.","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.","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>."},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/"}],"status":"public","date_created":"2018-12-11T11:54:01Z","type":"journal_article","_id":"1789","language":[{"iso":"eng"}],"volume":23,"month":"06","issue":"6","author":[{"full_name":"Kuechler, Alma","last_name":"Kuechler","first_name":"Alma"},{"first_name":"Alexander","last_name":"Zink","full_name":"Zink, Alexander"},{"last_name":"Wieland","first_name":"Thomas","full_name":"Wieland, Thomas"},{"first_name":"Hermann","last_name":"Lüdecke","full_name":"Lüdecke, Hermann"},{"last_name":"Cremer","first_name":"Kirsten","full_name":"Cremer, Kirsten"},{"first_name":"Leonardo","last_name":"Salviati","full_name":"Salviati, Leonardo"},{"last_name":"Magini","first_name":"Pamela","full_name":"Magini, Pamela"},{"last_name":"Najafi","first_name":"Kimia","full_name":"Najafi, Kimia"},{"full_name":"Zweier, Christiane","last_name":"Zweier","first_name":"Christiane"},{"full_name":"Czeschik, Johanna","first_name":"Johanna","last_name":"Czeschik"},{"full_name":"Aretz, Stefan","first_name":"Stefan","last_name":"Aretz"},{"full_name":"Endele, Sabine","first_name":"Sabine","last_name":"Endele"},{"last_name":"Tamburrino","first_name":"Federica","full_name":"Tamburrino, Federica"},{"full_name":"Pinato, Claudia","last_name":"Pinato","first_name":"Claudia"},{"full_name":"Clementi, Maurizio","first_name":"Maurizio","last_name":"Clementi"},{"full_name":"Gundlach, Jasmin","first_name":"Jasmin","last_name":"Gundlach"},{"last_name":"Maylahn","first_name":"Carina","full_name":"Maylahn, Carina"},{"first_name":"Laura","last_name":"Mazzanti","full_name":"Mazzanti, Laura"},{"first_name":"Eva","last_name":"Wohlleber","full_name":"Wohlleber, Eva"},{"full_name":"Schwarzmayr, Thomas","first_name":"Thomas","last_name":"Schwarzmayr"},{"full_name":"Kariminejad, Roxana","last_name":"Kariminejad","first_name":"Roxana"},{"last_name":"Schlessinger","first_name":"Avner","full_name":"Schlessinger, Avner"},{"first_name":"Dagmar","last_name":"Wieczorek","full_name":"Wieczorek, Dagmar"},{"first_name":"Tim","last_name":"Strom","full_name":"Strom, Tim"},{"last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia"},{"full_name":"Engels, Hartmut","last_name":"Engels","first_name":"Hartmut"}],"quality_controlled":"1","oa_version":"Submitted Version"},{"quality_controlled":"1","oa_version":"Published Version","author":[{"first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Topp, Christopher","last_name":"Topp","first_name":"Christopher"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"}],"month":"06","has_accepted_license":"1","file":[{"relation":"main_file","file_size":1850825,"access_level":"open_access","creator":"system","file_id":"5150","checksum":"d20f26461ca575276ad3ed9ce4bfc787","date_updated":"2020-07-14T12:45:16Z","date_created":"2018-12-12T10:15:30Z","content_type":"application/pdf","file_name":"IST-2016-454-v1+1_journal.pone.0127657.pdf"}],"article_number":"e0127657","issue":"6","language":[{"iso":"eng"}],"volume":10,"date_created":"2018-12-11T11:54:02Z","_id":"1793","type":"journal_article","status":"public","pubrep_id":"454","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"date_updated":"2023-02-23T14:06:33Z","citation":{"short":"O. Symonova, C. Topp, H. Edelsbrunner, PLoS One 10 (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>.","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>","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.","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>","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","abstract":[{"lang":"eng","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."}],"ddc":["000"],"file_date_updated":"2020-07-14T12:45:16Z","date_published":"2015-06-01T00:00:00Z","publisher":"Public Library of Science","title":"DynamicRoots: A software platform for the reconstruction and analysis of growing plant roots","oa":1,"doi":"10.1371/journal.pone.0127657","year":"2015","day":"01","scopus_import":1,"related_material":{"record":[{"relation":"research_data","id":"9737","status":"public"}]},"publist_id":"5318","intvolume":"        10","publication":"PLoS One"},{"language":[{"iso":"eng"}],"volume":5,"has_accepted_license":"1","month":"06","file":[{"relation":"main_file","creator":"system","file_id":"5280","checksum":"7716f582f8c9d82d8f2bf80bf896b440","file_size":2449723,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:16Z","date_created":"2018-12-12T10:17:26Z","file_name":"IST-2016-450-v1+1_srep10781.pdf"}],"article_number":"10781","author":[{"orcid":"0000-0001-5964-0203","last_name":"Altmeyer","first_name":"Sebastian","full_name":"Altmeyer, Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Do, Younghae","first_name":"Younghae","last_name":"Do"},{"last_name":"Lai","first_name":"Ying","full_name":"Lai, Ying"}],"quality_controlled":"1","oa_version":"Published Version","pubrep_id":"450","status":"public","date_created":"2018-12-11T11:54:06Z","type":"journal_article","_id":"1804","file_date_updated":"2020-07-14T12:45:16Z","date_published":"2015-06-12T00:00:00Z","publisher":"Nature Publishing Group","title":"Transition to turbulence in Taylor-Couette ferrofluidic flow","publication_status":"published","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"}],"ddc":["530"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BjHo"}],"date_updated":"2021-01-12T06:53:18Z","citation":{"short":"S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (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>.","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.","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>","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>","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>."},"publist_id":"5306","intvolume":"         5","publication":"Scientific Reports","scopus_import":1,"doi":"10.1038/srep10781","year":"2015","day":"12","oa":1},{"author":[{"first_name":"Michael","last_name":"Goldman","full_name":"Goldman, Michael"},{"last_name":"Royo-Letelier","first_name":"Jimena","id":"4D3BED28-F248-11E8-B48F-1D18A9856A87","full_name":"Royo-Letelier, Jimena"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"quality_controlled":"1","date_updated":"2021-01-12T06:53:20Z","citation":{"short":"M. Goldman, J. Royo-Letelier, ESAIM - Control, Optimisation and Calculus of Variations 21 (2015) 603–624.","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>.","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>","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.","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>","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."},"oa_version":"Preprint","publisher":"EDP Sciences","date_published":"2015-05-01T00:00:00Z","language":[{"iso":"eng"}],"volume":21,"title":"Sharp interface limit for two components Bose-Einstein condensates","publication_status":"published","month":"05","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"}],"issue":"3","status":"public","doi":"10.1051/cocv/2014040","day":"01","year":"2015","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1401.1727"}],"page":"603 - 624","date_created":"2018-12-11T11:54:07Z","oa":1,"type":"journal_article","_id":"1807","publist_id":"5303","intvolume":"        21","publication":"ESAIM - Control, Optimisation and Calculus of Variations","scopus_import":1},{"date_created":"2018-12-11T11:54:07Z","_id":"1809","type":"journal_article","status":"public","pubrep_id":"453","quality_controlled":"1","oa_version":"Published Version","author":[{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova"},{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"first_name":"Reinmar","last_name":"Hager","full_name":"Hager, Reinmar"}],"has_accepted_license":"1","month":"05","file":[{"relation":"main_file","creator":"system","file_id":"4730","checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","file_size":2748982,"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:09:07Z","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf"}],"issue":"5","language":[{"iso":"eng"}],"volume":10,"oa":1,"doi":"10.1371/journal.pone.0126907","year":"2015","day":"18","scopus_import":1,"related_material":{"record":[{"relation":"research_data","id":"9715","status":"public"},{"status":"public","relation":"research_data","id":"9772"}]},"publist_id":"5299","intvolume":"        10","publication":"PLoS One","department":[{"_id":"NiBa"}],"date_updated":"2023-02-23T14:07:48Z","citation":{"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>.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","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.","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>","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>.","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)."},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","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."}],"ddc":["570","576"],"date_published":"2015-05-18T00:00:00Z","file_date_updated":"2020-07-14T12:45:17Z","publisher":"Public Library of Science","title":"Indirect genetic effects and the dynamics of social interactions"},{"department":[{"_id":"ToBo"}],"date_updated":"2021-01-12T06:53:21Z","citation":{"short":"M.T. Bollenbach, Current Opinion in Microbiology 27 (2015) 1–9.","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>.","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.","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.","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>.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","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."}],"ddc":["570"],"file_date_updated":"2020-07-14T12:45:17Z","date_published":"2015-06-01T00:00:00Z","publisher":"Elsevier","title":"Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution","oa":1,"year":"2015","doi":"10.1016/j.mib.2015.05.008","page":"1 - 9","day":"01","scopus_import":1,"publist_id":"5298","intvolume":"        27","publication":"Current Opinion in Microbiology","quality_controlled":"1","project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","grant_number":"RGP0042/2013","name":"Revealing the fundamental limits of cell growth"}],"oa_version":"Published Version","author":[{"first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"}],"has_accepted_license":"1","month":"06","file":[{"file_name":"IST-2016-493-v1+1_1-s2.0-S1369527415000594-main.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:17:23Z","creator":"system","file_id":"5277","checksum":"1683bb0f42ef892a5b3b71a050d65d25","file_size":1047255,"access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":27,"date_created":"2018-12-11T11:54:08Z","type":"journal_article","_id":"1810","status":"public","pubrep_id":"493","ec_funded":1},{"month":"05","article_number":"052105","issue":"5","language":[{"iso":"eng"}],"volume":56,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Preprint","author":[{"full_name":"Safari, Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","first_name":"Laleh","last_name":"Safari"},{"full_name":"Santos, José","last_name":"Santos","first_name":"José"},{"last_name":"Amaro","first_name":"Pedro","full_name":"Amaro, Pedro"},{"first_name":"Kari","last_name":"Jänkälä","full_name":"Jänkälä, Kari"},{"first_name":"Filippo","last_name":"Fratini","full_name":"Fratini, Filippo"}],"ec_funded":1,"date_created":"2018-12-11T11:54:08Z","_id":"1811","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1409.0110"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms."}],"date_published":"2015-05-20T00:00:00Z","publisher":"American Institute of Physics","title":"Analytical evaluation of atomic form factors: Application to Rayleigh scattering","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:53:21Z","citation":{"ieee":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, and F. Fratini, “Analytical evaluation of atomic form factors: Application to Rayleigh scattering,” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5. American Institute of Physics, 2015.","ista":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. 2015. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. Journal of Mathematical Physics. 56(5), 052105.","ama":"Safari L, Santos J, Amaro P, Jänkälä K, Fratini F. Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. 2015;56(5). doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>","chicago":"Safari, Laleh, José Santos, Pedro Amaro, Kari Jänkälä, and Filippo Fratini. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>.","apa":"Safari, L., Santos, J., Amaro, P., Jänkälä, K., &#38; Fratini, F. (2015). Analytical evaluation of atomic form factors: Application to Rayleigh scattering. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4921227\">https://doi.org/10.1063/1.4921227</a>","mla":"Safari, Laleh, et al. “Analytical Evaluation of Atomic Form Factors: Application to Rayleigh Scattering.” <i>Journal of Mathematical Physics</i>, vol. 56, no. 5, 052105, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4921227\">10.1063/1.4921227</a>.","short":"L. Safari, J. Santos, P. Amaro, K. Jänkälä, F. Fratini, Journal of Mathematical Physics 56 (2015)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"publist_id":"5295","intvolume":"        56","publication":"Journal of Mathematical Physics","oa":1,"acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n◦ [291734]. F.F. acknowledges support by Fundação de Amparo à Pesquisa do estado de Minas Gerais (FAPEMIG), by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and by the Austrian Science Fund (FWF) through the START Grant No. Y 591-N16.","year":"2015","day":"20","doi":"10.1063/1.4921227"},{"oa":1,"doi":"10.1088/1367-2630/17/4/045005","year":"2015","day":"01","scopus_import":1,"publication":"New Journal of Physics","publist_id":"5294","intvolume":"        17","citation":{"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 Ltd., 2015.","chicago":"Lahrz, Martin, Mikhail Lemeshko, and Ludwig Mathey. “Exotic Roton Excitations in Quadrupolar Bose–Einstein Condensates .” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2015. <a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">https://doi.org/10.1088/1367-2630/17/4/045005</a>.","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>","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 Ltd. <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).","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 Ltd., 2015, doi:<a href=\"https://doi.org/10.1088/1367-2630/17/4/045005\">10.1088/1367-2630/17/4/045005</a>."},"department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:53:22Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"publication_status":"published","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"}],"title":"Exotic roton excitations in quadrupolar Bose–Einstein condensates ","file_date_updated":"2020-07-14T12:45:17Z","publisher":"IOP Publishing Ltd.","date_published":"2015-04-01T00:00:00Z","_id":"1812","type":"journal_article","date_created":"2018-12-11T11:54:09Z","status":"public","pubrep_id":"446","oa_version":"Published Version","quality_controlled":"1","author":[{"full_name":"Lahrz, Martin","last_name":"Lahrz","first_name":"Martin"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"last_name":"Mathey","first_name":"Ludwig","full_name":"Mathey, Ludwig"}],"file":[{"date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:15:59Z","content_type":"application/pdf","file_name":"IST-2016-446-v1+1_document.pdf","relation":"main_file","file_size":1900925,"access_level":"open_access","creator":"system","checksum":"551f751a75b39b89a1db2f7f498f9a49","file_id":"5184"}],"article_number":"045005","issue":"4","has_accepted_license":"1","month":"04","volume":17,"article_processing_charge":"No","language":[{"iso":"eng"}]},{"status":"public","doi":"10.1103/PhysRevLett.114.203001","main_file_link":[{"url":"http://arxiv.org/abs/1502.03447","open_access":"1"}],"year":"2015","day":"18","date_created":"2018-12-11T11:54:09Z","oa":1,"_id":"1813","type":"journal_article","publist_id":"5293","intvolume":"       114","publication":"Physical Review Letters","scopus_import":1,"author":[{"last_name":"Schmidt","first_name":"Richard","full_name":"Schmidt, Richard"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","department":[{"_id":"MiLe"}],"date_updated":"2021-01-12T06:53:22Z","citation":{"short":"R. Schmidt, M. Lemeshko, Physical Review Letters 114 (2015).","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>.","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>.","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."},"oa_version":"Preprint","language":[{"iso":"eng"}],"date_published":"2015-05-18T00:00:00Z","publisher":"American Physical Society","volume":114,"title":"Rotation of quantum impurities in the presence of a many-body environment","month":"05","publication_status":"published","abstract":[{"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.","lang":"eng"}],"article_number":"203001","issue":"20"},{"pubrep_id":"575","ec_funded":1,"_id":"1814","type":"journal_article","date_created":"2018-12-11T11:54:09Z","status":"public","issue":"3","article_number":"27","file":[{"relation":"main_file","access_level":"open_access","file_size":23712153,"file_id":"4933","checksum":"67c9f4fa370def68cdf31299e48bc91f","creator":"system","date_created":"2018-12-12T10:12:15Z","date_updated":"2020-07-14T12:45:17Z","content_type":"application/pdf","file_name":"IST-2016-575-v1+1_wavefront_preprint.pdf"}],"month":"04","has_accepted_license":"1","volume":34,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","project":[{"name":"Deep Pictures: Creating Visual and Haptic Vector Images","grant_number":"P 24352-N23","_id":"25357BD2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020"}],"quality_controlled":"1","author":[{"last_name":"Jeschke","first_name":"Stefan","full_name":"Jeschke, Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wojtan, Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J"}],"scopus_import":1,"publication":"ACM Transactions on Graphics","intvolume":"        34","publist_id":"5292","oa":1,"day":"01","doi":"10.1145/2714572","year":"2015","ddc":["000"],"abstract":[{"lang":"eng","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."}],"publication_status":"published","title":"Water wave animation via wavefront parameter interpolation","publisher":"ACM","date_published":"2015-04-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:17Z","citation":{"short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 34 (2015).","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>.","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>","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>","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>.","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."},"date_updated":"2023-02-23T10:15:40Z","department":[{"_id":"ChWo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4720436/"}],"date_created":"2018-12-11T11:54:10Z","_id":"1817","type":"journal_article","author":[{"full_name":"Porazinski, Sean","last_name":"Porazinski","first_name":"Sean"},{"first_name":"Huijia","last_name":"Wang","full_name":"Wang, Huijia"},{"full_name":"Asaoka, Yoichi","last_name":"Asaoka","first_name":"Yoichi"},{"full_name":"Behrndt, Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin"},{"full_name":"Miyamoto, Tatsuo","last_name":"Miyamoto","first_name":"Tatsuo"},{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi","last_name":"Morita","first_name":"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","first_name":"Gabriel","full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Osada","first_name":"Yumi","full_name":"Osada, Yumi"},{"last_name":"Asaka","first_name":"Satoshi","full_name":"Asaka, Satoshi"},{"full_name":"Momoi, Akihiro","last_name":"Momoi","first_name":"Akihiro"},{"full_name":"Linton, Sarah","last_name":"Linton","first_name":"Sarah"},{"last_name":"Miesfeld","first_name":"Joel","full_name":"Miesfeld, Joel"},{"full_name":"Link, Brian","first_name":"Brian","last_name":"Link"},{"full_name":"Senga, Takeshi","last_name":"Senga","first_name":"Takeshi"},{"first_name":"Atahualpa","last_name":"Castillo Morales","full_name":"Castillo Morales, Atahualpa"},{"first_name":"Araxi","last_name":"Urrutia","full_name":"Urrutia, Araxi"},{"first_name":"Nobuyoshi","last_name":"Shimizu","full_name":"Shimizu, Nobuyoshi"},{"full_name":"Nagase, Hideaki","last_name":"Nagase","first_name":"Hideaki"},{"last_name":"Matsuura","first_name":"Shinya","full_name":"Matsuura, Shinya"},{"full_name":"Bagby, Stefan","first_name":"Stefan","last_name":"Bagby"},{"first_name":"Hisato","last_name":"Kondoh","full_name":"Kondoh, Hisato"},{"last_name":"Nishina","first_name":"Hiroshi","full_name":"Nishina, Hiroshi"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Furutani Seiki, Makoto","last_name":"Furutani Seiki","first_name":"Makoto"}],"quality_controlled":"1","oa_version":"Submitted Version","language":[{"iso":"eng"}],"volume":521,"month":"03","issue":"7551","doi":"10.1038/nature14215","year":"2015","page":"217 - 221","day":"16","oa":1,"publist_id":"5289","intvolume":"       521","publication":"Nature","scopus_import":1,"external_id":{"pmid":["25778702"]},"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T06:53:23Z","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.","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.","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>."},"pmid":1,"publisher":"Nature Publishing Group","date_published":"2015-03-16T00:00:00Z","title":"YAP is essential for tissue tension to ensure vertebrate 3D body shape","publication_status":"published","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. "}]},{"language":[{"iso":"eng"}],"volume":112,"month":"05","issue":"20","author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka","last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"oa_version":"Submitted Version","ec_funded":1,"status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443383/"}],"date_created":"2018-12-11T11:54:11Z","type":"journal_article","_id":"1818","publisher":"National Academy of Sciences","date_published":"2015-05-19T00:00:00Z","pmid":1,"title":"Limits to adaptation along environmental gradients","abstract":[{"lang":"eng","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."}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["25941385"]},"date_updated":"2021-01-12T06:53:24Z","department":[{"_id":"NiBa"}],"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>.","short":"J. Polechova, N.H. Barton, PNAS 112 (2015) 6401–6406.","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.","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>.","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>","ista":"Polechova J, Barton NH. 2015. Limits to adaptation along environmental gradients. PNAS. 112(20), 6401–6406.","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>"},"intvolume":"       112","publist_id":"5288","publication":"PNAS","scopus_import":1,"doi":"10.1073/pnas.1421515112","page":"6401 - 6406","year":"2015","day":"19","oa":1},{"oa_version":"Preprint","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"quality_controlled":"1","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","first_name":"Martin"},{"full_name":"Gupta, Raghav","first_name":"Raghav","last_name":"Gupta"},{"full_name":"Kanodia, Ayush","first_name":"Ayush","last_name":"Kanodia"}],"month":"06","volume":5,"language":[{"iso":"eng"}],"_id":"1820","type":"conference","date_created":"2018-12-11T11:54:11Z","main_file_link":[{"url":"http://arxiv.org/abs/1411.3880","open_access":"1"}],"status":"public","conference":{"location":"Austin, TX, USA","name":"IAAI: Innovative Applications of Artificial Intelligence","end_date":"2015-01-30","start_date":"2015-01-25"},"ec_funded":1,"citation":{"apa":"Chatterjee, K., Chmelik, M., Gupta, R., &#38; Kanodia, A. (2015). Optimal cost almost-sure reachability in POMDPs. In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i> (Vol. 5, pp. 3496–3502). Austin, TX, USA: AAAI Press.","ista":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. 2015. Optimal cost almost-sure reachability in POMDPs. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence . IAAI: Innovative Applications of Artificial Intelligence, Artifical Intelligence, vol. 5, 3496–3502.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, Raghav Gupta, and Ayush Kanodia. “Optimal Cost Almost-Sure Reachability in POMDPs.” In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, 5:3496–3502. AAAI Press, 2015.","ama":"Chatterjee K, Chmelik M, Gupta R, Kanodia A. Optimal cost almost-sure reachability in POMDPs. In: <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>. Vol 5. AAAI Press; 2015:3496-3502.","ieee":"K. Chatterjee, M. Chmelik, R. Gupta, and A. Kanodia, “Optimal cost almost-sure reachability in POMDPs,” in <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, Austin, TX, USA, 2015, vol. 5, pp. 3496–3502.","mla":"Chatterjee, Krishnendu, et al. “Optimal Cost Almost-Sure Reachability in POMDPs.” <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence </i>, vol. 5, AAAI Press, 2015, pp. 3496–502.","short":"K. Chatterjee, M. Chmelik, R. Gupta, A. Kanodia, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence , AAAI Press, 2015, pp. 3496–3502."},"department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T10:02:57Z","alternative_title":["Artifical Intelligence"],"external_id":{"arxiv":["1411.3880"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with a set of target states and every transition is associated with an integer cost. The optimization objec- tive we study asks to minimize the expected total cost till the target set is reached, while ensuring that the target set is reached almost-surely (with probability 1). We show that for integer costs approximating the optimal cost is undecidable. For positive costs, our results are as follows: (i) we establish matching lower and upper bounds for the optimal cost and the bound is double exponential; (ii) we show that the problem of approximating the optimal cost is decidable and present ap- proximation algorithms developing on the existing algorithms for POMDPs with finite-horizon objectives. While the worst- case running time of our algorithm is double exponential, we present efficient stopping criteria for the algorithm and show experimentally that it performs well in many examples.","lang":"eng"}],"title":"Optimal cost almost-sure reachability in POMDPs","date_published":"2015-06-01T00:00:00Z","publisher":"AAAI Press","oa":1,"page":"3496-3502","year":"2015","day":"01","acknowledgement":" The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","scopus_import":1,"related_material":{"record":[{"status":"public","id":"1529","relation":"later_version"}]},"publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence ","arxiv":1,"publist_id":"5286","intvolume":"         5"},{"author":[{"first_name":"Guillaume","last_name":"Chevereau","full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","first_name":"Mark Tobias"}],"oa_version":"Published Version","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions"},{"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"}],"volume":11,"language":[{"iso":"eng"}],"article_number":"807","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:14:34Z","file_name":"IST-2015-395-v1+1_807.full.pdf","relation":"main_file","creator":"system","file_id":"5087","checksum":"4289b518fbe2166682fb1a1ef9b405f3","file_size":1273573,"access_level":"open_access"}],"issue":"4","has_accepted_license":"1","month":"04","status":"public","type":"journal_article","_id":"1823","date_created":"2018-12-11T11:54:12Z","ec_funded":1,"pubrep_id":"395","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>","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>.","ista":"Chevereau G, Bollenbach MT. 2015. Systematic discovery of drug interaction mechanisms. Molecular Systems Biology. 11(4), 807.","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>","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.","short":"G. Chevereau, M.T. Bollenbach, Molecular Systems Biology 11 (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>."},"department":[{"_id":"ToBo"}],"date_updated":"2021-01-12T06:53:26Z","title":"Systematic discovery of drug interaction mechanisms","date_published":"2015-04-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:17Z","publisher":"Nature Publishing Group","ddc":["570"],"publication_status":"published","abstract":[{"lang":"eng","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."}],"doi":"10.15252/msb.20156098","year":"2015","day":"01","oa":1,"publication":"Molecular Systems Biology","publist_id":"5283","intvolume":"        11","scopus_import":1},{"_id":"1824","type":"journal_article","date_created":"2018-12-11T11:54:13Z","status":"public","pubrep_id":"451","oa_version":"Published Version","quality_controlled":"1","author":[{"last_name":"Knebel","first_name":"Johannes","full_name":"Knebel, Johannes"},{"full_name":"Weber, Markus","last_name":"Weber","first_name":"Markus"},{"full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4821-3297","last_name":"Krüger","first_name":"Torben H"},{"full_name":"Frey, Erwin","last_name":"Frey","first_name":"Erwin"}],"file":[{"access_level":"open_access","file_size":1151501,"file_id":"5245","checksum":"c4cffb5c8b245e658a34eac71a03e7cc","creator":"system","relation":"main_file","file_name":"IST-2016-451-v1+1_ncomms7977.pdf","date_created":"2018-12-12T10:16:54Z","date_updated":"2020-07-14T12:45:17Z","content_type":"application/pdf"}],"article_number":"6977","has_accepted_license":"1","month":"04","volume":6,"language":[{"iso":"eng"}],"oa":1,"doi":"10.1038/ncomms7977","year":"2015","day":"24","scopus_import":1,"publication":"Nature Communications","publist_id":"5282","intvolume":"         6","citation":{"ista":"Knebel J, Weber M, Krüger TH, Frey E. 2015. Evolutionary games of condensates in coupled birth-death processes. Nature Communications. 6, 6977.","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>","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>.","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>","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.","short":"J. Knebel, M. Weber, T.H. Krüger, E. Frey, Nature Communications 6 (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>."},"department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T06:53:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"publication_status":"published","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"}],"title":"Evolutionary games of condensates in coupled birth-death processes","file_date_updated":"2020-07-14T12:45:17Z","publisher":"Nature Publishing Group","date_published":"2015-04-24T00:00:00Z"},{"status":"public","date_created":"2018-12-11T11:54:14Z","type":"journal_article","_id":"1827","ec_funded":1,"pubrep_id":"452","author":[{"last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mayo","first_name":"Avraham","full_name":"Mayo, Avraham"},{"full_name":"Tlusty, Tsvi","last_name":"Tlusty","first_name":"Tsvi"},{"full_name":"Alon, Uri","last_name":"Alon","first_name":"Uri"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"quality_controlled":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"article_processing_charge":"No","volume":11,"month":"03","has_accepted_license":"1","issue":"3","file":[{"file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf","date_created":"2018-12-12T10:15:39Z","date_updated":"2020-07-14T12:45:17Z","content_type":"application/pdf","access_level":"open_access","file_size":1811647,"file_id":"5161","checksum":"b8aa66f450ff8de393014b87ec7d2efb","creator":"system","relation":"main_file"}],"day":"23","year":"2015","doi":"10.1371/journal.pcbi.1004055","oa":1,"intvolume":"        11","publist_id":"5278","publication":"PLoS Computational Biology","related_material":{"record":[{"status":"public","relation":"research_data","id":"9718"},{"relation":"research_data","id":"9773","status":"public"}]},"scopus_import":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2023-02-23T14:07:51Z","department":[{"_id":"GaTk"}],"citation":{"ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” <i>PLoS Computational Biology</i>, vol. 11, no. 3. Public Library of Science, 2015.","apa":"Friedlander, T., Mayo, A., Tlusty, T., &#38; Alon, U. (2015). Evolution of bow-tie architectures in biology. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">https://doi.org/10.1371/journal.pcbi.1004055</a>","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. <i>PLoS Computational Biology</i>. 2015;11(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">10.1371/journal.pcbi.1004055</a>","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3).","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” <i>PLoS Computational Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">https://doi.org/10.1371/journal.pcbi.1004055</a>.","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” <i>PLoS Computational Biology</i>, vol. 11, no. 3, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004055\">10.1371/journal.pcbi.1004055</a>.","short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015)."},"file_date_updated":"2020-07-14T12:45:17Z","date_published":"2015-03-23T00:00:00Z","publisher":"Public Library of Science","title":"Evolution of bow-tie architectures in biology","abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"publication_status":"published","ddc":["576"]}]