[{"citation":{"chicago":"Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux, Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” <i>Medecine Sciences</i>. Éditions Médicales et Scientifiques, 2013. <a href=\"https://doi.org/10.1051/medsci/2013292011\">https://doi.org/10.1051/medsci/2013292011</a>.","ieee":"J.-L. Maître <i>et al.</i>, “Cell adhesion mechanics of zebrafish gastrulation,” <i>Medecine Sciences</i>, vol. 29, no. 2. Éditions Médicales et Scientifiques, pp. 147–150, 2013.","ama":"Maître J-L, Berthoumieux H, Krens G, et al. Cell adhesion mechanics of zebrafish gastrulation. <i>Medecine Sciences</i>. 2013;29(2):147-150. doi:<a href=\"https://doi.org/10.1051/medsci/2013292011\">10.1051/medsci/2013292011</a>","mla":"Maître, Jean-Léon, et al. “Cell Adhesion Mechanics of Zebrafish Gastrulation.” <i>Medecine Sciences</i>, vol. 29, no. 2, Éditions Médicales et Scientifiques, 2013, pp. 147–50, doi:<a href=\"https://doi.org/10.1051/medsci/2013292011\">10.1051/medsci/2013292011</a>.","ista":"Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg C-PJ. 2013. Cell adhesion mechanics of zebrafish gastrulation. Medecine Sciences. 29(2), 147–150.","short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Medecine Sciences 29 (2013) 147–150.","apa":"Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., &#38; Heisenberg, C.-P. J. (2013). Cell adhesion mechanics of zebrafish gastrulation. <i>Medecine Sciences</i>. Éditions Médicales et Scientifiques. <a href=\"https://doi.org/10.1051/medsci/2013292011\">https://doi.org/10.1051/medsci/2013292011</a>"},"department":[{"_id":"CaHe"}],"external_id":{"isi":["000315749700011"]},"publist_id":"3877","language":[{"iso":"eng"}],"issue":"2","_id":"2884","date_updated":"2025-09-29T13:33:31Z","article_processing_charge":"No","intvolume":"        29","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Medecine Sciences","isi":1,"publication_status":"published","publisher":"Éditions Médicales et Scientifiques","date_published":"2013-02-01T00:00:00Z","volume":29,"oa_version":"None","day":"01","page":"147 - 150","scopus_import":"1","project":[{"name":"Analysis of the Formation and Function of Different Cell Protusion Types During Cell Migration in Vivo","_id":"252064B8-B435-11E9-9278-68D0E5697425","grant_number":"HE_3231/6-1"},{"_id":"2527D5CC-B435-11E9-9278-68D0E5697425","grant_number":"I812-B12","call_identifier":"FWF","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation"}],"author":[{"orcid":"0000-0002-3688-1474","last_name":"Maître","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Berthoumieux, Hélène","last_name":"Berthoumieux","first_name":"Hélène"},{"first_name":"Gabriel","last_name":"Krens","orcid":"0000-0003-4761-5996","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel"},{"full_name":"Salbreux, Guillaume","first_name":"Guillaume","last_name":"Salbreux"},{"first_name":"Frank","last_name":"Julicher","full_name":"Julicher, Frank"},{"full_name":"Paluch, Ewa","first_name":"Ewa","last_name":"Paluch"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"doi":"10.1051/medsci/2013292011","year":"2013","title":"Cell adhesion mechanics of zebrafish gastrulation","month":"02","date_created":"2018-12-11T12:00:08Z","type":"journal_article","status":"public","quality_controlled":"1"},{"publist_id":"3874","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"page":"1 - 228","day":"09","citation":{"mla":"Kucera, Antonin, et al., editors. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol. 7721, Springer, 2013, pp. 1–228, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6\">10.1007/978-3-642-36046-6</a>.","ama":"Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D, eds. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol 7721. Springer; 2013:1-228. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6\">10.1007/978-3-642-36046-6</a>","ista":"Kucera A, Henzinger TA, Nesetril J, Vojnar T, Antos D eds. 2013. Mathematical and Engineering Methods in Computer Science, Springer,p.","short":"A. Kucera, T.A. Henzinger, J. Nesetril, T. Vojnar, D. Antos, eds., Mathematical and Engineering Methods in Computer Science, Springer, 2013.","apa":"Kucera, A., Henzinger, T. A., Nesetril, J., Vojnar, T., &#38; Antos, D. (Eds.). (2013). <i>Mathematical and Engineering Methods in Computer Science</i> (Vol. 7721, pp. 1–228). Presented at the MEMICS: Mathematical and Engineering methods in computer science, Znojmo, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36046-6\">https://doi.org/10.1007/978-3-642-36046-6</a>","chicago":"Kucera, Antonin, Thomas A Henzinger, Jaroslav Nesetril, Tomas Vojnar, and David Antos, eds. <i>Mathematical and Engineering Methods in Computer Science</i>. Vol. 7721. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6\">https://doi.org/10.1007/978-3-642-36046-6</a>.","ieee":"A. Kucera, T. A. Henzinger, J. Nesetril, T. Vojnar, and D. Antos, Eds., <i>Mathematical and Engineering Methods in Computer Science</i>, vol. 7721. Springer, 2013, pp. 1–228."},"doi":"10.1007/978-3-642-36046-6","year":"2013","title":"Mathematical and Engineering Methods in Computer Science","_id":"2885","month":"01","date_updated":"2019-08-02T12:37:55Z","series_title":"Lecture Notes in Computer Science","type":"conference_editor","conference":{"end_date":"2012-10-28","start_date":"2012-10-25","location":"Znojmo, Czech Republic","name":"MEMICS: Mathematical and Engineering methods in computer science"},"alternative_title":["LNCS"],"acknowledgement":"Red Hat Czech Republic, Y Soft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:00:08Z","intvolume":"      7721","editor":[{"first_name":"Antonin","last_name":"Kucera","full_name":"Kucera, Antonin"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nesetril, Jaroslav","last_name":"Nesetril","first_name":"Jaroslav"},{"first_name":"Tomas","last_name":"Vojnar","full_name":"Vojnar, Tomas"},{"full_name":"Antos, David","first_name":"David","last_name":"Antos"}],"abstract":[{"text":"This volume contains the post-proceedings of the 8th Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, MEMICS 2012, held in Znojmo, Czech Republic, in October, 2012. The 13 thoroughly revised papers were carefully selected out of 31 submissions and are presented together with 6 invited papers. The topics covered by the papers include: computer-aided analysis and verification, applications of game theory in computer science, networks and security, modern trends of graph theory in computer science, electronic systems design and testing, and quantum information processing.","lang":"eng"}],"volume":7721,"date_published":"2013-01-09T00:00:00Z","status":"public","oa_version":"None","quality_controlled":"1","publisher":"Springer","publication_status":"published"},{"volume":7721,"date_published":"2013-01-09T00:00:00Z","oa_version":"Submitted Version","ec_funded":1,"publisher":"Springer","publication_status":"published","conference":{"end_date":"2012-10-28","start_date":"2012-10-25","name":"MEMICS: Mathematical and Engineering Methods in Computer Science","location":"Znojmo, Czech Republic"},"alternative_title":["LNCS"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      7721","_id":"2886","article_processing_charge":"No","date_updated":"2025-06-11T08:05:09Z","publist_id":"3873","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"citation":{"ieee":"M. Chmelik and V. Řehák, “Controllable-choice message sequence graphs,” vol. 7721. Springer, pp. 118–130, 2013.","chicago":"Chmelik, Martin, and Vojtěch Řehák. “Controllable-Choice Message Sequence Graphs.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">https://doi.org/10.1007/978-3-642-36046-6_12</a>.","ista":"Chmelik M, Řehák V. 2013. Controllable-choice message sequence graphs. 7721, 118–130.","short":"M. Chmelik, V. Řehák, 7721 (2013) 118–130.","mla":"Chmelik, Martin, and Vojtěch Řehák. <i>Controllable-Choice Message Sequence Graphs</i>. Vol. 7721, Springer, 2013, pp. 118–30, doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">10.1007/978-3-642-36046-6_12</a>.","ama":"Chmelik M, Řehák V. Controllable-choice message sequence graphs. 2013;7721:118-130. doi:<a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">10.1007/978-3-642-36046-6_12</a>","apa":"Chmelik, M., &#38; Řehák, V. (2013). Controllable-choice message sequence graphs. Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Znojmo, Czech Republic: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36046-6_12\">https://doi.org/10.1007/978-3-642-36046-6_12</a>"},"external_id":{"arxiv":["1209.4499"]},"status":"public","quality_controlled":"1","arxiv":1,"corr_author":"1","type":"conference","oa":1,"date_created":"2018-12-11T12:00:09Z","main_file_link":[{"url":"http://arxiv.org/abs/1209.4499","open_access":"1"}],"abstract":[{"text":"We focus on the realizability problem of Message Sequence Graphs (MSG), i.e. the problem whether a given MSG specification is correctly distributable among parallel components communicating via messages. This fundamental problem of MSG is known to be undecidable. We introduce a well motivated restricted class of MSG, so called controllable-choice MSG, and show that all its models are realizable and moreover it is decidable whether a given MSG model is a member of this class. In more detail, this class of MSG specifications admits a deadlock-free realization by overloading existing messages with additional bounded control data. We also show that the presented class is the largest known subclass of MSG that allows for deadlock-free realization.","lang":"eng"}],"title":"Controllable-choice message sequence graphs","month":"01","series_title":"Lecture Notes in Computer Science","scopus_import":"1","page":"118 - 130","day":"09","year":"2013","doi":"10.1007/978-3-642-36046-6_12","author":[{"last_name":"Chmelik","first_name":"Martin","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vojtěch","last_name":"Řehák","full_name":"Řehák, Vojtěch"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}]},{"article_type":"original","scopus_import":"1","page":"2670 - 2675","day":"12","doi":"10.1073/pnas.1222821110","year":"2013","author":[{"first_name":"Suqin","last_name":"Fang","full_name":"Fang, Suqin"},{"last_name":"Clark","first_name":"Randy","full_name":"Clark, Randy"},{"last_name":"Zheng","first_name":"Ying","full_name":"Zheng, Ying"},{"first_name":"Anjali","last_name":"Iyer Pascuzzi","full_name":"Iyer Pascuzzi, Anjali"},{"full_name":"Weitz, Joshua","last_name":"Weitz","first_name":"Joshua"},{"first_name":"Leon","last_name":"Kochian","full_name":"Kochian, Leon"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Liao, Hong","last_name":"Liao","first_name":"Hong"},{"first_name":"Philip","last_name":"Benfey","full_name":"Benfey, Philip"}],"title":"Genotypic recognition and spatial responses by rice roots","month":"02","type":"journal_article","oa":1,"date_created":"2018-12-11T12:00:09Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574932/","open_access":"1"}],"abstract":[{"text":"Root system growth and development is highly plastic and is influenced by the surrounding environment. Roots frequently grow in heterogeneous environments that include interactions from neighboring plants and physical impediments in the rhizosphere. To investigate how planting density and physical objects affect root system growth, we grew rice in a transparent gel system in close proximity with another plant or a physical object. Root systems were imaged and reconstructed in three dimensions. Root-root interaction strength was calculated using quantitative metrics that characterize the extent towhich the reconstructed root systems overlap each other. Surprisingly, we found the overlap of root systems of the same genotype was significantly higher than that of root systems of different genotypes. Root systems of the same genotype tended to grow toward each other but those of different genotypes appeared to avoid each other. Shoot separation experiments excluded the possibility of aerial interactions, suggesting root communication. Staggered plantings indicated that interactions likely occur at root tips in close proximity. Recognition of obstacles also occurred through root tips, but through physical contact in a size-dependent manner. These results indicate that root systems use two different forms of communication to recognize objects and alter root architecture: root-root recognition, possibly mediated through root exudates, and root-object recognition mediated by physical contact at the root tips. This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes.","lang":"eng"}],"status":"public","quality_controlled":"1","publist_id":"3872","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"pmid":1,"citation":{"ieee":"S. Fang <i>et al.</i>, “Genotypic recognition and spatial responses by rice roots,” <i>PNAS</i>, vol. 110, no. 7. National Academy of Sciences, pp. 2670–2675, 2013.","chicago":"Fang, Suqin, Randy Clark, Ying Zheng, Anjali Iyer Pascuzzi, Joshua Weitz, Leon Kochian, Herbert Edelsbrunner, Hong Liao, and Philip Benfey. “Genotypic Recognition and Spatial Responses by Rice Roots.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1222821110\">https://doi.org/10.1073/pnas.1222821110</a>.","apa":"Fang, S., Clark, R., Zheng, Y., Iyer Pascuzzi, A., Weitz, J., Kochian, L., … Benfey, P. (2013). Genotypic recognition and spatial responses by rice roots. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1222821110\">https://doi.org/10.1073/pnas.1222821110</a>","short":"S. Fang, R. Clark, Y. Zheng, A. Iyer Pascuzzi, J. Weitz, L. Kochian, H. Edelsbrunner, H. Liao, P. Benfey, PNAS 110 (2013) 2670–2675.","ista":"Fang S, Clark R, Zheng Y, Iyer Pascuzzi A, Weitz J, Kochian L, Edelsbrunner H, Liao H, Benfey P. 2013. Genotypic recognition and spatial responses by rice roots. PNAS. 110(7), 2670–2675.","ama":"Fang S, Clark R, Zheng Y, et al. Genotypic recognition and spatial responses by rice roots. <i>PNAS</i>. 2013;110(7):2670-2675. doi:<a href=\"https://doi.org/10.1073/pnas.1222821110\">10.1073/pnas.1222821110</a>","mla":"Fang, Suqin, et al. “Genotypic Recognition and Spatial Responses by Rice Roots.” <i>PNAS</i>, vol. 110, no. 7, National Academy of Sciences, 2013, pp. 2670–75, doi:<a href=\"https://doi.org/10.1073/pnas.1222821110\">10.1073/pnas.1222821110</a>."},"external_id":{"isi":["000315812800060"],"pmid":["23362379"]},"_id":"2887","article_processing_charge":"No","date_updated":"2025-09-29T13:32:25Z","issue":"7","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       110","publication":"PNAS","date_published":"2013-02-12T00:00:00Z","volume":110,"oa_version":"Published Version","publisher":"National Academy of Sciences","publication_status":"published"},{"page":"514 - 515","day":"01","citation":{"chicago":"Azevedo, Ricardo, Rolf Lohaus, and Tiago Paixao. “Networking Networks.” <i>Evolution &#38; Development</i>. Wiley-Blackwell, 2013.","ieee":"R. Azevedo, R. Lohaus, and T. Paixao, “Networking networks,” <i>Evolution &#38; Development</i>, vol. 10, no. 5. Wiley-Blackwell, pp. 514–515, 2013.","mla":"Azevedo, Ricardo, et al. “Networking Networks.” <i>Evolution &#38; Development</i>, vol. 10, no. 5, Wiley-Blackwell, 2013, pp. 514–15.","ama":"Azevedo R, Lohaus R, Paixao T. Networking networks. <i>Evolution &#38; Development</i>. 2013;10(5):514-515.","short":"R. Azevedo, R. Lohaus, T. Paixao, Evolution &#38; Development 10 (2013) 514–515.","ista":"Azevedo R, Lohaus R, Paixao T. 2013. Networking networks. Evolution &#38; Development. 10(5), 514–515.","apa":"Azevedo, R., Lohaus, R., &#38; Paixao, T. (2013). Networking networks. <i>Evolution &#38; Development</i>. Wiley-Blackwell."},"year":"2013","author":[{"first_name":"Ricardo","last_name":"Azevedo","full_name":"Azevedo, Ricardo B"},{"last_name":"Lohaus","first_name":"Rolf","full_name":"Lohaus, Rolf"},{"orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Tiago Paixao"}],"extern":1,"publist_id":"3858","issue":"5","title":"Networking networks","_id":"2900","month":"01","date_updated":"2021-01-12T07:00:34Z","intvolume":"        10","date_created":"2018-12-11T12:00:14Z","main_file_link":[{"open_access":"0","url":"http://onlinelibrary.wiley.com/doi/10.1111/j.1525-142X.2008.00265.x/abstract"}],"publication":"Evolution & Development","type":"journal_article","publisher":"Wiley-Blackwell","publication_status":"published","date_published":"2013-01-01T00:00:00Z","status":"public","volume":10,"quality_controlled":0},{"alternative_title":[" JMLR: W&CP"],"oa":1,"conference":{"end_date":"2013-05-01","start_date":"2013-04-29","location":"Scottsdale, AZ, United States","name":"AISTATS: Conference on Uncertainty in Artificial Intelligence"},"type":"conference","abstract":[{"lang":"eng","text":" We introduce the M-modes problem for graphical models: predicting the M label configurations of highest probability that are at the same time local maxima of the probability landscape. M-modes have multiple possible applications: because they are intrinsically diverse, they provide a principled alternative to non-maximum suppression techniques for structured prediction, they can act as codebook vectors for quantizing the configuration space, or they can form component centers for mixture model approximation. We present two algorithms for solving the M-modes problem. The first algorithm solves the problem in polynomial time when the underlying graphical model is a simple chain. The second algorithm solves the problem for junction chains. In synthetic and real dataset, we demonstrate how M-modes can improve the performance of prediction. We also use the generated modes as a tool to understand the topography of the probability distribution of configurations, for example with relation to the training set size and amount of noise in the data. "}],"main_file_link":[{"open_access":"1","url":"http://jmlr.org/proceedings/papers/v31/chen13a.html"}],"date_created":"2018-12-11T12:00:14Z","intvolume":"        31","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","oa_version":"None","volume":31,"date_published":"2013-01-01T00:00:00Z","status":"public","publication_status":"published","publisher":"JMLR","language":[{"iso":"eng"}],"publist_id":"3846","author":[{"first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yan","first_name":"Zhu","full_name":"Yan, Zhu"},{"full_name":"Metaxas, Dimitris","first_name":"Dimitris","last_name":"Metaxas"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"year":"2013","day":"01","citation":{"ieee":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, and C. Lampert, “Computing the M most probable modes of a graphical model,” presented at the AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States, 2013, vol. 31, pp. 161–169.","chicago":"Chen, Chao, Vladimir Kolmogorov, Zhu Yan, Dimitris Metaxas, and Christoph Lampert. “Computing the M Most Probable Modes of a Graphical Model,” 31:161–69. JMLR, 2013.","short":"C. Chen, V. Kolmogorov, Z. Yan, D. Metaxas, C. Lampert, in:, JMLR, 2013, pp. 161–169.","ista":"Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. 2013. Computing the M most probable modes of a graphical model. AISTATS: Conference on Uncertainty in Artificial Intelligence,  JMLR: W&#38;CP, vol. 31, 161–169.","mla":"Chen, Chao, et al. <i>Computing the M Most Probable Modes of a Graphical Model</i>. Vol. 31, JMLR, 2013, pp. 161–69.","ama":"Chen C, Kolmogorov V, Yan Z, Metaxas D, Lampert C. Computing the M most probable modes of a graphical model. In: Vol 31. JMLR; 2013:161-169.","apa":"Chen, C., Kolmogorov, V., Yan, Z., Metaxas, D., &#38; Lampert, C. (2013). Computing the M most probable modes of a graphical model (Vol. 31, pp. 161–169). Presented at the AISTATS: Conference on Uncertainty in Artificial Intelligence, Scottsdale, AZ, United States: JMLR."},"scopus_import":"1","page":"161 - 169","department":[{"_id":"HeEd"},{"_id":"VlKo"},{"_id":"ChLa"}],"date_updated":"2025-07-10T11:52:23Z","month":"01","article_processing_charge":"No","_id":"2901","title":"Computing the M most probable modes of a graphical model"},{"file_date_updated":"2020-07-14T12:45:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments","alternative_title":["ALENEX"],"conference":{"end_date":"2013-01-07","start_date":"2013-01-07","name":"ALENEX: Algorithm Engineering and Experiments","location":"New Orleans, LA, United States"},"publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","date_published":"2013-01-01T00:00:00Z","oa_version":"Submitted Version","citation":{"apa":"Kerber, M., &#38; Edelsbrunner, H. (2013). 3D kinetic alpha complexes and their implementation. In <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i> (pp. 70–77). New Orleans, LA, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611972931.6\">https://doi.org/10.1137/1.9781611972931.6</a>","short":"M. Kerber, H. Edelsbrunner, in:, 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2013, pp. 70–77.","ista":"Kerber M, Edelsbrunner H. 2013. 3D kinetic alpha complexes and their implementation. 2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, ALENEX, , 70–77.","mla":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>, Society for Industrial and Applied Mathematics, 2013, pp. 70–77, doi:<a href=\"https://doi.org/10.1137/1.9781611972931.6\">10.1137/1.9781611972931.6</a>.","ama":"Kerber M, Edelsbrunner H. 3D kinetic alpha complexes and their implementation. In: <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>. Society for Industrial and Applied Mathematics; 2013:70-77. doi:<a href=\"https://doi.org/10.1137/1.9781611972931.6\">10.1137/1.9781611972931.6</a>","ieee":"M. Kerber and H. Edelsbrunner, “3D kinetic alpha complexes and their implementation,” in <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>, New Orleans, LA, United States, 2013, pp. 70–77.","chicago":"Kerber, Michael, and Herbert Edelsbrunner. “3D Kinetic Alpha Complexes and Their Implementation.” In <i>2013 Proceedings of the 15th Workshop on Algorithm Engineering and Experiments</i>, 70–77. Society for Industrial and Applied Mathematics, 2013. <a href=\"https://doi.org/10.1137/1.9781611972931.6\">https://doi.org/10.1137/1.9781611972931.6</a>."},"department":[{"_id":"HeEd"}],"publist_id":"3841","language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"2906","date_updated":"2025-06-03T11:47:11Z","article_processing_charge":"No","date_created":"2018-12-11T12:00:16Z","abstract":[{"text":"Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented\r\nusing CGAL, following the exact geometric computation paradigm. We report on several\r\ntechniques to accelerate the computation that turn our implementation applicable to the underlying biological\r\nproblem.","lang":"eng"}],"type":"conference","file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:08:57Z","file_name":"IST-2016-547-v1+1_2013-P-08-MedusaII.pdf","file_id":"4720","file_size":403013,"checksum":"a15a3ba22df9445731507f3e06c9fcee","date_updated":"2020-07-14T12:45:52Z","creator":"system","access_level":"open_access","relation":"main_file"}],"oa":1,"corr_author":"1","status":"public","quality_controlled":"1","day":"01","scopus_import":"1","page":"70 - 77","author":[{"full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael"},{"first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1137/1.9781611972931.6","year":"2013","pubrep_id":"547","ddc":["500"],"title":"3D kinetic alpha complexes and their implementation","month":"01"},{"date_created":"2018-12-11T12:00:16Z","abstract":[{"lang":"eng","text":"Sex and recombination are among the most striking features of the living world, and they play a crucial role in allowing the evolution of complex adaptation. The sharing of genomes through the sexual union of different individuals requires elaborate behavioral and physiological adaptations. At the molecular level, the alignment of two DNA double helices, followed by their precise cutting and rejoining, is an extraordinary feat. Sex and recombination have diverse—and often surprising—evolutionary consequences: distinct sexes, elaborate mating displays, selfish genetic elements, and so on."}],"type":"book_chapter","oa":1,"file":[{"file_id":"5237","file_size":79838,"checksum":"8332ca9cb40f7e66d1006b175ce36b60","date_updated":"2020-07-14T12:45:52Z","access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:16:47Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"IST-2013-119-v1+1_IV.4_Recombination_and_Sex_Barton_1-13-13-e.docx"},{"relation":"main_file","date_updated":"2020-07-14T12:45:52Z","access_level":"open_access","creator":"system","file_size":144131,"checksum":"849f418620fb78d6ba23bb4f488ee93f","file_id":"5238","date_created":"2018-12-12T10:16:48Z","content_type":"application/pdf","file_name":"IST-2017-119-v1+2_Barton_Recombination_Sex.pdf"}],"corr_author":"1","status":"public","quality_controlled":"1","day":"04","page":"328 - 333","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"year":"2013","pubrep_id":"119","ddc":["576"],"title":"Recombination and sex","month":"11","file_date_updated":"2020-07-14T12:45:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"The Princeton Guide to Evolution","publication_status":"published","publisher":"Princeton University Press","date_published":"2013-11-04T00:00:00Z","oa_version":"Submitted Version","publication_identifier":{"isbn":["9780691149776"]},"citation":{"mla":"Barton, Nicholas H. “Recombination and Sex.” <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–33.","ama":"Barton NH. Recombination and sex. In: <i>The Princeton Guide to Evolution</i>. Princeton University Press; 2013:328-333.","short":"N.H. Barton, in:, The Princeton Guide to Evolution, Princeton University Press, 2013, pp. 328–333.","ista":"Barton NH. 2013.Recombination and sex. In: The Princeton Guide to Evolution. , 328–333.","apa":"Barton, N. H. (2013). Recombination and sex. In <i>The Princeton Guide to Evolution</i> (pp. 328–333). Princeton University Press.","chicago":"Barton, Nicholas H. “Recombination and Sex.” In <i>The Princeton Guide to Evolution</i>, 328–33. Princeton University Press, 2013.","ieee":"N. H. Barton, “Recombination and sex,” in <i>The Princeton Guide to Evolution</i>, Princeton University Press, 2013, pp. 328–333."},"department":[{"_id":"NiBa"}],"publist_id":"3839","language":[{"iso":"eng"}],"has_accepted_license":"1","_id":"2907","date_updated":"2024-10-09T20:55:04Z"},{"publication":"Journal of Evolutionary Biology","file_date_updated":"2020-07-14T12:45:52Z","intvolume":"        26","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"publication_status":"published","publisher":"Wiley-Blackwell","oa_version":"Submitted Version","date_published":"2013-01-17T00:00:00Z","volume":26,"external_id":{"isi":["000313747600007"]},"citation":{"mla":"Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2, Wiley-Blackwell, 2013, pp. 267–69, doi:<a href=\"https://doi.org/10.1111/jeb.12015\">10.1111/jeb.12015</a>.","ama":"Barton NH. Does hybridisation influence speciation?  . <i>Journal of Evolutionary Biology</i>. 2013;26(2):267-269. doi:<a href=\"https://doi.org/10.1111/jeb.12015\">10.1111/jeb.12015</a>","ista":"Barton NH. 2013. Does hybridisation influence speciation?  . Journal of Evolutionary Biology. 26(2), 267–269.","short":"N.H. Barton, Journal of Evolutionary Biology 26 (2013) 267–269.","apa":"Barton, N. H. (2013). Does hybridisation influence speciation?  . <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/jeb.12015\">https://doi.org/10.1111/jeb.12015</a>","chicago":"Barton, Nicholas H. “Does Hybridisation Influence Speciation?  .” <i>Journal of Evolutionary Biology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/jeb.12015\">https://doi.org/10.1111/jeb.12015</a>.","ieee":"N. H. Barton, “Does hybridisation influence speciation?  ,” <i>Journal of Evolutionary Biology</i>, vol. 26, no. 2. Wiley-Blackwell, pp. 267–269, 2013."},"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publist_id":"3835","issue":"2","date_updated":"2025-09-29T13:31:43Z","article_processing_charge":"No","_id":"2908","abstract":[{"lang":"eng","text":"Hybridization is an almost inevitable component of speciation, and its study can tell us much about that process. However, hybridization itself may have a negligible influence on the origin of species: on the one hand, universally favoured alleles spread readily across hybrid zones, whilst on the other, spatially heterogeneous selection causes divergence despite gene flow. Thus, narrow hybrid zones or occasional hybridisation may hardly affect the process of divergence."}],"date_created":"2018-12-11T12:00:17Z","oa":1,"file":[{"file_id":"4762","file_size":13339,"checksum":"716e88714c3411cd0bd70928b14ea692","date_updated":"2020-07-14T12:45:52Z","access_level":"open_access","creator":"system","relation":"main_file","content_type":"text/rtf","date_created":"2018-12-12T10:09:38Z","file_name":"IST-2013-111-v1+1_Hybridisation_and_speciation_revised.rtf"},{"file_id":"4763","file_size":103437,"checksum":"957fd07c71c1b1eac2c65ae3311aca78","date_updated":"2020-07-14T12:45:52Z","creator":"system","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:09:39Z","content_type":"application/pdf","file_name":"IST-2017-111-v1+2_Hybridisation_and_speciation_revised.pdf"}],"type":"journal_article","corr_author":"1","quality_controlled":"1","status":"public","author":[{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"year":"2013","doi":"10.1111/jeb.12015","day":"17","scopus_import":"1","page":"267 - 269","ddc":["576"],"pubrep_id":"111","month":"01","title":"Does hybridisation influence speciation?  "},{"corr_author":"1","quality_controlled":"1","status":"public","abstract":[{"lang":"eng","text":"We survey a class of models for spatially structured populations\r\nwhich we have called spatial Λ-Fleming–Viot processes. They arise from a flexible\r\nframework for modelling in which the key innovation is that random genetic drift\r\nis driven by a Poisson point process of spatial ‘events’. We demonstrate how this\r\novercomes some of the obstructions to modelling populations which evolve in two-\r\n(and higher-) dimensional spatial continua, how its predictions match phenomena\r\nobserved in data and how it fits with classical models. Finally we outline some\r\ndirections for future research."}],"date_created":"2018-12-11T12:00:17Z","file":[{"date_updated":"2020-07-14T12:45:52Z","creator":"system","access_level":"open_access","relation":"main_file","file_id":"5242","file_size":702583,"checksum":"ce8a4424385b3086138a1e054e16e0e3","content_type":"application/pdf","date_created":"2018-12-12T10:16:52Z","file_name":"IST-2016-557-v1+1_BEVrevised.pdf"}],"oa":1,"type":"journal_article","ddc":["570"],"pubrep_id":"557","month":"01","title":"Modelling evolution in a spatial continuum","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"year":"2013","doi":"10.1088/1742-5468/2013/01/P01002","day":"16","scopus_import":"1","publication_status":"published","publisher":"IOP Publishing","ec_funded":1,"oa_version":"Submitted Version","volume":2013,"date_published":"2013-01-16T00:00:00Z","publication":"Journal of Statistical Mechanics Theory and Experiment","file_date_updated":"2020-07-14T12:45:52Z","intvolume":"      2013","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"issue":"1","date_updated":"2025-09-29T13:31:08Z","article_processing_charge":"No","_id":"2909","external_id":{"isi":["000315410500003"]},"citation":{"apa":"Barton, N. H., Etheridge, A., &#38; Véber, A. (2013). Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>","short":"N.H. Barton, A. Etheridge, A. Véber, Journal of Statistical Mechanics Theory and Experiment 2013 (2013).","ista":"Barton NH, Etheridge A, Véber A. 2013. Modelling evolution in a spatial continuum. Journal of Statistical Mechanics Theory and Experiment. 2013(1).","mla":"Barton, Nicholas H., et al. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1, IOP Publishing, 2013, doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>.","ama":"Barton NH, Etheridge A, Véber A. Modelling evolution in a spatial continuum. <i>Journal of Statistical Mechanics Theory and Experiment</i>. 2013;2013(1). doi:<a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">10.1088/1742-5468/2013/01/P01002</a>","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “Modelling evolution in a spatial continuum,” <i>Journal of Statistical Mechanics Theory and Experiment</i>, vol. 2013, no. 1. IOP Publishing, 2013.","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “Modelling Evolution in a Spatial Continuum.” <i>Journal of Statistical Mechanics Theory and Experiment</i>. IOP Publishing, 2013. <a href=\"https://doi.org/10.1088/1742-5468/2013/01/P01002\">https://doi.org/10.1088/1742-5468/2013/01/P01002</a>."},"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publist_id":"3834"},{"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:45:52Z","intvolume":"        29","publication":"Bioinformatics","volume":29,"date_published":"2013-02-07T00:00:00Z","oa_version":"Published Version","ec_funded":1,"publisher":"Oxford University Press","publication_status":"published","publist_id":"3833","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"citation":{"mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>.","ama":"Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. <i>Bioinformatics</i>. 2013;29(7):955-956. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>","ista":"Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956.","short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.","apa":"Kelleher, J., Barton, N. H., &#38; Etheridge, A. (2013). Coalescent simulation in continuous space. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>","chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>.","ieee":"J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” <i>Bioinformatics</i>, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013."},"external_id":{"isi":["000316695700020"]},"_id":"2910","article_processing_charge":"No","date_updated":"2025-09-29T13:30:36Z","issue":"7","type":"journal_article","oa":1,"file":[{"file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","date_created":"2018-12-12T10:16:04Z","content_type":"application/pdf","file_id":"5189","checksum":"a3b54d7477fac923815ac082403d9bd0","file_size":170197,"creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:45:52Z","relation":"main_file"}],"date_created":"2018-12-11T12:00:17Z","abstract":[{"lang":"eng","text":"Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module."}],"status":"public","quality_controlled":"1","corr_author":"1","scopus_import":"1","page":"955 - 956","day":"07","doi":"10.1093/bioinformatics/btt067","year":"2013","author":[{"full_name":"Kelleher, Jerome","first_name":"Jerome","last_name":"Kelleher"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152"}],"title":"Coalescent simulation in continuous space","month":"02","pubrep_id":"556","ddc":["570"]},{"corr_author":"1","quality_controlled":"1","arxiv":1,"status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.6598"}],"abstract":[{"lang":"eng","text":"The ability of an organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this &quot;neural metric&quot; tells us how distinguishable a pair of stimulus clips is to the retina, based on the similarity between the induced distributions of population responses. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the support-vector-machine- like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding."}],"date_created":"2018-12-11T12:00:18Z","oa":1,"type":"journal_article","month":"01","title":"Retinal metric: a stimulus distance measure derived from population neural responses","doi":"10.1103/PhysRevLett.110.058104","year":"2013","author":[{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"full_name":"Granot Atedgi, Einat","first_name":"Einat","last_name":"Granot Atedgi"},{"first_name":"Ronen","last_name":"Segev","full_name":"Segev, Ronen"},{"last_name":"Schneidman","first_name":"Elad","full_name":"Schneidman, Elad"}],"scopus_import":"1","day":"28","article_number":"058104","publisher":"American Physical Society","publication_status":"published","oa_version":"Preprint","date_published":"2013-01-28T00:00:00Z","volume":110,"publication":"Physical Review Letters","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       110","isi":1,"issue":"5","article_processing_charge":"No","date_updated":"2025-09-29T13:29:59Z","_id":"2913","external_id":{"isi":["000314090300012"],"arxiv":["1205.6598"]},"department":[{"_id":"GaTk"}],"citation":{"short":"G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).","ista":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 110(5), 058104.","ama":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus distance measure derived from population neural responses. <i>Physical Review Letters</i>. 2013;110(5). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">10.1103/PhysRevLett.110.058104</a>","mla":"Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” <i>Physical Review Letters</i>, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">10.1103/PhysRevLett.110.058104</a>.","apa":"Tkačik, G., Granot Atedgi, E., Segev, R., &#38; Schneidman, E. (2013). Retinal metric: a stimulus distance measure derived from population neural responses. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">https://doi.org/10.1103/PhysRevLett.110.058104</a>","ieee":"G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” <i>Physical Review Letters</i>, vol. 110, no. 5. American Physical Society, 2013.","chicago":"Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">https://doi.org/10.1103/PhysRevLett.110.058104</a>."},"language":[{"iso":"eng"}],"publist_id":"3830"},{"title":"Statistical thermodynamics of natural images","month":"01","pubrep_id":"401","ddc":["530"],"article_type":"original","article_number":"018701","day":"02","author":[{"first_name":"Greg","last_name":"Stephens","full_name":"Stephens, Greg"},{"full_name":"Mora, Thierry","first_name":"Thierry","last_name":"Mora"},{"first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"last_name":"Bialek","first_name":"William","full_name":"Bialek, William"}],"doi":"10.1103/PhysRevLett.110.018701","year":"2013","status":"public","arxiv":1,"quality_controlled":"1","type":"journal_article","oa":1,"file":[{"file_name":"IST-2016-401-v1+1_1281.full.pdf","date_created":"2018-12-12T10:18:44Z","content_type":"application/pdf","creator":"system","access_level":"open_access","date_updated":"2020-07-14T12:45:53Z","relation":"main_file","file_id":"5366","checksum":"72bfbc2094c4680e8a8a6bed668cd06d","file_size":416965}],"date_created":"2018-12-11T12:00:19Z","abstract":[{"text":"The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding thermodynamics. We find evidence for criticality in a diverging specific heat, which corresponds to large fluctuations in how &quot;surprising&quot; we find individual images, and in the quantitative form of the entropy vs energy. We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations.","lang":"eng"}],"_id":"2914","date_updated":"2025-09-29T13:29:28Z","article_processing_charge":"No","issue":"1","publist_id":"3829","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"short":"G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).","ista":"Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701.","ama":"Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. <i>Physical Review Letters</i>. 2013;110(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">10.1103/PhysRevLett.110.018701</a>","mla":"Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">10.1103/PhysRevLett.110.018701</a>.","apa":"Stephens, G., Mora, T., Tkačik, G., &#38; Bialek, W. (2013). Statistical thermodynamics of natural images. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>","ieee":"G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” <i>Physical Review Letters</i>, vol. 110, no. 1. American Physical Society, 2013.","chicago":"Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>."},"department":[{"_id":"GaTk"}],"external_id":{"isi":["000313006100058"],"arxiv":["0806.2694"]},"date_published":"2013-01-02T00:00:00Z","volume":110,"oa_version":"Published Version","publication_status":"published","publisher":"American Physical Society","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"acknowledgement":"This work was supported in part by NSF Grants No. IIS-0613435, No. IBN-0344678, and No. PHY-0957573, by NIH Grant No. T32 MH065214, by the Human Frontier Science Program, and by the Swartz Foundation.\r\nCC BY 3.0\r\n","isi":1,"file_date_updated":"2020-07-14T12:45:53Z","intvolume":"       110","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Physical Review Letters"},{"language":[{"iso":"eng"}],"publist_id":"3819","external_id":{"isi":["000312841300007"]},"citation":{"short":"I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot, M. González Gaitán, Nature Cell Biology 15 (2013) 28–39.","ista":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 15(1), 28–39.","ama":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. 2013;15(1):28-39. doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>","mla":"Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>, vol. 15, no. 1, Nature Publishing Group, 2013, pp. 28–39, doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>.","apa":"Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot, F., &#38; González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>","ieee":"I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot, and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,” <i>Nature Cell Biology</i>, vol. 15, no. 1. Nature Publishing Group, pp. 28–39, 2013.","chicago":"Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg, Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>."},"department":[{"_id":"CaHe"}],"date_updated":"2025-09-30T08:16:16Z","article_processing_charge":"No","_id":"2918","issue":"1","acknowledgement":"This work was supported by the SNSF, the Swiss SystemsX.ch initiative and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers in Genetics and Chemical Biology programmes and the Polish–Swiss research program (M.G-G.).","isi":1,"publication":"Nature Cell Biology","intvolume":"        15","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"None","volume":15,"date_published":"2013-01-01T00:00:00Z","publication_status":"published","publisher":"Nature Publishing Group","author":[{"full_name":"Castanon, Irinka","last_name":"Castanon","first_name":"Irinka"},{"last_name":"Abrami","first_name":"Laurence","full_name":"Abrami, Laurence"},{"last_name":"Holtzer","first_name":"Laurent","full_name":"Holtzer, Laurent"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"full_name":"Van Der Goot, Françoise","first_name":"Françoise","last_name":"Van Der Goot"},{"full_name":"González Gaitán, Marcos","first_name":"Marcos","last_name":"González Gaitán"}],"year":"2013","doi":"10.1038/ncb2632","day":"01","scopus_import":"1","page":"28 - 39","month":"01","title":"Anthrax toxin receptor 2a controls mitotic spindle positioning","type":"journal_article","abstract":[{"lang":"eng","text":"Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.\r\n"}],"date_created":"2018-12-11T12:00:20Z","quality_controlled":"1","status":"public"},{"publisher":"Wiley-Blackwell","publication_status":"published","oa_version":"Submitted Version","volume":32,"date_published":"2013-01-23T00:00:00Z","publication":"EMBO Journal","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        32","isi":1,"issue":"2","article_processing_charge":"No","date_updated":"2025-09-29T13:28:19Z","_id":"2919","external_id":{"pmid":["23211744"],"isi":["000316464500009"]},"department":[{"_id":"JiFr"}],"pmid":1,"citation":{"ieee":"P. Baster <i>et al.</i>, “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” <i>EMBO Journal</i>, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.","chicago":"Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste, Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>.","apa":"Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald, W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>","ista":"Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.","short":"P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald, B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274.","ama":"Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. 2013;32(2):260-274. doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>","mla":"Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>, vol. 32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>."},"language":[{"iso":"eng"}],"publist_id":"3818","corr_author":"1","quality_controlled":"1","status":"public","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/"}],"abstract":[{"text":"The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth.","lang":"eng"}],"date_created":"2018-12-11T12:00:20Z","oa":1,"type":"journal_article","month":"01","title":"SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism","doi":"10.1038/emboj.2012.310","year":"2013","author":[{"id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Baster, Pawel","last_name":"Baster","first_name":"Pawel"},{"full_name":"Robert, Stéphanie","last_name":"Robert","first_name":"Stéphanie"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine Vehn, Jürgen"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Kania, Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","last_name":"Kania","first_name":"Urszula"},{"last_name":"Grunewald","first_name":"Wim","full_name":"Grunewald, Wim"},{"first_name":"Bert","last_name":"De Rybel","full_name":"De Rybel, Bert"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"scopus_import":"1","page":"260 - 274","day":"23"},{"month":"01","title":"Neurulation coordinating cell polarisation and lumen formation","year":"2013","doi":"10.1038/emboj.2012.325","author":[{"last_name":"Compagnon","first_name":"Julien","full_name":"Compagnon, Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"scopus_import":"1","page":"1 - 3","day":"09","quality_controlled":"1","status":"public","corr_author":"1","oa":1,"type":"journal_article","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/","open_access":"1"}],"abstract":[{"text":"Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen.","lang":"eng"}],"date_created":"2018-12-11T12:00:20Z","article_processing_charge":"No","date_updated":"2025-09-29T13:27:27Z","_id":"2920","issue":"1","language":[{"iso":"eng"}],"publist_id":"3817","external_id":{"pmid":["23211745"],"isi":["000314141900001"]},"pmid":1,"department":[{"_id":"CaHe"}],"citation":{"ieee":"J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation and lumen formation,” <i>EMBO Journal</i>, vol. 32, no. 1. Wiley-Blackwell, pp. 1–3, 2013.","chicago":"Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>.","ista":"Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 32(1), 1–3.","short":"J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3.","mla":"Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 1–3, doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>.","ama":"Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. 2013;32(1):1-3. doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>","apa":"Compagnon, J., &#38; Heisenberg, C.-P. J. (2013). Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>"},"oa_version":"Submitted Version","date_published":"2013-01-09T00:00:00Z","volume":32,"publisher":"Wiley-Blackwell","publication_status":"published","isi":1,"publication":"EMBO Journal","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        32"},{"day":"01","page":"435 - 447","scopus_import":"1","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","last_name":"Chen","first_name":"Chao"},{"first_name":"Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299","full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"}],"year":"2013","doi":"10.1016/j.comgeo.2012.02.010","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3367"}]},"title":"An output sensitive algorithm for persistent homology","month":"05","date_created":"2018-12-11T12:00:27Z","abstract":[{"text":"In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ &gt; 0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number of homology classes with persistence at least (1 - δ) Γ, n is the total number of simplices in the complex, d its dimension, and R d (n) is the complexity of computing the rank of an n × n matrix with O (d n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ) Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C (1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} &gt; 0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n log n).","lang":"eng"}],"type":"journal_article","corr_author":"1","status":"public","quality_controlled":"1","citation":{"short":"C. Chen, M. Kerber, Computational Geometry: Theory and Applications 46 (2013) 435–447.","ista":"Chen C, Kerber M. 2013. An output sensitive algorithm for persistent homology. Computational Geometry: Theory and Applications. 46(4), 435–447.","ama":"Chen C, Kerber M. An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. 2013;46(4):435-447. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>","mla":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4, Elsevier, 2013, pp. 435–47, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>.","apa":"Chen, C., &#38; Kerber, M. (2013). An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>","ieee":"C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4. Elsevier, pp. 435–447, 2013.","chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>."},"department":[{"_id":"HeEd"}],"external_id":{"isi":["000314437000004"]},"publist_id":"3796","language":[{"iso":"eng"}],"issue":"4","_id":"2939","date_updated":"2025-09-29T13:26:21Z","article_processing_charge":"No","intvolume":"        46","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Computational Geometry: Theory and Applications","acknowledgement":"The authors thank Herbert Edelsbrunner for many helpful discussions and suggestions. Moreover, they are grateful for the careful reviews that helped to improve the quality of the paper.","isi":1,"publication_status":"published","publisher":"Elsevier","volume":46,"date_published":"2013-05-01T00:00:00Z","oa_version":"None"},{"citation":{"apa":"Krenn, S., Pietrzak, K. Z., &#38; Wadia, A. (2013). A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">https://doi.org/10.1007/978-3-642-36594-2_2</a>","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp. 23–39.","ista":"Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. TCC: Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.","mla":"Krenn, Stephan, et al. <i>A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It</i>. Edited by Amit Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:<a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">10.1007/978-3-642-36594-2_2</a>.","ama":"Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed. Vol 7785. Springer; 2013:23-39. doi:<a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">10.1007/978-3-642-36594-2_2</a>","ieee":"S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it,” presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol. 7785, pp. 23–39.","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">https://doi.org/10.1007/978-3-642-36594-2_2</a>."},"department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publist_id":"3795","date_updated":"2025-09-18T11:37:22Z","_id":"2940","file_date_updated":"2020-07-14T12:45:54Z","intvolume":"      7785","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"conference":{"location":"Tokyo, Japan","name":"TCC: Theory of Cryptography Conference","start_date":"2013-03-03","end_date":"2013-03-06"},"publication_status":"published","publisher":"Springer","ec_funded":1,"oa_version":"Submitted Version","date_published":"2013-01-29T00:00:00Z","volume":7785,"project":[{"call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"author":[{"id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","full_name":"Krenn, Stephan","last_name":"Krenn","first_name":"Stephan","orcid":"0000-0003-2835-9093"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"},{"first_name":"Akshay","last_name":"Wadia","full_name":"Wadia, Akshay"}],"year":"2013","doi":"10.1007/978-3-642-36594-2_2","day":"29","page":"23 - 39","scopus_import":1,"ddc":["000"],"related_material":{"record":[{"id":"1479","status":"public","relation":"later_version"}]},"month":"01","title":"A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it","abstract":[{"text":"A chain rule for an entropy notion H(.) states that the entropy H(X) of a variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)&gt;= H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)&gt;= H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability entropy and several variants of HILL entropy) satisfy the chain rule for conditional entropy, though here not only the quantity decreases by l, but also the quality of the entropy decreases exponentially in l. However, for \r\nthe standard notion of conditional HILL entropy (the computational equivalent of min-entropy) the existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that for conditional HILL entropy no meaningful chain rule exists, assuming the existence of one-way permutations: there exist distributions X,Y,A, where A is a distribution over a single bit, but  $H(X|Y)&gt;&gt;H(X|Y,A)$, even if we simultaneously allow for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying our construction is based on a surprising connection between the chain rule for HILL entropy and deniable encryption. ","lang":"eng"}],"editor":[{"full_name":"Sahai, Amit","first_name":"Amit","last_name":"Sahai"}],"date_created":"2018-12-11T12:00:27Z","oa":1,"file":[{"content_type":"application/pdf","date_created":"2019-01-22T14:11:11Z","file_name":"2013_LNCS_Krenn.pdf","file_size":414823,"checksum":"beb0cc1c0579da2d2e84394230a5da78","file_id":"5875","relation":"main_file","date_updated":"2020-07-14T12:45:54Z","creator":"dernst","access_level":"open_access"}],"type":"conference","quality_controlled":"1","status":"public"},{"issue":"4","_id":"2944","date_updated":"2025-09-29T13:25:36Z","article_processing_charge":"No","citation":{"apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>.","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. 2013;22(4):987-1002. doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>.","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” <i>Molecular Ecology</i>, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013."},"department":[{"_id":"NiBa"}],"external_id":{"isi":["000314220900008"]},"publist_id":"3788","language":[{"iso":"eng"}],"publication_status":"published","publisher":"Wiley-Blackwell","date_published":"2013-02-01T00:00:00Z","volume":22,"oa_version":"None","intvolume":"        22","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication":"Molecular Ecology","acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","isi":1,"related_material":{"record":[{"id":"9758","relation":"research_data","status":"public"}]},"title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","month":"02","day":"01","scopus_import":"1","page":"987 - 1002","author":[{"last_name":"Aeschbacher","first_name":"Simon","full_name":"Aeschbacher, Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Futschik, Andreas","first_name":"Andreas","last_name":"Futschik"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"}],"year":"2013","doi":"10.1111/mec.12165","corr_author":"1","status":"public","quality_controlled":"1","date_created":"2018-12-11T12:00:28Z","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"type":"journal_article","acknowledged_ssus":[{"_id":"ScienComp"}]},{"status":"public","quality_controlled":"1","date_created":"2018-12-11T12:00:30Z","abstract":[{"text":"Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance.","lang":"eng"}],"type":"conference","file":[{"relation":"main_file","date_updated":"2020-07-14T12:45:55Z","creator":"dernst","access_level":"open_access","file_size":1513620,"checksum":"a0a7234a89e2192af655b0d0ae3bf445","file_id":"5874","date_created":"2019-01-22T14:03:11Z","content_type":"application/pdf","file_name":"2012_ACCV_Tommasi.pdf"}],"oa":1,"series_title":"Lecture Notes in Computer Science","ddc":["000"],"title":"Beyond dataset bias: Multi-task unaligned shared knowledge transfer","month":"04","day":"04","page":"1 - 15","scopus_import":1,"author":[{"first_name":"Tatiana","last_name":"Tommasi","full_name":"Tommasi, Tatiana"},{"last_name":"Quadrianto","first_name":"Novi","full_name":"Quadrianto, Novi"},{"first_name":"Barbara","last_name":"Caputo","full_name":"Caputo, Barbara"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"year":"2013","doi":"10.1007/978-3-642-37331-2_1","publication_status":"published","publisher":"Springer","date_published":"2013-04-04T00:00:00Z","volume":7724,"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:55Z","intvolume":"      7724","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"acknowledgement":"This work was supported by the PASCAL 2 Network of Excellence (TT) and by the Newton International Fellowship (NQ)","conference":{"end_date":"2012-11-09","start_date":"2012-11-05","name":"ACCV: Asian Conference on Computer Vision","location":"Daejeon, Korea"},"_id":"2948","date_updated":"2020-08-11T10:09:54Z","citation":{"chicago":"Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert. “Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>.","ieee":"T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias: Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15, 2013.","apa":"Tommasi, T., Quadrianto, N., Caputo, B., &#38; Lampert, C. (2013). Beyond dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>","ama":"Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 2013;7724:1-15. doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>","mla":"Tommasi, Tatiana, et al. <i>Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer</i>. Vol. 7724, Springer, 2013, pp. 1–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>.","ista":"Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 7724, 1–15.","short":"T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15."},"department":[{"_id":"ChLa"}],"publist_id":"3784","language":[{"iso":"eng"}],"has_accepted_license":"1"}]