[{"corr_author":"1","language":[{"iso":"eng"}],"page":"1 - 29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2019-10-15T07:47:05Z","related_material":{"record":[{"id":"539","status":"public","relation":"dissertation_contains"}]},"oa":1,"publist_id":"6369","fulldoi":"https://doi.org/10.1007/978-1-4939-6831-2_1","publication_status":"published","project":[{"name":"Hormone cross-talk drives nutrient dependent plant development","_id":"2542D156-B435-11E9-9278-68D0E5697425","grant_number":"I 1774-B16","call_identifier":"FWF"}],"title":"Methodological advances in auxin and cytokinin biology","file":[{"creator":"system","file_id":"5068","file_size":840646,"access_level":"open_access","file_name":"IST-2018-1019-v1+1_Hurny_MethodsMolBiol_2017.pdf","date_created":"2018-12-12T10:14:18Z","content_type":"application/pdf","date_updated":"2019-10-15T07:47:05Z","relation":"main_file"}],"type":"journal_article","ddc":["575"],"status":"public","pubrep_id":"1019","publication_identifier":{"issn":["1064-3745"]},"volume":1569,"intvolume":" 1569","quality_controlled":"1","department":[{"_id":"EvBe"}],"alternative_title":["Methods in Molecular Biology"],"_id":"1024","publisher":"Springer","oa_version":"Submitted Version","month":"03","day":"17","date_published":"2017-03-17T00:00:00Z","doi":"10.1007/978-1-4939-6831-2_1","scopus_import":"1","abstract":[{"lang":"eng","text":"The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges."}],"publication":"Auxins and Cytokinins in Plant Biology","citation":{"chicago":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology. Springer, 2017. https://doi.org/10.1007/978-1-4939-6831-2_1.","short":"A. Hurny, E. Benková, Auxins and Cytokinins in Plant Biology 1569 (2017) 1–29.","ieee":"A. Hurny and E. Benková, “Methodological advances in auxin and cytokinin biology,” Auxins and Cytokinins in Plant Biology, vol. 1569. Springer, pp. 1–29, 2017.","mla":"Hurny, Andrej, and Eva Benková. “Methodological Advances in Auxin and Cytokinin Biology.” Auxins and Cytokinins in Plant Biology, vol. 1569, Springer, 2017, pp. 1–29, doi:10.1007/978-1-4939-6831-2_1.","ista":"Hurny A, Benková E. 2017. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 1569, 1–29.","ama":"Hurny A, Benková E. Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. 2017;1569:1-29. doi:10.1007/978-1-4939-6831-2_1","apa":"Hurny, A., & Benková, E. (2017). Methodological advances in auxin and cytokinin biology. Auxins and Cytokinins in Plant Biology. Springer. https://doi.org/10.1007/978-1-4939-6831-2_1"},"year":"2017","date_created":"2018-12-11T11:49:45Z","date_updated":"2026-10-20T22:31:07Z","author":[{"id":"4DC4AF46-F248-11E8-B48F-1D18A9856A87","first_name":"Andrej","last_name":"Hurny","full_name":"Hurny, Andrej","orcid":"0000-0003-3638-1426"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}]},{"ec_funded":1,"ddc":["540"],"type":"journal_article","status":"public","isi":1,"fulldoi":"https://doi.org/10.1002/anie.201611998","publist_id":"6362","file":[{"creator":"dernst","file_size":2614942,"file_id":"5845","date_created":"2019-01-18T09:39:55Z","content_type":"application/pdf","access_level":"open_access","file_name":"2017_communications_Kainrath.pdf","date_updated":"2019-01-18T09:39:55Z","success":1,"relation":"main_file"}],"title":"Green-light-induced inactivation of receptor signaling using cobalamin-binding domains","project":[{"name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","call_identifier":"FP7"},{"grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"}],"publication_status":"published","page":"4608-4611","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"related_material":{"record":[{"status":"public","id":"418","relation":"dissertation_contains"},{"id":"7680","status":"public","relation":"part_of_dissertation"}]},"article_processing_charge":"No","file_date_updated":"2019-01-18T09:39:55Z","has_accepted_license":"1","corr_author":"1","year":"2017","date_created":"2018-12-11T11:49:46Z","citation":{"mla":"Kainrath, Stephanie, et al. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie International Edition, vol. 56, no. 16, Wiley, 2017, pp. 4608–11, doi:10.1002/anie.201611998.","ieee":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, and H. L. Janovjak, “Green-light-induced inactivation of receptor signaling using cobalamin-binding domains,” Angewandte Chemie International Edition, vol. 56, no. 16. Wiley, pp. 4608–4611, 2017.","short":"S. Kainrath, M. Stadler, E. Gschaider-Reichhart, M. Distel, H.L. Janovjak, Angewandte Chemie International Edition 56 (2017) 4608–4611.","chicago":"Kainrath, Stephanie, Manuela Stadler, Eva Gschaider-Reichhart, Martin Distel, and Harald L Janovjak. “Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains.” Angewandte Chemie International Edition. Wiley, 2017. https://doi.org/10.1002/anie.201611998.","apa":"Kainrath, S., Stadler, M., Gschaider-Reichhart, E., Distel, M., & Janovjak, H. L. (2017). Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201611998","ama":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. 2017;56(16):4608-4611. doi:10.1002/anie.201611998","ista":"Kainrath S, Stadler M, Gschaider-Reichhart E, Distel M, Janovjak HL. 2017. Green-light-induced inactivation of receptor signaling using cobalamin-binding domains. Angewandte Chemie International Edition. 56(16), 4608–4611."},"publication":"Angewandte Chemie International Edition","author":[{"first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","full_name":"Kainrath, Stephanie","orcid":"0000-0002-6709-2195"},{"full_name":"Stadler, Manuela","last_name":"Stadler","first_name":"Manuela"},{"orcid":"0000-0002-7218-7738","full_name":"Gschaider-Reichhart, Eva","last_name":"Gschaider-Reichhart","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","last_name":"Distel","full_name":"Distel, Martin"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"}],"date_updated":"2026-10-20T22:31:08Z","das_tickbox":"1","abstract":[{"text":"Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes.","lang":"eng"}],"scopus_import":"1","doi":"10.1002/anie.201611998","day":"20","date_published":"2017-03-20T00:00:00Z","acknowledgement":"This work was supported by a grant from the European Unions Seventh Framework Programme (CIG-303564). E.R. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF), W1232) and a FemTech fellowship (Austrian Research Promotion Agency, 3580812)","_id":"1028","department":[{"_id":"CaGu"},{"_id":"HaJa"}],"oa_version":"Published Version","month":"03","publisher":"Wiley","external_id":{"isi":["000398154000038"]},"intvolume":" 56","volume":56,"publication_identifier":{"issn":["1433-7851"]},"quality_controlled":"1","issue":"16"},{"date_published":"2016-12-01T00:00:00Z","day":"01","abstract":[{"lang":"eng","text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y."}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1605.07332","open_access":"1"}],"citation":{"mla":"Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 1965–73.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 1965–1973.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems Foundation, 2016.","apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.","ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973."},"year":"2016","date_created":"2018-12-11T11:50:03Z","date_updated":"2025-06-03T11:33:51Z","author":[{"last_name":"Chalk","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"}],"volume":29,"intvolume":" 29","quality_controlled":"1","alternative_title":["Advances in Neural Information Processing Systems"],"department":[{"_id":"GaTk"}],"_id":"1082","external_id":{"arxiv":["1605.07332"]},"conference":{"end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05","location":"Barcelona, Spain"},"publisher":"Neural Information Processing Systems Foundation","oa_version":"Preprint","month":"12","arxiv":1,"publist_id":"6298","publication_status":"published","title":"Relevant sparse codes with variational information bottleneck","type":"conference","status":"public","language":[{"iso":"eng"}],"page":"1965-1973","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","related_material":{"link":[{"relation":"other","url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck"}]},"oa":1},{"isi":1,"publist_id":"6297","fulldoi":"https://doi.org/10.1093/cercor/bhw090","publication_status":"published","title":"KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons","type":"journal_article","status":"public","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"2318 - 2334","article_processing_charge":"No","abstract":[{"text":" Cholecystokinin-expressing interneurons (CCK-INs) mediate behavior state-dependent inhibition in cortical circuits and themselves receive strong GABAergic input. However, it remains unclear to what extent GABABreceptors (GABABRs) contribute to their inhibitory control. Using immunoelectron microscopy, we found that CCK-INs in the rat hippocampus possessed high levels of dendritic GABABRs and KCTD12 auxiliary proteins, whereas postsynaptic effector Kir3 channels were present at lower levels. Consistently, whole-cell recordings revealed slow GABABR-mediated inhibitory postsynaptic currents (IPSCs) in most CCK-INs. In spite of the higher surface density of GABABRs in CCK-INs than in CA1 principal cells, the amplitudes of IPSCs were comparable, suggesting that the expression of Kir3 channels is the limiting factor for the GABABR currents in these INs. Morphological analysis showed that CCK-INs were diverse, comprising perisomatic-targeting basket cells (BCs), as well as dendrite-targeting (DT) interneurons, including a previously undescribed DT type. GABABR-mediated IPSCs in CCK-INs were large in BCs, but small in DT subtypes. In response to prolonged activation, GABABR-mediated currents displayed strong desensitization, which was absent in KCTD12-deficient mice. This study highlights that GABABRs differentially control CCK-IN subtypes, and the kinetics and desensitization of GABABR-mediated currents are modulated by KCTD12 proteins. ","lang":"eng"}],"scopus_import":"1","day":"12","date_published":"2016-04-12T00:00:00Z","doi":"10.1093/cercor/bhw090","citation":{"mla":"Booker, Sam, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex, vol. 27, no. 3, Oxford University Press, 2016, pp. 2318–34, doi:10.1093/cercor/bhw090.","short":"S. Booker, D. Althof, A. Gross, D. Loreth, J. Müller, A. Unger, B. Fakler, A. Varro, M. Watanabe, M. Gassmann, B. Bettler, R. Shigemoto, I. Vida, Á. Kulik, Cerebral Cortex 27 (2016) 2318–2334.","ieee":"S. Booker et al., “KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons,” Cerebral Cortex, vol. 27, no. 3. Oxford University Press, pp. 2318–2334, 2016.","chicago":"Booker, Sam, Daniel Althof, Anna Gross, Desiree Loreth, Johanna Müller, Andreas Unger, Bernd Fakler, et al. “KCTD12 Auxiliary Proteins Modulate Kinetics of GABAB Receptor-Mediated Inhibition in Cholecystokinin-Containing Interneurons.” Cerebral Cortex. Oxford University Press, 2016. https://doi.org/10.1093/cercor/bhw090.","apa":"Booker, S., Althof, D., Gross, A., Loreth, D., Müller, J., Unger, A., … Kulik, Á. (2016). KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. Oxford University Press. https://doi.org/10.1093/cercor/bhw090","ista":"Booker S, Althof D, Gross A, Loreth D, Müller J, Unger A, Fakler B, Varro A, Watanabe M, Gassmann M, Bettler B, Shigemoto R, Vida I, Kulik Á. 2016. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 27(3), 2318–2334.","ama":"Booker S, Althof D, Gross A, et al. KCTD12 auxiliary proteins modulate kinetics of GABAB receptor-mediated inhibition in Cholecystokinin-containing interneurons. Cerebral Cortex. 2016;27(3):2318-2334. doi:10.1093/cercor/bhw090"},"date_created":"2018-12-11T11:50:03Z","year":"2016","publication":"Cerebral Cortex","author":[{"full_name":"Booker, Sam","last_name":"Booker","first_name":"Sam"},{"first_name":"Daniel","last_name":"Althof","full_name":"Althof, Daniel"},{"last_name":"Gross","first_name":"Anna","full_name":"Gross, Anna"},{"last_name":"Loreth","first_name":"Desiree","full_name":"Loreth, Desiree"},{"full_name":"Müller, Johanna","last_name":"Müller","first_name":"Johanna"},{"full_name":"Unger, Andreas","last_name":"Unger","first_name":"Andreas"},{"first_name":"Bernd","last_name":"Fakler","full_name":"Fakler, Bernd"},{"last_name":"Varro","first_name":"Andrea","full_name":"Varro, Andrea"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"last_name":"Gassmann","first_name":"Martin","full_name":"Gassmann, Martin"},{"full_name":"Bettler, Bernhard","first_name":"Bernhard","last_name":"Bettler"},{"last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Vida, Imre","first_name":"Imre","last_name":"Vida"},{"full_name":"Kulik, Ákos","first_name":"Ákos","last_name":"Kulik"}],"date_updated":"2025-09-22T14:19:11Z","intvolume":" 27","volume":27,"quality_controlled":"1","issue":"3","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (DFG SFB 780 A2, A.K.; SFB TR3 I.V. and EXC 257, I.V.; FOR 2143, A.K. and I.V.), Spemann Graduate School (D.A.), BIOSS-2 (A6, A.K.), the Swiss National Science Foundation (3100A0-117816, B.B.), The McNaught Bequest (S.A.B. and I.V.), and Tenovus Scotland (I.V.).\r\n\r\n\r\nWe thank Cheryl Hutton and Chinmaya Sadangi for their contributions to neuronal reconstruction as well as Natalie Wernet, Sigrun Nestel, Anikó Schneider, Ina Wolter, and Ulrich Noeller for their excellent technical support. VGAT-Venus transgenic rats were generated by Drs Y. Yanagawa, M. Hirabayashi, and Y. Kawaguchi in National Institute for Physiological Sciences, Okazaki, Japan, using pCS2-Venus provided by Dr A. Miyawaki. The monoclonal mouse CCK antibody was generously provided by Dr G.V. Ohning, CURE Center, UCLA, CA. ","department":[{"_id":"RySh"}],"_id":"1083","publisher":"Oxford University Press","oa_version":"None","month":"04","external_id":{"isi":["000397636600048"]}},{"_id":"1088","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"76 - 84","language":[{"iso":"eng"}],"oa_version":"None","month":"07","publisher":"Taylor & Francis","volume":6,"intvolume":" 6","extern":"1","issue":"4","quality_controlled":"1","type":"journal_article","publication":"BioArchitecture","year":"2016","date_created":"2018-12-11T11:50:05Z","citation":{"chicago":"Uhler, Caroline, and G V Shivashankar. “Geometric Control and Modeling of Genome Reprogramming.” BioArchitecture. Taylor & Francis, 2016. https://doi.org/10.1080/19490992.2016.1201620.","ieee":"C. Uhler and G. V. Shivashankar, “Geometric control and modeling of genome reprogramming,” BioArchitecture, vol. 6, no. 4. Taylor & Francis, pp. 76–84, 2016.","short":"C. Uhler, G.V. Shivashankar, BioArchitecture 6 (2016) 76–84.","mla":"Uhler, Caroline, and G. V. Shivashankar. “Geometric Control and Modeling of Genome Reprogramming.” BioArchitecture, vol. 6, no. 4, Taylor & Francis, 2016, pp. 76–84, doi:10.1080/19490992.2016.1201620.","ama":"Uhler C, Shivashankar GV. Geometric control and modeling of genome reprogramming. BioArchitecture. 2016;6(4):76-84. doi:10.1080/19490992.2016.1201620","ista":"Uhler C, Shivashankar GV. 2016. Geometric control and modeling of genome reprogramming. BioArchitecture. 6(4), 76–84.","apa":"Uhler, C., & Shivashankar, G. V. (2016). Geometric control and modeling of genome reprogramming. BioArchitecture. Taylor & Francis. https://doi.org/10.1080/19490992.2016.1201620"},"date_updated":"2021-01-12T06:48:11Z","status":"public","author":[{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler"},{"first_name":"G V","last_name":"Shivashankar","full_name":"Shivashankar, G V"}],"fulldoi":"https://doi.org/10.1080/19490992.2016.1201620","publist_id":"6289","doi":"10.1080/19490992.2016.1201620","day":"27","date_published":"2016-07-27T00:00:00Z","title":"Geometric control and modeling of genome reprogramming","abstract":[{"lang":"eng","text":"Cell geometry is tightly coupled to gene expression patterns within the tissue microenvironment. This perspective synthesizes evidence that the 3D organization of chromosomes is a critical intermediate for geometric control of genomic programs. Using a combination of experiments and modeling we outline approaches to decipher the mechano-genomic code that governs cellular homeostasis and reprogramming."}],"publication_status":"published"},{"file_date_updated":"2018-12-12T10:17:31Z","article_processing_charge":"No","has_accepted_license":"1","oa":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"conference","ddc":["004"],"ec_funded":1,"publication_status":"published","file":[{"date_updated":"2018-12-12T10:17:31Z","relation":"main_file","access_level":"open_access","file_name":"IST-2017-795-v1+1_LIPIcs-MFCS-2016-24.pdf","date_created":"2018-12-12T10:17:31Z","content_type":"application/pdf","file_size":564560,"file_id":"5286","creator":"system"}],"title":"Nested weighted limit-average automata of bounded width","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"publist_id":"6286","fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2016.24","conference":{"location":"Krakow; Poland","start_date":"2016-08-22","end_date":"2016-08-26","name":"MFCS: Mathematical Foundations of Computer Science"},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa_version":"Published Version","month":"08","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"alternative_title":["LIPIcs"],"_id":"1090","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23\r\n(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna\r\nScience and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre\r\n(NCN), Poland under grant 2014/15/D/ST6/04543.","article_number":"24","quality_controlled":"1","pubrep_id":"795","volume":58,"intvolume":" 58","date_updated":"2025-07-10T11:50:02Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"citation":{"ista":"Chatterjee K, Henzinger TA, Otop J. 2016. Nested weighted limit-average automata of bounded width. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 24.","ama":"Chatterjee K, Henzinger TA, Otop J. Nested weighted limit-average automata of bounded width. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.MFCS.2016.24","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2016). Nested weighted limit-average automata of bounded width (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, Krakow; Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.MFCS.2016.24","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Nested Weighted Limit-Average Automata of Bounded Width,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.MFCS.2016.24.","mla":"Chatterjee, Krishnendu, et al. Nested Weighted Limit-Average Automata of Bounded Width. Vol. 58, 24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.MFCS.2016.24.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Nested weighted limit-average automata of bounded width,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow; Poland, 2016, vol. 58.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016."},"date_created":"2018-12-11T11:50:05Z","year":"2016","date_published":"2016-08-01T00:00:00Z","day":"01","doi":"10.4230/LIPIcs.MFCS.2016.24","abstract":[{"text":" While weighted automata provide a natural framework to express quantitative properties, many basic properties like average response time cannot be expressed with weighted automata. Nested weighted automata extend weighted automata and consist of a master automaton and a set of slave automata that are invoked by the master automaton. Nested weighted automata are strictly more expressive than weighted automata (e.g., average response time can be expressed with nested weighted automata), but the basic decision questions have higher complexity (e.g., for deterministic automata, the emptiness question for nested weighted automata is PSPACE-hard, whereas the corresponding complexity for weighted automata is PTIME). We consider a natural subclass of nested weighted automata where at any point at most a bounded number k of slave automata can be active. We focus on automata whose master value function is the limit average. We show that these nested weighted automata with bounded width are strictly more expressive than weighted automata (e.g., average response time with no overlapping requests can be expressed with bound k=1, but not with non-nested weighted automata). We show that the complexity of the basic decision problems (i.e., emptiness and universality) for the subclass with k constant matches the complexity for weighted automata. Moreover, when k is part of the input given in unary we establish PSPACE-completeness.","lang":"eng"}],"scopus_import":"1"},{"ec_funded":1,"ddc":["004"],"type":"conference","status":"public","fulldoi":"https://doi.org/10.4230/LIPIcs.CONCUR.2016.20","publist_id":"6283","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"}],"title":"Linear distances between Markov chains","file":[{"access_level":"open_access","file_name":"IST-2017-794-v1+1_LIPIcs-CONCUR-2016-20.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:11:39Z","date_updated":"2018-12-12T10:11:39Z","relation":"main_file","creator":"system","file_id":"4895","file_size":501827}],"publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"oa":1,"related_material":{"record":[{"relation":"dissertation_contains","id":"1155","status":"public"}]},"file_date_updated":"2018-12-12T10:11:39Z","has_accepted_license":"1","date_created":"2018-12-11T11:50:06Z","year":"2016","citation":{"ama":"Daca P, Henzinger TA, Kretinsky J, Petrov T. Linear distances between Markov chains. In: Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.20","ista":"Daca P, Henzinger TA, Kretinsky J, Petrov T. 2016. Linear distances between Markov chains. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 20.","apa":"Daca, P., Henzinger, T. A., Kretinsky, J., & Petrov, T. (2016). Linear distances between Markov chains (Vol. 59). Presented at the CONCUR: Concurrency Theory, Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20","chicago":"Daca, Przemyslaw, Thomas A Henzinger, Jan Kretinsky, and Tatjana Petrov. “Linear Distances between Markov Chains,” Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.20.","mla":"Daca, Przemyslaw, et al. Linear Distances between Markov Chains. Vol. 59, 20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.20.","short":"P. Daca, T.A. Henzinger, J. Kretinsky, T. Petrov, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"P. Daca, T. A. Henzinger, J. Kretinsky, and T. Petrov, “Linear distances between Markov chains,” presented at the CONCUR: Concurrency Theory, Quebec City; Canada, 2016, vol. 59."},"author":[{"full_name":"Daca, Przemyslaw","last_name":"Daca","first_name":"Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","last_name":"Petrov","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2026-04-15T10:02:12Z","abstract":[{"text":"We introduce a general class of distances (metrics) between Markov chains, which are based on linear behaviour. This class encompasses distances given topologically (such as the total variation distance or trace distance) as well as by temporal logics or automata. We investigate which of the distances can be approximated by observing the systems, i.e. by black-box testing or simulation, and we provide both negative and positive results. ","lang":"eng"}],"scopus_import":1,"doi":"10.4230/LIPIcs.CONCUR.2016.20","date_published":"2016-08-01T00:00:00Z","day":"01","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989\r\n(QUAREM), the Austrian Science Fund (FWF) under grants project S11402-N23 (RiSE and SHiNE)\r\nand Z211-N23 (Wittgenstein Award), by the Czech Science Foundation Grant No. P202/12/G061, and\r\nby the SNSF Advanced Postdoc. Mobility Fellowship – grant number P300P2_161067.","_id":"1093","department":[{"_id":"ToHe"},{"_id":"KrCh"},{"_id":"CaGu"}],"alternative_title":["LIPIcs"],"month":"08","oa_version":"Published Version","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"start_date":"2016-08-23","end_date":"2016-08-26","name":"CONCUR: Concurrency Theory","location":"Quebec City; Canada"},"intvolume":" 59","volume":59,"pubrep_id":"794","quality_controlled":"1","article_number":"20"},{"type":"book_chapter","ec_funded":1,"status":"public","fulldoi":"https://doi.org/10.1007/978-1-4939-6352-2_12","publist_id":"6281","project":[{"call_identifier":"FP7","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","grant_number":"604102"}],"title":"Immunogold protein localization on grid-glued freeze-fracture replicas","publication_status":"published","page":"203 - 216","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"article_processing_charge":"No","publication":"High-Resolution Imaging of Cellular Proteins","year":"2016","date_created":"2018-12-11T11:50:06Z","citation":{"ama":"Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Vol 1474. Springer; 2016:203-216. doi:10.1007/978-1-4939-6352-2_12","ista":"Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods in Molecular Biology, vol. 1474, 203–216.","apa":"Harada, H., & Shigemoto, R. (2016). Immunogold protein localization on grid-glued freeze-fracture replicas. In High-Resolution Imaging of Cellular Proteins (Vol. 1474, pp. 203–216). Springer. https://doi.org/10.1007/978-1-4939-6352-2_12","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” In High-Resolution Imaging of Cellular Proteins, 1474:203–16. Springer, 2016. https://doi.org/10.1007/978-1-4939-6352-2_12.","mla":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” High-Resolution Imaging of Cellular Proteins, vol. 1474, Springer, 2016, pp. 203–16, doi:10.1007/978-1-4939-6352-2_12.","ieee":"H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued freeze-fracture replicas,” in High-Resolution Imaging of Cellular Proteins, vol. 1474, Springer, 2016, pp. 203–216.","short":"H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins, Springer, 2016, pp. 203–216."},"date_updated":"2025-04-15T07:12:21Z","author":[{"orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","last_name":"Harada","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"doi":"10.1007/978-1-4939-6352-2_12","date_published":"2016-08-12T00:00:00Z","day":"12","abstract":[{"text":"Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face.","lang":"eng"}],"_id":"1094","alternative_title":["Methods in Molecular Biology"],"department":[{"_id":"RySh"}],"acknowledgement":"We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron microscope imaging. This work was supported by the European Union (HBP—Project Ref. 604102). ","month":"08","oa_version":"None","publisher":"Springer","volume":1474,"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"]},"intvolume":" 1474","quality_controlled":"1"},{"file_date_updated":"2018-12-12T10:10:10Z","has_accepted_license":"1","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"title":"Local linearizability for concurrent container-type data structures","file":[{"date_created":"2018-12-12T10:10:10Z","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","relation":"main_file","date_updated":"2018-12-12T10:10:10Z","creator":"system","file_size":589747,"file_id":"4795"}],"publication_status":"published","fulldoi":"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6","publist_id":"6280","status":"public","type":"conference","ddc":["004"],"ec_funded":1,"article_number":"6","quality_controlled":"1","volume":59,"pubrep_id":"793","intvolume":" 59","conference":{"location":"Quebec City; Canada","start_date":"2016-08-23","end_date":"2016-08-26","name":"CONCUR: Concurrency Theory"},"oa_version":"Published Version","month":"08","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","_id":"1095","department":[{"_id":"ToHe"}],"alternative_title":["LIPIcs"],"acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","doi":"10.4230/LIPIcs.CONCUR.2016.6","date_published":"2016-08-01T00:00:00Z","day":"01","abstract":[{"lang":"eng","text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. "}],"scopus_import":1,"date_updated":"2025-04-15T06:25:58Z","author":[{"full_name":"Haas, Andreas","last_name":"Haas","first_name":"Andreas"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Andreas","last_name":"Holzer","full_name":"Holzer, Andreas"},{"last_name":"Kirsch","first_name":"Christoph","full_name":"Kirsch, Christoph"},{"full_name":"Lippautz, Michael","last_name":"Lippautz","first_name":"Michael"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"full_name":"Sezgin, Ali","last_name":"Sezgin","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali"},{"last_name":"Sokolova","first_name":"Ana","full_name":"Sokolova, Ana"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"}],"publication":"Leibniz International Proceedings in Informatics","year":"2016","date_created":"2018-12-11T11:50:07Z","citation":{"ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6.","ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: Leibniz International Proceedings in Informatics. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:10.4230/LIPIcs.CONCUR.2016.6","apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In Leibniz International Proceedings in Informatics (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6","chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In Leibniz International Proceedings in Informatics, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. https://doi.org/10.4230/LIPIcs.CONCUR.2016.6.","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"A. Haas et al., “Local linearizability for concurrent container-type data structures,” in Leibniz International Proceedings in Informatics, Quebec City; Canada, 2016, vol. 59.","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” Leibniz International Proceedings in Informatics, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:10.4230/LIPIcs.CONCUR.2016.6."}},{"scopus_import":"1","day":"20","date_published":"2016-06-20T00:00:00Z","doi":"10.1016/j.devcel.2016.05.024","citation":{"apa":"Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., & Heisenberg, C.-P. J. (2016). Actin rings of power. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.05.024","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024","ieee":"C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg, “Actin rings of power,” Developmental Cell, vol. 37, no. 6. Cell Press, pp. 493–506, 2016.","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.","chicago":"Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and Carl-Philipp J Heisenberg. “Actin Rings of Power.” Developmental Cell. Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.05.024."},"year":"2016","date_created":"2018-12-11T11:50:07Z","publication":"Developmental Cell","author":[{"full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","last_name":"Schwayer"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora"},{"full_name":"Slovakova, Jana","last_name":"Slovakova","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","first_name":"Jana"},{"full_name":"Kardos, Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"date_updated":"2026-04-08T13:55:28Z","intvolume":" 37","volume":37,"quality_controlled":"1","issue":"6","department":[{"_id":"CaHe"}],"_id":"1096","publisher":"Cell Press","month":"06","oa_version":"None","external_id":{"isi":["000378204200005"]},"isi":1,"publist_id":"6279","fulldoi":"https://doi.org/10.1016/j.devcel.2016.05.024","publication_status":"published","title":"Actin rings of power","type":"journal_article","status":"public","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"493 - 506","related_material":{"record":[{"id":"7186","status":"public","relation":"part_of_dissertation"}]},"article_processing_charge":"No"},{"title":"Computational multicopter design","file":[{"file_id":"5298","file_size":33114420,"creator":"system","relation":"main_file","date_updated":"2018-12-12T10:17:42Z","date_created":"2018-12-12T10:17:42Z","content_type":"application/pdf","file_name":"IST-2017-759-v1+1_copter.pdf","access_level":"open_access"}],"project":[{"call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599","name":"Soft-bodied intelligence for Manipulation"}],"publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1145/2980179.2982427","publist_id":"6278","status":"public","ec_funded":1,"ddc":["006"],"type":"conference","oa":1,"file_date_updated":"2018-12-12T10:17:42Z","article_processing_charge":"No","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"abstract":[{"text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics.","lang":"eng"}],"scopus_import":"1","doi":"10.1145/2980179.2982427","day":"01","date_published":"2016-11-01T00:00:00Z","author":[{"last_name":"Du","first_name":"Tao","full_name":"Du, Tao"},{"first_name":"Adriana","last_name":"Schulz","full_name":"Schulz, Adriana"},{"full_name":"Zhu, Bo","first_name":"Bo","last_name":"Zhu"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel"},{"first_name":"Wojciech","last_name":"Matusik","full_name":"Matusik, Wojciech"}],"date_updated":"2025-09-22T14:17:29Z","date_created":"2018-12-11T11:50:07Z","year":"2016","citation":{"chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982427.","mla":"Du, Tao, et al. Computational Multicopter Design. Vol. 35, no. 6, 227, ACM, 2016, doi:10.1145/2980179.2982427.","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016.","ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982427","apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., & Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982427"},"quality_controlled":"1","issue":"6","article_number":"227","intvolume":" 35","volume":35,"pubrep_id":"759","month":"11","oa_version":"Submitted Version","publisher":"ACM","conference":{"end_date":"2016-12-08","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","start_date":"2016-12-05","location":"Macao, China"},"external_id":{"isi":["000388446200069"]},"acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","_id":"1097","alternative_title":["ACM Transactions on Graphics"],"department":[{"_id":"BeBi"}]},{"day":"01","date_published":"2016-12-01T00:00:00Z","scopus_import":"1","abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"date_created":"2018-12-11T11:50:08Z","year":"2016","citation":{"ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3619-3627.","apa":"Pentina, A., & Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems Foundation, 2016.","mla":"Pentina, Anastasia, and Ruth Urner. Lifelong Learning with Weighted Majority Votes. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3619–27.","ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627.","short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems Foundation, 2016, pp. 3619–3627."},"date_updated":"2025-06-03T11:35:58Z","author":[{"full_name":"Pentina, Anastasia","last_name":"Pentina","first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Urner, Ruth","last_name":"Urner","first_name":"Ruth"}],"volume":29,"pubrep_id":"775","intvolume":" 29","quality_controlled":"1","_id":"1098","department":[{"_id":"ChLa"}],"alternative_title":["Advances in Neural Information Processing Systems"],"acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","conference":{"location":"Barcelona, Spain","start_date":"2016-12-05","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems"},"month":"12","oa_version":"Published Version","publisher":"Neural Information Processing Systems Foundation","publist_id":"6277","file":[{"relation":"main_file","date_updated":"2018-12-12T10:12:42Z","content_type":"application/pdf","date_created":"2018-12-12T10:12:42Z","access_level":"open_access","file_name":"IST-2017-775-v1+1_main.pdf","file_size":237111,"file_id":"4961","creator":"system"},{"relation":"main_file","date_updated":"2018-12-12T10:12:43Z","access_level":"open_access","file_name":"IST-2017-775-v1+2_supplementary.pdf","date_created":"2018-12-12T10:12:43Z","content_type":"application/pdf","file_id":"4962","file_size":185818,"creator":"system"}],"title":"Lifelong learning with weighted majority votes","project":[{"call_identifier":"FP7","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding"}],"publication_status":"published","type":"conference","ec_funded":1,"ddc":["006"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3619-3627","language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2018-12-12T10:12:43Z","article_processing_charge":"No","oa":1},{"ddc":["000","005"],"ec_funded":1,"type":"conference","status":"public","isi":1,"publist_id":"6276","fulldoi":"https://doi.org/10.1145/2980179.2982397","publication_status":"published","file":[{"creator":"system","file_id":"4918","file_size":11122029,"file_name":"IST-2017-760-v1+1_flexmolds.pdf","access_level":"open_access","date_created":"2018-12-12T10:12:01Z","content_type":"application/pdf","relation":"main_file","date_updated":"2018-12-12T10:12:01Z"}],"project":[{"call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425"}],"title":"FlexMolds: Automatic design of flexible shells for molding","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"file_date_updated":"2018-12-12T10:12:01Z","article_processing_charge":"No","has_accepted_license":"1","citation":{"chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. https://doi.org/10.1145/2980179.2982397.","ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","mla":"Malomo, Luigi, et al. FlexMolds: Automatic Design of Flexible Shells for Molding. Vol. 35, no. 6, 223, ACM, 2016, doi:10.1145/2980179.2982397.","ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:10.1145/2980179.2982397","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223.","apa":"Malomo, L., Pietroni, N., Bickel, B., & Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. https://doi.org/10.1145/2980179.2982397"},"date_created":"2018-12-11T11:50:08Z","year":"2016","author":[{"last_name":"Malomo","first_name":"Luigi","full_name":"Malomo, Luigi"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"first_name":"Paolo","last_name":"Cignoni","full_name":"Cignoni, Paolo"}],"date_updated":"2025-09-22T14:16:02Z","abstract":[{"lang":"eng","text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies."}],"scopus_import":"1","day":"01","date_published":"2016-11-01T00:00:00Z","doi":"10.1145/2980179.2982397","acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford 3D Scanning Repository. The bimba, fertility and elephant models are courtesy of the AIM@SHAPE Shape Repository. \r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement\r\nNo. 645599.","department":[{"_id":"BeBi"}],"alternative_title":["ACM Transactions on Graphics"],"_id":"1099","publisher":"ACM","oa_version":"Submitted Version","month":"11","external_id":{"isi":["000388446200065"]},"conference":{"name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","end_date":"2016-12-08","start_date":"2016-12-05","location":"Macao, China"},"intvolume":" 35","pubrep_id":"760","volume":35,"quality_controlled":"1","article_number":"223","issue":"6"},{"publisher":"American Chemical Society","oa_version":"None","month":"11","external_id":{"isi":["000388914800003"]},"acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","department":[{"_id":"HaJa"}],"_id":"1101","quality_controlled":"1","issue":"11","intvolume":" 1","volume":1,"author":[{"last_name":"Mitchell","first_name":"Joshua","full_name":"Mitchell, Joshua"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"last_name":"Zhang","first_name":"William","full_name":"Zhang, William"},{"last_name":"Henneberger","first_name":"Christian","full_name":"Henneberger, Christian"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","last_name":"Janovjak","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315"},{"first_name":"Megan","last_name":"O'Mara","full_name":"O'Mara, Megan"},{"full_name":"Jackson, Colin","last_name":"Jackson","first_name":"Colin"}],"date_updated":"2025-09-22T14:14:58Z","citation":{"ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 2016;1(11):1286-1290. doi:10.1021/acssensors.6b00576","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., & Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. American Chemical Society. https://doi.org/10.1021/acssensors.6b00576","chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” ACS SENSORS. American Chemical Society, 2016. https://doi.org/10.1021/acssensors.6b00576.","ieee":"J. Mitchell et al., “Rangefinder: A semisynthetic FRET sensor design algorithm,” ACS SENSORS, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290.","mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” ACS SENSORS, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:10.1021/acssensors.6b00576."},"date_created":"2018-12-11T11:50:09Z","year":"2016","publication":"ACS SENSORS","abstract":[{"lang":"eng","text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of >300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest."}],"scopus_import":"1","date_published":"2016-11-10T00:00:00Z","day":"10","doi":"10.1021/acssensors.6b00576","article_processing_charge":"No","language":[{"iso":"eng"}],"page":"1286 - 1290","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","type":"journal_article","publication_status":"published","title":"Rangefinder: A semisynthetic FRET sensor design algorithm","isi":1,"publist_id":"6274","fulldoi":"https://doi.org/10.1021/acssensors.6b00576"},{"scopus_import":"1","abstract":[{"text":"Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network\\'s mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation.","lang":"eng"}],"doi":"10.5244/C.30.92","date_published":"2016-09-01T00:00:00Z","day":"01","author":[{"full_name":"Kolesnikov, Alexander","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov"},{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"date_updated":"2026-06-18T10:46:30Z","date_created":"2018-12-11T11:50:09Z","year":"2016","citation":{"ama":"Kolesnikov A, Lampert C. Improving weakly-supervised object localization by micro-annotation. In: Proceedings of the British Machine Vision Conference 2016. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:10.5244/C.30.92","ista":"Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization by micro-annotation. Proceedings of the British Machine Vision Conference 2016. BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12.","apa":"Kolesnikov, A., & Lampert, C. (2016). Improving weakly-supervised object localization by micro-annotation. In Proceedings of the British Machine Vision Conference 2016 (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom: BMVA Press. https://doi.org/10.5244/C.30.92","chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” In Proceedings of the British Machine Vision Conference 2016, 2016–September:92.1-92.12. BMVA Press, 2016. https://doi.org/10.5244/C.30.92.","mla":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” Proceedings of the British Machine Vision Conference 2016, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12, doi:10.5244/C.30.92.","ieee":"A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization by micro-annotation,” in Proceedings of the British Machine Vision Conference 2016, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.","short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12."},"publication":"Proceedings of the British Machine Vision Conference 2016","main_file_link":[{"open_access":"1","url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf"}],"quality_controlled":"1","volume":"2016-September","oa_version":"Published Version","month":"09","publisher":"BMVA Press","conference":{"location":"York, United Kingdom","start_date":"2016-09-19","end_date":"2016-09-22","name":"BMVC: British Machine Vision Conference"},"acknowledgement":"This work was funded in parts by the European Research Council\r\nunder the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe donation of the GPUs used for this research.","_id":"1102","department":[{"_id":"ChLa"}],"title":"Improving weakly-supervised object localization by micro-annotation","project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"publication_status":"published","fulldoi":"https://doi.org/10.5244/C.30.92","publist_id":"6273","status":"public","ddc":["000"],"ec_funded":1,"type":"conference","oa":1,"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"92.1-92.12","language":[{"iso":"eng"}]},{"_id":"1103","department":[{"_id":"ToHe"}],"acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","conference":{"location":"Kanpur, India ","start_date":"2016-11-18","end_date":"2016-11-20","name":"MEMOCODE: Conference on Formal Methods and Models for System Design"},"external_id":{"arxiv":["1606.05473"]},"oa_version":"Preprint","month":"12","publisher":"IEEE","article_number":"7797741","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.05473"}],"date_created":"2018-12-11T11:50:09Z","year":"2016","citation":{"mla":"Gurung, Amit, et al. Parallel Reachability Analysis for Hybrid Systems. 7797741, IEEE, 2016, doi:10.1109/MEMCOD.2016.7797741.","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. https://doi.org/10.1109/MEMCOD.2016.7797741.","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., & Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. https://doi.org/10.1109/MEMCOD.2016.7797741","ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:10.1109/MEMCOD.2016.7797741","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: Conference on Formal Methods and Models for System Design, 7797741."},"date_updated":"2025-06-04T11:52:29Z","author":[{"last_name":"Gurung","first_name":"Amit","full_name":"Gurung, Amit"},{"full_name":"Deka, Arup","last_name":"Deka","first_name":"Arup"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy","last_name":"Bogomolov"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"},{"last_name":"Ray","first_name":"Rajarshi","full_name":"Ray, Rajarshi"}],"doi":"10.1109/MEMCOD.2016.7797741","day":"27","date_published":"2016-12-27T00:00:00Z","scopus_import":"1","abstract":[{"text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"type":"conference","ec_funded":1,"status":"public","fulldoi":"https://doi.org/10.1109/MEMCOD.2016.7797741","arxiv":1,"publist_id":"6272","title":"Parallel reachability analysis for hybrid systems","project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"publication_status":"published"},{"corr_author":"1","article_processing_charge":"No","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"3610-3618","language":[{"iso":"eng"}],"title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"publication_status":"published","publist_id":"6265","status":"public","type":"conference","ec_funded":1,"quality_controlled":"1","volume":29,"intvolume":" 29","conference":{"location":"Barcelona; Spain","name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10","start_date":"2016-12-05"},"oa_version":"None","month":"12","publisher":"Neural Information Processing Systems Foundation","_id":"1105","department":[{"_id":"GaTk"}],"alternative_title":["Advances in Neural Information Processing Systems"],"acknowledgement":"We thank Jozsef Csicsvari for kindly sharing the CA1 data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","day":"01","date_published":"2016-12-01T00:00:00Z","abstract":[{"text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions.","lang":"eng"}],"scopus_import":"1","date_updated":"2025-06-03T11:36:49Z","author":[{"full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods"}],"date_created":"2018-12-11T11:50:10Z","year":"2016","citation":{"ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3610-3618.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.","apa":"Savin, C., & Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems Foundation.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems Foundation, 2016.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 3610–3618.","mla":"Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3610–18."}},{"quality_controlled":"1","issue":"1","extern":"1","pmid":1,"intvolume":" 215","volume":215,"publication_identifier":{"issn":["0021-9525","1540-8140"]},"article_type":"original","oa_version":"Published Version","month":"10","publisher":"Rockefeller University Press","external_id":{"pmid":["27697922"]},"_id":"11069","scopus_import":"1","abstract":[{"lang":"eng","text":"Repeated rounds of nuclear envelope (NE) rupture and repair have been observed in laminopathy and cancer cells and result in intermittent loss of nucleus compartmentalization. Currently, the causes of NE rupture are unclear. Here, we show that NE rupture in cancer cells relies on the assembly of contractile actin bundles that interact with the nucleus via the linker of nucleoskeleton and cytoskeleton (LINC) complex. We found that the loss of actin bundles or the LINC complex did not rescue nuclear lamina defects, a previously identified determinant of nuclear membrane stability, but did decrease the number and size of chromatin hernias. Finally, NE rupture inhibition could be rescued in cells treated with actin-depolymerizing drugs by mechanically constraining nucleus height. These data suggest a model of NE rupture where weak membrane areas, caused by defects in lamina organization, rupture because of an increase in intranuclear pressure from actin-based nucleus confinement."}],"doi":"10.1083/jcb.201603053","day":"03","date_published":"2016-10-03T00:00:00Z","author":[{"first_name":"Emily M.","last_name":"Hatch","full_name":"Hatch, Emily M."},{"last_name":"HETZER","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"date_updated":"2024-10-14T11:20:38Z","date_created":"2022-04-07T07:47:42Z","year":"2016","citation":{"ama":"Hatch EM, Hetzer M. Nuclear envelope rupture is induced by actin-based nucleus confinement. Journal of Cell Biology. 2016;215(1):27-36. doi:10.1083/jcb.201603053","ista":"Hatch EM, Hetzer M. 2016. Nuclear envelope rupture is induced by actin-based nucleus confinement. Journal of Cell Biology. 215(1), 27–36.","apa":"Hatch, E. M., & Hetzer, M. (2016). Nuclear envelope rupture is induced by actin-based nucleus confinement. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201603053","chicago":"Hatch, Emily M., and Martin Hetzer. “Nuclear Envelope Rupture Is Induced by Actin-Based Nucleus Confinement.” Journal of Cell Biology. Rockefeller University Press, 2016. https://doi.org/10.1083/jcb.201603053.","ieee":"E. M. Hatch and M. Hetzer, “Nuclear envelope rupture is induced by actin-based nucleus confinement,” Journal of Cell Biology, vol. 215, no. 1. Rockefeller University Press, pp. 27–36, 2016.","short":"E.M. Hatch, M. Hetzer, Journal of Cell Biology 215 (2016) 27–36.","mla":"Hatch, Emily M., and Martin Hetzer. “Nuclear Envelope Rupture Is Induced by Actin-Based Nucleus Confinement.” Journal of Cell Biology, vol. 215, no. 1, Rockefeller University Press, 2016, pp. 27–36, doi:10.1083/jcb.201603053."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1083/jcb.201603053"}],"publication":"Journal of Cell Biology","keyword":["Cell Biology"],"oa":1,"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"27-36","language":[{"iso":"eng"}],"title":"Nuclear envelope rupture is induced by actin-based nucleus confinement","publication_status":"published","fulldoi":"https://doi.org/10.1083/jcb.201603053","status":"public","type":"journal_article"},{"date_updated":"2024-10-14T11:21:07Z","author":[{"full_name":"Ibarra, Arkaitz","last_name":"Ibarra","first_name":"Arkaitz"},{"last_name":"Benner","first_name":"Chris","full_name":"Benner, Chris"},{"last_name":"Tyagi","first_name":"Swati","full_name":"Tyagi, Swati"},{"full_name":"Cool, Jonah","last_name":"Cool","first_name":"Jonah"},{"last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W","orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/gad.287417.116"}],"publication":"Genes & Development","citation":{"apa":"Ibarra, A., Benner, C., Tyagi, S., Cool, J., & Hetzer, M. (2016). Nucleoporin-mediated regulation of cell identity genes. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.287417.116","ista":"Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. 2016. Nucleoporin-mediated regulation of cell identity genes. Genes & Development. 30(20), 2253–2258.","ama":"Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. Nucleoporin-mediated regulation of cell identity genes. Genes & Development. 2016;30(20):2253-2258. doi:10.1101/gad.287417.116","mla":"Ibarra, Arkaitz, et al. “Nucleoporin-Mediated Regulation of Cell Identity Genes.” Genes & Development, vol. 30, no. 20, Cold Spring Harbor Laboratory, 2016, pp. 2253–58, doi:10.1101/gad.287417.116.","ieee":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, and M. Hetzer, “Nucleoporin-mediated regulation of cell identity genes,” Genes & Development, vol. 30, no. 20. Cold Spring Harbor Laboratory, pp. 2253–2258, 2016.","short":"A. Ibarra, C. Benner, S. Tyagi, J. Cool, M. Hetzer, Genes & Development 30 (2016) 2253–2258.","chicago":"Ibarra, Arkaitz, Chris Benner, Swati Tyagi, Jonah Cool, and Martin Hetzer. “Nucleoporin-Mediated Regulation of Cell Identity Genes.” Genes & Development. Cold Spring Harbor Laboratory, 2016. https://doi.org/10.1101/gad.287417.116."},"year":"2016","date_created":"2022-04-07T07:48:08Z","day":"02","date_published":"2016-11-02T00:00:00Z","doi":"10.1101/gad.287417.116","abstract":[{"text":"The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.","lang":"eng"}],"scopus_import":"1","external_id":{"pmid":["27807035"]},"publisher":"Cold Spring Harbor Laboratory","month":"11","oa_version":"Published Version","_id":"11070","extern":"1","issue":"20","pmid":1,"quality_controlled":"1","article_type":"original","publication_identifier":{"issn":["0890-9369"],"eissn":["1549-5477"]},"volume":30,"intvolume":" 30","status":"public","type":"journal_article","publication_status":"published","title":"Nucleoporin-mediated regulation of cell identity genes","fulldoi":"https://doi.org/10.1101/gad.287417.116","article_processing_charge":"No","oa":1,"language":[{"iso":"eng"}],"page":"2253-2258","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Developmental Biology","Genetics"]},{"status":"public","type":"journal_article","title":"Evolution of a transcriptional regulator from a transmembrane nucleoporin","publication_status":"published","fulldoi":"https://doi.org/10.1101/gad.280941.116","oa":1,"article_processing_charge":"No","page":"1155-1171","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"keyword":["Developmental Biology","Genetics"],"author":[{"last_name":"Franks","first_name":"Tobias M.","full_name":"Franks, Tobias M."},{"last_name":"Benner","first_name":"Chris","full_name":"Benner, Chris"},{"first_name":"Iñigo","last_name":"Narvaiza","full_name":"Narvaiza, Iñigo"},{"full_name":"Marchetto, Maria C.N.","first_name":"Maria C.N.","last_name":"Marchetto"},{"first_name":"Janet M.","last_name":"Young","full_name":"Young, Janet M."},{"full_name":"Malik, Harmit S.","first_name":"Harmit S.","last_name":"Malik"},{"full_name":"Gage, Fred H.","last_name":"Gage","first_name":"Fred H."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","first_name":"Martin W"}],"date_updated":"2024-10-14T11:21:48Z","year":"2016","date_created":"2022-04-07T07:48:20Z","citation":{"apa":"Franks, T. M., Benner, C., Narvaiza, I., Marchetto, M. C. N., Young, J. M., Malik, H. S., … Hetzer, M. (2016). Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.280941.116","ista":"Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH, Hetzer M. 2016. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes & Development. 30(10), 1155–1171.","ama":"Franks TM, Benner C, Narvaiza I, et al. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes & Development. 2016;30(10):1155-1171. doi:10.1101/gad.280941.116","mla":"Franks, Tobias M., et al. “Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin.” Genes & Development, vol. 30, no. 10, Cold Spring Harbor Laboratory, 2016, pp. 1155–71, doi:10.1101/gad.280941.116.","short":"T.M. Franks, C. Benner, I. Narvaiza, M.C.N. Marchetto, J.M. Young, H.S. Malik, F.H. Gage, M. Hetzer, Genes & Development 30 (2016) 1155–1171.","ieee":"T. M. Franks et al., “Evolution of a transcriptional regulator from a transmembrane nucleoporin,” Genes & Development, vol. 30, no. 10. Cold Spring Harbor Laboratory, pp. 1155–1171, 2016.","chicago":"Franks, Tobias M., Chris Benner, Iñigo Narvaiza, Maria C.N. Marchetto, Janet M. Young, Harmit S. Malik, Fred H. Gage, and Martin Hetzer. “Evolution of a Transcriptional Regulator from a Transmembrane Nucleoporin.” Genes & Development. Cold Spring Harbor Laboratory, 2016. https://doi.org/10.1101/gad.280941.116."},"publication":"Genes & Development","main_file_link":[{"url":"https://doi.org/10.1101/gad.280941.116","open_access":"1"}],"scopus_import":"1","abstract":[{"text":"Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic transport, recent research suggests that certain NPC proteins have additionally acquired the role of affecting gene expression at the nuclear periphery and in the nucleoplasm in metazoans. Here we identify a widely expressed variant of the transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Interestingly, sPom121 transcripts appear independently in several mammalian species, suggesting convergent innovation of Nup-mediated transcription regulation during mammalian evolution. Our findings implicate alternate transcription initiation as a mechanism to increase the functional diversity of NPC components.","lang":"eng"}],"doi":"10.1101/gad.280941.116","day":"19","date_published":"2016-05-19T00:00:00Z","oa_version":"Published Version","month":"05","publisher":"Cold Spring Harbor Laboratory","external_id":{"pmid":["27198230"]},"_id":"11071","quality_controlled":"1","issue":"10","extern":"1","pmid":1,"intvolume":" 30","volume":30,"article_type":"original","publication_identifier":{"eissn":["1549-5477"],"issn":["0890-9369"]}}]