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Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002."},"date_updated":"2025-09-22T08:46:14Z","related_material":{"record":[{"id":"1270","relation":"used_in_publication","status":"public"}]},"title":"Computation of positional information in an Ising model","date_created":"2021-08-10T09:23:45Z","department":[{"_id":"GaTk"}],"abstract":[{"text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined.","lang":"eng"}],"year":"2016","article_processing_charge":"No","month":"09","oa_version":"Published Version","author":[{"last_name":"Hillenbrand","first_name":"Patrick","full_name":"Hillenbrand, Patrick"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"fulldoi":"https://doi.org/10.1371/journal.pone.0163628.s002","date_published":"2016-09-27T00:00:00Z","day":"27"},{"year":"2016","article_processing_charge":"No","oa_version":"Published Version","month":"09","author":[{"last_name":"Hillenbrand","first_name":"Patrick","full_name":"Hillenbrand, Patrick"},{"last_name":"Gerland","full_name":"Gerland, Ulrich","first_name":"Ulrich"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"fulldoi":"https://doi.org/10.1371/journal.pone.0163628.s003","day":"27","doi":"10.1371/journal.pone.0163628.s003","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","status":"public","_id":"9871","type":"research_data_reference","date_updated":"2025-09-22T08:46:14Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1270"}]},"citation":{"ama":"Hillenbrand P, Gerland U, Tkačik G. 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Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016."},"abstract":[{"text":"The positional information in a discrete morphogen field with Gaussian noise is computed.","lang":"eng"}],"date_created":"2021-08-10T09:27:35Z","title":"Computation of positional information in a discrete morphogen field","department":[{"_id":"GaTk"}]},{"month":"04","oa_version":"Published Version","year":"2016","article_processing_charge":"No","day":"19","author":[{"last_name":"Boehm","full_name":"Boehm, Alex","first_name":"Alex"},{"first_name":"Markus","full_name":"Arnoldini, Markus","last_name":"Arnoldini"},{"last_name":"Bergmiller","first_name":"Tobias","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","full_name":"Röösli, Thomas","last_name":"Röösli"},{"last_name":"Bigosch","first_name":"Colette","full_name":"Bigosch, Colette"},{"last_name":"Ackermann","full_name":"Ackermann, Martin","first_name":"Martin"}],"fulldoi":"https://doi.org/10.1371/journal.pgen.1005974.s015","status":"public","_id":"9873","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","doi":"10.1371/journal.pgen.1005974.s015","date_created":"2021-08-10T09:42:34Z","title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","department":[{"_id":"CaGu"}],"citation":{"ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Quantification of the growth rate reduction as a consequence of age-specific mortality, Public Library of Science, 10.1371/journal.pgen.1005974.s015.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification of the growth rate reduction as a consequence of age-specific mortality. 2016. doi:10.1371/journal.pgen.1005974.s015","mla":"Boehm, Alex, et al. Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality. Public Library of Science, 2016, doi:10.1371/journal.pgen.1005974.s015.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, (2016).","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., & Ackermann, M. (2016). Quantification of the growth rate reduction as a consequence of age-specific mortality. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005974.s015","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pgen.1005974.s015."},"date_updated":"2025-09-22T09:10:03Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1250"}]}},{"title":"Inference algorithms for pattern-based CRFs on sequence data","abstract":[{"text":"We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights.","lang":"eng"}],"page":"17 - 46","date_updated":"2025-09-29T14:28:47Z","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"type":"journal_article","_id":"1794","status":"public","publisher":"Springer","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1007/s00453-015-0017-7","date_published":"2016-09-01T00:00:00Z","day":"01","external_id":{"isi":["000381149500002"],"arxiv":["1210.0508"]},"fulldoi":"https://doi.org/10.1007/s00453-015-0017-7","isi":1,"publist_id":"5316","language":[{"iso":"eng"}],"scopus_import":"1","department":[{"_id":"VlKo"}],"date_created":"2018-12-11T11:54:02Z","publication":"Algorithmica","corr_author":"1","citation":{"chicago":"Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” Algorithmica. Springer, 2016. https://doi.org/10.1007/s00453-015-0017-7.","short":"V. Kolmogorov, R. Takhanov, Algorithmica 76 (2016) 17–46.","ieee":"V. Kolmogorov and R. Takhanov, “Inference algorithms for pattern-based CRFs on sequence data,” Algorithmica, vol. 76, no. 1. Springer, pp. 17–46, 2016.","apa":"Kolmogorov, V., & Takhanov, R. (2016). Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. Springer. https://doi.org/10.1007/s00453-015-0017-7","ama":"Kolmogorov V, Takhanov R. Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. 2016;76(1):17-46. doi:10.1007/s00453-015-0017-7","mla":"Kolmogorov, Vladimir, and Rustem Takhanov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” Algorithmica, vol. 76, no. 1, Springer, 2016, pp. 17–46, doi:10.1007/s00453-015-0017-7.","ista":"Kolmogorov V, Takhanov R. 2016. Inference algorithms for pattern-based CRFs on sequence data. Algorithmica. 76(1), 17–46."},"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2272"}]},"volume":76,"ec_funded":1,"quality_controlled":"1","arxiv":1,"acknowledgement":"This work has been partially supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no. 616160.","publication_status":"published","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Takhanov","full_name":"Takhanov, Rustem","first_name":"Rustem","id":"2CCAC26C-F248-11E8-B48F-1D18A9856A87"}],"month":"09","intvolume":" 76","issue":"1","oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1210.0508","open_access":"1"}],"article_processing_charge":"No","year":"2016","oa":1},{"doi":"10.1016/j.jmva.2015.10.005","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Elsevier","status":"public","_id":"1833","type":"journal_article","page":"440 - 452","date_updated":"2025-09-18T10:47:32Z","abstract":[{"text":"Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in the table, and not necessarily containing the overall effect, that is, a common parameter in every cell. Similarly to log-linear models, relational models can be extended to non-negative distributions, but the extension requires more complex methods. An extended relational model is defined as an algebraic variety, and it turns out to be the closure of the original model with respect to the Bregman divergence. In the extended relational model, the MLE of the cell parameters always exists and is unique, but some of its properties may be different from those of the MLE under log-linear models. The MLE can be computed using a generalized iterative scaling procedure based on Bregman projections. ","lang":"eng"}],"title":"On the closure of relational models","language":[{"iso":"eng"}],"publist_id":"5270","fulldoi":"https://doi.org/10.1016/j.jmva.2015.10.005","isi":1,"external_id":{"arxiv":["1501.00600"],"isi":["000366885300029"]},"date_published":"2016-01-01T00:00:00Z","day":"01","arxiv":1,"quality_controlled":"1","volume":143,"citation":{"mla":"Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal of Multivariate Analysis, vol. 143, Elsevier, 2016, pp. 440–52, doi:10.1016/j.jmva.2015.10.005.","ama":"Klimova A, Rudas T. On the closure of relational models. Journal of Multivariate Analysis. 2016;143:440-452. doi:10.1016/j.jmva.2015.10.005","ista":"Klimova A, Rudas T. 2016. On the closure of relational models. Journal of Multivariate Analysis. 143, 440–452.","chicago":"Klimova, Anna, and Tamás Rudas. “On the Closure of Relational Models.” Journal of Multivariate Analysis. Elsevier, 2016. https://doi.org/10.1016/j.jmva.2015.10.005.","apa":"Klimova, A., & Rudas, T. (2016). On the closure of relational models. Journal of Multivariate Analysis. Elsevier. https://doi.org/10.1016/j.jmva.2015.10.005","ieee":"A. Klimova and T. Rudas, “On the closure of relational models,” Journal of Multivariate Analysis, vol. 143. Elsevier, pp. 440–452, 2016.","short":"A. Klimova, T. Rudas, Journal of Multivariate Analysis 143 (2016) 440–452."},"corr_author":"1","publication":"Journal of Multivariate Analysis","date_created":"2018-12-11T11:54:15Z","scopus_import":"1","department":[{"_id":"CaUh"}],"oa":1,"year":"2016","article_processing_charge":"No","intvolume":" 143","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.00600"}],"month":"01","author":[{"full_name":"Klimova, Anna","first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","last_name":"Klimova"},{"first_name":"Tamás","full_name":"Rudas, Tamás","last_name":"Rudas"}],"publication_status":"published"},{"oa":1,"year":"2016","article_processing_charge":"No","month":"01","intvolume":" 6","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1408.3961"}],"issue":"3","oa_version":"Preprint","author":[{"first_name":"Richard","full_name":"Froese, Richard","last_name":"Froese"},{"first_name":"Darrick","full_name":"Lee, Darrick","last_name":"Lee"},{"last_name":"Sadel","id":"4760E9F8-F248-11E8-B48F-1D18A9856A87","full_name":"Sadel, Christian","orcid":"0000-0001-8255-3968","first_name":"Christian"},{"last_name":"Spitzer","first_name":"Wolfgang","full_name":"Spitzer, Wolfgang"},{"first_name":"Günter","full_name":"Stolz, Günter","last_name":"Stolz"}],"publication_status":"published","volume":6,"quality_controlled":"1","arxiv":1,"citation":{"ista":"Froese R, Lee D, Sadel C, Spitzer W, Stolz G. 2016. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 6(3), 557–600.","mla":"Froese, Richard, et al. “Localization for Transversally Periodic Random Potentials on Binary Trees.” Journal of Spectral Theory, vol. 6, no. 3, EMS Press, 2016, pp. 557–600, doi:10.4171/JST/132.","ama":"Froese R, Lee D, Sadel C, Spitzer W, Stolz G. Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. 2016;6(3):557-600. doi:10.4171/JST/132","ieee":"R. Froese, D. Lee, C. Sadel, W. Spitzer, and G. Stolz, “Localization for transversally periodic random potentials on binary trees,” Journal of Spectral Theory, vol. 6, no. 3. EMS Press, pp. 557–600, 2016.","apa":"Froese, R., Lee, D., Sadel, C., Spitzer, W., & Stolz, G. (2016). Localization for transversally periodic random potentials on binary trees. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/132","short":"R. Froese, D. Lee, C. Sadel, W. Spitzer, G. Stolz, Journal of Spectral Theory 6 (2016) 557–600.","chicago":"Froese, Richard, Darrick Lee, Christian Sadel, Wolfgang Spitzer, and Günter Stolz. “Localization for Transversally Periodic Random Potentials on Binary Trees.” Journal of Spectral Theory. EMS Press, 2016. https://doi.org/10.4171/JST/132."},"das_tickbox":"1","date_created":"2018-12-11T11:50:48Z","department":[{"_id":"LaEr"}],"scopus_import":"1","publication":"Journal of Spectral Theory","external_id":{"isi":["000388627000004"],"arxiv":["1408.3961"]},"language":[{"iso":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.4171/JST/132","publist_id":"6112","date_published":"2016-01-01T00:00:00Z","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"EMS Press","doi":"10.4171/JST/132","status":"public","_id":"1223","type":"journal_article","date_updated":"2026-07-06T11:55:04Z","page":"557 - 600","title":"Localization for transversally periodic random potentials on binary trees","abstract":[{"lang":"eng","text":"We consider a random Schrödinger operator on the binary tree with a random potential which is the sum of a random radially symmetric potential, Qr, and a random transversally periodic potential, κQt, with coupling constant κ. Using a new one-dimensional dynamical systems approach combined with Jensen's inequality in hyperbolic space (our key estimate) we obtain a fractional moment estimate proving localization for small and large κ. Together with a previous result we therefore obtain a model with two Anderson transitions, from localization to delocalization and back to localization, when increasing κ. As a by-product we also have a partially new proof of one-dimensional Anderson localization at any disorder."}]},{"file":[{"content_type":"application/pdf","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","access_level":"open_access","file_id":"5095","relation":"main_file","date_created":"2018-12-12T10:14:41Z","creator":"system","file_size":871964,"checksum":"781bc3ffd30b2dd65b7727c5a285fc78","date_updated":"2025-06-25T11:26:45Z"}],"fulldoi":"https://doi.org/10.1137/15M103306X","isi":1,"publist_id":"6186","language":[{"iso":"eng"}],"external_id":{"isi":["000391853100010"]},"day":"15","date_published":"2016-11-15T00:00:00Z","doi":"10.1137/15M103306X","publisher":"Society for Industrial and Applied Mathematics","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"1170","status":"public","date_updated":"2026-07-06T14:00:20Z","page":"B988 - B1008","file_date_updated":"2025-06-25T11:26:45Z","abstract":[{"text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.","lang":"eng"}],"title":"Modular parameter identification of biomolecular networks","article_processing_charge":"No","oa":1,"year":"2016","intvolume":" 38","oa_version":"Submitted Version","issue":"6","month":"11","publication_status":"published","article_type":"original","author":[{"first_name":"Moritz","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang"},{"last_name":"Stelling","first_name":"Jörg","full_name":"Stelling, Jörg"}],"pubrep_id":"811","ddc":["003","518","570","621"],"OA_type":"green","quality_controlled":"1","OA_place":"repository","volume":38,"has_accepted_license":"1","corr_author":"1","citation":{"chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics, 2016. https://doi.org/10.1137/15M103306X.","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics, pp. B988–B1008, 2016.","apa":"Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/15M103306X","mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society for Industrial and Applied Mathematics, 2016, pp. B988–1008, doi:10.1137/15M103306X.","ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008."},"publication":"SIAM Journal on Scientific Computing","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"scopus_import":"1","date_created":"2018-12-11T11:50:31Z","das_tickbox":"1"},{"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1137/15M1010257","publist_id":"5834","isi":1,"external_id":{"isi":["000385275400005"],"arxiv":["1502.07770"]},"date_published":"2016-05-03T00:00:00Z","day":"03","doi":"10.1137/15M1010257","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society for Industrial and Applied Mathematics","_id":"1377","status":"public","type":"journal_article","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160"}],"page":"605 - 636","date_updated":"2026-07-06T13:59:54Z","abstract":[{"text":"We consider the problem of minimizing the continuous valued total variation subject to different unary terms on trees and propose fast direct algorithms based on dynamic programming to solve these problems. We treat both the convex and the nonconvex case and derive worst-case complexities that are equal to or better than existing methods. We show applications to total variation based two dimensional image processing and computer vision problems based on a Lagrangian decomposition approach. The resulting algorithms are very effcient, offer a high degree of parallelism, and come along with memory requirements which are only in the order of the number of image pixels.","lang":"eng"}],"title":"Total variation on a tree","oa":1,"year":"2016","article_processing_charge":"No","oa_version":"Preprint","intvolume":" 9","issue":"2","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1502.07770"}],"month":"05","author":[{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","full_name":"Pock, Thomas","last_name":"Pock"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","first_name":"Michal","last_name":"Rolinek"}],"publication_status":"published","arxiv":1,"quality_controlled":"1","volume":9,"ec_funded":1,"citation":{"short":"V. Kolmogorov, T. Pock, M. Rolinek, SIAM Journal on Imaging Sciences 9 (2016) 605–636.","apa":"Kolmogorov, V., Pock, T., & Rolinek, M. (2016). Total variation on a tree. SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/15M1010257","ieee":"V. Kolmogorov, T. Pock, and M. Rolinek, “Total variation on a tree,” SIAM Journal on Imaging Sciences, vol. 9, no. 2. Society for Industrial and Applied Mathematics, pp. 605–636, 2016.","chicago":"Kolmogorov, Vladimir, Thomas Pock, and Michal Rolinek. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences. Society for Industrial and Applied Mathematics, 2016. https://doi.org/10.1137/15M1010257.","ista":"Kolmogorov V, Pock T, Rolinek M. 2016. Total variation on a tree. SIAM Journal on Imaging Sciences. 9(2), 605–636.","mla":"Kolmogorov, Vladimir, et al. “Total Variation on a Tree.” SIAM Journal on Imaging Sciences, vol. 9, no. 2, Society for Industrial and Applied Mathematics, 2016, pp. 605–36, doi:10.1137/15M1010257.","ama":"Kolmogorov V, Pock T, Rolinek M. Total variation on a tree. SIAM Journal on Imaging Sciences. 2016;9(2):605-636. doi:10.1137/15M1010257"},"publication":"SIAM Journal on Imaging Sciences","date_created":"2018-12-11T11:51:40Z","das_tickbox":"1","scopus_import":"1","department":[{"_id":"VlKo"}]},{"publist_id":"6048","fulldoi":"https://doi.org/10.1080/16864360.2016.1150718","file":[{"file_id":"5206","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-694-v1+1_Generalized_offsetting_of_planar_structures_using_skeletons.pdf","checksum":"c746f3a48edb62b588d92ea5d0fd2c0e","date_updated":"2020-07-14T12:44:42Z","file_size":1678369,"creator":"system","date_created":"2018-12-12T10:16:20Z","relation":"main_file"}],"language":[{"iso":"eng"}],"date_published":"2016-09-02T00:00:00Z","day":"02","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"page":"712 - 721","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_updated":"2026-07-07T05:34:31Z","file_date_updated":"2020-07-14T12:44:42Z","abstract":[{"lang":"eng","text":"We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams."}],"title":"Generalized offsetting of planar structures using skeletons","doi":"10.1080/16864360.2016.1150718","publisher":"Taylor & Francis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"1272","status":"public","publication_status":"published","author":[{"last_name":"Held","full_name":"Held, Martin","first_name":"Martin"},{"id":"4700A070-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","orcid":"0000-0002-8871-5814","full_name":"Huber, Stefan","last_name":"Huber"},{"last_name":"Palfrader","first_name":"Peter","full_name":"Palfrader, Peter"}],"pubrep_id":"694","ddc":["004","516"],"article_processing_charge":"No","year":"2016","oa":1,"issue":"5","intvolume":" 13","oa_version":"Published Version","month":"09","has_accepted_license":"1","citation":{"mla":"Held, Martin, et al. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications, vol. 13, no. 5, Taylor & Francis, 2016, pp. 712–21, doi:10.1080/16864360.2016.1150718.","ama":"Held M, Huber S, Palfrader P. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 2016;13(5):712-721. doi:10.1080/16864360.2016.1150718","ista":"Held M, Huber S, Palfrader P. 2016. Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. 13(5), 712–721.","chicago":"Held, Martin, Stefan Huber, and Peter Palfrader. “Generalized Offsetting of Planar Structures Using Skeletons.” Computer-Aided Design and Applications. Taylor & Francis, 2016. https://doi.org/10.1080/16864360.2016.1150718.","short":"M. Held, S. Huber, P. Palfrader, Computer-Aided Design and Applications 13 (2016) 712–721.","apa":"Held, M., Huber, S., & Palfrader, P. (2016). Generalized offsetting of planar structures using skeletons. Computer-Aided Design and Applications. Taylor & Francis. https://doi.org/10.1080/16864360.2016.1150718","ieee":"M. Held, S. Huber, and P. Palfrader, “Generalized offsetting of planar structures using skeletons,” Computer-Aided Design and Applications, vol. 13, no. 5. Taylor & Francis, pp. 712–721, 2016."},"publication":"Computer-Aided Design and Applications","department":[{"_id":"HeEd"}],"scopus_import":"1","das_tickbox":"1","date_created":"2018-12-11T11:51:04Z","acknowledgement":"This work was supported by Austrian Science Fund (FWF): P25816-N15.","quality_controlled":"1","volume":13},{"ec_funded":1,"volume":25,"quality_controlled":"1","arxiv":1,"acknowledgement":"AG and PP were partially supported by Abdus Salam International Centre for Theoretical Physics (ICTP). Additionally, AG was supported by BREUDS, and research conducted by PP has received funding from Fundo Europeu de Desenvolvimento Regional (FEDER) through COMPETE—Programa Operacional Factores de Competitividade (POFC) and from the Portuguese national funds through Fundação para a Ciência e a Tecnologia (FCT) in the framework of the research project FCOMP-01-0124-FEDER-010645 (ref. FCT PTDC/MAT/098871/2008); and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 622033. The authors gratefully acknowledge the Department of\r\nMathematics of Kyoto University for providing access\r\nto their server for conducting computations for this\r\nproject.","scopus_import":"1","department":[{"_id":"HeEd"}],"date_created":"2018-12-11T11:50:58Z","das_tickbox":"1","publication":"Experimental Mathematics","corr_author":"1","citation":{"chicago":"Golmakani, Ali, Stefano Luzzatto, and Pawel Pilarczyk. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics. Taylor & Francis, 2016. https://doi.org/10.1080/10586458.2015.1048011.","short":"A. Golmakani, S. Luzzatto, P. Pilarczyk, Experimental Mathematics 25 (2016) 116–124.","apa":"Golmakani, A., Luzzatto, S., & Pilarczyk, P. (2016). Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2015.1048011","ieee":"A. Golmakani, S. Luzzatto, and P. Pilarczyk, “Uniform expansivity outside a critical neighborhood in the quadratic family,” Experimental Mathematics, vol. 25, no. 2. Taylor & Francis, pp. 116–124, 2016.","mla":"Golmakani, Ali, et al. “Uniform Expansivity Outside a Critical Neighborhood in the Quadratic Family.” Experimental Mathematics, vol. 25, no. 2, Taylor & Francis, 2016, pp. 116–24, doi:10.1080/10586458.2015.1048011.","ama":"Golmakani A, Luzzatto S, Pilarczyk P. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 2016;25(2):116-124. doi:10.1080/10586458.2015.1048011","ista":"Golmakani A, Luzzatto S, Pilarczyk P. 2016. Uniform expansivity outside a critical neighborhood in the quadratic family. Experimental Mathematics. 25(2), 116–124."},"month":"04","oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1504.00116","open_access":"1"}],"issue":"2","intvolume":" 25","article_processing_charge":"No","year":"2016","oa":1,"publication_status":"published","author":[{"last_name":"Golmakani","first_name":"Ali","full_name":"Golmakani, Ali"},{"last_name":"Luzzatto","full_name":"Luzzatto, Stefano","first_name":"Stefano"},{"last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","full_name":"Pilarczyk, Pawel","first_name":"Pawel"}],"type":"journal_article","project":[{"grant_number":"622033","call_identifier":"FP7","name":"Persistent Homology - Images, Data and Maps","_id":"255F06BE-B435-11E9-9278-68D0E5697425"}],"status":"public","_id":"1254","publisher":"Taylor & Francis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1080/10586458.2015.1048011","title":"Uniform expansivity outside a critical neighborhood in the quadratic family","abstract":[{"text":"We use rigorous numerical techniques to compute a lower bound for the exponent of expansivity outside a neighborhood of the critical point for thousands of intervals of parameter values in the quadratic family. We first compute a radius of the critical neighborhood outside which the map is uniformly expanding. This radius is taken as small as possible, yet large enough for our numerical procedure to succeed in proving that the expansivity exponent outside this neighborhood is positive. Then, for each of the intervals, we compute a lower bound for this expansivity exponent, valid for all the parameters in that interval. We illustrate and study the distribution of the radii and the expansivity exponents. The results of our computations are mathematically rigorous. The source code of the software and the results of the computations are made publicly available at http://www.pawelpilarczyk.com/quadratic/.","lang":"eng"}],"page":"116 - 124","date_updated":"2026-07-07T05:34:16Z","date_published":"2016-04-02T00:00:00Z","day":"02","external_id":{"isi":["000372490500002"],"arxiv":["1504.00116"]},"fulldoi":"https://doi.org/10.1080/10586458.2015.1048011","publist_id":"6071","isi":1,"language":[{"iso":"eng"}]},{"author":[{"last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"},{"last_name":"Masoero","first_name":"Davide","full_name":"Masoero, Davide"}],"publication_status":"published","month":"12","main_file_link":[{"url":"https://arxiv.org/abs/1606.09048","open_access":"1"}],"issue":"12","intvolume":" 2016","oa_version":"Preprint","year":"2016","oa":1,"article_processing_charge":"No","date_created":"2018-12-11T11:50:37Z","das_tickbox":"1","scopus_import":"1","department":[{"_id":"GaTk"}],"publication":"Journal of Statistical Mechanics: Theory and Experiment","citation":{"chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.","short":"D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOP Publishing, 2016.","apa":"De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/aa4e8f","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOP Publishing, 2016, doi:10.1088/1742-5468/aa4e8f.","ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502."},"volume":2016,"ec_funded":1,"quality_controlled":"1","arxiv":1,"article_number":"123502","acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","date_published":"2016-12-30T00:00:00Z","day":"30","external_id":{"isi":["000391973900001"],"arxiv":["1606.09048"]},"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1088/1742-5468/aa4e8f","publist_id":"6165","isi":1,"title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth","abstract":[{"lang":"eng","text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations."}],"date_updated":"2026-07-07T13:11:22Z","_id":"1188","status":"public","type":"journal_article","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IOP Publishing","doi":"10.1088/1742-5468/aa4e8f"},{"month":"05","oa_version":"Submitted Version","issue":"21","intvolume":" 55","year":"2016","oa":1,"article_processing_charge":"No","ddc":["571","576"],"pubrep_id":"840","author":[{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","last_name":"Gschaider-Reichhart"},{"orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro","first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","last_name":"Inglés Prieto"},{"id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandra-Madelaine","full_name":"Tichy, Alexandra-Madelaine","last_name":"Tichy"},{"last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","full_name":"Mckenzie, Catherine"},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak"}],"publication_status":"published","volume":55,"ec_funded":1,"quality_controlled":"1","acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","date_created":"2018-12-11T11:52:02Z","das_tickbox":"1","department":[{"_id":"HaJa"}],"scopus_import":"1","publication":"Angewandte Chemie International Edition","citation":{"apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., & Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201601736","ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” Angewandte Chemie International Edition, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016.","short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie International Edition 55 (2016) 6339–6342.","chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” Angewandte Chemie International Edition. Wiley, 2016. https://doi.org/10.1002/anie.201601736.","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. 55(21), 6339–6342.","ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie International Edition. 2016;55(21):6339-6342. doi:10.1002/anie.201601736","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” Angewandte Chemie International Edition, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:10.1002/anie.201601736."},"corr_author":"1","has_accepted_license":"1","related_material":{"record":[{"id":"418","relation":"dissertation_contains","status":"public"}]},"date_published":"2016-05-17T00:00:00Z","day":"17","external_id":{"isi":["000377918400039"]},"language":[{"iso":"eng"}],"publist_id":"5755","fulldoi":"https://doi.org/10.1002/anie.201601736","isi":1,"file":[{"date_updated":"2020-07-14T12:44:55Z","checksum":"26da07960e57ac4750b54179197ce57f","file_size":1268662,"creator":"system","date_created":"2018-12-12T10:17:03Z","relation":"main_file","file_id":"5255","access_level":"open_access","file_name":"IST-2017-840-v1+1_reichhart.pdf","content_type":"application/pdf"}],"status":"public","_id":"1441","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564"},{"name":"Molecular Drug Targets","call_identifier":"FWF","_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","doi":"10.1002/anie.201601736","title":"A phytochrome sensory domain permits receptor activation by red light","abstract":[{"lang":"eng","text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1."}],"file_date_updated":"2020-07-14T12:44:55Z","page":"6339 - 6342","date_updated":"2026-07-08T05:54:25Z"},{"page":"674 - 703","date_updated":"2026-07-29T10:08:33Z","file_date_updated":"2020-07-14T12:45:10Z","abstract":[{"lang":"eng","text":"We introduce a modification of the classic notion of intrinsic volume using persistence moments of height functions. Evaluating the modified first intrinsic volume on digital approximations of a compact body with smoothly embedded boundary in Rn, we prove convergence to the first intrinsic volume of the body as the resolution of the approximation improves. We have weaker results for the other modified intrinsic volumes, proving they converge to the corresponding intrinsic volumes of the n-dimensional unit ball."}],"title":"Approximation and convergence of the intrinsic volume","doi":"10.1016/j.aim.2015.10.004","publisher":"Academic Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","project":[{"call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"status":"public","_id":"1662","fulldoi":"https://doi.org/10.1016/j.aim.2015.10.004","publist_id":"5488","file":[{"creator":"system","date_created":"2018-12-12T10:12:10Z","relation":"main_file","date_updated":"2020-07-14T12:45:10Z","checksum":"f8869ec110c35c852ef6a37425374af7","file_size":248985,"content_type":"application/pdf","file_name":"IST-2017-774-v1+1_2016-J-03-FirstIntVolume.pdf","file_id":"4928","access_level":"open_access"}],"isi":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000375634100016"]},"date_published":"2016-01-10T00:00:00Z","day":"10","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1399"}]},"has_accepted_license":"1","corr_author":"1","citation":{"ista":"Edelsbrunner H, Pausinger F. 2016. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 287, 674–703.","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” Advances in Mathematics, vol. 287, Academic Press, 2016, pp. 674–703, doi:10.1016/j.aim.2015.10.004.","ama":"Edelsbrunner H, Pausinger F. Approximation and convergence of the intrinsic volume. Advances in Mathematics. 2016;287:674-703. doi:10.1016/j.aim.2015.10.004","short":"H. Edelsbrunner, F. Pausinger, Advances in Mathematics 287 (2016) 674–703.","apa":"Edelsbrunner, H., & Pausinger, F. (2016). Approximation and convergence of the intrinsic volume. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2015.10.004","ieee":"H. Edelsbrunner and F. Pausinger, “Approximation and convergence of the intrinsic volume,” Advances in Mathematics, vol. 287. Academic Press, pp. 674–703, 2016.","chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Approximation and Convergence of the Intrinsic Volume.” Advances in Mathematics. Academic Press, 2016. https://doi.org/10.1016/j.aim.2015.10.004."},"publication":"Advances in Mathematics","department":[{"_id":"HeEd"}],"scopus_import":"1","date_created":"2018-12-11T11:53:20Z","acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, and by ESF under the ACAT Research Network Programme.\r\nBoth authors thank Anne Marie Svane for her comments on an early version of this paper. The second author wishes to thank Eva B. Vedel Jensen and Markus Kiderlen from Aarhus University for enlightening discussions and their kind hospitality during a visit of their department in 2014.","quality_controlled":"1","ec_funded":1,"volume":287,"publication_status":"published","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","last_name":"Pausinger"}],"pubrep_id":"774","ddc":["004"],"article_processing_charge":"No","year":"2016","oa":1,"intvolume":" 287","oa_version":"Published Version","month":"01"},{"article_processing_charge":"No","degree_awarded":"PhD","year":"2016","oa":1,"month":"12","oa_version":"Published Version","publication_status":"published","author":[{"last_name":"Acar","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","full_name":"Acar, Hande","orcid":"0000-0003-1986-9753","first_name":"Hande"}],"ddc":["570"],"acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","supervisor":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","corr_author":"1","citation":{"apa":"Acar, H. (2016). Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","mla":"Acar, Hande. Selective Barriers to Horizontal Gene Transfer. Institute of Science and Technology Austria, 2016."},"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","department":[{"_id":"JoBo"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:16Z","doi_confirm":"1","file":[{"file_id":"6814","access_level":"closed","file_name":"PhDThesis_HandeAcar_1230.pdf","content_type":"application/pdf","date_updated":"2019-08-13T11:17:50Z","checksum":"94bbbc754c36115bf37f8fc11fad43c4","file_size":3682711,"creator":"dernst","relation":"main_file","date_created":"2019-08-13T11:17:50Z"},{"content_type":"application/pdf","file_name":"2016_Thesis_HandeAcar.pdf","access_level":"open_access","file_id":"9184","relation":"main_file","date_created":"2021-02-22T11:51:13Z","creator":"dernst","success":1,"file_size":3682711,"checksum":"94bbbc754c36115bf37f8fc11fad43c4","date_updated":"2021-02-22T11:51:13Z"}],"publist_id":"6239","language":[{"iso":"eng"}],"date_published":"2016-12-01T00:00:00Z","day":"01","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"}],"_id":"1121","status":"public","page":"75","date_updated":"2026-07-29T11:17:47Z","title":"Selective barriers to horizontal gene transfer","file_date_updated":"2021-02-22T11:51:13Z","abstract":[{"text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments.","lang":"eng"}]},{"doi":"10.15479/AT:ISTA:th_640","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"dissertation","status":"public","_id":"1122","page":"114","license":"https://creativecommons.org/licenses/by/4.0/","date_updated":"2026-07-29T11:25:14Z","file_date_updated":"2018-12-12T10:13:02Z","abstract":[{"text":"Computer graphics is an extremely exciting field for two reasons. On the one hand,\r\nthere is a healthy injection of pragmatism coming from the visual effects industry\r\nthat want robust algorithms that work so they can produce results at an increasingly\r\nfrantic pace. On the other hand, they must always try to push the envelope and\r\nachieve the impossible to wow their audiences in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism, and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance that it will pan into something\r\nuseful.\r\nWater simulation has been in visual effects for decades, however it still remains\r\nextremely challenging because of its high computational cost and difficult artdirectability.\r\nThe work in this thesis tries to address some of these difficulties.\r\nSpecifically, we make the following three novel contributions to the state-of-the-art\r\nin water simulation for visual effects.\r\nFirst, we develop the first algorithm that can convert any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art methods at the time\r\ncould only handle surfaces with fixed connectivity, but we are the first to be able to\r\nhandle surfaces that merge and split apart. This is important for water simulation\r\npractitioners, because it allows them to convert splashy water surfaces extracted\r\nfrom particles or simulated using grid-based level sets into triangle meshes that can\r\nbe either textured and enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions of human performances.\r\nSecond, we formulate a surface-based energy that measures the deviation of a\r\nwater surface froma physically valid state. Such discrepancies arise when there is a\r\nmismatch in the degrees of freedom between the water surface and the underlying\r\nphysics solver. This commonly happens when practitioners use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution grid-based surfaces\r\nare combined with low-resolution physics. Following the direction of steepest\r\ndescent on our surface-based energy, we can either smooth these artifacts or turn\r\nthem into high-resolution waves by interpreting the energy as a physical potential.\r\nThird, we extend state-of-the-art techniques in non-reflecting boundaries to handle spatially and time-varying background flows. This allows a novel new\r\nworkflow where practitioners can re-simulate part of an existing simulation, such\r\nas removing a solid obstacle, adding a new splash or locally changing the resolution.\r\nSuch changes can easily lead to new waves in the re-simulated region that would\r\nreflect off of the new simulation boundary, effectively ruining the illusion of a\r\nseamless simulation boundary between the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure that such waves are absorbed.","lang":"eng"}],"title":"Tracking, correcting and absorbing water surface waves","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"doi_confirm":"1","file":[{"creator":"system","date_created":"2018-12-12T10:13:02Z","relation":"main_file","date_updated":"2018-12-12T10:13:02Z","file_size":13869345,"file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","content_type":"application/pdf","file_id":"4982","access_level":"open_access"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:th_640","publist_id":"6238","language":[{"iso":"eng"}],"day":"15","date_published":"2016-07-15T00:00:00Z","supervisor":[{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"acknowledgement":"First and foremost I would like to thank Chris. I have been incredibly lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right thing in all walks of\r\nlife is something I admire and aspire to. I also really appreciate the fact that when\r\nworking with you it felt like we were equals. I think we had a very synergetic work\r\nrelationship: I learned immensely from you, but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working with you. You showed me how to persevere and keep morale\r\nhigh when things were looking the most bleak before the deadline. You are an\r\nincredible motivator and super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing you by asking about your guitar playing that one\r\ntime. You really are quite awesome! Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have learned so much. The excellent discussions we had in reading\r\ngroups and research meetings really helped me become a better researcher!\r\nNext, I would like to thank all the amazing people that I met during my PhD\r\nstudies, both at IST Austria, in Vienna and elsewhere. ","OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","relation":"other","id":"5558"}]},"alternative_title":["ISTA Thesis"],"has_accepted_license":"1","corr_author":"1","citation":{"ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:10.15479/AT:ISTA:th_640","mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:th_640.","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:th_640.","short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","apa":"Bojsen-Hansen, M. (2016). Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_640","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016."},"department":[{"_id":"ChWo"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:16Z","article_processing_charge":"No","degree_awarded":"PhD","year":"2016","oa":1,"oa_version":"Published Version","month":"07","publication_status":"published","author":[{"last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","first_name":"Morten","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten"}],"ddc":["004","005","006","532","621"]},{"department":[{"_id":"KrCh"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:51:47Z","title":"Algorithms for partially observable markov decision processes","abstract":[{"lang":"eng","text":"We study partially observable Markov decision processes (POMDPs) with objectives used in verification and artificial intelligence. The qualitative analysis problem given a POMDP and an objective asks whether there is a strategy (policy) to ensure that the objective is satisfied almost surely (with probability 1), resp. with positive probability (with probability greater than 0). For POMDPs with limit-average payoff, where a reward value in the interval [0,1] is associated to every transition, and the payoff of an infinite path is the long-run average of the rewards, we consider two types of path constraints: (i) a quantitative limit-average constraint defines the set of paths where the payoff is at least a given threshold L1 = 1. Our main results for qualitative limit-average constraint under almost-sure winning are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative limit-average constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We present a prototype implementation of our EXPTIME algorithm. For POMDPs with w-regular conditions specified as parity objectives, while the qualitative analysis problems are known to be undecidable even for very special case of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. Based on our theoretical algorithms we also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of well-known POMDP examples for robotics applications. For POMDPs with a set of target states and an integer cost associated with every transition, we study the optimization objective that asks to minimize the expected total cost of reaching a state in the target set, while ensuring that the target set is reached almost surely. We show that for general 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, both double and exponential in the POMDP state space size; (ii) we show that the problem of approximating the optimal cost is decidable and present approximation algorithms that extend existing algorithms for POMDPs with finite-horizon objectives. We show experimentally that it performs well in many examples of interest. We study more deeply the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a strategy to ensure that the target set is reached almost surely. While in general the problem EXPTIME-complete, in many practical cases strategies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. We first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach. Decentralized POMDPs (DEC-POMDPs) extend POMDPs to a multi-agent setting, where several agents operate in an uncertain environment independently to achieve a joint objective. In this work we consider Goal DEC-POMDPs, where given a set of target states, the objective is to ensure that the target set is reached with minimal cost. We consider the indefinite-horizon (infinite-horizon with either discounted-sum, or undiscounted-sum, where absorbing goal states have zero-cost) problem. We present a new and novel method to solve the problem that extends methods for finite-horizon DEC-POMDPs and the real-time dynamic programming approach for POMDPs. We present experimental results on several examples, and show that our approach presents promising results. In the end we present a short summary of a few other results related to verification of MDPs and POMDPs."}],"corr_author":"1","citation":{"mla":"Chmelik, Martin. Algorithms for Partially Observable Markov Decision Processes. Institute of Science and Technology Austria, 2016.","ama":"Chmelik M. Algorithms for partially observable markov decision processes. 2016.","ista":"Chmelik M. 2016. Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria.","chicago":"Chmelik, Martin. “Algorithms for Partially Observable Markov Decision Processes.” Institute of Science and Technology Austria, 2016.","short":"M. Chmelik, Algorithms for Partially Observable Markov Decision Processes, Institute of Science and Technology Austria, 2016.","apa":"Chmelik, M. (2016). Algorithms for partially observable markov decision processes. Institute of Science and Technology Austria.","ieee":"M. Chmelik, “Algorithms for partially observable markov decision processes,” Institute of Science and Technology Austria, 2016."},"alternative_title":["ISTA Thesis"],"page":"232","date_updated":"2026-07-29T11:15:18Z","type":"dissertation","_id":"1397","status":"public","publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","supervisor":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"}],"date_published":"2016-02-01T00:00:00Z","day":"01","publication_status":"published","publist_id":"5810","author":[{"first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"}],"language":[{"iso":"eng"}],"month":"02","doi_confirm":"1","oa_version":"None","article_processing_charge":"No","degree_awarded":"PhD","year":"2016"},{"oa":1,"year":"2016","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa_version":"Published Version","month":"09","author":[{"last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","first_name":"Morten","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224"}],"file":[{"file_size":55237885,"date_updated":"2020-07-14T12:47:02Z","checksum":"5b1b256ad796fbddb4b7729f5e45e444","relation":"main_file","date_created":"2018-12-12T13:02:18Z","creator":"system","access_level":"open_access","file_id":"5589","content_type":"application/x-bzip2","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:48","publist_id":"6238","pubrep_id":"640","ddc":["004"],"date_published":"2016-09-23T00:00:00Z","day":"23","doi":"10.15479/AT:ISTA:48","datarep_id":"48","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","_id":"5558","status":"public","type":"research_data","date_updated":"2026-07-29T11:25:14Z","has_accepted_license":"1","related_material":{"record":[{"id":"1122","status":"public","relation":"other"}]},"citation":{"mla":"Bojsen-Hansen, Morten. Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:48.","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:10.15479/AT:ISTA:48","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 10.15479/AT:ISTA:48.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:48.","short":"M. Bojsen-Hansen, (2016).","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:48"},"abstract":[{"text":"PhD thesis LaTeX source code","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:02Z","title":"Tracking, Correcting and Absorbing Water Surface Waves","date_created":"2018-12-12T12:31:31Z","department":[{"_id":"ChWo"}]},{"file_date_updated":"2021-02-22T11:43:14Z","abstract":[{"lang":"eng","text":"Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms. Despite its importance, basic questions regarding force transduction\r\nor directional sensing are still heavily investigated. Directed migration of cells\r\nguided by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009), or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic migration by inducing adhesion to adhesive ligands and directional\r\nguidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the cellular response to immobilized guidance cues requires in vitro assays\r\nthat foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration of haptotactic cell migration through design and employment of such\r\nassays represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes, which after encountering danger\r\nsignals such as pathogens in peripheral organs instruct naïve T-cells and\r\nconsequently the adaptive immune response in the lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery, DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients have not yet been addressed. The main reason for this is the lack of\r\nan assay that offers diverse haptotactic environments, hence allowing the study\r\nof DC migration as a response to different signals of immobilized guidance cue.\r\nIn this work, we developed an in vitro assay that enables us to\r\nquantitatively assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis. We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration in combination with the local\r\nsteepness of the gradient. Our analysis suggests that the directionality of\r\nmigrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization (Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic guidance cues\r\noften coincide and compete with soluble chemotactic guidance cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess these complex coinciding immobilized and soluble\r\nguidance cues, we implemented our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing for chemotactic gradient generation. To validate\r\nthe assay, we observed DC migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis has been studied intensively over the\r\nlast century. However, quantitative studies leading to conceptual models are\r\nlargely missing, again due to the lack of a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished by stable passivation of the surface. In\r\naddition, controlled adhesion must be sustainable, quantifiable and dose\r\ndependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol (PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to direct cell migration. This\r\napproach allowed us to characterize the haptotactic migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue\r\nallowed us to control for cell shape and growth on a subcellular scale."}],"title":"Quantitative analysis of haptotactic cell migration","page":"178","date_updated":"2026-07-29T11:30:22Z","type":"dissertation","_id":"1129","status":"public","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2016-07-01T00:00:00Z","day":"01","publist_id":"6231","file":[{"relation":"main_file","date_created":"2019-08-13T10:55:35Z","creator":"dernst","file_size":32044069,"date_updated":"2019-08-13T10:55:35Z","checksum":"e3cd6b28f9c5cccb8891855565a2dade","content_type":"application/pdf","file_name":"Thesis_JSchwarz_final.pdf","access_level":"closed","file_id":"6813"},{"access_level":"open_access","file_id":"9181","content_type":"application/pdf","file_name":"2016_Thesis_JSchwarz.pdf","file_size":8396717,"checksum":"c3dbe219acf87eed2f46d21d5cca00de","date_updated":"2021-02-22T11:43:14Z","date_created":"2021-02-22T11:43:14Z","relation":"main_file","creator":"dernst","success":1}],"language":[{"iso":"eng"}],"doi_confirm":"1","department":[{"_id":"MiSi"},{"_id":"GradSch"}],"date_created":"2018-12-11T11:50:18Z","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"corr_author":"1","citation":{"chicago":"Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute of Science and Technology Austria, 2016.","apa":"Schwarz, J. (2016). Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria.","ieee":"J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute of Science and Technology Austria, 2016.","short":"J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute of Science and Technology Austria, 2016.","ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 2016.","mla":"Schwarz, Jan. Quantitative Analysis of Haptotactic Cell Migration. Institute of Science and Technology Austria, 2016.","ista":"Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria."},"OA_place":"publisher","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"}],"acknowledgement":"First, I would like to thank Michael Sixt for being a great supervisor, mentor and\r\nscientist. I highly appreciate his guidance and continued support. Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice and encouragement during our regular progress meetings.\r\nI also want to thank the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries, Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf, Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz, Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing time with many\r\nlegendary evenings and events. Along these lines I want to thank the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions. I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches. In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens, Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny, Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful after-lunch matches.\r\nI would not have been able to analyze the thousands of cell trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings, discussions and graphs and of course for proofreading and\r\nadvice for this thesis. For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS coated coverslips and help with anything\r\nmicro-fabrication related. And Maria Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva, Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for excellent technical support. At this\r\npoint I especially want to thank Robert for countless image analyses and\r\ntechnical ideas. Always interested and creative he played an essential role in all\r\nof my projects.\r\nAdditionally I want to thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for scientific and especially mental support in all\r\nthose years, countless coffee sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility","ddc":["570"],"publication_status":"published","author":[{"last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Schwarz, Jan"}],"oa_version":"Published Version","month":"07","article_processing_charge":"No","degree_awarded":"PhD","oa":1,"year":"2016"},{"acknowledgement":"Foremost, I would like to thank Uli Wagner for introducing me to the exciting interface between\r\ntopology and combinatorics, and for our subsequent years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner and Roman Karasev\r\nfor their careful reading of the present manuscript and for the many improvements they suggested.","supervisor":[{"full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner"}],"publication_identifier":{"issn":["2663-337X"]},"OA_place":"publisher","citation":{"ista":"Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","mla":"Mabillard, Isaac. Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture. Institute of Science and Technology Austria, 2016.","ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 2016.","ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” Institute of Science and Technology Austria, 2016.","apa":"Mabillard, I. (2016). Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016.","chicago":"Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and Technology Austria, 2016."},"corr_author":"1","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2159"}]},"date_created":"2018-12-11T11:50:16Z","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"oa":1,"year":"2016","degree_awarded":"PhD","article_processing_charge":"No","month":"08","oa_version":"Published Version","author":[{"first_name":"Isaac","full_name":"Mabillard, Isaac","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","last_name":"Mabillard"}],"publication_status":"published","ddc":["500"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","status":"public","_id":"1123","type":"dissertation","page":"55","date_updated":"2026-07-29T11:26:07Z","title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","abstract":[{"text":"Motivated by topological Tverberg-type problems in topological combinatorics and by classical\r\nresults about embeddings (maps without double points), we study the question whether a finite\r\nsimplicial complex K can be mapped into Rd without triple, quadruple, or, more generally, r-fold points (image points with at least r distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK = (r ≥ 1)k and d = rk \\ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN to Rd without r-Tverberg points when r not a prime power and\r\nN = (d + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K = σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension 3 obstacle" and\r\nto construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r + 1 and r not a prime power, by a reduction1 to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r not a prime power. ","lang":"eng"}],"file_date_updated":"2021-02-22T11:36:34Z","doi_confirm":"1","language":[{"iso":"eng"}],"publist_id":"6237","file":[{"creator":"dernst","relation":"main_file","date_created":"2019-08-13T08:45:27Z","checksum":"2d140cc924cd1b764544906fc22684ef","date_updated":"2019-08-13T08:45:27Z","file_size":2227916,"content_type":"application/pdf","file_name":"Thesis_final version_Mabillard_w_signature_page.pdf","file_id":"6809","access_level":"closed"},{"date_created":"2021-02-22T11:36:34Z","relation":"main_file","success":1,"creator":"dernst","file_size":2227916,"checksum":"2d140cc924cd1b764544906fc22684ef","date_updated":"2021-02-22T11:36:34Z","file_name":"2016_Mabillard_Thesis.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"9178"}],"date_published":"2016-08-01T00:00:00Z","day":"01"},{"day":"01","date_published":"2016-11-01T00:00:00Z","language":[{"iso":"eng"}],"file":[{"file_id":"5056","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-776-v1+1_Pentina_Thesis_2016.pdf","date_updated":"2018-12-12T10:14:07Z","file_size":2140062,"creator":"system","relation":"main_file","date_created":"2018-12-12T10:14:07Z"}],"fulldoi":"https://doi.org/10.15479/AT:ISTA:TH_776","publist_id":"6234","doi_confirm":"1","abstract":[{"lang":"eng","text":"Traditionally machine learning has been focusing on the problem of solving a single\r\ntask in isolation. While being quite well understood, this approach disregards an\r\nimportant aspect of human learning: when facing a new problem, humans are able to\r\nexploit knowledge acquired from previously learned tasks. Intuitively, access to several\r\nproblems simultaneously or sequentially could also be advantageous for a machine\r\nlearning system, especially if these tasks are closely related. Indeed, results of many\r\nempirical studies have provided justification for this intuition. However, theoretical\r\njustifications of this idea are rather limited.\r\nThe focus of this thesis is to expand the understanding of potential benefits of information\r\ntransfer between several related learning problems. We provide theoretical\r\nanalysis for three scenarios of multi-task learning - multiple kernel learning, sequential\r\nlearning and active task selection. We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate how the task generation process influences the generalization\r\nguarantees in this scenario. In addition, we show how some of the obtained\r\ntheoretical results can be used to derive principled multi-task and lifelong learning\r\nalgorithms and illustrate their performance on various synthetic and real-world datasets."}],"file_date_updated":"2018-12-12T10:14:07Z","title":"Theoretical foundations of multi-task lifelong learning","date_updated":"2026-07-29T11:28:23Z","page":"127","status":"public","_id":"1126","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}],"type":"dissertation","doi":"10.15479/AT:ISTA:TH_776","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","pubrep_id":"776","ddc":["006"],"author":[{"last_name":"Pentina","full_name":"Pentina, Anastasia","first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","oa_version":"Published Version","month":"11","oa":1,"year":"2016","degree_awarded":"PhD","article_processing_charge":"No","date_created":"2018-12-11T11:50:17Z","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"citation":{"ama":"Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:10.15479/AT:ISTA:TH_776","mla":"Pentina, Anastasia. Theoretical Foundations of Multi-Task Lifelong Learning. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_776.","ista":"Pentina A. 2016. Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria.","chicago":"Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_776.","ieee":"A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute of Science and Technology Austria, 2016.","apa":"Pentina, A. (2016). Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_776","short":"A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute of Science and Technology Austria, 2016."},"corr_author":"1","OA_place":"publisher","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"acknowledgement":"First and foremost I would like to express my gratitude to my supervisor, Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of doing research\r\n(including English grammar), for your trust in my capabilities and endless support. Thank\r\nyou for granting me freedom in my research and, at the same time, having time and\r\nhelping me cope with the consequences whenever I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it was a great pleasure and honor to be a part of\r\nit. There could not have been a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming me into his group at the University of Waterloo,\r\nfor inspiring discussions and support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful collaboration and for taking care of me during that not-so-sunny month of May.\r\nI thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding me with insightful comments.\r\nI would like to thank my colleagues for their support, entertaining conversations and\r\nendless table soccer games we shared together: Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas, Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo. Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible without funding from the European\r\nResearch Council under the European Union's Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036."}]