[{"date_updated":"2021-01-12T06:53:40Z","author":[{"first_name":"Neel","id":"31ABAF80-F248-11E8-B48F-1D18A9856A87","last_name":"Shah","full_name":"Shah, Neel"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir"},{"last_name":"Lampert","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph"}],"title":"A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_published":"2015-06-01T00:00:00Z","month":"06","publisher":"IEEE","language":[{"iso":"eng"}],"year":"2015","page":"2737 - 2745","department":[{"_id":"VlKo"},{"_id":"ChLa"}],"publist_id":"5240","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2015-06-12","start_date":"2015-06-07","location":"Boston, MA, USA"},"_id":"1859","date_created":"2018-12-11T11:54:24Z","quality_controlled":"1","status":"public","day":"01","citation":{"chicago":"Shah, Neel, Vladimir Kolmogorov, and Christoph Lampert. “A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle,” 2737–45. IEEE, 2015. <a href=\"https://doi.org/10.1109/CVPR.2015.7298890\">https://doi.org/10.1109/CVPR.2015.7298890</a>.","ieee":"N. Shah, V. Kolmogorov, and C. Lampert, “A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA, 2015, pp. 2737–2745.","ista":"Shah N, Kolmogorov V, Lampert C. 2015. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. CVPR: Computer Vision and Pattern Recognition, 2737–2745.","short":"N. Shah, V. Kolmogorov, C. Lampert, in:, IEEE, 2015, pp. 2737–2745.","ama":"Shah N, Kolmogorov V, Lampert C. A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle. In: IEEE; 2015:2737-2745. doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298890\">10.1109/CVPR.2015.7298890</a>","mla":"Shah, Neel, et al. <i>A Multi-Plane Block-Coordinate Frank-Wolfe Algorithm for Training Structural SVMs with a Costly Max-Oracle</i>. IEEE, 2015, pp. 2737–45, doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298890\">10.1109/CVPR.2015.7298890</a>.","apa":"Shah, N., Kolmogorov, V., &#38; Lampert, C. (2015). A multi-plane block-coordinate Frank-Wolfe algorithm for training structural SVMs with a costly max-oracle (pp. 2737–2745). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, USA: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2015.7298890\">https://doi.org/10.1109/CVPR.2015.7298890</a>"},"abstract":[{"lang":"eng","text":"Structural support vector machines (SSVMs) are amongst the best performing models for structured computer vision tasks, such as semantic image segmentation or human pose estimation. Training SSVMs, however, is computationally costly, because it requires repeated calls to a structured prediction subroutine (called \\emph{max-oracle}), which has to solve an optimization problem itself, e.g. a graph cut.\r\nIn this work, we introduce a new algorithm for SSVM training that is more efficient than earlier techniques when the max-oracle is computationally expensive, as it is frequently the case in computer vision tasks. The main idea is to (i) combine the recent stochastic Block-Coordinate Frank-Wolfe algorithm with efficient hyperplane caching, and (ii) use an automatic selection rule for deciding whether to call the exact max-oracle or to rely on an approximate one based on the cached hyperplanes.\r\nWe show experimentally that this strategy leads to faster convergence to the optimum with respect to the number of requires oracle calls, and that this translates into faster convergence with respect to the total runtime when the max-oracle is slow compared to the other steps of the algorithm. "}],"scopus_import":1,"type":"conference","oa_version":"Preprint","ec_funded":1,"project":[{"grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"},{"name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","call_identifier":"FP7"}],"doi":"10.1109/CVPR.2015.7298890","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1408.6804"}]},{"department":[{"_id":"ChLa"}],"publist_id":"5239","conference":{"end_date":"2015-06-12","start_date":"2015-06-07","name":"CVPR: Computer Vision and Pattern Recognition","location":"Boston, MA, United States"},"page":"1401 - 1409","year":"2015","language":[{"iso":"eng"}],"publisher":"IEEE","date_published":"2015-06-01T00:00:00Z","month":"06","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Amélie","last_name":"Royer","full_name":"Royer, Amélie"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph"}],"title":"Classifier adaptation at prediction time","date_updated":"2021-01-12T06:53:41Z","main_file_link":[{"url":"http://www.cv-foundation.org/openaccess/content_cvpr_2015/papers/Royer_Classifier_Adaptation_at_2015_CVPR_paper.pdf","open_access":"1"}],"publication_status":"published","doi":"10.1109/CVPR.2015.7298746","project":[{"grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"oa_version":"Submitted Version","ec_funded":1,"scopus_import":1,"abstract":[{"text":"Classifiers for object categorization are usually evaluated by their accuracy on a set of i.i.d. test examples. This provides us with an estimate of the expected error when applying the classifiers to a single new image. In real application, however, classifiers are rarely only used for a single image and then discarded. Instead, they are applied sequentially to many images, and these are typically not i.i.d. samples from a fixed data distribution, but they carry dependencies and their class distribution varies over time. In this work, we argue that the phenomenon of correlated data at prediction time is not a nuisance, but a blessing in disguise. We describe a probabilistic method for adapting classifiers at prediction time without having to retrain them. We also introduce a framework for creating realistically distributed image sequences, which offers a way to benchmark classifier adaptation methods, such as the one we propose. Experiments on the ILSVRC2010 and ILSVRC2012 datasets show that adapting object classification systems at prediction time can significantly reduce their error rate, even with no additional human feedback.","lang":"eng"}],"type":"conference","citation":{"mla":"Royer, Amélie, and Christoph Lampert. <i>Classifier Adaptation at Prediction Time</i>. IEEE, 2015, pp. 1401–09, doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298746\">10.1109/CVPR.2015.7298746</a>.","apa":"Royer, A., &#38; Lampert, C. (2015). Classifier adaptation at prediction time (pp. 1401–1409). Presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2015.7298746\">https://doi.org/10.1109/CVPR.2015.7298746</a>","chicago":"Royer, Amélie, and Christoph Lampert. “Classifier Adaptation at Prediction Time,” 1401–9. IEEE, 2015. <a href=\"https://doi.org/10.1109/CVPR.2015.7298746\">https://doi.org/10.1109/CVPR.2015.7298746</a>.","ama":"Royer A, Lampert C. Classifier adaptation at prediction time. In: IEEE; 2015:1401-1409. doi:<a href=\"https://doi.org/10.1109/CVPR.2015.7298746\">10.1109/CVPR.2015.7298746</a>","ista":"Royer A, Lampert C. 2015. Classifier adaptation at prediction time. CVPR: Computer Vision and Pattern Recognition, 1401–1409.","short":"A. Royer, C. Lampert, in:, IEEE, 2015, pp. 1401–1409.","ieee":"A. Royer and C. Lampert, “Classifier adaptation at prediction time,” presented at the CVPR: Computer Vision and Pattern Recognition, Boston, MA, United States, 2015, pp. 1401–1409."},"status":"public","day":"01","quality_controlled":"1","date_created":"2018-12-11T11:54:24Z","_id":"1860"},{"publication":"ACM Transactions on Modeling and Computer Simulation","publication_status":"published","doi":"10.1145/2688906","oa_version":"None","volume":25,"citation":{"mla":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2, 8, ACM, 2015, doi:<a href=\"https://doi.org/10.1145/2688906\">10.1145/2688906</a>.","apa":"Ruess, J., &#38; Lygeros, J. (2015). Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM. <a href=\"https://doi.org/10.1145/2688906\">https://doi.org/10.1145/2688906</a>","chicago":"Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” <i>ACM Transactions on Modeling and Computer Simulation</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2688906\">https://doi.org/10.1145/2688906</a>.","short":"J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015).","ieee":"J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” <i>ACM Transactions on Modeling and Computer Simulation</i>, vol. 25, no. 2. ACM, 2015.","ista":"Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8.","ama":"Ruess J, Lygeros J. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. <i>ACM Transactions on Modeling and Computer Simulation</i>. 2015;25(2). doi:<a href=\"https://doi.org/10.1145/2688906\">10.1145/2688906</a>"},"scopus_import":1,"abstract":[{"text":"Continuous-time Markov chains are commonly used in practice for modeling biochemical reaction networks in which the inherent randomness of themolecular interactions cannot be ignored. This has motivated recent research effort into methods for parameter inference and experiment design for such models. The major difficulty is that such methods usually require one to iteratively solve the chemical master equation that governs the time evolution of the probability distribution of the system. This, however, is rarely possible, and even approximation techniques remain limited to relatively small and simple systems. An alternative explored in this article is to base methods on only some low-order moments of the entire probability distribution. We summarize the theory behind such moment-based methods for parameter inference and experiment design and provide new case studies where we investigate their performance.","lang":"eng"}],"type":"journal_article","_id":"1861","date_created":"2018-12-11T11:54:25Z","quality_controlled":"1","day":"01","status":"public","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publist_id":"5238","language":[{"iso":"eng"}],"year":"2015","date_published":"2015-02-01T00:00:00Z","intvolume":"        25","month":"02","article_number":"8","publisher":"ACM","acknowledgement":"HYCON2; EC; European Commission\r\n","date_updated":"2021-01-12T06:53:41Z","author":[{"full_name":"Ruess, Jakob","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","last_name":"Ruess"},{"full_name":"Lygeros, John","first_name":"John","last_name":"Lygeros"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","issue":"2"},{"volume":16,"date_created":"2018-12-11T11:54:26Z","status":"public","day":"01","doi":"10.1007/s00023-014-0333-5","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.5107"}],"publication":"Annales Henri Poincare","ec_funded":1,"oa_version":"Preprint","month":"03","intvolume":"        16","date_published":"2015-03-01T00:00:00Z","date_updated":"2021-01-12T06:53:42Z","issue":"3","oa":1,"page":"709 - 799","year":"2015","citation":{"chicago":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” <i>Annales Henri Poincare</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00023-014-0333-5\">https://doi.org/10.1007/s00023-014-0333-5</a>.","ista":"Erdös L, Knowles A. 2015. The Altshuler–Shklovskii formulas for random band matrices II: The general case. Annales Henri Poincare. 16(3), 709–799.","ieee":"L. Erdös and A. Knowles, “The Altshuler–Shklovskii formulas for random band matrices II: The general case,” <i>Annales Henri Poincare</i>, vol. 16, no. 3. Springer, pp. 709–799, 2015.","short":"L. Erdös, A. Knowles, Annales Henri Poincare 16 (2015) 709–799.","ama":"Erdös L, Knowles A. The Altshuler–Shklovskii formulas for random band matrices II: The general case. <i>Annales Henri Poincare</i>. 2015;16(3):709-799. doi:<a href=\"https://doi.org/10.1007/s00023-014-0333-5\">10.1007/s00023-014-0333-5</a>","mla":"Erdös, László, and Antti Knowles. “The Altshuler–Shklovskii Formulas for Random Band Matrices II: The General Case.” <i>Annales Henri Poincare</i>, vol. 16, no. 3, Springer, 2015, pp. 709–99, doi:<a href=\"https://doi.org/10.1007/s00023-014-0333-5\">10.1007/s00023-014-0333-5</a>.","apa":"Erdös, L., &#38; Knowles, A. (2015). The Altshuler–Shklovskii formulas for random band matrices II: The general case. <i>Annales Henri Poincare</i>. Springer. <a href=\"https://doi.org/10.1007/s00023-014-0333-5\">https://doi.org/10.1007/s00023-014-0333-5</a>"},"type":"journal_article","abstract":[{"text":"The Altshuler–Shklovskii formulas (Altshuler and Shklovskii, BZh Eksp Teor Fiz 91:200, 1986) predict, for any disordered quantum system in the diffusive regime, a universal power law behaviour for the correlation functions of the mesoscopic eigenvalue density. In this paper and its companion (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013), we prove these formulas for random band matrices. In (Erdős and Knowles, The Altshuler–Shklovskii formulas for random band matrices I: the unimodular case, 2013) we introduced a diagrammatic approach and presented robust estimates on general diagrams under certain simplifying assumptions. In this paper, we remove these assumptions by giving a general estimate of the subleading diagrams. We also give a precise analysis of the leading diagrams which give rise to the Altschuler–Shklovskii power laws. Moreover, we introduce a family of general random band matrices which interpolates between real symmetric (β = 1) and complex Hermitian (β = 2) models, and track the transition for the mesoscopic density–density correlation. Finally, we address the higher-order correlation functions by proving that they behave asymptotically according to a Gaussian process whose covariance is given by the Altshuler–Shklovskii formulas.\r\n","lang":"eng"}],"scopus_import":1,"_id":"1864","project":[{"call_identifier":"FP7","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems"}],"publication_status":"published","publisher":"Springer","title":"The Altshuler–Shklovskii formulas for random band matrices II: The general case","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Erdös, László","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603"},{"full_name":"Knowles, Antti","first_name":"Antti","last_name":"Knowles"}],"publist_id":"5233","department":[{"_id":"LaEr"}],"language":[{"iso":"eng"}]},{"_id":"1865","quality_controlled":"1","citation":{"apa":"Robert, H., Grunewald, W., Sauer, M., Cannoot, B., Soriano, M., Swarup, R., … Friml, J. (2015). Plant embryogenesis requires AUX/LAX-mediated auxin influx. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.115832\">https://doi.org/10.1242/dev.115832</a>","mla":"Robert, Hélène, et al. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” <i>Development</i>, vol. 142, no. 4, Company of Biologists, 2015, pp. 702–11, doi:<a href=\"https://doi.org/10.1242/dev.115832\">10.1242/dev.115832</a>.","short":"H. Robert, W. Grunewald, M. Sauer, B. Cannoot, M. Soriano, R. Swarup, D. Weijers, M. Bennett, K. Boutilier, J. Friml, Development 142 (2015) 702–711.","ista":"Robert H, Grunewald W, Sauer M, Cannoot B, Soriano M, Swarup R, Weijers D, Bennett M, Boutilier K, Friml J. 2015. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development. 142(4), 702–711.","ieee":"H. Robert <i>et al.</i>, “Plant embryogenesis requires AUX/LAX-mediated auxin influx,” <i>Development</i>, vol. 142, no. 4. Company of Biologists, pp. 702–711, 2015.","ama":"Robert H, Grunewald W, Sauer M, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. <i>Development</i>. 2015;142(4):702-711. doi:<a href=\"https://doi.org/10.1242/dev.115832\">10.1242/dev.115832</a>","chicago":"Robert, Hélène, Wim Grunewald, Michael Sauer, Bernard Cannoot, Mercedes Soriano, Ranjan Swarup, Dolf Weijers, Malcolm Bennett, Kim Boutilier, and Jiří Friml. “Plant Embryogenesis Requires AUX/LAX-Mediated Auxin Influx.” <i>Development</i>. Company of Biologists, 2015. <a href=\"https://doi.org/10.1242/dev.115832\">https://doi.org/10.1242/dev.115832</a>."},"type":"journal_article","abstract":[{"text":"The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop betweenMONOPTEROS(ARF5)-dependent auxin signalling and auxin transport. ThisMONOPTEROSdependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.","lang":"eng"}],"scopus_import":1,"project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"publication_status":"published","author":[{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"last_name":"Sauer","first_name":"Michael","full_name":"Sauer, Michael"},{"full_name":"Cannoot, Bernard","first_name":"Bernard","last_name":"Cannoot"},{"full_name":"Soriano, Mercedes","last_name":"Soriano","first_name":"Mercedes"},{"full_name":"Swarup, Ranjan","last_name":"Swarup","first_name":"Ranjan"},{"first_name":"Dolf","last_name":"Weijers","full_name":"Weijers, Dolf"},{"first_name":"Malcolm","last_name":"Bennett","full_name":"Bennett, Malcolm"},{"full_name":"Boutilier, Kim","first_name":"Kim","last_name":"Boutilier"},{"full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Plant embryogenesis requires AUX/LAX-mediated auxin influx","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Company of Biologists","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"5231","date_created":"2018-12-11T11:54:26Z","status":"public","day":"15","volume":142,"ec_funded":1,"oa_version":"None","doi":"10.1242/dev.115832","publication":"Development","date_updated":"2021-01-12T06:53:43Z","issue":"4","intvolume":"       142","month":"02","date_published":"2015-02-15T00:00:00Z","acknowledgement":"W.G. is a post-doctoral fellow of the Research Foundation Flanders. H.S.R. is supported by Employment of Best Young Scientists for International Cooperation Empowerment [CZ.1.07/2.3.00/30.0037], co-financed by the European Social Fund and the state budget of the Czech Republic. Mi.S. was funded by the Ramón y Cajal program. This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], project ‘CEITEC – Central European Institute of Technology’ [CZ.1.05/1.1.00/02.0068], the European Social Fund [CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GACR [GA13-40637S] to J.F. We acknowledge funding from the Biological and Biotechnological Science Research Council (BBSRC) and Engineering Physics Science Research Council (EPSRC) to R.S. and M.B","year":"2015","page":"702 - 711"},{"date_published":"2015-01-28T00:00:00Z","month":"01","intvolume":"        58","publisher":"ACM","date_updated":"2021-01-12T06:53:43Z","title":"The equivalence problem for finite automata: Technical perspective","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Raskin, Jean","first_name":"Jean","last_name":"Raskin"}],"issue":"2","page":"86-86","department":[{"_id":"ToHe"}],"publist_id":"5232","language":[{"iso":"eng"}],"year":"2015","volume":58,"citation":{"chicago":"Henzinger, Thomas A, and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” <i>Communications of the ACM</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2701001\">https://doi.org/10.1145/2701001</a>.","ista":"Henzinger TA, Raskin J. 2015. The equivalence problem for finite automata: Technical perspective. Communications of the ACM. 58(2), 86–86.","ieee":"T. A. Henzinger and J. Raskin, “The equivalence problem for finite automata: Technical perspective,” <i>Communications of the ACM</i>, vol. 58, no. 2. ACM, pp. 86–86, 2015.","short":"T.A. Henzinger, J. Raskin, Communications of the ACM 58 (2015) 86–86.","ama":"Henzinger TA, Raskin J. The equivalence problem for finite automata: Technical perspective. <i>Communications of the ACM</i>. 2015;58(2):86-86. doi:<a href=\"https://doi.org/10.1145/2701001\">10.1145/2701001</a>","mla":"Henzinger, Thomas A., and Jean Raskin. “The Equivalence Problem for Finite Automata: Technical Perspective.” <i>Communications of the ACM</i>, vol. 58, no. 2, ACM, 2015, pp. 86–86, doi:<a href=\"https://doi.org/10.1145/2701001\">10.1145/2701001</a>.","apa":"Henzinger, T. A., &#38; Raskin, J. (2015). The equivalence problem for finite automata: Technical perspective. <i>Communications of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2701001\">https://doi.org/10.1145/2701001</a>"},"scopus_import":1,"type":"journal_article","date_created":"2018-12-11T11:54:26Z","_id":"1866","day":"28","status":"public","publication":"Communications of the ACM","publication_status":"published","doi":"10.1145/2701001","oa_version":"None"},{"publication_status":"published","project":[{"grant_number":"303564","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)","grant_number":"RGY0084/2012"}],"type":"journal_article","abstract":[{"text":"Cultured mammalian cells essential are model systems in basic biology research, production platforms of proteins for medical use, and testbeds in synthetic biology. Flavin cofactors, in particular flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), are critical for cellular redox reactions and sense light in naturally occurring photoreceptors and optogenetic tools. Here, we quantified flavin contents of commonly used mammalian cell lines. We first compared three procedures for extraction of free and noncovalently protein-bound flavins and verified extraction using fluorescence spectroscopy. For separation, two CE methods with different BGEs were established, and detection was performed by LED-induced fluorescence with limit of detections (LODs 0.5-3.8 nM). We found that riboflavin (RF), FMN, and FAD contents varied significantly between cell lines. RF (3.1-14 amol/cell) and FAD (2.2-17.0 amol/cell) were the predominant flavins, while FMN (0.46-3.4 amol/cell) was found at markedly lower levels. Observed flavin contents agree with those previously extracted from mammalian tissues, yet reduced forms of RF were detected that were not described previously. Quantification of flavins in mammalian cell lines will allow a better understanding of cellular redox reactions and optogenetic tools.","lang":"eng"}],"scopus_import":1,"citation":{"ama":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. <i>Electrophoresis</i>. 2015;36(4):518-525. doi:<a href=\"https://doi.org/10.1002/elps.201400451\">10.1002/elps.201400451</a>","short":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, H.L. Janovjak, Electrophoresis 36 (2015) 518–525.","ista":"Hühner J, Inglés Prieto Á, Neusüß C, Lämmerhofer M, Janovjak HL. 2015. Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. Electrophoresis. 36(4), 518–525.","ieee":"J. Hühner, Á. Inglés Prieto, C. Neusüß, M. Lämmerhofer, and H. L. Janovjak, “Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection,” <i>Electrophoresis</i>, vol. 36, no. 4. Wiley, pp. 518–525, 2015.","chicago":"Hühner, Jens, Álvaro Inglés Prieto, Christian Neusüß, Michael Lämmerhofer, and Harald L Janovjak. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” <i>Electrophoresis</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/elps.201400451\">https://doi.org/10.1002/elps.201400451</a>.","apa":"Hühner, J., Inglés Prieto, Á., Neusüß, C., Lämmerhofer, M., &#38; Janovjak, H. L. (2015). Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection. <i>Electrophoresis</i>. Wiley. <a href=\"https://doi.org/10.1002/elps.201400451\">https://doi.org/10.1002/elps.201400451</a>","mla":"Hühner, Jens, et al. “Quantification of Riboflavin, Flavin Mononucleotide, and Flavin Adenine Dinucleotide in Mammalian Model Cells by CE with LED-Induced Fluorescence Detection.” <i>Electrophoresis</i>, vol. 36, no. 4, Wiley, 2015, pp. 518–25, doi:<a href=\"https://doi.org/10.1002/elps.201400451\">10.1002/elps.201400451</a>."},"quality_controlled":"1","_id":"1867","publist_id":"5230","department":[{"_id":"HaJa"}],"pubrep_id":"836","language":[{"iso":"eng"}],"publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection","author":[{"full_name":"Hühner, Jens","first_name":"Jens","last_name":"Hühner"},{"full_name":"Inglés Prieto, Álvaro","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571","first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Neusüß, Christian","last_name":"Neusüß","first_name":"Christian"},{"first_name":"Michael","last_name":"Lämmerhofer","full_name":"Lämmerhofer, Michael"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"}],"doi":"10.1002/elps.201400451","publication":"Electrophoresis","oa_version":"None","ec_funded":1,"volume":36,"day":"01","status":"public","date_created":"2018-12-11T11:54:26Z","page":"518 - 525","year":"2015","intvolume":"        36","month":"02","date_published":"2015-02-01T00:00:00Z","issue":"4","date_updated":"2021-01-12T06:53:43Z"},{"publist_id":"5229","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"year":"2015","intvolume":"        91","month":"02","date_published":"2015-02-09T00:00:00Z","article_number":"022906","publisher":"American Physical Society","date_updated":"2021-01-12T06:53:44Z","issue":"2","author":[{"full_name":"Park, Youngyong","last_name":"Park","first_name":"Youngyong"},{"full_name":"Do, Younghae","first_name":"Younghae","last_name":"Do"},{"full_name":"Altmeyer, Sebastian","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Altmeyer","orcid":"0000-0001-5964-0203"},{"full_name":"Lai, Yingcheng","first_name":"Yingcheng","last_name":"Lai"},{"full_name":"Lee, Gyuwon","last_name":"Lee","first_name":"Gyuwon"}],"title":"Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1103/PhysRevE.91.022906","publication_status":"published","publication":"Physical Review E","oa_version":"None","publication_identifier":{"issn":["1539-3755"]},"citation":{"mla":"Park, Youngyong, et al. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” <i>Physical Review E</i>, vol. 91, no. 2, 022906, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022906\">10.1103/PhysRevE.91.022906</a>.","apa":"Park, Y., Do, Y., Altmeyer, S., Lai, Y., &#38; Lee, G. (2015). Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.91.022906\">https://doi.org/10.1103/PhysRevE.91.022906</a>","chicago":"Park, Youngyong, Younghae Do, Sebastian Altmeyer, Yingcheng Lai, and Gyuwon Lee. “Early Effect in Time-Dependent, High-Dimensional Nonlinear Dynamical Systems with Multiple Resonances.” <i>Physical Review E</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.91.022906\">https://doi.org/10.1103/PhysRevE.91.022906</a>.","ama":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. <i>Physical Review E</i>. 2015;91(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.022906\">10.1103/PhysRevE.91.022906</a>","short":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, G. Lee, Physical Review E 91 (2015).","ieee":"Y. Park, Y. Do, S. Altmeyer, Y. Lai, and G. Lee, “Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances,” <i>Physical Review E</i>, vol. 91, no. 2. American Physical Society, 2015.","ista":"Park Y, Do Y, Altmeyer S, Lai Y, Lee G. 2015. Early effect in time-dependent, high-dimensional nonlinear dynamical systems with multiple resonances. Physical Review E. 91(2), 022906."},"volume":91,"type":"journal_article","abstract":[{"text":"We investigate high-dimensional nonlinear dynamical systems exhibiting multiple resonances under adiabatic parameter variations. Our motivations come from experimental considerations where time-dependent sweeping of parameters is a practical approach to probing and characterizing the bifurcations of the system. The question is whether bifurcations so detected are faithful representations of the bifurcations intrinsic to the original stationary system. Utilizing a harmonically forced, closed fluid flow system that possesses multiple resonances and solving the Navier-Stokes equation under proper boundary conditions, we uncover the phenomenon of the early effect. Specifically, as a control parameter, e.g., the driving frequency, is adiabatically increased from an initial value, resonances emerge at frequency values that are lower than those in the corresponding stationary system. The phenomenon is established by numerical characterization of physical quantities through the resonances, which include the kinetic energy and the vorticity field, and a heuristic analysis based on the concept of instantaneous frequency. A simple formula is obtained which relates the resonance points in the time-dependent and time-independent systems. Our findings suggest that, in general, any true bifurcation of a nonlinear dynamical system can be unequivocally uncovered through adiabatic parameter sweeping, in spite of a shift in the bifurcation point, which is of value to experimental studies of nonlinear dynamical systems.","lang":"eng"}],"scopus_import":1,"_id":"1868","date_created":"2018-12-11T11:54:27Z","quality_controlled":"1","day":"09","status":"public"},{"file":[{"file_name":"IST-2016-563-v1+1_1.full.pdf","date_created":"2018-12-12T10:11:00Z","date_updated":"2020-07-14T12:45:19Z","file_size":1688844,"creator":"system","content_type":"application/pdf","file_id":"4852","relation":"main_file","checksum":"24c779f4cd9d549ca6833e26f486be27","access_level":"open_access"}],"title":"Auxin transporters and binding proteins at a glance","author":[{"first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones","full_name":"Grones, Peter"},{"full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Company of Biologists","has_accepted_license":"1","pubrep_id":"563","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"5225","quality_controlled":"1","_id":"1871","type":"journal_article","file_date_updated":"2020-07-14T12:45:19Z","abstract":[{"text":"The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.","lang":"eng"}],"scopus_import":1,"citation":{"ama":"Grones P, Friml J. Auxin transporters and binding proteins at a glance. <i>Journal of Cell Science</i>. 2015;128(1):1-7. doi:<a href=\"https://doi.org/10.1242/jcs.159418\">10.1242/jcs.159418</a>","ista":"Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7.","ieee":"P. Grones and J. Friml, “Auxin transporters and binding proteins at a glance,” <i>Journal of Cell Science</i>, vol. 128, no. 1. Company of Biologists, pp. 1–7, 2015.","short":"P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7.","chicago":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” <i>Journal of Cell Science</i>. Company of Biologists, 2015. <a href=\"https://doi.org/10.1242/jcs.159418\">https://doi.org/10.1242/jcs.159418</a>.","apa":"Grones, P., &#38; Friml, J. (2015). Auxin transporters and binding proteins at a glance. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.159418\">https://doi.org/10.1242/jcs.159418</a>","mla":"Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” <i>Journal of Cell Science</i>, vol. 128, no. 1, Company of Biologists, 2015, pp. 1–7, doi:<a href=\"https://doi.org/10.1242/jcs.159418\">10.1242/jcs.159418</a>."},"publication_status":"published","issue":"1","oa":1,"date_updated":"2021-01-12T06:53:45Z","acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP]; European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GAČR [grant number GA13-40637S]","month":"01","intvolume":"       128","date_published":"2015-01-01T00:00:00Z","year":"2015","page":"1 - 7","status":"public","day":"01","ddc":["570"],"date_created":"2018-12-11T11:54:28Z","volume":128,"oa_version":"Submitted Version","doi":"10.1242/jcs.159418","publication":"Journal of Cell Science"},{"month":"04","intvolume":"       221","date_published":"2015-04-01T00:00:00Z","oa":1,"date_updated":"2021-01-12T06:53:46Z","external_id":{"arxiv":["1408.2058"]},"page":"46 - 72","year":"2015","volume":221,"day":"01","status":"public","date_created":"2018-12-11T11:54:28Z","main_file_link":[{"url":"https://arxiv.org/abs/1408.2058","open_access":"1"}],"doi":"10.1016/j.artint.2014.12.009","publication":"Artificial Intelligence","oa_version":"Preprint","publisher":"Elsevier","title":"POMDPs under probabilistic semantics","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5224","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with 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 constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints 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 path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples.","lang":"eng"}],"scopus_import":1,"arxiv":1,"citation":{"chicago":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” <i>Artificial Intelligence</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.artint.2014.12.009\">https://doi.org/10.1016/j.artint.2014.12.009</a>.","ama":"Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. <i>Artificial Intelligence</i>. 2015;221:46-72. doi:<a href=\"https://doi.org/10.1016/j.artint.2014.12.009\">10.1016/j.artint.2014.12.009</a>","ieee":"K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” <i>Artificial Intelligence</i>, vol. 221. Elsevier, pp. 46–72, 2015.","short":"K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72.","ista":"Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial Intelligence. 221, 46–72.","mla":"Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” <i>Artificial Intelligence</i>, vol. 221, Elsevier, 2015, pp. 46–72, doi:<a href=\"https://doi.org/10.1016/j.artint.2014.12.009\">10.1016/j.artint.2014.12.009</a>.","apa":"Chatterjee, K., &#38; Chmelik, M. (2015). POMDPs under probabilistic semantics. <i>Artificial Intelligence</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.artint.2014.12.009\">https://doi.org/10.1016/j.artint.2014.12.009</a>"},"quality_controlled":"1","_id":"1873","publication_status":"published"},{"publist_id":"5222","department":[{"_id":"JoCs"}],"page":"838 - 857","year":"2015","language":[{"iso":"eng"}],"publisher":"Wiley","intvolume":"        25","month":"07","date_published":"2015-07-01T00:00:00Z","issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A three-plane architectonic atlas of the rat hippocampal region","author":[{"id":"3FC06552-F248-11E8-B48F-1D18A9856A87","first_name":"Charlotte","last_name":"Boccara","orcid":"0000-0001-7237-5109","full_name":"Boccara, Charlotte"},{"last_name":"Kjønigsen","first_name":"Lisa","full_name":"Kjønigsen, Lisa"},{"last_name":"Hammer","first_name":"Ingvild","full_name":"Hammer, Ingvild"},{"first_name":"Jan","last_name":"Bjaalie","full_name":"Bjaalie, Jan"},{"full_name":"Leergaard, Trygve","first_name":"Trygve","last_name":"Leergaard"},{"first_name":"Menno","last_name":"Witter","full_name":"Witter, Menno"}],"date_updated":"2021-01-12T06:53:46Z","doi":"10.1002/hipo.22407","publication_status":"published","publication":"Hippocampus","oa_version":"None","type":"journal_article","abstract":[{"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.","lang":"eng"}],"scopus_import":1,"citation":{"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.","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.","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>","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>.","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>","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>."},"volume":25,"quality_controlled":"1","status":"public","day":"01","_id":"1874","date_created":"2018-12-11T11:54:29Z"},{"volume":128,"citation":{"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>.","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>","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>.","short":"E. Cires Rodriguez, J. Prieto, Journal of Plant Research 128 (2015) 223–238.","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.","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>"},"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)."}],"scopus_import":1,"type":"journal_article","_id":"1878","date_created":"2018-12-11T11:54:30Z","quality_controlled":"1","status":"public","day":"24","publication":"Journal of Plant Research","doi":"10.1007/s10265-014-0691-6","publication_status":"published","oa_version":"None","date_published":"2015-01-24T00:00:00Z","intvolume":"       128","month":"01","publisher":"Springer","date_updated":"2021-01-12T06:53:47Z","author":[{"last_name":"Cires Rodriguez","id":"2AD56A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Eduardo","full_name":"Cires Rodriguez, Eduardo"},{"full_name":"Prieto, José","last_name":"Prieto","first_name":"José"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula","issue":"2","page":"223 - 238","department":[{"_id":"JiFr"}],"publist_id":"5217","language":[{"iso":"eng"}],"year":"2015"},{"has_accepted_license":"1","publisher":"Wiley-Blackwell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Developing 3D SEM in a broad biological context","author":[{"first_name":"A","last_name":"Kremer","full_name":"Kremer, A"},{"full_name":"Lippens, Stefaan","first_name":"Stefaan","last_name":"Lippens"},{"full_name":"Bartunkova, Sonia","first_name":"Sonia","last_name":"Bartunkova"},{"full_name":"Asselbergh, Bob","first_name":"Bob","last_name":"Asselbergh"},{"full_name":"Blanpain, Cendric","last_name":"Blanpain","first_name":"Cendric"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"full_name":"Goossens, A","first_name":"A","last_name":"Goossens"},{"full_name":"Holt, Matthew","first_name":"Matthew","last_name":"Holt"},{"full_name":"Janssens, Sophie","first_name":"Sophie","last_name":"Janssens"},{"full_name":"Krols, Michiel","last_name":"Krols","first_name":"Michiel"},{"full_name":"Larsimont, Jean","first_name":"Jean","last_name":"Larsimont"},{"last_name":"Mc Guire","first_name":"Conor","full_name":"Mc Guire, Conor"},{"full_name":"Nowack, Moritz","last_name":"Nowack","first_name":"Moritz"},{"first_name":"Xavier","last_name":"Saelens","full_name":"Saelens, Xavier"},{"full_name":"Schertel, Andreas","last_name":"Schertel","first_name":"Andreas"},{"last_name":"Schepens","first_name":"B","full_name":"Schepens, B"},{"first_name":"M","last_name":"Slezak","full_name":"Slezak, M"},{"last_name":"Timmerman","first_name":"Vincent","full_name":"Timmerman, Vincent"},{"full_name":"Theunis, Clara","last_name":"Theunis","first_name":"Clara"},{"last_name":"Van Brempt","first_name":"Ronald","full_name":"Van Brempt, Ronald"},{"first_name":"Y","last_name":"Visser","full_name":"Visser, Y"},{"full_name":"Guérin, Christophe","first_name":"Christophe","last_name":"Guérin"}],"file":[{"file_name":"IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:11:19Z","creator":"system","file_size":2899898,"content_type":"application/pdf","file_id":"4872","checksum":"3649c5372d1644062d728ea9287e367f","access_level":"open_access","relation":"main_file"}],"department":[{"_id":"JiFr"}],"publist_id":"5218","language":[{"iso":"eng"}],"pubrep_id":"459","citation":{"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.","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.","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>","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>.","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>","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>."},"scopus_import":1,"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"}],"file_date_updated":"2020-07-14T12:45:19Z","type":"journal_article","_id":"1879","quality_controlled":"1","publication_status":"published","date_published":"2015-08-01T00:00:00Z","intvolume":"       259","month":"08","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.","date_updated":"2021-01-12T06:53:48Z","oa":1,"issue":"2","page":"80 - 96","year":"2015","volume":259,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2018-12-11T11:54:30Z","day":"01","status":"public","publication":"Journal of Microscopy","doi":"10.1111/jmi.12211","oa_version":"Published Version"},{"volume":17,"day":"15","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:54:30Z","ddc":["530"],"publication":"New Journal of Physics","doi":"10.1088/1367-2630/17/1/013022","oa_version":"Published Version","article_number":"013022","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","date_published":"2015-01-15T00:00:00Z","month":"01","intvolume":"        17","oa":1,"date_updated":"2021-01-12T06:53:48Z","year":"2015","scopus_import":1,"abstract":[{"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","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:20Z","type":"journal_article","citation":{"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 Ltd., 2015, doi:<a href=\"https://doi.org/10.1088/1367-2630/17/1/013022\">10.1088/1367-2630/17/1/013022</a>.","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 Ltd. <a href=\"https://doi.org/10.1088/1367-2630/17/1/013022\">https://doi.org/10.1088/1367-2630/17/1/013022</a>","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 Ltd., 2015. <a href=\"https://doi.org/10.1088/1367-2630/17/1/013022\">https://doi.org/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>","short":"M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics 17 (2015).","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 Ltd., 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."},"quality_controlled":"1","_id":"1880","publication_status":"published","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"publisher":"IOP Publishing Ltd.","has_accepted_license":"1","title":"Superfluid behavior of a Bose-Einstein condensate in a random potential","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Könenberg, Martin","first_name":"Martin","last_name":"Könenberg"},{"first_name":"Thomas","id":"2B5FC9A4-F248-11E8-B48F-1D18A9856A87","last_name":"Moser","full_name":"Moser, Thomas"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"},{"full_name":"Yngvason, Jakob","last_name":"Yngvason","first_name":"Jakob"}],"file":[{"date_created":"2018-12-12T10:12:44Z","date_updated":"2020-07-14T12:45:20Z","file_name":"IST-2016-447-v1+1_document_1_.pdf","access_level":"open_access","relation":"main_file","checksum":"38fdf2b5ac30445e26a5d613abd84b16","creator":"system","file_size":768108,"content_type":"application/pdf","file_id":"4963"}],"publist_id":"5214","department":[{"_id":"RoSe"}],"pubrep_id":"447","language":[{"iso":"eng"}]},{"day":"30","status":"public","date_created":"2018-12-11T11:54:31Z","volume":8997,"ec_funded":1,"oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1408.1256","open_access":"1"}],"doi":"10.1007/978-3-319-15317-9_19","oa":1,"date_updated":"2021-01-12T06:53:49Z","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.","month":"01","intvolume":"      8997","alternative_title":["LNCS"],"date_published":"2015-01-30T00:00:00Z","year":"2015","conference":{"location":"Bertinoro, Italy","name":"FACS: Formal Aspects of Component Software","end_date":"2014-09-12","start_date":"2014-09-10"},"page":"306 - 324","quality_controlled":"1","_id":"1882","type":"conference","abstract":[{"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.","lang":"eng"}],"scopus_import":1,"citation":{"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>.","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>","short":"U. Fahrenberg, J. Kretinsky, A. Legay, L. Traonouez, in:, Springer, 2015, pp. 306–324.","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.","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.","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>.","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>"},"publication_status":"published","project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Compositionality for quantitative specifications","author":[{"last_name":"Fahrenberg","first_name":"Uli","full_name":"Fahrenberg, Uli"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"last_name":"Legay","first_name":"Axel","full_name":"Legay, Axel"},{"first_name":"Louis","last_name":"Traonouez","full_name":"Traonouez, Louis"}],"publisher":"Springer","language":[{"iso":"eng"}],"publist_id":"5216","department":[{"_id":"ToHe"},{"_id":"KrCh"}]},{"publisher":"American Institute of Physics","author":[{"first_name":"Stephanie","last_name":"Keller-Schmidt","full_name":"Keller-Schmidt, Stephanie"},{"id":"37C323C6-F248-11E8-B48F-1D18A9856A87","first_name":"Murat","orcid":"0000-0002-8523-0758","last_name":"Tugrul","full_name":"Tugrul, Murat"},{"last_name":"Eguíluz","first_name":"Víctor","full_name":"Eguíluz, Víctor"},{"full_name":"Hernandez Garcia, Emilio","first_name":"Emilio","last_name":"Hernandez Garcia"},{"full_name":"Klemm, Konstantin","first_name":"Konstantin","last_name":"Klemm"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Anomalous scaling in an age-dependent branching model","publist_id":"5213","department":[{"_id":"NiBa"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"type":"journal_article","arxiv":1,"scopus_import":1,"abstract":[{"lang":"eng","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"}],"citation":{"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>","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>.","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>","short":"S. Keller-Schmidt, M. Tugrul, V. Eguíluz, E. Hernandez Garcia, K. Klemm, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","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.","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.","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>."},"quality_controlled":"1","_id":"1883","publication_status":"published","article_number":"022803","intvolume":"        91","month":"02","date_published":"2015-02-02T00:00:00Z","issue":"2","oa":1,"date_updated":"2021-01-12T06:53:49Z","external_id":{"arxiv":["1012.3298"]},"year":"2015","volume":91,"day":"02","status":"public","date_created":"2018-12-11T11:54:31Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1012.3298"}],"doi":"10.1103/PhysRevE.91.022803","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","oa_version":"Preprint"},{"publisher":"Genetics Society of America","date_published":"2015-01-01T00:00:00Z","intvolume":"       199","month":"01","title":"Positional information, positional error, and readout precision in morphogenesis: A mathematical framework","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"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"}],"issue":"1","date_updated":"2021-01-12T06:53:50Z","publist_id":"5210","department":[{"_id":"GaTk"}],"page":"39 - 59","year":"2015","language":[{"iso":"eng"}],"abstract":[{"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. ","lang":"eng"}],"scopus_import":1,"type":"journal_article","volume":199,"citation":{"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>.","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>","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>.","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>","short":"G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59.","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.","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."},"status":"public","quality_controlled":"1","day":"01","date_created":"2018-12-11T11:54:32Z","_id":"1885","publication":"Genetics","publication_status":"published","main_file_link":[{"url":"http://arxiv.org/abs/1404.5599","open_access":"1"}],"doi":"10.1534/genetics.114.171850","oa_version":"Preprint"},{"department":[{"_id":"HeEd"}],"publist_id":"5152","page":"535 - 541","year":"2015","language":[{"iso":"eng"}],"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. ","publisher":"Elsevier","month":"03","intvolume":"       379","date_published":"2015-03-06T00:00:00Z","issue":"6","author":[{"full_name":"Pausinger, Florian","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8379-3768","last_name":"Pausinger"},{"full_name":"Steinerberger, Stefan","first_name":"Stefan","last_name":"Steinerberger"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"On the distribution of local extrema in quantum chaos","date_updated":"2021-01-12T06:54:12Z","publication_status":"published","doi":"10.1016/j.physleta.2014.12.010","publication":"Physics Letters, Section A","oa_version":"None","type":"journal_article","scopus_import":1,"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"}],"citation":{"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>.","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>","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>.","short":"F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.","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.","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>"},"volume":379,"quality_controlled":"1","status":"public","day":"06","_id":"1938","date_created":"2018-12-11T11:54:49Z"},{"publist_id":"5145","department":[{"_id":"GaTk"}],"year":"2015","language":[{"iso":"eng"}],"publisher":"American Institute of Physics","article_number":"062710","intvolume":"        91","month":"06","date_published":"2015-06-15T00:00:00Z","issue":"6","title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","author":[{"first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_updated":"2021-01-12T06:54:13Z","doi":"10.1103/PhysRevE.91.062710","main_file_link":[{"url":"http://arxiv.org/abs/1501.04015","open_access":"1"}],"publication_status":"published","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","oa_version":"Preprint","type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","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."}],"citation":{"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>.","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>","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>.","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.","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.","short":"T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","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>"},"volume":91,"quality_controlled":"1","day":"15","status":"public","date_created":"2018-12-11T11:54:49Z","_id":"1940"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","author":[{"full_name":"Rakusová, Hana","last_name":"Rakusová","first_name":"Hana"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","last_name":"Fendrych","orcid":"0000-0002-9767-8699"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"}],"issue":"2","date_updated":"2021-01-12T06:54:15Z","publisher":"Elsevier","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","date_published":"2015-02-01T00:00:00Z","month":"02","intvolume":"        23","year":"2015","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"5140","page":"116 - 123","day":"01","quality_controlled":"1","status":"public","date_created":"2018-12-11T11:54:51Z","_id":"1944","scopus_import":1,"type":"journal_article","volume":23,"citation":{"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>.","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.","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.","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>."},"oa_version":"None","ec_funded":1,"publication":"Current Opinion in Plant Biology","publication_status":"published","doi":"10.1016/j.pbi.2014.12.002","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}]}]