[{"month":"05","issue":"May-June","citation":{"ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. 2015;68/Part 2(May-June):285-296. doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>","apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>.","chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>.","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296."},"author":[{"id":"46870C74-F248-11E8-B48F-1D18A9856A87","last_name":"Noren","first_name":"Patrik","full_name":"Noren, Patrik"}],"corr_author":"1","year":"2015","publication_status":"published","oa_version":"Preprint","date_published":"2015-05-01T00:00:00Z","title":"The three-state toric homogeneous Markov chain model has Markov degree two","_id":"1997","quality_controlled":"1","publist_id":"5082","department":[{"_id":"CaUh"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.0077"}],"oa":1,"doi":"10.1016/j.jsc.2014.09.014","external_id":{"arxiv":["1207.0077"],"isi":["000347767600016"]},"volume":"68/Part 2","scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials."}],"type":"journal_article","day":"01","arxiv":1,"date_updated":"2025-09-23T14:17:34Z","status":"public","date_created":"2018-12-11T11:55:07Z","page":"285 - 296","isi":1,"publisher":"Elsevier","publication":"Journal of Symbolic Computation"},{"publication":"Experimental Mathematics","publisher":"Taylor & Francis","isi":1,"page":"261 - 269","date_created":"2018-12-11T11:55:10Z","status":"public","arxiv":1,"date_updated":"2025-09-23T14:07:49Z","day":"23","type":"journal_article","abstract":[{"text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. ","lang":"eng"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","volume":24,"external_id":{"isi":["000356873900001"],"arxiv":["1109.3436"]},"doi":"10.1080/10586458.2014.980044","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.3436"}],"department":[{"_id":"CaUh"}],"publist_id":"5070","intvolume":"        24","quality_controlled":"1","_id":"2006","title":"The monotone secant conjecture in the real Schubert calculus","date_published":"2015-06-23T00:00:00Z","oa_version":"Preprint","publication_status":"published","year":"2015","author":[{"full_name":"Hein, Nicolas","first_name":"Nicolas","last_name":"Hein"},{"full_name":"Hillar, Christopher","last_name":"Hillar","first_name":"Christopher"},{"first_name":"Abraham","last_name":"Martin Del Campo Sanchez","full_name":"Martin Del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sottile, Frank","first_name":"Frank","last_name":"Sottile"},{"full_name":"Teitler, Zach","first_name":"Zach","last_name":"Teitler"}],"issue":"3","citation":{"ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. 2015;24(3):261-269. doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>, vol. 24, no. 3, Taylor &#38; Francis, 2015, pp. 261–69, doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., &#38; Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>","ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” <i>Experimental Mathematics</i>, vol. 24, no. 3. Taylor &#38; Francis, pp. 261–269, 2015.","ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>. Taylor &#38; Francis, 2015. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>."},"month":"06"},{"volume":42,"doi":"10.1111/sjos.12139","external_id":{"isi":["000360077100012"],"arxiv":["1307.3282"]},"article_processing_charge":"No","abstract":[{"lang":"eng","text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","status":"public","date_created":"2018-12-11T11:55:11Z","date_updated":"2025-09-23T09:25:01Z","arxiv":1,"type":"journal_article","day":"01","publisher":"Wiley","publication":"Scandinavian Journal of Statistics","isi":1,"acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","page":"832 - 847","author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","full_name":"Klimova, Anna","first_name":"Anna","last_name":"Klimova"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"month":"09","citation":{"chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","apa":"Klimova, A., &#38; Rudas, T. (2015). Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. Wiley. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>","mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>.","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. 2015;42(3):832-847. doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>"},"issue":"3","date_published":"2015-09-01T00:00:00Z","year":"2015","oa_version":"Preprint","publication_status":"published","intvolume":"        42","quality_controlled":"1","title":"Iterative scaling in curved exponential families","_id":"2008","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3282"}],"publist_id":"5068","department":[{"_id":"CaUh"}]},{"corr_author":"1","date_published":"2015-07-01T00:00:00Z","publication_status":"published","oa_version":"Preprint","year":"2015","issue":"7","citation":{"ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics &#38; Data Analysis. 87(7), 57–72.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics &#38; Data Analysis 87 (2015) 57–72.","chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. 2015;87(7):57-72. doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>.","ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","apa":"Klimova, A., Uhler, C., &#38; Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>"},"month":"07","author":[{"full_name":"Klimova, Anna","last_name":"Klimova","first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","first_name":"Caroline","full_name":"Uhler, Caroline"},{"full_name":"Rudas, Tamás","last_name":"Rudas","first_name":"Tamás"}],"main_file_link":[{"url":"http://arxiv.org/abs/1404.6617","open_access":"1"}],"department":[{"_id":"CaUh"}],"publist_id":"5062","oa":1,"_id":"2014","title":"Faithfulness and learning hypergraphs from discrete distributions","intvolume":"        87","quality_controlled":"1","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000352661000005"],"arxiv":["1404.6617"]},"doi":"10.1016/j.csda.2015.01.017","volume":87,"page":"57 - 72","publication":"Computational Statistics & Data Analysis","publisher":"Elsevier","isi":1,"date_updated":"2025-09-23T08:45:54Z","arxiv":1,"day":"01","type":"journal_article","date_created":"2018-12-11T11:55:13Z","status":"public"},{"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins."}],"doi":"10.1016/j.bbamcr.2014.10.009","external_id":{"isi":["000347598100014"]},"pubrep_id":"615","volume":1853,"page":"144 - 156","file_date_updated":"2020-07-14T12:45:25Z","isi":1,"publisher":"Elsevier","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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","short":"CC BY-NC-ND (4.0)"},"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","type":"journal_article","day":"01","date_updated":"2025-09-23T14:51:55Z","date_created":"2018-12-11T11:55:17Z","status":"public","year":"2015","oa_version":"Submitted Version","publication_status":"published","date_published":"2015-01-01T00:00:00Z","month":"01","citation":{"mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>","ieee":"D. Kawada <i>et al.</i>, “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. 2015;1853(1):144-156. doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>."},"issue":"1","author":[{"full_name":"Kawada, Daiki","first_name":"Daiki","last_name":"Kawada"},{"full_name":"Kobayashi, Hiromu","first_name":"Hiromu","last_name":"Kobayashi"},{"first_name":"Tsuyoshi","last_name":"Tomita","full_name":"Tomita, Tsuyoshi"},{"first_name":"Eisuke","last_name":"Nakata","full_name":"Nakata, Eisuke"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353"},{"last_name":"Toshima","first_name":"Junko","full_name":"Toshima, Junko"},{"first_name":"Jiro","last_name":"Toshimaa","full_name":"Toshimaa, Jiro"}],"publist_id":"5047","department":[{"_id":"DaSi"}],"has_accepted_license":"1","ddc":["570"],"oa":1,"file":[{"content_type":"application/pdf","relation":"main_file","file_name":"IST-2016-615-v1+1_BBAMCR.pdf","checksum":"5bb328edebb6a91337cadd7d63f961b7","creator":"system","file_id":"4936","date_created":"2018-12-12T10:12:18Z","file_size":926685,"access_level":"open_access","date_updated":"2020-07-14T12:45:25Z"}],"title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","_id":"2025","quality_controlled":"1","intvolume":"      1853"},{"_id":"2030","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","intvolume":"       106","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1311.2481","open_access":"1"}],"department":[{"_id":"BjHo"}],"publist_id":"5042","oa":1,"citation":{"mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>.","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” <i>Computers and Fluids</i>, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","apa":"Shi, L., Rampp, M., Hof, B., &#38; Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. 2015;106(1):1-11. doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>","ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11."},"issue":"1","month":"01","author":[{"last_name":"Shi","first_name":"Liang","full_name":"Shi, Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markus","last_name":"Rampp","full_name":"Rampp, Markus"},{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"}],"date_published":"2015-01-01T00:00:00Z","publication_status":"published","oa_version":"Preprint","year":"2015","date_updated":"2025-09-22T14:31:33Z","arxiv":1,"day":"01","type":"journal_article","date_created":"2018-12-11T11:55:18Z","status":"public","page":"1 - 11","publication":"Computers and Fluids","publisher":"Elsevier","isi":1,"external_id":{"arxiv":["1311.2481"],"isi":["000346213200001"]},"doi":"10.1016/j.compfluid.2014.09.021","volume":106,"language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"doi":"10.1016/j.ipl.2014.09.001","external_id":{"isi":["000345478700010"],"arxiv":["1407.4225"]},"volume":115,"language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","abstract":[{"text":"Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers.","lang":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T09:54:42Z","arxiv":1,"type":"journal_article","day":"01","status":"public","date_created":"2018-12-11T11:55:20Z","page":"52 - 59","publisher":"Elsevier","ec_funded":1,"publication":" Information Processing Letters","isi":1,"month":"01","issue":"1","citation":{"apa":"Bérard, B., Chatterjee, K., &#38; Sznajder, N. (2015). Probabilistic opacity for Markov decision processes. <i> Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>","ieee":"B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov decision processes,” <i> Information Processing Letters</i>, vol. 115, no. 1. Elsevier, pp. 52–59, 2015.","mla":"Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.” <i> Information Processing Letters</i>, vol. 115, no. 1, Elsevier, 2015, pp. 52–59, doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>.","ama":"Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision processes. <i> Information Processing Letters</i>. 2015;115(1):52-59. doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>","chicago":"Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic Opacity for Markov Decision Processes.” <i> Information Processing Letters</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>.","short":"B. Bérard, K. Chatterjee, N. Sznajder,  Information Processing Letters 115 (2015) 52–59.","ista":"Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes.  Information Processing Letters. 115(1), 52–59."},"author":[{"full_name":"Bérard, Béatrice","first_name":"Béatrice","last_name":"Bérard"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Sznajder","first_name":"Nathalie","full_name":"Sznajder, Nathalie"}],"date_published":"2015-01-01T00:00:00Z","year":"2015","oa_version":"Preprint","publication_status":"published","title":"Probabilistic opacity for Markov decision processes","_id":"2034","intvolume":"       115","quality_controlled":"1","main_file_link":[{"url":"http://arxiv.org/abs/1407.4225","open_access":"1"}],"publist_id":"5025","department":[{"_id":"KrCh"}],"oa":1},{"acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","page":"1213 - 1244","ec_funded":1,"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Springer","publication":"Foundations of Computational Mathematics","file_date_updated":"2020-07-14T12:45:26Z","isi":1,"date_updated":"2025-09-23T14:08:54Z","type":"journal_article","day":"01","date_created":"2018-12-11T11:55:20Z","status":"public","language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility.\r\n"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"486","project":[{"grant_number":"318493","name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s10208-014-9223-y","external_id":{"isi":["000360862900004"]},"volume":15,"publist_id":"5022","department":[{"_id":"HeEd"}],"oa":1,"has_accepted_license":"1","ddc":["000"],"title":"The persistent homology of a self-map","_id":"2035","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"3566f3a8b0c1bc550e62914a88c584ff","file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","date_created":"2018-12-12T10:08:10Z","file_size":1317546,"file_id":"4670","creator":"system","date_updated":"2020-07-14T12:45:26Z","access_level":"open_access"}],"intvolume":"        15","quality_controlled":"1","date_published":"2015-10-01T00:00:00Z","year":"2015","license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","oa_version":"Published Version","month":"10","citation":{"ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. 2015;15(5):1213-1244. doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>","mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>.","ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","apa":"Edelsbrunner, H., Jablonski, G., &#38; Mrozek, M. (2015). The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>","ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244.","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>."},"issue":"5","author":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert"},{"first_name":"Grzegorz","last_name":"Jablonski","full_name":"Jablonski, Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866"},{"full_name":"Mrozek, Marian","first_name":"Marian","last_name":"Mrozek"}]},{"citation":{"mla":"Boccara, Charlotte N., et al. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” <i>Hippocampus</i>, vol. 25, no. 7, Wiley, 2015, pp. 838–57, doi:<a href=\"https://doi.org/10.1002/hipo.22407\">10.1002/hipo.22407</a>.","ieee":"C. N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, and M. Witter, “A three-plane architectonic atlas of the rat hippocampal region,” <i>Hippocampus</i>, vol. 25, no. 7. Wiley, pp. 838–857, 2015.","apa":"Boccara, C. N., Kjønigsen, L., Hammer, I., Bjaalie, J., Leergaard, T., &#38; Witter, M. (2015). A three-plane architectonic atlas of the rat hippocampal region. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.22407\">https://doi.org/10.1002/hipo.22407</a>","ama":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. A three-plane architectonic atlas of the rat hippocampal region. <i>Hippocampus</i>. 2015;25(7):838-857. doi:<a href=\"https://doi.org/10.1002/hipo.22407\">10.1002/hipo.22407</a>","ista":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. 2015. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 25(7), 838–857.","short":"C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857.","chicago":"Boccara, Charlotte N., Lisa Kjønigsen, Ingvild Hammer, Jan Bjaalie, Trygve Leergaard, and Menno Witter. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” <i>Hippocampus</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/hipo.22407\">https://doi.org/10.1002/hipo.22407</a>."},"issue":"7","month":"07","author":[{"full_name":"Boccara, Charlotte","first_name":"Charlotte","last_name":"Boccara","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7237-5109"},{"full_name":"Kjønigsen, Lisa","last_name":"Kjønigsen","first_name":"Lisa"},{"full_name":"Hammer, Ingvild","last_name":"Hammer","first_name":"Ingvild"},{"first_name":"Jan","last_name":"Bjaalie","full_name":"Bjaalie, Jan"},{"first_name":"Trygve","last_name":"Leergaard","full_name":"Leergaard, Trygve"},{"last_name":"Witter","first_name":"Menno","full_name":"Witter, Menno"}],"date_published":"2015-07-01T00:00:00Z","oa_version":"None","publication_status":"published","year":"2015","_id":"1874","title":"A three-plane architectonic atlas of the rat hippocampal region","intvolume":"        25","quality_controlled":"1","department":[{"_id":"JoCs"}],"publist_id":"5222","external_id":{"isi":["000356812700007"]},"doi":"10.1002/hipo.22407","volume":25,"language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"lang":"eng","text":"The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource."}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-23T07:29:29Z","day":"01","type":"journal_article","status":"public","date_created":"2018-12-11T11:54:29Z","page":"838 - 857","publication":"Hippocampus","publisher":"Wiley","isi":1},{"date_published":"2015-01-24T00:00:00Z","oa_version":"None","publication_status":"published","year":"2015","corr_author":"1","author":[{"full_name":"Cires Rodriguez, Eduardo","last_name":"Cires Rodriguez","first_name":"Eduardo","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Prieto","first_name":"José","full_name":"Prieto, José"}],"citation":{"short":"E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.","chicago":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” <i>Journal of Plant Research</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10265-014-0691-6\">https://doi.org/10.1007/s10265-014-0691-6</a>.","ista":"Cires Rodriguez E, Prieto J. 2015. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. Journal of Plant Research. 128(2), 223–238.","ama":"Cires Rodriguez E, Prieto J. Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. <i>Journal of Plant Research</i>. 2015;128(2):223-238. doi:<a href=\"https://doi.org/10.1007/s10265-014-0691-6\">10.1007/s10265-014-0691-6</a>","ieee":"E. Cires Rodriguez and J. Prieto, “Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula,” <i>Journal of Plant Research</i>, vol. 128, no. 2. Springer, pp. 223–238, 2015.","apa":"Cires Rodriguez, E., &#38; Prieto, J. (2015). Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula. <i>Journal of Plant Research</i>. Springer. <a href=\"https://doi.org/10.1007/s10265-014-0691-6\">https://doi.org/10.1007/s10265-014-0691-6</a>","mla":"Cires Rodriguez, Eduardo, and José Prieto. “Phylogenetic Relationships of Petrocoptis A. Braun Ex Endl. (Caryophyllaceae), a Discussed Genus from the Iberian Peninsula.” <i>Journal of Plant Research</i>, vol. 128, no. 2, Springer, 2015, pp. 223–38, doi:<a href=\"https://doi.org/10.1007/s10265-014-0691-6\">10.1007/s10265-014-0691-6</a>."},"issue":"2","month":"01","department":[{"_id":"JiFr"}],"publist_id":"5217","intvolume":"       128","quality_controlled":"1","_id":"1878","title":"Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula","abstract":[{"lang":"eng","text":"Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD, for rps16 intron)."}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"scopus_import":"1","volume":128,"external_id":{"isi":["000350826000001"]},"doi":"10.1007/s10265-014-0691-6","publication":"Journal of Plant Research","publisher":"Springer","isi":1,"page":"223 - 238","status":"public","date_created":"2018-12-11T11:54:30Z","date_updated":"2025-09-23T09:49:04Z","day":"24","type":"journal_article"},{"volume":259,"doi":"10.1111/jmi.12211","external_id":{"isi":["000358300600002"]},"pubrep_id":"459","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"text":"When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:54:30Z","status":"public","type":"journal_article","day":"01","date_updated":"2025-09-23T08:26:17Z","isi":1,"file_date_updated":"2020-07-14T12:45:19Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Wiley-Blackwell","publication":"Journal of Microscopy","page":"80 - 96","acknowledgement":"The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds Wetenschappelijk Onderzoek) of Flanders.","author":[{"full_name":"Kremer, A","last_name":"Kremer","first_name":"A"},{"last_name":"Lippens","first_name":"Stefaan","full_name":"Lippens, Stefaan"},{"last_name":"Bartunkova","first_name":"Sonia","full_name":"Bartunkova, Sonia"},{"first_name":"Bob","last_name":"Asselbergh","full_name":"Asselbergh, Bob"},{"full_name":"Blanpain, Cendric","first_name":"Cendric","last_name":"Blanpain"},{"full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"full_name":"Goossens, A","last_name":"Goossens","first_name":"A"},{"last_name":"Holt","first_name":"Matthew","full_name":"Holt, Matthew"},{"first_name":"Sophie","last_name":"Janssens","full_name":"Janssens, Sophie"},{"full_name":"Krols, Michiel","last_name":"Krols","first_name":"Michiel"},{"first_name":"Jean","last_name":"Larsimont","full_name":"Larsimont, Jean"},{"first_name":"Conor","last_name":"Mc Guire","full_name":"Mc Guire, Conor"},{"last_name":"Nowack","first_name":"Moritz","full_name":"Nowack, Moritz"},{"full_name":"Saelens, Xavier","first_name":"Xavier","last_name":"Saelens"},{"first_name":"Andreas","last_name":"Schertel","full_name":"Schertel, Andreas"},{"last_name":"Schepens","first_name":"B","full_name":"Schepens, B"},{"full_name":"Slezak, M","first_name":"M","last_name":"Slezak"},{"full_name":"Timmerman, Vincent","last_name":"Timmerman","first_name":"Vincent"},{"full_name":"Theunis, Clara","first_name":"Clara","last_name":"Theunis"},{"full_name":"Van Brempt, Ronald","last_name":"Van Brempt","first_name":"Ronald"},{"last_name":"Visser","first_name":"Y","full_name":"Visser, Y"},{"full_name":"Guérin, Christophe","first_name":"Christophe","last_name":"Guérin"}],"month":"08","issue":"2","citation":{"ista":"Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of Microscopy. 259(2), 80–96.","chicago":"Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain, Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.” <i>Journal of Microscopy</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1111/jmi.12211\">https://doi.org/10.1111/jmi.12211</a>.","short":"A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych, A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack, X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R. Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96.","ama":"Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological context. <i>Journal of Microscopy</i>. 2015;259(2):80-96. doi:<a href=\"https://doi.org/10.1111/jmi.12211\">10.1111/jmi.12211</a>","mla":"Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” <i>Journal of Microscopy</i>, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:<a href=\"https://doi.org/10.1111/jmi.12211\">10.1111/jmi.12211</a>.","apa":"Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych, M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. <i>Journal of Microscopy</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/jmi.12211\">https://doi.org/10.1111/jmi.12211</a>","ieee":"A. Kremer <i>et al.</i>, “Developing 3D SEM in a broad biological context,” <i>Journal of Microscopy</i>, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015."},"year":"2015","publication_status":"published","oa_version":"Published Version","date_published":"2015-08-01T00:00:00Z","quality_controlled":"1","intvolume":"       259","file":[{"file_name":"IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf","checksum":"3649c5372d1644062d728ea9287e367f","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:19Z","access_level":"open_access","file_id":"4872","date_created":"2018-12-12T10:11:19Z","file_size":2899898,"creator":"system"}],"title":"Developing 3D SEM in a broad biological context","_id":"1879","has_accepted_license":"1","ddc":["570"],"oa":1,"publist_id":"5218","department":[{"_id":"JiFr"}]},{"external_id":{"isi":["000348759300007"]},"doi":"10.1088/1367-2630/17/1/013022","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"pubrep_id":"447","volume":17,"scopus_import":"1","article_number":"013022","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder"}],"article_processing_charge":"No","day":"15","type":"journal_article","date_updated":"2025-09-23T10:51:00Z","status":"public","date_created":"2018-12-11T11:54:30Z","acknowledgement":"Support from the Natural Sciences and Engineering Research Council of Canada NSERC (MK and RS) and from the Austrian Science Fund FWF (JY, under project P 22929-N16) is gratefully acknowledged","isi":1,"file_date_updated":"2020-07-14T12:45:20Z","publication":"New Journal of Physics","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"IOP Publishing","citation":{"chicago":"Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” <i>New Journal of Physics</i>. IOP Publishing, 2015. <a href=\"https://doi.org/10.1088/1367-2630/17/1/013022\">https://doi.org/10.1088/1367-2630/17/1/013022</a>.","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics 17 (2015).","ista":"Könenberg M, Moser T, Seiringer R, Yngvason J. 2015. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 17, 013022.","apa":"Könenberg, M., Moser, T., Seiringer, R., &#38; Yngvason, J. (2015). Superfluid behavior of a Bose-Einstein condensate in a random potential. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/17/1/013022\">https://doi.org/10.1088/1367-2630/17/1/013022</a>","ieee":"M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluid behavior of a Bose-Einstein condensate in a random potential,” <i>New Journal of Physics</i>, vol. 17. IOP Publishing, 2015.","mla":"Könenberg, Martin, et al. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” <i>New Journal of Physics</i>, vol. 17, 013022, IOP Publishing, 2015, doi:<a href=\"https://doi.org/10.1088/1367-2630/17/1/013022\">10.1088/1367-2630/17/1/013022</a>.","ama":"Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluid behavior of a Bose-Einstein condensate in a random potential. <i>New Journal of Physics</i>. 2015;17. doi:<a href=\"https://doi.org/10.1088/1367-2630/17/1/013022\">10.1088/1367-2630/17/1/013022</a>"},"month":"01","author":[{"full_name":"Könenberg, Martin","last_name":"Könenberg","first_name":"Martin"},{"full_name":"Moser, Thomas","last_name":"Moser","first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"}],"publication_status":"published","oa_version":"Published Version","year":"2015","date_published":"2015-01-15T00:00:00Z","file":[{"file_name":"IST-2016-447-v1+1_document_1_.pdf","checksum":"38fdf2b5ac30445e26a5d613abd84b16","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:20Z","access_level":"open_access","file_id":"4963","date_created":"2018-12-12T10:12:44Z","file_size":768108,"creator":"system"}],"_id":"1880","title":"Superfluid behavior of a Bose-Einstein condensate in a random potential","quality_controlled":"1","intvolume":"        17","department":[{"_id":"RoSe"}],"publist_id":"5214","ddc":["530"],"has_accepted_license":"1","oa":1},{"date_created":"2018-12-11T11:54:31Z","status":"public","type":"conference","day":"30","arxiv":1,"date_updated":"2025-06-11T07:22:00Z","ec_funded":1,"publisher":"Springer","page":"306 - 324","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) project S11402-N23 (RiSE), and by the Czech Science Foundation, grant No. P202/12/G061.","volume":8997,"doi":"10.1007/978-3-319-15317-9_19","external_id":{"arxiv":["1408.1256"]},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations."}],"scopus_import":"1","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"quality_controlled":"1","intvolume":"      8997","title":"Compositionality for quantitative specifications","_id":"1882","oa":1,"publist_id":"5216","conference":{"location":"Bertinoro, Italy","start_date":"2014-09-10","end_date":"2014-09-12","name":"FACS: Formal Aspects of Component Software"},"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.1256"}],"author":[{"full_name":"Fahrenberg, Uli","first_name":"Uli","last_name":"Fahrenberg"},{"id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","first_name":"Jan","last_name":"Kretinsky","full_name":"Kretinsky, Jan"},{"last_name":"Legay","first_name":"Axel","full_name":"Legay, Axel"},{"full_name":"Traonouez, Louis","last_name":"Traonouez","first_name":"Louis"}],"month":"01","citation":{"ama":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. Compositionality for quantitative specifications. In: Vol 8997. Springer; 2015:306-324. doi:<a href=\"https://doi.org/10.1007/978-3-319-15317-9_19\">10.1007/978-3-319-15317-9_19</a>","mla":"Fahrenberg, Uli, et al. <i>Compositionality for Quantitative Specifications</i>. Vol. 8997, Springer, 2015, pp. 306–24, doi:<a href=\"https://doi.org/10.1007/978-3-319-15317-9_19\">10.1007/978-3-319-15317-9_19</a>.","ieee":"U. Fahrenberg, J. Kretinsky, A. Legay, and L. Traonouez, “Compositionality for quantitative specifications,” presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy, 2015, vol. 8997, pp. 306–324.","apa":"Fahrenberg, U., Kretinsky, J., Legay, A., &#38; Traonouez, L. (2015). Compositionality for quantitative specifications (Vol. 8997, pp. 306–324). Presented at the FACS: Formal Aspects of Component Software, Bertinoro, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-319-15317-9_19\">https://doi.org/10.1007/978-3-319-15317-9_19</a>","ista":"Fahrenberg U, Kretinsky J, Legay A, Traonouez L. 2015. Compositionality for quantitative specifications. FACS: Formal Aspects of Component Software, LNCS, vol. 8997, 306–324.","short":"U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015, pp. 306–324.","chicago":"Fahrenberg, Uli, Jan Kretinsky, Axel Legay, and Louis Traonouez. “Compositionality for Quantitative Specifications,” 8997:306–24. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-15317-9_19\">https://doi.org/10.1007/978-3-319-15317-9_19</a>."},"year":"2015","oa_version":"Preprint","publication_status":"published","date_published":"2015-01-30T00:00:00Z","corr_author":"1"},{"author":[{"full_name":"Keller-Schmidt, Stephanie","last_name":"Keller-Schmidt","first_name":"Stephanie"},{"last_name":"Tugrul","first_name":"Murat","full_name":"Tugrul, Murat","orcid":"0000-0002-8523-0758","id":"37C323C6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Eguíluz","first_name":"Víctor","full_name":"Eguíluz, Víctor"},{"first_name":"Emilio","last_name":"Hernandez Garcia","full_name":"Hernandez Garcia, Emilio"},{"last_name":"Klemm","first_name":"Konstantin","full_name":"Klemm, Konstantin"}],"issue":"2","citation":{"ista":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. 2015. Anomalous scaling in an age-dependent branching model. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(2), 022803.","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","chicago":"Keller-Schmidt, Stephanie, Murat Tugrul, Víctor Eguíluz, Emilio Hernandez Garcia, and Konstantin Klemm. “Anomalous Scaling in an Age-Dependent Branching Model.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">https://doi.org/10.1103/PhysRevE.91.022803</a>.","ama":"Keller-Schmidt S, Tugrul M, Eguíluz V, Hernandez Garcia E, Klemm K. Anomalous scaling in an age-dependent branching model. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2015;91(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">10.1103/PhysRevE.91.022803</a>","mla":"Keller-Schmidt, Stephanie, et al. “Anomalous Scaling in an Age-Dependent Branching Model.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 2, 022803, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">10.1103/PhysRevE.91.022803</a>.","apa":"Keller-Schmidt, S., Tugrul, M., Eguíluz, V., Hernandez Garcia, E., &#38; Klemm, K. (2015). Anomalous scaling in an age-dependent branching model. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.91.022803\">https://doi.org/10.1103/PhysRevE.91.022803</a>","ieee":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, and K. Klemm, “Anomalous scaling in an age-dependent branching model,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 2. American Institute of Physics, 2015."},"month":"02","publication_status":"published","oa_version":"Preprint","year":"2015","date_published":"2015-02-02T00:00:00Z","article_type":"original","quality_controlled":"1","intvolume":"        91","_id":"1883","title":"Anomalous scaling in an age-dependent branching model","oa":1,"department":[{"_id":"NiBa"}],"publist_id":"5213","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1012.3298"}],"volume":91,"external_id":{"arxiv":["1012.3298"],"isi":["000349860900006"]},"doi":"10.1103/PhysRevE.91.022803","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"We introduce a one-parametric family of tree growth models, in which branching probabilities decrease with branch age τ as τ-α. Depending on the exponent α, the scaling of tree depth with tree size n displays a transition between the logarithmic scaling of random trees and an algebraic growth. At the transition (α=1) tree depth grows as (logn)2. This anomalous scaling is in good agreement with the trend observed in evolution of biological species, thus providing a theoretical support for age-dependent speciation and associating it to the occurrence of a critical point.\r\n","lang":"eng"}],"article_processing_charge":"No","scopus_import":"1","article_number":"022803","language":[{"iso":"eng"}],"status":"public","date_created":"2018-12-11T11:54:31Z","day":"02","type":"journal_article","arxiv":1,"date_updated":"2025-09-23T07:53:52Z","isi":1,"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","publisher":"American Institute of Physics"},{"month":"01","citation":{"short":"G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.","chicago":"Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” <i>Genetics</i>. Genetics Society of America, 2015. <a href=\"https://doi.org/10.1534/genetics.114.171850\">https://doi.org/10.1534/genetics.114.171850</a>.","ista":"Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 199(1), 39–59.","ama":"Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. <i>Genetics</i>. 2015;199(1):39-59. doi:<a href=\"https://doi.org/10.1534/genetics.114.171850\">10.1534/genetics.114.171850</a>","ieee":"G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” <i>Genetics</i>, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.","apa":"Tkačik, G., Dubuis, J., Petkova, M., &#38; Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.114.171850\">https://doi.org/10.1534/genetics.114.171850</a>","mla":"Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” <i>Genetics</i>, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:<a href=\"https://doi.org/10.1534/genetics.114.171850\">10.1534/genetics.114.171850</a>."},"issue":"1","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper"},{"last_name":"Dubuis","first_name":"Julien","full_name":"Dubuis, Julien"},{"first_name":"Mariela","last_name":"Petkova","full_name":"Petkova, Mariela"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"}],"corr_author":"1","year":"2015","oa_version":"Preprint","publication_status":"published","date_published":"2015-01-01T00:00:00Z","title":"Positional information, positional error, and readout precision in morphogenesis: A mathematical framework","_id":"1885","quality_controlled":"1","intvolume":"       199","publist_id":"5210","department":[{"_id":"GaTk"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.5599"}],"oa":1,"doi":"10.1534/genetics.114.171850","external_id":{"arxiv":["1404.5599"],"isi":["000347712900004"]},"volume":199,"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. "}],"type":"journal_article","day":"01","arxiv":1,"date_updated":"2025-09-23T09:53:07Z","status":"public","date_created":"2018-12-11T11:54:32Z","page":"39 - 59","isi":1,"publisher":"Genetics Society of America","publication":"Genetics"},{"scopus_import":"1","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","abstract":[{"text":"We numerically investigate the distribution of extrema of 'chaotic' Laplacian eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a) we count extrema on grid graphs with a small number of randomly added edges and show the behavior to coincide with the 1957 prediction of Longuet-Higgins for the continuous case and (b) we compute the regularity of their spatial distribution using discrepancy, which is a classical measure from the theory of Monte Carlo integration. The first part suggests that grid graphs with randomly added edges should behave like two-dimensional surfaces with ergodic geodesic flow; in the second part we show that the extrema are more regularly distributed in space than the grid Z2.","lang":"eng"}],"doi":"10.1016/j.physleta.2014.12.010","external_id":{"isi":["000349586000006"]},"volume":379,"page":"535 - 541","acknowledgement":"F.P. was supported by the Graduate School of IST Austria. S.S. was partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and Michael Kerber for sharing their implementation of the persistence algorithm. ","isi":1,"publisher":"Elsevier","publication":"Physics Letters, Section A","type":"journal_article","day":"06","date_updated":"2025-09-23T09:44:12Z","date_created":"2018-12-11T11:54:49Z","status":"public","corr_author":"1","year":"2015","oa_version":"None","publication_status":"published","date_published":"2015-03-06T00:00:00Z","month":"03","issue":"6","citation":{"short":"F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.","chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” <i>Physics Letters, Section A</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.physleta.2014.12.010\">https://doi.org/10.1016/j.physleta.2014.12.010</a>.","ista":"Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 379(6), 535–541.","ama":"Pausinger F, Steinerberger S. On the distribution of local extrema in quantum chaos. <i>Physics Letters, Section A</i>. 2015;379(6):535-541. doi:<a href=\"https://doi.org/10.1016/j.physleta.2014.12.010\">10.1016/j.physleta.2014.12.010</a>","apa":"Pausinger, F., &#38; Steinerberger, S. (2015). On the distribution of local extrema in quantum chaos. <i>Physics Letters, Section A</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physleta.2014.12.010\">https://doi.org/10.1016/j.physleta.2014.12.010</a>","ieee":"F. Pausinger and S. Steinerberger, “On the distribution of local extrema in quantum chaos,” <i>Physics Letters, Section A</i>, vol. 379, no. 6. Elsevier, pp. 535–541, 2015.","mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” <i>Physics Letters, Section A</i>, vol. 379, no. 6, Elsevier, 2015, pp. 535–41, doi:<a href=\"https://doi.org/10.1016/j.physleta.2014.12.010\">10.1016/j.physleta.2014.12.010</a>."},"author":[{"full_name":"Pausinger, Florian","first_name":"Florian","last_name":"Pausinger","orcid":"0000-0002-8379-3768","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Stefan","last_name":"Steinerberger","full_name":"Steinerberger, Stefan"}],"publist_id":"5152","department":[{"_id":"HeEd"}],"title":"On the distribution of local extrema in quantum chaos","_id":"1938","quality_controlled":"1","intvolume":"       379"},{"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","publisher":"American Institute of Physics","isi":1,"arxiv":1,"date_updated":"2025-09-23T09:46:10Z","day":"15","type":"journal_article","date_created":"2018-12-11T11:54:49Z","status":"public","article_number":"062710","language":[{"iso":"eng"}],"scopus_import":"1","abstract":[{"text":"We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the &quot;input&quot;) by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.","lang":"eng"}],"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["1501.04015"],"isi":["000356131600006"]},"doi":"10.1103/PhysRevE.91.062710","volume":91,"main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"department":[{"_id":"GaTk"}],"publist_id":"5145","oa":1,"_id":"1940","title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","intvolume":"        91","quality_controlled":"1","corr_author":"1","date_published":"2015-06-15T00:00:00Z","oa_version":"Preprint","publication_status":"published","year":"2015","citation":{"ama":"Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2015;91(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">10.1103/PhysRevE.91.062710</a>","mla":"Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">10.1103/PhysRevE.91.062710</a>.","ieee":"T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 6. American Institute of Physics, 2015.","apa":"Sokolowski, T. R., &#38; Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">https://doi.org/10.1103/PhysRevE.91.062710</a>","ista":"Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.","short":"T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","chicago":"Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">https://doi.org/10.1103/PhysRevE.91.062710</a>."},"issue":"6","month":"06","author":[{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","last_name":"Sokolowski","first_name":"Thomas R","full_name":"Sokolowski, Thomas R"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper"}]},{"acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology (IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions) of the European Union","page":"116 - 123","publisher":"Elsevier","ec_funded":1,"publication":"Current Opinion in Plant Biology","isi":1,"date_updated":"2025-09-23T09:23:09Z","type":"journal_article","day":"01","status":"public","date_created":"2018-12-11T11:54:51Z","language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"doi":"10.1016/j.pbi.2014.12.002","external_id":{"isi":["000349880900017"]},"volume":23,"publist_id":"5140","department":[{"_id":"JiFr"}],"title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","_id":"1944","intvolume":"        23","quality_controlled":"1","corr_author":"1","date_published":"2015-02-01T00:00:00Z","year":"2015","publication_status":"published","oa_version":"None","month":"02","issue":"2","citation":{"ieee":"H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants,” <i>Current Opinion in Plant Biology</i>, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.","apa":"Rakusová, H., Fendrych, M., &#38; Friml, J. (2015). Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">https://doi.org/10.1016/j.pbi.2014.12.002</a>","mla":"Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” <i>Current Opinion in Plant Biology</i>, vol. 23, no. 2, Elsevier, 2015, pp. 116–23, doi:<a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">10.1016/j.pbi.2014.12.002</a>.","ama":"Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. <i>Current Opinion in Plant Biology</i>. 2015;23(2):116-123. doi:<a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">10.1016/j.pbi.2014.12.002</a>","chicago":"Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">https://doi.org/10.1016/j.pbi.2014.12.002</a>.","short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123.","ista":"Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 23(2), 116–123."},"author":[{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"},{"full_name":"Fendrych, Matyas","last_name":"Fendrych","first_name":"Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9767-8699"},{"first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}]},{"volume":2,"external_id":{"arxiv":["1411.4023"]},"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"text":"Simple board games, like Tic-Tac-Toe and CONNECT-4, play an important role not only in the development of mathematical and logical skills, but also in the emotional and social development. In this paper, we address the problem of generating targeted starting positions for such games. This can facilitate new approaches for bringing novice players to mastery, and also leads to discovery of interesting game variants. We present an approach that generates starting states of varying hardness levels for player 1 in a two-player board game, given rules of the board game, the desired number of steps required for player 1 to win, and the expertise levels of the two players. Our approach leverages symbolic methods and iterative simulation to efficiently search the extremely large state space. We present experimental results that include discovery of states of varying hardness levels for several simple grid-based board games. The presence of such states for standard game variants like 4×4 Tic-Tac-Toe opens up new games to be played that have never been played as the default start state is heavily biased. ","lang":"eng"}],"scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:52:16Z","status":"public","type":"conference","day":"01","arxiv":1,"date_updated":"2025-05-19T11:10:17Z","ec_funded":1,"publisher":"AAAI Press","publication":"Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence","page":"745 - 752","acknowledgement":"A Technical Report of this paper is available at: \r\nhttps://repository.ist.ac.at/id/eprint/146.\r\n","author":[{"last_name":"Ahmed","first_name":"Umair","full_name":"Ahmed, Umair"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Gulwani, Sumit","last_name":"Gulwani","first_name":"Sumit"}],"related_material":{"record":[{"id":"5410","relation":"earlier_version","status":"public"}]},"month":"01","citation":{"short":"U. Ahmed, K. Chatterjee, S. Gulwani, in:, Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence, AAAI Press, 2015, pp. 745–752.","chicago":"Ahmed, Umair, Krishnendu Chatterjee, and Sumit Gulwani. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i>, 2:745–52. AAAI Press, 2015.","ista":"Ahmed U, Chatterjee K, Gulwani S. 2015. Automatic generation of alternative starting positions for simple traditional board games. Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 2, 745–752.","ieee":"U. Ahmed, K. Chatterjee, and S. Gulwani, “Automatic generation of alternative starting positions for simple traditional board games,” in <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i>, Austin, TX, USA, 2015, vol. 2, pp. 745–752.","apa":"Ahmed, U., Chatterjee, K., &#38; Gulwani, S. (2015). Automatic generation of alternative starting positions for simple traditional board games. In <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i> (Vol. 2, pp. 745–752). Austin, TX, USA: AAAI Press.","mla":"Ahmed, Umair, et al. “Automatic Generation of Alternative Starting Positions for Simple Traditional Board Games.” <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i>, vol. 2, AAAI Press, 2015, pp. 745–52.","ama":"Ahmed U, Chatterjee K, Gulwani S. Automatic generation of alternative starting positions for simple traditional board games. In: <i>Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence</i>. Vol 2. AAAI Press; 2015:745-752."},"year":"2015","oa_version":"None","publication_status":"published","date_published":"2015-01-01T00:00:00Z","quality_controlled":"1","intvolume":"         2","title":"Automatic generation of alternative starting positions for simple traditional board games","_id":"1481","oa":1,"publist_id":"5713","conference":{"location":"Austin, TX, USA","name":"AAAI: Conference on Artificial Intelligence","end_date":"2015-01-30","start_date":"2015-01-25"},"department":[{"_id":"KrCh"}],"main_file_link":[{"open_access":"1","url":"https://www.aaai.org/ocs/index.php/AAAI/AAAI15/paper/download/9523/9300"}]},{"external_id":{"arxiv":["1412.6821"]},"doi":"10.1109/CVPR.2015.7299106","citation":{"ama":"Reininghaus J, Huber S, Bauer U, Kwitt R. A stable multi-scale kernel for topological machine learning. In: IEEE; 2015:4741-4748. doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7299106\">10.1109/CVPR.2015.7299106</a>","ieee":"J. Reininghaus, S. Huber, U. Bauer, and R. Kwitt, “A stable multi-scale kernel for topological machine learning,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 4741–4748.","apa":"Reininghaus, J., Huber, S., Bauer, U., &#38; Kwitt, R. (2015). A stable multi-scale kernel for topological machine learning (pp. 4741–4748). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2015.7299106\">https://doi.org/10.1109/CVPR.2015.7299106</a>","mla":"Reininghaus, Jan, et al. <i>A Stable Multi-Scale Kernel for Topological Machine Learning</i>. IEEE, 2015, pp. 4741–48, doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7299106\">10.1109/CVPR.2015.7299106</a>.","short":"J. Reininghaus, S. Huber, U. Bauer, R. Kwitt, in:, IEEE, 2015, pp. 4741–4748.","chicago":"Reininghaus, Jan, Stefan Huber, Ulrich Bauer, and Roland Kwitt. “A Stable Multi-Scale Kernel for Topological Machine Learning,” 4741–48. IEEE, 2015. <a href=\"https://doi.org/10.1109/CVPR.2015.7299106\">https://doi.org/10.1109/CVPR.2015.7299106</a>.","ista":"Reininghaus J, Huber S, Bauer U, Kwitt R. 2015. A stable multi-scale kernel for topological machine learning. CVPR: Computer Vision and Pattern Recognition, 4741–4748."},"month":"10","author":[{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"last_name":"Huber","first_name":"Stefan","full_name":"Huber, Stefan","orcid":"0000-0002-8871-5814","id":"4700A070-F248-11E8-B48F-1D18A9856A87"},{"id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9683-0724","full_name":"Bauer, Ulrich","first_name":"Ulrich","last_name":"Bauer"},{"full_name":"Kwitt, Roland","first_name":"Roland","last_name":"Kwitt"}],"scopus_import":"1","language":[{"iso":"eng"}],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2015","date_published":"2015-10-14T00:00:00Z","abstract":[{"text":"Topological data analysis offers a rich source of valuable information to study vision problems. Yet, so far we lack a theoretically sound connection to popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In this work, we establish such a connection by designing a multi-scale kernel for persistence diagrams, a stable summary representation of topological features in data. We show that this kernel is positive definite and prove its stability with respect to the 1-Wasserstein distance. Experiments on two benchmark datasets for 3D shape classification/retrieval and texture recognition show considerable performance gains of the proposed method compared to an alternative approach that is based on the recently introduced persistence landscapes.","lang":"eng"}],"article_processing_charge":"No","day":"14","type":"conference","publication_identifier":{"eisbn":["978-1-4673-6964-0 "]},"_id":"1483","arxiv":1,"date_updated":"2025-06-11T06:37:43Z","title":"A stable multi-scale kernel for topological machine learning","date_created":"2018-12-11T11:52:17Z","status":"public","page":"4741 - 4748","department":[{"_id":"HeEd"}],"publist_id":"5709","conference":{"location":"Boston, MA, USA","name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12","start_date":"2015-06-07"},"main_file_link":[{"url":"http://arxiv.org/abs/1412.6821","open_access":"1"}],"oa":1,"publisher":"IEEE"}]