[{"ec_funded":1,"publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"year":"2019","intvolume":"       102","date_published":"2019-04-03T00:00:00Z","day":"03","doi":"10.1016/j.neuron.2019.01.051","oa":1,"file":[{"file_size":7288572,"creator":"dernst","file_name":"2019_Neuron_Ortiz.pdf","date_created":"2019-05-15T09:28:41Z","access_level":"open_access","file_id":"6457","date_updated":"2020-07-14T12:47:30Z","relation":"main_file","content_type":"application/pdf","checksum":"1fb6e195c583eb0c5cabf26f69ff6675"}],"ddc":["570"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780"}],"publication":"Neuron","isi":1,"oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:30Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-04-14T07:43:05Z","page":"159-172.e7","author":[{"last_name":"Ortiz-Álvarez","full_name":"Ortiz-Álvarez, G","first_name":"G"},{"last_name":"Daclin","full_name":"Daclin, M","first_name":"M"},{"first_name":"A","full_name":"Shihavuddin, A","last_name":"Shihavuddin"},{"first_name":"P","last_name":"Lansade","full_name":"Lansade, P"},{"full_name":"Fortoul, A","last_name":"Fortoul","first_name":"A"},{"first_name":"M","full_name":"Faucourt, M","last_name":"Faucourt"},{"full_name":"Clavreul, S","last_name":"Clavreul","first_name":"S"},{"first_name":"ME","full_name":"Lalioti, ME","last_name":"Lalioti"},{"full_name":"Taraviras, S","last_name":"Taraviras","first_name":"S"},{"orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"full_name":"Livet, J","last_name":"Livet","first_name":"J"},{"last_name":"Meunier","full_name":"Meunier, A","first_name":"A"},{"first_name":"A","last_name":"Genovesio","full_name":"Genovesio, A"},{"last_name":"Spassky","full_name":"Spassky, N","first_name":"N"}],"title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","quality_controlled":"1","abstract":[{"text":"Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells.","lang":"eng"}],"type":"journal_article","pmid":1,"citation":{"ieee":"G. Ortiz-Álvarez <i>et al.</i>, “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” <i>Neuron</i>, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019.","ama":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. <i>Neuron</i>. 2019;102(1):159-172.e7. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">10.1016/j.neuron.2019.01.051</a>","apa":"Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt, M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">https://doi.org/10.1016/j.neuron.2019.01.051</a>","mla":"Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” <i>Neuron</i>, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">10.1016/j.neuron.2019.01.051</a>.","ista":"Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 102(1), 159–172.e7.","chicago":"Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt, S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.01.051\">https://doi.org/10.1016/j.neuron.2019.01.051</a>.","short":"G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt, S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A. Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7."},"publisher":"Elsevier","department":[{"_id":"SiHi"}],"volume":102,"external_id":{"pmid":["30824354"],"isi":["000463337900018"]},"date_created":"2019-05-14T13:06:30Z","publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"scopus_import":"1","issue":"1","month":"04","_id":"6454"},{"department":[{"_id":"SiHi"}],"volume":364,"main_file_link":[{"url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf","open_access":"1"}],"publisher":"AAAS","quality_controlled":"1","citation":{"short":"L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini, I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science 364 (2019).","ama":"Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. <i>Science</i>. 2019;364(6440). doi:<a href=\"https://doi.org/10.1126/science.aav2522\">10.1126/science.aav2522</a>","ieee":"L. Telley <i>et al.</i>, “Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex,” <i>Science</i>, vol. 364, no. 6440. AAAS, 2019.","apa":"Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., … Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aav2522\">https://doi.org/10.1126/science.aav2522</a>","mla":"Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” <i>Science</i>, vol. 364, no. 6440, eaav2522, AAAS, 2019, doi:<a href=\"https://doi.org/10.1126/science.aav2522\">10.1126/science.aav2522</a>.","chicago":"Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini, et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” <i>Science</i>. AAAS, 2019. <a href=\"https://doi.org/10.1126/science.aav2522\">https://doi.org/10.1126/science.aav2522</a>.","ista":"Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 364(6440), eaav2522."},"type":"journal_article","pmid":1,"abstract":[{"text":"During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity.","lang":"eng"}],"_id":"6455","issue":"6440","scopus_import":"1","month":"05","date_created":"2019-05-14T13:07:47Z","publication_status":"published","external_id":{"isi":["000467631800034"],"pmid":["31073041"]},"isi":1,"publication":"Science","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","grant_number":"725780","call_identifier":"H2020"},{"grant_number":"T01031","_id":"268F8446-B435-11E9-9278-68D0E5697425","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-05-10T00:00:00Z","intvolume":"       364","oa":1,"day":"10","doi":"10.1126/science.aav2522","article_type":"original","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"year":"2019","ec_funded":1,"article_number":"eaav2522","date_updated":"2025-04-15T07:50:01Z","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/","relation":"press_release"}]},"title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","author":[{"first_name":"L","full_name":"Telley, L","last_name":"Telley"},{"first_name":"G","last_name":"Agirman","full_name":"Agirman, G"},{"first_name":"J","full_name":"Prados, J","last_name":"Prados"},{"first_name":"Nicole","full_name":"Amberg, Nicole","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207"},{"first_name":"S","last_name":"Fièvre","full_name":"Fièvre, S"},{"first_name":"P","full_name":"Oberst, P","last_name":"Oberst"},{"full_name":"Bartolini, G","last_name":"Bartolini","first_name":"G"},{"last_name":"Vitali","full_name":"Vitali, I","first_name":"I"},{"full_name":"Cadilhac, C","last_name":"Cadilhac","first_name":"C"},{"first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"L","full_name":"Nguyen, L","last_name":"Nguyen"},{"first_name":"A","full_name":"Dayer, A","last_name":"Dayer"},{"full_name":"Jabaudon, D","last_name":"Jabaudon","first_name":"D"}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Published Version"},{"corr_author":"1","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"volume":11561,"quality_controlled":"1","type":"conference","abstract":[{"lang":"eng","text":"A controller is a device that interacts with a plant. At each time point,it reads the plant’s state and issues commands with the goal that the plant oper-ates optimally. Constructing optimal controllers is a fundamental and challengingproblem. Machine learning techniques have recently been successfully applied totrain controllers, yet they have limitations. Learned controllers are monolithic andhard to reason about. In particular, it is difficult to add features without retraining,to guarantee any level of performance, and to achieve acceptable performancewhen encountering untrained scenarios. These limitations can be addressed bydeploying quantitative run-timeshieldsthat serve as a proxy for the controller.At each time point, the shield reads the command issued by the controller andmay choose to alter it before passing it on to the plant. We show how optimalshields that interfere as little as possible while guaranteeing a desired level ofcontroller performance, can be generated systematically and automatically usingreactive  synthesis.  First,  we  abstract  the  plant  by  building  a  stochastic  model.Second, we consider the learned controller to be a black box. Third, we mea-surecontroller performanceandshield interferenceby two quantitative run-timemeasures that are formally defined using weighted automata. Then, the problemof constructing a shield that guarantees maximal performance with minimal inter-ference is the problem of finding an optimal strategy in a stochastic2-player game“controller versus shield” played on the abstract state space of the plant with aquantitative objective obtained from combining the performance and interferencemeasures. We illustrate the effectiveness of our approach by automatically con-structing lightweight shields for learned traffic-light controllers in various roadnetworks. The shields we generate avoid liveness bugs, improve controller per-formance in untrained and changing traffic situations, and add features to learnedcontrollers, such as giving priority to emergency vehicles."}],"citation":{"ama":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: <i>31st International Conference on Computer-Aided Verification</i>. Vol 11561. Springer; 2019:630-649. doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">10.1007/978-3-030-25540-4_36</a>","ieee":"G. Avni, R. Bloem, K. Chatterjee, T. A. Henzinger, B. Konighofer, and S. Pranger, “Run-time optimization for learned controllers through quantitative games,” in <i>31st International Conference on Computer-Aided Verification</i>, New York, NY, United States, 2019, vol. 11561, pp. 630–649.","apa":"Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., &#38; Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In <i>31st International Conference on Computer-Aided Verification</i> (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">https://doi.org/10.1007/978-3-030-25540-4_36</a>","ista":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. 2019. Run-time optimization for learned controllers through quantitative games. 31st International Conference on Computer-Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 11561, 630–649.","chicago":"Avni, Guy, Roderick Bloem, Krishnendu Chatterjee, Thomas A Henzinger, Bettina Konighofer, and Stefan Pranger. “Run-Time Optimization for Learned Controllers through Quantitative Games.” In <i>31st International Conference on Computer-Aided Verification</i>, 11561:630–49. Springer, 2019. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">https://doi.org/10.1007/978-3-030-25540-4_36</a>.","mla":"Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” <i>31st International Conference on Computer-Aided Verification</i>, vol. 11561, Springer, 2019, pp. 630–49, doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_36\">10.1007/978-3-030-25540-4_36</a>.","short":"G. Avni, R. Bloem, K. Chatterjee, T.A. Henzinger, B. Konighofer, S. Pranger, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 630–649."},"scopus_import":"1","month":"07","_id":"6462","external_id":{"isi":["000491468000036"]},"alternative_title":["LNCS"],"conference":{"end_date":"2019-07-18","start_date":"2019-07-13","location":"New York, NY, United States","name":"CAV: Computer Aided Verification"},"date_created":"2019-05-16T11:22:30Z","publication_status":"published","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"},"ddc":["000"],"project":[{"grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"31st International Conference on Computer-Aided Verification","isi":1,"year":"2019","publication_identifier":{"isbn":["9783030255398"],"issn":["0302-9743"]},"intvolume":"     11561","date_published":"2019-07-12T00:00:00Z","day":"12","doi":"10.1007/978-3-030-25540-4_36","file":[{"date_updated":"2020-07-14T12:47:31Z","file_id":"6816","content_type":"application/pdf","checksum":"c231579f2485c6fd4df17c9443a4d80b","relation":"main_file","creator":"dernst","file_size":659766,"file_name":"2019_CAV_Avni.pdf","date_created":"2019-08-14T09:35:24Z","access_level":"open_access"}],"oa":1,"file_date_updated":"2020-07-14T12:47:31Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-04-15T06:26:05Z","page":"630-649","author":[{"last_name":"Avni","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287","first_name":"Guy"},{"last_name":"Bloem","full_name":"Bloem, Roderick","first_name":"Roderick"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Konighofer, Bettina","last_name":"Konighofer","first_name":"Bettina"},{"last_name":"Pranger","full_name":"Pranger, Stefan","first_name":"Stefan"}],"title":"Run-time optimization for learned controllers through quantitative games","oa_version":"Published Version"},{"citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>. Royal Society of London, 2019. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>.","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>.","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” <i>Biology Letters</i>, vol. 15, no. 4. Royal Society of London, 2019.","apa":"Fraisse, C., &#38; Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019)."},"pmid":1,"abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"type":"journal_article","quality_controlled":"1","publisher":"Royal Society of London","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2018.0881"}],"volume":15,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"external_id":{"pmid":["31014191"],"isi":["000465405300010"]},"publication_status":"published","date_created":"2019-05-19T21:59:15Z","month":"04","scopus_import":"1","issue":"4","_id":"6467","article_number":"0881","year":"2019","article_type":"original","publication_identifier":{"eissn":["1744-957X"],"issn":["1744-9561"]},"ec_funded":1,"oa":1,"day":"03","doi":"10.1098/rsbl.2018.0881","date_published":"2019-04-03T00:00:00Z","intvolume":"        15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"publication":"Biology Letters","oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle"},{"first_name":"John J.","last_name":"Welch","full_name":"Welch, John J."}],"title":"The distribution of epistasis on simple fitness landscapes","date_updated":"2025-07-10T11:53:23Z","related_material":{"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008","relation":"supplementary_material"}],"record":[{"status":"public","id":"9799","relation":"research_data"},{"status":"public","id":"9798","relation":"research_data"}]}},{"quality_controlled":"1","citation":{"short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947.","ama":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. <i>Journal of Physiology</i>. 2019;597(11):2925–2947. doi:<a href=\"https://doi.org/10.1113/JP277681\">10.1113/JP277681</a>","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., &#38; Nusser, Z. (2019). Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. <i>Journal of Physiology</i>. Wiley. <a href=\"https://doi.org/10.1113/JP277681\">https://doi.org/10.1113/JP277681</a>","ieee":"T. Éltes, M. Szoboszlay, M. K. Szigeti, and Z. Nusser, “Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells,” <i>Journal of Physiology</i>, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","chicago":"Éltes, Tímea, Miklos Szoboszlay, Margit Katalin Szigeti, and Zoltan Nusser. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” <i>Journal of Physiology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1113/JP277681\">https://doi.org/10.1113/JP277681</a>.","ista":"Éltes T, Szoboszlay M, Szigeti MK, Nusser Z. 2019. Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells. Journal of Physiology. 597(11), 2925–2947.","mla":"Éltes, Tímea, et al. “Improved Spike Inference Accuracy by Estimating the Peak Amplitude of Unitary [Ca2+] Transients in Weakly GCaMP6f-Expressing Hippocampal Pyramidal Cells.” <i>Journal of Physiology</i>, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:<a href=\"https://doi.org/10.1113/JP277681\">10.1113/JP277681</a>."},"abstract":[{"lang":"eng","text":"Investigating neuronal activity using genetically encoded Ca2+ indicators in behaving animals is hampered by inaccuracies in spike inference from fluorescent tracers. Here we combine two‐photon [Ca2+] imaging with cell‐attached recordings, followed by post hoc determination of the expression level of GCaMP6f, to explore how it affects the amplitude, kinetics and temporal summation of somatic [Ca2+] transients in mouse hippocampal pyramidal cells (PCs). The amplitude of unitary [Ca2+] transients (evoked by a single action potential) negatively correlates with GCaMP6f expression, but displays large variability even among PCs with similarly low expression levels. The summation of fluorescence signals is frequency‐dependent, supralinear and also shows remarkable cell‐to‐cell variability. We performed experimental data‐based simulations and found that spike inference error rates using MLspike depend strongly on unitary peak amplitudes and GCaMP6f expression levels. We provide simple methods for estimating the unitary [Ca2+] transients in individual weakly GCaMP6f‐expressing PCs, with which we achieve spike inference error rates of ∼5%. "}],"type":"journal_article","pmid":1,"department":[{"_id":"GaNo"}],"volume":597,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1113/JP277681"}],"publisher":"Wiley","date_created":"2019-05-19T21:59:17Z","publication_status":"published","external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"_id":"6470","issue":"11","scopus_import":"1","month":"06","date_published":"2019-06-01T00:00:00Z","intvolume":"       597","oa":1,"doi":"10.1113/JP277681","day":"01","year":"2019","publication_identifier":{"eissn":["1469-7793"],"issn":["0022-3751"]},"article_type":"original","isi":1,"publication":"Journal of Physiology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_updated":"2025-07-10T11:53:24Z","page":"2925–2947","title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","author":[{"last_name":"Éltes","full_name":"Éltes, Tímea","first_name":"Tímea"},{"last_name":"Szoboszlay","full_name":"Szoboszlay, Miklos","first_name":"Miklos"},{"id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","last_name":"Szigeti","full_name":"Szigeti, Margit Katalin","orcid":"0000-0001-9500-8758","first_name":"Margit Katalin"},{"full_name":"Nusser, Zoltan","last_name":"Nusser","first_name":"Zoltan"}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}]},{"intvolume":"        91","date_published":"2019-05-22T00:00:00Z","doi":"10.1103/revmodphys.91.021001","day":"22","oa":1,"file":[{"date_updated":"2020-07-14T12:47:31Z","file_id":"6478","checksum":"4aec0e6662b09f6e0f828cd30ff2c3a6","content_type":"application/pdf","relation":"main_file","creator":"mserbyn","file_size":1695677,"file_name":"RevModPhys.91.021001.pdf","date_created":"2019-05-23T07:39:05Z","access_level":"open_access"}],"year":"2019","publication_identifier":{"issn":["1539-0756"],"eissn":["0034-6861"]},"article_type":"original","article_number":"021001","publication":"Reviews of Modern Physics","arxiv":1,"isi":1,"ddc":["530"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","date_updated":"2023-08-25T10:37:56Z","title":"Colloquium: Many-body localization, thermalization, and entanglement","author":[{"full_name":"Abanin, Dmitry A.","last_name":"Abanin","first_name":"Dmitry A."},{"first_name":"Ehud","full_name":"Altman, Ehud","last_name":"Altman"},{"last_name":"Bloch","full_name":"Bloch, Immanuel","first_name":"Immanuel"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym"}],"file_date_updated":"2020-07-14T12:47:31Z","has_accepted_license":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","abstract":[{"lang":"eng","text":"Thermalizing quantum systems are conventionallydescribed by statistical mechanics at equilib-rium. However, not all systems fall into this category, with many-body localization providinga generic mechanism for thermalization to fail in strongly disordered systems. Many-bodylocalized (MBL) systems remain perfect insulators at nonzero temperature, which do notthermalize and therefore cannot be describedusing statistical mechanics. This Colloquiumreviews recent theoretical and experimental advances in studies of MBL systems, focusing onthe new perspective provided by entanglement and nonequilibrium experimental probes suchas quantum quenches. Theoretically, MBL systems exhibit a new kind of robust integrability: anextensive set of quasilocal integrals of motion emerges, which provides an intuitive explanationof the breakdown of thermalization. A description based on quasilocal integrals of motion isused to predict dynamical properties of MBL systems, such as the spreading of quantumentanglement, the behavior of local observables, and the response to external dissipativeprocesses. Furthermore, MBL systems can exhibit eigenstate transitions and quantum ordersforbidden in thermodynamic equilibrium. An outline isgiven of the current theoretical under-standing of the quantum-to-classical transitionbetween many-body localized and ergodic phasesand anomalous transport in the vicinity of that transition. Experimentally, synthetic quantumsystems, which are well isolated from an external thermal reservoir, provide natural platforms forrealizing the MBL phase. Recent experiments with ultracold atoms, trapped ions, superconductingqubits, and quantum materials, in which different signatures of many-body localization have beenobserved, are reviewed. This Colloquium concludes by listing outstanding challenges andpromising future research directions."}],"type":"journal_article","citation":{"short":"D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019).","mla":"Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” <i>Reviews of Modern Physics</i>, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/revmodphys.91.021001\">10.1103/revmodphys.91.021001</a>.","chicago":"Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” <i>Reviews of Modern Physics</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/revmodphys.91.021001\">https://doi.org/10.1103/revmodphys.91.021001</a>.","ista":"Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.","apa":"Abanin, D. A., Altman, E., Bloch, I., &#38; Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. <i>Reviews of Modern Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/revmodphys.91.021001\">https://doi.org/10.1103/revmodphys.91.021001</a>","ama":"Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. <i>Reviews of Modern Physics</i>. 2019;91(2). doi:<a href=\"https://doi.org/10.1103/revmodphys.91.021001\">10.1103/revmodphys.91.021001</a>","ieee":"D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” <i>Reviews of Modern Physics</i>, vol. 91, no. 2. American Physical Society, 2019."},"department":[{"_id":"MaSe"}],"volume":91,"publisher":"American Physical Society","date_created":"2019-05-23T07:38:43Z","publication_status":"published","external_id":{"isi":["000469046900001"],"arxiv":["1804.11065"]},"_id":"6477","scopus_import":"1","issue":"2","month":"05"},{"quality_controlled":"1","abstract":[{"text":"Computer vision systems for automatic image categorization have become accurate and reliable enough that they can run continuously for days or even years as components of real-world commercial applications. A major open problem in this context, however, is quality control. Good classification performance can only be expected if systems run under the specific conditions, in particular data distributions, that they were trained for. Surprisingly, none of the currently used deep network architectures have a built-in functionality that could detect if a network operates on data from a distribution it was not trained for, such that potentially a warning to the human users could be triggered. In this work, we describe KS(conf), a procedure for detecting such outside of specifications (out-of-specs) operation, based on statistical testing of the network outputs. We show by extensive experiments using the ImageNet, AwA2 and DAVIS datasets on a variety of ConvNets architectures that KS(conf) reliably detects out-of-specs situations. It furthermore has a number of properties that make it a promising candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with all networks, including pretrained ones, and requires no a priori knowledge of how the data distribution could change. ","lang":"eng"}],"type":"conference","citation":{"ista":"Sun R, Lampert C. 2019. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. GCPR: Conference on Pattern Recognition, LNCS, vol. 11269, 244–259.","chicago":"Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications,” 11269:244–59. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-12939-2_18\">https://doi.org/10.1007/978-3-030-12939-2_18</a>.","mla":"Sun, Rémy, and Christoph Lampert. <i>KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications</i>. Vol. 11269, Springer Nature, 2019, pp. 244–59, doi:<a href=\"https://doi.org/10.1007/978-3-030-12939-2_18\">10.1007/978-3-030-12939-2_18</a>.","ieee":"R. Sun and C. Lampert, “KS(conf): A light-weight test if a ConvNet operates outside of Its specifications,” presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany, 2019, vol. 11269, pp. 244–259.","apa":"Sun, R., &#38; Lampert, C. (2019). KS(conf): A light-weight test if a ConvNet operates outside of Its specifications (Vol. 11269, pp. 244–259). Presented at the GCPR: Conference on Pattern Recognition, Stuttgart, Germany: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-12939-2_18\">https://doi.org/10.1007/978-3-030-12939-2_18</a>","ama":"Sun R, Lampert C. KS(conf): A light-weight test if a ConvNet operates outside of Its specifications. In: Vol 11269. Springer Nature; 2019:244-259. doi:<a href=\"https://doi.org/10.1007/978-3-030-12939-2_18\">10.1007/978-3-030-12939-2_18</a>","short":"R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259."},"main_file_link":[{"url":"https://arxiv.org/abs/1804.04171","open_access":"1"}],"publisher":"Springer Nature","department":[{"_id":"ChLa"}],"volume":11269,"alternative_title":["LNCS"],"external_id":{"arxiv":["1804.04171"]},"conference":{"end_date":"2018-10-12","location":"Stuttgart, Germany","name":"GCPR: Conference on Pattern Recognition","start_date":"2018-10-09"},"date_created":"2019-05-24T09:48:36Z","publication_status":"published","scopus_import":"1","month":"02","_id":"6482","ec_funded":1,"publication_identifier":{"eissn":["1611-3349"],"isbn":["9783030129385","9783030129392"],"issn":["0302-9743"]},"year":"2019","intvolume":"     11269","date_published":"2019-02-14T00:00:00Z","day":"14","doi":"10.1007/978-3-030-12939-2_18","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"arxiv":1,"oa_version":"Preprint","article_processing_charge":"No","language":[{"iso":"eng"}],"status":"public","related_material":{"record":[{"id":"6944","relation":"later_version","status":"public"}]},"page":"244-259","date_updated":"2025-04-15T07:10:25Z","author":[{"last_name":"Sun","full_name":"Sun, Rémy","first_name":"Rémy"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887"}],"title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications"},{"date_updated":"2024-12-11T11:42:22Z","_id":"6485","page":"417-418","author":[{"id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","full_name":"Koval, Nikita","first_name":"Nikita"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"first_name":"Roman","full_name":"Elizarov, Roman","last_name":"Elizarov"}],"title":"Lock-free channels for programming via communicating sequential processes","article_processing_charge":"No","language":[{"iso":"eng"}],"month":"02","status":"public","date_created":"2019-05-24T10:09:12Z","oa_version":"None","publication_status":"published","external_id":{"isi":["000587604600044"]},"conference":{"end_date":"2019-02-20","location":"Washington, NY, United States","name":"PPoPP: Principles and Practice of Parallel Programming","start_date":"2019-02-16"},"publication":"Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming","isi":1,"department":[{"_id":"DaAl"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","quality_controlled":"1","date_published":"2019-02-01T00:00:00Z","doi":"10.1145/3293883.3297000","day":"01","abstract":[{"text":"Traditional concurrent programming involves manipulating shared mutable state. Alternatives to this programming style are communicating sequential processes (CSP) [1] and actor [2] models, which share data via explicit communication. Rendezvous channelis the common abstraction for communication between several processes, where senders and receivers perform a rendezvous handshake as a part of their protocol (senders wait for receivers and vice versa). Additionally to this, channels support the select expression. In this work, we present the first efficient lock-free channel algorithm, and compare it against Go [3] and Kotlin [4] baseline implementations.","lang":"eng"}],"type":"conference_poster","citation":{"ama":"Koval N, Alistarh D-A, Elizarov R. <i>Lock-Free Channels for Programming via Communicating Sequential Processes</i>. ACM; 2019:417-418. doi:<a href=\"https://doi.org/10.1145/3293883.3297000\">10.1145/3293883.3297000</a>","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, <i>Lock-free channels for programming via communicating sequential processes</i>. ACM, 2019, pp. 417–418.","apa":"Koval, N., Alistarh, D.-A., &#38; Elizarov, R. (2019). <i>Lock-free channels for programming via communicating sequential processes</i>. <i>Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming</i> (pp. 417–418). Washington, NY, United States: ACM. <a href=\"https://doi.org/10.1145/3293883.3297000\">https://doi.org/10.1145/3293883.3297000</a>","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. <i>Lock-Free Channels for Programming via Communicating Sequential Processes</i>. <i>Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3293883.3297000\">https://doi.org/10.1145/3293883.3297000</a>.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM,p.","mla":"Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” <i>Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming</i>, ACM, 2019, pp. 417–18, doi:<a href=\"https://doi.org/10.1145/3293883.3297000\">10.1145/3293883.3297000</a>.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM, 2019."},"publication_identifier":{"isbn":["9781450362252"]},"year":"2019"},{"intvolume":"     11561","date_published":"2019-07-12T00:00:00Z","day":"12","doi":"10.1007/978-3-030-25540-4_16","oa":1,"file":[{"access_level":"open_access","creator":"dernst","file_size":674795,"date_created":"2019-08-14T11:05:30Z","file_name":"2019_CAV_GarciaSoto.pdf","checksum":"1f1d61b83a151031745ef70a501da3d6","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:47:32Z","file_id":"6817"}],"ec_funded":1,"year":"2019","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]},"publication":"31st International Conference on Computer-Aided Verification","isi":1,"ddc":["000"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","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"}],"oa_version":"Published Version","keyword":["Synthesis","Linear hybrid automaton","Membership"],"date_updated":"2025-04-15T06:26:13Z","page":"297-314","author":[{"orcid":"0000−0003−2936−5719","full_name":"Garcia Soto, Miriam","last_name":"Garcia Soto","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"last_name":"Zeleznik","full_name":"Zeleznik, Luka","id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","first_name":"Luka"}],"title":"Membership-based synthesis of linear hybrid automata","file_date_updated":"2020-07-14T12:47:32Z","article_processing_charge":"No","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","abstract":[{"lang":"eng","text":"We present two algorithmic approaches for synthesizing linear hybrid automata from experimental data. Unlike previous approaches, our algorithms work without a template and generate an automaton with nondeterministic guards and invariants, and with an arbitrary number and topology of modes. They thus construct a succinct model from the data and provide formal guarantees. In particular, (1) the generated automaton can reproduce the data up to a specified tolerance and (2) the automaton is tight, given the first guarantee. Our first approach encodes the synthesis problem as a logical formula in the theory of linear arithmetic, which can then be solved by an SMT solver. This approach minimizes the number of modes in the resulting model but is only feasible for limited data sets. To address scalability, we propose a second approach that does not enforce to find a minimal model. The algorithm constructs an initial automaton and then iteratively extends the automaton based on processing new data. Therefore the algorithm is well-suited for online and synthesis-in-the-loop applications. The core of the algorithm is a membership query that checks whether, within the specified tolerance, a given data set can result from the execution of a given automaton. We solve this membership problem for linear hybrid automata by repeated reachability computations. We demonstrate the effectiveness of the algorithm on synthetic data sets and on cardiac-cell measurements."}],"citation":{"chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In <i>31st International Conference on Computer-Aided Verification</i>, 11561:297–314. Springer, 2019. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_16\">https://doi.org/10.1007/978-3-030-25540-4_16</a>.","ista":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. 2019. Membership-based synthesis of linear hybrid automata. 31st International Conference on Computer-Aided Verification. CAV: Computer-Aided Verification, LNCS, vol. 11561, 297–314.","mla":"Garcia Soto, Miriam, et al. “Membership-Based Synthesis of Linear Hybrid Automata.” <i>31st International Conference on Computer-Aided Verification</i>, vol. 11561, Springer, 2019, pp. 297–314, doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_16\">10.1007/978-3-030-25540-4_16</a>.","apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., &#38; Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In <i>31st International Conference on Computer-Aided Verification</i> (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-030-25540-4_16\">https://doi.org/10.1007/978-3-030-25540-4_16</a>","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: <i>31st International Conference on Computer-Aided Verification</i>. Vol 11561. Springer; 2019:297-314. doi:<a href=\"https://doi.org/10.1007/978-3-030-25540-4_16\">10.1007/978-3-030-25540-4_16</a>","ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in <i>31st International Conference on Computer-Aided Verification</i>, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314."},"department":[{"_id":"ToHe"}],"volume":11561,"corr_author":"1","publisher":"Springer","date_created":"2019-05-27T07:09:53Z","publication_status":"published","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"},"external_id":{"isi":["000491468000016"]},"alternative_title":["LNCS"],"conference":{"end_date":"2019-07-18","start_date":"2019-07-15","location":"New York City, NY, USA","name":"CAV: Computer-Aided Verification"},"_id":"6493","scopus_import":"1","month":"07"},{"title":"Entropy solutions for stochastic porous media equations","author":[{"first_name":"Konstantinos","last_name":"Dareiotis","full_name":"Dareiotis, Konstantinos"},{"first_name":"Mate","full_name":"Gerencser, Mate","last_name":"Gerencser","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Benjamin","full_name":"Gess, Benjamin","last_name":"Gess"}],"date_updated":"2025-04-22T13:48:09Z","page":"3732-3763","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Preprint","publist_id":"7989","isi":1,"arxiv":1,"publication":"Journal of Differential Equations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"day":"05","doi":"10.1016/j.jde.2018.09.012","date_published":"2019-03-05T00:00:00Z","intvolume":"       266","year":"2019","article_type":"original","_id":"65","month":"03","issue":"6","scopus_import":"1","publication_status":"published","date_created":"2018-12-11T11:44:26Z","external_id":{"arxiv":["1803.06953"],"isi":["000456332500026"]},"volume":266,"department":[{"_id":"JaMa"}],"publisher":"Elsevier","main_file_link":[{"url":"http://arxiv.org/abs/1803.06953","open_access":"1"}],"citation":{"short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763.","chicago":"Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” <i>Journal of Differential Equations</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jde.2018.09.012\">https://doi.org/10.1016/j.jde.2018.09.012</a>.","ista":"Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763.","mla":"Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” <i>Journal of Differential Equations</i>, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:<a href=\"https://doi.org/10.1016/j.jde.2018.09.012\">10.1016/j.jde.2018.09.012</a>.","apa":"Dareiotis, K., Gerencser, M., &#38; Gess, B. (2019). Entropy solutions for stochastic porous media equations. <i>Journal of Differential Equations</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jde.2018.09.012\">https://doi.org/10.1016/j.jde.2018.09.012</a>","ieee":"K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” <i>Journal of Differential Equations</i>, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019.","ama":"Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. <i>Journal of Differential Equations</i>. 2019;266(6):3732-3763. doi:<a href=\"https://doi.org/10.1016/j.jde.2018.09.012\">10.1016/j.jde.2018.09.012</a>"},"type":"journal_article","abstract":[{"text":"We provide an entropy formulation for porous medium-type equations with a stochastic, non-linear, spatially inhomogeneous forcing. Well-posedness and L1-contraction is obtained in the class of entropy solutions. Our scope allows for porous medium operators Δ(|u|m−1u) for all m∈(1,∞), and Hölder continuous diffusion nonlinearity with exponent 1/2.","lang":"eng"}],"quality_controlled":"1"},{"oa_version":"Submitted Version","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","article_processing_charge":"No","file_date_updated":"2020-10-14T08:59:33Z","author":[{"first_name":"Yuzhou","last_name":"Zhang","full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2627-6956"},{"last_name":"He","full_name":"He, P","first_name":"P"},{"full_name":"Ma, X","last_name":"Ma","first_name":"X"},{"last_name":"Yang","full_name":"Yang, Z","first_name":"Z"},{"first_name":"C","full_name":"Pang, C","last_name":"Pang"},{"full_name":"Yu, J","last_name":"Yu","first_name":"J"},{"first_name":"G","last_name":"Wang","full_name":"Wang, G"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"},{"full_name":"Xiao, G","last_name":"Xiao","first_name":"G"}],"title":"Auxin-mediated statolith production for root gravitropism","date_updated":"2023-08-28T08:40:13Z","page":"761-774","year":"2019","article_type":"original","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646x"]},"file":[{"date_created":"2020-10-14T08:59:33Z","success":1,"file_name":"2019_NewPhytologist_Zhang_accepted.pdf","file_size":1099061,"creator":"dernst","access_level":"open_access","file_id":"8661","date_updated":"2020-10-14T08:59:33Z","relation":"main_file","content_type":"application/pdf","checksum":"6488243334538f5c39099a701cbf76b9"}],"oa":1,"day":"01","doi":"10.1111/nph.15932","date_published":"2019-10-01T00:00:00Z","intvolume":"       224","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["580"],"isi":1,"publication":"New Phytologist","external_id":{"isi":["000487184200024"],"pmid":["31111487"]},"publication_status":"published","date_created":"2019-05-28T14:33:26Z","month":"10","scopus_import":"1","issue":"2","_id":"6504","citation":{"ieee":"Y. Zhang <i>et al.</i>, “Auxin-mediated statolith production for root gravitropism,” <i>New Phytologist</i>, vol. 224, no. 2. Wiley, pp. 761–774, 2019.","apa":"Zhang, Y., He, P., Ma, X., Yang, Z., Pang, C., Yu, J., … Xiao, G. (2019). Auxin-mediated statolith production for root gravitropism. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.15932\">https://doi.org/10.1111/nph.15932</a>","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. <i>New Phytologist</i>. 2019;224(2):761-774. doi:<a href=\"https://doi.org/10.1111/nph.15932\">10.1111/nph.15932</a>","chicago":"Zhang, Yuzhou, P He, X Ma, Z Yang, C Pang, J Yu, G Wang, Jiří Friml, and G Xiao. “Auxin-Mediated Statolith Production for Root Gravitropism.” <i>New Phytologist</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/nph.15932\">https://doi.org/10.1111/nph.15932</a>.","ista":"Zhang Y, He P, Ma X, Yang Z, Pang C, Yu J, Wang G, Friml J, Xiao G. 2019. Auxin-mediated statolith production for root gravitropism. New Phytologist. 224(2), 761–774.","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” <i>New Phytologist</i>, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:<a href=\"https://doi.org/10.1111/nph.15932\">10.1111/nph.15932</a>.","short":"Y. Zhang, P. He, X. Ma, Z. Yang, C. Pang, J. Yu, G. Wang, J. Friml, G. Xiao, New Phytologist 224 (2019) 761–774."},"pmid":1,"abstract":[{"lang":"eng","text":"Root gravitropism is one of the most important processes allowing plant adaptation to the land environment. Auxin plays a central role in mediating root gravitropism, but how auxin contributes to gravitational perception and the subsequent response is still unclear.\r\n\r\nHere, we showed that the local auxin maximum/gradient within the root apex, which is generated by the PIN directional auxin transporters, regulates the expression of three key starch granule synthesis genes, SS4, PGM and ADG1, which in turn influence the accumulation of starch granules that serve as a statolith perceiving gravity.\r\n\r\nMoreover, using the cvxIAA‐ccvTIR1 system, we also showed that TIR1‐mediated auxin signaling is required for starch granule formation and gravitropic response within root tips. In addition, axr3 mutants showed reduced auxin‐mediated starch granule accumulation and disruption of gravitropism within the root apex.\r\n\r\nOur results indicate that auxin‐mediated statolith production relies on the TIR1/AFB‐AXR3‐mediated auxin signaling pathway. In summary, we propose a dual role for auxin in gravitropism: the regulation of both gravity perception and response."}],"type":"journal_article","quality_controlled":"1","publisher":"Wiley","volume":224,"department":[{"_id":"JiFr"}]},{"title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","author":[{"first_name":"Lianet","last_name":"Noda-García","full_name":"Noda-García, Lianet"},{"full_name":"Davidi, Dan","last_name":"Davidi","first_name":"Dan"},{"first_name":"Elisa","last_name":"Korenblum","full_name":"Korenblum, Elisa"},{"last_name":"Elazar","full_name":"Elazar, Assaf","first_name":"Assaf"},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina","id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina"},{"first_name":"Asaph","full_name":"Aharoni, Asaph","last_name":"Aharoni"},{"last_name":"Tawfik","full_name":"Tawfik, Dan S.","first_name":"Dan S."}],"date_updated":"2023-08-28T08:39:47Z","page":"1221–1230","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","oa_version":"Preprint","isi":1,"publication":"Nature Microbiology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"day":"01","doi":"10.1038/s41564-019-0412-y","date_published":"2019-07-01T00:00:00Z","intvolume":"         4","article_type":"original","year":"2019","publication_identifier":{"issn":["2058-5276"]},"_id":"6506","month":"07","scopus_import":"1","issue":"7","publication_status":"published","date_created":"2019-05-29T13:03:30Z","external_id":{"isi":["000480348200017"]},"volume":4,"department":[{"_id":"FyKo"}],"publisher":"Springer Nature","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/340828v2","open_access":"1"}],"citation":{"mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” <i>Nature Microbiology</i>, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:<a href=\"https://doi.org/10.1038/s41564-019-0412-y\">10.1038/s41564-019-0412-y</a>.","ista":"Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. 2019. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. 4(7), 1221–1230.","chicago":"Noda-García, Lianet, Dan Davidi, Elisa Korenblum, Assaf Elazar, Ekaterina Putintseva, Asaph Aharoni, and Dan S. Tawfik. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” <i>Nature Microbiology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41564-019-0412-y\">https://doi.org/10.1038/s41564-019-0412-y</a>.","apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., &#38; Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0412-y\">https://doi.org/10.1038/s41564-019-0412-y</a>","ieee":"L. Noda-García <i>et al.</i>, “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” <i>Nature Microbiology</i>, vol. 4, no. 7. Springer Nature, pp. 1221–1230, 2019.","ama":"Noda-García L, Davidi D, Korenblum E, et al. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. <i>Nature Microbiology</i>. 2019;4(7):1221–1230. doi:<a href=\"https://doi.org/10.1038/s41564-019-0412-y\">10.1038/s41564-019-0412-y</a>","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230."},"abstract":[{"lang":"eng","text":"How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments—from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost—across all the environments and conditions that we tested, the wild type was the fittest allele."}],"type":"journal_article","quality_controlled":"1"},{"ec_funded":1,"publication_identifier":{"issn":["0091-1798"]},"year":"2019","doi":"10.1214/18-AOP1284","day":"01","oa":1,"intvolume":"        47","date_published":"2019-05-01T00:00:00Z","project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Annals of Probability","arxiv":1,"isi":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","title":"Local single ring theorem on optimal scale","author":[{"orcid":"0000-0003-3036-1475","full_name":"Bao, Zhigang","last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang"},{"first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","last_name":"Erdös"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","first_name":"Kevin"}],"page":"1270-1334","date_updated":"2025-07-10T11:53:28Z","type":"journal_article","abstract":[{"lang":"eng","text":"Let U and V be two independent N by N random matrices that are distributed according to Haar measure on U(N). Let Σ be a nonnegative deterministic N by N matrix. The single ring theorem [Ann. of Math. (2) 174 (2011) 1189–1217] asserts that the empirical eigenvalue distribution of the matrix X:=UΣV∗ converges weakly, in the limit of large N, to a deterministic measure which is supported on a single ring centered at the origin in ℂ. Within the bulk regime, that is, in the interior of the single ring, we establish the convergence of the empirical eigenvalue distribution on the optimal local scale of order N−1/2+ε and establish the optimal convergence rate. The same results hold true when U and V are Haar distributed on O(N)."}],"citation":{"chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem on Optimal Scale.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2019. <a href=\"https://doi.org/10.1214/18-AOP1284\">https://doi.org/10.1214/18-AOP1284</a>.","ista":"Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale. Annals of Probability. 47(3), 1270–1334.","mla":"Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” <i>Annals of Probability</i>, vol. 47, no. 3, Institute of Mathematical Statistics, 2019, pp. 1270–334, doi:<a href=\"https://doi.org/10.1214/18-AOP1284\">10.1214/18-AOP1284</a>.","ama":"Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. <i>Annals of Probability</i>. 2019;47(3):1270-1334. doi:<a href=\"https://doi.org/10.1214/18-AOP1284\">10.1214/18-AOP1284</a>","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,” <i>Annals of Probability</i>, vol. 47, no. 3. Institute of Mathematical Statistics, pp. 1270–1334, 2019.","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2019). Local single ring theorem on optimal scale. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AOP1284\">https://doi.org/10.1214/18-AOP1284</a>","short":"Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334."},"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.05920"}],"volume":47,"department":[{"_id":"LaEr"}],"external_id":{"arxiv":["1612.05920"],"isi":["000466616100003"]},"publication_status":"published","date_created":"2019-06-02T21:59:13Z","month":"05","scopus_import":"1","issue":"3","_id":"6511"},{"publication":"Nature","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       570","date_published":"2019-06-06T00:00:00Z","doi":"10.1038/s41586-019-1212-5","day":"06","oa":1,"article_type":"original","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"year":"2019","page":"107-111","date_updated":"2025-07-10T11:53:29Z","title":"Tracing the origin of adult intestinal stem cells","author":[{"first_name":"Jordi","full_name":"Guiu, Jordi","last_name":"Guiu"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"full_name":"Yui, Shiro","last_name":"Yui","first_name":"Shiro"},{"full_name":"Demharter, Samuel","last_name":"Demharter","first_name":"Samuel"},{"last_name":"Ulyanchenko","full_name":"Ulyanchenko, Svetlana","first_name":"Svetlana"},{"first_name":"Martti","full_name":"Maimets, Martti","last_name":"Maimets"},{"full_name":"Jørgensen, Anne","last_name":"Jørgensen","first_name":"Anne"},{"full_name":"Perlman, Signe","last_name":"Perlman","first_name":"Signe"},{"full_name":"Lundvall, Lene","last_name":"Lundvall","first_name":"Lene"},{"full_name":"Mamsen, Linn Salto","last_name":"Mamsen","first_name":"Linn Salto"},{"last_name":"Larsen","full_name":"Larsen, Agnete","first_name":"Agnete"},{"first_name":"Rasmus H.","last_name":"Olesen","full_name":"Olesen, Rasmus H."},{"first_name":"Claus Yding","full_name":"Andersen, Claus Yding","last_name":"Andersen"},{"full_name":"Thuesen, Lea Langhoff","last_name":"Thuesen","first_name":"Lea Langhoff"},{"first_name":"Kristine Juul","last_name":"Hare","full_name":"Hare, Kristine Juul"},{"first_name":"Tune H.","last_name":"Pers","full_name":"Pers, Tune H."},{"first_name":"Konstantin","last_name":"Khodosevich","full_name":"Khodosevich, Konstantin"},{"last_name":"Simons","full_name":"Simons, Benjamin D.","first_name":"Benjamin D."},{"full_name":"Jensen, Kim B.","last_name":"Jensen","first_name":"Kim B."}],"article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"EdHa"}],"volume":570,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928"}],"publisher":"Springer Nature","quality_controlled":"1","type":"journal_article","pmid":1,"abstract":[{"text":"Adult intestinal stem cells are located at the bottom of crypts of Lieberkühn, where they express markers such as LGR5 1,2 and fuel the constant replenishment of the intestinal epithelium1. Although fetal LGR5-expressing cells can give rise to adult intestinal stem cells3,4, it remains unclear whether this population in the patterned epithelium represents unique intestinal stem-cell precursors. Here we show, using unbiased quantitative lineage-tracing approaches, biophysical modelling and intestinal transplantation, that all cells of the mouse intestinal epithelium—irrespective of their location and pattern of LGR5 expression in the fetal gut tube—contribute actively to the adult intestinal stem cell pool. Using 3D imaging, we find that during fetal development the villus undergoes gross remodelling and fission. This brings epithelial cells from the non-proliferative villus into the proliferative intervillus region, which enables them to contribute to the adult stem-cell niche. Our results demonstrate that large-scale remodelling of the intestinal wall and cell-fate specification are closely linked. Moreover, these findings provide a direct link between the observed plasticity and cellular reprogramming of differentiating cells in adult tissues following damage5,6,7,8,9, revealing that stem-cell identity is an induced rather than a hardwired property.","lang":"eng"}],"citation":{"apa":"Guiu, J., Hannezo, E. B., Yui, S., Demharter, S., Ulyanchenko, S., Maimets, M., … Jensen, K. B. (2019). Tracing the origin of adult intestinal stem cells. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1212-5\">https://doi.org/10.1038/s41586-019-1212-5</a>","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. <i>Nature</i>. 2019;570:107-111. doi:<a href=\"https://doi.org/10.1038/s41586-019-1212-5\">10.1038/s41586-019-1212-5</a>","ieee":"J. Guiu <i>et al.</i>, “Tracing the origin of adult intestinal stem cells,” <i>Nature</i>, vol. 570. Springer Nature, pp. 107–111, 2019.","ista":"Guiu J, Hannezo EB, Yui S, Demharter S, Ulyanchenko S, Maimets M, Jørgensen A, Perlman S, Lundvall L, Mamsen LS, Larsen A, Olesen RH, Andersen CY, Thuesen LL, Hare KJ, Pers TH, Khodosevich K, Simons BD, Jensen KB. 2019. Tracing the origin of adult intestinal stem cells. Nature. 570, 107–111.","chicago":"Guiu, Jordi, Edouard B Hannezo, Shiro Yui, Samuel Demharter, Svetlana Ulyanchenko, Martti Maimets, Anne Jørgensen, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1212-5\">https://doi.org/10.1038/s41586-019-1212-5</a>.","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” <i>Nature</i>, vol. 570, Springer Nature, 2019, pp. 107–11, doi:<a href=\"https://doi.org/10.1038/s41586-019-1212-5\">10.1038/s41586-019-1212-5</a>.","short":"J. Guiu, E.B. Hannezo, S. Yui, S. Demharter, S. Ulyanchenko, M. Maimets, A. Jørgensen, S. Perlman, L. Lundvall, L.S. Mamsen, A. Larsen, R.H. Olesen, C.Y. Andersen, L.L. Thuesen, K.J. Hare, T.H. Pers, K. Khodosevich, B.D. Simons, K.B. Jensen, Nature 570 (2019) 107–111."},"_id":"6513","scopus_import":"1","month":"06","date_created":"2019-06-02T21:59:14Z","publication_status":"published","external_id":{"pmid":["31092921"],"isi":["000470149000048"]}},{"month":"07","issue":"1","scopus_import":1,"_id":"6515","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"},"publication_status":"published","date_created":"2019-06-03T09:35:33Z","publisher":"Carleton University","volume":10,"department":[{"_id":"HeEd"}],"citation":{"short":"R. Dyer, G. Vegter, M. Wintraecken, Journal of Computational Geometry  10 (2019) 223–256.","mla":"Dyer, Ramsay, et al. “Simplices Modelled on Spaces of Constant Curvature.” <i>Journal of Computational Geometry </i>, vol. 10, no. 1, Carleton University, 2019, pp. 223–256, doi:<a href=\"https://doi.org/10.20382/jocg.v10i1a9\">10.20382/jocg.v10i1a9</a>.","chicago":"Dyer, Ramsay, Gert Vegter, and Mathijs Wintraecken. “Simplices Modelled on Spaces of Constant Curvature.” <i>Journal of Computational Geometry </i>. Carleton University, 2019. <a href=\"https://doi.org/10.20382/jocg.v10i1a9\">https://doi.org/10.20382/jocg.v10i1a9</a>.","ista":"Dyer R, Vegter G, Wintraecken M. 2019. Simplices modelled on spaces of constant curvature. Journal of Computational Geometry . 10(1), 223–256.","apa":"Dyer, R., Vegter, G., &#38; Wintraecken, M. (2019). Simplices modelled on spaces of constant curvature. <i>Journal of Computational Geometry </i>. Carleton University. <a href=\"https://doi.org/10.20382/jocg.v10i1a9\">https://doi.org/10.20382/jocg.v10i1a9</a>","ieee":"R. Dyer, G. Vegter, and M. Wintraecken, “Simplices modelled on spaces of constant curvature,” <i>Journal of Computational Geometry </i>, vol. 10, no. 1. Carleton University, pp. 223–256, 2019.","ama":"Dyer R, Vegter G, Wintraecken M. Simplices modelled on spaces of constant curvature. <i>Journal of Computational Geometry </i>. 2019;10(1):223–256. doi:<a href=\"https://doi.org/10.20382/jocg.v10i1a9\">10.20382/jocg.v10i1a9</a>"},"abstract":[{"lang":"eng","text":"We give non-degeneracy criteria for Riemannian simplices based on simplices in spaces of constant sectional curvature. It extends previous work on Riemannian simplices, where we developed Riemannian simplices with respect to Euclidean reference simplices. The criteria we give in this article are in terms of quality measures for spaces of constant curvature that we develop here. We see that simplices in spaces that have nearly constant curvature, are already non-degenerate under very weak quality demands. This is of importance because it allows for sampling of Riemannian manifolds based on anisotropy of the manifold and not (absolute) curvature."}],"type":"journal_article","quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:32Z","title":"Simplices modelled on spaces of constant curvature","author":[{"full_name":"Dyer, Ramsay","last_name":"Dyer","first_name":"Ramsay"},{"last_name":"Vegter","full_name":"Vegter, Gert","first_name":"Gert"},{"first_name":"Mathijs","last_name":"Wintraecken","full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220"}],"date_updated":"2021-01-12T08:07:50Z","page":"223–256","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"ddc":["510"],"publication":"Journal of Computational Geometry ","year":"2019","publication_identifier":{"issn":["1920-180X"]},"ec_funded":1,"oa":1,"file":[{"access_level":"open_access","date_created":"2019-06-03T09:30:01Z","file_name":"mainJournalFinal.pdf","creator":"mwintrae","file_size":2170882,"checksum":"57b4df2f16a74eb499734ec8ee240178","content_type":"application/pdf","relation":"main_file","date_updated":"2020-07-14T12:47:32Z","file_id":"6516"}],"day":"01","doi":"10.20382/jocg.v10i1a9","date_published":"2019-07-01T00:00:00Z","intvolume":"        10"},{"corr_author":"1","publisher":"Elsevier","department":[{"_id":"SaSi"}],"volume":707,"quality_controlled":"1","pmid":1,"abstract":[{"lang":"eng","text":"Microglia have emerged as a critical component of neurodegenerative diseases. Genetic manipulation of microglia can elucidate their functional impact in disease. In neuroscience, recombinant viruses such as lentiviruses and adeno-associated viruses (AAVs) have been successfully used to target various cell types in the brain, although effective transduction of microglia is rare. In this review, we provide a short background of lentiviruses and AAVs, and strategies for designing recombinant viral vectors. Then, we will summarize recent literature on successful microglial transductions in vitro and in vivo, and discuss the current challenges. Finally, we provide guidelines for reporting the efficiency and specificity of viral targeting in microglia, which will enable the microglial research community to assess and improve methodologies for future studies."}],"type":"journal_article","citation":{"ama":"Maes ME, Colombo G, Schulz R, Siegert S. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. <i>Neuroscience Letters</i>. 2019;707. doi:<a href=\"https://doi.org/10.1016/j.neulet.2019.134310\">10.1016/j.neulet.2019.134310</a>","apa":"Maes, M. E., Colombo, G., Schulz, R., &#38; Siegert, S. (2019). Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. <i>Neuroscience Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neulet.2019.134310\">https://doi.org/10.1016/j.neulet.2019.134310</a>","ieee":"M. E. Maes, G. Colombo, R. Schulz, and S. Siegert, “Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges,” <i>Neuroscience Letters</i>, vol. 707. Elsevier, 2019.","mla":"Maes, Margaret E., et al. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” <i>Neuroscience Letters</i>, vol. 707, 134310, Elsevier, 2019, doi:<a href=\"https://doi.org/10.1016/j.neulet.2019.134310\">10.1016/j.neulet.2019.134310</a>.","ista":"Maes ME, Colombo G, Schulz R, Siegert S. 2019. Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges. Neuroscience Letters. 707, 134310.","chicago":"Maes, Margaret E, Gloria Colombo, Rouven Schulz, and Sandra Siegert. “Targeting Microglia with Lentivirus and AAV: Recent Advances and Remaining Challenges.” <i>Neuroscience Letters</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neulet.2019.134310\">https://doi.org/10.1016/j.neulet.2019.134310</a>.","short":"M.E. Maes, G. Colombo, R. Schulz, S. Siegert, Neuroscience Letters 707 (2019)."},"scopus_import":"1","month":"08","_id":"6521","external_id":{"pmid":["31158432"],"isi":["000486094600037"]},"date_created":"2019-06-05T13:16:24Z","publication_status":"published","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"},"ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571"},{"name":"Modulating microglia through G protein-coupled receptor (GPCR) signaling","_id":"267F75D8-B435-11E9-9278-68D0E5697425"}],"publication":"Neuroscience Letters","isi":1,"ec_funded":1,"publication_identifier":{"issn":["0304-3940"]},"article_type":"original","year":"2019","article_number":"134310","intvolume":"       707","date_published":"2019-08-10T00:00:00Z","day":"10","doi":"10.1016/j.neulet.2019.134310","oa":1,"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"553c9dbd39727fbed55ee991c51ca4d1","file_id":"6551","date_updated":"2020-07-14T12:47:33Z","access_level":"open_access","date_created":"2019-06-08T11:44:20Z","file_name":"2019_Neuroscience_Maes.pdf","file_size":1779287,"creator":"dernst"}],"file_date_updated":"2020-07-14T12:47:33Z","article_processing_charge":"No","has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","date_updated":"2025-03-31T16:01:17Z","author":[{"orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E","last_name":"Maes","first_name":"Margaret E"},{"first_name":"Gloria","orcid":"0000-0001-9434-8902","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","last_name":"Colombo","full_name":"Colombo, Gloria"},{"first_name":"Rouven","orcid":"0000-0001-5297-733X","id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","last_name":"Schulz","full_name":"Schulz, Rouven"},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877"}],"title":"Targeting microglia with lentivirus and AAV: Recent advances and remaining challenges","oa_version":"Published Version"},{"month":"01","scopus_import":"1","_id":"6528","conference":{"start_date":"2019-01-10","location":"San Diego, CA, United States","name":"ITCS: Innovations in Theoretical Computer Science","end_date":"2019-01-12"},"alternative_title":["LIPIcs"],"publication_status":"published","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"},"date_created":"2019-06-06T14:12:36Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/627"}],"volume":124,"department":[{"_id":"KrPi"}],"abstract":[{"lang":"eng","text":"We construct a verifiable delay function (VDF) by showing how the Rivest-Shamir-Wagner time-lock puzzle can be made publicly verifiable. Concretely, we give a statistically sound public-coin protocol to prove that a tuple (N,x,T,y) satisfies y=x2T (mod N) where the prover doesn’t know the factorization of N and its running time is dominated by solving the puzzle, that is, compute x2T, which is conjectured to require T sequential squarings. To get a VDF we make this protocol non-interactive using the Fiat-Shamir heuristic.The motivation for this work comes from the Chia blockchain design, which uses a VDF as akey ingredient. For typical parameters (T≤2 40, N= 2048), our proofs are of size around 10K B, verification cost around three RSA exponentiations and computing the proof is 8000 times faster than solving the puzzle even without any parallelism."}],"type":"conference","citation":{"mla":"Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” <i>10th Innovations in Theoretical Computer Science Conference</i>, vol. 124, 60, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:<a href=\"https://doi.org/10.4230/LIPICS.ITCS.2019.60\">10.4230/LIPICS.ITCS.2019.60</a>.","ista":"Pietrzak KZ. 2019. Simple verifiable delay functions. 10th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science, LIPIcs, vol. 124, 60.","chicago":"Pietrzak, Krzysztof Z. “Simple Verifiable Delay Functions.” In <i>10th Innovations in Theoretical Computer Science Conference</i>, Vol. 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. <a href=\"https://doi.org/10.4230/LIPICS.ITCS.2019.60\">https://doi.org/10.4230/LIPICS.ITCS.2019.60</a>.","ieee":"K. Z. Pietrzak, “Simple verifiable delay functions,” in <i>10th Innovations in Theoretical Computer Science Conference</i>, San Diego, CA, United States, 2019, vol. 124.","ama":"Pietrzak KZ. Simple verifiable delay functions. In: <i>10th Innovations in Theoretical Computer Science Conference</i>. Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:<a href=\"https://doi.org/10.4230/LIPICS.ITCS.2019.60\">10.4230/LIPICS.ITCS.2019.60</a>","apa":"Pietrzak, K. Z. (2019). Simple verifiable delay functions. In <i>10th Innovations in Theoretical Computer Science Conference</i> (Vol. 124). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ITCS.2019.60\">https://doi.org/10.4230/LIPICS.ITCS.2019.60</a>","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019."},"quality_controlled":"1","status":"public","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:33Z","article_processing_charge":"No","has_accepted_license":"1","author":[{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"title":"Simple verifiable delay functions","date_updated":"2025-07-10T11:53:29Z","oa_version":"Published Version","project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"publication":"10th Innovations in Theoretical Computer Science Conference","article_number":"60","ec_funded":1,"year":"2019","publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"day":"10","doi":"10.4230/LIPICS.ITCS.2019.60","file":[{"relation":"main_file","checksum":"f0ae1bb161431d9db3dea5ace082bfb5","content_type":"application/pdf","file_id":"6529","date_updated":"2020-07-14T12:47:33Z","access_level":"open_access","file_name":"2019_LIPIcs_Pietrzak.pdf","date_created":"2019-06-06T14:22:04Z","file_size":558770,"creator":"dernst"}],"oa":1,"intvolume":"       124","date_published":"2019-01-10T00:00:00Z"},{"abstract":[{"text":"When animals become sick, infected cells and an armada of activated immune cells attempt to eliminate the pathogen from the body. Once infectious particles have breached the body's physical barriers of the skin or gut lining, an initially local response quickly escalates into a systemic response, attracting mobile immune cells to the site of infection. These cells complement the initial, unspecific defense with a more specialized, targeted response. This can also provide long-term immune memory and protection against future infection. The cell-autonomous defenses of the infected cells are thus aided by the actions of recruited immune cells. These specialized cells are the most mobile cells in the body, constantly patrolling through the otherwise static tissue to detect incoming pathogens. Such constant immune surveillance means infections are noticed immediately and can be rapidly cleared from the body. Some immune cells also remove infected cells that have succumbed to infection. All this prevents pathogen replication and spread to healthy tissues. Although this may involve the sacrifice of some somatic tissue, this is typically replaced quickly. Particular care is, however, given to the reproductive organs, which should always remain disease free (immune privilege). ","lang":"eng"}],"pmid":1,"type":"journal_article","citation":{"short":"S. Cremer, Current Biology 29 (2019) R458–R463.","apa":"Cremer, S. (2019). Social immunity in insects. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2019.03.035\">https://doi.org/10.1016/j.cub.2019.03.035</a>","ieee":"S. Cremer, “Social immunity in insects,” <i>Current Biology</i>, vol. 29, no. 11. Elsevier, pp. R458–R463, 2019.","ama":"Cremer S. Social immunity in insects. <i>Current Biology</i>. 2019;29(11):R458-R463. doi:<a href=\"https://doi.org/10.1016/j.cub.2019.03.035\">10.1016/j.cub.2019.03.035</a>","mla":"Cremer, Sylvia. “Social Immunity in Insects.” <i>Current Biology</i>, vol. 29, no. 11, Elsevier, 2019, pp. R458–63, doi:<a href=\"https://doi.org/10.1016/j.cub.2019.03.035\">10.1016/j.cub.2019.03.035</a>.","chicago":"Cremer, Sylvia. “Social Immunity in Insects.” <i>Current Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cub.2019.03.035\">https://doi.org/10.1016/j.cub.2019.03.035</a>.","ista":"Cremer S. 2019. Social immunity in insects. Current Biology. 29(11), R458–R463."},"quality_controlled":"1","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2019.03.035"}],"volume":29,"department":[{"_id":"SyCr"}],"external_id":{"pmid":["31163158"],"isi":["000470902000023"]},"publication_status":"published","date_created":"2019-06-09T21:59:10Z","month":"06","issue":"11","scopus_import":"1","_id":"6552","article_type":"original","publication_identifier":{"issn":["09609822"]},"year":"2019","doi":"10.1016/j.cub.2019.03.035","day":"03","oa":1,"intvolume":"        29","date_published":"2019-06-03T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"Current Biology","isi":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"status":"public","article_processing_charge":"No","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","first_name":"Sylvia"}],"title":"Social immunity in insects","page":"R458-R463","date_updated":"2023-08-28T09:38:00Z"},{"volume":41,"department":[{"_id":"ChLa"}],"publisher":"Institute of Electrical and Electronics Engineers","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1707.00600"}],"citation":{"ista":"Xian Y, Lampert C, Schiele B, Akata Z. 2019. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 41(9), 2251–2265.","chicago":"Xian, Yongqin, Christoph Lampert, Bernt Schiele, and Zeynep Akata. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. Institute of Electrical and Electronics Engineers, 2019. <a href=\"https://doi.org/10.1109/tpami.2018.2857768\">https://doi.org/10.1109/tpami.2018.2857768</a>.","mla":"Xian, Yongqin, et al. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 41, no. 9, Institute of Electrical and Electronics Engineers, 2019, pp. 2251–65, doi:<a href=\"https://doi.org/10.1109/tpami.2018.2857768\">10.1109/tpami.2018.2857768</a>.","ieee":"Y. Xian, C. Lampert, B. Schiele, and Z. Akata, “Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 41, no. 9. Institute of Electrical and Electronics Engineers, pp. 2251–2265, 2019.","ama":"Xian Y, Lampert C, Schiele B, Akata Z. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2019;41(9):2251-2265. doi:<a href=\"https://doi.org/10.1109/tpami.2018.2857768\">10.1109/tpami.2018.2857768</a>","apa":"Xian, Y., Lampert, C., Schiele, B., &#38; Akata, Z. (2019). Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/tpami.2018.2857768\">https://doi.org/10.1109/tpami.2018.2857768</a>","short":"Y. Xian, C. Lampert, B. Schiele, Z. Akata, IEEE Transactions on Pattern Analysis and Machine Intelligence 41 (2019) 2251–2265."},"type":"journal_article","abstract":[{"lang":"eng","text":"Due to the importance of zero-shot learning, i.e. classifying images where there is a lack of labeled training data, the number of proposed approaches has recently increased steadily. We argue that it is time to take a step back and to analyze the status quo of the area. The purpose of this paper is three-fold. First, given the fact that there is no agreed upon zero-shot learning benchmark, we first define a new benchmark by unifying both the evaluation protocols and data splits of publicly available datasets used for this task. This is an important contribution as published results are often not comparable and sometimes even flawed due to, e.g. pre-training on zero-shot test classes. Moreover, we propose a new zero-shot learning dataset, the Animals with Attributes 2 (AWA2) dataset which we make publicly available both in terms of image features and the images themselves. Second, we compare and analyze a significant number of the state-of-the-art methods in depth, both in the classic zero-shot setting but also in the more realistic generalized zero-shot setting. Finally, we discuss in detail the limitations of the current status of the area which can be taken as a basis for advancing it."}],"quality_controlled":"1","_id":"6554","month":"09","scopus_import":"1","issue":"9","publication_status":"published","date_created":"2019-06-11T14:05:59Z","external_id":{"arxiv":["1707.00600"],"isi":["000480343900015"]},"isi":1,"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"doi":"10.1109/tpami.2018.2857768","day":"01","date_published":"2019-09-01T00:00:00Z","intvolume":"        41","publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"year":"2019","article_type":"original","title":"Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly","author":[{"first_name":"Yongqin","last_name":"Xian","full_name":"Xian, Yongqin"},{"first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Bernt","last_name":"Schiele","full_name":"Schiele, Bernt"},{"first_name":"Zeynep","full_name":"Akata, Zeynep","last_name":"Akata"}],"date_updated":"2024-12-11T11:49:58Z","page":"2251 - 2265","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","oa_version":"Preprint"},{"article_type":"original","year":"2019","publication_identifier":{"eissn":["1089-8638"],"issn":["0022-2836"]},"intvolume":"       431","date_published":"2019-08-09T00:00:00Z","day":"09","doi":"10.1016/j.jmb.2019.05.033","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Molecular Biology","isi":1,"oa_version":"Preprint","article_processing_charge":"No","status":"public","language":[{"iso":"eng"}],"date_updated":"2025-07-10T11:53:33Z","page":"3046-3055","title":"Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions","author":[{"first_name":"Alexandra-Madelaine","last_name":"Tichy","full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gerrard","full_name":"Gerrard, Elliot J.","first_name":"Elliot J."},{"last_name":"Legrand","full_name":"Legrand, Julien M.D.","first_name":"Julien M.D."},{"last_name":"Hobbs","full_name":"Hobbs, Robin M.","first_name":"Robin M."},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L"}],"quality_controlled":"1","type":"journal_article","abstract":[{"lang":"eng","text":"Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology."}],"citation":{"short":"A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055.","apa":"Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., &#38; Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">https://doi.org/10.1016/j.jmb.2019.05.033</a>","ama":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. <i>Journal of Molecular Biology</i>. 2019;431(17):3046-3055. doi:<a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">10.1016/j.jmb.2019.05.033</a>","ieee":"A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” <i>Journal of Molecular Biology</i>, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019.","mla":"Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” <i>Journal of Molecular Biology</i>, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:<a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">10.1016/j.jmb.2019.05.033</a>.","ista":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.","chicago":"Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” <i>Journal of Molecular Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">https://doi.org/10.1016/j.jmb.2019.05.033</a>."},"main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/10.1101/583369v1"}],"publisher":"Elsevier","department":[{"_id":"HaJa"}],"volume":431,"external_id":{"isi":["000482872100002"]},"date_created":"2019-06-16T21:59:14Z","publication_status":"published","issue":"17","scopus_import":"1","month":"08","_id":"6564"}]