[{"license":"https://creativecommons.org/publicdomain/zero/1.0/","external_id":{"isi":["000341528300001"]},"tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"isi":1,"has_accepted_license":"1","status":"public","article_number":"663","publisher":"BioMed Central","publist_id":"5009","day":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","file_date_updated":"2020-07-14T12:45:26Z","oa_version":"Published Version","_id":"2042","citation":{"short":"A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>, vol. 15, no. 1, 663, BioMed Central, 2014, doi:<a href=\"https://doi.org/10.1186/1471-2164-15-663\">10.1186/1471-2164-15-663</a>.","ieee":"A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” <i>BMC Genomics</i>, vol. 15, no. 1. BioMed Central, 2014.","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663.","chicago":"Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>. BioMed Central, 2014. <a href=\"https://doi.org/10.1186/1471-2164-15-663\">https://doi.org/10.1186/1471-2164-15-663</a>.","ama":"Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. <i>BMC Genomics</i>. 2014;15(1). doi:<a href=\"https://doi.org/10.1186/1471-2164-15-663\">10.1186/1471-2164-15-663</a>","apa":"Kupczok, A., &#38; Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2164-15-663\">https://doi.org/10.1186/1471-2164-15-663</a>"},"article_processing_charge":"No","date_published":"2014-08-08T00:00:00Z","doi":"10.1186/1471-2164-15-663","volume":15,"oa":1,"date_updated":"2025-09-29T11:52:17Z","abstract":[{"text":"Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here.","lang":"eng"}],"quality_controlled":"1","scopus_import":"1","type":"journal_article","ddc":["570"],"publication":"BMC Genomics","corr_author":"1","intvolume":"        15","pubrep_id":"396","year":"2014","month":"08","issue":"1","author":[{"full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"department":[{"_id":"JoBo"}],"date_created":"2018-12-11T11:55:23Z","file":[{"relation":"main_file","file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf","date_updated":"2020-07-14T12:45:26Z","access_level":"open_access","file_id":"4878","file_size":1489769,"content_type":"application/pdf","creator":"system","checksum":"3f6d2776b90a842a28359cc957d3d04b","date_created":"2018-12-12T10:11:24Z"}]},{"article_processing_charge":"No","date_published":"2014-01-01T00:00:00Z","oa":1,"date_updated":"2025-06-11T08:03:07Z","doi":"10.1137/1.9781611973198.4","conference":{"start_date":"2014-01-05","location":"Portland, USA","end_date":"2014-01-05","name":"ALENEX: Algorithm Engineering and Experiments"},"ec_funded":1,"abstract":[{"text":"Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node.","lang":"eng"}],"quality_controlled":"1","publication":"Proceedings of the Workshop on Algorithm Engineering and Experiments","arxiv":1,"scopus_import":"1","type":"conference","year":"2014","editor":[{"last_name":" McGeoch","full_name":" McGeoch, Catherine","first_name":"Catherine"},{"first_name":"Ulrich","last_name":"Meyer","full_name":"Meyer, Ulrich"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.0710"}],"month":"01","page":"31 - 38","author":[{"orcid":"0000-0002-9683-0724","last_name":"Bauer","full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"orcid":"0000-0002-8030-9299","last_name":"Kerber","full_name":"Kerber, Michael","first_name":"Michael"},{"last_name":"Reininghaus","full_name":"Reininghaus, Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:23Z","external_id":{"arxiv":["1310.0710"]},"publisher":"Society for Industrial and Applied Mathematics","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publist_id":"5008","publication_status":"published","title":"Distributed computation of persistent homology","_id":"2043","oa_version":"Submitted Version","project":[{"call_identifier":"FP7","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","name":"Topological Complex Systems"}],"citation":{"apa":"Bauer, U., Kerber, M., &#38; Reininghaus, J. (2014). Distributed computation of persistent homology. In C.  McGeoch &#38; U. Meyer (Eds.), <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i> (pp. 31–38). Portland, USA: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611973198.4\">https://doi.org/10.1137/1.9781611973198.4</a>","ama":"Bauer U, Kerber M, Reininghaus J. Distributed computation of persistent homology. In:  McGeoch C, Meyer U, eds. <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>. Society for Industrial and Applied Mathematics; 2014:31-38. doi:<a href=\"https://doi.org/10.1137/1.9781611973198.4\">10.1137/1.9781611973198.4</a>","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Distributed computation of persistent homology,” in <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, Portland, USA, 2014, pp. 31–38.","ista":"Bauer U, Kerber M, Reininghaus J. 2014. Distributed computation of persistent homology. Proceedings of the Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, 31–38.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Distributed Computation of Persistent Homology.” In <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, edited by Catherine  McGeoch and Ulrich Meyer, 31–38. Society for Industrial and Applied Mathematics, 2014. <a href=\"https://doi.org/10.1137/1.9781611973198.4\">https://doi.org/10.1137/1.9781611973198.4</a>.","mla":"Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, edited by Catherine  McGeoch and Ulrich Meyer, Society for Industrial and Applied Mathematics, 2014, pp. 31–38, doi:<a href=\"https://doi.org/10.1137/1.9781611973198.4\">10.1137/1.9781611973198.4</a>.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, C.  McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society for Industrial and Applied Mathematics, 2014, pp. 31–38."}},{"publisher":"Springer","status":"public","external_id":{"arxiv":["1303.0477"]},"publication_status":"published","series_title":"Mathematics and Visualization","day":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5007","title":"Clear and Compress: Computing Persistent Homology in Chunks","citation":{"ama":"Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. <i>Topological Methods in Data Analysis and Visualization III</i>. Mathematics and Visualization. Springer; 2014:103-117. doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">10.1007/978-3-319-04099-8_7</a>","apa":"Bauer, U., Kerber, M., &#38; Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, &#38; R. Peikert (Eds.), <i>Topological Methods in Data Analysis and Visualization III</i> (pp. 103–117). Springer. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">https://doi.org/10.1007/978-3-319-04099-8_7</a>","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III, Springer, 2014, pp. 103–117.","mla":"Bauer, Ulrich, et al. “Clear and Compress: Computing Persistent Homology in Chunks.” <i>Topological Methods in Data Analysis and Visualization III</i>, edited by Peer-Timo Bremer et al., Springer, 2014, pp. 103–17, doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">10.1007/978-3-319-04099-8_7</a>.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in <i>Topological Methods in Data Analysis and Visualization III</i>, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Clear and Compress: Computing Persistent Homology in Chunks.” In <i>Topological Methods in Data Analysis and Visualization III</i>, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 103–17. Mathematics and Visualization. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">https://doi.org/10.1007/978-3-319-04099-8_7</a>.","ista":"Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117."},"_id":"2044","oa_version":"Submitted Version","project":[{"name":"Topological Complex Systems","call_identifier":"FP7","_id":"255D761E-B435-11E9-9278-68D0E5697425","grant_number":"318493"}],"date_updated":"2025-06-11T07:56:57Z","oa":1,"doi":"10.1007/978-3-319-04099-8_7","date_published":"2014-03-19T00:00:00Z","article_processing_charge":"No","corr_author":"1","publication":"Topological Methods in Data Analysis and Visualization III","type":"book_chapter","scopus_import":"1","arxiv":1,"quality_controlled":"1","ec_funded":1,"abstract":[{"text":"We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation.","lang":"eng"}],"year":"2014","editor":[{"first_name":"Peer-Timo","last_name":"Bremer","full_name":"Bremer, Peer-Timo"},{"last_name":"Hotz","full_name":"Hotz, Ingrid","first_name":"Ingrid"},{"last_name":"Pascucci","full_name":"Pascucci, Valerio","first_name":"Valerio"},{"last_name":"Peikert","full_name":"Peikert, Ronald","first_name":"Ronald"}],"page":"103 - 117","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:23Z","department":[{"_id":"HeEd"}],"author":[{"first_name":"Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","full_name":"Bauer, Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer"},{"full_name":"Kerber, Michael","last_name":"Kerber","orcid":"0000-0002-8030-9299","first_name":"Michael"},{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87"}],"month":"03","main_file_link":[{"url":"http://arxiv.org/abs/1303.0477","open_access":"1"}]},{"date_created":"2018-12-11T11:55:24Z","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Dachman Soled","full_name":"Dachman Soled, Dana","first_name":"Dana"},{"full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mohassel, Payman","last_name":"Mohassel","first_name":"Payman"},{"last_name":"O’Neill","full_name":"O’Neill, Adam","first_name":"Adam"}],"page":"329 - 344","month":"01","main_file_link":[{"url":"https://eprint.iacr.org/2012/543","open_access":"1"}],"alternative_title":["LNCS"],"editor":[{"full_name":"Krawczyk, Hugo","last_name":"Krawczyk","first_name":"Hugo"}],"year":"2014","scopus_import":1,"type":"conference","intvolume":"      8383","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","quality_controlled":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest."}],"conference":{"start_date":"2014-03-26","location":"Buenos Aires, Argentina","end_date":"2014-03-28","name":"PKC: Public Key Crypography"},"doi":"10.1007/978-3-642-54631-0_19","volume":8383,"date_updated":"2021-01-12T06:54:57Z","oa":1,"date_published":"2014-01-01T00:00:00Z","citation":{"ama":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. Enhanced chosen-ciphertext security and applications. In: Krawczyk H, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8383. Springer; 2014:329-344. doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">10.1007/978-3-642-54631-0_19</a>","apa":"Dachman Soled, D., Fuchsbauer, G., Mohassel, P., &#38; O’Neill, A. (2014). Enhanced chosen-ciphertext security and applications. In H. Krawczyk (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8383, pp. 329–344). Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">https://doi.org/10.1007/978-3-642-54631-0_19</a>","short":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344.","mla":"Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">10.1007/978-3-642-54631-0_19</a>.","ieee":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, and A. O’Neill, “Enhanced chosen-ciphertext security and applications,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Buenos Aires, Argentina, 2014, vol. 8383, pp. 329–344.","chicago":"Dachman Soled, Dana, Georg Fuchsbauer, Payman Mohassel, and Adam O’Neill. “Enhanced Chosen-Ciphertext Security and Applications.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, 8383:329–44. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">https://doi.org/10.1007/978-3-642-54631-0_19</a>.","ista":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. 2014. Enhanced chosen-ciphertext security and applications. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 329–344."},"project":[{"call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography"}],"oa_version":"Submitted Version","_id":"2045","title":"Enhanced chosen-ciphertext security and applications","publication_status":"published","publist_id":"5006","day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The second author was supported by EPSRC grant EP/H043454/1.","status":"public","publisher":"Springer"},{"conference":{"start_date":"2014-05-26","location":"Buenos Aires, Argentina","end_date":"2014-05-28","name":"PKC: Public Key Crypography"},"quality_controlled":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications."}],"intvolume":"      8383","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","scopus_import":1,"type":"conference","date_published":"2014-01-01T00:00:00Z","date_updated":"2021-01-12T06:54:57Z","oa":1,"doi":"10.1007/978-3-642-54631-0_30","volume":8383,"month":"01","main_file_link":[{"url":"https://eprint.iacr.org/2013/413","open_access":"1"}],"page":"520 - 537","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:24Z","department":[{"_id":"KrPi"}],"author":[{"last_name":"Bellare","full_name":"Bellare, Mihir","first_name":"Mihir"},{"full_name":"Fuchsbauer, Georg","last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"}],"year":"2014","editor":[{"last_name":"Krawczyk","full_name":"Krawczyk, Hugo","first_name":"Hugo"}],"alternative_title":["LNCS"],"day":"01","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1.","publist_id":"5005","publication_status":"published","publisher":"Springer","status":"public","oa_version":"Submitted Version","_id":"2046","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"citation":{"ista":"Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537.","ieee":"M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537.","chicago":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, 8383:520–37. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">https://doi.org/10.1007/978-3-642-54631-0_30</a>.","mla":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 520–37, doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">10.1007/978-3-642-54631-0_30</a>.","short":"M. Bellare, G. Fuchsbauer, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 520–537.","apa":"Bellare, M., &#38; Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">https://doi.org/10.1007/978-3-642-54631-0_30</a>","ama":"Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8383. Springer; 2014:520-537. doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">10.1007/978-3-642-54631-0_30</a>"},"title":"Policy-based signatures"},{"date_published":"2014-01-01T00:00:00Z","oa":1,"date_updated":"2024-11-04T13:35:21Z","doi":"10.1007/978-3-319-11257-2_14","volume":8744,"conference":{"end_date":"2014-09-19","name":"PSD: Privacy in Statistical Databases","start_date":"2014-09-17","location":"Ibiza, Spain"},"abstract":[{"lang":"eng","text":"Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance."}],"quality_controlled":"1","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","intvolume":"      8744","type":"conference","arxiv":1,"scopus_import":1,"year":"2014","editor":[{"full_name":"Domingo Ferrer, Josep","last_name":"Domingo Ferrer","first_name":"Josep"}],"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.8067"}],"month":"01","page":"170 - 184","author":[{"last_name":"Yu","full_name":"Yu, Fei","first_name":"Fei"},{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar","full_name":"Rybar, Michal"},{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","full_name":"Uhler, Caroline"},{"first_name":"Stephen","last_name":"Fienberg","full_name":"Fienberg, Stephen"}],"department":[{"_id":"KrPi"},{"_id":"CaUh"}],"date_created":"2018-12-11T11:55:24Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["1407.8067"]},"publisher":"Springer","status":"public","acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publist_id":"5004","publication_status":"published","title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","_id":"2047","oa_version":"Submitted Version","project":[{"grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425","name":"Genome-wide Analysis of Root Traits"}],"citation":{"chicago":"Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">https://doi.org/10.1007/978-3-319-11257-2_14</a>.","ieee":"F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Ibiza, Spain, 2014, vol. 8744, pp. 170–184.","ista":"Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.","short":"F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184.","mla":"Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:<a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">10.1007/978-3-319-11257-2_14</a>.","apa":"Yu, F., Rybar, M., Uhler, C., &#38; Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">https://doi.org/10.1007/978-3-319-11257-2_14</a>","ama":"Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8744. Springer; 2014:170-184. doi:<a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">10.1007/978-3-319-11257-2_14</a>"}},{"title":"Experimental investigation of transitional flow in a toroidal pipe","_id":"2050","oa_version":"Submitted Version","citation":{"apa":"Kühnen, J., Holzner, M., Hof, B., &#38; Kuhlmann, H. (2014). Experimental investigation of transitional flow in a toroidal pipe. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2013.603\">https://doi.org/10.1017/jfm.2013.603</a>","ama":"Kühnen J, Holzner M, Hof B, Kuhlmann H. Experimental investigation of transitional flow in a toroidal pipe. <i>Journal of Fluid Mechanics</i>. 2014;738:463-491. doi:<a href=\"https://doi.org/10.1017/jfm.2013.603\">10.1017/jfm.2013.603</a>","chicago":"Kühnen, Jakob, Markus Holzner, Björn Hof, and Hendrik Kuhlmann. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2014. <a href=\"https://doi.org/10.1017/jfm.2013.603\">https://doi.org/10.1017/jfm.2013.603</a>.","ieee":"J. Kühnen, M. Holzner, B. Hof, and H. Kuhlmann, “Experimental investigation of transitional flow in a toroidal pipe,” <i>Journal of Fluid Mechanics</i>, vol. 738. Cambridge University Press, pp. 463–491, 2014.","ista":"Kühnen J, Holzner M, Hof B, Kuhlmann H. 2014. Experimental investigation of transitional flow in a toroidal pipe. Journal of Fluid Mechanics. 738, 463–491.","mla":"Kühnen, Jakob, et al. “Experimental Investigation of Transitional Flow in a Toroidal Pipe.” <i>Journal of Fluid Mechanics</i>, vol. 738, Cambridge University Press, 2014, pp. 463–91, doi:<a href=\"https://doi.org/10.1017/jfm.2013.603\">10.1017/jfm.2013.603</a>.","short":"J. Kühnen, M. Holzner, B. Hof, H. Kuhlmann, Journal of Fluid Mechanics 738 (2014) 463–491."},"isi":1,"external_id":{"arxiv":["1508.06546"],"isi":["000328486400021"]},"publisher":"Cambridge University Press","status":"public","day":"10","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5001","publication_status":"published","year":"2014","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.06546"}],"page":"463 - 491","department":[{"_id":"BjHo"}],"date_created":"2018-12-11T11:55:25Z","language":[{"iso":"eng"}],"author":[{"full_name":"Kühnen, Jakob","last_name":"Kühnen","orcid":"0000-0003-4312-0179","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markus","last_name":"Holzner","full_name":"Holzner, Markus"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","full_name":"Hof, Björn"},{"last_name":"Kuhlmann","full_name":"Kuhlmann, Hendrik","first_name":"Hendrik"}],"date_published":"2014-01-10T00:00:00Z","article_processing_charge":"No","date_updated":"2025-09-29T11:51:23Z","oa":1,"volume":738,"doi":"10.1017/jfm.2013.603","quality_controlled":"1","abstract":[{"text":"The flow instability and further transition to turbulence in a toroidal pipe (torus) with curvature ratio (tube-to-coiling diameter) 0.049 is investigated experimentally. The flow inside the toroidal pipe is driven by a steel sphere fitted to the inner pipe diameter. The sphere is moved with constant azimuthal velocity from outside the torus by a moving magnet. The experiment is designed to investigate curved pipe flow by optical measurement techniques. Using stereoscopic particle image velocimetry, laser Doppler velocimetry and pressure drop measurements, the flow is measured for Reynolds numbers ranging from 1000 to 15 000. Time- and space-resolved velocity fields are obtained and analysed. The steady axisymmetric basic flow is strongly influenced by centrifugal effects. On an increase of the Reynolds number we find a sequence of bifurcations. For Re=4075±2% a supercritical bifurcation to an oscillatory flow is found in which waves travel in the streamwise direction with a phase velocity slightly faster than the mean flow. The oscillatory flow is superseded by a presumably quasi-periodic flow at a further increase of the Reynolds number before turbulence sets in. The results are found to be compatible, in general, with earlier experimental and numerical investigations on transition to turbulence in helical and curved pipes. However, important aspects of the bifurcation scenario differ considerably.","lang":"eng"}],"intvolume":"       738","corr_author":"1","publication":"Journal of Fluid Mechanics","type":"journal_article","arxiv":1,"scopus_import":"1"},{"conference":{"end_date":"2014-12-13","name":"NIPS: Neural Information Processing Systems","start_date":"2014-12-08","location":"Montreal, Canada"},"abstract":[{"text":"We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach.","lang":"eng"}],"intvolume":"        27","publication":"Advances in Neural Information Processing Systems","ddc":["000"],"OA_type":"gold","type":"conference","date_published":"2014-01-01T00:00:00Z","article_processing_charge":"No","date_updated":"2026-06-18T18:24:19Z","oa":1,"volume":27,"month":"01","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01065586","open_access":"1"}],"department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:26Z","author":[{"full_name":"Marchand, Mario","last_name":"Marchand","first_name":"Mario"},{"first_name":"Su","full_name":"Hongyu, Su","last_name":"Hongyu"},{"orcid":"0000-0002-8301-7240","last_name":"Morvant","full_name":"Morvant, Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","first_name":"Emilie"},{"full_name":"Rousu, Juho","last_name":"Rousu","first_name":"Juho"},{"first_name":"John","last_name":"Shawe Taylor","full_name":"Shawe Taylor, John"}],"year":"2014","publication_identifier":{"isbn":["9781510800410"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4996","publication_status":"published","publisher":"Neural Information Processing Systems Foundation","status":"public","oa_version":"Published Version","_id":"2051","citation":{"ama":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: <i>Advances in Neural Information Processing Systems</i>. Vol 27. Neural Information Processing Systems Foundation; 2014.","apa":"Marchand, M., Hongyu, S., Morvant, E., Rousu, J., &#38; Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. In <i>Advances in Neural Information Processing Systems</i> (Vol. 27). Montreal, Canada: Neural Information Processing Systems Foundation.","mla":"Marchand, Mario, et al. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” <i>Advances in Neural Information Processing Systems</i>, vol. 27, Neural Information Processing Systems Foundation, 2014.","short":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2014.","ieee":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2014, vol. 27.","chicago":"Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 27. Neural Information Processing Systems Foundation, 2014.","ista":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 27."},"OA_place":"repository","title":"Multilabel structured output learning with random spanning trees of max-margin Markov networks"},{"page":"109 - 124","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:26Z","department":[{"_id":"KrCh"}],"author":[{"first_name":"Benjamin","id":"4A55BD00-F248-11E8-B48F-1D18A9856A87","full_name":"Aminof, Benjamin","last_name":"Aminof"},{"full_name":"Kotek, Tomer","last_name":"Kotek","first_name":"Tomer"},{"first_name":"Sacha","full_name":"Rubin, Sacha","last_name":"Rubin"},{"full_name":"Spegni, Francesco","last_name":"Spegni","first_name":"Francesco"},{"last_name":"Veith","full_name":"Veith, Helmut","first_name":"Helmut"}],"month":"09","alternative_title":["LNCS"],"year":"2014","editor":[{"first_name":"Paolo","last_name":"Baldan","full_name":"Baldan, Paolo"},{"full_name":"Gorla, Daniele","last_name":"Gorla","first_name":"Daniele"}],"intvolume":"      8704","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","scopus_import":"1","type":"conference","conference":{"start_date":"2014-09-02","location":"Rome, Italy","end_date":"2014-09-05","name":"CONCUR: Concurrency Theory"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"A standard technique for solving the parameterized model checking problem is to reduce it to the classic model checking problem of finitely many finite-state systems. This work considers some of the theoretical power and limitations of this technique. We focus on concurrent systems in which processes communicate via pairwise rendezvous, as well as the special cases of disjunctive guards and token passing; specifications are expressed in indexed temporal logic without the next operator; and the underlying network topologies are generated by suitable Monadic Second Order Logic formulas and graph operations. First, we settle the exact computational complexity of the parameterized model checking problem for some of our concurrent systems, and establish new decidability results for others. Second, we consider the cases that model checking the parameterized system can be reduced to model checking some fixed number of processes, the number is known as a cutoff. We provide many cases for when such cutoffs can be computed, establish lower bounds on the size of such cutoffs, and identify cases where no cutoff exists. Third, we consider cases for which the parameterized system is equivalent to a single finite-state system (more precisely a Büchi word automaton), and establish tight bounds on the sizes of such automata."}],"date_updated":"2024-10-21T06:02:50Z","doi":"10.1007/978-3-662-44584-6_9","volume":8704,"date_published":"2014-09-01T00:00:00Z","citation":{"ieee":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, and H. Veith, “Parameterized model checking of rendezvous systems,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Rome, Italy, 2014, vol. 8704, pp. 109–124.","ista":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. 2014. Parameterized model checking of rendezvous systems. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 109–124.","chicago":"Aminof, Benjamin, Tomer Kotek, Sacha Rubin, Francesco Spegni, and Helmut Veith. “Parameterized Model Checking of Rendezvous Systems.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Paolo Baldan and Daniele Gorla, 8704:109–24. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. <a href=\"https://doi.org/10.1007/978-3-662-44584-6_9\">https://doi.org/10.1007/978-3-662-44584-6_9</a>.","mla":"Aminof, Benjamin, et al. “Parameterized Model Checking of Rendezvous Systems.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–24, doi:<a href=\"https://doi.org/10.1007/978-3-662-44584-6_9\">10.1007/978-3-662-44584-6_9</a>.","short":"B. Aminof, T. Kotek, S. Rubin, F. Spegni, H. Veith, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 109–124.","apa":"Aminof, B., Kotek, T., Rubin, S., Spegni, F., &#38; Veith, H. (2014). Parameterized model checking of rendezvous systems. In P. Baldan &#38; D. Gorla (Eds.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8704, pp. 109–124). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-662-44584-6_9\">https://doi.org/10.1007/978-3-662-44584-6_9</a>","ama":"Aminof B, Kotek T, Rubin S, Spegni F, Veith H. Parameterized model checking of rendezvous systems. In: Baldan P, Gorla D, eds. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:109-124. doi:<a href=\"https://doi.org/10.1007/978-3-662-44584-6_9\">10.1007/978-3-662-44584-6_9</a>"},"_id":"2052","oa_version":"None","title":"Parameterized model checking of rendezvous systems","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","day":"01","acknowledgement":"The second, third, fourth and fifth authors were supported by the Austrian National Research Network S11403-N23 (RiSE) of the Austrian Science Fund (FWF) and by the Vienna Science and Technology Fund (WWTF) through grants PROSEED, ICT12-059, and VRG11-005.","publist_id":"4994","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public"},{"conference":{"name":"CONCUR: Concurrency Theory","end_date":"2014-09-05","location":"Rome, Italy","start_date":"2014-09-02"},"ec_funded":1,"abstract":[{"lang":"eng","text":"In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a longstanding open problem concerning the representation of memoryless continuous time by memoryfull continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems."}],"intvolume":"      8704","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","type":"conference","arxiv":1,"scopus_import":"1","date_published":"2014-09-01T00:00:00Z","article_processing_charge":"No","date_updated":"2025-06-11T07:57:15Z","oa":1,"doi":"10.1007/978-3-662-44584-6_18","volume":8704,"month":"09","main_file_link":[{"url":"http://arxiv.org/abs/1404.5084","open_access":"1"}],"page":"249 - 265","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:27Z","author":[{"first_name":"Holger","full_name":"Hermanns, Holger","last_name":"Hermanns"},{"full_name":"Krčál, Jan","last_name":"Krčál","first_name":"Jan"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","last_name":"Kretinsky","orcid":"0000-0002-8122-2881"}],"year":"2014","editor":[{"first_name":"Paolo","full_name":"Baldan, Paolo","last_name":"Baldan"},{"last_name":"Gorla","full_name":"Gorla, Daniele","first_name":"Daniele"}],"alternative_title":["LNCS"],"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work is supported by the EU 7th Framework Programme under grant agreements 295261 (MEALS) and 318490 (SENSATION), Czech Science Foundation under grant agreement P202/12/G061, the DFG Transregional Collaborative Research Centre SFB/TR 14 AVACS, and by the CAS/SAFEA International Partnership Program for Creative Research Teams.","publist_id":"4993","publication_status":"published","external_id":{"arxiv":["1404.5084"]},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","_id":"2053","oa_version":"Submitted Version","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Hermanns, Holger, Jan Krčál, and Jan Kretinsky. “Probabilistic Bisimulation: Naturally on Distributions.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Paolo Baldan and Daniele Gorla, 8704:249–65. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. <a href=\"https://doi.org/10.1007/978-3-662-44584-6_18\">https://doi.org/10.1007/978-3-662-44584-6_18</a>.","ista":"Hermanns H, Krčál J, Kretinsky J. 2014. Probabilistic bisimulation: Naturally on distributions. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). CONCUR: Concurrency Theory, LNCS, vol. 8704, 249–265.","ieee":"H. Hermanns, J. Krčál, and J. Kretinsky, “Probabilistic bisimulation: Naturally on distributions,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Rome, Italy, 2014, vol. 8704, pp. 249–265.","mla":"Hermanns, Holger, et al. “Probabilistic Bisimulation: Naturally on Distributions.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Paolo Baldan and Daniele Gorla, vol. 8704, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–65, doi:<a href=\"https://doi.org/10.1007/978-3-662-44584-6_18\">10.1007/978-3-662-44584-6_18</a>.","short":"H. Hermanns, J. Krčál, J. Kretinsky, in:, P. Baldan, D. Gorla (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 249–265.","apa":"Hermanns, H., Krčál, J., &#38; Kretinsky, J. (2014). Probabilistic bisimulation: Naturally on distributions. In P. Baldan &#38; D. Gorla (Eds.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8704, pp. 249–265). Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-662-44584-6_18\">https://doi.org/10.1007/978-3-662-44584-6_18</a>","ama":"Hermanns H, Krčál J, Kretinsky J. Probabilistic bisimulation: Naturally on distributions. In: Baldan P, Gorla D, eds. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8704. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:249-265. doi:<a href=\"https://doi.org/10.1007/978-3-662-44584-6_18\">10.1007/978-3-662-44584-6_18</a>"},"title":"Probabilistic bisimulation: Naturally on distributions"},{"quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider a continuous-time Markov chain (CTMC) whose state space is partitioned into aggregates, and each aggregate is assigned a probability measure. A sufficient condition for defining a CTMC over the aggregates is presented as a variant of weak lumpability, which also characterizes that the measure over the original process can be recovered from that of the aggregated one. We show how the applicability of de-aggregation depends on the initial distribution. The application section is devoted to illustrate how the developed theory aids in reducing CTMC models of biochemical systems particularly in connection to protein-protein interactions. We assume that the model is written by a biologist in form of site-graph-rewrite rules. Site-graph-rewrite rules compactly express that, often, only a local context of a protein (instead of a full molecular species) needs to be in a certain configuration in order to trigger a reaction event. This observation leads to suitable aggregate Markov chains with smaller state spaces, thereby providing sufficient reduction in computational complexity. This is further exemplified in two case studies: simple unbounded polymerization and early EGFR/insulin crosstalk."}],"intvolume":"        69","publication":"Journal of Mathematical Biology","scopus_import":"1","type":"journal_article","arxiv":1,"date_published":"2014-11-20T00:00:00Z","article_processing_charge":"No","date_updated":"2025-09-29T11:50:22Z","oa":1,"doi":"10.1007/s00285-013-0738-7","volume":69,"issue":"3","month":"11","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.4532"}],"page":"767 - 797","date_created":"2018-12-11T11:55:28Z","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"ToHe"}],"author":[{"first_name":"Arnab","full_name":"Ganguly, Arnab","last_name":"Ganguly"},{"id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov","full_name":"Petrov, Tatjana"},{"last_name":"Koeppl","full_name":"Koeppl, Heinz","first_name":"Heinz"}],"year":"2014","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"20","acknowledgement":"T. Petrov is supported by SystemsX.ch—the Swiss Inititative for Systems Biology.","publist_id":"4990","publication_status":"published","isi":1,"external_id":{"isi":["000340588700008"],"arxiv":["1303.4532"]},"publisher":"Springer","status":"public","oa_version":"Submitted Version","_id":"2056","citation":{"apa":"Ganguly, A., Petrov, T., &#38; Koeppl, H. (2014). Markov chain aggregation and its applications to combinatorial reaction networks. <i>Journal of Mathematical Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s00285-013-0738-7\">https://doi.org/10.1007/s00285-013-0738-7</a>","ama":"Ganguly A, Petrov T, Koeppl H. Markov chain aggregation and its applications to combinatorial reaction networks. <i>Journal of Mathematical Biology</i>. 2014;69(3):767-797. doi:<a href=\"https://doi.org/10.1007/s00285-013-0738-7\">10.1007/s00285-013-0738-7</a>","ieee":"A. Ganguly, T. Petrov, and H. Koeppl, “Markov chain aggregation and its applications to combinatorial reaction networks,” <i>Journal of Mathematical Biology</i>, vol. 69, no. 3. Springer, pp. 767–797, 2014.","chicago":"Ganguly, Arnab, Tatjana Petrov, and Heinz Koeppl. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” <i>Journal of Mathematical Biology</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00285-013-0738-7\">https://doi.org/10.1007/s00285-013-0738-7</a>.","ista":"Ganguly A, Petrov T, Koeppl H. 2014. Markov chain aggregation and its applications to combinatorial reaction networks. Journal of Mathematical Biology. 69(3), 767–797.","mla":"Ganguly, Arnab, et al. “Markov Chain Aggregation and Its Applications to Combinatorial Reaction Networks.” <i>Journal of Mathematical Biology</i>, vol. 69, no. 3, Springer, 2014, pp. 767–97, doi:<a href=\"https://doi.org/10.1007/s00285-013-0738-7\">10.1007/s00285-013-0738-7</a>.","short":"A. Ganguly, T. Petrov, H. Koeppl, Journal of Mathematical Biology 69 (2014) 767–797."},"title":"Markov chain aggregation and its applications to combinatorial reaction networks"},{"title":"Majority vote of diverse classifiers for late fusion","project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding"}],"_id":"2057","oa_version":"Preprint","citation":{"apa":"Morvant, E., Habrard, A., &#38; Ayache, S. (2014). Majority vote of diverse classifiers for late fusion. In <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8621, pp. 153–162). Joensuu, Finland: Springer. <a href=\"https://doi.org/10.1007/978-3-662-44415-3_16\">https://doi.org/10.1007/978-3-662-44415-3_16</a>","ama":"Morvant E, Habrard A, Ayache S. Majority vote of diverse classifiers for late fusion. In: <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8621. Springer; 2014:153-162. doi:<a href=\"https://doi.org/10.1007/978-3-662-44415-3_16\">10.1007/978-3-662-44415-3_16</a>","ista":"Morvant E, Habrard A, Ayache S. 2014. Majority vote of diverse classifiers for late fusion. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition, LNCS, vol. 8621, 153–162.","chicago":"Morvant, Emilie, Amaury Habrard, and Stéphane Ayache. “Majority Vote of Diverse Classifiers for Late Fusion.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, 8621:153–62. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-662-44415-3_16\">https://doi.org/10.1007/978-3-662-44415-3_16</a>.","ieee":"E. Morvant, A. Habrard, and S. Ayache, “Majority vote of diverse classifiers for late fusion,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Joensuu, Finland, 2014, vol. 8621, pp. 153–162.","short":"E. Morvant, A. Habrard, S. Ayache, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 153–162.","mla":"Morvant, Emilie, et al. “Majority Vote of Diverse Classifiers for Late Fusion.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, vol. 8621, Springer, 2014, pp. 153–62, doi:<a href=\"https://doi.org/10.1007/978-3-662-44415-3_16\">10.1007/978-3-662-44415-3_16</a>."},"external_id":{"arxiv":["1404.7796"]},"status":"public","publisher":"Springer","publist_id":"4989","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2014","alternative_title":["LNCS"],"month":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.7796"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:28Z","department":[{"_id":"ChLa"}],"author":[{"first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","full_name":"Morvant, Emilie","last_name":"Morvant","orcid":"0000-0002-8301-7240"},{"last_name":"Habrard","full_name":"Habrard, Amaury","first_name":"Amaury"},{"first_name":"Stéphane","full_name":"Ayache, Stéphane","last_name":"Ayache"}],"page":"153 - 162","date_published":"2014-01-01T00:00:00Z","volume":8621,"doi":"10.1007/978-3-662-44415-3_16","date_updated":"2021-01-12T06:55:01Z","oa":1,"quality_controlled":"1","ec_funded":1,"abstract":[{"lang":"eng","text":"In the past few years, a lot of attention has been devoted to multimedia indexing by fusing multimodal informations. Two kinds of fusion schemes are generally considered: The early fusion and the late fusion. We focus on late classifier fusion, where one combines the scores of each modality at the decision level. To tackle this problem, we investigate a recent and elegant well-founded quadratic program named MinCq coming from the machine learning PAC-Bayesian theory. MinCq looks for the weighted combination, over a set of real-valued functions seen as voters, leading to the lowest misclassification rate, while maximizing the voters’ diversity. We propose an extension of MinCq tailored to multimedia indexing. Our method is based on an order-preserving pairwise loss adapted to ranking that allows us to improve Mean Averaged Precision measure while taking into account the diversity of the voters that we want to fuse. We provide evidence that this method is naturally adapted to late fusion procedures and confirm the good behavior of our approach on the challenging PASCAL VOC’07 benchmark."}],"conference":{"start_date":"2014-08-20","location":"Joensuu, Finland","end_date":"2014-08-22","name":"IAPR: International Workshop on Structural, Syntactic, and Statistical Pattern Recognition"},"scopus_import":1,"type":"conference","arxiv":1,"intvolume":"      8621","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)"},{"external_id":{"isi":["000340000100104"]},"isi":1,"has_accepted_license":"1","status":"public","publisher":"ACM","article_number":"137","publist_id":"4988","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","publication_status":"published","title":"Blending liquids","file_date_updated":"2020-07-14T12:45:27Z","project":[{"name":"Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425"}],"_id":"2058","oa_version":"Submitted Version","citation":{"apa":"Raveendran, K., Wojtan, C., Thuerey, N., &#38; Türk, G. (2014). Blending liquids. In <i>ACM Transactions on Graphics</i> (Vol. 33). Vancouver, Canada: ACM. <a href=\"https://doi.org/10.1145/2601097.2601126\">https://doi.org/10.1145/2601097.2601126</a>","ama":"Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: <i>ACM Transactions on Graphics</i>. Vol 33. ACM; 2014. doi:<a href=\"https://doi.org/10.1145/2601097.2601126\">10.1145/2601097.2601126</a>","ista":"Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33, 137.","chicago":"Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending Liquids.” In <i>ACM Transactions on Graphics</i>, Vol. 33. ACM, 2014. <a href=\"https://doi.org/10.1145/2601097.2601126\">https://doi.org/10.1145/2601097.2601126</a>.","ieee":"K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in <i>ACM Transactions on Graphics</i>, Vancouver, Canada, 2014, vol. 33, no. 4.","mla":"Raveendran, Karthik, et al. “Blending Liquids.” <i>ACM Transactions on Graphics</i>, vol. 33, no. 4, 137, ACM, 2014, doi:<a href=\"https://doi.org/10.1145/2601097.2601126\">10.1145/2601097.2601126</a>.","short":"K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014."},"article_processing_charge":"No","date_published":"2014-07-01T00:00:00Z","volume":33,"doi":"10.1145/2601097.2601126","oa":1,"date_updated":"2025-09-29T11:49:44Z","abstract":[{"text":"We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations.","lang":"eng"}],"quality_controlled":"1","conference":{"end_date":"2014-08-14","name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","start_date":"2014-08-10","location":"Vancouver, Canada"},"scopus_import":"1","type":"conference","ddc":["000"],"publication":"ACM Transactions on Graphics","intvolume":"        33","pubrep_id":"606","year":"2014","month":"07","issue":"4","author":[{"full_name":"Raveendran, Karthik","last_name":"Raveendran","first_name":"Karthik"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546"},{"first_name":"Nils","last_name":"Thuerey","full_name":"Thuerey, Nils"},{"full_name":"Türk, Greg","last_name":"Türk","first_name":"Greg"}],"date_created":"2018-12-11T11:55:28Z","department":[{"_id":"ChWo"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","file_size":8387384,"checksum":"1752760a2e71e254537f31c0d10d9c6c","creator":"system","date_created":"2018-12-12T10:08:27Z","file_name":"IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf","relation":"main_file","date_updated":"2020-07-14T12:45:27Z","file_id":"4688","access_level":"open_access"}]},{"file_date_updated":"2020-07-14T12:45:27Z","title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos","_id":"2059","oa_version":"Published Version","citation":{"mla":"Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” <i>Protoplasma</i>, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:<a href=\"https://doi.org/10.1007/s00709-014-0616-1\">10.1007/s00709-014-0616-1</a>.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087.","ieee":"E. Dubas <i>et al.</i>, “The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos,” <i>Protoplasma</i>, vol. 251, no. 5. Springer, pp. 1077–1087, 2014.","ista":"Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska M. 2014. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087.","chicago":"Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková, Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” <i>Protoplasma</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00709-014-0616-1\">https://doi.org/10.1007/s00709-014-0616-1</a>.","ama":"Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. <i>Protoplasma</i>. 2014;251(5):1077-1087. doi:<a href=\"https://doi.org/10.1007/s00709-014-0616-1\">10.1007/s00709-014-0616-1</a>","apa":"Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur, I., &#38; Krzewska, M. (2014). The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. <i>Protoplasma</i>. Springer. <a href=\"https://doi.org/10.1007/s00709-014-0616-1\">https://doi.org/10.1007/s00709-014-0616-1</a>"},"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"},"isi":1,"external_id":{"isi":["000340480300008"]},"publisher":"Springer","has_accepted_license":"1","status":"public","acknowledgement":"The research was supported by the IPP PAS-IPGB SAS bilateral project (“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547, and VEGA 2-0090-14.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"20","publist_id":"4987","publication_status":"published","year":"2014","pubrep_id":"394","issue":"5","month":"02","page":"1077 - 1087","file":[{"file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf","relation":"main_file","file_id":"5353","access_level":"open_access","date_updated":"2020-07-14T12:45:27Z","file_size":6377990,"content_type":"application/pdf","date_created":"2018-12-12T10:18:31Z","checksum":"d570a6073765118fc0bb83c31d96fa53","creator":"system"}],"author":[{"first_name":"Ewa","full_name":"Dubas, Ewa","last_name":"Dubas"},{"first_name":"Jana","full_name":"Moravčíková, Jana","last_name":"Moravčíková"},{"full_name":"Libantová, Jana","last_name":"Libantová","first_name":"Jana"},{"first_name":"Ildikó","last_name":"Matušíková","full_name":"Matušíková, Ildikó"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Iwona","last_name":"Zur","full_name":"Zur, Iwona"},{"full_name":"Krzewska, Monika","last_name":"Krzewska","first_name":"Monika"}],"department":[{"_id":"EvBe"}],"date_created":"2018-12-11T11:55:29Z","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2014-02-20T00:00:00Z","oa":1,"date_updated":"2025-09-29T11:49:12Z","volume":251,"doi":"10.1007/s00709-014-0616-1","abstract":[{"lang":"eng","text":"Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant."}],"quality_controlled":"1","ddc":["580"],"publication":"Protoplasma","intvolume":"       251","type":"journal_article","scopus_import":"1"},{"publisher":"Springer","status":"public","isi":1,"external_id":{"isi":["000340480300012"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"14","publist_id":"4985","title":"Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis","citation":{"ieee":"E. Mazur, E. Kurczyñska, and J. Friml, “Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis,” <i>Protoplasma</i>, vol. 251, no. 5. Springer, pp. 1125–1139, 2014.","chicago":"Mazur, Ewa, Ewa Kurczyñska, and Jiří Friml. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” <i>Protoplasma</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00709-014-0620-5\">https://doi.org/10.1007/s00709-014-0620-5</a>.","ista":"Mazur E, Kurczyñska E, Friml J. 2014. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 251(5), 1125–1139.","short":"E. Mazur, E. Kurczyñska, J. Friml, Protoplasma 251 (2014) 1125–1139.","mla":"Mazur, Ewa, et al. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” <i>Protoplasma</i>, vol. 251, no. 5, Springer, 2014, pp. 1125–39, doi:<a href=\"https://doi.org/10.1007/s00709-014-0620-5\">10.1007/s00709-014-0620-5</a>.","apa":"Mazur, E., Kurczyñska, E., &#38; Friml, J. (2014). Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. <i>Protoplasma</i>. Springer. <a href=\"https://doi.org/10.1007/s00709-014-0620-5\">https://doi.org/10.1007/s00709-014-0620-5</a>","ama":"Mazur E, Kurczyñska E, Friml J. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. <i>Protoplasma</i>. 2014;251(5):1125-1139. doi:<a href=\"https://doi.org/10.1007/s00709-014-0620-5\">10.1007/s00709-014-0620-5</a>"},"oa_version":"None","_id":"2061","date_updated":"2025-09-29T11:48:32Z","volume":251,"doi":"10.1007/s00709-014-0620-5","article_processing_charge":"No","date_published":"2014-02-14T00:00:00Z","publication":"Protoplasma","intvolume":"       251","scopus_import":"1","type":"journal_article","abstract":[{"text":"Development of cambium and its activity is important for our knowledge of the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model plant for such a kind of study. Thus, this paper reports on cellular events taking place in the interfascicular regions of inflorescence stems of A. thaliana, leading to the development of interfascicular cambium from differentiated interfascicular parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation, PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane and periclinal divisions. Distribution of auxin was observed to be higher in differentiating into cambium parenchyma cells compared to cells within the pith and cortex. Expression of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of PIN1 was already established in the cells prior to their periclinal division. These cellular events initiated within parenchyma cells adjacent to the vascular bundles and successively extended from that point towards the middle region of the interfascicular area, located between neighboring vascular bundles. The final consequence of which was the closure of the cambial ring within the stem. Changes in the chemical composition of IPC walls were also detected and included changes of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs). In summary, results presented in this paper describe interfascicular cambium ontogenesis in terms of successive cellular events in the interfascicular regions of inflorescence stems of Arabidopsis.","lang":"eng"}],"quality_controlled":"1","year":"2014","page":"1125 - 1139","author":[{"last_name":"Mazur","full_name":"Mazur, Ewa","first_name":"Ewa"},{"last_name":"Kurczyñska","full_name":"Kurczyñska, Ewa","first_name":"Ewa"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:29Z","issue":"5","month":"02"},{"date_updated":"2025-09-29T11:48:03Z","oa":1,"volume":345,"doi":"10.1126/science.1255263","date_published":"2014-08-01T00:00:00Z","article_processing_charge":"No","corr_author":"1","intvolume":"       345","publication":"Science","ddc":["570"],"type":"journal_article","scopus_import":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons (GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy. In 1995, the properties of these interneurons were completely unknown. Twenty years later, thanks to the massive use of subcellular patch-clamp techniques, simultaneous multiple-cell recording, optogenetics, in vivo measurements, and computational approaches, our knowledge about PV+ interneurons became more extensive than for several types of pyramidal neurons. These findings have implications beyond the “small world” of basic research on GABAergic cells. For example, the results provide a first proof of principle that neuroscientists might be able to close the gaps between the molecular, cellular, network, and behavioral levels, representing one of the main challenges at the present time. Furthermore, the results may form the basis for PV+ interneurons as therapeutic targets for brain disease in the future. However, much needs to be learned about the basic function of these interneurons before clinical neuroscientists will be able to use PV+ interneurons for therapeutic purposes."}],"ec_funded":1,"year":"2014","pubrep_id":"821","file":[{"relation":"main_file","file_name":"IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf","date_updated":"2020-07-14T12:45:27Z","access_level":"open_access","file_id":"5185","content_type":"application/pdf","file_size":215514,"creator":"system","checksum":"a0036a589037d37e86364fa25cc0a82f","date_created":"2018-12-12T10:16:00Z"},{"file_id":"5186","access_level":"open_access","date_updated":"2020-07-14T12:45:27Z","file_name":"IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf","relation":"main_file","date_created":"2018-12-12T10:16:01Z","checksum":"e1f57d2713725449cb898fdcb8ef47b8","creator":"system","content_type":"application/pdf","file_size":1732723}],"date_created":"2018-12-11T11:55:29Z","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"author":[{"first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","full_name":"Hu, Hua","last_name":"Hu"},{"last_name":"Gan","full_name":"Gan, Jian","id":"3614E438-F248-11E8-B48F-1D18A9856A87","first_name":"Jian"},{"full_name":"Jonas, Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"issue":"6196","month":"08","article_number":"1255263","publisher":"American Association for the Advancement of Science","has_accepted_license":"1","status":"public","isi":1,"external_id":{"isi":["000339651300036"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","publist_id":"4984","file_date_updated":"2020-07-14T12:45:27Z","title":"Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function","citation":{"mla":"Hu, Hua, et al. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” <i>Science</i>, vol. 345, no. 6196, 1255263, American Association for the Advancement of Science, 2014, doi:<a href=\"https://doi.org/10.1126/science.1255263\">10.1126/science.1255263</a>.","short":"H. Hu, J. Gan, P.M. Jonas, Science 345 (2014).","ista":"Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263.","chicago":"Hu, Hua, Jian Gan, and Peter M Jonas. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1255263\">https://doi.org/10.1126/science.1255263</a>.","ieee":"H. Hu, J. Gan, and P. M. Jonas, “Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function,” <i>Science</i>, vol. 345, no. 6196. American Association for the Advancement of Science, 2014.","ama":"Hu H, Gan J, Jonas PM. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. <i>Science</i>. 2014;345(6196). doi:<a href=\"https://doi.org/10.1126/science.1255263\">10.1126/science.1255263</a>","apa":"Hu, H., Gan, J., &#38; Jonas, P. M. (2014). Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1255263\">https://doi.org/10.1126/science.1255263</a>"},"_id":"2062","oa_version":"Submitted Version","project":[{"call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24","name":"Mechanisms of transmitter release at GABAergic synapses"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","grant_number":"268548","call_identifier":"FP7"}]},{"publisher":"Springer","status":"public","publication_status":"published","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4978","title":"CEGAR for qualitative analysis of probabilistic systems","related_material":{"record":[{"status":"public","id":"5412","relation":"earlier_version"},{"id":"5413","status":"public","relation":"earlier_version"},{"id":"5414","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","id":"1155","status":"public"}]},"citation":{"apa":"Chatterjee, K., Chmelik, M., &#38; Daca, P. (2014). CEGAR for qualitative analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">https://doi.org/10.1007/978-3-319-08867-9_31</a>","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic systems. In: Vol 8559. Springer; 2014:473-490. doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">10.1007/978-3-319-08867-9_31</a>","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 473–490.","ista":"Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">https://doi.org/10.1007/978-3-319-08867-9_31</a>.","mla":"Chatterjee, Krishnendu, et al. <i>CEGAR for Qualitative Analysis of Probabilistic Systems</i>. Vol. 8559, Springer, 2014, pp. 473–90, doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">10.1007/978-3-319-08867-9_31</a>.","short":"K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490."},"_id":"2063","oa_version":"None","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7"}],"date_updated":"2026-04-15T10:02:12Z","volume":8559,"doi":"10.1007/978-3-319-08867-9_31","date_published":"2014-07-01T00:00:00Z","corr_author":"1","intvolume":"      8559","type":"conference","scopus_import":"1","conference":{"start_date":"2014-07-18","location":"Vienna, Austria","end_date":"2014-07-22","name":"CAV: Computer Aided Verification"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements."}],"ec_funded":1,"alternative_title":["LNCS"],"year":"2014","page":"473 - 490","date_created":"2018-12-11T11:55:30Z","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chmelik","full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","last_name":"Daca","full_name":"Daca, Przemyslaw"}],"month":"07"},{"abstract":[{"text":"We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses.","lang":"eng"}],"quality_controlled":"1","publication":"Journal of Comparative Neurology","intvolume":"       522","scopus_import":"1","type":"journal_article","article_processing_charge":"No","date_published":"2014-07-29T00:00:00Z","oa":1,"date_updated":"2025-09-29T11:47:23Z","volume":522,"doi":"10.1002/cne.23654","issue":"18","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/"}],"month":"07","page":"4023 - 4042","author":[{"first_name":"Maía","last_name":"Rubio","full_name":"Rubio, Maía"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"last_name":"Kamasawa","full_name":"Kamasawa, Naomi","first_name":"Naomi"},{"full_name":"Clarkson, Cheryl","last_name":"Clarkson","first_name":"Cheryl"},{"first_name":"Elek","full_name":"Molnár, Elek","last_name":"Molnár"},{"last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"}],"language":[{"iso":"eng"}],"department":[{"_id":"RySh"}],"date_created":"2018-12-11T11:55:30Z","year":"2014","acknowledgement":"National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0; Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n","day":"29","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"4974","publication_status":"published","isi":1,"external_id":{"isi":["000343973100005"]},"publisher":"Wiley-Blackwell","status":"public","oa_version":"Submitted Version","_id":"2064","citation":{"apa":"Rubio, M., Fukazawa, Y., Kamasawa, N., Clarkson, C., Molnár, E., &#38; Shigemoto, R. (2014). Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. <i>Journal of Comparative Neurology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cne.23654\">https://doi.org/10.1002/cne.23654</a>","ama":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. <i>Journal of Comparative Neurology</i>. 2014;522(18):4023-4042. doi:<a href=\"https://doi.org/10.1002/cne.23654\">10.1002/cne.23654</a>","ieee":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, and R. Shigemoto, “Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus,” <i>Journal of Comparative Neurology</i>, vol. 522, no. 18. Wiley-Blackwell, pp. 4023–4042, 2014.","ista":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. 2014. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 522(18), 4023–4042.","chicago":"Rubio, Maía, Yugo Fukazawa, Naomi Kamasawa, Cheryl Clarkson, Elek Molnár, and Ryuichi Shigemoto. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” <i>Journal of Comparative Neurology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/cne.23654\">https://doi.org/10.1002/cne.23654</a>.","short":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto, Journal of Comparative Neurology 522 (2014) 4023–4042.","mla":"Rubio, Maía, et al. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” <i>Journal of Comparative Neurology</i>, vol. 522, no. 18, Wiley-Blackwell, 2014, pp. 4023–42, doi:<a href=\"https://doi.org/10.1002/cne.23654\">10.1002/cne.23654</a>."},"title":"Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus"},{"OA_place":"repository","title":"Clustered planarity testing revisited","place":"Cham","related_material":{"record":[{"relation":"later_version","id":"1642","status":"public"}]},"citation":{"ama":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited. In: <i>International Symposium on Graph Drawing</i>. Vol 8871. Cham: Springer Nature; 2014:428-436. doi:<a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">10.1007/978-3-662-45803-7_36</a>","apa":"Fulek, R., Kynčl, J., Malinović, I., &#38; Pálvölgyi, D. (2014). Clustered planarity testing revisited. In <i>International Symposium on Graph Drawing</i> (Vol. 8871, pp. 428–436). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">https://doi.org/10.1007/978-3-662-45803-7_36</a>","short":"R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.","mla":"Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” <i>International Symposium on Graph Drawing</i>, vol. 8871, Springer Nature, 2014, pp. 428–36, doi:<a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">10.1007/978-3-662-45803-7_36</a>.","chicago":"Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” In <i>International Symposium on Graph Drawing</i>, 8871:428–36. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">https://doi.org/10.1007/978-3-662-45803-7_36</a>.","ieee":"R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing revisited,” in <i>International Symposium on Graph Drawing</i>, 2014, vol. 8871, pp. 428–436.","ista":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436."},"_id":"10793","oa_version":"Preprint","publisher":"Springer Nature","status":"public","external_id":{"arxiv":["1305.4519"]},"publication_status":"published","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0302-9743"]},"alternative_title":["LNCS"],"year":"2014","page":"428-436","date_created":"2022-02-25T10:32:14Z","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"},{"last_name":"Malinović","full_name":"Malinović, Igor","first_name":"Igor"},{"first_name":"Dömötör","full_name":"Pálvölgyi, Dömötör","last_name":"Pálvölgyi"}],"month":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1305.4519","open_access":"1"}],"date_updated":"2025-06-26T07:57:46Z","oa":1,"volume":8871,"doi":"10.1007/978-3-662-45803-7_36","date_published":"2014-01-01T00:00:00Z","article_processing_charge":"No","intvolume":"      8871","publication":"International Symposium on Graph Drawing","OA_type":"green","arxiv":1,"scopus_import":"1","type":"conference","quality_controlled":"1","abstract":[{"text":"The Hanani–Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this classical result to clustered graphs with two disjoint clusters, and show that a straightforward extension of our result to flat clustered graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give a new and short proof for a related result by Di Battista and Frati based on the matroid intersection algorithm.","lang":"eng"}]},{"editor":[{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"place":"Vienna","year":"2014","title":"Auxin and Its Role in Plant Development","publication_identifier":{"isbn":["9783709115251"],"eisbn":["9783709115268"]},"edition":"1","month":"04","_id":"10811","oa_version":"None","citation":{"ama":"Zažímalová E, Petrášek J, Benková E, eds. <i>Auxin and Its Role in Plant Development</i>. 1st ed. Vienna: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">10.1007/978-3-7091-1526-8</a>","apa":"Zažímalová, E., Petrášek, J., &#38; Benková, E. (Eds.). (2014). <i>Auxin and Its Role in Plant Development</i> (1st ed.). Vienna: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">https://doi.org/10.1007/978-3-7091-1526-8</a>","mla":"Zažímalová, Eva, et al., editors. <i>Auxin and Its Role in Plant Development</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">10.1007/978-3-7091-1526-8</a>.","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014.","chicago":"Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. <i>Auxin and Its Role in Plant Development</i>. 1st ed. Vienna: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">https://doi.org/10.1007/978-3-7091-1526-8</a>.","ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., <i>Auxin and Its Role in Plant Development</i>, 1st ed. Vienna: Springer Nature, 2014."},"date_created":"2022-03-03T11:52:44Z","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"page":"444","article_processing_charge":"No","date_published":"2014-04-01T00:00:00Z","doi":"10.1007/978-3-7091-1526-8","status":"public","publisher":"Springer Nature","date_updated":"2022-03-04T07:38:15Z","abstract":[{"lang":"eng","text":"Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound  upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research."}],"quality_controlled":"1","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_editor","scopus_import":"1","publication_status":"published"}]