[{"publication_status":"draft","publisher":"ArXiv","main_file_link":[{"url":"https://arxiv.org/abs/1910.03372","open_access":"1"}],"oa":1,"department":[{"_id":"RoSe"}],"publication":"arXiv:1910.03372","status":"public","page":"61","article_processing_charge":"No","month":"10","_id":"7524","date_published":"2019-10-08T00:00:00Z","date_created":"2020-02-26T08:46:40Z","abstract":[{"lang":"eng","text":"We prove a lower bound for the free energy (per unit volume) of the two-dimensional Bose gas in the thermodynamic limit. We show that the free energy at density $\\rho$ and inverse temperature $\\beta$ differs from the one of the non-interacting system by the correction term $4 \\pi \\rho^2 |\\ln a^2 \\rho|^{-1} (2 - [1 - \\beta_{\\mathrm{c}}/\\beta]_+^2)$. Here $a$ is the scattering length of the interaction potential, $[\\cdot]_+ = \\max\\{ 0, \\cdot \\}$ and $\\beta_{\\mathrm{c}}$ is the inverse Berezinskii--Kosterlitz--Thouless critical temperature for superfluidity. The result is valid in the dilute limit\r\n$a^2\\rho \\ll 1$ and if $\\beta \\rho \\gtrsim 1$."}],"project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"status":"public","id":"7790","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"7514"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T13:12:41Z","language":[{"iso":"eng"}],"scopus_import":1,"ec_funded":1,"citation":{"short":"A. Deuchert, S. Mayer, R. Seiringer, ArXiv:1910.03372 (n.d.).","apa":"Deuchert, A., Mayer, S., &#38; Seiringer, R. (n.d.). The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv:1910.03372</i>. ArXiv.","ama":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. <i>arXiv:191003372</i>.","ieee":"A. Deuchert, S. Mayer, and R. Seiringer, “The free energy of the two-dimensional dilute Bose gas. I. Lower bound,” <i>arXiv:1910.03372</i>. ArXiv.","ista":"Deuchert A, Mayer S, Seiringer R. The free energy of the two-dimensional dilute Bose gas. I. Lower bound. arXiv:1910.03372, .","chicago":"Deuchert, Andreas, Simon Mayer, and Robert Seiringer. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv:1910.03372</i>. ArXiv, n.d.","mla":"Deuchert, Andreas, et al. “The Free Energy of the Two-Dimensional Dilute Bose Gas. I. Lower Bound.” <i>ArXiv:1910.03372</i>, ArXiv."},"title":"The free energy of the two-dimensional dilute Bose gas. I. Lower bound","day":"08","year":"2019","oa_version":"Preprint","type":"preprint","author":[{"full_name":"Deuchert, Andreas","first_name":"Andreas","last_name":"Deuchert","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3146-6746"},{"id":"30C4630A-F248-11E8-B48F-1D18A9856A87","last_name":"Mayer","full_name":"Mayer, Simon","first_name":"Simon"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert"}]},{"citation":{"apa":"Wendler, C., Alistarh, D.-A., &#38; Püschel, M. (2019). Powerset convolutional neural networks (Vol. 32, pp. 927–938). Presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada: Neural Information Processing Systems Foundation.","ama":"Wendler C, Alistarh D-A, Püschel M. Powerset convolutional neural networks. In: Vol 32. Neural Information Processing Systems Foundation; 2019:927-938.","short":"C. Wendler, D.-A. Alistarh, M. Püschel, in:, Neural Information Processing Systems Foundation, 2019, pp. 927–938.","mla":"Wendler, Chris, et al. <i>Powerset Convolutional Neural Networks</i>. Vol. 32, Neural Information Processing Systems Foundation, 2019, pp. 927–38.","ieee":"C. Wendler, D.-A. Alistarh, and M. Püschel, “Powerset convolutional neural networks,” presented at the NIPS: Conference on Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 927–938.","ista":"Wendler C, Alistarh D-A, Püschel M. 2019. Powerset convolutional neural networks. NIPS: Conference on Neural Information Processing Systems vol. 32, 927–938.","chicago":"Wendler, Chris, Dan-Adrian Alistarh, and Markus Püschel. “Powerset Convolutional Neural Networks,” 32:927–38. Neural Information Processing Systems Foundation, 2019."},"ec_funded":1,"title":"Powerset convolutional neural networks","conference":{"start_date":"2019-12-08","end_date":"2019-12-14","name":"NIPS: Conference on Neural Information Processing Systems","location":"Vancouver, Canada"},"day":"01","type":"conference","author":[{"last_name":"Wendler","full_name":"Wendler, Chris","first_name":"Chris"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"last_name":"Püschel","full_name":"Püschel, Markus","first_name":"Markus"}],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}],"language":[{"iso":"eng"}],"page":"927-938","month":"12","date_created":"2020-02-28T10:03:24Z","publisher":"Neural Information Processing Systems Foundation","isi":1,"department":[{"_id":"DaAl"}],"quality_controlled":"1","intvolume":"        32","status":"public","year":"2019","oa_version":"Published Version","external_id":{"isi":["000534424300084"],"arxiv":["1909.02253"]},"date_updated":"2023-09-08T11:13:52Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["1049-5258"]},"arxiv":1,"article_processing_charge":"No","_id":"7542","abstract":[{"text":"We present a novel class of convolutional neural networks (CNNs) for set functions,i.e., data indexed with the powerset of a finite set. The convolutions are derivedas linear, shift-equivariant functions for various notions of shifts on set functions.The framework is fundamentally different from graph convolutions based on theLaplacian, as it provides not one but several basic shifts, one for each element inthe ground set. Prototypical experiments with several set function classificationtasks on synthetic datasets and on datasets derived from real-world hypergraphsdemonstrate the potential of our new powerset CNNs.","lang":"eng"}],"date_published":"2019-12-01T00:00:00Z","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"http://papers.nips.cc/paper/8379-powerset-convolutional-neural-networks"}],"volume":32},{"oa_version":"Published Version","year":"2019","article_type":"original","publication_identifier":{"issn":["2160-1836"]},"external_id":{"pmid":["31519744"]},"date_updated":"2021-01-12T08:14:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7547","date_published":"2019-11-01T00:00:00Z","abstract":[{"text":"The BH3-only family of proteins is key for initiating apoptosis in a variety of contexts, and may also contribute to non-apoptotic cellular processes. Historically, the nematode Caenorhabditis elegans has provided a powerful system for studying and identifying conserved regulators of BH3-only proteins. In C. elegans, the BH3-only protein egl-1 is expressed during development to cell-autonomously trigger most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed after development in the sensory neuron pair URX without inducing apoptosis. We used genetic screening and epistasis analysis to determine that its transcription is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family proteins are also expressed in the adult nervous system of mammals, we suggest that studying egl-1 expression in URX may shed light on mechanisms that regulate conserved family members in higher organisms.","lang":"eng"}],"article_processing_charge":"No","issue":"11","volume":9,"publication_status":"published","author":[{"last_name":"Cohn","full_name":"Cohn, Jesse","first_name":"Jesse"},{"first_name":"Vivek","full_name":"Dwivedi, Vivek","last_name":"Dwivedi"},{"first_name":"Giulio","full_name":"Valperga, Giulio","last_name":"Valperga"},{"full_name":"Zarate, Nicole","first_name":"Nicole","last_name":"Zarate"},{"orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","full_name":"de Bono, Mario","first_name":"Mario"},{"full_name":"Horvitz, H. Robert","first_name":"H. Robert","last_name":"Horvitz"},{"first_name":"Jonathan T.","full_name":"Pierce, Jonathan T.","last_name":"Pierce"}],"type":"journal_article","day":"01","title":"Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans","citation":{"ista":"Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT. 2019. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. 9(11), 3703–3714.","ieee":"J. Cohn <i>et al.</i>, “Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans,” <i>G3: Genes, Genomes, Genetics</i>, vol. 9, no. 11. Genetics Society of America, pp. 3703–3714, 2019.","chicago":"Cohn, Jesse, Vivek Dwivedi, Giulio Valperga, Nicole Zarate, Mario de Bono, H. Robert Horvitz, and Jonathan T. Pierce. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America, 2019. <a href=\"https://doi.org/10.1534/g3.119.400654\">https://doi.org/10.1534/g3.119.400654</a>.","mla":"Cohn, Jesse, et al. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” <i>G3: Genes, Genomes, Genetics</i>, vol. 9, no. 11, Genetics Society of America, 2019, pp. 3703–14, doi:<a href=\"https://doi.org/10.1534/g3.119.400654\">10.1534/g3.119.400654</a>.","short":"J. Cohn, V. Dwivedi, G. Valperga, N. Zarate, M. de Bono, H.R. Horvitz, J.T. Pierce, G3: Genes, Genomes, Genetics 9 (2019) 3703–3714.","apa":"Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H. R., &#38; Pierce, J. T. (2019). Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. <i>G3: Genes, Genomes, Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/g3.119.400654\">https://doi.org/10.1534/g3.119.400654</a>","ama":"Cohn J, Dwivedi V, Valperga G, et al. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. <i>G3: Genes, Genomes, Genetics</i>. 2019;9(11):3703-3714. doi:<a href=\"https://doi.org/10.1534/g3.119.400654\">10.1534/g3.119.400654</a>"},"doi":"10.1534/g3.119.400654","language":[{"iso":"eng"}],"pmid":1,"date_created":"2020-02-28T10:44:27Z","month":"11","extern":"1","page":"3703-3714","status":"public","intvolume":"         9","publication":"G3: Genes, Genomes, Genetics","quality_controlled":"1","publisher":"Genetics Society of America"},{"publication_status":"published","publisher":"Public Library of Science","volume":14,"status":"public","intvolume":"        14","quality_controlled":"1","publication":"PLOS ONE","issue":"5","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils is a well-established hallmark of Alzheimer’s disease, the complex mechanisms linking this process to neurodegeneration are still incompletely understood. The nematode worm C. elegans is a valuable model organism through which to study these mechanisms because of its simple nervous system and its relatively short lifespan. Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study the toxic effects of the overexpression of Aβ in the muscle or nervous systems. However, the wide variety of effects associated with the tissue-level overexpression of Aβ makes it difficult to single out and study specific cellular mechanisms related to the onset of Alzheimer’s disease. Here, to better understand how to investigate the early events affecting neuronal signalling, we created a C. elegans model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural assays, we found that the Aβ42-expressing animals displayed a subtle modulation of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG neurons in young Aβ42-expressing nematodes were activated more strongly than in control animals, and that neuronal activation remained intact until old age. Taken together, our results suggest that Aβ42-expression in this very subtle model of AD is sufficient to modulate the behavioural response but not strong enough to generate significant neurotoxicity, suggesting that slightly more aggressive perturbations will enable effectively studies of the links between the modulation of a physiological response and its associated neurotoxicity."}],"_id":"7548","date_created":"2020-02-28T10:45:13Z","date_published":"2019-05-31T00:00:00Z","article_number":"e0217746","extern":"1","month":"05","doi":"10.1371/journal.pone.0217746","publication_identifier":{"issn":["1932-6203"]},"language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:14:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response","citation":{"ista":"Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. 2019. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. 14(5), e0217746.","ieee":"T. Sinnige, P. Ciryam, S. Casford, C. M. Dobson, M. de Bono, and M. Vendruscolo, “Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response,” <i>PLOS ONE</i>, vol. 14, no. 5. Public Library of Science, 2019.","chicago":"Sinnige, Tessa, Prashanth Ciryam, Samuel Casford, Christopher M. Dobson, Mario de Bono, and Michele Vendruscolo. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” <i>PLOS ONE</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pone.0217746\">https://doi.org/10.1371/journal.pone.0217746</a>.","mla":"Sinnige, Tessa, et al. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” <i>PLOS ONE</i>, vol. 14, no. 5, e0217746, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pone.0217746\">10.1371/journal.pone.0217746</a>.","short":"T. Sinnige, P. Ciryam, S. Casford, C.M. Dobson, M. de Bono, M. Vendruscolo, PLOS ONE 14 (2019).","apa":"Sinnige, T., Ciryam, P., Casford, S., Dobson, C. M., de Bono, M., &#38; Vendruscolo, M. (2019). Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. <i>PLOS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0217746\">https://doi.org/10.1371/journal.pone.0217746</a>","ama":"Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. <i>PLOS ONE</i>. 2019;14(5). doi:<a href=\"https://doi.org/10.1371/journal.pone.0217746\">10.1371/journal.pone.0217746</a>"},"oa_version":"Published Version","year":"2019","type":"journal_article","author":[{"last_name":"Sinnige","first_name":"Tessa","full_name":"Sinnige, Tessa"},{"first_name":"Prashanth","full_name":"Ciryam, Prashanth","last_name":"Ciryam"},{"first_name":"Samuel","full_name":"Casford, Samuel","last_name":"Casford"},{"last_name":"Dobson","full_name":"Dobson, Christopher M.","first_name":"Christopher M."},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","first_name":"Mario","full_name":"de Bono, Mario","last_name":"de Bono"},{"last_name":"Vendruscolo","first_name":"Michele","full_name":"Vendruscolo, Michele"}],"day":"31","article_type":"original"},{"date_updated":"2022-06-17T07:52:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1910.10050"]},"publication_identifier":{"issn":["1343-4373"]},"article_type":"original","year":"2019","oa_version":"Preprint","volume":28,"publication_status":"published","oa":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1910.10050","open_access":"1"}],"_id":"7550","abstract":[{"lang":"eng","text":"We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. "}],"date_published":"2019-10-22T00:00:00Z","arxiv":1,"issue":"2","article_processing_charge":"No","language":[{"iso":"eng"}],"acknowledgement":"This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375.","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"day":"22","type":"journal_article","author":[{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","full_name":"Portinale, Lorenzo","first_name":"Lorenzo"},{"last_name":"Stefanelli","full_name":"Stefanelli, Ulisse","first_name":"Ulisse"}],"citation":{"mla":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical Sciences and Applications</i>, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47.","ieee":"L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” <i>Advances in Mathematical Sciences and Applications</i>, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019.","ista":"Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447.","chicago":"Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” <i>Advances in Mathematical Sciences and Applications</i>. Gakko Tosho, 2019.","apa":"Portinale, L., &#38; Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>. Gakko Tosho.","ama":"Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. <i>Advances in Mathematical Sciences and Applications</i>. 2019;28(2):425-447.","short":"L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447."},"title":"Penalization via global functionals of optimal-control problems for dissipative evolution","quality_controlled":"1","department":[{"_id":"JaMa"}],"publication":"Advances in Mathematical Sciences and Applications","status":"public","intvolume":"        28","publisher":"Gakko Tosho","month":"10","date_created":"2020-02-28T10:54:41Z","page":"425-447"},{"arxiv":1,"page":"5","article_processing_charge":"No","month":"12","date_published":"2019-12-18T00:00:00Z","_id":"7552","date_created":"2020-02-28T10:57:08Z","abstract":[{"lang":"eng","text":"There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. "}],"publication_status":"submitted","publisher":"ArXiv","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.08579"}],"publication":"arXiv:1912.08579","department":[{"_id":"GaTk"}],"status":"public","citation":{"short":"W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.).","ama":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. <i>arXiv:191208579</i>.","apa":"Bialek, W., Gregor, T., &#38; Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. <i>arXiv:1912.08579</i>. ArXiv.","chicago":"Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv:1912.08579</i>. ArXiv, n.d.","ista":"Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, .","ieee":"W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” <i>arXiv:1912.08579</i>. ArXiv.","mla":"Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” <i>ArXiv:1912.08579</i>, ArXiv."},"title":"Action at a distance in transcriptional regulation","day":"18","type":"preprint","author":[{"last_name":"Bialek","full_name":"Bialek, William","first_name":"William"},{"last_name":"Gregor","full_name":"Gregor, Thomas","first_name":"Thomas"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"oa_version":"Preprint","year":"2019","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"external_id":{"arxiv":["1912.08579"]},"date_updated":"2021-01-12T08:14:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}]},{"publisher":"EasyChair Publications","publication":"EPiC Series in Computing","department":[{"_id":"ToHe"}],"quality_controlled":"1","status":"public","intvolume":"        61","page":"41-61","month":"05","date_created":"2020-03-08T23:00:49Z","language":[{"iso":"eng"}],"ddc":["000"],"doi":"10.29007/m75b","citation":{"short":"F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61.","ama":"Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: <i>EPiC Series in Computing</i>. Vol 61. EasyChair Publications; 2019:41-61. doi:<a href=\"https://doi.org/10.29007/m75b\">10.29007/m75b</a>","apa":"Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In <i>EPiC Series in Computing</i> (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. <a href=\"https://doi.org/10.29007/m75b\">https://doi.org/10.29007/m75b</a>","chicago":"Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In <i>EPiC Series in Computing</i>, 61:41–61. EasyChair Publications, 2019. <a href=\"https://doi.org/10.29007/m75b\">https://doi.org/10.29007/m75b</a>.","ieee":"F. Immler <i>et al.</i>, “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in <i>EPiC Series in Computing</i>, Montreal, Canada, 2019, vol. 61, pp. 41–61.","ista":"Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.","mla":"Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” <i>EPiC Series in Computing</i>, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:<a href=\"https://doi.org/10.29007/m75b\">10.29007/m75b</a>."},"title":"ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics","conference":{"location":"Montreal, Canada","name":"ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems","start_date":"2019-04-15","end_date":"2019-04-15"},"day":"25","author":[{"last_name":"Immler","first_name":"Fabian","full_name":"Immler, Fabian"},{"first_name":"Matthias","full_name":"Althoff, Matthias","last_name":"Althoff"},{"full_name":"Benet, Luis","first_name":"Luis","last_name":"Benet"},{"first_name":"Alexandre","full_name":"Chapoutot, Alexandre","last_name":"Chapoutot"},{"last_name":"Chen","full_name":"Chen, Xin","first_name":"Xin"},{"last_name":"Forets","first_name":"Marcelo","full_name":"Forets, Marcelo"},{"last_name":"Geretti","full_name":"Geretti, Luca","first_name":"Luca"},{"full_name":"Kochdumper, Niklas","first_name":"Niklas","last_name":"Kochdumper"},{"full_name":"Sanders, David P.","first_name":"David P.","last_name":"Sanders"},{"first_name":"Christian","full_name":"Schilling, Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"}],"type":"conference","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:48:00Z","volume":61,"article_processing_charge":"No","file":[{"checksum":"9138977a06fcd6a95976eb4bca875f0c","access_level":"open_access","date_updated":"2020-07-14T12:48:00Z","creator":"dernst","file_size":1934830,"file_name":"2019_ARCH19_Immler.pdf","date_created":"2020-03-24T07:36:36Z","file_id":"7617","relation":"main_file","content_type":"application/pdf"}],"_id":"7576","date_published":"2019-05-25T00:00:00Z","abstract":[{"text":"We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools.","lang":"eng"}],"scopus_import":1,"date_updated":"2021-01-12T08:14:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["23987340"]},"has_accepted_license":"1","year":"2019","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"doi":"10.1109/ITW44776.2019.8989292","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"15020","status":"public"}]},"day":"01","type":"conference","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","full_name":"Hledik, Michal","first_name":"Michal"},{"first_name":"Thomas R","full_name":"Sokolowski, Thomas R","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"citation":{"ieee":"M. Hledik, T. R. Sokolowski, and G. Tkačik, “A tight upper bound on mutual information,” in <i>IEEE Information Theory Workshop, ITW 2019</i>, Visby, Sweden, 2019.","ista":"Hledik M, Sokolowski TR, Tkačik G. 2019. A tight upper bound on mutual information. IEEE Information Theory Workshop, ITW 2019. Information Theory Workshop, 8989292.","chicago":"Hledik, Michal, Thomas R Sokolowski, and Gašper Tkačik. “A Tight Upper Bound on Mutual Information.” In <i>IEEE Information Theory Workshop, ITW 2019</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">https://doi.org/10.1109/ITW44776.2019.8989292</a>.","mla":"Hledik, Michal, et al. “A Tight Upper Bound on Mutual Information.” <i>IEEE Information Theory Workshop, ITW 2019</i>, 8989292, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">10.1109/ITW44776.2019.8989292</a>.","short":"M. Hledik, T.R. Sokolowski, G. Tkačik, in:, IEEE Information Theory Workshop, ITW 2019, IEEE, 2019.","apa":"Hledik, M., Sokolowski, T. R., &#38; Tkačik, G. (2019). A tight upper bound on mutual information. In <i>IEEE Information Theory Workshop, ITW 2019</i>. Visby, Sweden: IEEE. <a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">https://doi.org/10.1109/ITW44776.2019.8989292</a>","ama":"Hledik M, Sokolowski TR, Tkačik G. A tight upper bound on mutual information. In: <i>IEEE Information Theory Workshop, ITW 2019</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ITW44776.2019.8989292\">10.1109/ITW44776.2019.8989292</a>"},"conference":{"name":"Information Theory Workshop","start_date":"2019-08-25","end_date":"2019-08-28","location":"Visby, Sweden"},"title":"A tight upper bound on mutual information","department":[{"_id":"GaTk"}],"quality_controlled":"1","publication":"IEEE Information Theory Workshop, ITW 2019","status":"public","publisher":"IEEE","isi":1,"month":"08","date_created":"2020-03-22T23:00:47Z","date_updated":"2025-06-30T13:21:05Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000540384500015"],"arxiv":["1812.01475"]},"scopus_import":"1","publication_identifier":{"isbn":["9781538669006"]},"oa_version":"Preprint","year":"2019","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1812.01475","open_access":"1"}],"oa":1,"article_number":"8989292","_id":"7606","date_published":"2019-08-01T00:00:00Z","abstract":[{"text":"We derive a tight lower bound on equivocation (conditional entropy), or equivalently a tight upper bound on mutual information between a signal variable and channel outputs. The bound is in terms of the joint distribution of the signals and maximum a posteriori decodes (most probable signals given channel output). As part of our derivation, we describe the key properties of the distribution of signals, channel outputs and decodes, that minimizes equivocation and maximizes mutual information. This work addresses a problem in data analysis, where mutual information between signals and decodes is sometimes used to lower bound the mutual information between signals and channel outputs. Our result provides a corresponding upper bound.","lang":"eng"}],"arxiv":1,"article_processing_charge":"No"},{"date_updated":"2020-04-06T10:36:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"26","type":"preprint","author":[{"last_name":"Prehal","first_name":"Christian","full_name":"Prehal, Christian"},{"full_name":"Samojlov, Aleksej","first_name":"Aleksej","last_name":"Samojlov"},{"last_name":"Nachtnebel","full_name":"Nachtnebel, Manfred","first_name":"Manfred"},{"full_name":"Kriechbaum, Manfred","first_name":"Manfred","last_name":"Kriechbaum"},{"last_name":"Amenitsch","first_name":"Heinz","full_name":"Amenitsch, Heinz"},{"orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","last_name":"Freunberger"}],"oa_version":"Preprint","year":"2019","citation":{"short":"C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, (n.d.).","apa":"Prehal, C., Samojlov, A., Nachtnebel, M., Kriechbaum, M., Amenitsch, H., &#38; Freunberger, S. A. (n.d.). A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. ChemRxiv.","ama":"Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.","ista":"Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.","ieee":"C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, and S. A. Freunberger, “A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.” ChemRxiv.","chicago":"Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering.” ChemRxiv, n.d.","mla":"Prehal, Christian, et al. <i>A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering</i>. ChemRxiv."},"title":"A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering","status":"public","publication_status":"submitted","publisher":"ChemRxiv","main_file_link":[{"url":"https://doi.org/10.26434/chemrxiv.11447775.v1","open_access":"1"}],"oa":1,"month":"12","extern":"1","date_published":"2019-12-26T00:00:00Z","_id":"7627","abstract":[{"lang":"eng","text":"Electrodepositing  insulating  and  insoluble  Li2O2  is  the  key  process  during  discharge  of  aprotic  Li-O2 batteries  and  determines  rate,  capacity,  and  reversibility.  Current  understanding  states  that  the partition  between  surface  adsorbed  and  solvated  LiO2  governs  whether  Li2O2  grows  as  surface  film, leading to low capacity even at low rates, or in solution, leading to particles and high capacities. Here we show that Li2O2 forms to the widest extent as particles via solution mediated LiO2 disproportionation. We  describe  a  unified  Li2O2  growth  model  that  conclusively  explains  capacity  limitations  across  the whole range of electrolytes. Deciding for particle morphology, achievable rate and capacities are species mobilities,   electrode   specific   surface   area   (determining  true   areal   rate)   and   the  concentration distribution of associated LiO2 in solution. Provided that species mobilities and surface are high, high, capacities are possible even with low-donor-number electrolytes, previously considered prototypical for low   capacity   via   surface   growth.   The   tools   for   these   insights   are   microscopy,   hydrodynamic voltammetry, a numerical reaction model, and in situ small/wide angle X-ray scattering (SAXS/WAXS). Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative information from complex multi-phase systems. On a wider perspective, this SAXS method is a powerful in situ metrology with  atomic  to  sub-micron  resolution  to  study  mechanisms  in  complex  electrochemical  systems  and beyond. "}],"date_created":"2020-04-01T10:10:21Z","page":"50","article_processing_charge":"No"},{"article_processing_charge":"No","month":"10","article_number":"748-752","abstract":[{"text":"Deep neural networks (DNNs) have become increasingly important due to their excellent empirical performance on a wide range of problems. However, regularization is generally achieved by indirect means, largely due to the complex set of functions defined by a network and the difficulty in measuring function complexity. There exists no method in the literature for additive regularization based on a norm of the function, as is classically considered in statistical learning theory. In this work, we study the tractability of function norms for deep neural networks with ReLU activations. We provide, to the best of our knowledge, the first proof in the literature of the NP-hardness of computing function norms of DNNs of 3 or more layers. We also highlight a fundamental difference between shallow and deep networks. In the light on these results, we propose a new regularization strategy based on approximate function norms, and show its efficiency on a segmentation task with a DNN.","lang":"eng"}],"_id":"7639","date_published":"2019-10-01T00:00:00Z","date_created":"2020-04-05T22:00:50Z","publication_status":"published","publisher":"IEEE","isi":1,"publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","quality_controlled":"1","department":[{"_id":"VlKo"}],"status":"public","citation":{"ieee":"A. Rannen-Triki, M. Berman, V. Kolmogorov, and M. B. Blaschko, “Function norms for neural networks,” in <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, Seoul, South Korea, 2019.","ista":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. 2019. Function norms for neural networks. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 748–752.","chicago":"Rannen-Triki, Amal, Maxim Berman, Vladimir Kolmogorov, and Matthew B. Blaschko. “Function Norms for Neural Networks.” In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">https://doi.org/10.1109/ICCVW.2019.00097</a>.","mla":"Rannen-Triki, Amal, et al. “Function Norms for Neural Networks.” <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, 748–752, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">10.1109/ICCVW.2019.00097</a>.","short":"A. Rannen-Triki, M. Berman, V. Kolmogorov, M.B. Blaschko, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","apa":"Rannen-Triki, A., Berman, M., Kolmogorov, V., &#38; Blaschko, M. B. (2019). Function norms for neural networks. In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. Seoul, South Korea: IEEE. <a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">https://doi.org/10.1109/ICCVW.2019.00097</a>","ama":"Rannen-Triki A, Berman M, Kolmogorov V, Blaschko MB. Function norms for neural networks. In: <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00097\">10.1109/ICCVW.2019.00097</a>"},"title":"Function norms for neural networks","conference":{"location":"Seoul, South Korea","start_date":"2019-10-27","end_date":"2019-10-28","name":"ICCVW: International Conference on Computer Vision Workshop"},"day":"01","author":[{"full_name":"Rannen-Triki, Amal","first_name":"Amal","last_name":"Rannen-Triki"},{"full_name":"Berman, Maxim","first_name":"Maxim","last_name":"Berman"},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","first_name":"Vladimir"},{"full_name":"Blaschko, Matthew B.","first_name":"Matthew B.","last_name":"Blaschko"}],"type":"conference","oa_version":"None","year":"2019","external_id":{"isi":["000554591600090"]},"scopus_import":"1","date_updated":"2023-09-08T11:19:12Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"isbn":["9781728150239"]},"doi":"10.1109/ICCVW.2019.00097"},{"article_number":"1749-1753","abstract":[{"text":"We propose a new model for detecting visual relationships, such as \"person riding motorcycle\" or \"bottle on table\". This task is an important step towards comprehensive structured mage understanding, going beyond detecting individual objects. Our main novelty is a Box Attention mechanism that allows to model pairwise interactions between objects using standard object detection pipelines. The resulting model is conceptually clean, expressive and relies on well-justified training and prediction procedures. Moreover, unlike previously proposed approaches, our model does not introduce any additional complex components or hyperparameters on top of those already required by the underlying detection model. We conduct an experimental evaluation on two datasets, V-COCO and Open Images, demonstrating strong quantitative and qualitative results.","lang":"eng"}],"_id":"7640","date_published":"2019-10-01T00:00:00Z","arxiv":1,"article_processing_charge":"No","publication_status":"published","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1807.02136","open_access":"1"}],"year":"2019","oa_version":"Preprint","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-08T11:18:37Z","scopus_import":"1","external_id":{"arxiv":["1807.02136"],"isi":["000554591601098"]},"publication_identifier":{"isbn":["9781728150239"]},"month":"10","date_created":"2020-04-05T22:00:51Z","department":[{"_id":"ChLa"}],"quality_controlled":"1","publication":"Proceedings of the 2019 International Conference on Computer Vision Workshop","status":"public","publisher":"IEEE","isi":1,"day":"01","type":"conference","author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","last_name":"Kolesnikov","first_name":"Alexander","full_name":"Kolesnikov, Alexander"},{"last_name":"Kuznetsova","full_name":"Kuznetsova, Alina","first_name":"Alina"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"},{"last_name":"Ferrari","first_name":"Vittorio","full_name":"Ferrari, Vittorio"}],"ec_funded":1,"citation":{"chicago":"Kolesnikov, Alexander, Alina Kuznetsova, Christoph Lampert, and Vittorio Ferrari. “Detecting Visual Relationships Using Box Attention.” In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/ICCVW.2019.00217\">https://doi.org/10.1109/ICCVW.2019.00217</a>.","ista":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. 2019. Detecting visual relationships using box attention. Proceedings of the 2019 International Conference on Computer Vision Workshop. ICCVW: International Conference on Computer Vision Workshop, 1749–1753.","ieee":"A. Kolesnikov, A. Kuznetsova, C. Lampert, and V. Ferrari, “Detecting visual relationships using box attention,” in <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, Seoul, South Korea, 2019.","mla":"Kolesnikov, Alexander, et al. “Detecting Visual Relationships Using Box Attention.” <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>, 1749–1753, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00217\">10.1109/ICCVW.2019.00217</a>.","short":"A. Kolesnikov, A. Kuznetsova, C. Lampert, V. Ferrari, in:, Proceedings of the 2019 International Conference on Computer Vision Workshop, IEEE, 2019.","ama":"Kolesnikov A, Kuznetsova A, Lampert C, Ferrari V. Detecting visual relationships using box attention. In: <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/ICCVW.2019.00217\">10.1109/ICCVW.2019.00217</a>","apa":"Kolesnikov, A., Kuznetsova, A., Lampert, C., &#38; Ferrari, V. (2019). Detecting visual relationships using box attention. In <i>Proceedings of the 2019 International Conference on Computer Vision Workshop</i>. Seoul, South Korea: IEEE. <a href=\"https://doi.org/10.1109/ICCVW.2019.00217\">https://doi.org/10.1109/ICCVW.2019.00217</a>"},"conference":{"location":"Seoul, South Korea","end_date":"2019-10-28","start_date":"2019-10-27","name":"ICCVW: International Conference on Computer Vision Workshop"},"title":"Detecting visual relationships using box attention","language":[{"iso":"eng"}],"doi":"10.1109/ICCVW.2019.00217","project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:15:01Z","doi":"10.1038/s41467-019-13225-y","publication_identifier":{"issn":["2041-1723"]},"citation":{"short":"O. Delaneau, J.-F. Zagury, M.R. Robinson, J.L. Marchini, E.T. Dermitzakis, Nature Communications 10 (2019).","ama":"Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13225-y\">10.1038/s41467-019-13225-y</a>","apa":"Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., &#38; Dermitzakis, E. T. (2019). Accurate, scalable and integrative haplotype estimation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13225-y\">https://doi.org/10.1038/s41467-019-13225-y</a>","chicago":"Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative Haplotype Estimation.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13225-y\">https://doi.org/10.1038/s41467-019-13225-y</a>.","ieee":"O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis, “Accurate, scalable and integrative haplotype estimation,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","ista":"Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate, scalable and integrative haplotype estimation. Nature Communications. 10, 5436.","mla":"Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.” <i>Nature Communications</i>, vol. 10, 5436, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13225-y\">10.1038/s41467-019-13225-y</a>."},"title":"Accurate, scalable and integrative haplotype estimation","day":"28","article_type":"original","year":"2019","oa_version":"Published Version","author":[{"first_name":"Olivier","full_name":"Delaneau, Olivier","last_name":"Delaneau"},{"full_name":"Zagury, Jean-François","first_name":"Jean-François","last_name":"Zagury"},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","last_name":"Robinson"},{"last_name":"Marchini","first_name":"Jonathan L.","full_name":"Marchini, Jonathan L."},{"last_name":"Dermitzakis","full_name":"Dermitzakis, Emmanouil T.","first_name":"Emmanouil T."}],"type":"journal_article","publication_status":"published","publisher":"Springer Nature","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-019-13225-y"}],"quality_controlled":"1","publication":"Nature Communications","volume":10,"intvolume":"        10","status":"public","article_processing_charge":"No","article_number":"5436","extern":"1","month":"11","_id":"7710","date_created":"2020-04-30T10:40:32Z","date_published":"2019-11-28T00:00:00Z","abstract":[{"lang":"eng","text":"The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle."}]},{"publication":"Nature Metabolism","quality_controlled":"1","intvolume":"         1","status":"public","volume":1,"publication_status":"published","publisher":"Springer Nature","month":"12","extern":"1","date_published":"2019-12-09T00:00:00Z","_id":"7711","date_created":"2020-04-30T10:40:56Z","abstract":[{"lang":"eng","text":"The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies."}],"page":"1226-1242","article_processing_charge":"No","issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:15:01Z","publication_identifier":{"issn":["2522-5812"]},"doi":"10.1038/s42255-019-0147-3","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s42255-020-0202-0"}]},"article_type":"original","day":"09","type":"journal_article","author":[{"last_name":"Bevers","full_name":"Bevers, Roel P. J.","first_name":"Roel P. J."},{"first_name":"Maria","full_name":"Litovchenko, Maria","last_name":"Litovchenko"},{"last_name":"Kapopoulou","first_name":"Adamandia","full_name":"Kapopoulou, Adamandia"},{"last_name":"Braman","full_name":"Braman, Virginie S.","first_name":"Virginie S."},{"last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"last_name":"Auwerx","full_name":"Auwerx, Johan","first_name":"Johan"},{"last_name":"Hollis","full_name":"Hollis, Brian","first_name":"Brian"},{"full_name":"Deplancke, Bart","first_name":"Bart","last_name":"Deplancke"}],"oa_version":"None","year":"2019","citation":{"chicago":"Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” <i>Nature Metabolism</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s42255-019-0147-3\">https://doi.org/10.1038/s42255-019-0147-3</a>.","ista":"Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242.","ieee":"R. P. J. Bevers <i>et al.</i>, “Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,” <i>Nature Metabolism</i>, vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019.","mla":"Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” <i>Nature Metabolism</i>, vol. 1, no. 12, Springer Nature, 2019, pp. 1226–42, doi:<a href=\"https://doi.org/10.1038/s42255-019-0147-3\">10.1038/s42255-019-0147-3</a>.","short":"R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242.","ama":"Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. <i>Nature Metabolism</i>. 2019;1(12):1226-1242. doi:<a href=\"https://doi.org/10.1038/s42255-019-0147-3\">10.1038/s42255-019-0147-3</a>","apa":"Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. <i>Nature Metabolism</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42255-019-0147-3\">https://doi.org/10.1038/s42255-019-0147-3</a>"},"title":"Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel"},{"month":"06","date_created":"2018-12-11T11:44:06Z","page":"778-806","publication":"Journal of the London Mathematical Society","department":[{"_id":"TaHa"}],"quality_controlled":"1","intvolume":"        99","status":"public","publisher":"Wiley","isi":1,"day":"01","author":[{"id":"447491B8-F248-11E8-B48F-1D18A9856A87","full_name":"Ganev, Iordan V","first_name":"Iordan V","last_name":"Ganev"}],"type":"journal_article","citation":{"mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:<a href=\"https://doi.org/10.1112/jlms.12193\">10.1112/jlms.12193</a>.","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” <i>Journal of the London Mathematical Society</i>, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","chicago":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” <i>Journal of the London Mathematical Society</i>. Wiley, 2019. <a href=\"https://doi.org/10.1112/jlms.12193\">https://doi.org/10.1112/jlms.12193</a>.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. <i>Journal of the London Mathematical Society</i>. Wiley. <a href=\"https://doi.org/10.1112/jlms.12193\">https://doi.org/10.1112/jlms.12193</a>","ama":"Ganev IV. The wonderful compactification for quantum groups. <i>Journal of the London Mathematical Society</i>. 2019;99(3):778-806. doi:<a href=\"https://doi.org/10.1112/jlms.12193\">10.1112/jlms.12193</a>","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806."},"title":"The wonderful compactification for quantum groups","language":[{"iso":"eng"}],"doi":"10.1112/jlms.12193","ddc":["510"],"file":[{"file_name":"2019_Wiley_Ganev.pdf","creator":"kschuh","file_size":431754,"checksum":"1be56239b2cd740a0e9a084f773c22f6","date_updated":"2020-07-14T12:46:35Z","access_level":"open_access","content_type":"application/pdf","file_id":"7238","relation":"main_file","date_created":"2020-01-07T13:31:53Z"}],"abstract":[{"text":"In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2.","lang":"eng"}],"_id":"5","date_published":"2019-06-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","issue":"3","file_date_updated":"2020-07-14T12:46:35Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":99,"publication_status":"published","oa":1,"publist_id":"8052","year":"2019","has_accepted_license":"1","oa_version":"Published Version","external_id":{"isi":["000470025900008"]},"scopus_import":"1","date_updated":"2023-09-19T10:13:08Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:47:10Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"volume":62,"arxiv":1,"article_processing_charge":"Yes (via OA deal)","issue":"4","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:47:10Z","checksum":"f9d00e166efaccb5a76bbcbb4dcea3b4","creator":"dernst","file_size":599339,"file_name":"2018_DiscreteCompGeometry_Edelsbrunner.pdf","date_created":"2019-02-06T10:10:46Z","relation":"main_file","file_id":"5932","content_type":"application/pdf"}],"_id":"5678","abstract":[{"lang":"eng","text":"The order-k Voronoi tessellation of a locally finite set 𝑋⊆ℝ𝑛 decomposes ℝ𝑛 into convex domains whose points have the same k nearest neighbors in X. Assuming X is a stationary Poisson point process, we give explicit formulas for the expected number and total area of faces of a given dimension per unit volume of space. We also develop a relaxed version of discrete Morse theory and generalize by counting only faces, for which the k nearest points in X are within a given distance threshold."}],"date_published":"2019-12-01T00:00:00Z","scopus_import":"1","external_id":{"isi":["000494042900008"],"arxiv":["1709.09380"]},"date_updated":"2023-09-07T12:07:12Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"article_type":"original","year":"2019","has_accepted_license":"1","oa_version":"Published Version","publisher":"Springer","isi":1,"publication":"Discrete and Computational Geometry","quality_controlled":"1","department":[{"_id":"HeEd"}],"intvolume":"        62","status":"public","page":"865–878","month":"12","date_created":"2018-12-16T22:59:20Z","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6287"}]},"language":[{"iso":"eng"}],"ddc":["516"],"doi":"10.1007/s00454-018-0049-2","citation":{"apa":"Edelsbrunner, H., &#38; Nikitenko, A. (2019). Poisson–Delaunay Mosaics of Order k. <i>Discrete and Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-018-0049-2\">https://doi.org/10.1007/s00454-018-0049-2</a>","ama":"Edelsbrunner H, Nikitenko A. Poisson–Delaunay Mosaics of Order k. <i>Discrete and Computational Geometry</i>. 2019;62(4):865–878. doi:<a href=\"https://doi.org/10.1007/s00454-018-0049-2\">10.1007/s00454-018-0049-2</a>","short":"H. Edelsbrunner, A. Nikitenko, Discrete and Computational Geometry 62 (2019) 865–878.","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” <i>Discrete and Computational Geometry</i>, vol. 62, no. 4, Springer, 2019, pp. 865–878, doi:<a href=\"https://doi.org/10.1007/s00454-018-0049-2\">10.1007/s00454-018-0049-2</a>.","ieee":"H. Edelsbrunner and A. Nikitenko, “Poisson–Delaunay Mosaics of Order k,” <i>Discrete and Computational Geometry</i>, vol. 62, no. 4. Springer, pp. 865–878, 2019.","ista":"Edelsbrunner H, Nikitenko A. 2019. Poisson–Delaunay Mosaics of Order k. Discrete and Computational Geometry. 62(4), 865–878.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Poisson–Delaunay Mosaics of Order K.” <i>Discrete and Computational Geometry</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s00454-018-0049-2\">https://doi.org/10.1007/s00454-018-0049-2</a>."},"ec_funded":1,"title":"Poisson–Delaunay Mosaics of Order k","day":"01","type":"journal_article","author":[{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"last_name":"Nikitenko","full_name":"Nikitenko, Anton","first_name":"Anton","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0659-3201"}]},{"year":"2019","oa_version":"None","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-24T14:34:12Z","scopus_import":"1","external_id":{"isi":["000463802800009"]},"publication_identifier":{"issn":["23818107"],"eissn":["23818115"]},"issue":"1","article_processing_charge":"No","_id":"5680","abstract":[{"text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones.","lang":"eng"}],"date_published":"2019-01-01T00:00:00Z","publication_status":"published","volume":166,"citation":{"short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92.","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., &#38; Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. <i>Botany Letters</i>. Taylor and Francis. <a href=\"https://doi.org/10.1080/23818107.2018.1545142\">https://doi.org/10.1080/23818107.2018.1545142</a>","ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. <i>Botany Letters</i>. 2019;166(1):80-92. doi:<a href=\"https://doi.org/10.1080/23818107.2018.1545142\">10.1080/23818107.2018.1545142</a>","ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” <i>Botany Letters</i>, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92.","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” <i>Botany Letters</i>. Taylor and Francis, 2019. <a href=\"https://doi.org/10.1080/23818107.2018.1545142\">https://doi.org/10.1080/23818107.2018.1545142</a>.","mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” <i>Botany Letters</i>, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:<a href=\"https://doi.org/10.1080/23818107.2018.1545142\">10.1080/23818107.2018.1545142</a>."},"title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","day":"01","author":[{"first_name":"Christophe","full_name":"Andalo, Christophe","last_name":"Andalo"},{"full_name":"Burrus, Monique","first_name":"Monique","last_name":"Burrus"},{"full_name":"Paute, Sandrine","first_name":"Sandrine","last_name":"Paute"},{"last_name":"Lauzeral","full_name":"Lauzeral, Christine","first_name":"Christine"},{"last_name":"Field","full_name":"Field, David","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1080/23818107.2018.1545142","page":"80-92","month":"01","date_created":"2018-12-16T22:59:20Z","publisher":"Taylor and Francis","isi":1,"department":[{"_id":"NiBa"}],"quality_controlled":"1","publication":"Botany Letters","intvolume":"       166","status":"public"},{"abstract":[{"text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis.","lang":"eng"}],"_id":"5789","date_published":"2019-02-01T00:00:00Z","file":[{"relation":"main_file","file_id":"8685","content_type":"application/pdf","date_created":"2020-10-21T07:18:35Z","success":1,"creator":"dernst","file_size":71590590,"file_name":"2018_NatureCellBio_Petridou_accepted.pdf","checksum":"e38523787b3bc84006f2793de99ad70f","access_level":"open_access","date_updated":"2020-10-21T07:18:35Z"}],"article_processing_charge":"No","volume":21,"file_date_updated":"2020-10-21T07:18:35Z","oa":1,"publication_status":"published","oa_version":"Submitted Version","year":"2019","has_accepted_license":"1","article_type":"original","publication_identifier":{"issn":["14657392"]},"acknowledged_ssus":[{"_id":"Bio"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-11T14:03:28Z","scopus_import":"1","external_id":{"pmid":["30559456"],"isi":["000457468300011"]},"date_created":"2018-12-30T22:59:15Z","month":"02","page":"169–178","intvolume":"        21","status":"public","quality_controlled":"1","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publication":"Nature Cell Biology","isi":1,"publisher":"Nature Publishing Group","author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195","last_name":"Petridou","full_name":"Petridou, Nicoletta","first_name":"Nicoletta"},{"last_name":"Grigolon","first_name":"Silvia","full_name":"Grigolon, Silvia"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"},{"first_name":"Edouard B","full_name":"Hannezo, Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J"}],"type":"journal_article","day":"01","title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","ec_funded":1,"citation":{"ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. <i>Nature Cell Biology</i>. 2019;21:169–178. doi:<a href=\"https://doi.org/10.1038/s41556-018-0247-4\">10.1038/s41556-018-0247-4</a>","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41556-018-0247-4\">https://doi.org/10.1038/s41556-018-0247-4</a>","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178.","mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” <i>Nature Cell Biology</i>, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:<a href=\"https://doi.org/10.1038/s41556-018-0247-4\">10.1038/s41556-018-0247-4</a>.","chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2019. <a href=\"https://doi.org/10.1038/s41556-018-0247-4\">https://doi.org/10.1038/s41556-018-0247-4</a>.","ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178.","ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” <i>Nature Cell Biology</i>, vol. 21. Nature Publishing Group, pp. 169–178, 2019."},"ddc":["570"],"doi":"10.1038/s41556-018-0247-4","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/"}]},"pmid":1,"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants (EMBO fellowship)"}]},{"volume":91,"main_file_link":[{"url":"https://arxiv.org/abs/1309.2399","open_access":"1"}],"oa":1,"publication_status":"published","abstract":[{"text":"The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest.","lang":"eng"}],"_id":"5790","date_published":"2019-08-01T00:00:00Z","issue":"4","article_processing_charge":"No","arxiv":1,"publication_identifier":{"issn":["03649024"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-24T14:30:43Z","scopus_import":"1","external_id":{"isi":["000485392800004"],"arxiv":["1309.2399"]},"year":"2019","oa_version":"Preprint","article_type":"original","intvolume":"        91","status":"public","department":[{"_id":"UlWa"}],"quality_controlled":"1","publication":"Journal of Graph Theory","isi":1,"publisher":"Wiley","date_created":"2018-12-30T22:59:15Z","month":"08","page":"365-394","doi":"10.1002/jgt.22436","language":[{"iso":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"type":"journal_article","author":[{"last_name":"Chaplick","full_name":"Chaplick, Steven","first_name":"Steven"},{"orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","full_name":"Fulek, Radoslav","last_name":"Fulek"},{"full_name":"Klavík, Pavel","first_name":"Pavel","last_name":"Klavík"}],"day":"01","title":"Extending partial representations of circle graphs","ec_funded":1,"citation":{"apa":"Chaplick, S., Fulek, R., &#38; Klavík, P. (2019). Extending partial representations of circle graphs. <i>Journal of Graph Theory</i>. Wiley. <a href=\"https://doi.org/10.1002/jgt.22436\">https://doi.org/10.1002/jgt.22436</a>","ama":"Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. <i>Journal of Graph Theory</i>. 2019;91(4):365-394. doi:<a href=\"https://doi.org/10.1002/jgt.22436\">10.1002/jgt.22436</a>","short":"S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394.","mla":"Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” <i>Journal of Graph Theory</i>, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:<a href=\"https://doi.org/10.1002/jgt.22436\">10.1002/jgt.22436</a>.","ieee":"S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” <i>Journal of Graph Theory</i>, vol. 91, no. 4. Wiley, pp. 365–394, 2019.","ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394.","chicago":"Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” <i>Journal of Graph Theory</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/jgt.22436\">https://doi.org/10.1002/jgt.22436</a>."}},{"page":"167-181","abstract":[{"text":"The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis.","lang":"eng"}],"_id":"5793","date_created":"2019-01-06T22:59:11Z","series_title":"Methods in Molecular Biology","date_published":"2019-01-01T00:00:00Z","month":"01","publisher":"Springer","publication_status":"published","intvolume":"      1893","status":"public","volume":1893,"publication":"The hippo pathway","quality_controlled":"1","department":[{"_id":"CaHe"}],"title":"Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids","editor":[{"last_name":"Hergovich","full_name":"Hergovich, Alexander","first_name":"Alexander"}],"citation":{"short":"Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181.","apa":"Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., &#38; Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), <i>The hippo pathway</i> (Vol. 1893, pp. 167–181). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-8910-2_14\">https://doi.org/10.1007/978-1-4939-8910-2_14</a>","ama":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. <i>The Hippo Pathway</i>. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:<a href=\"https://doi.org/10.1007/978-1-4939-8910-2_14\">10.1007/978-1-4939-8910-2_14</a>","ieee":"Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in <i>The hippo pathway</i>, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181.","ista":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181.","chicago":"Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In <i>The Hippo Pathway</i>, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. <a href=\"https://doi.org/10.1007/978-1-4939-8910-2_14\">https://doi.org/10.1007/978-1-4939-8910-2_14</a>.","mla":"Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” <i>The Hippo Pathway</i>, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:<a href=\"https://doi.org/10.1007/978-1-4939-8910-2_14\">10.1007/978-1-4939-8910-2_14</a>."},"author":[{"first_name":"Yoichi","full_name":"Asaoka, Yoichi","last_name":"Asaoka"},{"first_name":"Hitoshi","full_name":"Morita, Hitoshi","last_name":"Morita"},{"last_name":"Furumoto","first_name":"Hiroko","full_name":"Furumoto, Hiroko"},{"first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Furutani-Seiki, Makoto","first_name":"Makoto","last_name":"Furutani-Seiki"}],"type":"book_chapter","year":"2019","alternative_title":["MIMB"],"oa_version":"None","day":"01","publication_identifier":{"isbn":["978-1-4939-8909-6"]},"doi":"10.1007/978-1-4939-8910-2_14","scopus_import":1,"date_updated":"2021-01-12T08:03:30Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file_date_updated":"2020-10-09T11:00:05Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"volume":15,"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","publication_status":"published","oa":1,"file":[{"file_size":5370762,"creator":"bkavcic","file_name":"lmt_sftmtr_V8.pdf","access_level":"open_access","date_updated":"2020-10-09T11:00:05Z","checksum":"614c337d6424ccd3d48d1b1f9513510d","relation":"main_file","file_id":"8641","content_type":"application/pdf","success":1,"date_created":"2020-10-09T11:00:05Z"}],"abstract":[{"lang":"eng","text":"We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion."}],"_id":"5817","date_published":"2019-01-10T00:00:00Z","article_processing_charge":"No","issue":"4","external_id":{"pmid":["30629082"],"isi":["000457329700003"]},"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-13T08:47:16Z","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"article_type":"original","year":"2019","has_accepted_license":"1","oa_version":"Submitted Version","publication":"Soft Matter","quality_controlled":"1","department":[{"_id":"GaTk"}],"intvolume":"        15","status":"public","publisher":"Royal Society of Chemistry","isi":1,"month":"01","date_created":"2019-01-11T07:37:47Z","page":"602-614","language":[{"iso":"eng"}],"doi":"10.1039/c8sm01956h","ddc":["530"],"pmid":1,"day":"10","author":[{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor","full_name":"Kavcic, Bor"},{"last_name":"Sakashita","first_name":"A.","full_name":"Sakashita, A."},{"last_name":"Noguchi","first_name":"H.","full_name":"Noguchi, H."},{"full_name":"Ziherl, P.","first_name":"P.","last_name":"Ziherl"}],"type":"journal_article","citation":{"mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” <i>Soft Matter</i>, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:<a href=\"https://doi.org/10.1039/c8sm01956h\">10.1039/c8sm01956h</a>.","chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” <i>Soft Matter</i>. Royal Society of Chemistry, 2019. <a href=\"https://doi.org/10.1039/c8sm01956h\">https://doi.org/10.1039/c8sm01956h</a>.","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” <i>Soft Matter</i>, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019.","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. <i>Soft Matter</i>. 2019;15(4):602-614. doi:<a href=\"https://doi.org/10.1039/c8sm01956h\">10.1039/c8sm01956h</a>","apa":"Kavcic, B., Sakashita, A., Noguchi, H., &#38; Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/c8sm01956h\">https://doi.org/10.1039/c8sm01956h</a>","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614."},"title":"Limiting shapes of confined lipid vesicles"}]