[{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:45:52Z","ec_funded":1,"title":"Coalescent simulation in continuous space","publist_id":"3833","citation":{"short":"J. Kelleher, N.H. Barton, A. Etheridge, Bioinformatics 29 (2013) 955–956.","ieee":"J. Kelleher, N. H. Barton, and A. Etheridge, “Coalescent simulation in continuous space,” <i>Bioinformatics</i>, vol. 29, no. 7. Oxford University Press, pp. 955–956, 2013.","mla":"Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>, vol. 29, no. 7, Oxford University Press, 2013, pp. 955–56, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>.","ama":"Kelleher J, Barton NH, Etheridge A. Coalescent simulation in continuous space. <i>Bioinformatics</i>. 2013;29(7):955-956. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btt067\">10.1093/bioinformatics/btt067</a>","ista":"Kelleher J, Barton NH, Etheridge A. 2013. Coalescent simulation in continuous space. Bioinformatics. 29(7), 955–956.","apa":"Kelleher, J., Barton, N. H., &#38; Etheridge, A. (2013). Coalescent simulation in continuous space. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>","chicago":"Kelleher, Jerome, Nicholas H Barton, and Alison Etheridge. “Coalescent Simulation in Continuous Space.” <i>Bioinformatics</i>. Oxford University Press, 2013. <a href=\"https://doi.org/10.1093/bioinformatics/btt067\">https://doi.org/10.1093/bioinformatics/btt067</a>."},"oa":1,"corr_author":"1","quality_controlled":"1","date_created":"2018-12-11T12:00:17Z","year":"2013","volume":29,"page":"955 - 956","day":"07","type":"journal_article","article_processing_charge":"No","issue":"7","publication":"Bioinformatics","publisher":"Oxford University Press","pubrep_id":"556","_id":"2910","intvolume":"        29","abstract":[{"text":"Coalescent simulation has become an indispensable tool in population genetics and many complex evolutionary scenarios have been incorporated into the basic algorithm. Despite many years of intense interest in spatial structure, however, there are no available methods to simulate the ancestry of a sample of genes that occupy a spatial continuum. This is mainly due to the severe technical problems encountered by the classical model of isolation\r\nby distance. A recently introduced model solves these technical problems and provides a solid theoretical basis for the study of populations evolving in continuous space. We present a detailed algorithm to simulate the coalescent process in this model, and provide an efficient implementation of a generalised version of this algorithm as a freely available Python module.","lang":"eng"}],"status":"public","publication_status":"published","file":[{"access_level":"open_access","file_id":"5189","checksum":"a3b54d7477fac923815ac082403d9bd0","file_size":170197,"date_updated":"2020-07-14T12:45:52Z","creator":"system","file_name":"IST-2016-556-v1+1_bioinformatics-2013.pdf","date_created":"2018-12-12T10:16:04Z","content_type":"application/pdf","relation":"main_file"}],"department":[{"_id":"NiBa"}],"isi":1,"doi":"10.1093/bioinformatics/btt067","oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","month":"02","external_id":{"isi":["000316695700020"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"date_updated":"2025-09-29T13:30:36Z","author":[{"last_name":"Kelleher","full_name":"Kelleher, Jerome","first_name":"Jerome"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"}],"date_published":"2013-02-07T00:00:00Z","ddc":["570"]},{"language":[{"iso":"eng"}],"external_id":{"isi":["000314090300012"],"arxiv":["1205.6598"]},"month":"01","scopus_import":"1","oa_version":"Preprint","date_published":"2013-01-28T00:00:00Z","author":[{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455"},{"first_name":"Einat","full_name":"Granot Atedgi, Einat","last_name":"Granot Atedgi"},{"first_name":"Ronen","last_name":"Segev","full_name":"Segev, Ronen"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"}],"date_updated":"2025-09-29T13:29:59Z","article_number":"058104","isi":1,"department":[{"_id":"GaTk"}],"doi":"10.1103/PhysRevLett.110.058104","issue":"5","publication":"Physical Review Letters","publisher":"American Physical Society","article_processing_charge":"No","type":"journal_article","volume":110,"day":"28","arxiv":1,"publication_status":"published","intvolume":"       110","_id":"2913","abstract":[{"text":"The ability of an organism to distinguish between various stimuli is limited by the structure and noise in the population code of its sensory neurons. Here we infer a distance measure on the stimulus space directly from the recorded activity of 100 neurons in the salamander retina. In contrast to previously used measures of stimulus similarity, this &quot;neural metric&quot; tells us how distinguishable a pair of stimulus clips is to the retina, based on the similarity between the induced distributions of population responses. We show that the retinal distance strongly deviates from Euclidean, or any static metric, yet has a simple structure: we identify the stimulus features that the neural population is jointly sensitive to, and show the support-vector-machine- like kernel function relating the stimulus and neural response spaces. We show that the non-Euclidean nature of the retinal distance has important consequences for neural decoding.","lang":"eng"}],"status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.6598"}],"publist_id":"3830","title":"Retinal metric: a stimulus distance measure derived from population neural responses","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T12:00:18Z","year":"2013","corr_author":"1","quality_controlled":"1","oa":1,"citation":{"chicago":"Tkačik, Gašper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">https://doi.org/10.1103/PhysRevLett.110.058104</a>.","apa":"Tkačik, G., Granot Atedgi, E., Segev, R., &#38; Schneidman, E. (2013). Retinal metric: a stimulus distance measure derived from population neural responses. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">https://doi.org/10.1103/PhysRevLett.110.058104</a>","ista":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. 2013. Retinal metric: a stimulus distance measure derived from population neural responses. Physical Review Letters. 110(5), 058104.","ama":"Tkačik G, Granot Atedgi E, Segev R, Schneidman E. Retinal metric: a stimulus distance measure derived from population neural responses. <i>Physical Review Letters</i>. 2013;110(5). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">10.1103/PhysRevLett.110.058104</a>","short":"G. Tkačik, E. Granot Atedgi, R. Segev, E. Schneidman, Physical Review Letters 110 (2013).","mla":"Tkačik, Gašper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” <i>Physical Review Letters</i>, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.058104\">10.1103/PhysRevLett.110.058104</a>.","ieee":"G. Tkačik, E. Granot Atedgi, R. Segev, and E. Schneidman, “Retinal metric: a stimulus distance measure derived from population neural responses,” <i>Physical Review Letters</i>, vol. 110, no. 5. American Physical Society, 2013."}},{"doi":"10.1103/PhysRevLett.110.018701","license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"This work was supported in part by NSF Grants No. IIS-0613435, No. IBN-0344678, and No. PHY-0957573, by NIH Grant No. T32 MH065214, by the Human Frontier Science Program, and by the Swartz Foundation.\r\nCC BY 3.0\r\n","article_number":"018701","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"GaTk"}],"isi":1,"author":[{"first_name":"Greg","last_name":"Stephens","full_name":"Stephens, Greg"},{"first_name":"Thierry","full_name":"Mora, Thierry","last_name":"Mora"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"}],"date_published":"2013-01-02T00:00:00Z","ddc":["530"],"date_updated":"2025-09-29T13:29:28Z","external_id":{"arxiv":["0806.2694"],"isi":["000313006100058"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","month":"01","quality_controlled":"1","article_type":"original","date_created":"2018-12-11T12:00:19Z","year":"2013","citation":{"apa":"Stephens, G., Mora, T., Tkačik, G., &#38; Bialek, W. (2013). Statistical thermodynamics of natural images. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>","chicago":"Stephens, Greg, Thierry Mora, Gašper Tkačik, and William Bialek. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>. American Physical Society, 2013. <a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">https://doi.org/10.1103/PhysRevLett.110.018701</a>.","ama":"Stephens G, Mora T, Tkačik G, Bialek W. Statistical thermodynamics of natural images. <i>Physical Review Letters</i>. 2013;110(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">10.1103/PhysRevLett.110.018701</a>","ista":"Stephens G, Mora T, Tkačik G, Bialek W. 2013. Statistical thermodynamics of natural images. Physical Review Letters. 110(1), 018701.","short":"G. Stephens, T. Mora, G. Tkačik, W. Bialek, Physical Review Letters 110 (2013).","ieee":"G. Stephens, T. Mora, G. Tkačik, and W. Bialek, “Statistical thermodynamics of natural images,” <i>Physical Review Letters</i>, vol. 110, no. 1. American Physical Society, 2013.","mla":"Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” <i>Physical Review Letters</i>, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.110.018701\">10.1103/PhysRevLett.110.018701</a>."},"oa":1,"publist_id":"3829","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:45:53Z","title":"Statistical thermodynamics of natural images","publication_status":"published","file":[{"checksum":"72bfbc2094c4680e8a8a6bed668cd06d","file_size":416965,"file_id":"5366","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:18:44Z","file_name":"IST-2016-401-v1+1_1281.full.pdf","creator":"system","date_updated":"2020-07-14T12:45:53Z"}],"arxiv":1,"pubrep_id":"401","abstract":[{"lang":"eng","text":"The scale invariance of natural images suggests an analogy to the statistical mechanics of physical systems at a critical point. Here we examine the distribution of pixels in small image patches and show how to construct the corresponding thermodynamics. We find evidence for criticality in a diverging specific heat, which corresponds to large fluctuations in how &quot;surprising&quot; we find individual images, and in the quantitative form of the entropy vs energy. We identify special image configurations as local energy minima and show that average patches within each basin are interpretable as lines and edges in all orientations."}],"_id":"2914","intvolume":"       110","status":"public","article_processing_charge":"No","publication":"Physical Review Letters","issue":"1","publisher":"American Physical Society","volume":110,"day":"02","type":"journal_article"},{"department":[{"_id":"CaHe"}],"isi":1,"doi":"10.1038/ncb2632","acknowledgement":"This work was supported by the SNSF, the Swiss SystemsX.ch initiative and LipidX-2008/011 (M.G-G. and F.G.v.d.G.), by the Fondation SANTE-Vaduz/Aide au Soutien des Nouvelles Thérapies (F.G.v.d.G.) and by the ERC, the NCCR Frontiers in Genetics and Chemical Biology programmes and the Polish–Swiss research program (M.G-G.).","language":[{"iso":"eng"}],"external_id":{"isi":["000312841300007"]},"month":"01","oa_version":"None","scopus_import":"1","date_published":"2013-01-01T00:00:00Z","author":[{"full_name":"Castanon, Irinka","last_name":"Castanon","first_name":"Irinka"},{"first_name":"Laurence","full_name":"Abrami, Laurence","last_name":"Abrami"},{"full_name":"Holtzer, Laurent","last_name":"Holtzer","first_name":"Laurent"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"},{"full_name":"Van Der Goot, Françoise","last_name":"Van Der Goot","first_name":"Françoise"},{"last_name":"González Gaitán","full_name":"González Gaitán, Marcos","first_name":"Marcos"}],"date_updated":"2025-09-30T08:16:16Z","publist_id":"3819","title":"Anthrax toxin receptor 2a controls mitotic spindle positioning","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T12:00:20Z","year":"2013","quality_controlled":"1","citation":{"short":"I. Castanon, L. Abrami, L. Holtzer, C.-P.J. Heisenberg, F. Van Der Goot, M. González Gaitán, Nature Cell Biology 15 (2013) 28–39.","ieee":"I. Castanon, L. Abrami, L. Holtzer, C.-P. J. Heisenberg, F. Van Der Goot, and M. González Gaitán, “Anthrax toxin receptor 2a controls mitotic spindle positioning,” <i>Nature Cell Biology</i>, vol. 15, no. 1. Nature Publishing Group, pp. 28–39, 2013.","mla":"Castanon, Irinka, et al. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>, vol. 15, no. 1, Nature Publishing Group, 2013, pp. 28–39, doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>.","ama":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. 2013;15(1):28-39. doi:<a href=\"https://doi.org/10.1038/ncb2632\">10.1038/ncb2632</a>","ista":"Castanon I, Abrami L, Holtzer L, Heisenberg C-PJ, Van Der Goot F, González Gaitán M. 2013. Anthrax toxin receptor 2a controls mitotic spindle positioning. Nature Cell Biology. 15(1), 28–39.","apa":"Castanon, I., Abrami, L., Holtzer, L., Heisenberg, C.-P. J., Van Der Goot, F., &#38; González Gaitán, M. (2013). Anthrax toxin receptor 2a controls mitotic spindle positioning. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>","chicago":"Castanon, Irinka, Laurence Abrami, Laurent Holtzer, Carl-Philipp J Heisenberg, Françoise Van Der Goot, and Marcos González Gaitán. “Anthrax Toxin Receptor 2a Controls Mitotic Spindle Positioning.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/ncb2632\">https://doi.org/10.1038/ncb2632</a>."},"issue":"1","publication":"Nature Cell Biology","publisher":"Nature Publishing Group","article_processing_charge":"No","type":"journal_article","volume":15,"day":"01","page":"28 - 39","publication_status":"published","_id":"2918","abstract":[{"text":"Oriented mitosis is essential during tissue morphogenesis. The Wnt/planar cell polarity (Wnt/PCP) pathway orients mitosis in a number of developmental systems, including dorsal epiblast cell divisions along the animal-vegetal (A-V) axis during zebrafish gastrulation. How Wnt signalling orients the mitotic plane is, however, unknown. Here we show that, in dorsal epiblast cells, anthrax toxin receptor 2a (Antxr2a) accumulates in a polarized cortical cap, which is aligned with the embryonic A-V axis and forecasts the division plane. Filamentous actin (F-actin) also forms an A-V polarized cap, which depends on Wnt/PCP and its effectors RhoA and Rock2. Antxr2a is recruited to the cap by interacting with actin. Antxr2a also interacts with RhoA and together they activate the diaphanous-related formin zDia2. Mechanistically, Antxr2a functions as a Wnt-dependent polarized determinant, which, through the action of RhoA and zDia2, exerts torque on the spindle to align it with the A-V axis.\r\n","lang":"eng"}],"intvolume":"        15","status":"public"},{"oa_version":"Submitted Version","scopus_import":"1","month":"01","external_id":{"pmid":["23211744"],"isi":["000316464500009"]},"language":[{"iso":"eng"}],"date_updated":"2025-09-29T13:28:19Z","author":[{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Baster, Pawel","last_name":"Baster"},{"last_name":"Robert","full_name":"Robert, Stéphanie","first_name":"Stéphanie"},{"last_name":"Kleine Vehn","full_name":"Kleine Vehn, Jürgen","first_name":"Jürgen"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"last_name":"Kania","full_name":"Kania, Urszula","id":"4AE5C486-F248-11E8-B48F-1D18A9856A87","first_name":"Urszula"},{"first_name":"Wim","last_name":"Grunewald","full_name":"Grunewald, Wim"},{"last_name":"De Rybel","full_name":"De Rybel, Bert","first_name":"Bert"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"date_published":"2013-01-23T00:00:00Z","isi":1,"department":[{"_id":"JiFr"}],"doi":"10.1038/emboj.2012.310","page":"260 - 274","day":"23","volume":32,"type":"journal_article","article_processing_charge":"No","publisher":"Wiley-Blackwell","publication":"EMBO Journal","issue":"2","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3553380/"}],"status":"public","_id":"2919","intvolume":"        32","pmid":1,"abstract":[{"text":"The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth.","lang":"eng"}],"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism","publist_id":"3818","citation":{"chicago":"Baster, Pawel, Stéphanie Robert, Jürgen Kleine Vehn, Steffen Vanneste, Urszula Kania, Wim Grunewald, Bert De Rybel, Tom Beeckman, and Jiří Friml. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>.","apa":"Baster, P., Robert, S., Kleine Vehn, J., Vanneste, S., Kania, U., Grunewald, W., … Friml, J. (2013). SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.310\">https://doi.org/10.1038/emboj.2012.310</a>","ista":"Baster P, Robert S, Kleine Vehn J, Vanneste S, Kania U, Grunewald W, De Rybel B, Beeckman T, Friml J. 2013. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. EMBO Journal. 32(2), 260–274.","ama":"Baster P, Robert S, Kleine Vehn J, et al. SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism. <i>EMBO Journal</i>. 2013;32(2):260-274. doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>","ieee":"P. Baster <i>et al.</i>, “SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism,” <i>EMBO Journal</i>, vol. 32, no. 2. Wiley-Blackwell, pp. 260–274, 2013.","mla":"Baster, Pawel, et al. “SCF^TIR1 AFB-Auxin Signalling Regulates PIN Vacuolar Trafficking and Auxin Fluxes during Root Gravitropism.” <i>EMBO Journal</i>, vol. 32, no. 2, Wiley-Blackwell, 2013, pp. 260–74, doi:<a href=\"https://doi.org/10.1038/emboj.2012.310\">10.1038/emboj.2012.310</a>.","short":"P. Baster, S. Robert, J. Kleine Vehn, S. Vanneste, U. Kania, W. Grunewald, B. De Rybel, T. Beeckman, J. Friml, EMBO Journal 32 (2013) 260–274."},"oa":1,"corr_author":"1","quality_controlled":"1","year":"2013","date_created":"2018-12-11T12:00:20Z"},{"citation":{"ama":"Compagnon J, Heisenberg C-PJ. Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. 2013;32(1):1-3. doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>","ista":"Compagnon J, Heisenberg C-PJ. 2013. Neurulation coordinating cell polarisation and lumen formation. EMBO Journal. 32(1), 1–3.","apa":"Compagnon, J., &#38; Heisenberg, C.-P. J. (2013). Neurulation coordinating cell polarisation and lumen formation. <i>EMBO Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>","chicago":"Compagnon, Julien, and Carl-Philipp J Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1038/emboj.2012.325\">https://doi.org/10.1038/emboj.2012.325</a>.","ieee":"J. Compagnon and C.-P. J. Heisenberg, “Neurulation coordinating cell polarisation and lumen formation,” <i>EMBO Journal</i>, vol. 32, no. 1. Wiley-Blackwell, pp. 1–3, 2013.","mla":"Compagnon, Julien, and Carl-Philipp J. Heisenberg. “Neurulation Coordinating Cell Polarisation and Lumen Formation.” <i>EMBO Journal</i>, vol. 32, no. 1, Wiley-Blackwell, 2013, pp. 1–3, doi:<a href=\"https://doi.org/10.1038/emboj.2012.325\">10.1038/emboj.2012.325</a>.","short":"J. Compagnon, C.-P.J. Heisenberg, EMBO Journal 32 (2013) 1–3."},"oa":1,"corr_author":"1","quality_controlled":"1","date_created":"2018-12-11T12:00:20Z","year":"2013","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Neurulation coordinating cell polarisation and lumen formation","publist_id":"3817","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3545307/","open_access":"1"}],"_id":"2920","intvolume":"        32","pmid":1,"abstract":[{"text":"Cell polarisation in development is a common and fundamental process underlying embryo patterning and morphogenesis, and has been extensively studied over the past years. Our current knowledge of cell polarisation in development is predominantly based on studies that have analysed polarisation of single cells, such as eggs, or cellular aggregates with a stable polarising interface, such as cultured epithelial cells (St Johnston and Ahringer, 2010). However, in embryonic development, particularly of vertebrates, cell polarisation processes often encompass large numbers of cells that are placed within moving and proliferating tissues, and undergo mesenchymal-to-epithelial transitions with a highly complex spatiotemporal choreography. How such intricate cell polarisation processes in embryonic development are achieved has only started to be analysed. By using live imaging of neurulation in the transparent zebrafish embryo, Buckley et al (2012) now describe a novel polarisation strategy by which cells assemble an apical domain in the part of their cell body that intersects with the midline of the forming neural rod. This mechanism, along with the previously described mirror-symmetric divisions (Tawk et al, 2007), is thought to trigger formation of both neural rod midline and lumen.","lang":"eng"}],"status":"public","publication_status":"published","volume":32,"page":"1 - 3","day":"09","type":"journal_article","article_processing_charge":"No","issue":"1","publication":"EMBO Journal","publisher":"Wiley-Blackwell","doi":"10.1038/emboj.2012.325","department":[{"_id":"CaHe"}],"isi":1,"date_updated":"2025-09-29T13:27:27Z","author":[{"id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","full_name":"Compagnon, Julien","last_name":"Compagnon","first_name":"Julien"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"date_published":"2013-01-09T00:00:00Z","scopus_import":"1","oa_version":"Submitted Version","month":"01","external_id":{"isi":["000314141900001"],"pmid":["23211745"]},"language":[{"iso":"eng"}]},{"external_id":{"isi":["000314437000004"]},"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"None","month":"05","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chao","first_name":"Chao"},{"first_name":"Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael","last_name":"Kerber"}],"date_published":"2013-05-01T00:00:00Z","date_updated":"2025-09-29T13:26:21Z","department":[{"_id":"HeEd"}],"isi":1,"doi":"10.1016/j.comgeo.2012.02.010","acknowledgement":"The authors thank Herbert Edelsbrunner for many helpful discussions and suggestions. Moreover, they are grateful for the careful reviews that helped to improve the quality of the paper.","article_processing_charge":"No","publisher":"Elsevier","publication":"Computational Geometry: Theory and Applications","issue":"4","page":"435 - 447","day":"01","volume":46,"type":"journal_article","publication_status":"published","status":"public","abstract":[{"text":"In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ &gt; 0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0, 1), the running time is O (C (1 - δ) Γ R d (n) log n), where C (1 - δ) Γ is the number of homology classes with persistence at least (1 - δ) Γ, n is the total number of simplices in the complex, d its dimension, and R d (n) is the complexity of computing the rank of an n × n matrix with O (d n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O (C (1 - δ) Γ n 2.376) algorithm, an O (C (1 - δ) Γ n 2.28) Las-Vegas algorithm, or an O (C (1 - δ) Γ n 2 + ε{lunate}) Monte-Carlo algorithm for an arbitrary ε{lunate} &gt; 0. The space complexity of the Monte-Carlo version is bounded by O (d n) = O (n log n).","lang":"eng"}],"_id":"2939","intvolume":"        46","publist_id":"3796","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"relation":"earlier_version","id":"3367","status":"public"}]},"title":"An output sensitive algorithm for persistent homology","corr_author":"1","quality_controlled":"1","year":"2013","date_created":"2018-12-11T12:00:27Z","citation":{"ista":"Chen C, Kerber M. 2013. An output sensitive algorithm for persistent homology. Computational Geometry: Theory and Applications. 46(4), 435–447.","ama":"Chen C, Kerber M. An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. 2013;46(4):435-447. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>","chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>.","apa":"Chen, C., &#38; Kerber, M. (2013). An output sensitive algorithm for persistent homology. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">https://doi.org/10.1016/j.comgeo.2012.02.010</a>","ieee":"C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4. Elsevier, pp. 435–447, 2013.","mla":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology.” <i>Computational Geometry: Theory and Applications</i>, vol. 46, no. 4, Elsevier, 2013, pp. 435–47, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2012.02.010\">10.1016/j.comgeo.2012.02.010</a>.","short":"C. Chen, M. Kerber, Computational Geometry: Theory and Applications 46 (2013) 435–447."}},{"project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"}],"date_updated":"2025-09-18T11:37:22Z","author":[{"orcid":"0000-0003-2835-9093","first_name":"Stephan","last_name":"Krenn","full_name":"Krenn, Stephan","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"},{"full_name":"Wadia, Akshay","last_name":"Wadia","first_name":"Akshay"}],"alternative_title":["LNCS"],"ddc":["000"],"date_published":"2013-01-29T00:00:00Z","has_accepted_license":"1","oa_version":"Submitted Version","scopus_import":1,"month":"01","conference":{"name":"TCC: Theory of Cryptography Conference","location":"Tokyo, Japan","start_date":"2013-03-03","end_date":"2013-03-06"},"language":[{"iso":"eng"}],"editor":[{"full_name":"Sahai, Amit","last_name":"Sahai","first_name":"Amit"}],"doi":"10.1007/978-3-642-36594-2_2","department":[{"_id":"KrPi"}],"status":"public","abstract":[{"text":"A chain rule for an entropy notion H(.) states that the entropy H(X) of a variable X decreases by at most l if conditioned on an l-bit string A, i.e., H(X|A)&gt;= H(X)-l. More generally, it satisfies a chain rule for conditional entropy if H(X|Y,A)&gt;= H(X|Y)-l.\r\n\r\nAll natural information theoretic entropy notions we are aware of (like Shannon or min-entropy) satisfy some kind of chain rule for conditional entropy. Moreover, many computational entropy notions (like Yao entropy, unpredictability entropy and several variants of HILL entropy) satisfy the chain rule for conditional entropy, though here not only the quantity decreases by l, but also the quality of the entropy decreases exponentially in l. However, for \r\nthe standard notion of conditional HILL entropy (the computational equivalent of min-entropy) the existence of such a rule was unknown so far.\r\n\r\nIn this paper, we prove that for conditional HILL entropy no meaningful chain rule exists, assuming the existence of one-way permutations: there exist distributions X,Y,A, where A is a distribution over a single bit, but  $H(X|Y)&gt;&gt;H(X|Y,A)$, even if we simultaneously allow for a massive degradation in the quality of the entropy.\r\n\r\nThe idea underlying our construction is based on a surprising connection between the chain rule for HILL entropy and deniable encryption. ","lang":"eng"}],"_id":"2940","intvolume":"      7785","file":[{"date_updated":"2020-07-14T12:45:54Z","creator":"dernst","file_name":"2013_LNCS_Krenn.pdf","date_created":"2019-01-22T14:11:11Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"5875","file_size":414823,"checksum":"beb0cc1c0579da2d2e84394230a5da78"}],"publication_status":"published","page":"23 - 39","day":"29","volume":7785,"type":"conference","publisher":"Springer","citation":{"ista":"Krenn S, Pietrzak KZ, Wadia A. 2013. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. TCC: Theory of Cryptography Conference, LNCS, vol. 7785, 23–39.","ama":"Krenn S, Pietrzak KZ, Wadia A. A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In: Sahai A, ed. Vol 7785. Springer; 2013:23-39. doi:<a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">10.1007/978-3-642-36594-2_2</a>","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, and Akshay Wadia. “A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It.” edited by Amit Sahai, 7785:23–39. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">https://doi.org/10.1007/978-3-642-36594-2_2</a>.","apa":"Krenn, S., Pietrzak, K. Z., &#38; Wadia, A. (2013). A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it. In A. Sahai (Ed.) (Vol. 7785, pp. 23–39). Presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan: Springer. <a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">https://doi.org/10.1007/978-3-642-36594-2_2</a>","mla":"Krenn, Stephan, et al. <i>A Counterexample to the Chain Rule for Conditional HILL Entropy, and What Deniable Encryption Has to Do with It</i>. Edited by Amit Sahai, vol. 7785, Springer, 2013, pp. 23–39, doi:<a href=\"https://doi.org/10.1007/978-3-642-36594-2_2\">10.1007/978-3-642-36594-2_2</a>.","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, in:, A. Sahai (Ed.), Springer, 2013, pp. 23–39.","ieee":"S. Krenn, K. Z. Pietrzak, and A. Wadia, “A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it,” presented at the TCC: Theory of Cryptography Conference, Tokyo, Japan, 2013, vol. 7785, pp. 23–39."},"oa":1,"quality_controlled":"1","year":"2013","date_created":"2018-12-11T12:00:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"later_version","id":"1479","status":"public"}]},"ec_funded":1,"title":"A counterexample to the chain rule for conditional HILL entropy, and what deniable encryption has to do with it","file_date_updated":"2020-07-14T12:45:54Z","publist_id":"3795"},{"acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","doi":"10.1111/mec.12165","department":[{"_id":"NiBa"}],"isi":1,"date_updated":"2025-09-29T13:25:36Z","date_published":"2013-02-01T00:00:00Z","author":[{"first_name":"Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","full_name":"Aeschbacher, Simon","last_name":"Aeschbacher"},{"last_name":"Futschik","full_name":"Futschik, Andreas","first_name":"Andreas"},{"full_name":"Beaumont, Mark","last_name":"Beaumont","first_name":"Mark"}],"month":"02","scopus_import":"1","oa_version":"None","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000314220900008"]},"citation":{"short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” <i>Molecular Ecology</i>, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.","mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. 2013;22(4):987-1002. doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>.","apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>"},"year":"2013","date_created":"2018-12-11T12:00:28Z","quality_controlled":"1","corr_author":"1","title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"status":"public","id":"9758","relation":"research_data"}]},"publist_id":"3788","status":"public","_id":"2944","intvolume":"        22","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"publication_status":"published","type":"journal_article","day":"01","page":"987 - 1002","volume":22,"publisher":"Wiley-Blackwell","publication":"Molecular Ecology","issue":"4","article_processing_charge":"No"},{"acknowledgement":"This work was supported by the PASCAL 2 Network of Excellence (TT) and by the Newton International Fellowship (NQ)","doi":"10.1007/978-3-642-37331-2_1","department":[{"_id":"ChLa"}],"date_updated":"2020-08-11T10:09:54Z","date_published":"2013-04-04T00:00:00Z","ddc":["000"],"alternative_title":["LNCS"],"author":[{"last_name":"Tommasi","full_name":"Tommasi, Tatiana","first_name":"Tatiana"},{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"first_name":"Barbara","full_name":"Caputo, Barbara","last_name":"Caputo"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph"}],"month":"04","scopus_import":1,"oa_version":"Submitted Version","has_accepted_license":"1","language":[{"iso":"eng"}],"conference":{"end_date":"2012-11-09","start_date":"2012-11-05","location":"Daejeon, Korea","name":"ACCV: Asian Conference on Computer Vision"},"oa":1,"citation":{"ista":"Tommasi T, Quadrianto N, Caputo B, Lampert C. 2013. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 7724, 1–15.","ama":"Tommasi T, Quadrianto N, Caputo B, Lampert C. Beyond dataset bias: Multi-task unaligned shared knowledge transfer. 2013;7724:1-15. doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>","chicago":"Tommasi, Tatiana, Novi Quadrianto, Barbara Caputo, and Christoph Lampert. “Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>.","apa":"Tommasi, T., Quadrianto, N., Caputo, B., &#38; Lampert, C. (2013). Beyond dataset bias: Multi-task unaligned shared knowledge transfer. Presented at the ACCV: Asian Conference on Computer Vision, Daejeon, Korea: Springer. <a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">https://doi.org/10.1007/978-3-642-37331-2_1</a>","mla":"Tommasi, Tatiana, et al. <i>Beyond Dataset Bias: Multi-Task Unaligned Shared Knowledge Transfer</i>. Vol. 7724, Springer, 2013, pp. 1–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-37331-2_1\">10.1007/978-3-642-37331-2_1</a>.","ieee":"T. Tommasi, N. Quadrianto, B. Caputo, and C. Lampert, “Beyond dataset bias: Multi-task unaligned shared knowledge transfer,” vol. 7724. Springer, pp. 1–15, 2013.","short":"T. Tommasi, N. Quadrianto, B. Caputo, C. Lampert, 7724 (2013) 1–15."},"date_created":"2018-12-11T12:00:30Z","year":"2013","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:55Z","title":"Beyond dataset bias: Multi-task unaligned shared knowledge transfer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3784","_id":"2948","intvolume":"      7724","abstract":[{"text":"Many visual datasets are traditionally used to analyze the performance of different learning techniques. The evaluation is usually done within each dataset, therefore it is questionable if such results are a reliable indicator of true generalization ability. We propose here an algorithm to exploit the existing data resources when learning on a new multiclass problem. Our main idea is to identify an image representation that decomposes orthogonally into two subspaces: a part specific to each dataset, and a part generic to, and therefore shared between, all the considered source sets. This allows us to use the generic representation as un-biased reference knowledge for a novel classification task. By casting the method in the multi-view setting, we also make it possible to use different features for different databases. We call the algorithm MUST, Multitask Unaligned Shared knowledge Transfer. Through extensive experiments on five public datasets, we show that MUST consistently improves the cross-datasets generalization performance.","lang":"eng"}],"status":"public","publication_status":"published","file":[{"access_level":"open_access","file_id":"5874","checksum":"a0a7234a89e2192af655b0d0ae3bf445","file_size":1513620,"date_updated":"2020-07-14T12:45:55Z","creator":"dernst","file_name":"2012_ACCV_Tommasi.pdf","date_created":"2019-01-22T14:03:11Z","content_type":"application/pdf","relation":"main_file"}],"type":"conference","series_title":"Lecture Notes in Computer Science","volume":7724,"page":"1 - 15","day":"04","publisher":"Springer"},{"date_updated":"2021-01-12T07:40:10Z","status":"public","abstract":[{"text":"Efficient zero-knowledge proofs of knowledge (ZK-PoK) are basic building blocks of many practical cryptographic applications such as identification schemes, group signatures, and secure multiparty computation. Currently, first applications that critically rely on ZK-PoKs are being deployed in the real world. The most prominent example is Direct Anonymous Attestation (DAA), which was adopted by the Trusted Computing Group (TCG) and implemented as one of the functionalities of the cryptographic Trusted Platform Module (TPM) chip.\n\nImplementing systems using ZK-PoK turns out to be challenging, since ZK-PoK are, loosely speaking, significantly more complex than standard crypto primitives, such as encryption and signature schemes. As a result, implementation cycles of ZK-PoK are time-consuming and error-prone, in particular for developers with minor or no cryptographic skills. \n\nIn this paper we report on our ongoing and future research vision with the goal to bring ZK-PoK to practice by making them accessible to crypto and security engineers. To this end we are developing compilers and related tools that support and partially automate the design, implementation, verification and secure implementation of ZK-PoK protocols.","lang":"eng"}],"_id":"2973","intvolume":"      7028","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2009/211.pdf"}],"alternative_title":["LNCS"],"date_published":"2013-01-08T00:00:00Z","author":[{"first_name":"Endre","full_name":"Bangerter, Endre","last_name":"Bangerter"},{"last_name":"Barzan","full_name":"Barzan, Stefania","first_name":"Stefania"},{"full_name":"Stephan Krenn","last_name":"Krenn","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2835-9093","first_name":"Stephan"},{"last_name":"Sadeghi","full_name":"Sadeghi, Ahmad-Reza","first_name":"Ahmad"},{"first_name":"Thomas","full_name":"Schneider, Thomas","last_name":"Schneider"},{"first_name":"Joe","full_name":"Tsay, Joe-Kai","last_name":"Tsay"}],"publication_status":"published","type":"conference","month":"01","page":"51 - 62","day":"08","volume":7028,"publisher":"Springer","conference":{"name":"SPW: Security Protocols Workshop"},"extern":1,"oa":1,"acknowledgement":"This work is being performed within the FP7 EU project CACE (Computer Aided Cryptography Engineering).","editor":[{"first_name":"Bruce","full_name":"Christianson, Bruce","last_name":"Christianson"},{"full_name":"Malcolm, James A.","last_name":"Malcolm","first_name":"James"},{"first_name":"Vashek","last_name":"Matyas","full_name":"Matyas, Vashek"},{"first_name":"Michael","full_name":"Roe, Michael","last_name":"Roe"}],"citation":{"short":"E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, J. Tsay, in:, B. Christianson, J. Malcolm, V. Matyas, M. Roe (Eds.), Springer, 2013, pp. 51–62.","ieee":"E. Bangerter, S. Barzan, S. Krenn, A. Sadeghi, T. Schneider, and J. Tsay, “Bringing Zero-Knowledge Proofs of Knowledge to Practice,” presented at the SPW: Security Protocols Workshop, 2013, vol. 7028, pp. 51–62.","mla":"Bangerter, Endre, et al. <i>Bringing Zero-Knowledge Proofs of Knowledge to Practice</i>. Edited by Bruce Christianson et al., vol. 7028, Springer, 2013, pp. 51–62, doi:<a href=\"https://doi.org/10.1007/978-3-642-36213-2_9\">10.1007/978-3-642-36213-2_9</a>.","chicago":"Bangerter, Endre, Stefania Barzan, Stephan Krenn, Ahmad Sadeghi, Thomas Schneider, and Joe Tsay. “Bringing Zero-Knowledge Proofs of Knowledge to Practice.” edited by Bruce Christianson, James Malcolm, Vashek Matyas, and Michael Roe, 7028:51–62. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-36213-2_9\">https://doi.org/10.1007/978-3-642-36213-2_9</a>.","apa":"Bangerter, E., Barzan, S., Krenn, S., Sadeghi, A., Schneider, T., &#38; Tsay, J. (2013). Bringing Zero-Knowledge Proofs of Knowledge to Practice. In B. Christianson, J. Malcolm, V. Matyas, &#38; M. Roe (Eds.) (Vol. 7028, pp. 51–62). Presented at the SPW: Security Protocols Workshop, Springer. <a href=\"https://doi.org/10.1007/978-3-642-36213-2_9\">https://doi.org/10.1007/978-3-642-36213-2_9</a>","ista":"Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. 2013. Bringing Zero-Knowledge Proofs of Knowledge to Practice. SPW: Security Protocols Workshop, LNCS, vol. 7028, 51–62.","ama":"Bangerter E, Barzan S, Krenn S, Sadeghi A, Schneider T, Tsay J. Bringing Zero-Knowledge Proofs of Knowledge to Practice. In: Christianson B, Malcolm J, Matyas V, Roe M, eds. Vol 7028. Springer; 2013:51-62. doi:<a href=\"https://doi.org/10.1007/978-3-642-36213-2_9\">10.1007/978-3-642-36213-2_9</a>"},"year":"2013","date_created":"2018-12-11T12:00:38Z","doi":"10.1007/978-3-642-36213-2_9","quality_controlled":0,"title":"Bringing Zero-Knowledge Proofs of Knowledge to Practice","publist_id":"3732"},{"doi":"10.1007/s10703-012-0170-4","acknowledgement":"This research was supported in part by the National Science Foundation CAREER award CCR-0132780, by the ONR grant N00014-02-1-0671, by the National Science Foundation grants CCR-0427202 and CCR-0234690, and by the ARP award TO.030.MM.D.","isi":1,"department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"De Alfaro","full_name":"De Alfaro, Luca","first_name":"Luca"},{"first_name":"Marco","full_name":"Faella, Marco","last_name":"Faella"},{"first_name":"Ritankar","full_name":"Majumdar, Ritankar","last_name":"Majumdar"},{"full_name":"Raman, Vishwanath","last_name":"Raman","first_name":"Vishwanath"}],"date_published":"2013-04-01T00:00:00Z","date_updated":"2025-09-29T13:24:54Z","external_id":{"isi":["000316677500002"]},"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"None","month":"04","quality_controlled":"1","year":"2013","date_created":"2018-12-11T12:01:29Z","citation":{"chicago":"Chatterjee, Krishnendu, Luca De Alfaro, Marco Faella, Ritankar Majumdar, and Vishwanath Raman. “Code Aware Resource Management.” <i>Formal Methods in System Design</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s10703-012-0170-4\">https://doi.org/10.1007/s10703-012-0170-4</a>.","apa":"Chatterjee, K., De Alfaro, L., Faella, M., Majumdar, R., &#38; Raman, V. (2013). Code aware resource management. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-012-0170-4\">https://doi.org/10.1007/s10703-012-0170-4</a>","ista":"Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. 2013. Code aware resource management. Formal Methods in System Design. 42(2), 142–174.","ama":"Chatterjee K, De Alfaro L, Faella M, Majumdar R, Raman V. Code aware resource management. <i>Formal Methods in System Design</i>. 2013;42(2):142-174. doi:<a href=\"https://doi.org/10.1007/s10703-012-0170-4\">10.1007/s10703-012-0170-4</a>","ieee":"K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, and V. Raman, “Code aware resource management,” <i>Formal Methods in System Design</i>, vol. 42, no. 2. Springer, pp. 142–174, 2013.","mla":"Chatterjee, Krishnendu, et al. “Code Aware Resource Management.” <i>Formal Methods in System Design</i>, vol. 42, no. 2, Springer, 2013, pp. 142–74, doi:<a href=\"https://doi.org/10.1007/s10703-012-0170-4\">10.1007/s10703-012-0170-4</a>.","short":"K. Chatterjee, L. De Alfaro, M. Faella, R. Majumdar, V. Raman, Formal Methods in System Design 42 (2013) 142–174."},"publist_id":"3583","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Code aware resource management","publication_status":"published","status":"public","intvolume":"        42","_id":"3116","abstract":[{"lang":"eng","text":"Multithreaded programs coordinate their interaction through synchronization primitives like mutexes and semaphores, which are managed by an OS-provided resource manager. We propose algorithms for the automatic construction of code-aware resource managers for multithreaded embedded applications. Such managers use knowledge about the structure and resource usage (mutex and semaphore usage) of the threads to guarantee deadlock freedom and progress while managing resources in an efficient way. Our algorithms compute managers as winning strategies in certain infinite games, and produce a compact code description of these strategies. We have implemented the algorithms in the tool Cynthesis. Given a multithreaded program in C, the tool produces C code implementing a code-aware resource manager. We show in experiments that Cynthesis produces compact resource managers within a few minutes on a set of embedded benchmarks with up to 6 threads. © 2012 Springer Science+Business Media, LLC."}],"article_processing_charge":"No","publisher":"Springer","publication":"Formal Methods in System Design","issue":"2","day":"01","page":"142 - 174","volume":42,"type":"journal_article"},{"doi":"10.1073/pnas.1315642110","department":[{"_id":"GaTk"}],"isi":1,"date_published":"2013-10-08T00:00:00Z","ddc":["570"],"author":[{"first_name":"Julien","full_name":"Dubuis, Julien","last_name":"Dubuis"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455"},{"full_name":"Wieschaus, Eric","last_name":"Wieschaus","first_name":"Eric"},{"last_name":"Gregor","full_name":"Gregor, Thomas","first_name":"Thomas"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"}],"date_updated":"2025-09-29T13:24:21Z","language":[{"iso":"eng"}],"external_id":{"pmid":["24089448"],"isi":["000325395600021"]},"month":"10","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","date_created":"2018-12-11T12:02:19Z","year":"2013","quality_controlled":"1","oa":1,"citation":{"ieee":"J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, and W. Bialek, “Positional information, in bits,” <i>PNAS</i>, vol. 110, no. 41. National Academy of Sciences, pp. 16301–16308, 2013.","short":"J. Dubuis, G. Tkačik, E. Wieschaus, T. Gregor, W. Bialek, PNAS 110 (2013) 16301–16308.","mla":"Dubuis, Julien, et al. “Positional Information, in Bits.” <i>PNAS</i>, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:<a href=\"https://doi.org/10.1073/pnas.1315642110\">10.1073/pnas.1315642110</a>.","ista":"Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. 2013. Positional information, in bits. PNAS. 110(41), 16301–16308.","ama":"Dubuis J, Tkačik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. <i>PNAS</i>. 2013;110(41):16301-16308. doi:<a href=\"https://doi.org/10.1073/pnas.1315642110\">10.1073/pnas.1315642110</a>","chicago":"Dubuis, Julien, Gašper Tkačik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.” <i>PNAS</i>. National Academy of Sciences, 2013. <a href=\"https://doi.org/10.1073/pnas.1315642110\">https://doi.org/10.1073/pnas.1315642110</a>.","apa":"Dubuis, J., Tkačik, G., Wieschaus, E., Gregor, T., &#38; Bialek, W. (2013). Positional information, in bits. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1315642110\">https://doi.org/10.1073/pnas.1315642110</a>"},"publist_id":"3387","file_date_updated":"2020-07-14T12:46:06Z","title":"Positional information, in bits","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","file":[{"date_created":"2019-01-22T13:53:23Z","file_name":"2013_PNAS_Dubuis.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:46:06Z","creator":"dernst","checksum":"ecd859fe52a562193027d428b5524a8d","file_size":1670548,"access_level":"open_access","file_id":"5873"}],"pmid":1,"_id":"3261","abstract":[{"text":"Cells in a developing embryo have no direct way of &quot;measuring&quot; their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for &quot;positional information.&quot; We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1% along the anterior-posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.","lang":"eng"}],"intvolume":"       110","status":"public","issue":"41","publication":"PNAS","publisher":"National Academy of Sciences","article_processing_charge":"No","type":"journal_article","volume":110,"page":"16301 - 16308","day":"08"},{"status":"public","date_updated":"2021-01-12T07:42:33Z","_id":"331","abstract":[{"lang":"eng","text":"We report a procedure to prepare highly monodisperse copper telluride nanocubes, nanoplates, and nanorods. The procedure is based on the reaction of a copper salt with trioctylphosphine telluride in the presence of lithium bis(trimethylsilyl)amide and oleylamine. CuTe nanocrystals display a strong near-infrared optical absorption associated with localized surface plasmon resonances. We exploit this plasmon resonance for the design of surface-enhanced Raman scattering sensors for unconventional optical probes. Furthermore, we also report here our preliminary analysis of the use of CuTe nanocrystals as cytotoxic and photothermal agents."}],"intvolume":"       135","date_published":"2013-04-30T00:00:00Z","author":[{"first_name":"Wenhua","full_name":"Li, Wenhua","last_name":"Li"},{"first_name":"Reza","full_name":"Zamani, Reza","last_name":"Zamani"},{"full_name":"Rivera Gil, Pilar","last_name":"Rivera Gil","first_name":"Pilar"},{"first_name":"Beatriz","last_name":"Pelaz","full_name":"Pelaz, Beatriz"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Doris","full_name":"Cadavid, Doris","last_name":"Cadavid"},{"full_name":"Shavel, Alexey","last_name":"Shavel","first_name":"Alexey"},{"full_name":"Alvarez Puebla, Ramon","last_name":"Alvarez Puebla","first_name":"Ramon"},{"first_name":"Wolfgang","full_name":"Parak, Wolfgang","last_name":"Parak"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"first_name":"Andreu","last_name":"Cabot","full_name":"Cabot, Andreu"}],"publication_status":"published","type":"journal_article","month":"04","page":"7098 - 7101","day":"30","oa_version":"None","volume":135,"publisher":"ACS","language":[{"iso":"eng"}],"extern":"1","publication":"Journal of the American Chemical Society","issue":"19","article_processing_charge":"No","citation":{"short":"W. Li, R. Zamani, P. Rivera Gil, B. Pelaz, M. Ibáñez, D. Cadavid, A. Shavel, R. Alvarez Puebla, W. Parak, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 7098–7101.","ieee":"W. Li <i>et al.</i>, “CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents,” <i>Journal of the American Chemical Society</i>, vol. 135, no. 19. ACS, pp. 7098–7101, 2013.","mla":"Li, Wenhua, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” <i>Journal of the American Chemical Society</i>, vol. 135, no. 19, ACS, 2013, pp. 7098–101, doi:<a href=\"https://doi.org/10.1021/ja401428e\">10.1021/ja401428e</a>.","ama":"Li W, Zamani R, Rivera Gil P, et al. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. <i>Journal of the American Chemical Society</i>. 2013;135(19):7098-7101. doi:<a href=\"https://doi.org/10.1021/ja401428e\">10.1021/ja401428e</a>","ista":"Li W, Zamani R, Rivera Gil P, Pelaz B, Ibáñez M, Cadavid D, Shavel A, Alvarez Puebla R, Parak W, Arbiol J, Cabot A. 2013. CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. Journal of the American Chemical Society. 135(19), 7098–7101.","apa":"Li, W., Zamani, R., Rivera Gil, P., Pelaz, B., Ibáñez, M., Cadavid, D., … Cabot, A. (2013). CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents. <i>Journal of the American Chemical Society</i>. ACS. <a href=\"https://doi.org/10.1021/ja401428e\">https://doi.org/10.1021/ja401428e</a>","chicago":"Li, Wenhua, Reza Zamani, Pilar Rivera Gil, Beatriz Pelaz, Maria Ibáñez, Doris Cadavid, Alexey Shavel, et al. “CuTe Nanocrystals: Shape and Size Control, Plasmonic Properties, and Use as SERS Probes and Photothermal Agents.” <i>Journal of the American Chemical Society</i>. ACS, 2013. <a href=\"https://doi.org/10.1021/ja401428e\">https://doi.org/10.1021/ja401428e</a>."},"year":"2013","doi":"10.1021/ja401428e","date_created":"2018-12-11T11:45:51Z","article_type":"original","quality_controlled":"1","title":"CuTe nanocrystals: Shape and size control, plasmonic properties, and use as SERS probes and photothermal agents","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7521"},{"department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Kernel based learning","publist_id":"3314","citation":{"mla":"Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” <i>Encyclopedia of Systems Biology</i>, edited by Werner Dubitzky et al., vol. 3, Springer, 2013, pp. 1069–1069, doi:<a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">10.1007/978-1-4419-9863-7_604</a>.","ieee":"N. Quadrianto and C. Lampert, “Kernel based learning,” in <i>Encyclopedia of Systems Biology</i>, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota, Eds. Springer, 2013, pp. 1069–1069.","short":"N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota (Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069.","ista":"Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of Systems Biology. vol. 3, 1069–1069.","ama":"Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer O, Cho K, Yokota H, eds. <i>Encyclopedia of Systems Biology</i>. Vol 3. Springer; 2013:1069-1069. doi:<a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">10.1007/978-1-4419-9863-7_604</a>","chicago":"Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In <i>Encyclopedia of Systems Biology</i>, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho, and Hiroki Yokota, 3:1069–1069. Springer, 2013. <a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">https://doi.org/10.1007/978-1-4419-9863-7_604</a>.","apa":"Quadrianto, N., &#38; Lampert, C. (2013). Kernel based learning. In W. Dubitzky, O. Wolkenhauer, K. Cho, &#38; H. Yokota (Eds.), <i>Encyclopedia of Systems Biology</i> (Vol. 3, pp. 1069–1069). Springer. <a href=\"https://doi.org/10.1007/978-1-4419-9863-7_604\">https://doi.org/10.1007/978-1-4419-9863-7_604</a>"},"editor":[{"first_name":"Werner","last_name":"Dubitzky","full_name":"Dubitzky, Werner"},{"full_name":"Wolkenhauer, Olaf","last_name":"Wolkenhauer","first_name":"Olaf"},{"full_name":"Cho, Kwang","last_name":"Cho","first_name":"Kwang"},{"last_name":"Yokota","full_name":"Yokota, Hiroki","first_name":"Hiroki"}],"quality_controlled":"1","doi":"10.1007/978-1-4419-9863-7_604","date_created":"2018-12-11T12:02:39Z","year":"2013","oa_version":"None","volume":3,"page":"1069 - 1069","day":"01","month":"01","type":"encyclopedia_article","publication":"Encyclopedia of Systems Biology","language":[{"iso":"eng"}],"publisher":"Springer","_id":"3321","intvolume":"         3","date_updated":"2021-01-12T07:42:38Z","status":"public","publication_status":"published","author":[{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"date_published":"2013-01-01T00:00:00Z"},{"date_updated":"2021-01-12T07:43:21Z","status":"public","intvolume":"       135","_id":"342","abstract":[{"lang":"eng","text":"Morphology is a key parameter in the design of novel nanocrystals and nanomaterials with controlled functional properties. Here, we demonstrate the potential of foreign metal ions to tune the morphology of colloidal semiconductor nanoparticles. We illustrate the underlying mechanism by preparing copper selenide nanocubes in the presence of Al ions. We further characterize the plasmonic properties of the obtained nanocrystals and demonstrate their potential as a platform to produce cubic nanoparticles with different composition by cation exchange. © 2013 American Chemical Society."}],"date_published":"2013-03-07T00:00:00Z","author":[{"first_name":"Wenhua","full_name":"Li, Wenhua","last_name":"Li"},{"last_name":"Zamani","full_name":"Zamani, Reza","first_name":"Reza"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez"},{"first_name":"Doris","full_name":"Cadavid, Doris","last_name":"Cadavid"},{"last_name":"Shavel","full_name":"Shavel, Alexey","first_name":"Alexey"},{"first_name":"Joan","last_name":"Morante","full_name":"Morante, Joan"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"publication_status":"published","type":"journal_article","month":"03","day":"07","page":"4664 - 4667","volume":135,"oa_version":"None","publisher":"American Chemical Society","extern":"1","issue":"12","publication":"Journal of the American Chemical Society","language":[{"iso":"eng"}],"article_processing_charge":"No","acknowledgement":"The research was supported by the European Regional Development Funds. M.I. thanks the Spanish MICINN for her Ph.D. grant. J.A. and R.Z. also acknowledge MAT2010-15138.","citation":{"ieee":"W. Li <i>et al.</i>, “Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes,” <i>Journal of the American Chemical Society</i>, vol. 135, no. 12. American Chemical Society, pp. 4664–4667, 2013.","short":"W. Li, R. Zamani, M. Ibáñez, D. Cadavid, A. Shavel, J. Morante, J. Arbiol, A. Cabot, Journal of the American Chemical Society 135 (2013) 4664–4667.","mla":"Li, Wenhua, et al. “Metal Ions to Control the Morphology of Semiconductor Nanoparticles: Copper Selenide Nanocubes.” <i>Journal of the American Chemical Society</i>, vol. 135, no. 12, American Chemical Society, 2013, pp. 4664–67, doi:<a href=\"https://doi.org/10.1021/ja400472m\">10.1021/ja400472m</a>.","chicago":"Li, Wenhua, Reza Zamani, Maria Ibáñez, Doris Cadavid, Alexey Shavel, Joan Morante, Jordi Arbiol, and Andreu Cabot. “Metal Ions to Control the Morphology of Semiconductor Nanoparticles: Copper Selenide Nanocubes.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2013. <a href=\"https://doi.org/10.1021/ja400472m\">https://doi.org/10.1021/ja400472m</a>.","apa":"Li, W., Zamani, R., Ibáñez, M., Cadavid, D., Shavel, A., Morante, J., … Cabot, A. (2013). Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja400472m\">https://doi.org/10.1021/ja400472m</a>","ista":"Li W, Zamani R, Ibáñez M, Cadavid D, Shavel A, Morante J, Arbiol J, Cabot A. 2013. Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. Journal of the American Chemical Society. 135(12), 4664–4667.","ama":"Li W, Zamani R, Ibáñez M, et al. Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes. <i>Journal of the American Chemical Society</i>. 2013;135(12):4664-4667. doi:<a href=\"https://doi.org/10.1021/ja400472m\">10.1021/ja400472m</a>"},"year":"2013","date_created":"2018-12-11T11:45:55Z","doi":"10.1021/ja400472m","article_type":"original","quality_controlled":"1","title":"Metal ions to control the morphology of semiconductor nanoparticles: Copper selenide nanocubes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7482"},{"language":[{"iso":"eng"}],"month":"10","scopus_import":"1","oa_version":"None","date_published":"2013-10-22T00:00:00Z","author":[{"first_name":"Tal","full_name":"Ely, Tal","last_name":"Ely"},{"last_name":"Das","full_name":"Das, Sanjib","first_name":"Sanjib"},{"first_name":"Wenjie","last_name":"Li","full_name":"Li, Wenjie"},{"first_name":"Pintu","last_name":"Kundu","full_name":"Kundu, Pintu"},{"full_name":"Tirosh, Einat","last_name":"Tirosh","first_name":"Einat"},{"first_name":"David","last_name":"Cahen","full_name":"Cahen, David"},{"last_name":"Vilan","full_name":"Vilan, Ayelet","first_name":"Ayelet"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"date_updated":"2024-10-14T12:21:03Z","doi":"10.1055/s-0033-1340087","publication_identifier":{"eissn":["1437-2096"],"issn":["0936-5214"]},"publisher":"Georg Thieme Verlag","publication":"Synlett","issue":"18","extern":"1","article_processing_charge":"No","type":"journal_article","day":"22","keyword":["Organic Chemistry"],"page":"2370-2374","volume":24,"publication_status":"published","status":"public","abstract":[{"lang":"eng","text":"We report a method for preparing electrode–molecule–electrode junctions that incorporate nonsymmetrical azobenzene dithiols. Our approach is based on sequential deprotection of thiol moieties originally carrying two different protecting groups. The azobenzene derivatives retained their switching properties within monolayers and permitted the photocontrol of electrical conductance."}],"intvolume":"        24","_id":"13405","title":"Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","date_created":"2023-08-01T09:47:17Z","article_type":"original","quality_controlled":"1","citation":{"apa":"Ely, T., Das, S., Li, W., Kundu, P., Tirosh, E., Cahen, D., … Klajn, R. (2013). Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. <i>Synlett</i>. Georg Thieme Verlag. <a href=\"https://doi.org/10.1055/s-0033-1340087\">https://doi.org/10.1055/s-0033-1340087</a>","chicago":"Ely, Tal, Sanjib Das, Wenjie Li, Pintu Kundu, Einat Tirosh, David Cahen, Ayelet Vilan, and Rafal Klajn. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” <i>Synlett</i>. Georg Thieme Verlag, 2013. <a href=\"https://doi.org/10.1055/s-0033-1340087\">https://doi.org/10.1055/s-0033-1340087</a>.","ama":"Ely T, Das S, Li W, et al. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. <i>Synlett</i>. 2013;24(18):2370-2374. doi:<a href=\"https://doi.org/10.1055/s-0033-1340087\">10.1055/s-0033-1340087</a>","ista":"Ely T, Das S, Li W, Kundu P, Tirosh E, Cahen D, Vilan A, Klajn R. 2013. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. 24(18), 2370–2374.","short":"T. Ely, S. Das, W. Li, P. Kundu, E. Tirosh, D. Cahen, A. Vilan, R. Klajn, Synlett 24 (2013) 2370–2374.","mla":"Ely, Tal, et al. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” <i>Synlett</i>, vol. 24, no. 18, Georg Thieme Verlag, 2013, pp. 2370–74, doi:<a href=\"https://doi.org/10.1055/s-0033-1340087\">10.1055/s-0033-1340087</a>.","ieee":"T. Ely <i>et al.</i>, “Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol,” <i>Synlett</i>, vol. 24, no. 18. Georg Thieme Verlag, pp. 2370–2374, 2013."}},{"type":"journal_article","volume":25,"day":"18","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"page":"422-426","extern":"1","issue":"3","publication":"Advanced Materials","publisher":"Wiley","article_processing_charge":"No","pmid":1,"_id":"13406","abstract":[{"text":"Dual-responsive nanoparticles are designed by functionalizing magnetic cores with light-responsive ligands. These materials respond to both light and magnetic fields and can be assembled into various higher-order structures, depending on the relative contributions of these two stimuli.","lang":"eng"}],"intvolume":"        25","status":"public","publication_status":"published","title":"Dual-responsive nanoparticles and their self-assembly","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Das, P. Ranjan, P.S. Maiti, G. Singh, G. Leitus, R. Klajn, Advanced Materials 25 (2013) 422–426.","mla":"Das, Sanjib, et al. “Dual-Responsive Nanoparticles and Their Self-Assembly.” <i>Advanced Materials</i>, vol. 25, no. 3, Wiley, 2013, pp. 422–26, doi:<a href=\"https://doi.org/10.1002/adma.201201734\">10.1002/adma.201201734</a>.","ieee":"S. Das, P. Ranjan, P. S. Maiti, G. Singh, G. Leitus, and R. Klajn, “Dual-responsive nanoparticles and their self-assembly,” <i>Advanced Materials</i>, vol. 25, no. 3. Wiley, pp. 422–426, 2013.","apa":"Das, S., Ranjan, P., Maiti, P. S., Singh, G., Leitus, G., &#38; Klajn, R. (2013). Dual-responsive nanoparticles and their self-assembly. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201201734\">https://doi.org/10.1002/adma.201201734</a>","chicago":"Das, Sanjib, Priyadarshi Ranjan, Pradipta Sankar Maiti, Gurvinder Singh, Gregory Leitus, and Rafal Klajn. “Dual-Responsive Nanoparticles and Their Self-Assembly.” <i>Advanced Materials</i>. Wiley, 2013. <a href=\"https://doi.org/10.1002/adma.201201734\">https://doi.org/10.1002/adma.201201734</a>.","ama":"Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. Dual-responsive nanoparticles and their self-assembly. <i>Advanced Materials</i>. 2013;25(3):422-426. doi:<a href=\"https://doi.org/10.1002/adma.201201734\">10.1002/adma.201201734</a>","ista":"Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. 2013. Dual-responsive nanoparticles and their self-assembly. Advanced Materials. 25(3), 422–426."},"date_created":"2023-08-01T09:47:30Z","year":"2013","quality_controlled":"1","article_type":"original","month":"01","scopus_import":"1","oa_version":"None","language":[{"iso":"eng"}],"external_id":{"pmid":["22933327"]},"date_updated":"2024-10-14T12:21:16Z","date_published":"2013-01-18T00:00:00Z","author":[{"last_name":"Das","full_name":"Das, Sanjib","first_name":"Sanjib"},{"last_name":"Ranjan","full_name":"Ranjan, Priyadarshi","first_name":"Priyadarshi"},{"first_name":"Pradipta Sankar","full_name":"Maiti, Pradipta Sankar","last_name":"Maiti"},{"first_name":"Gurvinder","full_name":"Singh, Gurvinder","last_name":"Singh"},{"first_name":"Gregory","last_name":"Leitus","full_name":"Leitus, Gregory"},{"first_name":"Rafal","full_name":"Klajn, Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn"}],"publication_identifier":{"issn":["0935-9648"]},"doi":"10.1002/adma.201201734"},{"department":[{"_id":"KrCh"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.4230/LIPIcs.CSL.2013.181","has_accepted_license":"1","oa_version":"Published Version","scopus_import":1,"month":"09","conference":{"name":"CSL: Computer Science Logic","location":"Torino, Italy","start_date":"203-09-02","end_date":"2013-09-05"},"language":[{"iso":"eng"}],"date_updated":"2024-10-09T20:55:23Z","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Nathanaël","full_name":"Fijalkow, Nathanaël","last_name":"Fijalkow"}],"ddc":["000"],"alternative_title":["LIPIcs"],"date_published":"2013-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"title":"Infinite-state games with finitary conditions","file_date_updated":"2020-07-14T12:44:47Z","publist_id":"5837","citation":{"short":"K. Chatterjee, N. Fijalkow, in:, 22nd EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–196.","ieee":"K. Chatterjee and N. Fijalkow, “Infinite-state games with finitary conditions,” in <i>22nd EACSL Annual Conference on Computer Science Logic</i>, Torino, Italy, 2013, vol. 23, pp. 181–196.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” <i>22nd EACSL Annual Conference on Computer Science Logic</i>, vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–96, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2013). Infinite-state games with finitary conditions. In <i>22nd EACSL Annual Conference on Computer Science Logic</i> (Vol. 23, pp. 181–196). Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” In <i>22nd EACSL Annual Conference on Computer Science Logic</i>, 23:181–96. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>.","ama":"Chatterjee K, Fijalkow N. Infinite-state games with finitary conditions. In: <i>22nd EACSL Annual Conference on Computer Science Logic</i>. Vol 23. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2013:181-196. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>","ista":"Chatterjee K, Fijalkow N. 2013. Infinite-state games with finitary conditions. 22nd EACSL Annual Conference on Computer Science Logic. CSL: Computer Science LogicLeibniz International Proceedings in Informatics, LIPIcs, vol. 23, 181–196."},"oa":1,"quality_controlled":"1","corr_author":"1","year":"2013","date_created":"2018-12-11T11:51:39Z","day":"01","page":"181 - 196","volume":23,"series_title":"Leibniz International Proceedings in Informatics","type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication":"22nd EACSL Annual Conference on Computer Science Logic","pubrep_id":"624","status":"public","intvolume":"        23","_id":"1374","abstract":[{"text":"We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.","lang":"eng"}],"file":[{"file_size":547296,"checksum":"b7091a3866db573c0db5ec486952255e","access_level":"open_access","file_id":"5023","date_created":"2018-12-12T10:13:38Z","file_name":"IST-2016-624-v1+1_ChKr_Infinite-state_games_2013_17.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:44:47Z","creator":"system"}],"publication_status":"published"},{"doi":"10.1109/FMCAD.2013.6679386","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_published":"2013-12-11T00:00:00Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"}],"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"date_updated":"2025-06-26T08:33:43Z","OA_place":"repository","conference":{"name":"FMCAD: Formal Methods in Computer-Aided Design","location":"Portland, OR, United States","start_date":"2013-10-20","end_date":"2013-10-23"},"language":[{"iso":"eng"}],"month":"12","scopus_import":"1","oa_version":"Preprint","year":"2013","date_created":"2018-12-11T11:51:40Z","quality_controlled":"1","corr_author":"1","oa":1,"citation":{"apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In <i>13th International Conference on Formal Methods in Computer-Aided Design</i> (pp. 18–25). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, 18–25. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>.","ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: <i>13th International Conference on Formal Methods in Computer-Aided Design</i>. IEEE; 2013:18-25. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 18–25.","mla":"Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 18–25, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>."},"publist_id":"5835","title":"Distributed synthesis for LTL fragments","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"5406","relation":"earlier_version","status":"public"}]},"publication_status":"published","status":"public","_id":"1376","abstract":[{"text":"We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.15479/AT:IST-2013-130-v1-1","open_access":"1"}],"publisher":"IEEE","publication":"13th International Conference on Formal Methods in Computer-Aided Design","article_processing_charge":"No","OA_type":"green","type":"conference","day":"11","page":"18 - 25"}]