[{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"date_created":"2019-04-30T15:24:22Z","pmid":1,"external_id":{"isi":["000470086100019"],"pmid":["31000634"]},"year":"2019","department":[{"_id":"JiFr"}],"publisher":"ASPB","page":"757-766","quality_controlled":"1","article_processing_charge":"No","issue":"2","citation":{"ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","ieee":"J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 757–766, 2019.","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377","mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377.","chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377.","ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766."},"volume":180,"oa":1,"_id":"6366","publication":"Plant Physiology","article_type":"original","title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","date_updated":"2023-09-05T12:25:19Z","day":"01","author":[{"first_name":"Julia","full_name":"Bellstaedt, Julia","last_name":"Bellstaedt"},{"last_name":"Trenner","first_name":"Jana","full_name":"Trenner, Jana"},{"last_name":"Lippmann","first_name":"Rebecca","full_name":"Lippmann, Rebecca"},{"full_name":"Poeschl, Yvonne","first_name":"Yvonne","last_name":"Poeschl"},{"full_name":"Zhang, Xixi","first_name":"Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Quint, Marcel","first_name":"Marcel","last_name":"Quint"},{"first_name":"Carolin","full_name":"Delker, Carolin","last_name":"Delker"}],"main_file_link":[{"url":"www.doi.org/10.1104/pp.18.01377","open_access":"1"}],"date_published":"2019-06-01T00:00:00Z","scopus_import":"1","abstract":[{"text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl.","lang":"eng"}],"type":"journal_article","month":"06","isi":1,"status":"public","intvolume":" 180","doi":"10.1104/pp.18.01377","oa_version":"Published Version","publication_status":"published","language":[{"iso":"eng"}]},{"volume":33,"citation":{"ama":"Cremer S. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 2019;33:63-68. doi:10.1016/j.cois.2019.03.011","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” Current Opinion in Insect Science, vol. 33. Elsevier, pp. 63–68, 2019.","apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. Elsevier. https://doi.org/10.1016/j.cois.2019.03.011","chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science. Elsevier, 2019. https://doi.org/10.1016/j.cois.2019.03.011.","mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” Current Opinion in Insect Science, vol. 33, Elsevier, 2019, pp. 63–68, doi:10.1016/j.cois.2019.03.011.","ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68."},"scopus_import":"1","article_processing_charge":"No","date_published":"2019-06-01T00:00:00Z","quality_controlled":"1","page":"63-68","department":[{"_id":"SyCr"}],"publisher":"Elsevier","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","full_name":"Cremer, Sylvia","first_name":"Sylvia","orcid":"0000-0002-2193-3868"}],"year":"2019","external_id":{"isi":["000477666000012"]},"day":"01","date_updated":"2025-07-10T11:53:22Z","title":"Pathogens and disease defense of invasive ants","date_created":"2019-05-13T07:58:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2214-5745"],"eissn":["2214-5753"]},"language":[{"iso":"eng"}],"publication_status":"published","oa_version":"None","doi":"10.1016/j.cois.2019.03.011","publication":"Current Opinion in Insect Science","intvolume":" 33","status":"public","month":"06","isi":1,"_id":"6415","abstract":[{"lang":"eng","text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success."}],"type":"journal_article"},{"year":"2019","external_id":{"isi":["000476569800003"]},"date_created":"2019-05-13T07:58:38Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1759-6653"]},"volume":11,"oa":1,"citation":{"mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:10.1093/gbe/evz053.","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz053.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 2019;11(4):1033-1044. doi:10.1093/gbe/evz053","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” Genome biology and evolution, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., & Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz053"},"project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"}],"issue":"4","article_processing_charge":"No","quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"BeVi"}],"page":"1033-1044","file":[{"file_size":1256303,"date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-14T08:29:38Z","checksum":"7d0ede297b6741f3dc89cd59017c7642","file_name":"2019_GBE_Huylmans.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"6446","creator":"dernst","relation":"main_file"}],"publisher":"Oxford University Press","acknowledged_ssus":[{"_id":"ScienComp"}],"_id":"6418","ddc":["570"],"publication":"Genome biology and evolution","day":"01","date_updated":"2025-04-14T07:41:21Z","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","file_date_updated":"2020-07-14T12:47:29Z","date_published":"2019-04-01T00:00:00Z","author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","full_name":"Huylmans, Ann K","first_name":"Ann K","orcid":"0000-0001-8871-4961"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"first_name":"Ariana","full_name":"Macon, Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"William J","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz"}],"intvolume":" 11","status":"public","isi":1,"month":"04","abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"type":"journal_article","related_material":{"record":[{"status":"public","relation":"popular_science","id":"6060"}]},"language":[{"iso":"eng"}],"publication_status":"published","oa_version":"Published Version","doi":"10.1093/gbe/evz053","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"conference":{"start_date":"2019-04-16","location":"Montreal, Canada","name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2019-04-18"},"publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","ddc":["000"],"_id":"6428","article_processing_charge":"No","quality_controlled":"1","file":[{"relation":"main_file","file_id":"8633","content_type":"application/pdf","access_level":"open_access","creator":"dernst","success":1,"file_name":"2019_ACM_Ferrere.pdf","checksum":"b8e967081e051d1c55ca5d18fb187890","date_created":"2020-10-08T17:25:45Z","file_size":1055421,"date_updated":"2020-10-08T17:25:45Z"}],"publisher":"ACM","department":[{"_id":"ToHe"}],"page":"57-66","oa":1,"citation":{"ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 57–66.","mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66, doi:10.1145/3302504.3311800.","chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, 57–66. ACM, 2019. https://doi.org/10.1145/3302504.3311800.","apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., & Kapinski, J. (2019). Interface-aware signal temporal logic. In Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control (pp. 57–66). Montreal, Canada: ACM. https://doi.org/10.1145/3302504.3311800","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, Montreal, Canada, 2019, pp. 57–66.","ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. ACM; 2019:57-66. doi:10.1145/3302504.3311800","short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66."},"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"}],"date_created":"2019-05-13T08:13:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"isbn":["9781450362825"]},"year":"2019","external_id":{"isi":["000516713900007"]},"publication_status":"published","oa_version":"Submitted Version","doi":"10.1145/3302504.3311800","language":[{"iso":"eng"}],"type":"conference","abstract":[{"text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system.","lang":"eng"}],"status":"public","month":"04","isi":1,"file_date_updated":"2020-10-08T17:25:45Z","date_published":"2019-04-16T00:00:00Z","author":[{"id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","full_name":"Ferrere, Thomas","first_name":"Thomas","orcid":"0000-0001-5199-3143"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"},{"last_name":"Donzé","full_name":"Donzé, Alexandre","first_name":"Alexandre"},{"last_name":"Ito","first_name":"Hisahiro","full_name":"Ito, Hisahiro"},{"last_name":"Kapinski","first_name":"James","full_name":"Kapinski, James"}],"has_accepted_license":"1","scopus_import":"1","title":"Interface-aware signal temporal logic","date_updated":"2025-07-10T11:53:22Z","day":"16"},{"publication":"ACM Transactions on Graphics","ddc":["000","005"],"_id":"6442","article_number":"130","acknowledged_ssus":[{"_id":"ScienComp"}],"article_processing_charge":"No","quality_controlled":"1","file":[{"file_size":44328918,"date_updated":"2020-07-14T12:47:30Z","checksum":"1b737dfe3e051aba8f3f4ab1dceda673","date_created":"2019-05-14T07:03:55Z","file_name":"2019_ACM_Schreck.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"6443","creator":"dernst","relation":"main_file"}],"publisher":"ACM","department":[{"_id":"ChWo"}],"oa":1,"volume":38,"citation":{"ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics, vol. 38, no. 4, 130, ACM, 2019, doi:10.1145/3306346.3323002.","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323002.","apa":"Schreck, C., Hafner, C., & Wojtan, C. (2019). Fundamental solutions for water wave animation. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323002","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323002"},"project":[{"name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"}],"issue":"4","date_created":"2019-05-14T07:04:06Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","external_id":{"isi":["000475740600104"]},"publication_status":"published","oa_version":"Submitted Version","doi":"10.1145/3306346.3323002","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples."}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/"}]},"intvolume":" 38","status":"public","month":"07","isi":1,"file_date_updated":"2020-07-14T12:47:30Z","date_published":"2019-07-01T00:00:00Z","author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","first_name":"Camille","full_name":"Schreck, Camille"},{"full_name":"Hafner, Christian","first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","first_name":"Christopher J","full_name":"Wojtan, Christopher J"}],"ec_funded":1,"has_accepted_license":"1","scopus_import":"1","date_updated":"2024-10-22T09:58:22Z","title":"Fundamental solutions for water wave animation","day":"01"},{"ddc":["570"],"publication":"iScience","_id":"6451","oa":1,"volume":15,"citation":{"chicago":"Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger, Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience. Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.04.018.","mla":"Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” IScience, vol. 15, Elsevier, 2019, pp. 243–56, doi:10.1016/j.isci.2019.04.018.","ista":"Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 15, 243–256.","ama":"Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 2019;15:243-256. doi:10.1016/j.isci.2019.04.018","short":"N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann, B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience 15 (2019) 243–256.","apa":"Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann, M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation in a p53-independent manner. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.04.018","ieee":"N. Amberg et al., “EGFR controls hair shaft differentiation in a p53-independent manner,” iScience, vol. 15. Elsevier, pp. 243–256, 2019."},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file":[{"file_name":"2019_iScience_Amberg.pdf","date_created":"2019-05-14T11:51:51Z","checksum":"a9ad2296726c9474ad5860c9c2f53622","file_size":8365970,"date_updated":"2020-07-14T12:47:30Z","relation":"main_file","creator":"dernst","file_id":"6452","content_type":"application/pdf","access_level":"open_access"}],"page":"243-256","publisher":"Elsevier","department":[{"_id":"SiHi"}],"article_processing_charge":"No","quality_controlled":"1","external_id":{"isi":["000470104600022"]},"year":"2019","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2589-0042"]},"date_created":"2019-05-14T11:47:40Z","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1016/j.isci.2019.04.018","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)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"publication_status":"published","status":"public","isi":1,"month":"05","intvolume":" 15","abstract":[{"text":"Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis.","lang":"eng"}],"type":"journal_article","has_accepted_license":"1","author":[{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207"},{"first_name":"Panagiota A.","full_name":"Sotiropoulou, Panagiota A.","last_name":"Sotiropoulou"},{"last_name":"Heller","full_name":"Heller, Gerwin","first_name":"Gerwin"},{"last_name":"Lichtenberger","full_name":"Lichtenberger, Beate M.","first_name":"Beate M."},{"last_name":"Holcmann","first_name":"Martin","full_name":"Holcmann, Martin"},{"last_name":"Camurdanoglu","full_name":"Camurdanoglu, Bahar","first_name":"Bahar"},{"last_name":"Baykuscheva-Gentscheva","first_name":"Temenuschka","full_name":"Baykuscheva-Gentscheva, Temenuschka"},{"first_name":"Cedric","full_name":"Blanpain, Cedric","last_name":"Blanpain"},{"last_name":"Sibilia","full_name":"Sibilia, Maria","first_name":"Maria"}],"file_date_updated":"2020-07-14T12:47:30Z","date_published":"2019-05-31T00:00:00Z","day":"31","title":"EGFR controls hair shaft differentiation in a p53-independent manner","date_updated":"2023-09-08T11:38:04Z"},{"language":[{"iso":"eng"}],"publication_status":"published","doi":"10.1016/j.neuron.2019.01.051","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)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"oa_version":"Published Version","intvolume":" 102","month":"04","isi":1,"status":"public","type":"journal_article","abstract":[{"lang":"eng","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."}],"ec_funded":1,"has_accepted_license":"1","scopus_import":"1","date_published":"2019-04-03T00:00:00Z","file_date_updated":"2020-07-14T12:47:30Z","author":[{"last_name":"Ortiz-Álvarez","first_name":"G","full_name":"Ortiz-Álvarez, G"},{"last_name":"Daclin","full_name":"Daclin, M","first_name":"M"},{"last_name":"Shihavuddin","full_name":"Shihavuddin, A","first_name":"A"},{"first_name":"P","full_name":"Lansade, P","last_name":"Lansade"},{"last_name":"Fortoul","full_name":"Fortoul, A","first_name":"A"},{"first_name":"M","full_name":"Faucourt, M","last_name":"Faucourt"},{"last_name":"Clavreul","first_name":"S","full_name":"Clavreul, S"},{"last_name":"Lalioti","full_name":"Lalioti, ME","first_name":"ME"},{"full_name":"Taraviras, S","first_name":"S","last_name":"Taraviras"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Livet, J","first_name":"J","last_name":"Livet"},{"last_name":"Meunier","first_name":"A","full_name":"Meunier, A"},{"last_name":"Genovesio","first_name":"A","full_name":"Genovesio, A"},{"first_name":"N","full_name":"Spassky, N","last_name":"Spassky"}],"day":"03","title":"Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members","date_updated":"2025-04-14T07:43:05Z","ddc":["570"],"publication":"Neuron","_id":"6454","citation":{"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.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.051.","mla":"Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:10.1016/j.neuron.2019.01.051.","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. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.051","ieee":"G. Ortiz-Álvarez et al., “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” Neuron, 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. Neuron. 2019;102(1):159-172.e7. doi:10.1016/j.neuron.2019.01.051","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."},"volume":102,"oa":1,"issue":"1","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","article_processing_charge":"No","file":[{"date_updated":"2020-07-14T12:47:30Z","file_size":7288572,"date_created":"2019-05-15T09:28:41Z","checksum":"1fb6e195c583eb0c5cabf26f69ff6675","file_name":"2019_Neuron_Ortiz.pdf","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_id":"6457","relation":"main_file"}],"page":"159-172.e7","department":[{"_id":"SiHi"}],"publisher":"Elsevier","year":"2019","pmid":1,"external_id":{"isi":["000463337900018"],"pmid":["30824354"]},"date_created":"2019-05-14T13:06:30Z","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"_id":"6455","article_number":"eaav2522","publication":"Science","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"date_created":"2019-05-14T13:07:47Z","external_id":{"isi":["000467631800034"],"pmid":["31073041"]},"pmid":1,"year":"2019","department":[{"_id":"SiHi"}],"publisher":"AAAS","article_processing_charge":"No","quality_controlled":"1","project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T01031","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression"}],"issue":"6440","oa":1,"volume":364,"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. Science. 2019;364(6440). doi:10.1126/science.aav2522","ieee":"L. Telley et al., “Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex,” Science, 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. Science. AAAS. https://doi.org/10.1126/science.aav2522","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.” Science. AAAS, 2019. https://doi.org/10.1126/science.aav2522.","mla":"Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science, vol. 364, no. 6440, eaav2522, AAAS, 2019, doi:10.1126/science.aav2522.","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."},"related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/","description":"News on IST Homepage","relation":"press_release"}]},"type":"journal_article","abstract":[{"lang":"eng","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."}],"status":"public","month":"05","isi":1,"intvolume":" 364","oa_version":"Published Version","doi":"10.1126/science.aav2522","publication_status":"published","language":[{"iso":"eng"}],"date_updated":"2025-04-15T07:50:01Z","title":"Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex","article_type":"original","day":"10","main_file_link":[{"open_access":"1","url":"https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf"}],"author":[{"full_name":"Telley, L","first_name":"L","last_name":"Telley"},{"last_name":"Agirman","first_name":"G","full_name":"Agirman, G"},{"first_name":"J","full_name":"Prados, J","last_name":"Prados"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","orcid":"0000-0002-3183-8207","first_name":"Nicole","full_name":"Amberg, Nicole"},{"first_name":"S","full_name":"Fièvre, S","last_name":"Fièvre"},{"last_name":"Oberst","full_name":"Oberst, P","first_name":"P"},{"last_name":"Bartolini","first_name":"G","full_name":"Bartolini, G"},{"first_name":"I","full_name":"Vitali, I","last_name":"Vitali"},{"full_name":"Cadilhac, C","first_name":"C","last_name":"Cadilhac"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"},{"full_name":"Nguyen, L","first_name":"L","last_name":"Nguyen"},{"last_name":"Dayer","first_name":"A","full_name":"Dayer, A"},{"first_name":"D","full_name":"Jabaudon, D","last_name":"Jabaudon"}],"date_published":"2019-05-10T00:00:00Z","scopus_import":"1","ec_funded":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."}],"status":"public","month":"07","isi":1,"intvolume":" 11561","oa_version":"Published Version","doi":"10.1007/978-3-030-25540-4_36","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","language":[{"iso":"eng"}],"title":"Run-time optimization for learned controllers through quantitative games","date_updated":"2025-04-15T06:26:05Z","day":"12","author":[{"id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","last_name":"Avni","full_name":"Avni, Guy","first_name":"Guy","orcid":"0000-0001-5588-8287"},{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konighofer, Bettina","first_name":"Bettina","last_name":"Konighofer"},{"first_name":"Stefan","full_name":"Pranger, Stefan","last_name":"Pranger"}],"file_date_updated":"2020-07-14T12:47:31Z","date_published":"2019-07-12T00:00:00Z","scopus_import":"1","has_accepted_license":"1","_id":"6462","conference":{"start_date":"2019-07-13","location":"New York, NY, United States","end_date":"2019-07-18","name":"CAV: Computer Aided Verification"},"corr_author":"1","publication":"31st International Conference on Computer-Aided Verification","ddc":["000"],"publication_identifier":{"isbn":["9783030255398"],"issn":["0302-9743"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-05-16T11:22:30Z","alternative_title":["LNCS"],"external_id":{"isi":["000491468000036"]},"year":"2019","file":[{"file_name":"2019_CAV_Avni.pdf","date_updated":"2020-07-14T12:47:31Z","file_size":659766,"date_created":"2019-08-14T09:35:24Z","checksum":"c231579f2485c6fd4df17c9443a4d80b","relation":"main_file","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_id":"6816"}],"page":"630-649","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer","article_processing_charge":"No","quality_controlled":"1","project":[{"grant_number":"M02369","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","_id":"264B3912-B435-11E9-9278-68D0E5697425"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"oa":1,"volume":11561,"citation":{"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 31st International Conference on Computer-Aided Verification, 11561:630–49. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_36.","mla":"Avni, Guy, et al. “Run-Time Optimization for Learned Controllers through Quantitative Games.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 630–49, doi:10.1007/978-3-030-25540-4_36.","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.","ama":"Avni G, Bloem R, Chatterjee K, Henzinger TA, Konighofer B, Pranger S. Run-time optimization for learned controllers through quantitative games. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:630-649. doi:10.1007/978-3-030-25540-4_36","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.","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 31st International Conference on Computer-Aided Verification, New York, NY, United States, 2019, vol. 11561, pp. 630–649.","apa":"Avni, G., Bloem, R., Chatterjee, K., Henzinger, T. A., Konighofer, B., & Pranger, S. (2019). Run-time optimization for learned controllers through quantitative games. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 630–649). New York, NY, United States: Springer. https://doi.org/10.1007/978-3-030-25540-4_36"}},{"oa_version":"Published Version","doi":"10.1098/rsbl.2018.0881","publication_status":"published","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9799"},{"status":"public","relation":"research_data","id":"9798"}],"link":[{"url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008","relation":"supplementary_material"}]},"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","status":"public","month":"04","isi":1,"intvolume":" 15","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2018.0881"}],"author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John J.","full_name":"Welch, John J.","last_name":"Welch"}],"date_published":"2019-04-03T00:00:00Z","scopus_import":"1","ec_funded":1,"title":"The distribution of epistasis on simple fitness landscapes","date_updated":"2025-07-10T11:53:23Z","article_type":"original","day":"03","publication":"Biology Letters","_id":"6467","article_number":"0881","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Royal Society of London","article_processing_charge":"No","quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"issue":"4","volume":15,"oa":1,"citation":{"ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","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.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881."},"publication_identifier":{"issn":["1744-9561"],"eissn":["1744-957X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-05-19T21:59:15Z","external_id":{"pmid":["31014191"],"isi":["000465405300010"]},"pmid":1,"year":"2019"},{"intvolume":" 597","month":"06","isi":1,"status":"public","type":"journal_article","abstract":[{"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%. ","lang":"eng"}],"language":[{"iso":"eng"}],"publication_status":"published","doi":"10.1113/JP277681","oa_version":"Published Version","day":"01","article_type":"original","title":"Improved spike inference accuracy by estimating the peak amplitude of unitary [Ca2+] transients in weakly GCaMP6f-expressing hippocampal pyramidal cells","date_updated":"2025-07-10T11:53:24Z","scopus_import":"1","date_published":"2019-06-01T00:00:00Z","author":[{"last_name":"Éltes","full_name":"Éltes, Tímea","first_name":"Tímea"},{"full_name":"Szoboszlay, Miklos","first_name":"Miklos","last_name":"Szoboszlay"},{"id":"44F4BDC0-F248-11E8-B48F-1D18A9856A87","last_name":"Szigeti","full_name":"Szigeti, Margit Katalin","first_name":"Margit Katalin","orcid":"0000-0001-9500-8758"},{"first_name":"Zoltan","full_name":"Nusser, Zoltan","last_name":"Nusser"}],"main_file_link":[{"url":"https://doi.org/10.1113/JP277681","open_access":"1"}],"_id":"6470","publication":"Journal of Physiology","year":"2019","pmid":1,"external_id":{"pmid":["31006863"],"isi":["000470780400013"]},"date_created":"2019-05-19T21:59:17Z","publication_identifier":{"issn":["0022-3751"],"eissn":["1469-7793"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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. Journal of Physiology. 2019;597(11):2925–2947. doi:10.1113/JP277681","short":"T. Éltes, M. Szoboszlay, M.K. Szigeti, Z. Nusser, Journal of Physiology 597 (2019) 2925–2947.","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,” Journal of Physiology, vol. 597, no. 11. Wiley, pp. 2925–2947, 2019.","apa":"Éltes, T., Szoboszlay, M., Szigeti, M. K., & 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. Wiley. https://doi.org/10.1113/JP277681","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.” Journal of Physiology. Wiley, 2019. https://doi.org/10.1113/JP277681.","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.” Journal of Physiology, vol. 597, no. 11, Wiley, 2019, pp. 2925–2947, doi:10.1113/JP277681.","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."},"oa":1,"volume":597,"issue":"11","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"GaNo"}],"publisher":"Wiley","page":"2925–2947"},{"article_type":"original","title":"Colloquium: Many-body localization, thermalization, and entanglement","date_updated":"2023-08-25T10:37:56Z","day":"22","author":[{"first_name":"Dmitry A.","full_name":"Abanin, Dmitry A.","last_name":"Abanin"},{"last_name":"Altman","first_name":"Ehud","full_name":"Altman, Ehud"},{"first_name":"Immanuel","full_name":"Bloch, Immanuel","last_name":"Bloch"},{"first_name":"Maksym","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2019-05-22T00:00:00Z","file_date_updated":"2020-07-14T12:47:31Z","scopus_import":"1","has_accepted_license":"1","type":"journal_article","abstract":[{"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.","lang":"eng"}],"month":"05","isi":1,"status":"public","intvolume":" 91","doi":"10.1103/revmodphys.91.021001","oa_version":"Published Version","publication_status":"published","arxiv":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1539-0756"],"eissn":["0034-6861"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-05-23T07:38:43Z","external_id":{"isi":["000469046900001"],"arxiv":["1804.11065"]},"year":"2019","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","file":[{"file_name":"RevModPhys.91.021001.pdf","date_updated":"2020-07-14T12:47:31Z","file_size":1695677,"checksum":"4aec0e6662b09f6e0f828cd30ff2c3a6","date_created":"2019-05-23T07:39:05Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6478","creator":"mserbyn"}],"quality_controlled":"1","article_processing_charge":"No","issue":"2","citation":{"ista":"Abanin DA, Altman E, Bloch I, Serbyn M. 2019. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 91(2), 021001.","chicago":"Abanin, Dmitry A., Ehud Altman, Immanuel Bloch, and Maksym Serbyn. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics. American Physical Society, 2019. https://doi.org/10.1103/revmodphys.91.021001.","mla":"Abanin, Dmitry A., et al. “Colloquium: Many-Body Localization, Thermalization, and Entanglement.” Reviews of Modern Physics, vol. 91, no. 2, 021001, American Physical Society, 2019, doi:10.1103/revmodphys.91.021001.","ieee":"D. A. Abanin, E. Altman, I. Bloch, and M. Serbyn, “Colloquium: Many-body localization, thermalization, and entanglement,” Reviews of Modern Physics, vol. 91, no. 2. American Physical Society, 2019.","apa":"Abanin, D. A., Altman, E., Bloch, I., & Serbyn, M. (2019). Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. American Physical Society. https://doi.org/10.1103/revmodphys.91.021001","ama":"Abanin DA, Altman E, Bloch I, Serbyn M. Colloquium: Many-body localization, thermalization, and entanglement. Reviews of Modern Physics. 2019;91(2). doi:10.1103/revmodphys.91.021001","short":"D.A. Abanin, E. Altman, I. Bloch, M. Serbyn, Reviews of Modern Physics 91 (2019)."},"oa":1,"volume":91,"_id":"6477","article_number":"021001","publication":"Reviews of Modern Physics","ddc":["530"]},{"_id":"6482","conference":{"location":"Stuttgart, Germany","end_date":"2018-10-12","name":"GCPR: Conference on Pattern Recognition","start_date":"2018-10-09"},"date_created":"2019-05-24T09:48:36Z","alternative_title":["LNCS"],"publication_identifier":{"isbn":["9783030129385","9783030129392"],"eissn":["1611-3349"],"issn":["0302-9743"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2019","external_id":{"arxiv":["1804.04171"]},"quality_controlled":"1","article_processing_charge":"No","publisher":"Springer Nature","department":[{"_id":"ChLa"}],"page":"244-259","citation":{"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. https://doi.org/10.1007/978-3-030-12939-2_18.","mla":"Sun, Rémy, and Christoph Lampert. KS(Conf): A Light-Weight Test If a ConvNet Operates Outside of Its Specifications. Vol. 11269, Springer Nature, 2019, pp. 244–59, doi:10.1007/978-3-030-12939-2_18.","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.","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:10.1007/978-3-030-12939-2_18","short":"R. Sun, C. Lampert, in:, Springer Nature, 2019, pp. 244–259.","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., & 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. https://doi.org/10.1007/978-3-030-12939-2_18"},"oa":1,"volume":11269,"project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"6944"}]},"type":"conference","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"}],"intvolume":" 11269","month":"02","status":"public","publication_status":"published","doi":"10.1007/978-3-030-12939-2_18","oa_version":"Preprint","arxiv":1,"language":[{"iso":"eng"}],"title":"KS(conf): A light-weight test if a ConvNet operates outside of Its specifications","date_updated":"2025-04-15T07:10:25Z","day":"14","date_published":"2019-02-14T00:00:00Z","author":[{"last_name":"Sun","full_name":"Sun, Rémy","first_name":"Rémy"},{"last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph"}],"main_file_link":[{"url":"https://arxiv.org/abs/1804.04171","open_access":"1"}],"ec_funded":1,"scopus_import":"1"},{"language":[{"iso":"eng"}],"publication_status":"published","oa_version":"None","conference":{"start_date":"2019-02-16","location":"Washington, NY, United States","name":"PPoPP: Principles and Practice of Parallel Programming","end_date":"2019-02-20"},"publication":"Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming","doi":"10.1145/3293883.3297000","status":"public","isi":1,"month":"02","_id":"6485","abstract":[{"lang":"eng","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."}],"type":"conference_poster","citation":{"ama":"Koval N, Alistarh D-A, Elizarov R. Lock-Free Channels for Programming via Communicating Sequential Processes. ACM; 2019:417-418. doi:10.1145/3293883.3297000","short":"N. Koval, D.-A. Alistarh, R. Elizarov, Lock-Free Channels for Programming via Communicating Sequential Processes, ACM, 2019.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2019). Lock-free channels for programming via communicating sequential processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming (pp. 417–418). Washington, NY, United States: ACM. https://doi.org/10.1145/3293883.3297000","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, Lock-free channels for programming via communicating sequential processes. ACM, 2019, pp. 417–418.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. Lock-Free Channels for Programming via Communicating Sequential Processes. Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming. ACM, 2019. https://doi.org/10.1145/3293883.3297000.","mla":"Koval, Nikita, et al. “Lock-Free Channels for Programming via Communicating Sequential Processes.” Proceedings of the 24th Symposium on Principles and Practice of Parallel Programming, ACM, 2019, pp. 417–18, doi:10.1145/3293883.3297000.","ista":"Koval N, Alistarh D-A, Elizarov R. 2019. Lock-free channels for programming via communicating sequential processes, ACM,p."},"article_processing_charge":"No","date_published":"2019-02-01T00:00:00Z","quality_controlled":"1","publisher":"ACM","page":"417-418","department":[{"_id":"DaAl"}],"author":[{"last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","full_name":"Koval, Nikita","first_name":"Nikita"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Elizarov","full_name":"Elizarov, Roman","first_name":"Roman"}],"year":"2019","external_id":{"isi":["000587604600044"]},"day":"01","date_updated":"2024-12-11T11:42:22Z","title":"Lock-free channels for programming via communicating sequential processes","date_created":"2019-05-24T10:09:12Z","publication_identifier":{"isbn":["9781450362252"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"isi":1,"month":"07","status":"public","keyword":["Synthesis","Linear hybrid automaton","Membership"],"intvolume":" 11561","abstract":[{"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.","lang":"eng"}],"type":"conference","language":[{"iso":"eng"}],"doi":"10.1007/978-3-030-25540-4_16","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","publication_status":"published","day":"12","date_updated":"2025-04-15T06:26:13Z","title":"Membership-based synthesis of linear hybrid automata","scopus_import":"1","ec_funded":1,"has_accepted_license":"1","author":[{"last_name":"Garcia Soto","id":"4B3207F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0003−2936−5719","full_name":"Garcia Soto, Miriam","first_name":"Miriam"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Schilling","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3658-1065","full_name":"Schilling, Christian","first_name":"Christian"},{"first_name":"Luka","full_name":"Zeleznik, Luka","id":"3ADCA2E4-F248-11E8-B48F-1D18A9856A87","last_name":"Zeleznik"}],"date_published":"2019-07-12T00:00:00Z","file_date_updated":"2020-07-14T12:47:32Z","_id":"6493","ddc":["000"],"publication":"31st International Conference on Computer-Aided Verification","conference":{"start_date":"2019-07-15","name":"CAV: Computer-Aided Verification","end_date":"2019-07-18","location":"New York City, NY, USA"},"corr_author":"1","external_id":{"isi":["000491468000016"]},"year":"2019","publication_identifier":{"issn":["0302-9743"],"isbn":["9783030255398"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-05-27T07:09:53Z","alternative_title":["LNCS"],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems"}],"citation":{"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.” 31st International Conference on Computer-Aided Verification, vol. 11561, Springer, 2019, pp. 297–314, doi:10.1007/978-3-030-25540-4_16.","chicago":"Garcia Soto, Miriam, Thomas A Henzinger, Christian Schilling, and Luka Zeleznik. “Membership-Based Synthesis of Linear Hybrid Automata.” In 31st International Conference on Computer-Aided Verification, 11561:297–314. Springer, 2019. https://doi.org/10.1007/978-3-030-25540-4_16.","apa":"Garcia Soto, M., Henzinger, T. A., Schilling, C., & Zeleznik, L. (2019). Membership-based synthesis of linear hybrid automata. In 31st International Conference on Computer-Aided Verification (Vol. 11561, pp. 297–314). New York City, NY, USA: Springer. https://doi.org/10.1007/978-3-030-25540-4_16","ieee":"M. Garcia Soto, T. A. Henzinger, C. Schilling, and L. Zeleznik, “Membership-based synthesis of linear hybrid automata,” in 31st International Conference on Computer-Aided Verification, New York City, NY, USA, 2019, vol. 11561, pp. 297–314.","ama":"Garcia Soto M, Henzinger TA, Schilling C, Zeleznik L. Membership-based synthesis of linear hybrid automata. In: 31st International Conference on Computer-Aided Verification. Vol 11561. Springer; 2019:297-314. doi:10.1007/978-3-030-25540-4_16","short":"M. Garcia Soto, T.A. Henzinger, C. Schilling, L. Zeleznik, in:, 31st International Conference on Computer-Aided Verification, Springer, 2019, pp. 297–314."},"oa":1,"volume":11561,"file":[{"relation":"main_file","creator":"dernst","file_id":"6817","content_type":"application/pdf","access_level":"open_access","file_name":"2019_CAV_GarciaSoto.pdf","checksum":"1f1d61b83a151031745ef70a501da3d6","date_created":"2019-08-14T11:05:30Z","file_size":674795,"date_updated":"2020-07-14T12:47:32Z"}],"page":"297-314","publisher":"Springer","department":[{"_id":"ToHe"}],"quality_controlled":"1","article_processing_charge":"No"},{"intvolume":" 266","status":"public","month":"03","isi":1,"type":"journal_article","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"arxiv":1,"publist_id":"7989","publication_status":"published","oa_version":"Preprint","doi":"10.1016/j.jde.2018.09.012","day":"05","date_updated":"2025-04-22T13:48:09Z","title":"Entropy solutions for stochastic porous media equations","article_type":"original","scopus_import":"1","date_published":"2019-03-05T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1803.06953"}],"author":[{"full_name":"Dareiotis, Konstantinos","first_name":"Konstantinos","last_name":"Dareiotis"},{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Gerencser","full_name":"Gerencser, Mate","first_name":"Mate"},{"last_name":"Gess","first_name":"Benjamin","full_name":"Gess, Benjamin"}],"_id":"65","publication":"Journal of Differential Equations","year":"2019","external_id":{"isi":["000456332500026"],"arxiv":["1803.06953"]},"date_created":"2018-12-11T11:44:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"volume":266,"citation":{"mla":"Dareiotis, Konstantinos, et al. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations, vol. 266, no. 6, Elsevier, 2019, pp. 3732–63, doi:10.1016/j.jde.2018.09.012.","chicago":"Dareiotis, Konstantinos, Mate Gerencser, and Benjamin Gess. “Entropy Solutions for Stochastic Porous Media Equations.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.09.012.","ista":"Dareiotis K, Gerencser M, Gess B. 2019. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 266(6), 3732–3763.","short":"K. Dareiotis, M. Gerencser, B. Gess, Journal of Differential Equations 266 (2019) 3732–3763.","ama":"Dareiotis K, Gerencser M, Gess B. Entropy solutions for stochastic porous media equations. Journal of Differential Equations. 2019;266(6):3732-3763. doi:10.1016/j.jde.2018.09.012","apa":"Dareiotis, K., Gerencser, M., & Gess, B. (2019). Entropy solutions for stochastic porous media equations. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.09.012","ieee":"K. Dareiotis, M. Gerencser, and B. Gess, “Entropy solutions for stochastic porous media equations,” Journal of Differential Equations, vol. 266, no. 6. Elsevier, pp. 3732–3763, 2019."},"issue":"6","article_processing_charge":"No","quality_controlled":"1","department":[{"_id":"JaMa"}],"publisher":"Elsevier","page":"3732-3763"},{"_id":"6504","publication":"New Phytologist","ddc":["580"],"publication_identifier":{"issn":["0028-646x"],"eissn":["1469-8137"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2019-05-28T14:33:26Z","pmid":1,"external_id":{"pmid":["31111487"],"isi":["000487184200024"]},"year":"2019","department":[{"_id":"JiFr"}],"publisher":"Wiley","file":[{"checksum":"6488243334538f5c39099a701cbf76b9","date_created":"2020-10-14T08:59:33Z","date_updated":"2020-10-14T08:59:33Z","file_size":1099061,"success":1,"file_name":"2019_NewPhytologist_Zhang_accepted.pdf","file_id":"8661","access_level":"open_access","content_type":"application/pdf","creator":"dernst","relation":"main_file"}],"page":"761-774","quality_controlled":"1","article_processing_charge":"No","issue":"2","citation":{"ieee":"Y. Zhang et al., “Auxin-mediated statolith production for root gravitropism,” New Phytologist, 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. New Phytologist. Wiley. https://doi.org/10.1111/nph.15932","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.","ama":"Zhang Y, He P, Ma X, et al. Auxin-mediated statolith production for root gravitropism. New Phytologist. 2019;224(2):761-774. doi:10.1111/nph.15932","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.","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.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.15932.","mla":"Zhang, Yuzhou, et al. “Auxin-Mediated Statolith Production for Root Gravitropism.” New Phytologist, vol. 224, no. 2, Wiley, 2019, pp. 761–74, doi:10.1111/nph.15932."},"volume":224,"oa":1,"type":"journal_article","abstract":[{"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.","lang":"eng"}],"month":"10","isi":1,"status":"public","intvolume":" 224","doi":"10.1111/nph.15932","oa_version":"Submitted Version","publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","title":"Auxin-mediated statolith production for root gravitropism","date_updated":"2023-08-28T08:40:13Z","day":"01","author":[{"orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"He","first_name":"P","full_name":"He, P"},{"last_name":"Ma","first_name":"X","full_name":"Ma, X"},{"full_name":"Yang, Z","first_name":"Z","last_name":"Yang"},{"last_name":"Pang","full_name":"Pang, C","first_name":"C"},{"full_name":"Yu, J","first_name":"J","last_name":"Yu"},{"last_name":"Wang","first_name":"G","full_name":"Wang, G"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří"},{"last_name":"Xiao","first_name":"G","full_name":"Xiao, G"}],"date_published":"2019-10-01T00:00:00Z","file_date_updated":"2020-10-14T08:59:33Z","scopus_import":"1","has_accepted_license":"1"},{"publication":"Nature Microbiology","_id":"6506","article_processing_charge":"No","quality_controlled":"1","page":"1221–1230","publisher":"Springer Nature","department":[{"_id":"FyKo"}],"oa":1,"volume":4,"citation":{"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.","mla":"Noda-García, Lianet, et al. “Chance and Pleiotropy Dominate Genetic Diversity in Complex Bacterial Environments.” Nature Microbiology, vol. 4, no. 7, Springer Nature, 2019, pp. 1221–1230, doi:10.1038/s41564-019-0412-y.","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.” Nature Microbiology. Springer Nature, 2019. https://doi.org/10.1038/s41564-019-0412-y.","apa":"Noda-García, L., Davidi, D., Korenblum, E., Elazar, A., Putintseva, E., Aharoni, A., & Tawfik, D. S. (2019). Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-019-0412-y","ieee":"L. Noda-García et al., “Chance and pleiotropy dominate genetic diversity in complex bacterial environments,” Nature Microbiology, 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. Nature Microbiology. 2019;4(7):1221–1230. doi:10.1038/s41564-019-0412-y","short":"L. Noda-García, D. Davidi, E. Korenblum, A. Elazar, E. Putintseva, A. Aharoni, D.S. Tawfik, Nature Microbiology 4 (2019) 1221–1230."},"issue":"7","date_created":"2019-05-29T13:03:30Z","publication_identifier":{"issn":["2058-5276"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2019","external_id":{"isi":["000480348200017"]},"publication_status":"published","oa_version":"Preprint","doi":"10.1038/s41564-019-0412-y","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"type":"journal_article","intvolume":" 4","status":"public","month":"07","isi":1,"date_published":"2019-07-01T00:00:00Z","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/340828v2","open_access":"1"}],"author":[{"last_name":"Noda-García","full_name":"Noda-García, Lianet","first_name":"Lianet"},{"last_name":"Davidi","first_name":"Dan","full_name":"Davidi, Dan"},{"first_name":"Elisa","full_name":"Korenblum, Elisa","last_name":"Korenblum"},{"full_name":"Elazar, Assaf","first_name":"Assaf","last_name":"Elazar"},{"id":"2EF67C84-F248-11E8-B48F-1D18A9856A87","last_name":"Putintseva","full_name":"Putintseva, Ekaterina","first_name":"Ekaterina"},{"last_name":"Aharoni","first_name":"Asaph","full_name":"Aharoni, Asaph"},{"full_name":"Tawfik, Dan S.","first_name":"Dan S.","last_name":"Tawfik"}],"scopus_import":"1","title":"Chance and pleiotropy dominate genetic diversity in complex bacterial environments","date_updated":"2023-08-28T08:39:47Z","article_type":"original","day":"01"},{"day":"01","title":"Local single ring theorem on optimal scale","date_updated":"2025-07-10T11:53:28Z","ec_funded":1,"scopus_import":"1","date_published":"2019-05-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.05920"}],"author":[{"last_name":"Bao","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475"},{"last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","full_name":"Erdös, László"},{"id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","last_name":"Schnelli","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","first_name":"Kevin"}],"intvolume":" 47","status":"public","isi":1,"month":"05","type":"journal_article","abstract":[{"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).","lang":"eng"}],"language":[{"iso":"eng"}],"arxiv":1,"publication_status":"published","oa_version":"Preprint","doi":"10.1214/18-AOP1284","year":"2019","external_id":{"arxiv":["1612.05920"],"isi":["000466616100003"]},"date_created":"2019-06-02T21:59:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0091-1798"]},"oa":1,"volume":47,"citation":{"apa":"Bao, Z., Erdös, L., & Schnelli, K. (2019). Local single ring theorem on optimal scale. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AOP1284","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local single ring theorem on optimal scale,” Annals of Probability, vol. 47, no. 3. Institute of Mathematical Statistics, pp. 1270–1334, 2019.","ama":"Bao Z, Erdös L, Schnelli K. Local single ring theorem on optimal scale. Annals of Probability. 2019;47(3):1270-1334. doi:10.1214/18-AOP1284","short":"Z. Bao, L. Erdös, K. Schnelli, Annals of Probability 47 (2019) 1270–1334.","ista":"Bao Z, Erdös L, Schnelli K. 2019. Local single ring theorem on optimal scale. Annals of Probability. 47(3), 1270–1334.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AOP1284.","mla":"Bao, Zhigang, et al. “Local Single Ring Theorem on Optimal Scale.” Annals of Probability, vol. 47, no. 3, Institute of Mathematical Statistics, 2019, pp. 1270–334, doi:10.1214/18-AOP1284."},"project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"issue":"3","article_processing_charge":"No","quality_controlled":"1","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"page":"1270-1334","_id":"6511","publication":"Annals of Probability"},{"oa":1,"volume":570,"citation":{"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.","mla":"Guiu, Jordi, et al. “Tracing the Origin of Adult Intestinal Stem Cells.” Nature, vol. 570, Springer Nature, 2019, pp. 107–11, doi:10.1038/s41586-019-1212-5.","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.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1212-5.","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. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1212-5","ieee":"J. Guiu et al., “Tracing the origin of adult intestinal stem cells,” Nature, vol. 570. Springer Nature, pp. 107–111, 2019.","ama":"Guiu J, Hannezo EB, Yui S, et al. Tracing the origin of adult intestinal stem cells. Nature. 2019;570:107-111. doi:10.1038/s41586-019-1212-5","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."},"department":[{"_id":"EdHa"}],"page":"107-111","publisher":"Springer Nature","article_processing_charge":"No","quality_controlled":"1","external_id":{"pmid":["31092921"],"isi":["000470149000048"]},"pmid":1,"year":"2019","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-06-02T21:59:14Z","publication":"Nature","_id":"6513","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986928"}],"author":[{"first_name":"Jordi","full_name":"Guiu, Jordi","last_name":"Guiu"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Yui","first_name":"Shiro","full_name":"Yui, Shiro"},{"full_name":"Demharter, Samuel","first_name":"Samuel","last_name":"Demharter"},{"last_name":"Ulyanchenko","first_name":"Svetlana","full_name":"Ulyanchenko, Svetlana"},{"last_name":"Maimets","full_name":"Maimets, Martti","first_name":"Martti"},{"last_name":"Jørgensen","full_name":"Jørgensen, Anne","first_name":"Anne"},{"full_name":"Perlman, Signe","first_name":"Signe","last_name":"Perlman"},{"last_name":"Lundvall","first_name":"Lene","full_name":"Lundvall, Lene"},{"full_name":"Mamsen, Linn Salto","first_name":"Linn Salto","last_name":"Mamsen"},{"first_name":"Agnete","full_name":"Larsen, Agnete","last_name":"Larsen"},{"last_name":"Olesen","full_name":"Olesen, Rasmus H.","first_name":"Rasmus H."},{"last_name":"Andersen","full_name":"Andersen, Claus Yding","first_name":"Claus Yding"},{"full_name":"Thuesen, Lea Langhoff","first_name":"Lea Langhoff","last_name":"Thuesen"},{"first_name":"Kristine Juul","full_name":"Hare, Kristine Juul","last_name":"Hare"},{"last_name":"Pers","full_name":"Pers, Tune H.","first_name":"Tune H."},{"first_name":"Konstantin","full_name":"Khodosevich, Konstantin","last_name":"Khodosevich"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"full_name":"Jensen, Kim B.","first_name":"Kim B.","last_name":"Jensen"}],"date_published":"2019-06-06T00:00:00Z","day":"06","title":"Tracing the origin of adult intestinal stem cells","date_updated":"2025-07-10T11:53:29Z","article_type":"original","language":[{"iso":"eng"}],"oa_version":"Submitted Version","doi":"10.1038/s41586-019-1212-5","publication_status":"published","status":"public","month":"06","isi":1,"intvolume":" 570","type":"journal_article","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"}]}]